<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Szmuc, Eric</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Kireev, Dmitry</style></author><author><style face="normal" font="default" size="100%">Akinwande, Deji</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Keitz, Benjamin</style></author><author><style face="normal" font="default" size="100%">Ellington, Andrew</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Engineering Geobacter pili to produce metal:organic filaments.</style></title><secondary-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biosensing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Gold</style></keyword><keyword><style  face="normal" font="default" size="100%">Metal Nanoparticles</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2023 Feb 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">222</style></volume><pages><style face="normal" font="default" size="100%">114993</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The organized self-assembly of conductive biological structures holds promise for creating new bioelectronic devices. In particular, Geobacter sulfurreducens type IVa pili have proven to be a versatile material for fabricating protein nanowire-based devices. To scale the production of conductive pili, we designed a strain of Shewanella oneidensis that heterologously expressed abundant, conductive Geobacter pili when grown aerobically in liquid culture. S. oneidensis expressing a cysteine-modified pilin, designed to enhance the capability to bind to gold, generated conductive pili that self-assembled into biohybrid filaments in the presence of gold nanoparticles. Elemental composition analysis confirmed the filament-metal interactions within the structures, which were several orders of magnitude larger than previously described metal:organic filaments. The results demonstrate that the S. oneidensis chassis significantly advances the possibilities for facile conductive protein nanowire design and fabrication.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/36525710?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">H Is a Major Intermediate in  Corrosion of Iron.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Corrosion</style></keyword><keyword><style  face="normal" font="default" size="100%">Desulfovibrio</style></keyword><keyword><style  face="normal" font="default" size="100%">Desulfovibrio vulgaris</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Lactic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2023 Apr 25</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">e0007623</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Desulfovibrio vulgaris has been a primary pure culture sulfate reducer for developing microbial corrosion concepts. Multiple mechanisms for how it accepts electrons from Fe have been proposed. We investigated Fe oxidation with a mutant of  in which hydrogenase genes were deleted. The hydrogenase mutant grew as well as the parental strain with lactate as the electron donor, but unlike the parental strain, it was not able to grow on H. The parental strain reduced sulfate with Fe as the sole electron donor, but the hydrogenase mutant did not. H accumulated over time in Fe cultures of the hydrogenase mutant and sterile controls but not in parental strain cultures. Sulfide stimulated H production in uninoculated controls apparently by both reacting with Fe to generate H and facilitating electron transfer from Fe to H. Parental strain supernatants did not accelerate H production from Fe, ruling out a role for extracellular hydrogenases. Previously proposed electron transfer between Fe and  via soluble electron shuttles was not evident. The hydrogenase mutant did not reduce sulfate in the presence of Fe and either riboflavin or anthraquinone-2,6-disulfonate, and these potential electron shuttles did not stimulate parental strain sulfate reduction with Fe as the electron donor. The results demonstrate that  primarily accepts electrons from Fe via H as an intermediary electron carrier. These findings clarify the interpretation of previous  corrosion studies and suggest that H-mediated electron transfer is an important mechanism for iron corrosion under sulfate-reducing conditions.  Microbial corrosion of iron in the presence of sulfate-reducing microorganisms is economically significant. There is substantial debate over how microbes accelerate iron corrosion. Tools for genetic manipulation have only been developed for a few Fe(III)-reducing and methanogenic microorganisms known to corrode iron and in each case those microbes were found to accept electrons from Fe via direct electron transfer. However, iron corrosion is often most intense in the presence of sulfate-reducing microbes. The finding that Desulfovibrio vulgaris relies on H to shuttle electrons between Fe and cells revives the concept, developed in some of the earliest studies on microbial corrosion, that sulfate reducers consumption of H is a major microbial corrosion mechanism. The results further emphasize that direct Fe-to-microbe electron transfer has yet to be rigorously demonstrated in sulfate-reducing microbes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/36786581?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lekbach, Yassir</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Liu, Xiaomeng</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor</style></author><author><style face="normal" font="default" size="100%">Yao, Jun</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial nanowires with genetically modified peptide ligands to sustainably fabricate electronic sensing devices.</style></title><secondary-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Ammonia</style></keyword><keyword><style  face="normal" font="default" size="100%">Biosensing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Electronics</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Ligands</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2023 Apr 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">226</style></volume><pages><style face="normal" font="default" size="100%">115147</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Nanowires have substantial potential as the sensor component in electronic sensing devices. However, surface functionalization of traditional nanowire and nanotube materials with short peptides that increase sensor selectivity and sensitivity requires complex chemistries with toxic reagents. In contrast, microorganisms can assemble pilin monomers into protein nanowires with intrinsic conductivity from renewable feedstocks, yielding an electronic material that is robust and stable in applications, but also biodegradable. Here we report that the sensitivity and selectivity of protein nanowire-based sensors can be modified with a simple plug and play genetic approach in which a short peptide sequence, designed to bind the analyte of interest, is incorporated into the pilin protein that is microbially assembled into nanowires. We employed a scalable Escherichia coli chassis to fabricate protein nanowires that displayed either a peptide previously demonstrated to effectively bind ammonia, or a peptide known to bind acetic acid. Sensors comprised of thin films of the nanowires amended with the ammonia-specific peptide had a ca. 100-fold greater response to ammonia than sensors made with unmodified protein nanowires. Protein nanowires with the peptide that binds acetic acid yielded a 4-fold higher response than nanowires without the peptide. The protein nanowire-based sensors had greater responses than previously reported sensors fabricated with other nanomaterials. The results demonstrate that protein nanowires with enhanced sensor response for analytes of interest can be fabricated with a flexible genetic strategy that sustainably eliminates the energy, environmental, and health concerns associated with other common nanomaterials.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/36804664?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Response to Wang et al.: evidence contradicting the cytochrome-only model.</style></title><secondary-title><style face="normal" font="default" size="100%">Trends Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Trends Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2023 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">31</style></volume><pages><style face="normal" font="default" size="100%">548-549</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/37005158?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhou, Enze</style></author><author><style face="normal" font="default" size="100%">Li, Feng</style></author><author><style face="normal" font="default" size="100%">Zhang, Dawei</style></author><author><style face="normal" font="default" size="100%">Xu, Dake</style></author><author><style face="normal" font="default" size="100%">Li, Zhong</style></author><author><style face="normal" font="default" size="100%">Jia, Ru</style></author><author><style face="normal" font="default" size="100%">Jin, Yuting</style></author><author><style face="normal" font="default" size="100%">Song, Hao</style></author><author><style face="normal" font="default" size="100%">Li, Huabing</style></author><author><style face="normal" font="default" size="100%">Wang, Qiang</style></author><author><style face="normal" font="default" size="100%">Wang, Jianjun</style></author><author><style face="normal" font="default" size="100%">Li, Xiaogang</style></author><author><style face="normal" font="default" size="100%">Gu, Tingyue</style></author><author><style face="normal" font="default" size="100%">Homborg, Axel M</style></author><author><style face="normal" font="default" size="100%">Mol, Johannes M C</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Wang, Fuhui</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Direct microbial electron uptake as a mechanism for stainless steel corrosion in aerobic environments.</style></title><secondary-title><style face="normal" font="default" size="100%">Water Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Water Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Corrosion</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Stainless Steel</style></keyword><keyword><style  face="normal" font="default" size="100%">Steel</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Jul 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">219</style></volume><pages><style face="normal" font="default" size="100%">118553</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Shewanella oneidensis MR-1 is an attractive model microbe for elucidating the biofilm-metal interactions that contribute to the billions of dollars in corrosion damage to industrial applications each year. Multiple mechanisms for S. oneidensis-enhanced corrosion have been proposed, but none of these mechanisms have previously been rigorously investigated with methods that rule out alternative routes for electron transfer. We found that S. oneidensis grown under aerobic conditions formed thick biofilms (∼50 µm) on stainless steel coupons, accelerating corrosion over sterile controls. H and flavins were ruled out as intermediary electron carriers because stainless steel did not reduce riboflavin and previous studies have demonstrated stainless does not generate H. Strain ∆mtrCBA, in which the genes for the most abundant porin-cytochrome conduit in S. oneidensis were deleted, corroded stainless steel substantially less than wild-type in aerobic cultures. Wild-type biofilms readily reduced nitrate with stainless steel as the sole electron donor under anaerobic conditions, but strain ∆mtrCBA did not. These results demonstrate that S. oneidensis can directly consume electrons from iron-containing metals and illustrate how direct metal-to-microbe electron transfer can be an important route for corrosion, even in aerobic environments.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/35561622?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Rev Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Rev Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Physiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">5-19</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34316046?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioresour Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioresour Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">345</style></volume><pages><style face="normal" font="default" size="100%">126553</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H is actually the electron donor supporting growth has not been rigorously excluded.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34906705?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">On the Existence of Pilin-Based Microbial Nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">872610</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/35733974?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genetic Manipulation of Desulfovibrio ferrophilus and Evaluation of Fe(III) Oxide Reduction Mechanisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiol Spectr</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiol Spectr</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Dec 21</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">e0392222</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The sulfate-reducing microbe Desulfovibrio ferrophilus is of interest due to its relatively rare ability to also grow with Fe(III) oxide as an electron acceptor and its rapid corrosion of metallic iron. Previous studies have suggested multiple agents for  extracellular electron exchange including a soluble electron shuttle, electrically conductive pili, and outer surface multiheme -type cytochromes. However, the previous lack of a strategy for genetic manipulation of  limited mechanistic investigations. We developed an electroporation-mediated transformation method that enabled replacement of  genes of interest with an antibiotic resistance gene via double-crossover homologous recombination. Genes were identified that are essential for flagellum-based motility and the expression of the two types of  pili. Disrupting flagellum-based motility or expression of either of the two pili did not inhibit Fe(III) oxide reduction, nor did deleting genes for multiheme -type cytochromes predicted to be associated with the outer membrane. Although redundancies in cytochrome or pilus function might explain some of these phenotypes, overall, the results are consistent with  primarily reducing Fe(III) oxide via an electron shuttle. The finding that  is genetically tractable not only will aid in elucidating further details of its mechanisms for Fe(III) oxide reduction but also provides a new experimental approach for developing a better understanding of some of its other unique features, such as the ability to corrode metallic iron at high rates and accept electrons from negatively poised electrodes.   is an important pure culture model for Fe(III) oxide reduction and the corrosion of iron-containing metals in anaerobic marine environments. This study demonstrates that  is genetically tractable, an important advance for elucidating the mechanisms by which it interacts with extracellular electron acceptors and donors. The results demonstrate that there is not one specific outer surface multiheme -type cytochrome that is essential for Fe(III) oxide reduction. This finding, coupled with the lack of apparent porin-cytochrome conduits encoded in the  genome and the finding that deleting genes for pilus and flagellum expression did not inhibit Fe(III) oxide reduction, suggests that  has adopted strategies for extracellular electron exchange that are different from those of intensively studied electroactive microbes like  and  species. Thus, the ability to genetically manipulate  is likely to lead to new mechanistic concepts in electromicrobiology.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/36445123?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbe Profile: : a model for novel physiologies of biogeochemical and technological significance.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology (Reading)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">168</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt; has served as the initial model for a substantial number of newly recognized microbial physiologies that play an important role in biogeochemical cycling of carbon, metals and nutrients. The strategies used by  for microbial interaction with minerals, contaminants, other microbes and electrodes have led to new technologies for bioremediation, bioenergy conversion and the sustainable production of 'green' electronics.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/35171087?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xiaomeng</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Gao, Hongyan</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Fu, Tianda</style></author><author><style face="normal" font="default" size="100%">Fu, Shuai</style></author><author><style face="normal" font="default" size="100%">Sun, Lu</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Yao, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial biofilms for electricity generation from water evaporation and power to wearables.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Wearable Electronic Devices</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Jul 28</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">4369</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Employing renewable materials for fabricating clean energy harvesting devices can further improve sustainability. Microorganisms can be mass produced with renewable feedstocks. Here, we demonstrate that it is possible to engineer microbial biofilms as a cohesive, flexible material for long-term continuous electricity production from evaporating water. Single biofilm sheet (~40 µm thick) serving as the functional component in an electronic device continuously produces power density (~1 μW/cm) higher than that achieved with thicker engineered materials. The energy output is comparable to that achieved with similar sized biofilms catalyzing current production in microbial fuel cells, without the need for an organic feedstock or maintaining cell viability. The biofilm can be sandwiched between a pair of mesh electrodes for scalable device integration and current production. The devices maintain the energy production in ionic solutions and can be used as skin-patch devices to harvest electricity from sweat and moisture on skin to continuously power wearable devices. Biofilms made from different microbial species show generic current production from water evaporation. These results suggest that we can harness the ubiquity of biofilms in nature as additional sources of biomaterial for evaporation-based electricity generation in diverse aqueous environments.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/35902587?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Feb 07</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">32</style></volume><pages><style face="normal" font="default" size="100%">R110-R112</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;In this Quick guide, Derek Lovley introduces microbial nanowires-conductive extracellular appendages made by some bacteria and archaea.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/35134353?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Untangling Geobacter sulfurreducens Nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Jun 28</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">e0085022</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/35642973?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhou, Jinjie</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Tang, Hai-Yan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Correlation of Key Physiological Properties of  Isolates with Environment of Origin.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioreactors</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Archaeal</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Jun 11</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">87</style></volume><pages><style face="normal" font="default" size="100%">e0073121</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;It is known that the physiology of  species can differ significantly, but the ecological impact of these differences is unclear. We recovered two strains of  from two different ecosystems with a similar enrichment and isolation method. Both strains had the same ability to metabolize organic substrates and participate in direct interspecies electron transfer but also had major physiological differences. Strain DH-1, which was isolated from an anaerobic digester, used H as an electron donor. Genome analysis indicated that it lacks an Rnf complex and conserves energy from acetate metabolism via intracellular H cycling. In contrast, strain DH-2, a subsurface isolate, lacks hydrogenases required for H uptake and cycling and has an Rnf complex for energy conservation when growing on acetate. Further analysis of the genomes of previously described isolates, as well as phylogenetic and metagenomic data on uncultured  in anaerobic digesters and diverse soils and sediments, revealed a physiological dichotomy that corresponded with environment of origin. The physiology of type I  revolves around H production and consumption. In contrast, type II  species eschew H and have genes for an Rnf complex and the multiheme, membrane-bound -type cytochrome MmcA, shown to be essential for extracellular electron transfer. The distribution of  species in diverse environments suggests that the type I H-based physiology is well suited for high-energy environments, like anaerobic digesters, whereas type II Rnf/cytochrome-based physiology is an adaptation to the slower, steady-state carbon and electron fluxes common in organic-poor anaerobic soils and sediments.  Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane is an important bioenergy process.  species play an important role in methane production in many methanogenic soils and sediments as well as anaerobic waste digesters. The studies reported here emphasize that the genus  is composed of two physiologically distinct groups. This is important to recognize when interpreting the role of  in methanogenic environments, especially regarding H metabolism. Furthermore, the finding that type I  species predominate in environments with high rates of carbon and electron flux and that type II  species predominate in lower-energy environments suggests that evaluating the relative abundance of type I and type II  may provide further insights into rates of carbon and electron flux in methanogenic environments.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">13</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33931421?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xinying</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Sun, Dezhi</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Direct Observation of Electrically Conductive Pili Emanating from .</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Atomic Force</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Aug 31</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">e0220921</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter sulfurreducens is a model microbe for elucidating the mechanisms for extracellular electron transfer in several biogeochemical cycles, bioelectrochemical applications, and microbial metal corrosion. Multiple lines of evidence previously suggested that electrically conductive pili (e-pili) are an essential conduit for long-range extracellular electron transport in G. sulfurreducens. However, it has recently been reported that G. sulfurreducens does not express e-pili and that filaments comprised of multi-heme -type cytochromes are responsible for long-range electron transport. This possibility was directly investigated by examining cells, rather than filament preparations, with atomic force microscopy. Approximately 90% of the filaments emanating from wild-type cells had a diameter (3 nm) and conductance consistent with previous reports of e-pili harvested from G. sulfurreducens or heterologously expressed in Escherichia coli from the G. sulfurreducens pilin gene. The remaining 10% of filaments had a morphology consistent with filaments comprised of the -type cytochrome OmcS. A strain expressing a modified pilin gene designed to yield poorly conductive pili expressed 90% filaments with a 3-nm diameter, but greatly reduced conductance, further indicating that the 3-nm diameter conductive filaments in the wild-type strain were e-pili. A strain in which genes for five of the most abundant outer-surface -type cytochromes, including OmcS, were deleted yielded only 3-nm-diameter filaments with the same conductance as in the wild type. These results demonstrate that e-pili are the most abundant conductive filaments expressed by G. sulfurreducens, consistent with previous functional studies demonstrating the need for e-pili for long-range extracellular electron transfer.  Electroactive microbes have significant environmental impacts, as well as applications in bioenergy and bioremediation. The composition, function, and even existence of electrically conductive pili (e-pili) has been one of the most contentious areas of investigation in electromicrobiology, in part because e-pili offer a mechanism for long-range electron transport that does not involve the metal cofactors common in much of biological electron transport. This study demonstrates that e-pili are abundant filaments emanating from Geobacter sulfurreducens, which serves as a model for long-range extracellular electron transfer in direct interspecies electron transfer, dissimilatory metal reduction, microbe-electrode exchange, and corrosion caused by direct electron uptake from Fe(0). The methods described in this study provide a simple strategy for evaluating the distribution of conductive filaments throughout the microbial world with an approach that avoids artifactual production and/or enrichment of filaments that may not be physiologically relevant.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34465020?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liang, Dandan</style></author><author><style face="normal" font="default" size="100%">Liu, Xinying</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Feng, Yujie</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extracellular Electron Exchange Capabilities of  and .</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Desulfovibrio</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Dec 07</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">55</style></volume><pages><style face="normal" font="default" size="100%">16195-16203</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial extracellular electron transfer plays an important role in diverse biogeochemical cycles, metal corrosion, bioelectrochemical technologies, and anaerobic digestion. Evaluation of electron uptake from pure Fe(0) and stainless steel indicated that, in contrast to previous speculation in the literature,  and  are not able to directly extract electrons from solid-phase electron-donating surfaces.  grew with Fe(III) as the electron acceptor, but  did not.  reduced Fe(III) oxide occluded within porous alginate beads, suggesting that it released a soluble electron shuttle to promote Fe(III) oxide reduction. Conductive atomic force microscopy revealed that the  pili are electrically conductive and the expression of a gene encoding an aromatics-rich putative pilin was upregulated during growth on Fe(III) oxide. The expression of genes for multi-heme -type cytochromes was not upregulated during growth with Fe(III) as the electron acceptor, and genes for a porin-cytochrome conduit across the outer membrane were not apparent in the genome. The results suggest that  has adopted a novel combination of strategies to enable extracellular electron transport, which may be of biogeochemical and technological significance.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">23</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34748326?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Generation of High Current Densities in Geobacter sulfurreducens Lacking the Putative Gene for the PilB Pilus Assembly Motor.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiol Spectr</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiol Spectr</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Atomic Force</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Oct 31</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">e0087721</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter sulfurreducens is commonly employed as a model for the study of extracellular electron transport mechanisms in the  species. Deletion of , which is known to encode the pilus assembly motor protein for type IV pili in other bacteria, has been proposed as an effective strategy for evaluating the role of electrically conductive pili (e-pili) in G. sulfurreducens extracellular electron transfer. In those studies, the inhibition of e-pili expression associated with  deletion was not demonstrated directly but was inferred from the observation that  deletion mutants produced lower current densities than wild-type cells. Here, we report that deleting  did not diminish current production. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-type G. sulfurreducens or when e-pili are expressed heterologously from the G. sulfurreducens pilin gene in Escherichia coli. Immunogold labeling demonstrated that a G. sulfurreducens strain expressing a pilin monomer with a His tag continued to express His tag-labeled filaments when  was deleted. These results suggest that a reinterpretation of the results of previous studies on G. sulfurreducens  deletion strains may be necessary.  Geobacter sulfurreducens is a model microbe for the study of biogeochemically and technologically significant processes, such as the reduction of Fe(III) oxides in soils and sediments, bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity, direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments, and metal corrosion. Elucidating the phenotypes associated with gene deletions is an important strategy for determining the mechanisms for extracellular electron transfer in G. sulfurreducens. The results reported here demonstrate that we cannot replicate the key phenotype reported for a gene deletion that has been central to the development of models for long-range electron transport in G. sulfurreducens.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34585977?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Yao, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Intrinsically Conductive Microbial Nanowires for 'Green' Electronics with Novel Functions.</style></title><secondary-title><style face="normal" font="default" size="100%">Trends Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Trends Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electronics</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">940-952</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Intrinsically conductive protein nanowires, microbially produced from inexpensive, renewable feedstocks, are a sustainable alternative to traditional nanowire electronic materials, which require high energy inputs and hazardous conditions/chemicals for fabrication and can be highly toxic. Pilin-based nanowires can be tailored for specific functions via the design of synthetic pilin genes to tune wire conductivity or introduce novel functionalities. Other microbially produced nanowire options for electronics may include cytochrome wires, curli fibers, and the conductive fibers of cable bacteria. Proof-of-concept protein nanowire electronics that have been successfully demonstrated include biomedical sensors, neuromorphic devices, and a device that generates electricity from ambient humidity. Further development of applications will require interdisciplinary teams of engineers, biophysicists, and synthetic biologists.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33419586?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Zhou, Jinjie</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mechanisms for Electron Uptake by Methanosarcina acetivorans during Direct Interspecies Electron Transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaeal Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Oct 26</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">e0234421</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here, we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in coculture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in  grown in coculture versus pure-culture growth on acetate revealed that transcripts for the outer-surface multiheme type cytochrome MmcA were higher during DIET-based growth. Deletion of  inhibited DIET. The high aromatic amino acid content of  archaellins suggests that they might assemble into electrically conductive archaella. A mutant that could not express archaella was deficient in DIET. However, this mutant grew in DIET-based coculture as well as the archaellum-expressing parental strain in the presence of granular activated carbon, which was previously shown to serve as a substitute for electrically conductive pili as a conduit for long-range interspecies electron transfer in other DIET-based cocultures. Transcriptomic data suggesting that the membrane-bound Rnf, Fpo, and HdrED complexes also play a role in DIET were incorporated into a charge-balanced model illustrating how electrons entering the cell through MmcA can yield energy to support growth from carbon dioxide reduction. The results are the first genetics-based functional demonstration of likely outer-surface electrical contacts for DIET in a methanogen.  The conversion of organic matter to methane plays an important role in the global carbon cycle and is an effective strategy for converting wastes to a useful biofuel. The reduction of carbon dioxide to methane accounts for approximately a third of the methane produced in anaerobic soils and sediments as well as waste digesters. Potential electron donors for carbon dioxide reduction are H or electrons derived from direct interspecies electron transfer (DIET) between bacteria and methanogens. Elucidating the relative importance of these electron donors has been difficult due to a lack of information on the electrical connections on the outer surfaces of methanogens and how they process the electrons received from DIET. Transcriptomic patterns and gene deletion phenotypes reported here provide insight into how a group of  organisms that play an important role in methane production in soils and sediments participate in DIET.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34607451?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lekbach, Yassir</style></author><author><style face="normal" font="default" size="100%">Liu, Tao</style></author><author><style face="normal" font="default" size="100%">Li, Yingchao</style></author><author><style face="normal" font="default" size="100%">Moradi, Masoumeh</style></author><author><style face="normal" font="default" size="100%">Dou, Wenwen</style></author><author><style face="normal" font="default" size="100%">Xu, Dake</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial corrosion of metals: The corrosion microbiome.</style></title><secondary-title><style face="normal" font="default" size="100%">Adv Microb Physiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Adv Microb Physiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Corrosion</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbiota</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">317-390</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbially catalyzed corrosion of metals is a substantial economic concern. Aerobic microbes primarily enhance Fe oxidation through indirect mechanisms and their impact appears to be limited compared to anaerobic microbes. Several anaerobic mechanisms are known to accelerate Fe oxidation. Microbes can consume H abiotically generated from the oxidation of Fe. Microbial H removal makes continued Fe oxidation more thermodynamically favorable. Extracellular hydrogenases further accelerate Fe oxidation. Organic electron shuttles such as flavins, phenazines, and possibly humic substances may replace H as the electron carrier between Fe and cells. Direct Fe-to-microbe electron transfer is also possible. Which of these anaerobic mechanisms predominates in model pure culture isolates is typically poorly documented because of a lack of functional genetic studies. Microbial mechanisms for Fe oxidation may also apply to some other metals. An ultimate goal of microbial metal corrosion research is to develop molecular tools to diagnose the occurrence, mechanisms, and rates of metal corrosion to guide the implementation of the most effective mitigation strategies. A systems biology approach that includes innovative isolation and characterization methods, as well as functional genomic investigations, will be required in order to identify the diagnostic features to be gleaned from meta-omic analysis of corroding materials. A better understanding of microbial metal corrosion mechanisms is expected to lead to new corrosion mitigation strategies. The understanding of the corrosion microbiome is clearly in its infancy, but interdisciplinary electrochemical, microbiological, and molecular tools are available to make rapid progress in this field.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34147188?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fu, Tianda</style></author><author><style face="normal" font="default" size="100%">Liu, Xiaomeng</style></author><author><style face="normal" font="default" size="100%">Fu, Shuai</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor</style></author><author><style face="normal" font="default" size="100%">Gao, Hongyan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Yao, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Self-sustained green neuromorphic interfaces.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biocompatible Materials</style></keyword><keyword><style  face="normal" font="default" size="100%">Electronics</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Neural Networks, Computer</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Synapses</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Jun 07</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">3351</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Incorporating neuromorphic electronics in bioelectronic interfaces can provide intelligent responsiveness to environments. However, the signal mismatch between the environmental stimuli and driving amplitude in neuromorphic devices has limited the functional versatility and energy sustainability. Here we demonstrate multifunctional, self-sustained neuromorphic interfaces by achieving signal matching at the biological level. The advances rely on the unique properties of microbially produced protein nanowires, which enable both bio-amplitude (e.g., &lt;100 mV) signal processing and energy harvesting from ambient humidity. Integrating protein nanowire-based sensors, energy devices and memristors of bio-amplitude functions yields flexible, self-powered neuromorphic interfaces that can intelligently interpret biologically relevant stimuli for smart responses. These features, coupled with the fact that protein nanowires are a green biomaterial of potential diverse functionalities, take the interfaces a step closer to biological integration.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34099691?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sun, Yun-Lu</style></author><author><style face="normal" font="default" size="100%">Montz, Brian J</style></author><author><style face="normal" font="default" size="100%">Selhorst, Ryan</style></author><author><style face="normal" font="default" size="100%">Tang, Hai-Yan</style></author><author><style face="normal" font="default" size="100%">Zhu, Jiaxin</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Ribbe, Alexander E</style></author><author><style face="normal" font="default" size="100%">Russell, Thomas P</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Emrick, Todd</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Solvent-Induced Assembly of Microbial Protein Nanowires into Superstructured Bundles.</style></title><secondary-title><style face="normal" font="default" size="100%">Biomacromolecules</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biomacromolecules</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Solvents</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Mar 08</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">1305-1311</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Protein-based electronic biomaterials represent an attractive alternative to traditional metallic and semiconductor materials due to their environmentally benign production and purification. However, major challenges hindering further development of these materials include (1) limitations associated with processing proteins in organic solvents and (2) difficulties in forming higher-order structures or scaffolds with multilength scale control. This paper addresses both challenges, resulting in the formation of one-dimensional bundles composed of electrically conductive protein nanowires harvested from the microbes  and . Processing these bionanowires from common organic solvents, such as hexane, cyclohexane, and DMF, enabled the production of multilength scale structures composed of distinctly visible pili. Transmission electron microscopy revealed striking images of bundled protein nanowires up to 10 μm in length and with widths ranging from 50-500 nm (representing assembly of tens to hundreds of nanowires). Conductive atomic force microscopy confirmed the presence of an appreciable nanowire conductivity in their bundled state. These results greatly expand the possibilities for fabricating a diverse array of protein nanowire-based electronic device architectures.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33591727?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tang, Hai-Yan</style></author><author><style face="normal" font="default" size="100%">Yang, Chuntian</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Pittman, Conor C</style></author><author><style face="normal" font="default" size="100%">Xu, Dake</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Gu, Tingyue</style></author><author><style face="normal" font="default" size="100%">Wang, Fuhui</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Corrosion</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Stainless Steel</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">3084-3093</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial corrosion of iron-based materials is a substantial economic problem. A mechanistic understanding is required to develop mitigation strategies, but previous mechanistic studies have been limited to investigations with relatively pure Fe(0), which is not a common structural material. We report here that the mechanism for microbial corrosion of stainless steel, the metal of choice for many actual applications, can be significantly different from that for Fe(0). Although H is often an intermediary electron carrier between the metal and microbes during Fe(0) corrosion, we found that H is not abiotically produced from stainless steel, making this corrosion mechanism unlikely. Geobacter sulfurreducens and Geobacter metallireducens, electrotrophs that are known to directly accept electrons from other microbes or electrodes, extracted electrons from stainless steel via direct iron-to-microbe electron transfer. Genetic modification to prevent H consumption did not negatively impact on stainless steel corrosion. Corrosion was inhibited when genes for outer-surface cytochromes that are key electrical contacts were deleted. These results indicate that a common model of microbial Fe(0) corrosion by hydrogenase-positive microbes, in which H serves as an intermediary electron carrier between the metal surface and the microbe, may not apply to the microbial corrosion of stainless steel. However, direct iron-to-microbe electron transfer is a feasible route for stainless steel corrosion.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33972726?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fu, Tianda</style></author><author><style face="normal" font="default" size="100%">Liu, Xiaomeng</style></author><author><style face="normal" font="default" size="100%">Gao, Hongyan</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Liu, Xiaorong</style></author><author><style face="normal" font="default" size="100%">Yin, Bing</style></author><author><style face="normal" font="default" size="100%">Wang, Zhongrui</style></author><author><style face="normal" font="default" size="100%">Zhuo, Ye</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Joshua Yang, J</style></author><author><style face="normal" font="default" size="100%">Chen, Jianhan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Yao, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Bioinspired bio-voltage memristors.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Action Potentials</style></keyword><keyword><style  face="normal" font="default" size="100%">Biosensing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electronics</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Design</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Dynamics Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Neural Networks, Computer</style></keyword><keyword><style  face="normal" font="default" size="100%">Neurons</style></keyword><keyword><style  face="normal" font="default" size="100%">Synapses</style></keyword><keyword><style  face="normal" font="default" size="100%">Wearable Electronic Devices</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Apr 20</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">1861</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Memristive devices are promising candidates to emulate biological computing. However, the typical switching voltages (0.2-2 V) in previously described devices are much higher than the amplitude in biological counterparts. Here we demonstrate a type of diffusive memristor, fabricated from the protein nanowires harvested from the bacterium Geobacter sulfurreducens, that functions at the biological voltages of 40-100 mV. Memristive function at biological voltages is possible because the protein nanowires catalyze metallization. Artificial neurons built from these memristors not only function at biological action potentials (e.g., 100 mV, 1 ms) but also exhibit temporal integration close to that in biological neurons. The potential of using the memristor to directly process biosensing signals is also demonstrated.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32313096?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zheng, Shiling</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Wang, Bingchen</style></author><author><style face="normal" font="default" size="100%">Zhang, Yuechao</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%"> Capable of Direct Interspecies Electron Transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanobacterium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Dec 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">54</style></volume><pages><style face="normal" font="default" size="100%">15347-15354</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) from bacteria to methanogens is a revolutionary concept for syntrophic metabolism in methanogenic soils/sediments and anaerobic digestion. Previous studies have indicated that the potential for DIET is limited to methanogens in the , leading to the assumption that an abundance of other types of methanogens, such as  species, indicates a lack of DIET. We report here on a strain of , designated strain YSL, that grows via DIET in defined cocultures with . The cocultures formed aggregates, in which cells of strain YSL and  were uniformly dispersed throughout. This close association of the two species is the likely explanation for the ability of a strain of  that could not express electrically conductive pili to grow in coculture with strain YSL. Granular activated carbon promoted the initial formation of the DIET-based cocultures. The discovery of DIET in , the genus of methanogens that has been the exemplar for interspecies electron transfer  H, suggests that the capacity for DIET is much more broadly distributed among methanogens than previously considered. More innovative approaches to microbial isolation and characterization are needed in order to better understand how methanogenic communities function.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">23</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33205658?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An  Chassis for Production of Electrically Conductive Protein Nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">ACS Synth Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ACS Synth Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Microorganisms, Genetically-Modified</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Atomic Force</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Engineering</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Mar 20</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">647-654</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt; pilin-based electrically conductive protein nanowires (e-PNs) are a revolutionary electronic material. They offer novel options for electronic sensing applications and have the remarkable ability to harvest electrical energy from atmospheric humidity. However, technical constraints limit mass cultivation and genetic manipulation of . Therefore, we designed a strain of  to express e-PNs by introducing a plasmid that contained an inducible operon with  genes for type IV pili biogenesis machinery and a synthetic gene designed to yield a peptide monomer that could be assembled into e-PNs. The e-PNs expressed in  and harvested with a simple filtration method had the same diameter (3 nm) and conductance as e-PNs expressed in . These results, coupled with the robustness of  for mass cultivation and the extensive  toolbox for genetic manipulation, greatly expand the opportunities for large-scale fabrication of novel e-PNs.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32125829?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xiaomeng</style></author><author><style face="normal" font="default" size="100%">Gao, Hongyan</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Liu, Xiaorong</style></author><author><style face="normal" font="default" size="100%">Yin, Bing</style></author><author><style face="normal" font="default" size="100%">Fu, Tianda</style></author><author><style face="normal" font="default" size="100%">Chen, Jianhan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Yao, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Power generation from ambient humidity using protein nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">578</style></volume><pages><style face="normal" font="default" size="100%">550-554</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Harvesting energy from the environment offers the promise of clean power for self-sustained systems. Known technologies-such as solar cells, thermoelectric devices and mechanical generators-have specific environmental requirements that restrict where they can be deployed and limit their potential for continuous energy production. The ubiquity of atmospheric moisture offers an alternative. However, existing moisture-based energy-harvesting technologies can produce only intermittent, brief (shorter than 50 seconds) bursts of power in the ambient environment, owing to the lack of a sustained conversion mechanism. Here we show that thin-film devices made from nanometre-scale protein wires harvested from the microbe Geobacter sulfurreducens can generate continuous electric power in the ambient environment. The devices produce a sustained voltage of around 0.5 volts across a 7-micrometre-thick film, with a current density of around 17 microamperes per square centimetre. We find the driving force behind this energy generation to be a self-maintained moisture gradient that forms within the film when the film is exposed to the humidity that is naturally present in air. Connecting several devices linearly scales up the voltage and current to power electronics. Our results demonstrate the feasibility of a continuous energy-harvesting strategy that is less restricted by location or environmental conditions than other sustainable approaches.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7796</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32066937?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Protein Nanowires: the Electrification of the Microbial World and Maybe Our Own.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Bacteriol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Engineering</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Sep 23</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">202</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Electrically conductive protein nanowires appear to be widespread in the microbial world and are a revolutionary &quot;green&quot; material for the fabrication of electronic devices. Electrically conductive pili (e-pili) assembled from type IV pilin monomers have independently evolved multiple times in microbial history as have electrically conductive archaella (e-archaella) assembled from homologous archaellin monomers. A role for e-pili in long-range (micrometer) extracellular electron transport has been demonstrated in some microbes. The surprising finding of e-pili in syntrophic bacteria and the role of e-pili as conduits for direct interspecies electron transfer have necessitated a reassessment of routes for electron flux in important methanogenic environments, such as anaerobic digesters and terrestrial wetlands. Pilin monomers similar to those found in e-pili may also be a major building block of the conductive &quot;cables&quot; that transport electrons over centimeter distances through continuous filaments of cable bacteria consisting of a thousand cells or more. Protein nanowires harvested from microbes have many functional and sustainability advantages over traditional nanowire materials and have already yielded novel electronic devices for sustainable electricity production, neuromorphic memory, and sensing. e-pili can be mass produced with an  chassis, providing a ready source of material for electronics as well as for studies on the basic mechanisms for long-range electron transport along protein nanowires. Continued exploration is required to better understand the electrification of microbial communities with microbial nanowires and to expand the &quot;green toolbox&quot; of sustainable materials for wiring and powering the emerging &quot;Internet of things.&quot;&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">20</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32747429?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhao, Zhiqiang</style></author><author><style face="normal" font="default" size="100%">Li, Yang</style></author><author><style face="normal" font="default" size="100%">Zhang, Yaobin</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sparking Anaerobic Digestion: Promoting Direct Interspecies Electron Transfer to Enhance Methane Production.</style></title><secondary-title><style face="normal" font="default" size="100%">iScience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">iScience</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Dec 18</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">23</style></volume><pages><style face="normal" font="default" size="100%">101794</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Anaerobic digestion was one of the first bioenergy strategies developed, yet the interactions of the microbial community that is responsible for the production of methane are still poorly understood. For example, it has only recently been recognized that the bacteria that oxidize organic waste components can forge electrical connections with methane-producing microbes through biologically produced, protein-based, conductive circuits. This direct interspecies electron transfer (DIET) is faster than interspecies electron exchange via diffusive electron carriers, such as H. DIET is also more resilient to perturbations such as increases in organic load inputs or toxic compounds. However, with current digester practices DIET rarely predominates. Improvements in anaerobic digestion associated with the addition of electrically conductive materials have been attributed to increased DIET, but experimental verification has been lacking. This deficiency may soon be overcome with improved understanding of the diversity of microbes capable of DIET, which is leading to molecular tools for determining the extent of DIET. Here we review the microbiology of DIET, suggest molecular strategies for monitoring DIET in anaerobic digesters, and propose approaches for re-engineering digester design and practices to encourage DIET.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33294801?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Zhu, Jiaxin</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">McInerney, Michael J</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Formates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">837-846</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Syntrophic interspecies electron exchange is essential for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron transfer because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Here we report that Syntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Heterologous expression of the putative S. aciditrophicus type IV pilin gene in Geobacter sulfurreducens yielded conductive pili of the same diameter (4 nm) and conductance of the native S. aciditrophicus pili and enabled long-range electron transport in G. sulfurreducens. S. aciditrophicus lacked abundant c-type cytochromes often associated with DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The finding that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31896792?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Martz, Eric</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Zhou, Zimu</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Archaellum of Methanospirillum hungatei Is Electrically Conductive.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Flagella</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanospirillum</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenylalanine</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 Apr 16</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbially produced electrically conductive protein filaments are of interest because they can function as conduits for long-range biological electron transfer. They also show promise as sustainably produced electronic materials. Until now, microbially produced conductive protein filaments have been reported only for bacteria. We report here that the archaellum of  is electrically conductive. This is the first demonstration that electrically conductive protein filaments have evolved in  Furthermore, the structure of the  archaellum was previously determined (N. Poweleit, P. Ge, H. N. Nguyen, R. R. O. Loo, et al., Nat Microbiol 2:16222, 2016, https://doi.org/10.1038/nmicrobiol.2016.222). Thus, the archaellum of  is the first microbially produced electrically conductive protein filament for which a structure is known. We analyzed the previously published structure and identified a core of tightly packed phenylalanines that is one likely route for electron conductance. The availability of the  archaellum structure is expected to substantially advance mechanistic evaluation of long-range electron transport in microbially produced electrically conductive filaments and to aid in the design of &quot;green&quot; electronic materials that can be microbially produced with renewable feedstocks. Microbially produced electrically conductive protein filaments are a revolutionary, sustainably produced, electronic material with broad potential applications. The design of new protein nanowires based on the known  archaellum structure could be a major advance over the current empirical design of synthetic protein nanowires from electrically conductive bacterial pili. An understanding of the diversity of outer-surface protein structures capable of electron transfer is important for developing models for microbial electrical communication with other cells and minerals in natural anaerobic environments. Extracellular electron exchange is also essential in engineered environments such as bioelectrochemical devices and anaerobic digesters converting wastes to methane. The finding that the archaellum of  is electrically conductive suggests that some archaea might be able to make long-range electrical connections with their external environment.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/30992355?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Filman, David J</style></author><author><style face="normal" font="default" size="100%">Marino, Stephen F</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Yang, Lu</style></author><author><style face="normal" font="default" size="100%">Mester, Zoltán</style></author><author><style face="normal" font="default" size="100%">Bullitt, Esther</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Strauss, Mike</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire.</style></title><secondary-title><style face="normal" font="default" size="100%">Commun Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Commun Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cryoelectron Microscopy</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">219</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Electrically conductive pili from  species, termed bacterial nanowires, are intensely studied for their biological significance and potential in the development of new materials. Using cryo-electron microscopy, we have characterized nanowires from conductive  pili preparations that are composed solely of head-to-tail stacked monomers of the six-heme C-type cytochrome OmcS. The unique fold of OmcS - closely wrapped around a continuous stack of hemes that can serve as an uninterrupted path for electron transport - generates a scaffold that supports the unbranched chain of hemes along the central axis of the filament. We present here, at 3.4 Å resolution, the structure of this cytochrome-based filament and discuss its possible role in long-range biological electron transport.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31240257?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Decorating the Outer Surface of Microbially Produced Protein Nanowires with Peptides.</style></title><secondary-title><style face="normal" font="default" size="100%">ACS Synth Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ACS Synth Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carboxy-Lyases</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethylene Glycols</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Structure</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxygenases</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptides</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenylalanine Ammonia-Lyase</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmids</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Saccharomyces cerevisiae</style></keyword><keyword><style  face="normal" font="default" size="100%">Saccharomyces cerevisiae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Styrenes</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 Aug 16</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">1809-1817</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The potential applications of electrically conductive protein nanowires (e-PNs) harvested from  might be greatly expanded if the outer surface of the wires could be modified to confer novel sensing capabilities or to enhance binding to other materials. We developed a simple strategy for functionalizing e-PNs with surface-exposed peptides. The  gene for the monomer that assembles into e-PNs was modified to add peptide tags at the carboxyl terminus of the monomer. Strains of  were constructed that fabricated synthetic e-PNs with a six-histidine &quot;His-tag&quot; or both the His-tag and a nine-peptide &quot;HA-tag&quot; exposed on the outer surface. Addition of the peptide tags did not diminish e-PN conductivity. The abundance of HA-tag in e-PNs was controlled by placing expression of the gene for the synthetic monomer with the HA-tag under transcriptional regulation. These studies suggest broad possibilities for tailoring e-PN properties for diverse applications.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31298834?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tang, Hai-Yan</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Palacios, Paola A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Iron Corrosion via Direct Metal-Microbe Electron Transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Corrosion</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Formate Dehydrogenases</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 May 14</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The concept that anaerobic microorganisms can directly accept electrons from Fe(0) has been controversial because direct metal-microbe electron transfer has previously only been indirectly inferred. Fe(0) oxidation was studied with  strain ACL, an autotrophic strain that was previously shown to grow with electrons derived from a graphite cathode as the sole electron donor. Strain ACL grew with Fe(0) as the sole electron donor and fumarate as the electron acceptor. However, it appeared that at least a portion of the electron transfer was via H produced nonenzymatically from the oxidation of Fe(0) to Fe(II). H, which accumulated in abiotic controls, was consumed during the growth of strain ACL, the cells were predominately planktonic, and genes for the uptake hydrogenase were highly expressed. Strain ACL was constructed to prevent growth on H or formate by deleting the genes for the uptake of hydrogenase and formate dehydrogenases from strain ACL. Strain ACL also grew with Fe(0) as the sole electron donor, but H accumulated in the culture, and cells heavily colonized Fe(0) surfaces with no visible planktonic growth. Transcriptomics suggested that the outer surface -type cytochromes OmcS and OmcZ were important during growth of strain ACL on Fe(0). Strain ACL did not grow on Fe(0) if the gene for either of these cytochromes was deleted. The specific attachment of strain ACL to Fe(0), coupled with requirements for known extracellular electrical contacts, suggest that direct metal-microbe electron transfer is the most likely option for Fe(0) serving as an electron donor. The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environmental concern. It has been known for over 100 years that the presence of anaerobic respiratory microorganisms can accelerate iron corrosion. Multiple studies have suggested that there are sulfate reducers, methanogens, and acetogens that can directly accept electrons from Fe(0) to support sulfate or carbon dioxide reduction. However, all of the strains studied can also use H as an electron donor for growth, which is known to be abiotically produced from Fe(0). Furthermore, no proteins definitely shown to function as extracellular electrical contacts with Fe(0) were identified. The studies described here demonstrate that direct electron transfer from Fe(0) can support anaerobic respiration. They also map out a simple genetic approach to the study of iron corrosion mechanisms in other microorganisms. A better understanding of how microorganisms promote iron corrosion is expected to lead to the development of strategies that can help reduce adverse impacts from this process.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31088920?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Tang, Hai-Yan</style></author><author><style face="normal" font="default" size="100%">Zhou, Jinjie</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Chaput, Gina</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Membrane-Bound Cytochrome Enables  To Conserve Energy from Extracellular Electron Transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Anthraquinones</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Archaeal</style></keyword><keyword><style  face="normal" font="default" size="100%">Gram-Negative Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Membranes</style></keyword><keyword><style  face="normal" font="default" size="100%">Mesna</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 Aug 20</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Extracellular electron exchange in  species and closely related  plays an important role in the global carbon cycle and enhances the speed and stability of anaerobic digestion by facilitating efficient syntrophic interactions. Here, we grew  with methanol provided as the electron donor and the humic analogue, anthraquione-2,6-disulfonate (AQDS), provided as the electron acceptor when methane production was inhibited with bromoethanesulfonate. AQDS was reduced with simultaneous methane production in the absence of bromoethanesulfonate. Transcriptomics revealed that expression of the gene for the transmembrane, multiheme, -type cytochrome MmcA was higher in AQDS-respiring cells than in cells performing methylotrophic methanogenesis. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction but grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenzyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable the survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation of  makes it an excellent model microbe for evaluating -type cytochrome-dependent extracellular electron transfer in  The discovery of a methanogen that can conserve energy to support growth solely from the oxidation of organic carbon coupled to the reduction of an extracellular electron acceptor expands the possible environments in which methanogens might thrive. The potential importance of -type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some  was previously proposed, but these studies with  provide the first genetic evidence for cytochrome-based extracellular electron transfer in  The results suggest parallels with Gram-negative bacteria, such as  and  species, in which multiheme outer-surface -type cytochromes are an essential component for electrical communication with the extracellular environment.  offers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in  with implications not only for methanogens but possibly also for  that anaerobically oxidize methane.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31431545?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xing</style></author><author><style face="normal" font="default" size="100%">Zhan, Ji</style></author><author><style face="normal" font="default" size="100%">Jing, Xianyue</style></author><author><style face="normal" font="default" size="100%">Zhou, Shungui</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A pilin chaperone required for the expression of electrically conductive Geobacter sulfurreducens pili.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Chaperones</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">2511-2522</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Mechanisms controlling the expression of the electrically conductive pili (e-pili) of Geobacter species are of interest because of the important role of e-pili in diverse biogeochemical processes, anaerobic digestion and electromicrobiological applications. We investigated the function of the protein, designated Spc (short pilin chaperone), encoded by the gene immediately downstream from the gene for PilA, the monomer that assembles into e-pili. Multiple lines of evidence suggest that Spc forms an oligomer that is associated with the inner membrane. Mutating the start codon of spc to prevent translation increased the transcript abundance of pilA but greatly diminished the abundance of PilA, and e-pili could no longer be detected. Cross-linking, protein capture and two-hybrid studies demonstrated that Spc and PilA interacted. Two sites in PilA for electrostatic interaction with Spc were identified. The results demonstrate that Spc is required for PilA stability prior to incorporation into e-pili, suggesting that Spc has a chaperone function that may be specific to the relatively short PilA monomers that assemble into e-pili. These results are important for identifying microorganisms likely to express e-pili from (meta)genomic data and for the construction of microbial strains expressing e-pili.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31012224?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%"> Protein Nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">2078</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The study of electrically conductive protein nanowires in  has led to new concepts for long-range extracellular electron transport, as well as for the development of sustainable conductive materials and electronic devices with novel functions. Until recently, electrically conductive pili (e-pili), assembled from the PilA pilin monomer, were the only known  protein nanowires. However, filaments comprised of the multi-heme -type cytochrome, OmcS, are present in some preparations of  outer-surface proteins. The purpose of this review is to evaluate the available evidence on the  expression of e-pili and OmcS filaments and their biological function. Abundant literature demonstrates that  expresses e-pili, which are required for long-range electron transport to Fe (III) oxides and through conductive biofilms. In contrast, there is no definitive evidence yet that wild-type  express long filaments of OmcS extending from the cells, and deleting the gene for OmcS actually  biofilm conductivity. The literature does not support the concern that many previous studies on e-pili were mistakenly studying OmcS filaments. For example, heterologous expression of the aromatic-rich pilin monomer of  in  increases the conductivity of individual nanowires more than 5,000-fold, whereas expression of an aromatic-poor pilin reduced conductivity more than 1,000-fold. This more than million-fold range in nanowire conductivity was achieved while maintaining the 3-nm diameter characteristic of e-pili. Purification methods that eliminate all traces of OmcS yield highly conductive e-pili, as does heterologous expression of the e-pilin monomer in microbes that do not produce OmcS or any other outer-surface cytochromes. Future studies of  expression of protein nanowires need to be cognizant of the importance of maintaining environmentally relevant growth conditions because artificial laboratory culture conditions can rapidly select against e-pili expression. Principles derived from the study of e-pili have enabled identification of non-cytochrome protein nanowires in diverse bacteria and archaea. A similar search for cytochrome appendages is warranted. Both e-pili and OmcS filaments offer design options for the synthesis of protein-based &quot;green&quot; electronics, which may be the primary driving force for the study of these structures in the near future.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31608018?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sun, Yun-Lu</style></author><author><style face="normal" font="default" size="100%">Tang, Hai-Yan</style></author><author><style face="normal" font="default" size="100%">Ribbe, Alexander</style></author><author><style face="normal" font="default" size="100%">Duzhko, Volodimyr</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Bai, Ying</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Nonnenmann, Stephen S</style></author><author><style face="normal" font="default" size="100%">Russell, Thomas</style></author><author><style face="normal" font="default" size="100%">Emrick, Todd</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Conductive Composite Materials Fabricated from Microbially Produced Protein Nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">Small</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Small</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanocomposites</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymers</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">e1802624</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Protein-based electronic materials have numerous potential advantages with respect to sustainability and biocompatibility over electronic materials that are synthesized using harsh chemical processes and/or which contain toxic components. The microorganism Geobacter sulfurreducens synthesizes electrically conductive protein nanowires (e-PNs) with high aspect ratios (3 nm × 10-30 µm) from renewable organic feedstocks. Here, the integration of G. Sulfurreducens e-PNs into poly(vinyl alcohol) (PVA) as a host polymer matrix is described. The resultant e-PN/PVA composites exhibit conductivities comparable to PVA-based composites containing synthetic nanowires. The relationship between e-PN density and conductivity of the resultant composites is consistent with percolation theory. These e-PNs confer conductivity to the composites even under extreme conditions, with the highest conductivities achieved from materials prepared at pH 1.5 and temperatures greater than 100 °C. These results demonstrate that e-PNs represent viable and sustainable nanowire compositions for the fabrication of electrically conductive composite materials.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">44</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/30260563?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Aklujkar, Muktak A</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Construction of a  Strain With Exceptional Growth on Cathodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">1512</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Insoluble extracellular electron donors are important sources of energy for anaerobic respiration in biogeochemical cycling and in diverse practical applications. The previous lack of a genetically tractable model microorganism that could be grown to high densities under anaerobic conditions in pure culture with an insoluble extracellular electron donor has stymied efforts to better understand this form of respiration. We report here on the design of a strain of , designated strain ACL, which grows as thick (ca. 35 μm) confluent biofilms on graphite cathodes poised at -500 mV ( Ag/AgCl) with fumarate as the electron acceptor. Sustained maximum current consumption rates were &gt;0.8 A/m, which is &gt;10-fold higher than the current consumption of the wild-type strain. The improved function on the cathode was achieved by introducing genes for an ATP-dependent citrate lyase, completing the complement of enzymes needed for a reverse TCA cycle for the synthesis of biosynthetic precursors from carbon dioxide. Strain ACL provides an important model organism for elucidating the mechanisms for effective anaerobic growth with an insoluble extracellular electron donor and may offer unique possibilities as a chassis for the introduction of synthetic metabolic pathways for the production of commodities with electrons derived from electrodes.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/30057572?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Walker, David Jf</style></author><author><style face="normal" font="default" size="100%">Adhikari, Ramesh Y</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrically conductive pili from pilin genes of phylogenetically diverse microorganisms.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">48-58</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The possibility that bacteria other than Geobacter species might contain genes for electrically conductive pili (e-pili) was investigated by heterologously expressing pilin genes of interest in Geobacter sulfurreducens. Strains of G. sulfurreducens producing high current densities, which are only possible with e-pili, were obtained with pilin genes from Flexistipes sinusarabici, Calditerrivibrio nitroreducens and Desulfurivibrio alkaliphilus. The conductance of pili from these strains was comparable to native G. sulfurreducens e-pili. The e-pili derived from C. nitroreducens, and D. alkaliphilus pilin genes are the first examples of relatively long (&gt;100 amino acids) pilin monomers assembling into e-pili. The pilin gene from Candidatus Desulfofervidus auxilii did not yield e-pili, suggesting that the hypothesis that this sulfate reducer wires itself with e-pili to methane-oxidizing archaea to enable anaerobic methane oxidation should be reevaluated. A high density of aromatic amino acids and a lack of substantial aromatic-free gaps along the length of long pilins may be important characteristics leading to e-pili. This study demonstrates a simple method to screen pilin genes from difficult-to-culture microorganisms for their potential to yield e-pili; reveals new sources for biologically based electronic materials; and suggests that a wide phylogenetic diversity of microorganisms may use e-pili for extracellular electron exchange.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28872631?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Ferry, James G</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electron and Proton Flux for Carbon Dioxide Reduction in  During Direct Interspecies Electron Transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">3109</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) is important in diverse methanogenic environments, but how methanogens participate in DIET is poorly understood. Therefore, the transcriptome of  grown via DIET in co-culture with  was compared with its transcriptome when grown via H interspecies transfer (HIT) with . Notably, transcripts for the FH dehydrogenase, Fpo, and the heterodisulfide reductase, HdrABC, were more abundant during growth on DIET. A model for CO reduction was developed from these results in which electrons delivered to methanophenazine in the cell membrane are transferred to Fpo. The external proton gradient necessary to drive the otherwise thermodynamically unfavorable reverse electron transport for Fpo-catalyzed F reduction is derived from protons released from  metabolism. Reduced F is a direct electron donor in the carbon dioxide reduction pathway and also serves as the electron donor for the proposed HdrABC-catalyzed electron bifurcation reaction in which reduced ferredoxin (also required for carbon dioxide reduction) is generated with simultaneous reduction of CoM-S-S-CoB. Expression of genes for putative redox-active proteins predicted to be localized on the outer cell surface was higher during growth on DIET, but further analysis will be required to identify the electron transfer route to methanophenazine. The results indicate that the pathways for electron and proton flux for CO reduction during DIET are substantially different than for HIT and suggest that gene expression patterns may also be useful for determining whether  are directly accepting electrons from other extracellular electron donors, such as corroding metals or electrodes.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/30631315?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Hydrogen Economy of Methanosarcina barkeri: Life in the Fast Lane.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Bacteriol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina barkeri</style></keyword><keyword><style  face="normal" font="default" size="100%">Proton-Motive Force</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 Oct 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">200</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Two recent studies (T. D. Mand, G. Kulkarni, and W. W. Metcalf, J. Bacteriol 200:e00342-18, 2018, https://doi.org/10.1128/JB.00342-18, and G. Kulkarni, T. D. Mand, and W. W. Metcalf, mBio 9:e01256-18, 2018, https://doi.org/10.1128/mBio.01256-18) analyzed an impressive array of hydrogenase-deficient mutant strains of  not only to describe H-based growth but also to demonstrate the conservation of energy with intracellular hydrogen cycling, a novel strategy for creating a proton motive force to support ATP synthesis.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">20</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/30082458?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Orelana, Roberto</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Wang, Li-Ying</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Ecol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb Ecol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">76</style></volume><pages><style face="normal" font="default" size="100%">660-667</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40 days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29500492?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Wang, Li-Ying</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%"> Strains Expressing Poorly Conductive Pili Reveal Constraints on Direct Interspecies Electron Transfer Mechanisms.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 Jul 10</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Cytochrome-to-cytochrome electron transfer and electron transfer along conduits of multiple extracellular magnetite grains are often proposed as strategies for direct interspecies electron transfer (DIET) that do not require electrically conductive pili (e-pili). However, physical evidence for these proposed DIET mechanisms has been lacking. To investigate these possibilities further, we constructed  strain Aro-5, in which the wild-type pilin gene was replaced with the  pilin gene that was previously shown to yield poorly conductive pili in  strain Aro-5.  strain Aro-5 did not reduce Fe(III) oxide and produced only low current densities, phenotypes consistent with expression of poorly conductive pili. Like  strain Aro-5,  strain Aro-5 displayed abundant outer surface cytochromes. Cocultures initiated with wild-type  as the electron-donating strain and  strain Aro-5 as the electron-accepting strain grew via DIET. However,  Aro-5/ wild-type cocultures did not. Cocultures initiated with the Aro-5 strains of both species grew only when amended with granular activated carbon (GAC), a conductive material known to be a conduit for DIET. Magnetite could not substitute for GAC. The inability of the two Aro-5 strains to adapt for DIET in the absence of GAC suggests that there are physical constraints on establishing DIET solely through cytochrome-to-cytochrome electron transfer or along chains of magnetite. The finding that DIET is possible with electron-accepting partners that lack highly conductive pili greatly expands the range of potential electron-accepting partners that might participate in DIET. DIET is thought to be an important mechanism for interspecies electron exchange in natural anaerobic soils and sediments in which methane is either produced or consumed, as well as in some photosynthetic mats and anaerobic digesters converting organic wastes to methane. Understanding the potential mechanisms for DIET will not only aid in modeling carbon and electron flow in these geochemically significant environments but will also be helpful for interpreting meta-omic data from as-yet-uncultured microbes in DIET-based communities and for designing strategies to promote DIET in anaerobic digesters. The results demonstrate the need to develop a better understanding of the diversity of types of e-pili in the microbial world to identify potential electron-donating partners for DIET. Novel methods for recovering as-yet-uncultivated microorganisms capable of DIET in culture will be needed to further evaluate whether DIET is possible without e-pili in the absence of conductive materials such as GAC.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29991583?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Philips, Jo</style></author><author><style face="normal" font="default" size="100%">Rabaey, Korneel</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Vargas, Madeline</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS One</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Flagella</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Glass</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Osmotic Pressure</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Sodium Chloride</style></keyword><keyword><style  face="normal" font="default" size="100%">Spores, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Stress, Physiological</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">e0170406</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28118386?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">e-Biologics: Fabrication of Sustainable Electronics with &quot;Green&quot; Biological Materials.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biological Products</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrical Equipment and Supplies</style></keyword><keyword><style  face="normal" font="default" size="100%">Electronics</style></keyword><keyword><style  face="normal" font="default" size="100%">Green Chemistry Technology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Jun 27</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial components as the guide for synthesis, are a potential green solution. Some e-biologics can be fabricated from renewable feedstocks with relatively low energy inputs, often while avoiding the harsh chemicals used for synthesizing more traditional electronic materials. Several are completely free of toxic components, can be readily recycled, and offer unique features not found in traditional electronic materials in terms of size, performance, and opportunities for diverse functionalization. An appropriate investment in the concerted multidisciplinary collaborative research required to identify and characterize e-biologics and to engineer materials and devices based on e-biologics could be rewarded with a new &quot;green age&quot; of sustainable electronic materials and devices.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28655820?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tan, Yang</style></author><author><style face="normal" font="default" size="100%">Adhikari, Ramesh Y</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Expressing the Geobacter metallireducens PilA in Geobacter sulfurreducens Yields Pili with Exceptional Conductivity.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombinant Proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Jan 17</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;The electrically conductive pili (e-pili) of Geobacter sulfurreducens serve as a model for a novel strategy for long-range extracellular electron transfer. e-pili are also a new class of bioelectronic materials. However, the only other Geobacter pili previously studied, which were from G. uraniireducens, were poorly conductive. In order to obtain more information on the range of pili conductivities in Geobacter species, the pili of G. metallireducens were investigated. Heterologously expressing the PilA gene of G. metallireducens in G. sulfurreducens yielded a G. sulfurreducens strain, designated strain MP, that produced abundant pili. Strain MP exhibited phenotypes consistent with the presence of e-pili, such as high rates of Fe(III) oxide reduction and high current densities on graphite anodes. Individual pili prepared at physiologically relevant pH 7 had conductivities of 277 ± 18.9 S/cm (mean ± standard deviation), which is 5,000-fold higher than the conductivity of G. sulfurreducens pili at pH 7 and nearly 1 million-fold higher than the conductivity of G. uraniireducens pili at the same pH. A potential explanation for the higher conductivity of the G. metallireducens pili is their greater density of aromatic amino acids, which are known to be important components in electron transport along the length of the pilus. The G. metallireducens pili represent the most highly conductive pili found to date and suggest strategies for designing synthetic pili with even higher conductivities.&lt;/p&gt;&lt;p&gt;&lt;b&gt;IMPORTANCE: &lt;/b&gt;e-pili are a remarkable electrically conductive material that can be sustainably produced without harsh chemical processes from renewable feedstocks and that contain no toxic components in the final product. Thus, e-pili offer an unprecedented potential for developing novel materials, electronic devices, and sensors for diverse applications with a new &quot;green&quot; technology. Increasing e-pili conductivity will even further expand their potential applications. A proven strategy is to design synthetic e-pili that contain tryptophan, an aromatic amino acid not found in previously studied e-pili. The studies reported here demonstrate that a productive alternative approach is to search more broadly in the microbial world. Surprisingly, even though G. metallireducens and G. sulfurreducens are closely related, the conductivities of their e-pili differ by more than 3 orders of magnitude. The ability to produce e-pili with high conductivity without generating a genetically modified product enhances the attractiveness of this novel electronic material.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28096491?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Happy together: microbial communities that hook up to swap electrons.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Consortia</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">327-336</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The discovery of direct interspecies electron transfer (DIET) and cable bacteria has demonstrated that microbial cells can exchange electrons over long distances (μm-cm) through electrical connections. For example, in the presence of cable bacteria electrons are rapidly transported over centimeter distances, coupling the oxidation of reduced sulfur compounds in anoxic sediments to oxygen reduction in overlying surficial sediments. Bacteria and archaea wired for DIET are found in anaerobic methane-producing and methane-consuming communities. Electrical connections between gut microbes and host cells have also been proposed. Iterative environmental and defined culture studies on methanogenic communities revealed the importance of electrically conductive pili and c-type cytochromes in natural electrical grids, and demonstrated that conductive carbon materials and magnetite can substitute for these biological connectors to facilitate DIET. This understanding has led to strategies to enhance and stabilize anaerobic digestion. Key unknowns warranting further investigation include elucidation of the archaeal electrical connections facilitating DIET-based methane production and consumption; and the mechanisms for long-range electron transfer through cable bacteria. A better understanding of mechanisms for cell-to-cell electron transfer could facilitate the hunt for additional electrically connected microbial communities with omics approaches and could advance spin-off applications such as the development of sustainable bioelectronics materials and bioelectrochemical technologies.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27801905?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Dang, Yan</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Metagenome</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcinaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Oryza</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 May 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">83</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The possibility that  (formerly ) and  species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of  accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with  species, but sequences most closely related to putative e-pilin genes from genera such as , , , and , were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with  species, and the finding that  spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed  genes. In addition, homologs of genes encoding OmcS, a -type cytochrome associated with the e-pili of  and required for DIET, were also highly expressed in the soils.  species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO reduction in  Thus, these results are consistent with a model in which  species were providing electrons to  species for methane production through electrical connections of e-pili. species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for  in methanogenic rice paddy soils is important because it demonstrates that the contribution that  makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when  species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus,  growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that  species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with  spp., and possibly other methanogens, via DIET.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28258137?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Syntrophy Goes Electric: Direct Interspecies Electron Transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Annu Rev Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Annu Rev Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Industrial Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Sep 08</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">643-664</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) has biogeochemical significance, and practical applications that rely on DIET or DIET-based aspects of microbial physiology are growing. Mechanisms for DIET have primarily been studied in defined cocultures in which Geobacter species are one of the DIET partners. Electrically conductive pili (e-pili) can be an important electrical conduit for DIET. However, there may be instances in which electrical contacts are made between electron transport proteins associated with the outer membranes of the partners. Alternatively, DIET partners can plug into conductive carbon materials, such as granular activated carbon, carbon cloth, and biochar, for long-range electron exchange without the need for e-pili. Magnetite promotes DIET, possibly by acting as a substitute for outer-surface c-type cytochromes. DIET is the primary mode of interspecies electron exchange in some anaerobic digesters converting wastes to methane. Promoting DIET with conductive materials shows promise for stabilizing and accelerating methane production in digesters, permitting higher organic loading rates. Various lines of evidence suggest that DIET is important in terrestrial wetlands, which are an important source of atmospheric methane. DIET may also have a role in anaerobic methane oxidation coupled to sulfate reduction, an important control on methane releases. The finding that DIET can serve as the source of electrons for anaerobic photosynthesis further broadens its potential environmental significance. Microorganisms capable of DIET are good catalysts for several bioelectrochemical technologies and e-pili are a promising renewable source of electronic materials. The study of DIET is in its early stages, and additional investigation is required to better understand the diversity of microorganisms that are capable of DIET, the importance of DIET to carbon and electron flow in anaerobic environments, and the biochemistry and physiology of DIET.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28697668?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">DiDonato, Laurie N</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Toward establishing minimum requirements for extracellular electron transfer in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">FEMS Microbiol Lett</style></secondary-title><alt-title><style face="normal" font="default" size="100%">FEMS Microbiol Lett</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Periplasm</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 May 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">364</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The highly redundant pathways for extracellular electron transfer in Geobacter sulfurreducens must be simplified for this microorganism to serve as an effective chassis for applications such as the development of sensors and biocomputing. Five homologs of the periplasmic c-type cytochromes, PpcA-E, offer the possibility of multiple routes of electron transfer across the periplasm. The presence of a large number of outer membrane c-type cytochromes allows G. sulfurreducens to adapt to disruption of an electron transfer pathway in the outer membrane. A strain in which genes for all five periplasmic cytochromes, PpcA-E, were deleted did not reduce Fe(III). Introducing ppcA under the control of an IPTG-inducible system in the quintuple deletion strain yielded a strain that reduced Fe(III) only in the presence of IPTG. A strain lacking known major outer membrane cytochromes, OmcB, OmcE, OmcS and OmcT, and putative functional homologs of OmcB, did not reduce Fe(III). Introduction of omcB in this septuple deletion strain restored the ability to reduce Fe(III). These results demonstrate that it is possible to trim redundancy from the extracellular electron transfer pathways in G. sulfurreducens in order to construct strains with defined extracellular electron transfer routes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28472266?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Shrestha, Minita</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H and CO compared to organotrophic growth with fructose.</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Sci Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Monoxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Fructose</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">NADP</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2017 Oct 13</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">13135</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H), carbon dioxide (CO), and carbon monoxide (CO), or with H and CO. Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H/CO was compared by RNA-Seq. Upregulated genes with both syngas and H/CO (compared to fructose) point to the urea cycle, uptake and degradation of peptides and amino acids, response to sulfur starvation, potentially NADPH-producing pathways involving (S)-malate and ornithine, quorum sensing, sporulation, and cell wall remodeling, suggesting a global and multicellular response to lithotrophic conditions. With syngas, the upregulated (R)-lactate dehydrogenase gene represents a route of electron transfer from ferredoxin to NAD. With H/CO, flavodoxin and histidine biosynthesis genes were upregulated. Downregulated genes corresponded to an intracytoplasmic microcompartment for disposal of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several cytoplasmic and membrane-associated redox-active protein genes were differentially regulated. The transcriptomic profiles of C. ljungdahlii in lithotrophic and organotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide biofuel and commodity chemical production with this species.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29030620?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Dang, Yan</style></author><author><style face="normal" font="default" size="100%">Walker, David J F</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The electrically conductive pili of pecies are a recently evolved feature for extracellular electron transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Genom</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb Genom</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electromagnetic Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">e000072</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The electrically conductive pili (e-pili) of  have environmental and practical significance because they can facilitate electron transfer to insoluble Fe(III) oxides; to other microbial species; and through electrically conductive biofilms. E-pili conductivity has been attributed to the truncated PilA monomer, which permits tight packing of aromatic amino acids to form a conductive path along the length of e-pili. In order to better understand the evolution and distribution of e-pili in the microbial world, type IVa PilA proteins from various Gram-negative and Gram-positive bacteria were examined with a particular emphasis on Fe(III)-respiring bacteria. E-pilin genes are primarily restricted to a tight phylogenetic group in the order Desulfuromonadales. The downstream gene in all but one of the Desulfuromonadales that possess an e-pilin gene is a gene previously annotated as '' that has characteristics suggesting that it may encode an outer-membrane protein. Other genes associated with pilin function are clustered with e-pilin and '' genes in the Desulfuromonadales. In contrast, in the few bacteria outside the Desulfuromonadales that contain e-pilin genes, the other genes required for pilin function may have been acquired through horizontal gene transfer. Of the 95 known Fe(III)-reducing micro-organisms for which genomes are available, 80 % lack e-pilin genes, suggesting that e-pili are just one of several mechanisms involved in extracellular electron transport. These studies provide insight into where and when e-pili are likely to contribute to extracellular electron transport processes that are biogeochemically important and involved in bioenergy conversions.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/28348867?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Dang, Yan</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Zhao, Zhiqiang</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Zhang, Yaobin</style></author><author><style face="normal" font="default" size="100%">Sun, Dezhi</style></author><author><style face="normal" font="default" size="100%">Wang, Li-Ying</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Enhancing anaerobic digestion of complex organic waste with carbon-based conductive materials.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioresour Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioresour Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioreactors</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Fiber</style></keyword><keyword><style  face="normal" font="default" size="100%">Charcoal</style></keyword><keyword><style  face="normal" font="default" size="100%">Dogs</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Fatty Acids, Volatile</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Organic Chemicals</style></keyword><keyword><style  face="normal" font="default" size="100%">Waste Products</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">220</style></volume><pages><style face="normal" font="default" size="100%">516-522</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The aim of this work was to study the methanogenic metabolism of dog food, a food waste surrogate, in laboratory-scale reactors with different carbon-based conductive materials. Carbon cloth, carbon felt, and granular activated carbon all permitted higher organic loading rates and promoted faster recovery of soured reactors than the control reactors. Microbial community analysis revealed that specific and substantial enrichments of Sporanaerobacter and Methanosarcina were present on the carbon cloth surface. These results, and the known ability of Sporanaerobacter species to transfer electrons to elemental sulfur, suggest that Sporanaerobacter species can participate in direct interspecies electron transfer with Methanosarcina species when carbon cloth is available as an electron transfer mediator.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27611035?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wang, Li-Ying</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Mu, Bo-Zhong</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Expanding the Diet for DIET: Electron Donors Supporting Direct Interspecies Electron Transfer (DIET) in Defined Co-Cultures.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">236</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) has been recognized as an alternative to interspecies H2 transfer as a mechanism for syntrophic growth, but previous studies on DIET with defined co-cultures have only documented DIET with ethanol as the electron donor in the absence of conductive materials. Co-cultures of Geobacter metallireducens and Geobacter sulfurreducens metabolized propanol, butanol, propionate, and butyrate with the reduction of fumarate to succinate. G. metallireducens utilized each of these substrates whereas only electrons available from DIET supported G. sulfurreducens respiration. A co-culture of G. metallireducens and a strain of G. sulfurreducens that could not metabolize acetate oxidized acetate with fumarate as the electron acceptor, demonstrating that acetate can also be syntrophically metabolized via DIET. A co-culture of G. metallireducens and Methanosaeta harundinacea previously shown to syntrophically convert ethanol to methane via DIET metabolized propanol or butanol as the sole electron donor, but not propionate or butyrate. The stoichiometric accumulation of propionate or butyrate in the propanol- or butanol-fed cultures demonstrated that M. harundinaceae could conserve energy to support growth solely from electrons derived from DIET. Co-cultures of G. metallireducens and Methanosarcina barkeri could also incompletely metabolize propanol and butanol and did not metabolize propionate or butyrate as sole electron donors. These results expand the range of substrates that are known to be syntrophically metabolized through DIET, but suggest that claims of propionate and butyrate metabolism via DIET in mixed microbial communities warrant further validation.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/26973614?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yun, Jiae</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">310-20</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/26140532?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genetic switches and related tools for controlling gene expression and electrical outputs of Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Ind Microbiol Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Ind Microbiol Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Acetyl Coenzyme A</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Isopropyl Thiogalactoside</style></keyword><keyword><style  face="normal" font="default" size="100%">L-Lactate Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Lac Repressors</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Transferases</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">43</style></volume><pages><style face="normal" font="default" size="100%">1561-1575</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Physiological studies and biotechnology applications of Geobacter species have been limited by a lack of genetic tools. Therefore, potential additional molecular strategies for controlling metabolism were explored. When the gene for citrate synthase, or acetyl-CoA transferase, was placed under the control of a LacI/IPTG regulator/inducer system, cells grew on acetate only in the presence of IPTG. The TetR/AT system could also be used to control citrate synthase gene expression and acetate metabolism. A strain that required IPTG for growth on D-lactate was constructed by placing the gene for D-lactate dehydrogenase under the control of the LacI/IPTG system. D-Lactate served as an inducer in a strain in which a D-lactate responsive promoter and transcription repressor were used to control citrate synthase expression. Iron- and potassium-responsive systems were successfully incorporated to regulate citrate synthase expression and growth on acetate. Linking the appropriate degradation tags on the citrate synthase protein made it possible to control acetate metabolism with either the endogenous ClpXP or exogenous Lon protease and tag system. The ability to control current output from Geobacter biofilms and the construction of an AND logic gate for acetate metabolism suggested that the tools developed may be applicable for biosensor and biocomputing applications.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27659960?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Caitlyn S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">How to Sustainably Feed a Microbe: Strategies for Biological Production of Carbon-Based Commodities with Renewable Electricity.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">1879</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;As interest and application of renewable energy grows, strategies are needed to align the asynchronous supply and demand. Microbial metabolisms are a potentially sustainable mechanism for transforming renewable electrical energy into biocommodities that are easily stored and transported. Acetogens and methanogens can reduce carbon dioxide to organic products including methane, acetic acid, and ethanol. The library of biocommodities is expanded when engineered metabolisms of acetogens are included. Typically, electrochemical systems are employed to integrate renewable energy sources with biological systems for production of carbon-based commodities. Within these systems, there are three prevailing mechanisms for delivering electrons to microorganisms for the conversion of carbon dioxide to reduce organic compounds: (1) electrons can be delivered to microorganisms via H produced separately in a electrolyzer, (2) H produced at a cathode can convey electrons to microorganisms supported on the cathode surface, and (3) a cathode can directly feed electrons to microorganisms. Each of these strategies has advantages and disadvantages that must be considered in designing full-scale processes. This review considers the evolving understanding of each of these approaches and the state of design for advancing these strategies toward viability.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27965629?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tan, Yang</style></author><author><style face="normal" font="default" size="100%">Adhikari, Ramesh Y</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Snoeyenbos-West, Oona L</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Low Conductivity of Geobacter uraniireducens Pili Suggests a Diversity of Extracellular Electron Transfer Mechanisms in the Genus Geobacter.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">980</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Studies on the mechanisms for extracellular electron transfer in Geobacter species have primarily focused on Geobacter sulfurreducens, but the poor conservation of genes for some electron transfer components within the Geobacter genus suggests that there may be a diversity of extracellular electron transport strategies among Geobacter species. Examination of the gene sequences for PilA, the type IV pilus monomer, in Geobacter species revealed that the PilA sequence of Geobacter uraniireducens was much longer than that of G. sulfurreducens. This is of interest because it has been proposed that the relatively short PilA sequence of G. sulfurreducens is an important feature conferring conductivity to G. sulfurreducens pili. In order to investigate the properties of the G. uraniireducens pili in more detail, a strain of G. sulfurreducens that expressed pili comprised the PilA of G. uraniireducens was constructed. This strain, designated strain GUP, produced abundant pili, but generated low current densities and reduced Fe(III) very poorly. At pH 7, the conductivity of the G. uraniireducens pili was 3 × 10(-4) S/cm, much lower than the previously reported 5 × 10(-2) S/cm conductivity of G. sulfurreducens pili at the same pH. Consideration of the likely voltage difference across pili during Fe(III) oxide reduction suggested that G. sulfurreducens pili can readily accommodate maximum reported rates of respiration, but that G. uraniireducens pili are not sufficiently conductive to be an effective mediator of long-range electron transfer. In contrast to G. sulfurreducens and G. metallireducens, which require direct contact with Fe(III) oxides in order to reduce them, G. uraniireducens reduced Fe(III) oxides occluded within microporous beads, demonstrating that G. uraniireducens produces a soluble electron shuttle to facilitate Fe(III) oxide reduction. The results demonstrate that Geobacter species may differ substantially in their mechanisms for long-range electron transport and that it is important to have information beyond a phylogenetic affiliation in order to make conclusions about the mechanisms by which Geobacter species are transferring electrons to extracellular electron acceptors.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27446021?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xiao, Ke</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Shu, Chuanjun</style></author><author><style face="normal" font="default" size="100%">Martz, Eric</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Sun, Xiao</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili.</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Sci Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Theoretical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Mar 22</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">23385</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27001169?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhao, Zhiqiang</style></author><author><style face="normal" font="default" size="100%">Zhang, Yaobin</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Dang, Yan</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Potential enhancement of direct interspecies electron transfer for syntrophic metabolism of propionate and butyrate with biochar in up-flow anaerobic sludge blanket reactors.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioresour Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioresour Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioreactors</style></keyword><keyword><style  face="normal" font="default" size="100%">Butyric Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Charcoal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Consortia</style></keyword><keyword><style  face="normal" font="default" size="100%">Propionates</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sewage</style></keyword><keyword><style  face="normal" font="default" size="100%">Waste Disposal, Fluid</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">209</style></volume><pages><style face="normal" font="default" size="100%">148-56</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Promoting direct interspecies electron transfer (DIET) to enhance syntrophic metabolism may be a strategy for accelerating the conversion of organic wastes to methane, but microorganisms capable of metabolizing propionate and butyrate via DIET under methanogenic conditions have yet to be identified. In an attempt to establish methanogenic communities metabolizing propionate or butyrate with DIET, enrichments were initiated with up-flow anaerobic sludge blanket (UASB), similar to those that were previously reported to support communities that metabolized ethanol with DIET that relied on direct biological electrical connections. In the absence of any amendments, microbial communities enriched were dominated by microorganisms closely related to pure cultures that are known to metabolize propionate or butyrate to acetate with production of H2. When biochar was added to the reactors there was a substantial enrichment on the biochar surface of 16S rRNA gene sequences closely related to Geobacter and Methanosaeta species known to participate in DIET.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/26967338?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Rotello, Vincent M</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reply to 'Measuring conductivity of living Geobacter sulfurreducens biofilms'.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Nanotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Nanotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Nov 08</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">913-914</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27821844?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tan, Yang</style></author><author><style face="normal" font="default" size="100%">Adhikari, Ramesh Y</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Pi, Shuang</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Xia, Qiangfei</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Synthetic Biological Protein Nanowires with High Conductivity.</style></title><secondary-title><style face="normal" font="default" size="100%">Small</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Small</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Tryptophan</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">4481-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Genetic modification to add tryptophan to PilA, the monomer for the electrically conductive pili of Geobacter sulfurreducens, yields conductive protein filaments 2000-fold more conductive than the wild-type pili while cutting the diameter in half to 1.5 nm.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">33</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27409066?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">King, Gary M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Centimeter-long electron transport in marine sediments via conductive minerals.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Minerals</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">527-31</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Centimeter-long electron conduction through marine sediments, in which electrons derived from sulfide in anoxic sediments are transported to oxygen in surficial sediments, may have an important influence on sediment geochemistry. Filamentous bacteria have been proposed to mediate the electron transport, but the filament conductivity could not be verified and other mechanisms are possible. Surprisingly, previous investigations have never actually measured the sediment conductivity or its basic physical properties. Here we report direct measurements that demonstrate centimeter-long electron flow through marine sediments, with conductivities sufficient to account for previously estimated electron fluxes. Conductivity was lost for oxidized sediments, which contrasts with the previously described increase in the conductivity of microbial biofilms upon oxidation. Adding pyrite to the sediments significantly enhanced the conductivity. These results suggest that the role of conductive minerals, which are more commonly found in sediments than centimeter-long microbial filaments, need to be considered when modeling marine sediment biogeochemistry.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25050525?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Chaurasia, Akhilesh K</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Luef, Birgit</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Wrighton, Kelly C</style></author><author><style face="normal" font="default" size="100%">Thompson, Courtney A</style></author><author><style face="normal" font="default" size="100%">Comolli, Luis R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriophages</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Viral</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Metagenome</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Viral Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">333-46</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25083935?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Link between capacity for current production and syntrophic growth in Geobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">744</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Electrodes are unnatural electron acceptors, and it is yet unknown how some Geobacter species evolved to use electrodes as terminal electron acceptors. Analysis of different Geobacter species revealed that they varied in their capacity for current production. Geobacter metallireducens and G. hydrogenophilus generated high current densities (ca. 0.2 mA/cm(2)), comparable to G. sulfurreducens. G. bremensis, G. chapellei, G. humireducens, and G. uraniireducens, produced much lower currents (ca. 0.05 mA/cm(2)) and G. bemidjiensis was previously found to not produce current. There was no correspondence between the effectiveness of current generation and Fe(III) oxide reduction rates. Some high-current-density strains (G. metallireducens and G. hydrogenophilus) reduced Fe(III)-oxides as fast as some low-current-density strains (G. bremensis, G. humireducens, and G. uraniireducens) whereas other low-current-density strains (G. bemidjiensis and G. chapellei) reduced Fe(III) oxide as slowly as G. sulfurreducens, a high-current-density strain. However, there was a correspondence between the ability to produce higher currents and the ability to grow syntrophically. G. hydrogenophilus was found to grow in co-culture with Methanosarcina barkeri, which is capable of direct interspecies electron transfer (DIET), but not with Methanospirillum hungatei capable only of H2 or formate transfer. Conductive granular activated carbon (GAC) stimulated metabolism of the G. hydrogenophilus - M. barkeri co-culture, consistent with electron exchange via DIET. These findings, coupled with the previous finding that G. metallireducens and G. sulfurreducens are also capable of DIET, suggest that evolution to optimize DIET has fortuitously conferred the capability for high-density current production to some Geobacter species.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/26284037?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Magnetite compensates for the lack of a pilin-associated c-type cytochrome in extracellular electron exchange.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferrosoferric Oxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Heme</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">648-55</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Nanoscale magnetite can facilitate microbial extracellular electron transfer that plays an important role in biogeochemical cycles, bioremediation and several bioenergy strategies, but the mechanisms for the stimulation of extracellular electron transfer are poorly understood. Further investigation revealed that magnetite attached to the electrically conductive pili of Geobacter species in a manner reminiscent of the association of the multi-heme c-type cytochrome OmcS with the pili of Geobacter sulfurreducens. Magnetite conferred extracellular electron capabilities on an OmcS-deficient strain unable to participate in interspecies electron transfer or Fe(III) oxide reduction. In the presence of magnetite wild-type cells repressed expression of the OmcS gene, suggesting that cells might need to produce less OmcS when magnetite was available. The finding that magnetite can compensate for the lack of the electron transfer functions of a multi-heme c-type cytochrome has implications not only for the function of modern microbes, but also for the early evolution of microbial electron transport mechanisms.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24725505?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Snoeyenbos-West, Oona L</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Strickland, Justin N</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Protozoan grazing reduces the current output of microbial fuel cells.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioresour Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioresour Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Eukaryota</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">193</style></volume><pages><style face="normal" font="default" size="100%">8-14</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/26115527?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Seeing is believing: novel imaging techniques help clarify microbial nanowire structure and function.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Atomic Force</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword><keyword><style  face="normal" font="default" size="100%">Periplasm</style></keyword><keyword><style  face="normal" font="default" size="100%">Shewanella</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">2209-15</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Novel imaging approaches have recently helped to clarify the properties of 'microbial nanowires'. Geobacter sulfurreducens pili are actual wires. They possess metallic-like conductivity, which can be attributed to overlapping pi-pi orbitals of key aromatic amino acids. Electrostatic force microscopy recently confirmed charge propagation along the pili, in a manner similar to carbon nanotubes. The pili are essential for long-range electron transport to insoluble electron acceptors and interspecies electron transfer. Previous claims that Shewanella oneidensis also produce conductive pili have recently been recanted, based on novel live-imaging studies. The putative pili are, in fact, long extensions of the cytochrome-rich outer membrane and periplasm that, when dried, collapse to form filaments with dimensions similar to pili. It has yet to be demonstrated whether the cytochrome-to-cytochrome electron hopping documented in the dried membrane extensions takes place in intact hydrated membrane extensions or whether the membrane extensions enhance electron transport to insoluble electron acceptors such as Fe(III) oxides or electrodes. These findings demonstrate that G. sulfurreducens conductive pili and the outer membrane extensions of S. oneidensis are fundamentally different in composition, mechanism of electron transport and physiological role. New methods for evaluating filament conductivity will facilitate screening the microbial world for nanowires and elucidating their function.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25384844?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Giddings, Cloelle G S</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodward, Trevor</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Butler, Caitlyn S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Simplifying microbial electrosynthesis reactor design.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">468</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial electrosynthesis, an artificial form of photosynthesis, can efficiently convert carbon dioxide into organic commodities; however, this process has only previously been demonstrated in reactors that have features likely to be a barrier to scale-up. Therefore, the possibility of simplifying reactor design by both eliminating potentiostatic control of the cathode and removing the membrane separating the anode and cathode was investigated with biofilms of Sporomusa ovata. S. ovata reduces carbon dioxide to acetate and acts as the microbial catalyst for plain graphite stick cathodes as the electron donor. In traditional 'H-cell' reactors, where the anode and cathode chambers were separated with a proton-selective membrane, the rates and columbic efficiencies of microbial electrosynthesis remained high when electron delivery at the cathode was powered with a direct current power source rather than with a potentiostat-poised cathode utilized in previous studies. A membrane-less reactor with a direct-current power source with the cathode and anode positioned to avoid oxygen exposure at the cathode, retained high rates of acetate production as well as high columbic and energetic efficiencies. The finding that microbial electrosynthesis is feasible without a membrane separating the anode from the cathode, coupled with a direct current power source supplying the energy for electron delivery, is expected to greatly simplify future reactor design and lower construction costs.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/26029199?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Vargas, Madeline</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Evans-Lutterodt, Kenneth</style></author><author><style face="normal" font="default" size="100%">Nykypanchuk, Dmytro</style></author><author><style face="normal" font="default" size="100%">Martz, Eric</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Structural basis for metallic-like conductivity in microbial nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acids, Aromatic</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophysiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">X-Ray Diffraction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015 Mar 03</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">e00084</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;Direct measurement of multiple physical properties of Geobacter sulfurreducens pili have demonstrated that they possess metallic-like conductivity, but several studies have suggested that metallic-like conductivity is unlikely based on the structures of the G. sulfurreducens pilus predicted from homology models. In order to further evaluate this discrepancy, pili were examined with synchrotron X-ray microdiffraction and rocking-curve X-ray diffraction. Both techniques revealed a periodic 3.2-Å spacing in conductive, wild-type G. sulfurreducens pili that was missing in the nonconductive pili of strain Aro5, which lack key aromatic acids required for conductivity. The intensity of the 3.2-Å peak increased 100-fold when the pH was shifted from 10.5 to 2, corresponding with a previously reported 100-fold increase in pilus conductivity with this pH change. These results suggest a clear structure-function correlation for metallic-like conductivity that can be attributed to overlapping π-orbitals of aromatic amino acids. A homology model of the G. sulfurreducens pilus was constructed with a Pseudomonas aeruginosa pilus model as a template as an alternative to previous models, which were based on a Neisseria gonorrhoeae pilus structure. This alternative model predicted that aromatic amino acids in G. sulfurreducens pili are packed within 3 to 4 Å, consistent with the experimental results. Thus, the predictions of homology modeling are highly sensitive to assumptions inherent in the model construction. The experimental results reported here further support the concept that the pili of G. sulfurreducens represent a novel class of electronically functional proteins in which aromatic amino acids promote long-distance electron transport.&lt;/p&gt;&lt;p&gt;&lt;b&gt;IMPORTANCE: &lt;/b&gt;The mechanism for long-range electron transport along the conductive pili of Geobacter sulfurreducens is of interest because these &quot;microbial nanowires&quot; are important in biogeochemical cycling as well as applications in bioenergy and bioelectronics. Although proteins are typically insulators, G. sulfurreducens pilus proteins possess metallic-like conductivity. The studies reported here provide important structural insights into the mechanism of the metallic-like conductivity of G. sulfurreducens pili. This information is expected to be useful in the design of novel bioelectronic materials.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25736881?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Syntrophic growth via quinone-mediated interspecies electron transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2015</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2015</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">121</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The mechanisms by which microbial species exchange electrons are of interest because interspecies electron transfer can expand the metabolic capabilities of microbial communities. Previous studies with the humic substance analog anthraquinone-2,6-disulfonate (AQDS) suggested that quinone-mediated interspecies electron transfer (QUIET) is feasible, but it was not determined if sufficient energy is available from QUIET to support the growth of both species. Furthermore, there have been no previous studies on the mechanisms for the oxidation of anthrahydroquinone-2,6-disulfonate (AHQDS). A co-culture of Geobacter metallireducens and G. sulfurreducens metabolized ethanol with the reduction of fumarate much faster in the presence of AQDS, and there was an increase in cell protein. G. sulfurreducens was more abundant, consistent with G. sulfurreducens obtaining electrons from acetate that G. metallireducens produced from ethanol, as well as from AHQDS. Co-cultures initiated with a citrate synthase-deficient strain of G. sulfurreducens that was unable to use acetate as an electron donor also metabolized ethanol with the reduction of fumarate and cell growth, but acetate accumulated over time. G. sulfurreducens and G. metallireducens were equally abundant in these co-cultures reflecting the inability of the citrate synthase-deficient strain of G. sulfurreducens to metabolize acetate. Evaluation of the mechanisms by which G. sulfurreducens accepts electrons from AHQDS demonstrated that a strain deficient in outer-surface c-type cytochromes that are required for AQDS reduction was as effective at QUIET as the wild-type strain. Deletion of additional genes previously implicated in extracellular electron transfer also had no impact on QUIET. These results demonstrate that QUIET can yield sufficient energy to support the growth of both syntrophic partners, but that the mechanisms by which electrons are derived from extracellular hydroquinones require further investigation.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25741332?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chen, Shanshan</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Philips, Jo</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Carbon cloth stimulates direct interspecies electron transfer in syntrophic co-cultures.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioresour Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioresour Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Communication</style></keyword><keyword><style  face="normal" font="default" size="100%">Coculture Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Materials Testing</style></keyword><keyword><style  face="normal" font="default" size="100%">Membranes, Artificial</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Consortia</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Symbiosis</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">173</style></volume><pages><style face="normal" font="default" size="100%">82-86</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;This study investigated the possibility that the electrical conductivity of carbon cloth accelerates direct interspecies electron transfer (DIET) in co-cultures. Carbon cloth accelerated metabolism of DIET co-cultures (Geobacter metallireducens-Geobacter sulfurreducens and G.metallireducens-Methanosarcina barkeri) but did not promote metabolism of co-cultures performing interspecies H2 transfer (Desulfovibrio vulgaris-G.sulfurreducens). On the other hand, DIET co-cultures were not stimulated by poorly conductive cotton cloth. Mutant strains lacking electrically conductive pili, or pili-associated cytochromes participated in DIET only in the presence of carbon cloth. In co-cultures promoted by carbon cloth, cells were primarily associated with the cloth although the syntrophic partners were too far apart for cell-to-cell biological electrical connections to be feasible. Carbon cloth seemingly mediated interspecies electron transfer between the distant syntrophic partners. These results suggest that the ability of carbon cloth to accelerate DIET should be considered in anaerobic digester designs that incorporate carbon cloth.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25285763?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Feist, Adam M</style></author><author><style face="normal" font="default" size="100%">Nagarajan, Harish</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">e1003575</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24762737?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetyl Coenzyme A</style></keyword><keyword><style  face="normal" font="default" size="100%">Butyrates</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Engineering</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Flux Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombinant Proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Oct 21</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">e01636-14</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahlii chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. Importance: The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors for C. ljungdahlii include carbon monoxide, which can be derived from industrial waste gases or the conversion of recalcitrant biomass to syngas, as well as hydrogen, another syngas component. The finding that carbon and electron flow in C. ljungdahlii can be diverted from the production of acetate to butyrate synthesis is an important step toward the goal of renewable commodity production from carbon dioxide with this organism.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25336453?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Werner, Jeffrey J</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Elena-Rotaru, Amelia</style></author><author><style face="normal" font="default" size="100%">Shrestha, Minita</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Angenent, Largus T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Correlation between microbial community and granule conductivity in anaerobic bioreactors for brewery wastewater treatment.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioresour Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioresour Technol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Alcoholic Beverages</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioreactors</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Sewage</style></keyword><keyword><style  face="normal" font="default" size="100%">Waste Disposal, Fluid</style></keyword><keyword><style  face="normal" font="default" size="100%">Wastewater</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Purification</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">174</style></volume><pages><style face="normal" font="default" size="100%">306-10</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Prior investigation of an upflow anaerobic sludge blanket (UASB) reactor treating brewery wastes suggested that direct interspecies electron transfer (DIET) significantly contributed to interspecies electron transfer to methanogens. To investigate DIET in granules further, the electrical conductivity and bacterial community composition of granules in fourteen samples from four different UASB reactors treating brewery wastes were investigated. All of the UASB granules were electrically conductive whereas control granules from ANAMMOX (ANaerobic AMMonium OXidation) reactors and microbial granules from an aerobic bioreactor designed for phosphate removal were not. There was a moderate correlation (r=0.67) between the abundance of Geobacter species in the UASB granules and granule conductivity, suggesting that Geobacter contributed to granule conductivity. These results, coupled with previous studies, which have demonstrated that Geobacter species can donate electrons to methanogens that are typically predominant in anaerobic digesters, suggest that DIET may be a widespread phenomenon in UASB reactors treating brewery wastes.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25443621?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Markovaite, Beatrice</style></author><author><style face="normal" font="default" size="100%">Chen, Shanshan</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biological Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina barkeri</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">80</style></volume><pages><style face="normal" font="default" size="100%">4599-605</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) is potentially an effective form of syntrophy in methanogenic communities, but little is known about the diversity of methanogens capable of DIET. The ability of Methanosarcina barkeri to participate in DIET was evaluated in coculture with Geobacter metallireducens. Cocultures formed aggregates that shared electrons via DIET during the stoichiometric conversion of ethanol to methane. Cocultures could not be initiated with a pilin-deficient G. metallireducens strain, suggesting that long-range electron transfer along pili was important for DIET. Amendments of granular activated carbon permitted the pilin-deficient G. metallireducens isolates to share electrons with M. barkeri, demonstrating that this conductive material could substitute for pili in promoting DIET. When M. barkeri was grown in coculture with the H2-producing Pelobacter carbinolicus, incapable of DIET, M. barkeri utilized H2 as an electron donor but metabolized little of the acetate that P.carbinolicus produced. This suggested that H2, but not electrons derived from DIET, inhibited acetate metabolism. P. carbinolicus-M. barkeri cocultures did not aggregate, demonstrating that, unlike DIET, close physical contact was not necessary for interspecies H2 transfer. M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2 or electrons derived from DIET for CO2 reduction. Furthermore, M. barkeri is genetically tractable,making it a model organism for elucidating mechanisms by which methanogens make biological electrical connections with other cells.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">15</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24837373?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shanmugam, Raghuvaran</style></author><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Schäfer, Matthias</style></author><author><style face="normal" font="default" size="100%">Reinhardt, Richard</style></author><author><style face="normal" font="default" size="100%">Nickel, Olaf</style></author><author><style face="normal" font="default" size="100%">Reuter, Gunter</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Ehrenhofer-Murray, Ann</style></author><author><style face="normal" font="default" size="100%">Nellen, Wolfgang</style></author><author><style face="normal" font="default" size="100%">Ankri, Serge</style></author><author><style face="normal" font="default" size="100%">Helm, Mark</style></author><author><style face="normal" font="default" size="100%">Jurkowski, Tomasz P</style></author><author><style face="normal" font="default" size="100%">Jeltsch, Albert</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Methylation</style></keyword><keyword><style  face="normal" font="default" size="100%">Mice</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Transfer, Asp</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Transfer, Glu</style></keyword><keyword><style  face="normal" font="default" size="100%">Substrate Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">tRNA Methyltransferases</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">42</style></volume><pages><style face="normal" font="default" size="100%">6487-96</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24711368?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liu, Xing</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Vargas, Madeline</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A Geobacter sulfurreducens strain expressing pseudomonas aeruginosa type IV pili localizes OmcS on pili but is deficient in Fe(III) oxide reduction and current production.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcinaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Pseudomonas aeruginosa</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">80</style></volume><pages><style face="normal" font="default" size="100%">1219-24</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The conductive pili of Geobacter species play an important role in electron transfer to Fe(III) oxides, in long-range electron transport through current-producing biofilms, and in direct interspecies electron transfer. Although multiple lines of evidence have indicated that the pili of Geobacter sulfurreducens have a metal-like conductivity, independent of the presence of c-type cytochromes, this claim is still controversial. In order to further investigate this phenomenon, a strain of G. sulfurreducens, designated strain PA, was constructed in which the gene for the native PilA, the structural pilin protein, was replaced with the PilA gene of Pseudomonas aeruginosa PAO1. Strain PA expressed and properly assembled P. aeruginosa PilA subunits into pili and exhibited a profile of outer surface c-type cytochromes similar to that of a control strain expressing the G. sulfurreducens PilA. Surprisingly, the strain PA pili were decorated with the c-type cytochrome OmcS in a manner similar to the control strain. However, the strain PA pili were 14-fold less conductive than the pili of the control strain, and strain PA was severely impaired in Fe(III) oxide reduction and current production. These results demonstrate that the presence of OmcS on pili is not sufficient to confer conductivity to pili and suggest that there are unique structural features of the G. sulfurreducens PilA that are necessary for conductivity.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24296506?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Snoeyenbos-West, Oona L</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Going wireless: Fe(III) oxide reduction without pili by Geobacter sulfurreducens strain JS-1.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">80</style></volume><pages><style face="normal" font="default" size="100%">4331-40</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Previous studies have suggested that the conductive pili of Geobacter sulfurreducens are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of G. sulfurreducens reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (&gt;30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the c-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through G. sulfurreducens biofilms is more effective via pili.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">14</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24814783?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Chaurasia, Akhilesh K</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Bain, Timothy S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">245</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Although the biochemical pathways for the anaerobic degradation of many of the hydrocarbon constituents in petroleum reservoirs have been elucidated, the mechanisms for anaerobic activation of benzene, a very stable molecule, are not known. Previous studies have demonstrated that Geobacter metallireducens can anaerobically oxidize benzene to carbon dioxide with Fe(III) as the sole electron acceptor and that phenol is an intermediate in benzene oxidation. In an attempt to identify enzymes that might be involved in the conversion of benzene to phenol, whole-genome gene transcript abundance was compared in cells metabolizing benzene and cells metabolizing phenol. Eleven genes had significantly higher transcript abundance in benzene-metabolizing cells. Five of these genes had annotations suggesting that they did not encode proteins that could be involved in benzene metabolism and were not further studied. Strains were constructed in which one of the remaining six genes was deleted. The strain in which the monocistronic gene Gmet 0232 was deleted metabolized phenol, but not benzene. Transcript abundance of the adjacent monocistronic gene, Gmet 0231, predicted to encode a zinc-containing oxidoreductase, was elevated in cells metabolizing benzene, although not at a statistically significant level. However, deleting Gmet 0231 also yielded a strain that could metabolize phenol, but not benzene. Although homologs of Gmet 0231 and Gmet 0232 are found in microorganisms not known to anaerobically metabolize benzene, the adjacent localization of these genes is unique to G. metallireducens. The discovery of genes that are specifically required for the metabolism of benzene, but not phenol in G. metallireducens is an important step in potentially identifying the mechanisms for anaerobic benzene activation.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24904558?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Banerjee, Areen</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Lactose-inducible system for metabolic engineering of Clostridium ljungdahlii.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Acetone</style></keyword><keyword><style  face="normal" font="default" size="100%">Acetyl Coenzyme A</style></keyword><keyword><style  face="normal" font="default" size="100%">Alcohol Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Fructose</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Lactose</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Engineering</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Flux Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptional Activation</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">80</style></volume><pages><style face="normal" font="default" size="100%">2410-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The development of tools for genetic manipulation of Clostridium ljungdahlii has increased its attractiveness as a chassis for autotrophic production of organic commodities and biofuels from syngas and microbial electrosynthesis and established it as a model organism for the study of the basic physiology of acetogenesis. In an attempt to expand the genetic toolbox for C. ljungdahlii, the possibility of adapting a lactose-inducible system for gene expression, previously reported for Clostridium perfringens, was investigated. The plasmid pAH2, originally developed for C. perfringens with a gusA reporter gene, functioned as an effective lactose-inducible system in C. ljungdahlii. Lactose induction of C. ljungdahlii containing pB1, in which the gene for the aldehyde/alcohol dehydrogenase AdhE1 was downstream of the lactose-inducible promoter, increased expression of adhE1 30-fold over the wild-type level, increasing ethanol production 1.5-fold, with a corresponding decrease in acetate production. Lactose-inducible expression of adhE1 in a strain in which adhE1 and the adhE1 homolog adhE2 had been deleted from the chromosome restored ethanol production to levels comparable to those in the wild-type strain. Inducing expression of adhE2 similarly failed to restore ethanol production, suggesting that adhE1 is the homolog responsible for ethanol production. Lactose-inducible expression of the four heterologous genes necessary to convert acetyl coenzyme A (acetyl-CoA) to acetone diverted ca. 60% of carbon flow to acetone production during growth on fructose, and 25% of carbon flow went to acetone when carbon monoxide was the electron donor. These studies demonstrate that the lactose-inducible system described here will be useful for redirecting carbon and electron flow for the biosynthesis of products more valuable than acetate. Furthermore, this tool should aid in optimizing microbial electrosynthesis and for basic studies on the physiology of acetogenesis.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24509933?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Orellana, Roberto</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Robbins, Mark J</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">366</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Previous studies have suggested that protozoa prey on Fe(III)- and sulfate-reducing bacteria that are enriched when acetate is added to uranium contaminated subsurface sediments to stimulate U(VI) reduction. In order to determine whether protozoa continue to impact subsurface biogeochemistry after these acetate amendments have stopped, 18S rRNA and ß-tubulin sequences from this phase of an in situ uranium bioremediation field experiment were analyzed. Sequences most similar to Metopus species predominated, with the majority of sequences most closely related to M. palaeformis, a cilitated protozoan known to harbor methanogenic symbionts. Quantification of mcrA mRNA transcripts in the groundwater suggested that methanogens closely related to Metopus endosymbionts were metabolically active at this time. There was a strong correlation between the number of mcrA transcripts from the putative endosymbiotic methanogen and Metopus ß-tubulin mRNA transcripts during the course of the field experiment, suggesting that the activity of the methanogens was dependent upon the activity of the Metopus species. Addition of the eukaryotic inhibitors cyclohexamide and colchicine to laboratory incubations of acetate-amended subsurface sediments significantly inhibited methane production and there was a direct correlation between methane concentration and Metopus ß-tubulin and putative symbiont mcrA gene copies. These results suggest that, following the stimulation of subsurface microbial growth with acetate, protozoa harboring methanogenic endosymbionts become important members of the microbial community, feeding on moribund biomass and producing methane.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25147543?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial nanowires for bioenergy applications.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Shewanella</style></keyword><keyword><style  face="normal" font="default" size="100%">Synthetic Biology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">27</style></volume><pages><style face="normal" font="default" size="100%">88-95</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial nanowires are electrically conductive filaments that facilitate long-range extracellular electron transfer. The model for electron transport along Shewanella oneidensis nanowires is electron hopping/tunneling between cytochromes adorning the filaments. Geobacter sulfurreducens nanowires are comprised of pili that have metal-like conductivity attributed to overlapping pi-pi orbitals of aromatic amino acids. The nanowires of Geobacter species have been implicated in direct interspecies electron transfer (DIET), which may be an important mode of syntrophy in the conversion of organic wastes to methane. Nanowire networks confer conductivity to Geobacter biofilms converting organic compounds to electricity in microbial fuel cells (MFCs) and increasing nanowire production is the only genetic manipulation shown to yield strains with improved current-producing capabilities. Introducing nanowires, or nanowire mimetics, might improve other bioenergy strategies that rely on extracellular electron exchange, such as microbial electrosynthesis. Similarities between microbial nanowires and synthetic conducting polymers suggest additional energy-related applications.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24863901?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chen, Shanshan</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Fan, Wei</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Promoting interspecies electron transfer with biochar.</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Sci Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Charcoal</style></keyword><keyword><style  face="normal" font="default" size="100%">Coculture Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Methanosarcina barkeri</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 May 21</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">5019</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Biochar, a charcoal-like product of the incomplete combustion of organic materials, is an increasingly popular soil amendment designed to improve soil fertility. We investigated the possibility that biochar could promote direct interspecies electron transfer (DIET) in a manner similar to that previously reported for granular activated carbon (GAC). Although the biochars investigated were 1000 times less conductive than GAC, they stimulated DIET in co-cultures of Geobacter metallireducens with Geobacter sulfurreducens or Methanosarcina barkeri in which ethanol was the electron donor. Cells were attached to the biochar, yet not in close contact, suggesting that electrons were likely conducted through the biochar, rather than biological electrical connections. The finding that biochar can stimulate DIET may be an important consideration when amending soils with biochar and can help explain why biochar may enhance methane production from organic wastes under anaerobic conditions.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24846283?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Orellana, Roberto</style></author><author><style face="normal" font="default" size="100%">Hixson, Kim K</style></author><author><style face="normal" font="default" size="100%">Murphy, Sean</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Sharma, Manju L</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Proteome of Geobacter sulfurreducens in the presence of U(VI).</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology (Reading)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Organometallic Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">160</style></volume><pages><style face="normal" font="default" size="100%">2607-2617</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of Geobacter sulfurreducens exposed to 100 µM U(VI) acetate was compared to control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared with the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) on the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND (resistance-nodulation-cell division) family, and membrane protection, and other proteins, such as chaperones and proteins involved in secretion systems, were found in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in a higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew more slowly than the WT strain in the presence of U(VI), but not in its absence. The results suggested that there is no specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Pt 12</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25273002?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wardman, Colin</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Real-time monitoring of subsurface microbial metabolism with graphite electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Front Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Front Microbiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">621</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μM range. In order to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2-(14)C]-acetate metabolism. There was a direct correlation between current production and the rate that [2-(14)C]-acetate was metabolized to (14)CO2 and (14)CH4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. The results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25484879?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Bain, Timothy S</style></author><author><style face="normal" font="default" size="100%">Barlett, Melissa A</style></author><author><style face="normal" font="default" size="100%">Dar, Shabir A</style></author><author><style face="normal" font="default" size="100%">Snoeyenbos-West, Oona L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sulfur oxidation to sulfate coupled with electron transfer to electrodes by Desulfuromonas strain TZ1.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology (Reading)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Desulfuromonas</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">160</style></volume><pages><style face="normal" font="default" size="100%">123-129</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial oxidation of elemental sulfur with an electrode serving as the electron acceptor is of interest because this may play an important role in the recovery of electrons from sulfidic wastes and for current production in marine benthic microbial fuel cells. Enrichments initiated with a marine sediment inoculum, with elemental sulfur as the electron donor and a positively poised (+300 mV versus Ag/AgCl) anode as the electron acceptor, yielded an anode biofilm with a diversity of micro-organisms, including Thiobacillus, Sulfurimonas, Pseudomonas, Clostridium and Desulfuromonas species. Further enrichment of the anode biofilm inoculum in medium with elemental sulfur as the electron donor and Fe(III) oxide as the electron acceptor, followed by isolation in solidified sulfur/Fe(III) medium yielded a strain of Desulfuromonas, designated strain TZ1. Strain TZ1 effectively oxidized elemental sulfur to sulfate with an anode serving as the sole electron acceptor, at rates faster than Desulfobulbus propionicus, the only other organism in pure culture previously shown to oxidize S° with current production. The abundance of Desulfuromonas species enriched on the anodes of marine benthic fuel cells has previously been interpreted as acetate oxidation driving current production, but the results presented here suggest that sulfur-driven current production is a likely alternative.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Pt 1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24169815?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Yalcin, Sibel Ebru</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Visualization of charge propagation along individual pili proteins using ambient electrostatic force microscopy.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Nanotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Nanotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electrochemical, Scanning</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">1012-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The nanoscale imaging of charge flow in proteins is crucial to understanding several life processes, including respiration, metabolism and photosynthesis. However, existing imaging methods are only effective under non-physiological conditions or are limited to photosynthetic proteins. Here, we show that electrostatic force microscopy can be used to directly visualize charge propagation along pili of Geobacter sulfurreducens with nanometre resolution and under ambient conditions. Charges injected at a single point into individual, untreated pili, which are still attached to cells, propagated over the entire filament. The mobile charge density in the pili, as well as the temperature and pH dependence of the charge density, were similar to those of carbon nanotubes and other organic conductors. These findings, coupled with a lack of charge propagation in mutated pili that were missing key aromatic amino acids, suggest that the pili of G. sulfurreducens function as molecular wires with transport via delocalized charges, rather than the hopping mechanism that is typical of biological electron transport.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/25326694?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Chaurasia, Akhilesh Kumar</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Bain, Timothy S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Anaerobic benzene oxidation via phenol in Geobacter metallireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzene</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenol</style></keyword><keyword><style  face="normal" font="default" size="100%">Water</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">7800-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated in Geobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (&lt;0.5 μM) of phenol accumulated in cultures of Geobacter metallireducens anaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures of Geobacter sulfurreducens, a Geobacter species that cannot metabolize benzene. The phenol produced in G. metallireducens cultures was labeled with (18)O during growth in H2(18)O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in which Geobacter species are considered to play an important role in anaerobic benzene degradation.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">24</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24096430?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Vargas, Madeline</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Patel, Pranav</style></author><author><style face="normal" font="default" size="100%">Snoeyenbos-West, Oona</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Aromatic amino acids required for pili conductivity and long-range extracellular electron transport in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acids, Aromatic</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Mar 12</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">e00105-13</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;It has been proposed that Geobacter sulfurreducens requires conductive pili for long-range electron transport to Fe(III) oxides and for high-density current production in microbial fuel cells. In order to investigate this further, we constructed a strain of G. sulfurreducens, designated Aro-5, which produced pili with diminished conductivity. This was accomplished by modifying the amino acid sequence of PilA, the structural pilin protein. An alanine was substituted for each of the five aromatic amino acids in the carboxyl terminus of PilA, the region in which G. sulfurreducens PilA differs most significantly from the PilAs of microorganisms incapable of long-range extracellular electron transport. Strain Aro-5 produced pili that were properly decorated with the multiheme c-type cytochrome OmcS, which is essential for Fe(III) oxide reduction. However, pili preparations of the Aro-5 strain had greatly diminished conductivity and Aro-5 cultures were severely limited in their capacity to reduce Fe(III) compared to the control strain. Current production of the Aro-5 strain, with a graphite anode serving as the electron acceptor, was less than 10% of that of the control strain. The conductivity of the Aro-5 biofilms was 10-fold lower than the control strain's. These results demonstrate that the pili of G. sulfurreducens must be conductive in order for the cells to be effective in extracellular long-range electron transport.&lt;/p&gt;&lt;p&gt;&lt;b&gt;IMPORTANCE: &lt;/b&gt;Extracellular electron transfer by Geobacter species plays an important role in the biogeochemistry of soils and sediments and has a number of bioenergy applications. For example, microbial reduction of Fe(III) oxide is one of the most geochemically significant processes in anaerobic soils, aquatic sediments, and aquifers, and Geobacter organisms are often abundant in such environments. Geobacter sulfurreducens produces the highest current densities of any known pure culture, and close relatives are often the most abundant organisms colonizing anodes in microbial fuel cells that harvest electricity from wastewater or aquatic sediments. The finding that a strain of G. sulfurreducens that produces pili with low conductivity is limited in these extracellular electron transport functions provides further insight into these environmentally significant processes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23481602?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Bargar, John R</style></author><author><style face="normal" font="default" size="100%">Lloyd, Jonathan R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">489-97</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Adding organic electron donors to stimulate microbial reduction of highly soluble U(VI) to less soluble U(IV) is a promising strategy for immobilizing uranium in contaminated subsurface environments. Studies suggest that diagnosing the in situ physiological status of the subsurface community during uranium bioremediation with environmental transcriptomic and proteomic techniques can identify factors potentially limiting U(VI) reduction activity. Models which couple genome-scale in silico representations of the metabolism of key microbial populations with geochemical and hydrological models may be able to predict the outcome of bioremediation strategies and aid in the development of new approaches. Concerns remain about the long-term stability of sequestered U(IV) minerals and the release of co-contaminants associated with Fe(III) oxides, which might be overcome through targeted delivery of electrons to select microorganisms using in situ electrodes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23159488?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nagarajan, Harish</style></author><author><style face="normal" font="default" size="100%">Embree, Mallory</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Feist, Adam M</style></author><author><style face="normal" font="default" size="100%">Palsson, Bernhard Ø</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Symbiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">2809</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Syntrophic associations are central to microbial communities and thus have a fundamental role in the global carbon cycle. Despite biochemical approaches describing the physiological activity of these communities, there has been a lack of a mechanistic understanding of the relationship between complex nutritional and energetic dependencies and their functioning. Here we apply a multi-omic modelling workflow that combines genomic, transcriptomic and physiological data with genome-scale models to investigate dynamics and electron flow mechanisms in the syntrophic association of Geobacter metallireducens and Geobacter sulfurreducens. Genome-scale modelling of direct interspecies electron transfer reveals insights into the energetics of electron transfer mechanisms. While G. sulfurreducens adapts to rapid syntrophic growth by changes at the genomic and transcriptomic level, G. metallireducens responds only at the transcriptomic level. This multi-omic approach enhances our understanding of adaptive responses and factors that shape the evolution of syntrophic communities.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24264237?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wrighton, Kelly C</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Montgomery, Alison P</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Orellana, Roberto</style></author><author><style face="normal" font="default" size="100%">Thompson, Courtney A</style></author><author><style face="normal" font="default" size="100%">Roper, Thomas J</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Characterization and transcription of arsenic respiration and resistance genes during in situ uranium bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Arsenate Reductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Arsenic</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Colorado</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">370-83</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the α-subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative reverse transcription-PCR. Most of the arrA (&gt;60%) and acr3-1 (&gt;90%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (&gt;50%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated the transcription of arrA in situ, even though the presence of As(V) increased the transcription of arrA in cultures of Geobacter lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23038171?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nagarajan, Harish</style></author><author><style face="normal" font="default" size="100%">Sahin, Merve</style></author><author><style face="normal" font="default" size="100%">Nogales, Juan</style></author><author><style face="normal" font="default" size="100%">Latif, Haythem</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Ebrahim, Ali</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Cell Fact</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb Cell Fact</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofuels</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Engineering</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Nov 25</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">118</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24274140?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Qiu, Yu</style></author><author><style face="normal" font="default" size="100%">Nagarajan, Harish</style></author><author><style face="normal" font="default" size="100%">Embree, Mallory</style></author><author><style face="normal" font="default" size="100%">Shieu, Wendy</style></author><author><style face="normal" font="default" size="100%">Abate, Elisa</style></author><author><style face="normal" font="default" size="100%">Juárez, Katy</style></author><author><style face="normal" font="default" size="100%">Cho, Byung-Kwan</style></author><author><style face="normal" font="default" size="100%">Elkins, James G</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Barrett, Christian L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Palsson, Bernhard O</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Regulatory Networks</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Regulon</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">1755</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σ(N) being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23612296?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrobiocommodities: powering microbial production of fuels and commodity chemicals from carbon dioxide with electricity.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Respiration</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemical Industry</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxygen</style></keyword><keyword><style  face="normal" font="default" size="100%">Renewable Energy</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">385-90</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Electricity can be an energy source for microbially catalyzed production of fuels and other organic commodities from carbon dioxide. These electrobiocommodities (E-BCs) can be produced directly via electrode-to-microbe electron transfer or indirectly with electrochemically generated electron donors such as H2 or formate. Producing E-BCs may be a more efficient and environmentally sustainable strategy for converting solar energy to biocommodities than approaches that rely on biological photosynthesis. A diversity of microbial physiologies could potentially be adapted for E-BC production, but to date acetogenic microorganisms are the only organisms shown to covert electrically generated low potential electrons and carbon dioxide into multi-carbon organic products with high recovery of electrons in product. Substantial research and development will be required for E-BC commercialization.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23465755?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wrighton, Kelly C</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Thompson, Courtney A</style></author><author><style face="normal" font="default" size="100%">Roper, Thomas J</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Eukaryota</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 18S</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">1286-98</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23446832?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">N'Guessan, A Lucie</style></author><author><style face="normal" font="default" size="100%">Arey, Bruce</style></author><author><style face="normal" font="default" size="100%">Dodova, Elena</style></author><author><style face="normal" font="default" size="100%">Dohnalkova, Alice</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Field evidence of selenium bioreduction in a uranium-contaminated aquifer.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Microbiol Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Betaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Colorado</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Consortia</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxygen</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Selenic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Selenium</style></keyword><keyword><style  face="normal" font="default" size="100%">Selenium Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Thauera</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">444-52</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Removal of selenium from groundwater was documented during injection of acetate into a uranium-contaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm. Accumulation of Se0 within biofilms occurred over a three-week interval at a rate of c. 9 mg Se0 m(-2) tubing day(-1). Removal was inferred to result from the activity of a mixed microbial community within the biofilms capable of coupling acetate oxidation to the reduction of oxygen, nitrate and selenate. Phylogenetic analysis of the biofilm revealed a community dominated by strains of Dechloromonas sp. and Thauera sp., with isolates exhibiting genetic similarity to the latter known to reduce selenate to Se0. Enrichment cultures of selenate-respiring microorganisms were readily established using Rifle site groundwater and acetate, with cultures dominated by strains closely related to D. aromatica (96-99% similarity). Predominance of Dechloromonas sp. in recovered biofilms and enrichments suggests this microorganism may play a role in the removal of selenium oxyanions present in Se-impacted groundwaters and sediments.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23905166?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Wrighton, Kelly C</style></author><author><style face="normal" font="default" size="100%">Nicora, Carrie D</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">McCue, Lee Ann</style></author><author><style face="normal" font="default" size="100%">Handley, Kim M</style></author><author><style face="normal" font="default" size="100%">Miller, Chris S</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Montgomery, Alison P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Banfield, Jillian F</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS One</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Environment</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Humic Substances</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphates</style></keyword><keyword><style  face="normal" font="default" size="100%">Plankton</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Tandem Mass Spectrometry</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Vanadium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">e57819</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23472107?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Electroporation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Complementation Test</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Vectors</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetics, Microbial</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Engineering</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Plasmids</style></keyword><keyword><style  face="normal" font="default" size="100%">Transformation, Bacterial</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">1102-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Methods for genetic manipulation of Clostridium ljungdahlii are of interest because of the potential for production of fuels and other biocommodities from carbon dioxide via microbial electrosynthesis or more traditional modes of autotrophy with hydrogen or carbon monoxide as the electron donor. Furthermore, acetogenesis plays an important role in the global carbon cycle. Gene deletion strategies required for physiological studies of C. ljungdahlii have not previously been demonstrated. An electroporation procedure for introducing plasmids was optimized, and four different replicative origins for plasmid propagation in C. ljungdahlii were identified. Chromosomal gene deletion via double-crossover homologous recombination with a suicide vector was demonstrated initially with deletion of the gene for FliA, a putative sigma factor involved in flagellar biogenesis and motility in C. ljungdahlii. Deletion of fliA yielded a strain that lacked flagella and was not motile. To evaluate the potential utility of gene deletions for functional genomic studies and to redirect carbon and electron flow, the genes for the putative bifunctional aldehyde/alcohol dehydrogenases, adhE1 and adhE2, were deleted individually or together. Deletion of adhE1, but not adhE2, diminished ethanol production with a corresponding carbon recovery in acetate. The double deletion mutant had a phenotype similar to that of the adhE1-deficient strain. Expression of adhE1 in trans partially restored the capacity for ethanol production. These results demonstrate the feasibility of genetic investigations of acetogen physiology and the potential for genetic manipulation of C. ljungdahlii to optimize autotrophic biocommodity production.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23204413?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nie, Huarong</style></author><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Cui, Mengmeng</style></author><author><style face="normal" font="default" size="100%">Lu, Haiyun</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Russell, Thomas P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Improved cathode for high efficient microbial-catalyzed reduction in microbial electrosynthesis cells.</style></title><secondary-title><style face="normal" font="default" size="100%">Phys Chem Chem Phys</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Phys Chem Chem Phys</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biocatalysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrochemical Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Nickel</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Veillonellaceae</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Sep 14</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">14290-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Microbial electrosynthesis cells (MECs) are devices wherein microorganisms can electrochemically interact with electrodes, directly donating or accepting electrons from electrode surfaces. Here, we developed a novel cathode by using nickel nanowires anchored to graphite for the improvement of microbial-catalyzed reduction in MEC cathode chamber. This porous nickel-nanowire-network-coated graphite electrode increased the interfacial area and interfacial interactions between the cathode surface and the microbial biofilm. A 2.3 fold increase in bio-reduction rate over the untreated graphite was observed. Around 282 mM day(-1) m(-2) of acetate resulting from the bio-reduction of carbon dioxide by Sporomusa was produced with 82 ± 14% of the electrons consumed being recovered in acetate.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">34</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23881181?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Barlett, Melissa</style></author><author><style face="normal" font="default" size="100%">Chavan, Milind A</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael</style></author><author><style face="normal" font="default" size="100%">Long, Philip</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular analysis of the in situ growth rates of subsurface Geobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">In Situ Hybridization, Fluorescence</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Ribosomal Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">1646-53</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r(2) = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23275510?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Outer cell surface components essential for Fe(III) oxide reduction by Geobacter metallireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microarray Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">901-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter species are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail in Geobacter sulfurreducens, but a number of the most thoroughly studied outer surface components of G. sulfurreducens, particularly c-type cytochromes, are not well conserved among Geobacter species. In order to identify cellular components potentially important for Fe(III) oxide reduction in Geobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes for c-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified six c-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of the c-type cytochromes which were essential for Fe(III) oxide reduction in G. metallireducens have homologs in G. sulfurreducens that are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1-HT2A-Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer between G. metallireducens and G. sulfurreducens but the outer-surface c-type cytochromes involved in Fe(III) oxide reduction are different.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23183974?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Shrestha, Minita</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil</style></author><author><style face="normal" font="default" size="100%">Flores, Dan Carlo</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Syntrophic growth with direct interspecies electron transfer as the primary mechanism for energy exchange.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ Microbiol Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Formate Dehydrogenases</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">904-10</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) through biological electrical connections is an alternative to interspecies H2 transfer as a mechanism for electron exchange in syntrophic cultures. However, it has not previously been determined whether electrons received via DIET yield energy to support cell growth. In order to investigate this, co-cultures of Geobacter metallireducens, which can transfer electrons to wild-type G. sulfurreducens via DIET, were established with a citrate synthase-deficient G. sulfurreducens strain that can receive electrons for respiration through DIET only. In a medium with ethanol as the electron donor and fumarate as the electron acceptor, co-cultures with the citrate synthase-deficient G. sulfurreducens strain metabolized ethanol as fast as co-cultures with wild-type, but the acetate that G. metallireducens generated from ethanol oxidation accumulated. The lack of acetate metabolism resulted in less fumarate reduction and lower cell abundance of G. sulfurreducens. RNAseq analysis of transcript abundance was consistent with a lack of acetate metabolism in G. sulfurreducens and revealed gene expression levels for the uptake hydrogenase, formate dehydrogenase, the pilus-associated c-type cytochrome OmcS and pili consistent with electron transfer via DIET. These results suggest that electrons transferred via DIET can serve as the sole energy source to support anaerobic respiration.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/24249299?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Shrestha, Minita</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Transcriptomic and genetic analysis of direct interspecies electron transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">2397-404</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2 interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in cocultures in which Geobacter sulfurreducens was the electron-accepting partner for either Geobacter metallireducens, which performs DIET, or Pelobacter carbinolicus, which relies on HIT. Transcript abundance for G. sulfurreducens uptake hydrogenase genes was 7-fold lower in cocultures with G. metallireducens than in cocultures with P. carbinolicus, consistent with DIET and HIT, respectively, in the two cocultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET but not for HIT, was 240-fold higher in the cocultures with G. metallireducens than in cocultures with P. carbinolicus. The pilin gene pilA was moderately expressed despite a mutation that might be expected to repress pilA expression. Lower transcript abundance for G. sulfurreducens genes associated with acetate metabolism in the cocultures with P. carbinolicus was consistent with the repression of these genes by H2 during HIT. Genes for the biogenesis of pili and flagella and several c-type cytochrome genes were among the most highly expressed in G. metallireducens. Mutant strains that lacked the ability to produce pili, flagella, or the outer surface c-type cytochrome encoded by Gmet_2896 were not able to form cocultures with G. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more-complex environments.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23377933?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Orellana, Roberto</style></author><author><style face="normal" font="default" size="100%">Leavitt, Janet J</style></author><author><style face="normal" font="default" size="100%">Comolli, Luis R</style></author><author><style face="normal" font="default" size="100%">Csencsits, Roseann</style></author><author><style face="normal" font="default" size="100%">Janot, Noemie</style></author><author><style face="normal" font="default" size="100%">Flanagan, Kelly A</style></author><author><style face="normal" font="default" size="100%">Gray, Arianna S</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Izallalen, Mounir</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">U(VI) reduction by diverse outer surface c-type cytochromes of Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Transmission</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">X-Ray Absorption Spectroscopy</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">79</style></volume><pages><style face="normal" font="default" size="100%">6369-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Early studies with Geobacter sulfurreducens suggested that outer-surface c-type cytochromes might play a role in U(VI) reduction, but it has recently been suggested that there is substantial U(VI) reduction at the surface of the electrically conductive pili known as microbial nanowires. This phenomenon was further investigated. A strain of G. sulfurreducens, known as Aro-5, which produces pili with substantially reduced conductivity reduced U(VI) nearly as well as the wild type, as did a strain in which the gene for PilA, the structural pilin protein, was deleted. In order to reduce rates of U(VI) reduction to levels less than 20% of the wild-type rates, it was necessary to delete the genes for the five most abundant outer surface c-type cytochromes of G. sulfurreducens. X-ray absorption near-edge structure spectroscopy demonstrated that whereas 83% ± 10% of the uranium associated with wild-type cells correspond to U(IV) after 4 h of incubation, with the quintuple mutant, 89% ± 10% of uranium was U(VI). Transmission electron microscopy and X-ray energy dispersion spectroscopy revealed that wild-type cells did not precipitate uranium along pili as previously reported, but U(IV) was precipitated at the outer cell surface. These findings are consistent with those of previous studies, which have suggested that G. sulfurreducens requires outer-surface c-type cytochromes but not pili for the reduction of soluble extracellular electron acceptors.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">20</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23934497?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shrestha, Pravin Malla</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Shrestha, Minita</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">When is a microbial culture &quot;pure&quot;? Persistent cryptic contaminant escapes detection even with deep genome sequencing.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Coinfection</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">High-Throughput Nucleotide Sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Mar 12</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">e00591-12</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;Geobacter sulfurreducens strain KN400 was recovered in previous studies in which a culture of the DL1 strain of G. sulfurreducens served as the inoculum in investigations of microbial current production at low anode potentials (-400 mV versus Ag/AgCl). Differences in the genome sequences of KN400 and DL1 were too great to have arisen from adaptive evolution during growth on the anode. Previous deep sequencing (80-fold coverage) of the DL1 culture failed to detect sequences specific to KN400, suggesting that KN400 was an external contaminant inadvertently introduced into the anode culturing system. In order to evaluate this further, a portion of the gene for OmcS, a c-type cytochrome that both KN400 and DL1 possess, was amplified from the DL1 culture. HiSeq-2000 Illumina sequencing of the PCR product detected the KN400 sequence, which differs from the DL1 sequence at 14 bp, at a frequency of ca. 1 in 10(5) copies of the DL1 sequence. A similar low frequency of KN400 was detected with quantitative PCR of a KN400-specific gene. KN400 persisted at this frequency after intensive restreaking of isolated colonies from the DL1 culture. However, a culture in which KN400 could no longer be detected was obtained by serial dilution to extinction in liquid medium. The KN400-free culture could not grow on an anode poised at -400 mV. Thus, KN400 cryptically persisted in the culture dominated by DL1 for more than a decade, undetected by even deep whole-genome sequencing, and was only fortuitously uncovered by the unnatural selection pressure of growth on a low-potential electrode.&lt;/p&gt;&lt;p&gt;&lt;b&gt;IMPORTANCE: &lt;/b&gt;Repeated streaking of isolated colonies on solidified medium remains a common strategy for obtaining pure cultures, especially of difficult-to-cultivate microorganisms such as strict anaerobes. The results presented here demonstrate that verifying the purity of cultures obtained in this manner may be difficult because extremely rare variants can persist, undetectable with even deep genomic DNA sequencing. The only way to ensure that a culture is pure is to cultivate it from an initial single cell, which may be technically difficult for many environmentally significant microbes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23481604?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Bain, Timothy S</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Barlett, Melissa A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Anaerobic benzene oxidation by Geobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzene</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">8304-10</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The abundance of Geobacter species in contaminated aquifers in which benzene is anaerobically degraded has led to the suggestion that some Geobacter species might be capable of anaerobic benzene degradation, but this has never been documented. A strain of Geobacter, designated strain Ben, was isolated from sediments from the Fe(III)-reducing zone of a petroleum-contaminated aquifer in which there was significant capacity for anaerobic benzene oxidation. Strain Ben grew in a medium with benzene as the sole electron donor and Fe(III) oxide as the sole electron acceptor. Furthermore, additional evaluation of Geobacter metallireducens demonstrated that it could also grow in benzene-Fe(III) medium. In both strain Ben and G. metallireducens the stoichiometry of benzene metabolism and Fe(III) reduction was consistent with the oxidation of benzene to carbon dioxide with Fe(III) serving as the sole electron acceptor. With benzene as the electron donor, and Fe(III) oxide (strain Ben) or Fe(III) citrate (G. metallireducens) as the electron acceptor, the cell yields of strain Ben and G. metallireducens were 3.2 × 10(9) and 8.4 × 10(9) cells/mmol of Fe(III) reduced, respectively. Strain Ben also oxidized benzene with anthraquinone-2,6-disulfonate (AQDS) as the sole electron acceptor with cell yields of 5.9 × 10(9) cells/mmol of AQDS reduced. Strain Ben serves as model organism for the study of anaerobic benzene metabolism in petroleum-contaminated aquifers, and G. metallireducens is the first anaerobic benzene-degrading organism that can be genetically manipulated.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">23</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23001648?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Young, Nelson D</style></author><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Comparative Genomic Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Annotation</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Sep 12</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">471</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;Both genomes were re-annotated, resulting in 14 fewer genes (net) in the PCA genome; 28 fewer (net) in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in PCA. Most of the remaining genes were in regions of genomic mobility and were strain-specific or conserved in other Geobacteraceae, indicating that the changes occurred post-divergence. There were 27,270 single nucleotide polymorphisms (SNP) between the genomes. There was significant enrichment for SNP locations in non-coding or synonymous amino acid sites, indicating significant selective pressure since the divergence. 25% of orthologs had sequence differences, and this set was enriched in phosphorylation and ATP-dependent enzymes. Substantial sequence differences (at least 12 non-synonymous SNP/kb) were found in 3.6% of the orthologs, and this set was enriched in cytochromes and integral membrane proteins. Genes known to be involved in electron transport, those used in the metabolic cell model, and those that exhibit changes in expression during growth in microbial fuel cells were examined in detail.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;The improvement in external electron transfer in the KN400 strain does not appear to be due to novel gene acquisition, but rather to changes in the common metabolic network. The increase in electron transfer rate and yield in KN400 may be due to changes in carbon flux towards oxidation pathways and to changes in ATP metabolism, both of which indicate that the overall energy state of the cell may be different. The electrically conductive pili appear to be unchanged, but cytochrome folding, localization, and redox potentials may all be affected, which would alter the electrical connection between the cell and the substrate.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22967216?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhuang, K</style></author><author><style face="normal" font="default" size="100%">Ma, E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The design of long-term effective uranium bioremediation strategy using a community metabolic model.</style></title><secondary-title><style face="normal" font="default" size="100%">Biotechnol Bioeng</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biotechnol. Bioeng.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">109</style></volume><pages><style face="normal" font="default" size="100%">2475-83</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Acetate amendment at uranium contaminated sites in Rifle, CO. leads to an initial bloom of Geobacter accompanied by the removal of U(VI) from the groundwater, followed by an increase of sulfate-reducing bacteria (SRBs) which are poor reducers of U(VI). One of the challenges associated with bioremediation is the decay in Geobacter abundance, which has been attributed to the depletion of bio-accessible Fe(III), motivating the investigation of simultaneous amendments of acetate and Fe(III) as an alternative bioremediation strategy. In order to understand the community metabolism of Geobacter and SRBs during artificial substrate amendment, we have created a genome-scale dynamic community model of Geobacter and SRBs using the previously described Dynamic Multi-species Metabolic Modeling framework. Optimization techniques are used to determine the optimal acetate and Fe(III) addition profile. Field-scale simulation of acetate addition accurately predicted the in situ data. The simulations suggest that batch amendment of Fe(III) along with continuous acetate addition is insufficient to promote long-term bioremediation, while continuous amendment of Fe(III) along with continuous acetate addition is sufficient to promote long-term bioremediation. By computationally minimizing the acetate and Fe(III) addition rates as well as the difference between the predicted and target uranium concentration, we showed that it is possible to maintain the uranium concentration below the environmental safety standard while minimizing the cost of chemical additions. These simulations show that simultaneous addition of acetate and Fe(III) has the potential to be an effective uranium bioremediation strategy. They also show that computational modeling of microbial community is an important tool to design effective strategies for practical applications in environmental biotechnology. Biotechnol. Bioeng. 2012; 109: 2475-2483. © 2012 Wiley Periodicals, Inc.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22510989?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Lau, Joanne</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrical conductivity in a mixed-species biofilm.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Consortia</style></keyword><keyword><style  face="normal" font="default" size="100%">Sewage</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">5967-71</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Geobacter sulfurreducens can form electrically conductive biofilms, but the potential for conductivity through mixed-species biofilms has not been examined. A current-producing biofilm grown from a wastewater sludge inoculum was highly conductive with low charge transfer resistance even though microorganisms other than Geobacteraceae accounted for nearly half the microbial community.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">16</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22706052?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electromicrobiology.</style></title><secondary-title><style face="normal" font="default" size="100%">Annu Rev Microbiol</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jun 28</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">Electromicrobiology deals with the interactions between microorganisms and electronic devices and with the novel electrical properties of microorganisms. A diversity of microorganisms can donate electrons to, or accept electrons from, electrodes without the addition of artificial electron shuttles. However, the mechanisms for microbe-electrode electron exchange have been seriously studied in only a few microorganisms. Shewanella oneidensis interacts with electrodes primarily via flavins that function as soluble electron shuttles. Geobacter sulfurreducens makes direct electrical contacts with electrodes via outer-surface, c-type cytochromes. G. sulfurreducens is also capable of long-range electron transport along pili, known as microbial nanowires, that have metallic-like conductivity similar to that previously described in synthetic conducting polymers. Pili networks confer conductivity to G. sulfurreducens biofilms, which function as a conducting polymer, with supercapacitor and transistor functionalities. Conductive microorganisms and/or their nanowires have a number of potential practical applications, but additional basic research will be necessary for rational optimization. Expected final online publication date for the Annual Review of Microbiology Volume 66 is September 08, 2012. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22746334?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Haveman, Shelley A</style></author><author><style face="normal" font="default" size="100%">DiDonato, Raymond</style></author><author><style face="normal" font="default" size="100%">Chertkov, Olga</style></author><author><style face="normal" font="default" size="100%">Han, Cliff S</style></author><author><style face="normal" font="default" size="100%">Land, Miriam L</style></author><author><style face="normal" font="default" size="100%">Brown, Peter</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Base Pairing</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Butylene Glycols</style></keyword><keyword><style  face="normal" font="default" size="100%">Choline</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanolamine</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethylene Glycol</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Glycerol</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Annotation</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Propylene Glycols</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Transfer, Asn</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Dec 10</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">690</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23227809?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria, Anaerobic</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzoates</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenol</style></keyword><keyword><style  face="normal" font="default" size="100%">Rhodopseudomonas</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">146-57</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (&gt;80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21776029?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Inoue, Kengo</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identification of multicomponent histidine-aspartate phosphorelay system controlling flagellar and motility gene expression in Geobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">J Biol Chem</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Biol. Chem.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Mar 30</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">287</style></volume><pages><style face="normal" font="default" size="100%">10958-66</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species play an important role in the natural biogeochemical cycles of aquatic sediments and subsurface environments as well as in subsurface bioremediation by oxidizing organic compounds with the reduction of insoluble Fe(III) oxides. Flagellum-based motility is considered to be critical for Geobacter species to locate fresh sources of Fe(III) oxides. Functional and comparative genomic approaches, coupled with genetic and biochemical methods, identified key regulators for flagellar gene expression in Geobacter species. A master transcriptional regulator, designated FgrM, is a member of the enhancer-binding protein family. The fgrM gene in the most studied strain of Geobacter species, Geobacter sulfurreducens strain DL-1, is truncated by a transposase gene, preventing flagellar biosynthesis. Integrating a functional FgrM homolog restored flagellar biosynthesis and motility in G. sulfurreducens DL-1 and enhanced the ability to reduce insoluble Fe(III) oxide. Interrupting the fgrM gene in G. sulfurreducens strain KN400, which is motile, removed the capacity for flagellar production and inhibited Fe(III) oxide reduction. FgrM, which is also a response regulator of the two-component His-Asp phosphorelay system, was phosphorylated by histidine kinase GHK4, which was essential for flagellar production and motility. GHK4, which is a hybrid kinase with a receiver domain at the N terminus, was phosphorylated by another histidine kinase, GHK3. Therefore, the multicomponent His-Asp phosphorelay system appears to control flagellar gene expression in Geobacter species.</style></abstract><issue><style face="normal" font="default" size="100%">14</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22362768?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Liu, Fanghua</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Coculture Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Formates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">7645-51</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Direct interspecies electron transfer (DIET) is an alternative to interspecies H(2)/formate transfer as a mechanism for microbial species to cooperatively exchange electrons during syntrophic metabolism. To understand what specific properties contribute to DIET, studies were conducted with Pelobacter carbinolicus, a close relative of Geobacter metallireducens, which is capable of DIET. P. carbinolicus grew in coculture with Geobacter sulfurreducens with ethanol as the electron donor and fumarate as the electron acceptor, conditions under which G. sulfurreducens formed direct electrical connections with G. metallireducens. In contrast to the cell aggregation associated with DIET, P. carbinolicus and G. sulfurreducens did not aggregate. Attempts to initiate cocultures with a genetically modified strain of G. sulfurreducens incapable of both H(2) and formate utilization were unsuccessful, whereas cocultures readily grew with mutant strains capable of formate but not H(2) uptake or vice versa. The hydrogenase mutant of G. sulfurreducens compensated, in cocultures, with significantly increased formate dehydrogenase gene expression. In contrast, the transcript abundance of a hydrogenase gene was comparable in cocultures with that for the formate dehydrogenase mutant of G. sulfurreducens or the wild type, suggesting that H(2) was the primary electron carrier in the wild-type cocultures. Cocultures were also initiated with strains of G. sulfurreducens that could not produce pili or OmcS, two essential components for DIET. The finding that P. carbinolicus exchanged electrons with G. sulfurreducens via interspecies transfer of H(2)/formate rather than DIET demonstrates that not all microorganisms that can grow syntrophically are capable of DIET and that closely related microorganisms may use significantly different strategies for interspecies electron exchange.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">21</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22923399?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Ismail, Wael</style></author><author><style face="normal" font="default" size="100%">Haveman, Shelley A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">975-83</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The addition of organic compounds to groundwater in order to promote bioremediation may represent a new selective pressure on subsurface microorganisms. The ability of Geobacter sulfurreducens, which serves as a model for the Geobacter species that are important in various types of anaerobic groundwater bioremediation, to adapt for rapid metabolism of lactate, a common bioremediation amendment, was evaluated. Serial transfer of five parallel cultures in a medium with lactate as the sole electron donor yielded five strains that could metabolize lactate faster than the wild-type strain. Genome sequencing revealed that all five strains had non-synonymous single-nucleotide polymorphisms in the same gene, GSU0514, a putative transcriptional regulator. Introducing the single-base-pair mutation from one of the five strains into the wild-type strain conferred rapid growth on lactate. This strain and the five adaptively evolved strains had four to eight-fold higher transcript abundance than wild-type cells for genes for the two subunits of succinyl-CoA synthase, an enzyme required for growth on lactate. DNA-binding assays demonstrated that the protein encoded by GSU0514 bound to the putative promoter of the succinyl-CoA synthase operon. The binding sequence was not apparent elsewhere in the genome. These results demonstrate that a single-base-pair mutation in a transcriptional regulator can have a significant impact on the capacity for substrate utilization and suggest that adaptive evolution should be considered as a potential response of microorganisms to environmental change(s) imposed during bioremediation.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22113376?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Long-range electron transport to Fe(III) oxide via pili with metallic-like conductivity.</style></title><secondary-title><style face="normal" font="default" size="100%">Biochem Soc Trans</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biochem Soc Trans</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Dec 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">40</style></volume><pages><style face="normal" font="default" size="100%">1186-90</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The mechanisms for Fe(III) oxide reduction by Geobacter species are of interest because Geobacter species have been shown to play an important role in Fe(III) oxide reduction in a diversity of environments in which Fe(III) reduction is a geochemically significant process. Geobacter species specifically express pili during growth on Fe(III) oxide compared with growth on soluble chelated Fe(III), and mutants that cannot produce pili are unable to effectively reduce Fe(III) oxide. The pili of Geobacter sulfurreducens are electrically conductive along their length under physiologically relevant conditions and exhibit a metallic-like conductivity similar to that observed previously in synthetic organic metals. Metallic-like conductivity in a biological protein filament is a previously unrecognized mechanism for electron transport that differs significantly from the more well-known biological strategy of electron hopping/tunnelling between closely spaced redox-active proteins. The multihaem c-type cytochrome OmcS is specifically associated with pili and is necessary for Fe(III) oxide reduction. However, multiple lines of evidence, including the metallic-like conductivity of the pili and the fact that OmcS molecules are spaced too far apart for electron hopping/tunnelling, indicate that OmcS is not responsible for long-range electron conduction along the pili. The role of OmcS may be to facilitate electron transfer from the pili to Fe(III) oxide. Long-range electron transport via pili with metallic-like conductivity is a paradigm shift that has important implications not only for Fe(III) oxide reduction, but also for interspecies electron exchange in syntrophic microbial communities as well as microbe-electrode interactions and the emerging field of bioelectronics.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23176452?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Liang, Yuting</style></author><author><style face="normal" font="default" size="100%">Van Nostrand, Joy D</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Peacock, Aaron D</style></author><author><style face="normal" font="default" size="100%">Deng, Ye</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Resch, C Tom</style></author><author><style face="normal" font="default" size="100%">Wu, Liyou</style></author><author><style face="normal" font="default" size="100%">He, Zhili</style></author><author><style face="normal" font="default" size="100%">Li, Guanghe</style></author><author><style face="normal" font="default" size="100%">Hazen, Terry C</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Zhou, Jizhong</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biota</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Microarray Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">78</style></volume><pages><style face="normal" font="default" size="100%">2966-72</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (E(h)) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22327592?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial nanowires: a new paradigm for biological electron transfer and bioelectronics.</style></title><secondary-title><style face="normal" font="default" size="100%">ChemSusChem</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ChemSusChem</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Physiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Biotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanostructures</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">1039-46</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The discovery that Geobacter sulfurreducens can produce protein filaments with metallic-like conductivity, known as microbial nanowires, that facilitate long-range electron transport is a paradigm shift in biological electron transfer and has important implications for biogeochemistry, microbial ecology, and the emerging field of bioelectronics. Although filaments in a wide diversity of microorganisms have been called microbial nanowires, the type IV pili of G. sulfurreducens and G. metallireducens are the only filaments that have been shown to be required for extracellular electron transport to extracellular electron acceptors or for conduction of electrons through biofilms. Studies of G. sulfurreducens pili preparations and intact biofilms under physiologically relevant conditions have provided multiple lines of evidence for metallic-like conduction along the length of pili and for the possibility of pili networks to confer high conductivity within biofilms. This mechanism of electron conduction contrasts with the previously known mechanism for biological electron transfer via electron tunneling or hopping between closely associated molecules, a strategy unlikely to be well adapted for long-range electron transport outside the cell. In addition to promoting electron exchange with abiotic electron acceptors, microbial nanowires have recently been shown to be involved in direct interspecies electron transfer between syntrophic partners. An improved understanding of the mechanisms for metallic-like conductivity in microbial nanowires, as well as engineering microorganisms with desirable catalytic abilities with nanowires, could lead to new applications in microbial electrosynthesis and bioelectronics.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22614997?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Qu, Yanhua</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic classification of diverse LysR-type transcriptional regulators of a model prokaryote Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Mol Evol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Mol. Evol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">74</style></volume><pages><style face="normal" font="default" size="100%">187-205</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The protein family of LysR-type transcriptional regulators (LTTRs) is highly abundant among prokaryotes. We analyzed 10,145 non-redundant microbial sequences with homology to eight LysR family regulators of a model prokaryote, Geobacter sulfurreducens, and employed phylogenetic tree inference for LTTR classification. We also analyzed the arrangement of genome clusters containing G. sulfurreducens LTTR genes and searched for LTTR regulatory motifs, suggesting likely regulatory targets of G. sulfurreducens LTTRs. This is the first study to date providing a detailed classification of LTTRs in the deltaproteobacterial family Geobacteraceae.</style></abstract><issue><style face="normal" font="default" size="100%">3-4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22526031?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Real-time spatial gene expression analysis within current-producing biofilms.</style></title><secondary-title><style face="normal" font="default" size="100%">ChemSusChem</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ChemSusChem</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Quaternary Ammonium Compounds</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">1092-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The expression of genes involved in central metabolism and extracellular electron transfer was examined in real-time in current-producing anode biofilms of Geobacter sulfurreducens. Strains of G. sulfurreducens were generated, in which the expression of the gene for a short half-life fluorescent protein was placed under control of the promoter of the genes of interest. Anode biofilms were grown in a chamber that permitted direct examination of the cell fluorescence with confocal scanning laser microscopy. Studies on nifD and citrate synthase expression in response to environmental changes demonstrated that the reporter system revealed initiation and termination of gene transcription. Uniform expression throughout the biofilms was noted for the genes for citrate synthase; PilA, the structural protein of the conductive pili; and OmcZ, a c-type cytochrome essential for optimal current production, which was localized at the anode-biofilm interface. These results demonstrate that even cells at great distance from the anode, or within expected low-pH zones, are metabolically active and likely to contribute to current production and that there are factors other than gene expression differences influencing the distribution of OmcZ. This real-time reporter approach is likely to be a useful tool in optimizing the design of technologies relying on microbe-electrode interactions.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22577044?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Dar, Shabir A</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase essential for autotrophic growth.</style></title><secondary-title><style face="normal" font="default" size="100%">mBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">mBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adenosine Triphosphate</style></keyword><keyword><style  face="normal" font="default" size="100%">Autotrophic Processes</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Fructose</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Knockout Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Essential</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Proton-Motive Force</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Dec 26</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">e00406-12</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;It has been predicted that the Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD(+) oxidoreductase which contributes to ATP synthesis by an H(+)-translocating ATPase under both autotrophic and heterotrophic growth conditions. The recent development of methods for genetic manipulation of C. ljungdahlii made it possible to evaluate the possible role of the Rnf complex in energy conservation. Disruption of the C. ljungdahlii rnf operon inhibited autotrophic growth. ATP synthesis, proton gradient, membrane potential, and proton motive force collapsed in the Rnf-deficient mutant with H(2) as the electron source and CO(2) as the electron acceptor. Heterotrophic growth was hindered in the absence of a functional Rnf complex, as ATP synthesis, proton gradient, and proton motive force were significantly reduced with fructose as the electron donor. Growth of the Rnf-deficient mutant was also inhibited when no source of fixed nitrogen was provided. These results demonstrate that the Rnf complex of C. ljungdahlii is responsible for translocation of protons across the membrane to elicit energy conservation during acetogenesis and is a multifunctional device also implicated in nitrogen fixation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;IMPORTANCE: &lt;/b&gt;Mechanisms for energy conservation in the acetogen Clostridium ljungdahlii are of interest because of its potential value as a chassis for the production of biocommodities with novel electron donors such as carbon monoxide, syngas, and electrons derived from electrodes. Characterizing the components implicated in the chemiosmotic ATP synthesis during acetogenesis by C. ljungdahlii is a prerequisite for the development of highly productive strains. The Rnf complex has been considered the prime candidate to be the pump responsible for the formation of an ion gradient coupled with ATP synthesis in multiple acetogens. However, experimental evidence for a proton-pumping Rnf complex has been lacking. This study establishes the C. ljungdahlii Rnf complex as a proton-translocating ferredoxin:NAD(+) oxidoreductase and demonstrates that C. ljungdahlii has the potential of becoming a model organism to study proton translocation, electron transport, and other functions of the Rnf complex in energy conservation or other processes.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23269825?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen Peroxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidative Stress</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxygen</style></keyword><keyword><style  face="normal" font="default" size="100%">Reactive Oxygen Species</style></keyword><keyword><style  face="normal" font="default" size="100%">Reverse Transcriptase Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Xanthine Oxidase</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">194</style></volume><pages><style face="normal" font="default" size="100%">2248-53</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H(2) in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen peroxide. Hya was also required to safeguard Hyb hydrogen oxidation activity after exposure to O(2). Overexpression studies demonstrated that Hya was more resistant to oxidative stress than Hyb. Overexpression of Hya also resulted in the creation of a recombinant strain better fitted for exposure to oxidative stress than wild-type G. sulfurreducens. These results demonstrate that one of the physiological roles of the O(2)-resistant Hya is to participate in the oxidative stress defense of G. sulfurreducens.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22366414?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Supercapacitors based on c-type cytochromes using conductive nanostructured networks of living bacteria.</style></title><secondary-title><style face="normal" font="default" size="100%">Chemphyschem</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Chemphyschem</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Dielectric Spectroscopy</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Capacitance</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanostructures</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">463-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Supercapacitors have attracted interest in energy storage because they have the potential to complement or replace batteries. Here, we report that c-type cytochromes, naturally immersed in a living, electrically conductive microbial biofilm, greatly enhance the device capacitance by over two orders of magnitude. We employ genetic engineering, protein unfolding and Nernstian modeling for in vivo demonstration of charge storage capacity of c-type cytochromes and perform electrochemical impedance spectroscopy, cyclic voltammetry and charge-discharge cycling to confirm the pseudocapacitive, redox nature of biofilm capacitance. The biofilms also show low self-discharge and good charge/discharge reversibility. The superior electrochemical performance of the biofilm is related to its high abundance of cytochromes, providing large electron storage capacity, its nanostructured network with metallic-like conductivity, and its porous architecture with hydrous nature, offering prospects for future low cost and environmentally sustainable energy storage devices.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22253215?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Smith, Jessica A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Anaerobic oxidation of benzene by the hyperthermophilic archaeon Ferroglobus placidus.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaeoglobales</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzene</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Radioisotopes</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Isotope Labeling</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">77</style></volume><pages><style face="normal" font="default" size="100%">5926-33</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [(14)C]benzene to [(14)C]carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism, and [(14)C]benzoate was produced from [(14)C]benzene. Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not upregulated during growth on benzene. A gene for a putative carboxylase that was more highly expressed in benzene- than in benzoate-grown cells was identified. These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus. This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways. Thus, F. placidus provides a much-needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms.</style></abstract><issue><style face="normal" font="default" size="100%">17</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21742914?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Qian, Xinlei</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Morgado, Leonor</style></author><author><style face="normal" font="default" size="100%">Arakawa, Tsutomu</style></author><author><style face="normal" font="default" size="100%">Sharma, Manju L</style></author><author><style face="normal" font="default" size="100%">Inoue, Kengo</style></author><author><style face="normal" font="default" size="100%">Joseph, Crisjoe</style></author><author><style face="normal" font="default" size="100%">Salgueiro, Carlos A</style></author><author><style face="normal" font="default" size="100%">Maroney, Michael J</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Biochemical characterization of purified OmcS, a c-type cytochrome required for insoluble Fe(III) reduction in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Biochim Biophys Acta</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biochim. Biophys. Acta</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Circular Dichroism</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Heme</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Weight</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1807</style></volume><pages><style face="normal" font="default" size="100%">404-12</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies with Geobacter sulfurreducens have demonstrated that OmcS, an abundant c-type cytochrome that is only loosely bound to the outer surface, plays an important role in electron transfer to Fe(III) oxides as well as other extracellular electron acceptors. In order to further investigate the function of OmcS, it was purified from a strain that overproduces the protein. Purified OmcS had a molecular mass of 47015 Da, and six low-spin bis-histidinyl hexacoordinated heme groups. Its midpoint redox potential was -212 mV. A thermal stability analysis showed that the cooperative melting of purified OmcS occurs in the range of 65-82 °C. Far UV circular dichroism spectroscopy indicated that the secondary structure of purified OmcS consists of about 10% α-helix and abundant disordered structures. Dithionite-reduced OmcS was able to transfer electrons to a variety of substrates of environmental importance including insoluble Fe(III) oxide, Mn(IV) oxide and humic substances. Stopped flow analysis revealed that the reaction rate of OmcS oxidation has a hyperbolic dependence on the concentration of the studied substrates. A ten-fold faster reaction rate with anthraquinone-2,6-disulfonate (AQDS) (25.2 s⁻¹) was observed as compared to that with Fe(III) citrate (2.9 s⁻¹). The results, coupled with previous localization and gene deletion studies, suggest that OmcS is well-suited to play an important role in extracellular electron transfer.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21236241?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tremblay, Pier-Luc</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author><author><style face="normal" font="default" size="100%">Barrett, Christian L</style></author><author><style face="normal" font="default" size="100%">Qiu, Yu</style></author><author><style face="normal" font="default" size="100%">Palsson, Bernhard O</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutagenesis, Insertional</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Riboswitch</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">13-23</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The stimulation of subsurface microbial metabolism often associated with engineered bioremediation of groundwater contaminants presents subsurface microorganisms, which are adapted for slow growth and metabolism in the subsurface, with new selective pressures. In order to better understand how Geobacter species might adapt to selective pressure for faster metal reduction in the subsurface, Geobacter sulfurreducens was put under selective pressure for rapid Fe(III) oxide reduction. The genomes of two resultant strains with rates of Fe(III) oxide reduction that were 10-fold higher than those of the parent strain were resequenced. Both strains contain either a single base-pair change or a 1 nucleotide insertion in a GEMM riboswitch upstream of GSU1761, a gene coding for the periplasmic c-type cytochrome designated PgcA. GSU1771, a gene coding for a SARP regulator, was also mutated in both strains. Introduction of either of the GEMM riboswitch mutations upstream of pgcA in the wild-type increased the abundance of pgcA transcripts, consistent with increased expression of pgcA in the adapted strains. One of the mutations doubled the rate of Fe(III) oxide reduction. Interruption of GSU1771 doubled the Fe(III) oxide reduction rate. This was associated with an increased in expression of pilA, the gene encoding the structural protein for the pili thought to function as microbial nanowires. The combination of the GSU1771 interruption with either of the pgcA mutations resulted in a strain that reduced Fe(III) as fast as the comparable adapted strain. These results suggest that the accumulation of a small number of beneficial mutations under selective pressure, similar to that potentially present during bioremediation, can greatly enhance the capacity for Fe(III) oxide reduction in G. sulfurreducens. Furthermore, the results emphasize the importance of the c-type cytochrome PgcA and pili in Fe(III) oxide reduction and demonstrate how adaptive evolution studies can aid in the elucidation of complex mechanisms, such as extracellular electron transfer.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20636372?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Callister, Stephen J</style></author><author><style face="normal" font="default" size="100%">Miletto, Marzia</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Nicora, Carrie D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Markers</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Groundwater</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">55-63</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21255372?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fang, Yilin</style></author><author><style face="normal" font="default" size="100%">Scheibe, Timothy D</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">Garg, Srinath</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.</style></title><secondary-title><style face="normal" font="default" size="100%">J Contam Hydrol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Contam. Hydrol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Colorado</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Mar 25</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">122</style></volume><pages><style face="normal" font="default" size="100%">96-103</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment.</style></abstract><issue><style face="normal" font="default" size="100%">1-4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21172725?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Hensley, Sarah A</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Ou, Jianhong</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Snoeyenbos-West, Oona L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetobacterium</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Clostridium</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Moorella</style></keyword><keyword><style  face="normal" font="default" size="100%">Organic Chemicals</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Veillonellaceae</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">77</style></volume><pages><style face="normal" font="default" size="100%">2882-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Microbial electrosynthesis, a process in which microorganisms use electrons derived from electrodes to reduce carbon dioxide to multicarbon, extracellular organic compounds, is a potential strategy for capturing electrical energy in carbon-carbon bonds of readily stored and easily distributed products, such as transportation fuels. To date, only one organism, the acetogen Sporomusa ovata, has been shown to be capable of electrosynthesis. The purpose of this study was to determine if a wider range of microorganisms is capable of this process. Several other acetogenic bacteria, including two other Sporomusa species, Clostridium ljungdahlii, Clostridium aceticum, and Moorella thermoacetica, consumed current with the production of organic acids. In general acetate was the primary product, but 2-oxobutyrate and formate also were formed, with 2-oxobutyrate being the predominant identified product of electrosynthesis by C. aceticum. S. sphaeroides, C. ljungdahlii, and M. thermoacetica had high (&gt;80%) efficiencies of electrons consumed and recovered in identified products. The acetogen Acetobacterium woodii was unable to consume current. These results expand the known range of microorganisms capable of electrosynthesis, providing multiple options for the further optimization of this process.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21378039?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Strycharz, Sarah M</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Gannon, Sarah M</style></author><author><style face="normal" font="default" size="100%">Perpetua, Lorrie A</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Gene expression and deletion analysis of mechanisms for electron transfer from electrodes to Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioelectrochemistry</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioelectrochemistry</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Deletion</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">80</style></volume><pages><style face="normal" font="default" size="100%">142-50</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens is one of the few microorganisms available in pure culture known to directly accept electrons from a negatively poised electrode. Microarray analysis was used to compare gene transcript abundance in biofilms of G. sulfurreducens using a graphite electrode as the sole electron donor for fumarate reduction compared with transcript abundance in biofilms growing on the same material, but not consuming current. Surprisingly, genes for putative cell-electrode connections, such as outer-surface cytochromes and pili, which are highly expressed in current-producing biofilms, were not highly expressed in current-consuming biofilms. Microarray analysis of G. sulfurreducens gene transcript abundance in current-consuming biofilms versus current-producing biofilms gave similar results. In both comparative studies current-consuming biofilms had greater transcript abundance for a gene (GSU3274) encoding a putative monoheme, c-type cytochrome. Deletion of genes for outer-surface proteins previously shown to be essential for optimal electron transfer to electrodes had no impact on electron transfer from electrodes. Deletion of GSU3274 completely inhibited electron transfer from electrodes, but had no impact on electron transfer to electrodes. These differences in gene expression patterns and the impact of gene deletions suggest that the mechanisms for electron transfer from electrodes to G. sulfurreducens differ significantly from the mechanisms for electron transfer to electrodes.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20696622?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Sontineni, Sreedhar</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Qu, Yanhua</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome diversity of the TetR family of transcriptional regulators in a metal-reducing bacterial family Geobacteraceae and other microbial species.</style></title><secondary-title><style face="normal" font="default" size="100%">OMICS</style></secondary-title><alt-title><style face="normal" font="default" size="100%">OMICS</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Gram-Negative Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jul-Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">495-506</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role of TetR family proteins in Geobacteraceae in regulatory cascades involving a variety of sigma factors. In order to understand the role of the TetR regulatory family in Geobacteraceae, we have inferred phylogenetic relationships among the Geobacteraceae TetR proteins and their homologs in other microbial species.</style></abstract><issue><style face="normal" font="default" size="100%">7-8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21699403?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhuang, Kai</style></author><author><style face="normal" font="default" size="100%">Izallalen, Mounir</style></author><author><style face="normal" font="default" size="100%">Mouser, Paula</style></author><author><style face="normal" font="default" size="100%">Richter, Hanno</style></author><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Comamonadaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen Fixation</style></keyword><keyword><style  face="normal" font="default" size="100%">Quaternary Ammonium Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">305-16</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20668487?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Shrestha, Pravin M</style></author><author><style face="normal" font="default" size="100%">Flanagan, Kelly A</style></author><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Giloteaux, Ludovic</style></author><author><style face="normal" font="default" size="100%">Rotaru, Amelia-Elena</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Orellana, Roberto</style></author><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter: the microbe electric's physiology, ecology, and practical applications.</style></title><secondary-title><style face="normal" font="default" size="100%">Adv Microb Physiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Adv. Microb. Physiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecology</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Remediation</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">59</style></volume><pages><style face="normal" font="default" size="100%">1-100</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique &quot;microbial nanowires,&quot; pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22114840?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">Palsson, Bernhard Ø</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Rev Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Rev. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Environment</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">39-50</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21132020?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yun, Jiae</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Miletto, Marzia</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Monitoring the metabolic status of geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Antibodies, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Quaternary Ammonium Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">77</style></volume><pages><style face="normal" font="default" size="100%">4597-602</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.</style></abstract><issue><style face="normal" font="default" size="100%">13</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21551286?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A shift in the current: new applications and concepts for microbe-electrode electron exchange.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr. Opin. Biotechnol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofuels</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Fungi</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Organic Chemicals</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">441-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Perceived applications of microbe-electrode interactions are shifting from production of electric power to other technologies, some of which even consume current. Electrodes can serve as stable, long-term electron acceptors for contaminant-degrading microbes to promote rapid degradation of organic pollutants in anaerobic subsurface environments. Solar and other forms of renewable electrical energy can be used to provide electrons extracted from water to microorganisms on electrodes at suitably low potentials for a number of groundwater bioremediation applications as well as for the production of fuels and other organic compounds from carbon dioxide. The understanding of how microorganisms exchange electrons with electrodes has improved substantially and is expected to be helpful in optimizing practical applications of microbe-electrode interactions, as well as yielding insights into related natural environmental phenomena.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21333524?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Vargas, Madeline</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Inoue, Kengo</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Covalla, Sean F</style></author><author><style face="normal" font="default" size="100%">Johnson, Jessica P</style></author><author><style face="normal" font="default" size="100%">Rotello, Vincent M</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Tunable metallic-like conductivity in microbial nanowire networks.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Nanotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Nanotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword><keyword><style  face="normal" font="default" size="100%">Transistors, Electronic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">573-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Electronic nanostructures made from natural amino acids are attractive because of their relatively low cost, facile processing and absence of toxicity. However, most materials derived from natural amino acids are electronically insulating. Here, we report metallic-like conductivity in films of the bacterium Geobacter sulfurreducens and also in pilin nanofilaments (known as microbial nanowires) extracted from these bacteria. These materials have electronic conductivities of ∼5 mS cm(-1), which are comparable to those of synthetic metallic nanostructures. They can also conduct over distances on the centimetre scale, which is thousands of times the size of a bacterium. Moreover, the conductivity of the biofilm can be tuned by regulating gene expression, and also by varying the gate voltage in a transistor configuration. The conductivity of the nanofilaments has a temperature dependence similar to that of a disordered metal, and the conductivity could be increased by processing.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21822253?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Qian, Xinlei</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Alignment of the c-type cytochrome OmcS along pili of Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Immunohistochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Immunoelectron</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">76</style></volume><pages><style face="normal" font="default" size="100%">4080-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Immunogold localization revealed that OmcS, a cytochrome that is required for Fe(III) oxide reduction by Geobacter sulfurreducens, was localized along the pili. The apparent spacing between OmcS molecules suggests that OmcS facilitates electron transfer from pili to Fe(III) oxides rather than promoting electron conduction along the length of the pili.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20400557?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Callister, Stephen J</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Nicora, Carrie D</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Banfield, Jillian F</style></author><author><style face="normal" font="default" size="100%">VerBerkmoes, Nathan C</style></author><author><style face="normal" font="default" size="100%">Hettich, Robert L</style></author><author><style face="normal" font="default" size="100%">N'Guessan, Lucie</style></author><author><style face="normal" font="default" size="100%">Mouser, Paula J</style></author><author><style face="normal" font="default" size="100%">Elifantz, Hila</style></author><author><style face="normal" font="default" size="100%">Smith, Richard D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodiversity</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Plankton</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteome</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Dec 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">44</style></volume><pages><style face="normal" font="default" size="100%">8897-903</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or &quot;pseudo-metagenomes&quot;, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.</style></abstract><issue><style face="normal" font="default" size="100%">23</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21058662?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sun, Jun</style></author><author><style face="normal" font="default" size="100%">Haveman, Shelley A</style></author><author><style face="normal" font="default" size="100%">Bui, Olivia</style></author><author><style face="normal" font="default" size="100%">Fahland, Tom R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Constraint-based modeling analysis of the metabolism of two Pelobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Syst Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Syst Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Desulfuromonas</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Reproducibility of Results</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">174</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells.

RESULTS: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models.

CONCLUSIONS: We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21182788?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nagarajan, Harish</style></author><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Klimes, Anna</style></author><author><style face="normal" font="default" size="100%">Qiu, Yu</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author><author><style face="normal" font="default" size="100%">Ward, Joy</style></author><author><style face="normal" font="default" size="100%">Young, Nelson D</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Palsson, Bernhard Ø</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Barrett, Christian L</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS ONE</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">e10922</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated.We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454) to assemble a complete microbial genome de novo. We applied this approach to completely assemble the 3.7 Mb genome of a rare Geobacter variant (KN400) that is capable of unprecedented current production at an electrode. Two key components of our strategy enabled us to achieve this result. First, we integrated the two data types early in the process to maximally leverage their complementary characteristics. And second, we used the output of different short read assembly programs in such a way so as to leverage the complementary nature of their different underlying algorithms or of their different implementations of the same underlying algorithm.The significance of our result is that it demonstrates a general approach for maximizing the efficiency and success of genome assembly projects as new sequencing technologies and new assembly algorithms are introduced. The general approach is a meta strategy, wherein sequencing data are integrated as early as possible and in particular ways and wherein multiple assembly algorithms are judiciously applied such that the deficiencies in one are complemented by another.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20544019?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Fogarty, Heather E</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Malvankar, Nikhil S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria.</style></title><secondary-title><style face="normal" font="default" size="100%">Science</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Science</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Consortia</style></keyword><keyword><style  face="normal" font="default" size="100%">Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Selection, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Dec 3</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">330</style></volume><pages><style face="normal" font="default" size="100%">1413-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Microbial consortia that cooperatively exchange electrons play a key role in the anaerobic processing of organic matter. Interspecies hydrogen transfer is a well-documented strategy for electron exchange in dispersed laboratory cultures, but cooperative partners in natural environments often form multispecies aggregates. We found that laboratory evolution of a coculture of Geobacter metallireducens and Geobacter sulfurreducens metabolizing ethanol favored the formation of aggregates that were electrically conductive. Sequencing aggregate DNA revealed selection for a mutation that enhances the production of a c-type cytochrome involved in extracellular electron transfer and accelerates the formation of aggregates. Aggregate formation was also much faster in mutants that were deficient in interspecies hydrogen transfer, further suggesting direct interspecies electron transfer.</style></abstract><issue><style face="normal" font="default" size="100%">6009</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21127257?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley</style></author><author><style face="normal" font="default" size="100%">Englert, Andreas</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrode-based approach for monitoring in situ microbial activity during subsurface bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Monitoring</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Remediation</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jan 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">44</style></volume><pages><style face="normal" font="default" size="100%">47-54</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Current production by microorganisms colonizing subsurface electrodes and its relationship to substrate availability and microbial activity was evaluated in an aquifer undergoing bioremediation. Borehole graphite anodes were installed downgradient from a region of acetate injection designed to stimulate bioreduction of U(VI); cathodes consisted of graphite electrodes embedded at the ground surface. Significant increases in current density (&lt; or =50 mA/m2) tracked delivery of acetate to the electrodes, dropping rapidly when acetate inputs were discontinued. An upgradient control electrode not exposed to acetate produced low, steady currents (&lt; or =0.2 mA/m2). Elevated current was strongly correlated with uranium removal but minimal correlation existed with elevated Fe(II). Confocal laser scanning microscopy of electrodes revealed firmly attached biofilms, and analysis of 16S rRNA gene sequences indicated the electrode surfaces were dominated (67-80%) by Geobacter species. This is the first demonstration that electrodes can produce readily detectable currents despite long-range (6 m) separation of anode and cathode, and these results suggest that oxidation of acetate coupled to electron transfer to electrodes by Geobacter species was the primary source of current. Thus it is expected that current production may serve as an effective proxy for monitoring in situ microbial activity in a variety of subsurface anoxic environments.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19921843?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Young, Nelson D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proton-Translocating ATPases</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Comparative Genomic Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Duplication</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Transfer, Horizontal</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">NADH Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">40</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter species grow by transferring electrons out of the cell--either to Fe(III)-oxides or to man-made substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments.

RESULTS: The results showed that enzymes for acetate transport and oxidation, and for proton transport across the inner membrane were well conserved. An NADH dehydrogenase, the ATP synthase, and several TCA cycle enzymes were among the best conserved in the genomes. However, most of the cytochromes required for Fe(III)-reduction were not, including many of the outer-membrane cytochromes. While conservation of cytochromes was poor, an abundance and diversity of cytochromes were found in every genome, with duplications apparent in several species.

CONCLUSIONS: These results indicate there is a common pathway for acetate oxidation and energy generation across the family and in the last common ancestor. They also suggest that while cytochromes are important for extracellular electron transport, the path of electrons across the periplasm and outer membrane is variable. This combination of abundant cytochromes with weak sequence conservation suggests they may not be specific terminal reductases, but rather may be important in their heme-bearing capacity, as sinks for electrons between the inner-membrane electron transport chain and the extracellular acceptor.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20078895?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Elifantz, Hila</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Mouser, Paula J</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Expression of acetate permease-like (apl ) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations.</style></title><secondary-title><style face="normal" font="default" size="100%">FEMS Microbiol Ecol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">FEMS Microbiol. Ecol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Library</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Membrane Transport Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">73</style></volume><pages><style face="normal" font="default" size="100%">441-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high acetate) weakly correlated with the acetate concentration over time, the transcript levels for this gene were relatively constant in well D08 (low acetate). At the lowest acetate concentrations during the groundwater flush, the transcript levels of aplII were the highest. The expression of aplII decreased 2-10-fold upon acetate reintroduction. However, the overall instability of acetate concentrations throughout the experiment could not support a robust conclusion regarding the role of apl genes in response to acetate limitation under field conditions, in contrast to previous chemostat studies, suggesting that the function of a microbial community cannot be inferred based on lab experiments alone.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20533942?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Young, Nelson D</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn</style></author><author><style face="normal" font="default" size="100%">Chavan, Milind</style></author><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Kiss, Hajnalka E</style></author><author><style face="normal" font="default" size="100%">Han, Cliff S</style></author><author><style face="normal" font="default" size="100%">Land, Miriam L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Aldehyde Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbohydrate Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Wall</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Fatty Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Frameshift Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Glucose</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Multienzyme Complexes</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Osmosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxo-Acid-Lyases</style></keyword><keyword><style  face="normal" font="default" size="100%">Propionic Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Pyruvic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Surface Properties</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">490</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species.

RESULTS: Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen.

CONCLUSION: Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in subsurface environments, compared to non-subsurface Geobacter species, such as the ability to disproportionate fumarate, more efficient oxidation of propionate, enhanced responses to oxygen stress, and dependence on the environment for a vitamin requirement. Therefore, an understanding of the activity of Geobacter species in the subsurface is more likely to benefit from studies of subsurface isolates such as G. bemidjiensis than from the non-subsurface model species studied so far.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20828392?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Repressor Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">38</style></volume><pages><style face="normal" font="default" size="100%">810-21</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species play important roles in bioremediation of contaminated environments and in electricity production from waste organic matter in microbial fuel cells. To better understand physiology of Geobacter species, expression and function of citrate synthase, a key enzyme in the TCA cycle that is important for organic acid oxidation in Geobacter species, was investigated. Geobacter sulfurreducens did not require citrate synthase for growth with hydrogen as the electron donor and fumarate as the electron acceptor. Expression of the citrate synthase gene, gltA, was repressed by a transcription factor under this growth condition. Functional and comparative genomics approaches, coupled with genetic and biochemical assays, identified a novel transcription factor termed HgtR that acts as a repressor for gltA. Further analysis revealed that HgtR is a global regulator for genes involved in biosynthesis and energy generation in Geobacter species. The hgtR gene was essential for growth with hydrogen, during which hgtR expression was induced. These findings provide important new insights into the mechanisms by which Geobacter species regulate their central metabolism under different environmental conditions.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19939938?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Juárez, Katy</style></author><author><style face="normal" font="default" size="100%">Barbe, Jose F</style></author><author><style face="normal" font="default" size="100%">Qu, Yanhua</style></author><author><style face="normal" font="default" size="100%">Andrade, Angel</style></author><author><style face="normal" font="default" size="100%">Puljic, Marko</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-wide survey for PilR recognition sites of the metal-reducing prokaryote Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Gene</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Gene</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Dec 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">469</style></volume><pages><style face="normal" font="default" size="100%">31-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens is a species from the bacterial family Geobacteraceae, members of which participate in bioenergy production and in environmental bioremediation. G. sulfurreducens pili are electrically conductive and are required for Fe(III) oxide reduction and for optimal current production in microbial fuel cells. PilR is an enhancer binding protein, which is an activator acting together with the alternative sigma factor, RpoN, in transcriptional regulation. Both RpoN and PilR are involved in regulation of expression of the pilA gene, whose product is pilin, a structural component of a pilus. Using bioinformatic approaches, we predicted G. sulfurreducens sequence elements that are likely to be regulated by PilR. The functional importance of the genome region containing a PilR binding site predicted upstream of the pilA gene was experimentally validated. The predicted G. sulfurreducens PilR binding sites are similar to PilR binding sites of Pseudomonas and Moraxella. While the number of predicted PilR-regulated sites did not deviate from that expected by chance, multiple sites were predicted upstream of genes with roles in biosynthesis and function of pili and flagella, in secretory pathways, and in cell wall biogenesis, suggesting the possible involvement of G. sulfurreducens PilR in regulation of production and assembly of pili and flagella.</style></abstract><issue><style face="normal" font="default" size="100%">1-2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20708667?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Evol Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Evol. Biol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Comparative Genomic Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Intergenic</style></keyword><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacillus</style></keyword><keyword><style  face="normal" font="default" size="100%">Histidine-tRNA Ligase</style></keyword><keyword><style  face="normal" font="default" size="100%">Inverted Repeat Sequences</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">230</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Pelobacter carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III) directly or produce electricity like its relatives. How P. carbinolicus evolved is an intriguing problem. The genome of P. carbinolicus contains clustered regularly interspaced short palindromic repeats (CRISPR) separated by unique spacer sequences, which recent studies have shown to produce RNA molecules that interfere with genes containing identical sequences.

RESULTS: CRISPR spacer #1, which matches a sequence within hisS, the histidyl-tRNA synthetase gene of P. carbinolicus, was shown to be expressed. Phylogenetic analysis and genetics demonstrated that a gene paralogous to hisS in the genomes of Geobacteraceae is unlikely to compensate for interference with hisS. Spacer #1 inhibited growth of a transgenic strain of Geobacter sulfurreducens in which the native hisS was replaced with that of P. carbinolicus. The prediction that interference with hisS would result in an attenuated histidyl-tRNA pool insufficient for translation of proteins with multiple closely spaced histidines, predisposing them to mutation and elimination during evolution, was investigated by comparative genomics of P. carbinolicus and related species. Several ancestral genes with high histidine demand have been lost or modified in the P. carbinolicus lineage, providing an explanation for its physiological differences from other Geobacteraceae.

CONCLUSIONS: The disappearance of multiheme c-type cytochromes and other genes typical of a metal-respiring ancestor from the P. carbinolicus lineage may be the consequence of spacer #1 interfering with hisS, a condition that can be reproduced in a heterologous host. This is the first successful co-introduction of an active CRISPR spacer and its target in the same cell, the first application of a chimeric CRISPR construct consisting of a spacer from one species in the context of repeats of another species, and the first report of a potential impact of CRISPR on genome-scale evolution by interference with an essential gene.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20667132?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yang, Tae Hoon</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Sun, Jun</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Metabolic response of Geobacter sulfurreducens towards electron donor/acceptor variation.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Cell Fact</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb. Cell Fact.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Acetyl Coenzyme A</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Isotopes</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Gluconeogenesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphoenolpyruvate Carboxykinase (GTP)</style></keyword><keyword><style  face="normal" font="default" size="100%">Pyruvates</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">90</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen) and acceptors (Fe(III), fumarate) was investigated via (13)C-based metabolic flux analysis. We examined the (13)C-labeling patterns of proteinogenic amino acids obtained from G. sulfurreducens cultured with (13)C-acetate.

RESULTS: Using (13)C-based metabolic flux analysis, we observed that donor and acceptor variations gave rise to differences in gluconeogenetic initiation, tricarboxylic acid cycle activity, and amino acid biosynthesis pathways. Culturing G. sulfurreducens cells with Fe(III) as the electron acceptor and acetate as the electron donor resulted in pyruvate as the primary carbon source for gluconeogenesis. When fumarate was provided as the electron acceptor and acetate as the electron donor, the flux analysis suggested that fumarate served as both an electron acceptor and, in conjunction with acetate, a carbon source. Growth on fumarate and acetate resulted in the initiation of gluconeogenesis by phosphoenolpyruvate carboxykinase and a slightly elevated flux through the oxidative tricarboxylic acid cycle as compared to growth with Fe(III) as the electron acceptor. In addition, the direction of net flux between acetyl-CoA and pyruvate was reversed during growth on fumarate relative to Fe(III), while growth in the presence of Fe(III) and acetate which provided hydrogen as an electron donor, resulted in decreased flux through the tricarboxylic acid cycle.

CONCLUSIONS: We gained detailed insight into the metabolism of G. sulfurreducens cells under various electron donor/acceptor conditions using (13)C-based metabolic flux analysis. Our results can be used for the development of G. sulfurreducens as a chassis for a variety of applications including bioremediation and renewable biofuel production.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21092215?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Summers, Zarath M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial electrosynthesis: feeding microbes electricity to convert carbon dioxide and water to multicarbon extracellular organic compounds.</style></title><secondary-title><style face="normal" font="default" size="100%">MBio</style></secondary-title><alt-title><style face="normal" font="default" size="100%">MBio</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Organic Chemicals</style></keyword><keyword><style  face="normal" font="default" size="100%">Veillonellaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Water</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The possibility of providing the acetogenic microorganism Sporomusa ovata with electrons delivered directly to the cells with a graphite electrode for the reduction of carbon dioxide to organic compounds was investigated. Biofilms of S. ovata growing on graphite cathode surfaces consumed electrons with the reduction of carbon dioxide to acetate and small amounts of 2-oxobutyrate. Electrons appearing in these products accounted for over 85% of the electrons consumed. These results demonstrate that microbial production of multicarbon organic compounds from carbon dioxide and water with electricity as the energy source is feasible.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20714445?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Tetrazolium Salts</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">509-19</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. Cells throughout anode biofilms of Geobacter sulfurreducens reduced the metabolic stains: 5-cyano-2,3-ditolyl tetrazolium chloride and Redox Green, suggesting metabolic activity throughout the biofilm. To compare the metabolic status of cells growing close to the anode versus cells in the outer portion of the anode biofilm, anode biofilms were encased in resin and sectioned into inner (0-20 microm from anode surface) and outer (30-60 microm) fractions. Transcriptional analysis revealed that, at a twofold threshold, 146 genes had significant (P&lt;0.05) differences in transcript abundance between the inner and outer biofilm sections. Only 1 gene, GSU0093, a hypothetical ATP-binding cassette transporter, had significantly higher transcript abundances in the outer biofilm. Genes with lower transcript abundance in the outer biofilm included genes for ribosomal proteins and NADH dehydrogenase, suggesting lower metabolic rates. However, differences in transcript abundance were relatively low (&lt;threefold) and the expression of genes for the tricarboxylic acid cycle enzymes was not significantly lower. Lower expression of genes involved in stress responses in the outer biofilm may reflect the development of low pH near the surface of the anode. The results of this study suggest that cells throughout the biofilm are metabolically active and can potentially contribute to current production. The microtoming/microarray strategy described here may be useful for evaluating gene expression with depth in a diversity of microbial biofilms.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20033069?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhao, Jiao</style></author><author><style face="normal" font="default" size="100%">Fang, Yilin</style></author><author><style face="normal" font="default" size="100%">Scheibe, Timothy D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Mahadevan, R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments.</style></title><secondary-title><style face="normal" font="default" size="100%">J Contam Hydrol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Contam. Hydrol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Capacitance</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Mar 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">112</style></volume><pages><style face="normal" font="default" size="100%">30-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In situ stimulation of the metabolic activity of Geobacter species through acetate amendment has been shown to be a promising bioremediation strategy to reduce and immobilize hexavalent uranium [U(VI)] as insoluble U(IV). Although Geobacter species are reducing U(VI), they primarily grow via Fe(III) reduction. Unfortunately, the biogeochemistry and the physiology of simultaneous reduction of multiple metals are still poorly understood. A detailed model is therefore required to better understand the pathways leading to U(VI) and Fe(III) reduction by Geobacter species. Based on recent experimental evidence of temporary electron capacitors in Geobacter we propose a novel kinetic model that physically distinguishes planktonic cells into electron-loaded and -unloaded states. Incorporation of an electron load-unload cycle into the model provides insight into U(VI) reduction efficiency, and elucidates the relationship between U(VI)- and Fe(III)-reducing activity and further explains the correlation of high U(VI) removal with high fractions of planktonic cells in subsurface environments. Global sensitivity analysis was used to determine the level of importance of geochemical and microbial processes controlling Geobacter growth and U(VI) reduction, suggesting that the electron load-unload cycle and the resulting repartition of the microbes between aqueous and attached phases are critical for U(VI) reduction. As compared with conventional Monod modeling approaches without inclusion of the electron capacitance, the new model attempts to incorporate a novel cellular mechanism that has a significant impact on the outcome of in situ bioremediation.</style></abstract><issue><style face="normal" font="default" size="100%">1-4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19892431?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Elifantz, Hila</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Mouser, Paula J</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Manley, Kimberly</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Larsen, Joern T</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphates</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">253-66</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified by microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high-affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU upregulated the most. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium-bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve because of the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20010635?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen Fixation</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Kinases</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">38</style></volume><pages><style face="normal" font="default" size="100%">7485-99</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His-Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of nitrogen-fixation genes and represses a gene encoding glutamate dehydrogenase during nitrogen fixation. The other system whose expression is directly activated by the master regulatory system appears to control by antitermination the expression of a subset of the nitrogen-fixation genes whose transcription is activated by the master regulatory system and whose promoter contains transcription termination signals. This study provides a new paradigm for nitrogen-fixation gene regulation.</style></abstract><issue><style face="normal" font="default" size="100%">21</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20660485?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Klimes, Anna</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Tran, Hoa</style></author><author><style face="normal" font="default" size="100%">Barrett, Christian L</style></author><author><style face="normal" font="default" size="100%">Qiu, Yu</style></author><author><style face="normal" font="default" size="100%">Zengler, Karsten</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA.</style></title><secondary-title><style face="normal" font="default" size="100%">FEMS Microbiol Lett</style></secondary-title><alt-title><style face="normal" font="default" size="100%">FEMS Microbiol. Lett.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Adhesion</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Glass</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Transmission</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Sep 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">310</style></volume><pages><style face="normal" font="default" size="100%">62-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The pili of Geobacter sulfurreducens are of interest because of the apparent importance of the type IV pili in extracellular electron transfer. A strain of G. sulfurreducens, designated strain MA, produced many more pili than the previously studied DL-1 strain even though genome resequencing indicated that the MA and DL-1 genome sequences were identical. Filaments that looked similar to type IV pili in transmission electron micrographs were abundant even after the gene encoding PilA, the structural pilin protein, was deleted. The results of proteinase K treatment indicated that the filaments were proteinaceous. The simultaneous deletion of several genes encoding homologues of type II pseudopilins was required before the filaments were significantly depleted. The pilA-deficient MA strain attached to glass as well as the wild-type MA did, but strains in which three or four pseudopilin genes were deleted in addition to pilA had impaired attachment capabilities. These results demonstrate that there are several proteins that can yield pilin-like filaments in G. sulfurreducens and that some means other than microscopic observation is required before the composition of filaments can be unambiguously specified.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20629752?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Inoue, Kengo</style></author><author><style face="normal" font="default" size="100%">Qian, Xinlei</style></author><author><style face="normal" font="default" size="100%">Morgado, Leonor</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Izallalen, Mounir</style></author><author><style face="normal" font="default" size="100%">Salgueiro, Carlos A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Purification and characterization of OmcZ, an outer-surface, octaheme c-type cytochrome essential for optimal current production by Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Heme</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Weight</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Binding</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Stability</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, Protein</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">76</style></volume><pages><style face="normal" font="default" size="100%">3999-4007</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have demonstrated that Geobacter sulfurreducens requires the c-type cytochrome OmcZ, which is present in large (OmcZ(L); 50-kDa) and small (OmcZ(S); 30-kDa) forms, for optimal current production in microbial fuel cells. This protein was further characterized to aid in understanding its role in current production. Subcellular-localization studies suggested that OmcZ(S) was the predominant extracellular form of OmcZ. N- and C-terminal amino acid sequence analysis of purified OmcZ(S) and molecular weight measurements indicated that OmcZ(S) is a cleaved product of OmcZ(L) retaining all 8 hemes, including 1 heme with the unusual c-type heme-binding motif CX(14)CH. The purified OmcZ(S) was remarkably thermally stable (thermal-denaturing temperature, 94.2 degrees C). Redox titration analysis revealed that the midpoint reduction potential of OmcZ(S) is approximately -220 mV (versus the standard hydrogen electrode [SHE]) with nonequivalent heme groups that cover a large reduction potential range (-420 to -60 mV). OmcZ(S) transferred electrons in vitro to a diversity of potential extracellular electron acceptors, such as Fe(III) citrate, U(VI), Cr(VI), Au(III), Mn(IV) oxide, and the humic substance analogue anthraquinone-2,6-disulfonate, but not Fe(III) oxide. The biochemical properties and extracellular localization of OmcZ suggest that it is well suited for promoting electron transfer in current-producing biofilms of G. sulfurreducens.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20400562?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Voordeckers, James W</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Izallalen, Mounir</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Role of Geobacter sulfurreducens outer surface c-type cytochromes in reduction of soil humic acid and anthraquinone-2,6-disulfonate.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anthraquinones</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Humic Substances</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">76</style></volume><pages><style face="normal" font="default" size="100%">2371-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20154112?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhang, Tian</style></author><author><style face="normal" font="default" size="100%">Gannon, Sarah M</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Stimulating the anaerobic degradation of aromatic hydrocarbons in contaminated sediments by providing an electrode as the electron acceptor.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzene</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Naphthalenes</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Toluene</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">1011-20</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The possibility that electrodes might serve as an electron acceptor to simulate the degradation of aromatic hydrocarbons in anaerobic contaminated sediments was investigated. Initial studies with Geobacter metallireducens demonstrated that although toluene was rapidly adsorbed onto the graphite electrodes it was rapidly oxidized to carbon dioxide with the electrode serving as the sole electron acceptor. Providing graphite electrodes as an electron acceptor in hydrocarbon-contaminated sediments significantly stimulated the removal of added toluene and benzene. Rates of toluene and benzene removal accelerated with continued additions of toluene and benzene. [(14)C]-Toluene and [(14)C]-benzene were quantitatively recovered as [(14)C]-CO(2), demonstrating that even though the graphite adsorbed toluene and benzene they were degraded. Introducing an electrode as an electron acceptor also accelerated the loss of added naphthalene and [(14)C]-naphthalene was converted to [(14)C]-CO(2). The results suggest that graphite electrodes can serve as an electron acceptor for the degradation of aromatic hydrocarbon contaminants in sediments, co-localizing the contaminants, the degradative organisms and the electron acceptor. Once in position, they provide a permanent, low-maintenance source of electron acceptor. Thus, graphite electrodes may offer an attractive alternative for enhancing contaminant degradation in anoxic environments.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20105223?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Johnson, Jessica P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Didonato, Raymond J</style></author><author><style face="normal" font="default" size="100%">Covalla, Sean F</style></author><author><style face="normal" font="default" size="100%">Franks, Ashley E</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS ONE</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Complementation Test</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Confocal</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Up-Regulation</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">e5628</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The mechanisms by which Geobacter sulfurreducens transfers electrons through relatively thick (&gt;50 microm) biofilms to electrodes acting as a sole electron acceptor were investigated. Biofilms of Geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. Fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantial physiological differences from current-producing biofilms. Microarray analysis revealed 13 genes in current-harvesting biofilms that had significantly higher transcript levels. The greatest increases were for pilA, the gene immediately downstream of pilA, and the genes for two outer c-type membrane cytochromes, OmcB and OmcZ. Down-regulated genes included the genes for the outer-membrane c-type cytochromes, OmcS and OmcT. Results of quantitative RT-PCR of gene transcript levels during biofilm growth were consistent with microarray results. OmcZ and the outer-surface c-type cytochrome, OmcE, were more abundant and OmcS was less abundant in current-harvesting cells. Strains in which pilA, the gene immediately downstream from pilA, omcB, omcS, omcE, or omcZ was deleted demonstrated that only deletion of pilA or omcZ severely inhibited current production and biofilm formation in current-harvesting mode. In contrast, these gene deletions had no impact on biofilm formation on graphite surfaces when fumarate served as the electron acceptor. These results suggest that biofilms grown harvesting current are specifically poised for electron transfer to electrodes and that, in addition to pili, OmcZ is a key component in electron transfer through differentiated G. sulfurreducens biofilms to electrodes.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19461962?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Scheibe, Timothy D</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">Fang, Yilin</style></author><author><style face="normal" font="default" size="100%">Garg, Srinath</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">274-86</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The increasing availability of the genome sequences of microorganisms involved in important bioremediation processes makes it feasible to consider developing genome-scale models that can aid in predicting the likely outcome of potential subsurface bioremediation strategies. Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction. Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation. In order to simplify the modelling, the influence of only three growth factors was considered: acetate, the electron donor added to stimulate U(VI) reduction; Fe(III), the electron acceptor primarily supporting growth of Geobacter; and ammonium, a key nutrient. The constraint-based model predicted that growth yields of Geobacter varied significantly based on the availability of these three growth factors and that there are minimum thresholds of acetate and Fe(III) below which growth and activity are not possible. This contrasts with typical, empirical microbial models that assume fixed growth yields and the possibility for complete metabolism of the substrates. The coupled genome-scale and reactive transport model predicted acetate concentrations and U(VI) reduction rates in a field trial of in situ uranium bioremediation that were comparable to the predictions of a calibrated conventional model, but without the need for empirical calibration, other than specifying the initial biomass of Geobacter. These results suggest that coupling genome-scale metabolic models with reactive transport models may be a good approach to developing models that can be truly predictive, without empirical calibration, for evaluating the probable response of subsurface microorganisms to possible bioremediation approaches prior to implementation.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21261921?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Barbe, Jose F</style></author><author><style face="normal" font="default" size="100%">Qu, Yanhua</style></author><author><style face="normal" font="default" size="100%">Yan, Bin</style></author><author><style face="normal" font="default" size="100%">Puljic, Marko</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer.</style></title><secondary-title><style face="normal" font="default" size="100%">Funct Integr Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Funct. Integr. Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">15-25</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The delta-proteobacterium, Geobacter sulfurreducens, can obtain energy by coupling the oxidation of organic matter to the reduction of insoluble Fe(III) or the anode of a microbial fuel cell. Because Fe(III) oxide or the anode surface, in contrast to oxygen, nitrate, or sulfate, is not soluble nor can it be reduced readily, Geobacter species have developed mechanisms which allow electrons to be delivered across outer membrane to the cell surface. OmcB is an outer-membrane c-type cytochrome important for G. sulfurreducens Fe(III) respiration. In the absence of OmcB, cells lost the ability to reduce soluble or insoluble Fe(III). However, the omcB deletion mutant can slowly adapt to growth on soluble Fe(III) over prolonged incubation in the medium with acetate as the electron donor. We discuss available information about predicted or experimentally validated promoters and transcription regulatory sites identified upstream of operons with transcriptional expression significantly changed in the adapted omcB mutant. DNA sequences of upstream regions of coregulated operons in the adapted mutant are divergent, suggesting the presence of recognition sites for different transcriptional regulators and indicating that adaptation of the omcB mutant to growth on soluble Fe(III) has shifted the relevant expression networks involved to a more diverse molecular basis.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18677521?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Young, Nelson D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria, Anaerobic</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Fermentation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Transfer, Horizontal</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">103</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration.

RESULTS: In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer.

CONCLUSION: The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19284579?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Future shock from the microbe electric.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb Biotechnol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy-Generating Resources</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">139-41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/21261897?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Aklujkar, Muktak</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">DiBartolo, Genevieve</style></author><author><style face="normal" font="default" size="100%">Lapidus, Alla</style></author><author><style face="normal" font="default" size="100%">Land, Miriam L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">109</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences.

RESULTS: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes.

CONCLUSION: The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19473543?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Sun, Jun</style></author><author><style face="normal" font="default" size="100%">Zhuang, Kai</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">DeBoy, Robert</style></author><author><style face="normal" font="default" size="100%">Ismail, Wael</style></author><author><style face="normal" font="default" size="100%">Shrivastava, Susmita</style></author><author><style face="normal" font="default" size="100%">Huot, Heather</style></author><author><style face="normal" font="default" size="100%">Kothari, Sagar</style></author><author><style face="normal" font="default" size="100%">Daugherty, Sean</style></author><author><style face="normal" font="default" size="100%">Bui, Olivia</style></author><author><style face="normal" font="default" size="100%">Schilling, Christophe H</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Comamonadaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Comparative Genomic Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">447</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Rhodoferax ferrireducens is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies.

RESULTS: The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why R. ferrireducens is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that R. ferrireducens is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress.

CONCLUSION: This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19772637?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sun, Jun</style></author><author><style face="normal" font="default" size="100%">Sayyar, Bahareh</style></author><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Pharkya, Priti</style></author><author><style face="normal" font="default" size="100%">Fahland, Tom R</style></author><author><style face="normal" font="default" size="100%">Famili, Iman</style></author><author><style face="normal" font="default" size="100%">Schilling, Christophe H</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-scale constraint-based modeling of Geobacter metallireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Syst Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Syst Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Biology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">15</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens.

RESULTS: The genome-scale metabolic model of G. metallireducens was constructed to include 747 genes and 697 reactions. Compared to the G. sulfurreducens model, the G. metallireducens metabolic model contains 118 unique reactions that reflect many of G. metallireducens' specific metabolic capabilities. Detailed examination of the G. metallireducens model suggests that its central metabolism contains several energy-inefficient reactions that are not present in the G. sulfurreducens model. Experimental biomass yield of G. metallireducens growing on pyruvate was lower than the predicted optimal biomass yield. Microarray data of G. metallireducens growing with benzoate and acetate indicated that genes encoding these energy-inefficient reactions were up-regulated by benzoate. These results suggested that the energy-inefficient reactions were likely turned off during G. metallireducens growth with acetate for optimal biomass yield, but were up-regulated during growth with complex electron donors such as benzoate for rapid energy generation. Furthermore, several computational modeling approaches were applied to accelerate G. metallireducens research. For example, growth of G. metallireducens with different electron donors and electron acceptors were studied using the genome-scale metabolic model, which provided a fast and cost-effective way to understand the metabolism of G. metallireducens.

CONCLUSION: We have developed a genome-scale metabolic model for G. metallireducens that features both metabolic similarities and differences to the published model for its close relative, G. sulfurreducens. Together these metabolic models provide an important resource for improving strategies on bioremediation and bioenergy generation.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19175927?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Puljic, Marko</style></author><author><style face="normal" font="default" size="100%">Sun, Jun</style></author><author><style face="normal" font="default" size="100%">Juárez, Katy</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">DiDonato, Raymond</style></author><author><style face="normal" font="default" size="100%">Postier, Bradley</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome-Wide Association Study</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Regulon</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA Polymerase Sigma 54</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">331</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.

RESULTS: An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III), which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT.

CONCLUSION: The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19624843?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Qu, Yanhua</style></author><author><style face="normal" font="default" size="100%">Brown, Peter</style></author><author><style face="normal" font="default" size="100%">Barbe, Jose F</style></author><author><style face="normal" font="default" size="100%">Puljic, Marko</style></author><author><style face="normal" font="default" size="100%">Merino, Enrique</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">OMICS</style></secondary-title><alt-title><style face="normal" font="default" size="100%">OMICS</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Online Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Regulatory Sequences, Nucleic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">439-49</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens is a model organism within the delta-Proteobacterial family Geobacteraceae, members of which can participate in environmental bioremediation of metal and organic waste contaminants and in production of bioenergy. In this report, we describe a new, significantly expanded and updated, version 2 of the GSEL (Geobacter Sequence Elements) database ( http://geobacter.org/research/gsel2/ and http://geobacter.org/refs/gsel2/ ) and its accompanying online query system, which compiles information on operon organization and regulatory sequence elements in the genome of G. sulfurreducens. It incorporates a new online graphical browser, provides novel search capabilities, and includes updated operon predictions along with new information on predicted and experimentally validated genome regulatory sites. The GSEL database and online search system provides a unique and comprehensive tool cataloging information about gene regulation in G. sulfurreducens, aiding in investigation of mechanisms that regulate its ability to generate electric power, bioremediate environmental waste, and adapt to environmental changes.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19792871?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mouser, Paula J</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Elifantz, Hila</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carrier Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Remediation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Library</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen Fixation</style></keyword><keyword><style  face="normal" font="default" size="100%">Quaternary Ammonium Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Time Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jun 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">43</style></volume><pages><style face="normal" font="default" size="100%">4386-92</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by 2 orders of magnitude (&lt; 4 to 400 microM) across th study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during uranium reduction. The abundance of amtB was inversely correlated to ammonium levels, whereas nifD transcript levels were similar across all sites examined. These results suggest that nifD and amtB expression are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB transcript expression appears to be a useful approach for monitoring the nitrogen-related physiological status of subsurface Geobacter species. This study also emphasizes the need for more detailed analysis of geochemical and physiological interactions at the field scale in order to adequately model subsurface microbial processes during bioremediation.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19603651?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Juárez, Katy</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly</style></author><author><style face="normal" font="default" size="100%">Olvera, Leticia</style></author><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Mol Microbiol Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Mol. Microbiol. Biotechnol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Regulator</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">146-58</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Growth using Fe(III) as a terminal electron acceptor is a critical physiological process in Geobacter sulfurreducens. However, the mechanisms of electron transfer during Fe(III) reduction are only now being understood. It has been demonstrated that the pili in G. sulfurreducens function as microbial nanowires conducting electrons onto Fe(III) oxides. A number of c-type cytochromes have also been shown to play important roles in Fe(III) reduction. However, the regulatory networks controlling the expression of the genes involved in such processes are not well known. Here we report that the expression of pilA, which encodes the pilistructural protein, is directly regulated by a two-component regulatory system in which PilR functions as an RpoN-dependent enhancer binding protein. Surprisingly, a deletion of the pilR gene affected not only insoluble Fe(III) reduction, which requires pili, but also soluble Fe(III) reduction, which, in contrast, does not require pili. Gene expression profiling using whole-genome DNA microarray and quantitative RT-PCR analyses obtained with a PilR-deficient mutant revealed that the expression of pilA and other pilin-related genes are downregulated, while many c-type cytochromes involved in Fe(III) reduction were differentially regulated. This is the first instance of an enhancer binding protein implicated in regulating genes involved in Fe(III) respiratory functions.</style></abstract><issue><style face="normal" font="default" size="100%">3-4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18253022?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wilkins, Michael J</style></author><author><style face="normal" font="default" size="100%">VerBerkmoes, Nathan C</style></author><author><style face="normal" font="default" size="100%">Williams, Kenneth H</style></author><author><style face="normal" font="default" size="100%">Callister, Stephen J</style></author><author><style face="normal" font="default" size="100%">Mouser, Paula J</style></author><author><style face="normal" font="default" size="100%">Elifantz, Hila</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Thomas, Brian C</style></author><author><style face="normal" font="default" size="100%">Nicora, Carrie D</style></author><author><style face="normal" font="default" size="100%">Shah, Manesh B</style></author><author><style face="normal" font="default" size="100%">Abraham, Paul</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Hettich, Robert L</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Banfield, Jillian F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptide Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">Plankton</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">75</style></volume><pages><style face="normal" font="default" size="100%">6591-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.</style></abstract><issue><style face="normal" font="default" size="100%">20</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19717633?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mouser, Paula J</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Perpetua, Lorrie A</style></author><author><style face="normal" font="default" size="100%">DiDonato, Raymond</style></author><author><style face="normal" font="default" size="100%">Postier, Brad</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Colorado</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidative Stress</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">454-65</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">As part of an effort to diagnose the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater, transcript levels for two genes potentially associated with oxidative stress, cydA and sodA, were quantified throughout a bioremediation field study in Rifle, CO, USA. Despite the accumulation of Fe(II) in the groundwater, which is inconsistent with the presence of dissolved oxygen, both genes were highly expressed during the bioremediation process. Therefore, the response to oxidative stress was further evaluated with Geobacter uraniireducens, an isolate from the Rifle site. When G. uraniireducens cultured with fumarate as the electron acceptor was exposed to 5% oxygen for 8 h, there was a significant increase in cydA and sodA transcripts as well as other genes associated with oxygen respiration or oxidative stress. Oxygen-exposed cells had lower transcript abundance for genes associated with anaerobic respiration, metabolism and motility. Short-term oxygen exposure had little impact on cydA transcript levels, as more than 1 h was required for increases to levels comparable to the subsurface. Abundance of cydA and sodA transcripts for the isolate G. sulfurreducens were always higher in cells cultured with Fe(III) compared with fumarate as an electron acceptor, even when fumarate-grown cells were exposed to oxygen, and Fe(III)-grown cells were grown anaerobically. These results suggest that the apparently high Geobacter cydA and sodA expression during bioremediation cannot necessarily be attributed to oxidative stress and demonstrate that diagnosis of the metabolic status of subsurface microorganisms through transcript analysis should be coupled with appropriate geochemical analyses.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19129865?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yi, Hana</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Franks, Ashely E</style></author><author><style face="normal" font="default" size="100%">Klimes, Anna</style></author><author><style face="normal" font="default" size="100%">Tender, Leonard M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells.</style></title><secondary-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Design</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Failure Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Aug 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">3498-503</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens produces current densities in microbial fuel cells that are among the highest known for pure cultures. The possibility of adapting this organism to produce even higher current densities was evaluated. A system in which a graphite anode was poised at -400 mV (versus Ag/AgCl) was inoculated with the wild-type strain of G. sulfurreducens, strain DL-1. An isolate, designated strain KN400, was recovered from the biofilm after 5 months of growth on the electrode. KN400 was much more effective in current production than strain DL-1. This was apparent with anodes poised at -400 mV, as well as in systems run in true fuel cell mode. KN400 had current (7.6A/m(2)) and power (3.9 W/m(2)) densities that respectively were substantially higher than those of DL1 (1.4A/m(2) and 0.5 W/m(2)). On a per cell basis KN400 was more effective in current production than DL1, requiring thinner biofilms to make equivalent current. The enhanced capacity for current production in KN400 was associated with a greater abundance of electrically conductive microbial nanowires than DL1 and lower internal resistance (0.015 versus 0.130 Omega/m(2)) and mass transfer limitation in KN400 fuel cells. KN400 produced flagella, whereas DL1 does not. Surprisingly, KN400 had much less outer-surface c-type cytochromes than DL1. KN400 also had a greater propensity to form biofilms on glass or graphite than DL1, even when growing with the soluble electron acceptor, fumarate. These results demonstrate that it is possible to enhance the ability of microorganisms to electrochemically interact with electrodes with the appropriate selective pressure and that improved current production is associated with clear differences in the properties of the outer surface of the cell that may provide insights into the mechanisms for microbe-electrode interactions.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19487117?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Chavan, Milind A</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Perpetua, Lorrie A</style></author><author><style face="normal" font="default" size="100%">Larrahondo, M Juliana</style></author><author><style face="normal" font="default" size="100%">DiDonato, Raymond</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Colorado</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">216-30</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18843300?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tran, Hoa T</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Antommattei, Frances M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Weis, Robert M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemotaxis</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Amino Acid</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">471</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Geobacter species are delta-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells.

RESULTS: The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors sigma28 and sigma54 play a role in regulating the Geobacter chemotaxis gene expression.

CONCLUSION: The numerous chemoreceptors and chemotaxis-like gene clusters of Geobacter appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18844997?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Segura, Daniel</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">Juárez, Katy</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Comput. Biol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Multienzyme Complexes</style></keyword><keyword><style  face="normal" font="default" size="100%">Signal Transduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">e36</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous model-based analysis of the metabolic network of Geobacter sulfurreducens suggested the existence of several redundant pathways. Here, we identified eight sets of redundant pathways that included redundancy for the assimilation of acetate, and for the conversion of pyruvate into acetyl-CoA. These equivalent pathways and two other sub-optimal pathways were studied using 5 single-gene deletion mutants in those pathways for the evaluation of the predictive capacity of the model. The growth phenotypes of these mutants were studied under 12 different conditions of electron donor and acceptor availability. The comparison of the model predictions with the resulting experimental phenotypes indicated that pyruvate ferredoxin oxidoreductase is the only activity able to convert pyruvate into acetyl-CoA. However, the results and the modeling showed that the two acetate activation pathways present are not only active, but needed due to the additional role of the acetyl-CoA transferase in the TCA cycle, probably reflecting the adaptation of these bacteria to acetate utilization. In other cases, the data reconciliation suggested additional capacity constraints that were confirmed with biochemical assays. The results demonstrate the need to experimentally verify the activity of key enzymes when developing in silico models of microbial physiology based on sequence-based reconstruction of metabolic networks.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18266464?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richter, Hanno</style></author><author><style face="normal" font="default" size="100%">McCarthy, Kevin</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Johnson, Jessica P</style></author><author><style face="normal" font="default" size="100%">Rotello, Vincent M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electricity generation by Geobacter sulfurreducens attached to gold electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Langmuir</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Langmuir</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Gold</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Confocal</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Scanning</style></keyword><keyword><style  face="normal" font="default" size="100%">Surface Properties</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Apr 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><pages><style face="normal" font="default" size="100%">4376-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The versatility of gold for electrode manufacture suggests that it could be an ideal material for some microbial fuel cell applications. However, previous studies have suggested that microorganisms that readily transfer electrons to graphite do not transfer electrons to gold. Investigations with Geobacter sulfurreducens demonstrated that it could grow on gold anodes producing current nearly as effectively as with graphite anodes. Current production was associated with the development of G. sulfurreducens biofilms up to 40 microm thick. No current was produced if pilA, the gene for the structural protein of the conductive pili of G. sulfurreducens, was deleted. The finding that gold is a suitable anode material for microbial fuel cells offers expanded possibilities for the construction of microbial fuel cells and the electrochemical analysis of microbe-electrode interactions.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18303924?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Van Dien, Stephen J</style></author><author><style face="normal" font="default" size="100%">Orloff, Amber</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetyl Coenzyme A</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biosynthetic Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Butyric Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Isotopes</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Isoleucine</style></keyword><keyword><style  face="normal" font="default" size="100%">Malates</style></keyword><keyword><style  face="normal" font="default" size="100%">Pyruvic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Threonine</style></keyword><keyword><style  face="normal" font="default" size="100%">Threonine Dehydratase</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">190</style></volume><pages><style face="normal" font="default" size="100%">2266-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor fraction of isoleucine biosynthesis and that the majority of isoleucine was instead derived from acetyl-coenzyme A and pyruvate, possibly via the citramalate pathway. Genes encoding citramalate synthase (GSU1798), which catalyzes the first dedicated step in the citramalate pathway, and threonine ammonia-lyase (GSU0486), which catalyzes the conversion of threonine to 2-oxobutanoate, were identified and knocked out. Mutants lacking both of these enzymes were auxotrophs for isoleucine, whereas single mutants were capable of growth in the absence of isoleucine. Biochemical characterization of the single mutants revealed deficiencies in citramalate synthase and threonine ammonia-lyase activity. Thus, in G. sulfurreducens, 2-oxobutanoate can be synthesized either from citramalate or threonine, with the former being the main pathway for isoleucine biosynthesis. The citramalate synthase of G. sulfurreducens constitutes the first characterized member of a phylogenetically distinct clade of citramalate synthases, which contains representatives from a wide variety of microorganisms.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18245290?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extracellular electron transfer: wires, capacitors, iron lungs, and more.</style></title><secondary-title><style face="normal" font="default" size="100%">Geobiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Geobiology</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cell Surface Extensions</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Shewanella</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">225-31</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18393985?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Sosnik, Julian</style></author><author><style face="normal" font="default" size="100%">Visconti, Pablo</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Fluorescent properties of c-type cytochromes reveal their potential role as an extracytoplasmic electron sink in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anthraquinones</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Flagella</style></keyword><keyword><style  face="normal" font="default" size="100%">Fluorescence</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Fluorescence</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">497-505</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A novel fluorescence technique for monitoring the redox status of c-type cytochromes in Geobacter sulfurreducens was developed in order to evaluate the capacity of these extracytoplasmic cytochromes to store electrons during periods in which an external electron acceptor is not available. When intact cells in which the cytochromes were in a reduced state were excited at a wavelength of 350 nm, they fluoresced with maxima at 402 and 437 nm. Oxidation of the cytochromes resulted in a loss of fluorescence. This method was much more sensitive than the traditional approach of detecting c-type cytochromes via visible light absorbance. Furthermore, fluorescence of reduced cytochromes in individual cells could be detected via fluorescence microscopy, and the cytochromes in a G. sulfurreducens biofilm, remotely excited with an optical fibre, could be detected at distances as far as 5 cm. Fluorescence analysis of cytochrome oxidation and reduction of the external electron acceptor, anthraquinone-2,6-disulfonate, suggested that the extracytoplasmic cytochromes of G. sulfurreducens could store approximately 10(7) electrons per cell. Independent analysis of the haem content of the cells determined from analysis of incorporation of (55)Fe into cytochromes provided a similar estimate of cytochrome electron-storage capacity. This electron-storage capacity could, in the absence of an external electron acceptor, permit continued electron transfer across the inner membrane sufficient to supply the maintenance energy requirements for G. sulfurreducens for up to 8 min or enough proton motive force to power flagella motors for G. sulfurreducens motility. The fluorescence approach described here provides a sensitive method for evaluating the redox status of Geobacter species in culture and/or its environments. Furthermore, these results suggest that the periplasmic and outer-membrane cytochromes of Geobacter species act as capacitors, allowing continued electron transport, and thus viability and motility, for Geobacter species as they move between heterogeneously dispersed Fe(III) oxides during growth in the subsurface.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18093163?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Adams, Lorrie A</style></author><author><style face="normal" font="default" size="100%">Larrahondo, M Juliana</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferrous Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Repressor Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Reverse Transcriptase Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollution, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">1218-30</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Limitations on the availability of Fe(III) as an electron acceptor are thought to play an important role in restricting the growth and activity of Geobacter species during bioremediation of contaminated subsurface environments, but the possibility that these organisms might also be limited in the subsurface by the availability of iron for assimilatory purposes was not previously considered because copious quantities of Fe(II) are produced as the result of Fe(III) reduction. Analysis of multiple Geobacteraceae genomes revealed the presence of a three-gene cluster consisting of homologues of two iron-dependent regulators, fur and dtxR (ideR), separated by a homologue of feoB, which encodes an Fe(II) uptake protein. This cluster appears to be conserved among members of the Geobacteraceae and was detected in several environments. Expression of the fur-feoB-ideR cluster decreased as Fe(II) concentrations increased in chemostat cultures. The number of Geobacteraceae feoB transcripts in groundwater samples from a site undergoing in situ uranium bioremediation was relatively high until the concentration of dissolved Fe(II) increased near the end of the field experiment. These results suggest that, because much of the Fe(II) is sequestered in solid phases, Geobacter species, which have a high requirement for iron for iron-sulfur proteins, may be limited by the amount of iron available for assimilatory purposes. These results demonstrate the ability of transcript analysis to reveal previously unsuspected aspects of the in situ physiology of microorganisms in subsurface environments.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18279349?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Perpetua, Lorrie A</style></author><author><style face="normal" font="default" size="100%">Larrahondo, M Juliana</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard</style></author><author><style face="normal" font="default" size="100%">Sharma, Manju L</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Nucleic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">154</style></volume><pages><style face="normal" font="default" size="100%">1422-35</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have shown that Geobacter sulfurreducens requires the outer-membrane, multicopper protein OmpB for Fe(III) oxide reduction. A homologue of OmpB, designated OmpC, which is 36 % similar to OmpB, has been discovered in the G. sulfurreducens genome. Deletion of ompC inhibited reduction of insoluble, but not soluble Fe(III). Analysis of multiple Geobacter and Pelobacter genomes, as well as in situ Geobacter, indicated that genes encoding multicopper proteins are conserved in Geobacter species but are not found in Pelobacter species. Levels of ompB transcripts were similar in G. sulfurreducens at different growth rates in chemostats and during growth on a microbial fuel cell anode. In contrast, ompC transcript levels increased at higher growth rates in chemostats and with increasing current production in fuel cells. Constant levels of Geobacter ompB transcripts were detected in groundwater during a field experiment in which acetate was added to the subsurface to promote in situ uranium bioremediation. In contrast, ompC transcript levels increased during the rapid phase of growth of Geobacter species following addition of acetate to the groundwater and then rapidly declined. These results demonstrate that more than one multicopper protein is required for optimal Fe(III) oxide reduction in G. sulfurreducens and suggest that, in environmental studies, quantifying OmpB/OmpC-related genes could help alleviate the problem that Pelobacter genes may be inadvertently quantified via quantitative analysis of 16S rRNA genes. Furthermore, comparison of differential expression of ompB and ompC may provide insight into the in situ metabolic state of Geobacter species in environments of interest.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18451051?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Haveman, Shelley A</style></author><author><style face="normal" font="default" size="100%">Didonato, Raymond J</style></author><author><style face="normal" font="default" size="100%">Villanueva, Laura</style></author><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Postier, Bradley L</style></author><author><style face="normal" font="default" size="100%">Xu, Bo</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetoin</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethanol</style></keyword><keyword><style  face="normal" font="default" size="100%">Fermentation</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrilotriacetic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Reverse Transcriptase Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Substrate Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfides</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur-Reducing Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Thioredoxins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">74</style></volume><pages><style face="normal" font="default" size="100%">4277-84</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Although Pelobacter species are closely related to Geobacter species, recent studies suggested that Pelobacter carbinolicus may reduce Fe(III) via a different mechanism because it lacks the outer-surface c-type cytochromes that are required for Fe(III) reduction by Geobacter sulfurreducens. Investigation into the mechanisms for Fe(III) reduction demonstrated that P. carbinolicus had growth yields on both soluble and insoluble Fe(III) consistent with those of other Fe(III)-reducing bacteria. Comparison of whole-genome transcript levels during growth on Fe(III) versus fermentative growth demonstrated that the greatest apparent change in gene expression was an increase in transcript levels for four contiguous genes. These genes encode two putative periplasmic thioredoxins; a putative outer-membrane transport protein; and a putative NAD(FAD)-dependent dehydrogenase with homology to disulfide oxidoreductases in the N terminus, rhodanese (sulfurtransferase) in the center, and uncharacterized conserved proteins in the C terminus. Unlike G. sulfurreducens, transcript levels for cytochrome genes did not increase in P. carbinolicus during growth on Fe(III). P. carbinolicus could use sulfate as the sole source of sulfur during fermentative growth, but required elemental sulfur or sulfide for growth on Fe(III). The increased expression of genes potentially involved in sulfur reduction, coupled with the requirement for sulfur or sulfide during growth on Fe(III), suggests that P. carbinolicus reduces Fe(III) via an indirect mechanism in which (i) elemental sulfur is reduced to sulfide and (ii) the sulfide reduces Fe(III) with the regeneration of elemental sulfur. This contrasts with the direct reduction of Fe(III) that has been proposed for Geobacter species.</style></abstract><issue><style face="normal" font="default" size="100%">14</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18515480?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Izallalen, Mounir</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Radhakrishnan</style></author><author><style face="normal" font="default" size="100%">Burgard, Anthony</style></author><author><style face="normal" font="default" size="100%">Postier, Bradley</style></author><author><style face="normal" font="default" size="100%">DiDonato, Raymond</style></author><author><style face="normal" font="default" size="100%">Sun, Jun</style></author><author><style face="normal" font="default" size="100%">Schilling, Christopher H</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter sulfurreducens strain engineered for increased rates of respiration.</style></title><secondary-title><style face="normal" font="default" size="100%">Metab Eng</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Metab. Eng.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adenosine Triphosphate</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">NADH Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">NADP</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxygen Consumption</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphates</style></keyword><keyword><style  face="normal" font="default" size="100%">Proton-Translocating ATPases</style></keyword><keyword><style  face="normal" font="default" size="100%">Radioactive Pollutants</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">267-75</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species are among the most effective microorganisms known for the bioremediation of radioactive and toxic metals in contaminated subsurface environments and for converting organic compounds to electricity in microbial fuel cells. However, faster rates of electron transfer could aid in optimizing these processes. Therefore, the Optknock strain design methodology was applied in an iterative manner to the constraint-based, in silico model of Geobacter sulfurreducens to identify gene deletions predicted to increase respiration rates. The common factor in the Optknock predictions was that each resulted in a predicted increase in the cellular ATP demand, either by creating ATP-consuming futile cycles or decreasing the availability of reducing equivalents and inorganic phosphate for ATP biosynthesis. The in silico model predicted that increasing the ATP demand would result in higher fluxes of acetate through the TCA cycle and higher rates of NADPH oxidation coupled with decreases in flux in reactions that funnel acetate toward biosynthetic pathways. A strain of G. sulfurreducens was constructed in which the hydrolytic, F(1) portion of the membrane-bound F(0)F(1) (H(+))-ATP synthase complex was expressed when IPTG was added to the medium. Induction of the ATP drain decreased the ATP content of the cell by more than half. The cells with the ATP drain had higher rates of respiration, slower growth rates, and a lower cell yield. Genome-wide analysis of gene transcript levels indicated that when the higher rate of respiration was induced transcript levels were higher for genes involved in energy metabolism, especially in those encoding TCA cycle enzymes, subunits of the NADH dehydrogenase, and proteins involved in electron acceptor reduction. This was accompanied by lower transcript levels for genes encoding proteins involved in amino acid biosynthesis, cell growth, and motility. Several changes in gene expression that involve processes not included in the in silico model were also detected, including increased expression of a number of redox-active proteins, such as c-type cytochromes and a putative multicopper outer-surface protein. The results demonstrate that it is possible to genetically engineer increased respiration rates in G. sulfurreducens in accordance with predictions from in silico metabolic modeling. To our knowledge, this is the first report of metabolic engineering to increase the respiratory rate of a microorganism.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18644460?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Findlay, Robert H</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Typing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, rRNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Genotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">58</style></volume><pages><style face="normal" font="default" size="100%">1075-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A Gram-negative, rod-shaped, motile bacterium, strain Rf4T, which conserves energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation, was isolated from subsurface sediment undergoing uranium bioremediation. The 16S rRNA gene sequence of strain Rf4T matched sequences recovered in 16S rRNA gene clone libraries constructed from DNA extracted from groundwater sampled at the same time as the source sediment. Cells of strain Rf4T were regular, motile rods, 1.2-2.0 microm long and 0.5-0.6 microm in diameter, with rounded ends. Cells had one lateral flagellum. Growth was optimal at pH 6.5-7.0 and 32 degrees C. With acetate as the electron donor, strain Rf4T used Fe(III), Mn(IV), anthraquinone-2,6-disulfonate, malate and fumarate as electron acceptors and reduced U(VI) in cell suspensions. With poorly crystalline Fe(III) oxide as the electron acceptor, strain Rf4T oxidized the following electron donors: acetate, lactate, pyruvate and ethanol. Phylogenetic analysis of the 16S rRNA gene sequence of strain Rf4T placed it in the genus Geobacter. Strain Rf4T was most closely related to 'Geobacter humireducens' JW3 (95.9 % sequence similarity), Geobacter bremensis Dfr1T (95.4 %) and Geobacter bemidjiensis BemT (95.1 %). Based on phylogenetic analysis and phenotypic differences between strain Rf4T and closely related Geobacter species, this strain is described as a representative of a novel species, Geobacter uraniireducens sp. nov. The type strain is Rf4T (=ATCC BAA-1134T =JCM 13001T).</style></abstract><issue><style face="normal" font="default" size="100%">Pt 5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18450691?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Strycharz, Sarah M</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Johnson, Jessica P</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Sanford, Robert A</style></author><author><style face="normal" font="default" size="100%">Löffler, Frank E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Graphite electrode as a sole electron donor for reductive dechlorination of tetrachlorethene by Geobacter lovleyi.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ethylene Dichlorides</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Scanning</style></keyword><keyword><style  face="normal" font="default" size="100%">Succinic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Tetrachloroethylene</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">74</style></volume><pages><style face="normal" font="default" size="100%">5943-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The possibility that graphite electrodes can serve as the direct electron donor for microbially catalyzed reductive dechlorination was investigated with Geobacter lovleyi. In an initial evaluation of whether G. lovleyi could interact electronically with graphite electrodes, cells were provided with acetate as the electron donor and an electrode as the sole electron acceptor. Current was produced at levels that were ca. 10-fold lower than those previously reported for Geobacter sulfurreducens under similar conditions, and G. lovleyi anode biofilms were correspondingly thinner. When an electrode poised at -300 mV (versus a standard hydrogen electrode) was provided as the electron donor, G. lovleyi effectively reduced fumarate to succinate. The stoichiometry of electrons consumed to succinate produced was 2:1, the ratio expected if the electrode served as the sole electron donor for fumarate reduction. G. lovleyi effectively reduced tetrachloroethene (PCE) to cis-dichloroethene with a poised electrode as the sole electron donor at rates comparable to those obtained when acetate serves as the electron donor. Cells were less abundant on the electrodes when the electrodes served as an electron donor than when they served as an electron acceptor. PCE was not reduced in controls without cells or when the current supply to cells was interrupted. These results demonstrate that G. lovleyi can use a poised electrode as a direct electron donor for reductive dechlorination of PCE. The ability to colocalize dechlorinating microorganisms with electrodes has several potential advantages for bioremediation of subsurface chlorinated contaminants, especially in source zones where electron donor delivery is challenging and often limits dechlorination.</style></abstract><issue><style face="normal" font="default" size="100%">19</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18658278?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kashefi, Kazem</style></author><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Elliott, W Crawford</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Growth of thermophilic and hyperthermophilic Fe(III)-reducing microorganisms on a ferruginous smectite as the sole electron acceptor.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Silicates</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">74</style></volume><pages><style face="normal" font="default" size="100%">251-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Recent studies have suggested that the structural Fe(III) within phyllosilicate minerals, including smectite and illite, is an important electron acceptor for Fe(III)-reducing microorganisms in sedimentary environments at moderate temperatures. The reduction of structural Fe(III) by thermophiles, however, has not previously been described. A wide range of thermophilic and hyperthermophilic Archaea and Bacteria from marine and freshwater environments that are known to reduce poorly crystalline Fe(III) oxides were tested for their ability to reduce structural (octahedrally coordinated) Fe(III) in smectite (SWa-1) as the sole electron acceptor. Two out of the 10 organisms tested, Geoglobus ahangari and Geothermobacterium ferrireducens, were not able to conserve energy to support growth by reduction of Fe(III) in SWa-1 despite the fact that both organisms were originally isolated with solid-phase Fe(III) as the electron acceptor. The other organisms tested were able to grow on SWa-1 and reduced 6.3 to 15.1% of the Fe(III). This is 20 to 50% less than the reported amounts of Fe(III) reduced in the same smectite (SWa-1) by mesophilic Fe(III) reducers. Two organisms, Geothermobacter ehrlichii and archaeal strain 140, produced copious amounts of an exopolysaccharide material, which may have played an active role in the dissolution of the structural iron in SWa-1 smectite. The reduction of structural Fe(III) in SWa-1 by archaeal strain 140 was studied in detail. Microbial Fe(III) reduction was accompanied by an increase in interlayer and octahedral charges and some incorporation of potassium and magnesium into the smectite structure. However, these changes in the major element chemistry of SWa-1 smectite did not result in the formation of an illite-like structure, as reported for a mesophilic Fe(III) reducer. These results suggest that thermophilic Fe(III)-reducing organisms differ in their ability to reduce and solubilize structural Fe(III) in SWa-1 smectite and that SWa-1 is not easily transformed to illite by these organisms.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17981937?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lanthier, Martin</style></author><author><style face="normal" font="default" size="100%">Gregory, Kelvin B</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Growth with high planktonic biomass in Shewanella oneidensis fuel cells.</style></title><secondary-title><style face="normal" font="default" size="100%">FEMS Microbiol Lett</style></secondary-title><alt-title><style face="normal" font="default" size="100%">FEMS Microbiol. Lett.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Lactic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Plankton</style></keyword><keyword><style  face="normal" font="default" size="100%">Shewanella</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">278</style></volume><pages><style face="normal" font="default" size="100%">29-35</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Shewanella oneidensis MR-1 grew for over 50 days in microbial fuel cells, incompletely oxidizing lactate to acetate with high recovery of the electrons derived from this reaction as electricity. Electricity was produced with lactate or hydrogen and current was comparable to that of electricigens which completely oxidize organic substrates. However, unlike fuel cells with previously described electricigens, in which cells are primarily attached to the anode, at least as many of the S. oneidensis cells were planktonic as were attached to the anode. These results demonstrate that S. oneidensis may conserve energy for growth with an electrode serving as an electron acceptor and suggest that multiple strategies for electron transfer to fuel cell anodes exist.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17995953?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Risso, Carla</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Elifantz, Hila</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Highly conserved genes in Geobacter species with expression patterns indicative of acetate limitation.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Membrane Transport Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">154</style></volume><pages><style face="normal" font="default" size="100%">2589-99</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Analysis of the genome of Geobacter sulfurreducens revealed four genes encoding putative symporters with homology to ActP, an acetate transporter in Escherichia coli. Three of these genes, aplA, aplB and aplC, are highly similar (over 90 % identical) and fell within a tight phylogenetic cluster (Group I) consisting entirely of Geobacter homologues. Transcript levels for all three genes increased in response to acetate limitation. The fourth gene, aplD, is phylogenetically distinct (Group II) and its expression was not influenced by acetate availability. Deletion of any one of the three genes in Group I did not significantly affect acetate-dependent growth, suggesting functional redundancy. Attempts to recover mutants in which various combinations of two of these genes were deleted were unsuccessful, suggesting that at least two of these three transporter genes are required to support growth. Closely related Group I apl genes were found in the genomes of other Geobacter species whose genome sequences are available. Furthermore, related genes could be detected in genomic DNA extracted from a subsurface environment undergoing in situ uranium bioremediation. The transporter genes recovered from the subsurface were most closely related to Group I apl genes found in the genomes of cultured Geobacter species that were isolated from contaminated subsurface environments. The increased expression of these genes in response to acetate limitation, their high degree of conservation among Geobacter species and the ease with which they can be detected in environmental samples suggest that Group I apl genes of the Geobacteraceae may be suitable biomarkers for acetate limitation. Monitoring the expression of these genes could aid in the design of strategies for acetate-mediated in situ bioremediation of uranium-contaminated groundwater.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18757793?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Postier, Bradley L</style></author><author><style face="normal" font="default" size="100%">Didonato, Raymond J</style></author><author><style face="normal" font="default" size="100%">Chaudhuri, Swades K</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioelectrochemistry</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioelectrochemistry</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Down-Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">73</style></volume><pages><style face="normal" font="default" size="100%">70-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens effectively produces electricity in microbial fuel cells by oxidizing acetate with an electrode serving as the sole electron acceptor. Deletion of the gene encoding OmcF, a monoheme outer membrane c-type cytochrome, substantially decreased current production. Previous studies demonstrated that inhibition of Fe(III) reduction in the OmcF-deficient mutant could be attributed to poor transcription of the gene for OmcB, an outer membrane c-type cytochrome that is required for Fe(III) reduction. However, a mutant in which omcB was deleted produced electricity as well as wild type. Microarray analysis of the OmcF-deficient mutant versus the wild type revealed that many of the genes with the greatest decreases in transcript levels were genes whose expression was previously reported to be upregulated in cells grown with an electrode as the sole electron acceptor. These included genes with putative functions related to metal efflux and/or type I secretion and two hypothetical proteins. The outer membrane cytochromes, OmcS and OmcE, which previous studies have demonstrated are required for optimal current generation, were not detected on the outer surface of the OmcF-deficient mutant even though the omcS and omcE genes were still transcribed, suggesting that the putative secretion system could be involved in the export of outer membrane proteins necessary for electron transfer to the fuel cell anode. These results suggest that the requirement for OmcF for optimal current production is not because OmcF is directly involved in extracellular electron transfer but because OmcF is required for the appropriate transcription of other genes either directly or indirectly involved in electricity production.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18538641?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Investigation of direct vs. indirect involvement of the c-type cytochrome MacA in Fe(III) reduction by Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">FEMS Microbiol Lett</style></secondary-title><alt-title><style face="normal" font="default" size="100%">FEMS Microbiol. Lett.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">ATP-Binding Cassette Transporters</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">286</style></volume><pages><style face="normal" font="default" size="100%">39-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The electron transfer pathway to Fe(III) reduction in Geobacter sulfurreducens has been hypothesized to consist of a series of c-type cytochromes. Previous genetic studies suggested that the inner membrane-associated, c-type cytochrome, MacA, was a component of the electron transfer chain leading to Fe(III) reduction in the dissimilatory Fe(III)-reducer, G. sulfurreducens. However, investigation of the expression of OmcB, an outer-membrane c-type cytochrome demonstrated previously to be critical for optimal Fe(III) reduction, revealed that both omcB transcript and protein levels were dramatically reduced in the MacA-deficient mutant. Expression of the omcB gene in trans enabled the MacA-deficient mutant to reduce Fe(III) at a rate that was proportional to the level of omcB expression. These results suggest that MacA is not directly involved in electron transfer to Fe(III) and further confirm the importance of OmcB in Fe(III) reduction by G. sulfurreducens.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18616590?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The microbe electric: conversion of organic matter to electricity.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr. Opin. Biotechnol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Organic Chemicals</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">564-71</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Broad application of microbial fuel cells will require substantial increases in current density. A better understanding of the microbiology of these systems may help. Recent studies have greatly expanded the range of microorganisms known to function either as electrode-reducing microorganisms at the anode or as electrode-oxidizing microorganisms at the cathode. Microorganisms that can completely oxidize organic compounds with an electrode serving as the sole electron acceptor are expected to be the primary contributors to power production. Several mechanisms for electron transfer to anodes have been proposed including: direct electron transfer via outer-surface c-type cytochromes, long-range electron transfer via microbial nanowires, electron flow through a conductive biofilm matrix containing cytochromes, and soluble electron shuttles. Which mechanisms are most important depend on the microorganisms and the thickness of the anode biofilm. Emerging systems biology approaches to the study, design, and evolution of microorganisms interacting with electrodes are expected to contribute to improved microbial fuel cells.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19000760?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ding, Yan-Huai R</style></author><author><style face="normal" font="default" size="100%">Hixson, Kim K</style></author><author><style face="normal" font="default" size="100%">Aklujkar, Muktak A</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author><author><style face="normal" font="default" size="100%">Smith, Richard D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor.</style></title><secondary-title><style face="normal" font="default" size="100%">Biochim Biophys Acta</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biochim. Biophys. Acta</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1784</style></volume><pages><style face="normal" font="default" size="100%">1935-41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The mechanisms for Fe(III) oxide reduction in Geobacter species are of interest because Fe(III) oxides are the most abundant form of Fe(III) in many soils and sediments and Geobacter species are prevalent Fe(III)-reducing microorganisms in many of these environments. Protein abundance in G. sulfurreducens grown on poorly crystalline Fe(III) oxide or on soluble Fe(III) citrate was compared with a global accurate mass and time tag proteomic approach in order to identify proteins that might be specifically associated with Fe(III) oxide reduction. A total of 2991 proteins were detected in G. sulfurreducens grown with acetate as the electron donor and either Fe(III) oxide or soluble Fe(III) citrate as the electron acceptor, resulting in 86% recovery of the genes predicted to encode proteins. Of the total expressed proteins 76% were less abundant in Fe(III) oxide cultures than in Fe(III) citrate cultures, which is consistent with the overall slower rate of metabolism during growth with an insoluble electron acceptor. A total of 269 proteins were more abundant in Fe(III) oxide-grown cells than in cells grown on Fe(III) citrate. Most of these proteins were in the energy metabolism category: primarily electron transport proteins, including 13 c-type cytochromes and PilA, the structural protein for electrically conductive pili. Several of the cytochromes that were more abundant in Fe(III) oxide-grown cells were previously shown with genetic approaches to be essential for optimal Fe(III) oxide reduction. Other proteins that were more abundant during growth on Fe(III) oxide included transport and binding proteins, proteins involved in regulation and signal transduction, cell envelope proteins, and enzymes for amino acid and protein biosynthesis, among others. There were also a substantial number of proteins of unknown function that were more abundant during growth on Fe(III) oxide. These results indicate that electron transport to Fe(III) oxide requires additional and/or different proteins than electron transfer to soluble, chelated Fe(III) and suggest proteins whose functions should be further investigated in order to better understand the mechanisms of electron transfer to Fe(III) oxide in G. sulfurreducens.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18638577?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Villanueva, Laura</style></author><author><style face="normal" font="default" size="100%">Haveman, Shelley A</style></author><author><style face="normal" font="default" size="100%">Summers, Zara M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Quantification of Desulfovibrio vulgaris dissimilatory sulfite reductase gene expression during electron donor- and electron acceptor-limited growth.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Desulfovibrio vulgaris</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogensulfite Reductase</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">74</style></volume><pages><style face="normal" font="default" size="100%">5850-3</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have suggested that levels of transcripts for dsrA, a gene encoding a subunit of the dissimilatory sulfite reductase, are not directly related to the rates of sulfate reduction in sediments under all conditions. This phenomenon was further investigated with chemostat-grown Desulfovibrio vulgaris. Under sulfate-limiting conditions, dsrA transcript levels increased as the bulk rates of sulfate reduction in the chemostat increased, but transcript levels were similar at all sulfate reduction rates under electron donor-limiting conditions. When both electron donor- and electron acceptor-limiting conditions were considered, there was a direct correspondence between dsrA transcript levels and the rates of sulfate reduction per cell. These results suggest that dsrA transcript levels may provide important information on the metabolic state of sulfate reducers.</style></abstract><issue><style face="normal" font="default" size="100%">18</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18658285?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chin, Kuk-Jeong</style></author><author><style face="normal" font="default" size="100%">Sharma, Manju L</style></author><author><style face="normal" font="default" size="100%">Russell, Lyndsey A</style></author><author><style face="normal" font="default" size="100%">O'Neill, Kathleen R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Quantifying expression of a dissimilatory (bi)sulfite reductase gene in petroleum-contaminated marine harbor sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Ecol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb. Ecol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Desulfitobacterium</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogensulfite Reductase</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Temperature</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">55</style></volume><pages><style face="normal" font="default" size="100%">489-99</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The possibility of quantifying in situ levels of transcripts for dissimilatory (bi)sulfite reductase (dsr) genes to track the activity of sulfate-reducing microorganisms in petroleum-contaminated marine harbor sediments was evaluated. Phylogenetic analysis of the cDNA generated from mRNA for a ca. 1.4 kbp portion of the contiguous dsrA and dsrB genes suggested that Desulfosarcina species, closely related to cultures known to anaerobically oxidize aromatic hydrocarbons, were active sulfate reducers in the sediments. The levels of dsrA transcripts (per mug total mRNA) were quantified in sediments incubated anaerobically at the in situ temperature as well as in sediments incubated at higher temperatures and/or with added acetate to increase the rate of sulfate reduction. Levels of dsrA transcripts were low when there was no sulfate reduction because the sediments were depleted of sulfate or if sulfate reduction was inhibited with added molybdate. There was a direct correlation between dsrA transcript levels and rates of sulfate reduction when sulfate was at ca. 10 mM in the various sediment treatments, but it was also apparent that within a given sediment, dsrA levels increased over time as long as sulfate was available, even when sulfate reduction rates did not increase. These results suggest that phylogenetic analysis of dsr transcript sequences may provide insight into the active sulfate reducers in marine sediments and that quantifying levels of dsrA transcripts can indicate whether sulfate reducers are active in particular sediment. Furthermore, it may only be possible to use dsrA transcript levels to compare the relative rates of sulfate reduction in sediments when sulfate concentrations, and possibly other environmental conditions, are comparable.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17786505?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Resch, Charles T</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Adsorption</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Colorado</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Supply</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Apr 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">42</style></volume><pages><style face="normal" font="default" size="100%">2999-3004</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous field studies on in situ bioremediation of uranium-contaminated groundwater in an aquifer in Rifle, Colorado identified two distinct phases following the addition of acetate to stimulate microbial respiration. In phase I, Geobacter species are the predominant organisms, Fe(III) is reduced, and microbial reduction of soluble U(VI) to insoluble U(IV) removes uranium from the groundwater. In phase II, Fe(III) is depleted, sulfate is reduced, and sulfate-reducing bacteria predominate. Long-term monitoring revealed an unexpected third phase during which U(VI) removal continues even after acetate additions are stopped. All three of these phases were successfully reproduced in flow-through sediment columns. When sediments from the third phase were heat sterilized, the capacity for U(VI) removal was lost. In the live sediments U(VI) removed from the groundwater was recovered as U(VI) in the sediments. This contrasts to the recovery of U(IV) in sediments resulting from the reduction of U(VI) to U(IV) during the Fe(III) reduction phase in acetate-amended sediments. Analysis of 16S rRNA gene sequences in the sediments in which U(VI) was being adsorbed indicated that members of the Firmicutes were the predominant organisms whereas no Firmicutes sequences were detected in background sediments which did not have the capacity to sorb U(VI), suggesting that the U(VI) adsorption might be due to the presence of these living organisms or at least their intact cell components. This unexpected enhanced adsorption of U(VI) onto sediments following the stimulation of microbial growth in the subsurface may potentially enhance the cost effectiveness of in situ uranium bioremediation.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18497157?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Qian, Xinlei</style></author><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evidence that OmcB and OmpB of Geobacter sulfurreducens are outer membrane surface proteins.</style></title><secondary-title><style face="normal" font="default" size="100%">FEMS Microbiol Lett</style></secondary-title><alt-title><style face="normal" font="default" size="100%">FEMS Microbiol. Lett.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Membrane</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Transmission</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptide Hydrolases</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">277</style></volume><pages><style face="normal" font="default" size="100%">21-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The c-type cytochrome (OmcB) and the multicopper protein (OmpB) required for Fe(III) oxide reduction by Geobacter sulfurreducens were predicted previously to be outer membrane proteins, but it is not clear whether they are positioned in a manner that permits the interaction with Fe(III). Treatment of whole cells with proteinase K inhibited Fe(III) reduction, but had no impact on the inner membrane-associated fumarate reduction. OmcB was digested by protease, resulting in a smaller peptide. However, immunogold labeling coupled with transmission electron microscopy did not detect OmcB, suggesting that it is only partially exposed on the cell surface. In contrast, OmpB was completely digested with protease. OmpB was loosely associated with the cell surface as a substantial portion of it was recovered in the culture supernatant. Immunogold labeling demonstrated that OmpB associated with the cell was evenly distributed on the cell surface rather than localized to one side of the cell like the conductive pili. Although several proteins required for Fe(III) oxide reduction are shown to be exposed on the outer surface of G. sulfurreducens, the finding that OmcB is also surface exposed is the first report of a protein required for optimal Fe(III) citrate reduction at least partially accessible on the cell surface.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17986080?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author><author><style face="normal" font="default" size="100%">Yan, Bin</style></author><author><style face="normal" font="default" size="100%">DiDonato, Laurie N</style></author><author><style face="normal" font="default" size="100%">Puljic, Marko</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.</style></title><secondary-title><style face="normal" font="default" size="100%">Funct Integr Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Funct. Integr. Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Ligases</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Regulatory Sequences, Nucleic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Repressor Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">229-55</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Rel(Gsu) is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3', 5' bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel(Gsu) deletion mutant to identify putative regulatory sites involved in transcription networks modulated by Rel(Gsu) or ppGpp. Differential gene expression in the rel(Gsu) deletion mutant, as compared to the wild type, was available from two growth conditions, steady state chemostat cultures and stationary phase batch cultures. Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely co-regulated. Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur- and RpoS-regulated sites. These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by Rel(Gsu)-mediated signaling.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17406915?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yan, Bin</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Biosystems</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BioSystems</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">False Positive Reactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Statistical</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Sep-Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">90</style></volume><pages><style face="normal" font="default" size="100%">421-41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The knowledge obtained from understanding individual elements involved in gene regulation is important for reconstructing gene regulatory networks, a key for understanding cellular behavior. To study gene regulatory interactions in a model microorganism, Geobacter sulfurreducens, which participates in metal reduction and energy harvesting, we investigated the presence of 59 known Escherichia coli transcription factors and predicted transcription regulatory sites in its genome. The supplementary material, available at http://www.geobacter.org/research/genomescan/, provides the results of similarity comparisons that identified regulatory proteins of G. sulfurreducens and the genome locations of the predicted regulatory sites, including the list of putative regulatory elements in the upstream regions of every predicted operon and singleton open reading frame. Regulatory sequence elements, predicted using genome similarity searches to matrices of established transcription regulatory elements from E. coli, provide an initial insight into regulation of genes and operons in G. sulfurreducens. The predicted regulatory elements were predominantly located in the upstream regions of operons and singleton open reading frames. The validity of the predictions was examined using a permutation approach. Sequence similarity searches indicate that E. coli transcription factors ArgR, CytR, DeoR, FlhCD (both FlhC and FlhD subunits), FruR, GalR, GlpR, H-NS, LacI, MetJ, PurR, TrpR, and Tus are likely missing from G. sulfurreducens. Phylogenetic analysis suggests that one HU subunit is present in G. sulfurreducens as compared to two subunits in E. coli, while each of the two E. coli IHF subunits, HimA and HimD, have two homologs in G. sulfurreducens. The closest homolog of E. coli RpoE in G. sulfurreducens may be more similar to FecI than to RpoE. These findings represent the first step in the understanding of the regulatory relationships in G. sulfurreducens on the genome scale.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17184904?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">He, Qiang</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">He, Zhili</style></author><author><style face="normal" font="default" size="100%">Zhou, Jizhong</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrocarbons, Aromatic</style></keyword><keyword><style  face="normal" font="default" size="100%">Microarray Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Chemical</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Multigene Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">180</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known.

RESULTS: The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation.

CONCLUSION: G. metallireducens appears to convert aromatic compounds to benzoyl-CoA, then to acetyl-CoA via fatty acid oxidation, and then to carbon dioxide via the TCA cycle. The enzyme responsible for dearomatizing the aromatic ring may be novel, and energetic investments at this step may be offset by a change in succinate metabolism. Analysis of a field isolate suggests that the pathways inferred for G. metallireducens may be applicable to modeling in situ bioremediation.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17578578?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Blakeney-Hayward, Jessie D</style></author><author><style face="normal" font="default" size="100%">Johnsen, Claudia V</style></author><author><style face="normal" font="default" size="100%">Plaia, Todd W</style></author><author><style face="normal" font="default" size="100%">Krader, Paul</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Vanpraagh, Catherine Gaw</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter pickeringii sp. nov., Geobacter argillaceus sp. nov. and Pelosinus fermentans gen. nov., sp. nov., isolated from subsurface kaolin lenses.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Typing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Composition</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, rRNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Georgia</style></keyword><keyword><style  face="normal" font="default" size="100%">Kaolin</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Russia</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">126-35</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The goal of this project was to isolate representative Fe(III)-reducing bacteria from kaolin clays that may influence iron mineralogy in kaolin. Two novel dissimilatory Fe(III)-reducing bacteria, strains G12(T) and G13(T), were isolated from sedimentary kaolin strata in Georgia (USA). Cells of strains G12(T) and G13(T) were motile, non-spore-forming regular rods, 1-2 mum long and 0.6 mum in diameter. Cells had one lateral flagellum. Phylogenetic analyses using the 16S rRNA gene sequence of the novel strains demonstrated their affiliation to the genus Geobacter. Strain G12(T) was most closely related to Geobacter pelophilus (94.7 %) and Geobacter chapellei (94.1 %). Strain G13(T) was most closely related to Geobacter grbiciae (95.3 %) and Geobacter metallireducens (95.1 %). Based on phylogenetic analyses and phenotypic differences between the novel isolates and other closely related species of the genus Geobacter, the isolates are proposed as representing two novel species, Geobacter argillaceus sp. nov. (type strain G12(T)=ATCC BAA-1139(T)=JCM 12999(T)) and Geobacter pickeringii sp. nov. (type strain G13(T)=ATCC BAA-1140(T)=DSM 17153(T)=JCM 13000(T)). Another isolate, strain R7(T), was derived from a primary kaolin deposit in Russia. The cells of strain R7(T) were motile, spore-forming, slightly curved rods, 0.6 x 2.0-6.0 microm in size and with up to six peritrichous flagella. Strain R7(T) was capable of reducing Fe(III) only in the presence of a fermentable substrate. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing less than 92 % similarity to bacteria of the Sporomusa-Pectinatus-Selenomomas phyletic group, including 'Anaerospora hongkongensis' (90.2 %), Acetonema longum (90.6 %), Dendrosporobacter quercicolus (90.9 %) and Anaerosinus glycerini (91.5 %). On the basis of phylogenetic analysis and physiological tests, strain R7(T) is proposed to represent a novel genus and species, Pelosinus fermentans gen. nov., sp. nov. (type strain R7(T)=DSM 17108(T)=ATCC BAA-1133(T)), in the Sporomusa-Pectinatus-Selenomonas group.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17220454?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Heat-shock sigma factor RpoH from Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Binding Sites</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Heat-Shock Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">153</style></volume><pages><style face="normal" font="default" size="100%">838-46</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Recent studies with Myxococcus xanthus have suggested that homologues of the Escherichia coli heat-shock sigma factor, RpoH, may not be involved in the heat-shock response in this delta-proteobacterium. The genome of another delta-proteobacterium, Geobacter sulfurreducens, which is considered to be a representative of the Fe(III)-reducing Geobacteraceae that predominate in a diversity of subsurface environments, contains an rpoH homologue. Characterization of the G. sulfurreducens rpoH homologue revealed that it was induced by a temperature shift from 30 degrees C to 42 degrees C and that an rpoH-deficient mutant was unable to grow at 42 degrees C. The predicted heat-shock genes, hrcA, grpE, dnaK, groES and htpG, were heat-shock inducible in an rpoH-dependent manner, and comparison of promoter regions of these genes identified the consensus sequences for the -10 and -35 promoter elements. In addition, DNA elements identical to the CIRCE consensus sequence were found in promoters of rpoH, hrcA and groES, suggesting that these genes are regulated by a homologue of the repressor HrcA, which is known to bind the CIRCE element. These results suggest that the G. sulfurreducens RpoH homologue is the heat-shock sigma factor and that heat-shock response in G. sulfurreducens is regulated positively by RpoH as well as negatively by the HrcA/CIRCE system.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17322204?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Korenevsky, Anton A</style></author><author><style face="normal" font="default" size="100%">DiDonato, Laurie N</style></author><author><style face="normal" font="default" size="100%">Sullivan, Sara A</style></author><author><style face="normal" font="default" size="100%">Konishi, Hiromi</style></author><author><style face="normal" font="default" size="100%">Xu, Huifang</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Importance of c-Type cytochromes for U(VI) reduction by Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Transmission</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Periplasm</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">16</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: In order to study the mechanism of U(VI) reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI) with acetate serving as the electron donor was investigated.

RESULTS: The ability of several c-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50-60%) the ability of G. sulfurreducens to reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI) reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI) reduction. A subpopulation of both wild type and U(VI) reduction-impaired cells, 24-30%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI) reduction-impaired and wild type G. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III) revealed no correlation between the impact of cytochrome deletion on U(VI) reduction and reduction of Fe(III) hydroxide and chelated Fe(III).

CONCLUSION: This study indicates that c-type cytochromes are involved in U(VI) reduction by Geobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction by G. sulfurreducens but do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI) reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI) reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium reduction. Periplasmic uranium accumulation may reflect the ability of uranium to penetrate the outer membrane rather than the occurrence of enzymatic U(VI) reduction. Elimination of cytochromes rarely had a similar impact on both Fe(III) and U(VI) reduction, suggesting that there are differences in the routes of electron transfer to U(VI) and Fe(III). Further studies are required to clarify the pathways leading to U(VI) reduction in G. sulfurreducens.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17346345?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Kaufmann, Franz</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Involvement of Geobacter sulfurreducens SfrAB in acetate metabolism rather than intracellular, respiration-linked Fe(III) citrate reduction.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acid Transport Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Membrane</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytoplasm</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Formic Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">NADH, NADPH Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">153</style></volume><pages><style face="normal" font="default" size="100%">3572-85</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A soluble ferric reductase, SfrAB, which catalysed the NADPH-dependent reduction of chelated Fe(III), was previously purified from the dissimilatory Fe(III)-reducing micro-organism Geobacter sulfurreducens, suggesting that reduction of chelated forms of Fe(III) might be cytoplasmic. However, metabolically active spheroplast suspensions could not catalyse acetate-dependent Fe(III) citrate reduction, indicating that periplasmic and/or outer-membrane components were required for Fe(III) citrate reduction. Furthermore, phenotypic analysis of an SfrAB knockout mutant suggested that SfrAB was involved in acetate metabolism rather than respiration-linked Fe(III) reduction. The mutant could not grow via the reduction of either Fe(III) citrate or fumarate when acetate was the electron donor but could grow with either acceptor if either hydrogen or formate served as the electron donor. Following prolonged incubation in acetate : fumarate medium in the absence of hydrogen and formate, an 'acetate-adapted' SfrAB-null strain was isolated that was capable of growth on acetate : fumarate medium but not acetate : Fe(III) citrate medium. Comparison of gene expression in this strain with that of the wild-type revealed upregulation of a potential NADPH-dependent ferredoxin oxidoreductase as well as genes involved in energy generation and amino acid uptake, suggesting that NADPH homeostasis and the tricarboxylic acid (TCA) cycle were perturbed in the 'acetate-adapted' SfrAB-null strain. Membrane and soluble fractions prepared from the 'acetate-adapted' strain were depleted of NADPH-dependent Fe(III), viologen and quinone reductase activities. These results indicate that cytoplasmic, respiration-linked reduction of Fe(III) by SfrAB in vivo is unlikely and suggest that deleting SfrAB may interfere with growth via acetate oxidation by interfering with NADP regeneration.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17906154?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richter, Hanno</style></author><author><style face="normal" font="default" size="100%">Lanthier, Martin</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Lack of electricity production by Pelobacter carbinolicus indicates that the capacity for Fe(III) oxide reduction does not necessarily confer electron transfer ability to fuel cell anodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteriological Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferrous Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">In Situ Hybridization, Fluorescence</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Confocal</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">73</style></volume><pages><style face="normal" font="default" size="100%">5347-53</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The ability of Pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to Pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. P. carbinolicus could not produce current in a microbial fuel cell with electron donors which support Fe(III) oxide reduction by this organism. Current was produced using a coculture of P. carbinolicus and Geobacter sulfurreducens with ethanol as the fuel. Ethanol consumption was associated with the transitory accumulation of acetate and hydrogen. G. sulfurreducens alone could not metabolize ethanol, suggesting that P. carbinolicus grew in the fuel cell by converting ethanol to hydrogen and acetate, which G. sulfurreducens oxidized with electron transfer to the anode. Up to 83% of the electrons available in ethanol were recovered as electricity and in the metabolic intermediate acetate. Hydrogen consumption by G. sulfurreducens was important for ethanol metabolism by P. carbinolicus. Confocal microscopy and analysis of 16S rRNA genes revealed that half of the cells growing on the anode surface were P. carbinolicus, but there was a nearly equal number of planktonic cells of P. carbinolicus. In contrast, G. sulfurreducens was primarily attached to the anode. P. carbinolicus represents the first Fe(III) oxide-reducing microorganism found to be unable to produce current in a microbial fuel cell, providing the first suggestion that the mechanisms for extracellular electron transfer to Fe(III) oxides and fuel cell anodes may be different.</style></abstract><issue><style face="normal" font="default" size="100%">16</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17574993?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">Pollina, Rachael B</style></author><author><style face="normal" font="default" size="100%">Nicoll, Julie S</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Possible nonconductive role of Geobacter sulfurreducens pilus nanowires in biofilm formation.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Agglutination</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">189</style></volume><pages><style face="normal" font="default" size="100%">2125-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens required expression of electrically conductive pili to form biofilms on Fe(III) oxide surfaces, but pili were also essential for biofilm development on plain glass when fumarate was the sole electron acceptor. Furthermore, pili were needed for cell aggregation in agglutination studies. These results suggest that the pili of G. sulfurreducens also have a structural role in biofilm formation.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17158673?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Peacock, Aaron D</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteroidetes</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbohydrate Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Cold Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy-Generating Resources</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Seawater</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">701-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A Gram-negative, non-motile, filamentous, rod-shaped, non-spore-forming bacterium (strain F2(T)) was isolated from the surface of an electricity-harvesting electrode incubated in marine sediments. Strain F2(T) does not contain c-type cytochromes, flexirubin or carotenoids. It is a facultative anaerobe that can ferment sugars by using a mixed acid fermentation pathway and it can grow over a wide range of temperatures (4-42 degrees C). The DNA G+C (44.9 mol%) content and chemotaxonomic characteristics (major fatty acids, a-15 : 0 and 15 : 0) were consistent with those of species within the phylum Bacteroidetes. Phylogenetic analysis of the 16S rRNA nucleotide and elongation factor G amino acid sequences indicated that strain F2(T) represents a unique phylogenetic cluster within the phylum Bacteroidetes. On the basis of 16S rRNA gene sequence phylogeny, the closest relative available in pure culture, Alkaliflexus imshenetskii, is only 87.5 % similar to strain F2(T). Results from physiological, biochemical and phylogenetic analyses showed that strain F2(T) should be classified as a novel genus and species within the phylum Bacteroidetes, for which the name Prolixibacter bellariivorans gen. nov., sp. nov. is proposed. The type strain is F2(T) (=ATCC BAA-1284(T)=JCM 13498(T)).</style></abstract><issue><style face="normal" font="default" size="100%">Pt 4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17392190?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Covalla, Sean F</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Temperature</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">463-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1(T)=ATCC BAA-34(T)=JCM 14045(T)) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 degrees C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17329769?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ahrendt, Angela J</style></author><author><style face="normal" font="default" size="100%">Tollaksen, Sandra L</style></author><author><style face="normal" font="default" size="100%">Lindberg, Carl</style></author><author><style face="normal" font="default" size="100%">Zhu, Wenhong</style></author><author><style face="normal" font="default" size="100%">Yates, John R</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Babnigg, György</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Giometti, Carol S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Steady state protein levels in Geobacter metallireducens grown with iron (III) citrate or nitrate as terminal electron acceptor.</style></title><secondary-title><style face="normal" font="default" size="100%">Proteomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proteomics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Proliferation</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophoresis, Gel, Two-Dimensional</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrates</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Tandem Mass Spectrometry</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">4148-57</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species predominate in aquatic sediments and submerged soils where organic carbon sources are oxidized with the reduction of Fe(III). The natural occurrence of Geobacter in some waste sites suggests this microorganism could be useful for bioremediation if growth and metabolic activity can be regulated. 2-DE was used to monitor the steady state protein levels of Geobacter metallireducens grown with either Fe(III) citrate or nitrate to elucidate metabolic differences in response to different terminal electron acceptors present in natural environments populated by Geobacter. Forty-six protein spots varied significantly in abundance (p&lt;0.05) between the two growth conditions; proteins were identified by tryptic peptide mass and peptide sequence determined by MS/MS. Enzymes involved in pyruvate metabolism and the tricarboxylic acid (TCA) cycle were more abundant in cells grown with Fe(III) citrate, while proteins associated with nitrate metabolism and sensing cellular redox status along with several proteins of unknown function were more abundant in cells grown with nitrate. These results indicate a higher level of flux through the TCA cycle in the presence of Fe(III) compared to nitrate. The oxidative stress response observed in previous studies of Geobacter sulfurreducens grown with Fe(III) citrate was not seen in G. metallireducens.</style></abstract><issue><style face="normal" font="default" size="100%">22</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17994620?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">N'guessan, Lucie A</style></author><author><style face="normal" font="default" size="100%">Ortiz-Bernad, Irene</style></author><author><style face="normal" font="default" size="100%">Larrahondo, Maria J</style></author><author><style face="normal" font="default" size="100%">Adams, Lorrie A</style></author><author><style face="normal" font="default" size="100%">Ward, Joy A</style></author><author><style face="normal" font="default" size="100%">Nicoll, Julie S</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Chavan, Milind A</style></author><author><style face="normal" font="default" size="100%">Johnson, Jessica P</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments.</style></title><secondary-title><style face="normal" font="default" size="100%">ISME J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">ISME J</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrocarbons, Aromatic</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1</style></volume><pages><style face="normal" font="default" size="100%">663-77</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18059491?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Nicoll, Julie S</style></author><author><style face="normal" font="default" size="100%">Covalla, Sean F</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Biofilm and nanowire production leads to increased current in Geobacter sulfurreducens fuel cells.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biofilms</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Confocal</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanowires</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">72</style></volume><pages><style face="normal" font="default" size="100%">7345-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens developed highly structured, multilayer biofilms on the anode surface of a microbial fuel cell converting acetate to electricity. Cells at a distance from the anode remained viable, and there was no decrease in the efficiency of current production as the thickness of the biofilm increased. Genetic studies demonstrated that efficient electron transfer through the biofilm required the presence of electrically conductive pili. These pili may represent an electronic network permeating the biofilm that can promote long-range electrical transfer in an energy-efficient manner, increasing electricity production more than 10-fold.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16936064?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Bug juice: harvesting electricity with microorganisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Rev Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Rev. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">497-508</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It is well established that some reduced fermentation products or microbially reduced artificial mediators can abiotically react with electrodes to yield a small electrical current. This type of metabolism does not typically result in an efficient conversion of organic compounds to electricity because only some metabolic end products will react with electrodes, and the microorganisms only incompletely oxidize their organic fuels. A new form of microbial respiration has recently been discovered in which microorganisms conserve energy to support growth by oxidizing organic compounds to carbon dioxide with direct quantitative electron transfer to electrodes. These organisms, termed electricigens, offer the possibility of efficiently converting organic compounds into electricity in self-sustaining systems with long-term stability.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16778836?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yan, Bin</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Ueki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Puljic, Marko</style></author><author><style face="normal" font="default" size="100%">Adkins, Ronald M</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.</style></title><secondary-title><style face="normal" font="default" size="100%">Gene</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Gene</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrates</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Directed RNA Polymerases</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli</style></keyword><keyword><style  face="normal" font="default" size="100%">Escherichia coli Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Dec 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">384</style></volume><pages><style face="normal" font="default" size="100%">73-95</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">RpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely -35 and -10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative -35/-10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of -35/-10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between -35/-10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17014972?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Haveman, Shelley A</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Ding, Yan-Huai R</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Didonato, Raymond J</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">c-Type cytochromes in Pelobacter carbinolicus.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Heme</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Reverse Transcriptase Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">72</style></volume><pages><style face="normal" font="default" size="100%">6980-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies failed to detect c-type cytochromes in Pelobacter species despite the fact that other close relatives in the Geobacteraceae, such as Geobacter and Desulfuromonas species, have abundant c-type cytochromes. Analysis of the recently completed genome sequence of Pelobacter carbinolicus revealed 14 open reading frames that could encode c-type cytochromes. Transcripts for all but one of these open reading frames were detected in acetoin-fermenting and/or Fe(III)-reducing cells. Three putative c-type cytochrome genes were expressed specifically during Fe(III) reduction, suggesting that the encoded proteins may participate in electron transfer to Fe(III). One of these proteins was a periplasmic triheme cytochrome with a high level of similarity to PpcA, which has a role in Fe(III) reduction in Geobacter sulfurreducens. Genes for heme biosynthesis and system II cytochrome c biogenesis were identified in the genome and shown to be expressed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of protein extracted from acetoin-fermenting P. carbinolicus cells contained three heme-staining bands which were confirmed by mass spectrometry to be among the 14 predicted c-type cytochromes. The number of cytochrome genes, the predicted amount of heme c per protein, and the ratio of heme-stained protein to total protein were much smaller in P. carbinolicus than in G. sulfurreducens. Furthermore, many of the c-type cytochromes that genetic studies have indicated are required for optimal Fe(III) reduction in G. sulfurreducens were not present in the P. carbinolicus genome. These results suggest that further evaluation of the functions of c-type cytochromes in the Geobacteraceae is warranted.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16936056?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Giometti, Carol</style></author><author><style face="normal" font="default" size="100%">Tollaksen, Sandra</style></author><author><style face="normal" font="default" size="100%">Khare, Tripti</style></author><author><style face="normal" font="default" size="100%">Lin, Winston</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">DNA microarray and proteomic analyses of the RpoS regulon in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Citric Acid Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophoresis, Gel, Two-Dimensional</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Mass Spectrometry</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutagenesis, Insertional</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidative Stress</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Biosynthesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteome</style></keyword><keyword><style  face="normal" font="default" size="100%">Regulon</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Signal Transduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">188</style></volume><pages><style face="normal" font="default" size="100%">2792-800</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The regulon of the sigma factor RpoS was defined in Geobacter sulfurreducens by using a combination of DNA microarray expression profiles and proteomics. An rpoS mutant was examined under steady-state conditions with acetate as an electron donor and fumarate as an electron acceptor and with additional transcriptional profiling using Fe(III) as an electron acceptor. Expression analysis revealed that RpoS acts as both a positive and negative regulator. Many of the RpoS-dependent genes determined play roles in energy metabolism, including the tricarboxylic acid cycle, signal transduction, transport, protein synthesis and degradation, and amino acid metabolism and transport. As expected, RpoS activated genes involved in oxidative stress resistance and adaptation to nutrient limitation. Transcription of the cytochrome c oxidase operon, necessary for G. sulfurreducens growth using oxygen as an electron acceptor, and expression of at least 13 c-type cytochromes, including one previously shown to participate in Fe(III) reduction (MacA), were RpoS dependent. Analysis of a subset of the rpoS mutant proteome indicated that 15 major protein species showed reproducible differences in abundance relative to those of the wild-type strain. Protein identification using mass spectrometry indicated that the expression of seven of these proteins correlated with the microarray data. Collectively, these results indicate that RpoS exerts global effects on G. sulfurreducens physiology and that RpoS is vital to G. sulfurreducens survival under conditions typically encountered in its native subsurface environments.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16585740?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in Geobacter sulfurreducens and engineering of fumarate reduction in Geobacter metallireducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Dicarboxylic Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombinant Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Substrate Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Succinate Dehydrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Succinic Acid</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">188</style></volume><pages><style face="normal" font="default" size="100%">450-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The mechanism of fumarate reduction in Geobacter sulfurreducens was investigated. The genome contained genes encoding a heterotrimeric fumarate reductase, FrdCAB, with homology to the fumarate reductase of Wolinella succinogenes and the succinate dehydrogenase of Bacillus subtilis. Mutation of the putative catalytic subunit of the enzyme resulted in a strain that lacked fumarate reductase activity and was unable to grow with fumarate as the terminal electron acceptor. The mutant strain also lacked succinate dehydrogenase activity and did not grow with acetate as the electron donor and Fe(III) as the electron acceptor. The mutant strain could grow with acetate as the electron donor and Fe(III) as the electron acceptor if fumarate was provided to alleviate the need for succinate dehydrogenase activity in the tricarboxylic acid cycle. The growth rate of the mutant strain under these conditions was faster and the cell yields were higher than for wild type grown under conditions requiring succinate dehydrogenase activity, suggesting that the succinate dehydrogenase reaction consumes energy. An orthologous frdCAB operon was present in Geobacter metallireducens, which cannot grow with fumarate as the terminal electron acceptor. When a putative dicarboxylic acid transporter from G. sulfurreducens was expressed in G. metallireducens, growth with fumarate as the sole electron acceptor was possible. These results demonstrate that, unlike previously described organisms, G. sulfurreducens and possibly G. metallireducens use the same enzyme for both fumarate reduction and succinate oxidation in vivo.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16385034?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lowy, Daniel A</style></author><author><style face="normal" font="default" size="100%">Tender, Leonard M</style></author><author><style face="normal" font="default" size="100%">Zeikus, J Gregory</style></author><author><style face="normal" font="default" size="100%">Park, Doo Hyun</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Harvesting energy from the marine sediment-water interface II. Kinetic activity of anode materials.</style></title><secondary-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biosens Bioelectron</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electrochemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy-Generating Resources</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferumoxytol</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Oceans and Seas</style></keyword><keyword><style  face="normal" font="default" size="100%">Seawater</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 May 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">2058-63</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Here, we report a comparative study on the kinetic activity of various anodes of a recently described microbial fuel cell consisting of an anode imbedded in marine sediment and a cathode in overlying seawater. Using plain graphite anodes, it was demonstrated that a significant portion of the anodic current results from oxidation of sediment organic matter catalyzed by microorganisms colonizing the anode and capable of directly reducing the anode without added exogenous electron-transfer mediators. Here, graphite anodes incorporating microbial oxidants are evaluated in the laboratory relative to plain graphite with the goal of increasing power density by increasing current density. Anodes evaluated include graphite modified by adsorption of anthraquinone-1,6-disulfonic acid (AQDS) or 1,4-naphthoquinone (NQ), a graphite-ceramic composite containing Mn2+ and Ni2+, and graphite modified with a graphite paste containing Fe3O4 or Fe3O4 and Ni2+. It was found that these anodes possess between 1.5- and 2.2-fold greater kinetic activity than plain graphite. Fuel cells were deployed in a coastal site near Tuckerton, NJ (USA) that utilized two of these anodes. These fuel cells generated ca. 5-fold greater current density than a previously characterized fuel cell equipped with a plain graphite anode, and operated at the same site.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16574400?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Chaudhuri, Swades K</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Mehta, Teena</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Liu, Anna</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Webster, Jennifer</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Blotting, Northern</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophysiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Reverse Transcriptase Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">1805-15</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Whole-genome analysis of gene expression in Geobacter sulfurreducens revealed 474 genes with transcript levels that were significantly different during growth with an electrode as the sole electron acceptor versus growth on Fe(III) citrate. The greatest response was a more than 19-fold increase in transcript levels for omcS, which encodes an outer-membrane cytochrome previously shown to be required for Fe(III) oxide reduction. Quantitative reverse transcription polymerase chain reaction and Northern analyses confirmed the higher levels of omcS transcripts, which increased as power production increased. Deletion of omcS inhibited current production that was restored when omcS was expressed in trans. Transcript expression and genetic analysis suggested that OmcE, another outer-membrane cytochrome, is also involved in electron transfer to electrodes. Surprisingly, genes for other proteins known to be important in Fe(III) reduction such as the outer-membrane c-type cytochrome, OmcB, and the electrically conductive pilin &quot;nanowires&quot; did not have higher transcript levels on electrodes, and deletion of the relevant genes did not inhibit power production. Changes in the transcriptome suggested that cells growing on electrodes were subjected to less oxidative stress than cells growing on Fe(III) citrate and that a number of genes annotated as encoding metal efflux proteins or proteins of unknown function may be important for growth on electrodes. These results demonstrate for the first time that it is possible to evaluate gene expression, and hence the metabolic state, of microorganisms growing on electrodes on a genome-wide basis and suggest that OmcS, and to a lesser extent OmcE, are important in electron transfer to electrodes. This has important implications for the design of electrode materials and the genetic engineering of microorganisms to improve the function of microbial fuel cells.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16958761?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial fuel cells: novel microbial physiologies and engineering approaches.</style></title><secondary-title><style face="normal" font="default" size="100%">Curr Opin Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr. Opin. Biotechnol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Physiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomass</style></keyword><keyword><style  face="normal" font="default" size="100%">Biosensing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Engineering</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">327-32</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The possibility of generating electricity with microbial fuel cells has been recognized for some time, but practical applications have been slow to develop. The recent development of a microbial fuel cell that can harvest electricity from the organic matter stored in marine sediments has demonstrated the feasibility of producing useful amounts of electricity in remote environments. Further study of these systems has led to the discovery of microorganisms that conserve energy to support their growth by completely oxidizing organic compounds to carbon dioxide with direct electron transfer to electrodes. This suggests that self-sustaining microbial fuel cells that can effectively convert a diverse range of waste organic matter or renewable biomass to electricity are feasible. Significant progress has recently been made to increase the power output of systems designed to convert organic wastes to electricity, but substantial additional optimization will be required for large-scale electricity production.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16679010?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ding, Yan-Huai R</style></author><author><style face="normal" font="default" size="100%">Hixson, Kim K</style></author><author><style face="normal" font="default" size="100%">Giometti, Carol S</style></author><author><style face="normal" font="default" size="100%">Stanley, Ann</style></author><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Khare, Tripti</style></author><author><style face="normal" font="default" size="100%">Tollaksen, Sandra L</style></author><author><style face="normal" font="default" size="100%">Zhu, Wenhong</style></author><author><style face="normal" font="default" size="100%">Adkins, Joshua N</style></author><author><style face="normal" font="default" size="100%">Lipton, Mary S</style></author><author><style face="normal" font="default" size="100%">Smith, Richard D</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions.</style></title><secondary-title><style face="normal" font="default" size="100%">Biochim Biophys Acta</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biochim. Biophys. Acta</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteriological Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromatography, High Pressure Liquid</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophoresis, Gel, Two-Dimensional</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptide Fragments</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteome</style></keyword><keyword><style  face="normal" font="default" size="100%">Spectrometry, Mass, Electrospray Ionization</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1764</style></volume><pages><style face="normal" font="default" size="100%">1198-206</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The proteome of Geobacter sulfurreducens, a model for the Geobacter species that predominate in many Fe(III)-reducing subsurface environments, was characterized with ultra high-pressure liquid chromatography and mass spectrometry using accurate mass and time (AMT) tags as well as with more traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Cells were grown under six different growth conditions in order to enhance the potential that a wide range of genes would be expressed. The AMT tag approach was able to identify a much greater number of proteins than could be detected with the 2-D PAGE approach. With the AMT approach over 3,000 gene products were identified, representing about 90% of the total predicted gene products in the genome. A high proportion of predicted proteins in most protein role categories were detected; the highest number of proteins was identified in the hypothetical protein role category. Furthermore, 91 c-type cytochromes of 111 predicted genes in the G. sulfurreducens genome were identified. Differences in the abundance of cytochromes and other proteins under different growth conditions provided information for future functional analysis of these proteins. These results demonstrate that a high percentage of the predicted proteins in the G. sulfurreducens genome are produced and that the AMT tag approach provides a rapid method for comparing differential expression of proteins under different growth conditions in this organism.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16797259?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Mehta, Teena</style></author><author><style face="normal" font="default" size="100%">Childers, Susan E</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Manganese Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">152</style></volume><pages><style face="normal" font="default" size="100%">2257-64</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Extracellular electron transfer onto Fe(III) oxides in Geobacter sulfurreducens is considered to require proteins that must be exported to the outer surface of the cell. In order to investigate this, the putative gene for OxpG, the pseudopilin involved in a type II general secretion pathway of Gram-negative bacteria, was deleted. The mutant was unable to grow with insoluble Fe(III) oxide as the electron acceptor. Growth on soluble Fe(III) was not affected. An analysis of proteins that accumulated in the periplasm of the oxpG mutant, but not in the wild-type, led to the identification of a secreted protein, OmpB. OmpB is predicted to be a multicopper protein, with highest homology to the manganese oxidase, MofA, from Leptothrix discophora. OmpB contains a potential Fe(III)-binding site and a fibronectin type III domain, suggesting a possible role for this protein in accessing Fe(III) oxides. OmpB was localized to the membrane fraction of G. sulfurreducens and in the supernatant of growing cultures, consistent with the type II secretion system exporting OmpB. A mutant in which ompB was deleted had the same phenotype as the oxpG mutant, suggesting that the failure to export OmpB was responsible for the inability of the oxpG-deficient mutant to reduce Fe(III) oxide. This is the first report that proposes a role for a multicopper oxidase-like protein in an anaerobic organism. These results further emphasize the importance of outer-membrane proteins in Fe(III) oxide reduction and suggest that outer-membrane proteins other than c-type cytochromes are required for Fe(III) oxide reduction in Geobacter species.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16849792?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">DiDonato, Laurie N</style></author><author><style face="normal" font="default" size="100%">Sullivan, Sara A</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">England, Reg</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Guanosine Tetraphosphate</style></keyword><keyword><style  face="normal" font="default" size="100%">Heat-Shock Response</style></keyword><keyword><style  face="normal" font="default" size="100%">Ligases</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Reverse Transcriptase Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">188</style></volume><pages><style face="normal" font="default" size="100%">8469-78</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome of Geobacter sulfurreducens contains a gene designated rel(Gsu), which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3',5'-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of Rel(Gsu) in G. sulfurreducens, a rel(Gsu) mutant was constructed and characterized, and ppGpp levels were monitored under various conditions in both the wild-type and rel(Gsu) mutant strains. In the wild-type strain, ppGpp and ppGp were produced in response to acetate and nitrogen deprivation, whereas exposure to oxygen resulted in an accumulation of ppGpp alone. Neither ppGpp nor ppGp could be detected in the rel(Gsu) mutant. The rel(Gsu) mutant consistently grew to a higher cell density than the wild type in acetate-fumarate medium and was less tolerant of oxidative stress than the wild type. The capacity for Fe(III) reduction was substantially diminished in the mutant. Microarray and quantitative reverse transcription-PCR analyses indicated that during stationary-phase growth, protein synthesis genes were up-regulated in the rel(Gsu) mutant and genes involved in stress responses and electron transport, including several implicated in Fe(III) reduction, were down-regulated in the mutant. The results are consistent with a role for Rel(Gsu) in regulating growth, stress responses, and Fe(III) reduction in G. sulfurreducens under conditions likely to be prevalent in subsurface environments.</style></abstract><issue><style face="normal" font="default" size="100%">24</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17041036?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Qian, Xinlei</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Two putative c-type multiheme cytochromes required for the expression of OmcB, an outer membrane protein essential for optimal Fe(III) reduction in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Blotting, Northern</style></keyword><keyword><style  face="normal" font="default" size="100%">Blotting, Western</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">188</style></volume><pages><style face="normal" font="default" size="100%">3138-42</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Deletion of two homologous Geobacter sulfurreducens c-type cytochrome genes, omcG and omcH, decreased the rate of Fe(III) reduction and decreased the level of an outer membrane cytochrome critical for Fe(III) reduction, OmcB, without affecting its transcription. Expression of either gene restored Fe(III) reduction and OmcB expression, suggesting functional similarity.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16585776?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Mester, Tünde</style></author><author><style face="normal" font="default" size="100%">Nesbø, Camilla L</style></author><author><style face="normal" font="default" size="100%">Izquierdo-Lopez, Andrea V</style></author><author><style face="normal" font="default" size="100%">Collart, Frank L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Characterization of citrate synthase from Geobacter sulfurreducens and evidence for a family of citrate synthases similar to those of eukaryotes throughout the Geobacteraceae.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Eukaryotic Cells</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">3858-65</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Members of the family Geobacteraceae are commonly the predominant Fe(III)-reducing microorganisms in sedimentary environments, as well as on the surface of energy-harvesting electrodes, and are able to effectively couple the oxidation of acetate to the reduction of external electron acceptors. Citrate synthase activity of these organisms is of interest due to its key role in acetate metabolism. Prior sequencing of the genome of Geobacter sulfurreducens revealed a putative citrate synthase sequence related to the citrate synthases of eukaryotes. All citrate synthase activity in G. sulfurreducens could be resolved to a single 49-kDa protein via affinity chromatography. The enzyme was successfully expressed at high levels in Escherichia coli with similar properties as the native enzyme, and kinetic parameters were comparable to related citrate synthases (kcat= 8.3 s(-1); Km= 14.1 and 4.3 microM for acetyl coenzyme A and oxaloacetate, respectively). The enzyme was dimeric and was slightly inhibited by ATP (Ki= 1.9 mM for acetyl coenzyme A), which is a known inhibitor for many eukaryotic, dimeric citrate synthases. NADH, an allosteric inhibitor of prokaryotic hexameric citrate synthases, did not affect enzyme activity. Unlike most prokaryotic dimeric citrate synthases, the enzyme did not have any methylcitrate synthase activity. A unique feature of the enzyme, in contrast to citrate synthases from both eukaryotes and prokaryotes, was a lack of stimulation by K+ ions. Similar citrate synthase sequences were detected in a diversity of other Geobacteraceae members. This first characterization of a eukaryotic-like citrate synthase from a prokaryote provides new insight into acetate metabolism in Geobacteraceae members and suggests a molecular target for tracking the presence and activity of these organisms in the environment.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16000798?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Crystal ball. In silico biology meets in situ phenomenology.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Physiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">478-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15816920?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Webster, Jennifer</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly</style></author><author><style face="normal" font="default" size="100%">Butler, Jessica</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microarray Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen Fixation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">2530-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A DNA microarray representing the genome of Geobacter sulfurreducens was constructed for use in global gene expression profiling of cells under steady-state conditions with acetate as the electron donor and Fe(III) or fumarate as the electron acceptor. Reproducible differences in transcript levels were also observed in comparisons between cells grown with ammonia and those fixing atmospheric nitrogen. There was a high correlation between changes in transcript levels determined with microarray analyses and an evaluation of a subset of the genome with quantitative PCR. As expected, cells required to fix nitrogen had higher levels of transcripts of genes associated with nitrogen fixation, further demonstrating that the microarray approach could reliably detect important physiological changes. Cells grown with Fe(III) as the electron acceptor had higher levels of transcripts for omcB, a gene coding for an outer membrane c-type cytochrome that is essential for Fe(III) reduction. Several other c-type cytochrome genes also appeared to be up-regulated. An unexpected result was significantly higher levels of transcripts for genes which have a role in metal efflux, potentially suggesting the importance of maintaining metal homeostasis during release of soluble metals when reducing Fe(III). A substantial proportion (30%) of significantly expressed genes during Fe(III) reduction were genes of unknown function or hypothetical proteins, suggesting differences in Fe(III) reduction physiology among microorganisms which perform this metabolic process.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15870343?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evidence for involvement of an electron shuttle in electricity generation by Geothrix fermentans.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Scanning</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">2186-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In experiments performed using graphite electrodes poised by a potentiostat (+200 mV versus Ag/AgCl) or in a microbial fuel cell (with oxygen as the electron acceptor), the Fe(III)-reducing organism Geothrix fermentans conserved energy to support growth by coupling the complete oxidation of acetate to reduction of a graphite electrode. Other organic compounds, such as lactate, malate, propionate, and succinate as well as components of peptone and yeast extract, were utilized for electricity production. However, electrical characteristics and the results of shuttling assays indicated that unlike previously described electrode-reducing microorganisms, G. fermentans produced a compound that promoted electrode reduction. This is the first report of complete oxidation of organic compounds linked to electrode reduction by an isolate outside of the Proteobacteria.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15812057?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">McCarthy, Kevin D</style></author><author><style face="normal" font="default" size="100%">Mehta, Teena</style></author><author><style face="normal" font="default" size="100%">Nicoll, Julie S</style></author><author><style face="normal" font="default" size="100%">Tuominen, Mark T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extracellular electron transfer via microbial nanowires.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Electric Conductivity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Atomic Force</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Transmission</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Nanostructures</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jun 23</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">435</style></volume><pages><style face="normal" font="default" size="100%">1098-101</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Microbes that can transfer electrons to extracellular electron acceptors, such as Fe(iii) oxides, are important in organic matter degradation and nutrient cycling in soils and sediments. Previous investigations on electron transfer to Fe(iii) have focused on the role of outer-membrane c-type cytochromes. However, some Fe(iii) reducers lack c-cytochromes. Geobacter species, which are the predominant Fe(iii) reducers in many environments, must directly contact Fe(iii) oxides to reduce them, and produce monolateral pili that were proposed, on the basis of the role of pili in other organisms, to aid in establishing contact with the Fe(iii) oxides. Here we report that a pilus-deficient mutant of Geobacter sulfurreducens could not reduce Fe(iii) oxides but could attach to them. Conducting-probe atomic force microscopy revealed that the pili were highly conductive. These results indicate that the pili of G. sulfurreducens might serve as biological nanowires, transferring electrons from the cell surface to the surface of Fe(iii) oxides. Electron transfer through pili indicates possibilities for other unique cell-surface and cell-cell interactions, and for bioengineering of novel conductive materials.</style></abstract><issue><style face="normal" font="default" size="100%">7045</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15973408?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Hinlein, Erich S</style></author><author><style face="normal" font="default" size="100%">Ostendorf, David W</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Typing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Cold Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, rRNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Massachusetts</style></keyword><keyword><style  face="normal" font="default" size="100%">Minnesota</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Supply</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">55</style></volume><pages><style face="normal" font="default" size="100%">1667-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Fe(III)-reducing isolates were recovered from two aquifers in which Fe(III) reduction is known to be important. Strain Bem(T) was enriched from subsurface sediments collected in Bemidji, MN, USA, near a site where Fe(III) reduction is important in aromatic hydrocarbon degradation. Strains P11, P35(T) and P39 were isolated from the groundwater of an aquifer in Plymouth, MA, USA, in which Fe(III) reduction is important because of long-term inputs of acetate as a highway de-icing agent to the subsurface. All four isolates were Gram-negative, slightly curved rods that grew best in freshwater media. Strains P11, P35(T) and P39 exhibited motility via means of monotrichous flagella. Analysis of the 16S rRNA and nifD genes indicated that all four strains are delta-proteobacteria and members of the Geobacter cluster of the Geobacteraceae. Differences in phenotypic and phylogenetic characteristics indicated that the four isolates represent two novel species within the genus Geobacter. All of the isolates coupled the oxidation of acetate to the reduction of Fe(III) [iron(III) citrate, amorphous iron(III) oxide, iron(III) pyrophosphate and iron(III) nitrilotriacetate]. All four strains utilized ethanol, lactate, malate, pyruvate and succinate as electron donors and malate and fumarate as electron acceptors. Strain Bem(T) grew fastest at 30 degrees C, whereas strains P11, P35(T) and P39 grew equally well at 17, 22 and 30 degrees C. In addition, strains P11, P35(T) and P39 were capable of growth at 4 degrees C. The names Geobacter bemidjiensis sp. nov. (type strain Bem(T)=ATCC BAA-1014(T)=DSM 16622(T)=JCM 12645(T)) and Geobacter psychrophilus sp. nov. (strains P11, P35(T) and P39; type strain P35(T)=ATCC BAA-1013(T)=DSM 16674(T)=JCM 12644(T)) are proposed.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16014499?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chang, Yun-Juan</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Geyer, Roland</style></author><author><style face="normal" font="default" size="100%">Peacock, Aaron D</style></author><author><style face="normal" font="default" size="100%">Resch, Charles T</style></author><author><style face="normal" font="default" size="100%">Sublette, Kerry</style></author><author><style face="normal" font="default" size="100%">Pfiffner, Susan</style></author><author><style face="normal" font="default" size="100%">Smithgall, Amanda</style></author><author><style face="normal" font="default" size="100%">Anderson, Robert T</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Stephen, John R</style></author><author><style face="normal" font="default" size="100%">Dayvault, Richard</style></author><author><style face="normal" font="default" size="100%">Ortiz-Bernad, Irene</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">White, David C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI).</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Isotopes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophoresis, Polyacrylamide Gel</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Dec 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">9039-48</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A field-scale acetate amendment experiment was performed in a contaminated aquifer at Old Rifle, CO to stimulate in situ microbial reduction of U(VI) in groundwater. To evaluate the microorganisms responsible for microbial uranium reduction during the experiment, 13C-labeled acetate was introduced into well bores via bio-traps containing porous activated carbon beads (Bio-Sep). Incorporation of the 13C from labeled acetate into cellular DNA and phospholipid fatty acid (PLFA) biomarkers was analyzed in parallel with geochemical parameters. An enrichment of active sigma-proteobacteria was demonstrated in downgradient monitoring wells: Geobacter dominated in wells closer to the acetate injection gallery, while various sulfate reducers were prominent in different downgradient wells. These results were consistent with the geochemical evidence of Fe(III), U(VI), and SO(4)2- reduction. PLFA profiling of bio-traps suspended in the monitoring wells also showed the incorporation of 13C into bacterial cellular lipids. Community composition of downgradient monitoring wells based on quinone and PLFA profiling was in general agreement with the 13C-DNA result. The direct application of 13C label to biosystems, coupled with DNA and PLFA analysis,</style></abstract><issue><style face="normal" font="default" size="100%">23</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16382923?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Anderson, Robert T</style></author><author><style face="normal" font="default" size="100%">Ortiz-Bernad, Irene</style></author><author><style face="normal" font="default" size="100%">O'Neill, Kathleen R</style></author><author><style face="normal" font="default" size="100%">Resch, Charles T</style></author><author><style face="normal" font="default" size="100%">Peacock, Aaron D</style></author><author><style face="normal" font="default" size="100%">Dayvault, Richard</style></author><author><style face="normal" font="default" size="100%">White, David C</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollution</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">6308-18</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16204552?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Afkar, Eman</style></author><author><style face="normal" font="default" size="100%">Reguera, Gemma</style></author><author><style face="normal" font="default" size="100%">Schiffer, Marianne</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Primers</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Manganese Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptide Fragments</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Structure, Secondary</style></keyword><keyword><style  face="normal" font="default" size="100%">Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Metal reduction is thought to take place at or near the bacterial outer membrane and, thus, outer membrane proteins in the model dissimilatory metal-reducing organism Geobacter sulfurreducens are of interest to understand the mechanisms of Fe(III) reduction in the Geobacter species that are the predominant Fe(III) reducers in many environments. Previous studies have implicated periplasmic and outer membrane cytochromes in electron transfer to metals. Here we show that the most abundant outer membrane protein of G. sulfurreducens, OmpJ, is not a cytochrome yet it is required for metal respiration.

RESULTS: When outer membrane proteins of G. sulfurreducens were separated via SDS-PAGE, one protein, designated OmpJ (outer membrane protein J), was particularly abundant. The encoding gene, which was identified from mass spectrometry analysis of peptide fragments, is present in other Geobacteraceae, but not in organisms outside this family. The predicted localization and structure of the OmpJ protein suggested that it was a porin. Deletion of the ompJ gene in G. sulfurreducens produced a strain that grew as well as the wild-type strain with fumarate as the electron acceptor but could not grow with metals, such as soluble or insoluble Fe(III) and insoluble Mn(IV) oxide, as the electron acceptor. The heme c content in the mutant strain was ca. 50% of the wild-type and there was a widespread loss of multiple cytochromes from soluble and membrane fractions. Transmission electron microscopy analyses of mutant cells revealed an unusually enlarged periplasm, which is likely to trigger extracytoplasmic stress response mechanisms leading to the degradation of periplasmic and/or outer membrane proteins, such as cytochromes, required for metal reduction. Thus, the loss of the capacity for extracellular electron transport in the mutant could be due to the missing c-type cytochromes, or some more direct, but as yet unknown, role of OmpJ in metal reduction.

CONCLUSION: OmpJ is a putative porin found in the outer membrane of the model metal reducer G. sulfurreducens that is required for respiration of extracellular electron acceptors such as soluble and insoluble metals. The effect of OmpJ in extracellular electron transfer is indirect, as OmpJ is required to keep the integrity of the periplasmic space necessary for proper folding and functioning of periplasmic and outer membrane electron transport components. The exclusive presence of ompJ in members of the Geobacteraceae family as well as its role in metal reduction suggest that the ompJ sequence may be useful in tracking the growth or activity of Geobacteraceae in sedimentary environments.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16000176?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kim, Byoung-Chan</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Ding, Yan-Huai R</style></author><author><style face="normal" font="default" size="100%">Glaven, Richard H</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">OmcF, a putative c-Type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes c</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">187</style></volume><pages><style face="normal" font="default" size="100%">4505-13</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Outer membrane cytochromes are often proposed as likely agents for electron transfer to extracellular electron acceptors, such as Fe(III). The omcF gene in the dissimilatory Fe(III)-reducing microorganism Geobacter sulfurreducens is predicted to code for a small outer membrane monoheme c-type cytochrome. An OmcF-deficient strain was constructed, and its ability to reduce and grow on Fe(III) citrate was found to be impaired. Following a prolonged lag phase (150 h), the OmcF-deficient strain developed the ability to grow in Fe(III) citrate medium with doubling times and yields that were ca. 145% and 70% of those of the wild type, respectively. Comparison of the c-type cytochrome contents of outer membrane-enriched fractions prepared from wild-type and OmcF-deficient cultures confirmed the outer membrane association of OmcF and revealed multiple changes in the cytochrome content of the OmcF-deficient strain. These changes included loss of expression of two previously characterized outer membrane cytochromes, OmcB and OmcC, and overexpression of a third previously characterized outer membrane cytochrome, OmcS, during growth on Fe(III) citrate. The omcB and omcC transcripts could not be detected in the OmcF-deficient mutant by either reverse transcriptase PCR or Northern blot analyses. Expression of the omcF gene in trans restored both the capacity of the OmcF-deficient mutant to reduce Fe(III) and wild-type levels of omcB and omcC mRNA and protein. Thus, elimination of OmcF may impair Fe(III) reduction by influencing expression of OmcB, which has previously been demonstrated to play a critical role in Fe(III) reduction.</style></abstract><issue><style face="normal" font="default" size="100%">13</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15968061?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Ward, Joy E</style></author><author><style face="normal" font="default" size="100%">Adams, Lorrie A</style></author><author><style face="normal" font="default" size="100%">Woodard, Trevor L</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrate (si)-Synthase</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">71</style></volume><pages><style face="normal" font="default" size="100%">6870-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16269721?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Regulation of two highly similar genes, omcB and omcC, in a 10 kb chromosomal duplication in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Microbiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microbiology (Reading, Engl.)</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Outer Membrane Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Blotting, Northern</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">151</style></volume><pages><style face="normal" font="default" size="100%">1761-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Fe(III)-reducing micro-organism Geobacter sulfurreducens requires an outer-membrane c-type cytochrome, OmcB, for Fe(III) reduction, but a related cytochrome, OmcC, which is 73 % identical to OmcB, is not required. The omcB and omcC genes are part of a tandem chromosomal duplication consisting of two repeated clusters of four genes. The 2.7 kb sequences preceding omcB and omcC are identical with the exception of a single base pair change. Studies that combined genetic, Northern blotting and primer extension analyses demonstrated that both omcB and omcC are transcribed as monocistronic and polycistronic (orf1-orf2-omcB/omcC) transcripts. All of the promoters for the various transcripts were found to be located within the 2.7 kb identical region upstream of omcB and omcC. The sequences of the promoter regions for the two monocistronic transcripts are identical and equidistant from the omcB or omcC start codons. The promoters for the two polycistronic transcripts, in contrast, are distinct. One is specific for transcription of orf1-orf2-omcB and the other is associated with transcription of orf1-orf2-omcC. Studies with an RpoS-deficient mutant suggested that transcription from all four promoters is RpoS dependent under one or more growth conditions. Deletion of orfR, a gene immediately upstream of orf1-orf2-omcB that encodes a putative transcriptional regulator, significantly lowered the omcB transcription when Fe(III) was the electron acceptor and partially inhibited Fe(III) reduction. In contrast, levels of omcC transcripts were unaffected in the orfR mutant. These results indicate that omcB and omcC operons represent a rare instance in which duplicated operons, located in tandem on the chromosome, have different transcriptional regulation.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15941985?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gregory, Kelvin B</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Remediation and recovery of uranium from contaminated subsurface environments with electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Nov 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">8943-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have demonstrated that Geobacter species can effectively remove uranium from contaminated groundwater by reducing soluble U(VI) to the relatively insoluble U(IV) with organic compounds serving as the electron donor. Studies were conducted to determine whether electrodes might serve as an alternative electron donor for U(VI) reduction by a pure culture of Geobacter sulfurreducens and microorganisms in uranium-contaminated sediments. Electrodes poised at -500 mV (vs a Ag/AgCl reference) rapidly removed U(VI) from solution in the absence of cells. However, when the poise at the electrode was removed, all of the U(VI) returned to solution, demonstrating that the electrode did not reduce U(VI). If G. sulfurreducens was present on the electrode, U(VI) did not return to solution until the electrode was exposed to dissolved oxygen. This suggeststhat G. sulfurreducens on the electrode reduced U(VI) to U(IV) which was stably precipitated until reoxidized in the presence of oxygen. When an electrode was placed in uranium-contaminated subsurface sediments, U(VI) was removed and recovered from groundwater using poised electrodes. Electrodes emplaced in flow-through columns of uranium-contaminated sediments readily removed U(VI) from the groundwater, and 87% of the uranium that had been removed was recovered from the electrode surface after the electrode was pulled from the sediments. These results suggest that microorganisms can use electrons derived from electrodes to reduce U(VI) and that it may be possible to remove and recover uranium from contaminated groundwater with poised electrodes.</style></abstract><issue><style face="normal" font="default" size="100%">22</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16323798?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Desulfuromonas</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Gyrase</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Directed RNA Polymerases</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, rRNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen Fixation</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptide Elongation Factor G</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Rec A Recombinases</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">54</style></volume><pages><style face="normal" font="default" size="100%">1591-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The sequences of five conserved genes, in addition to the 16S rRNA gene, were investigated in 30 members of the Geobacteraceae fam. nov. All members of the Geobacteraceae examined contained nifD, suggesting that they are capable of nitrogen fixation, which may explain their ability to compete effectively in nitrogen-poor subsurface environments undergoing remediation for petroleum or metal contamination. The phylogenies predicted from rpoB, gyrB, fusA, recA and nifD were generally in agreement with the phylogeny predicted from 16S rRNA gene sequences. Furthermore, phylogenetic analysis of concatemers constructed from all five protein-coding genes corresponded closely with the 16S rRNA gene-based phylogeny. This study demonstrated that the Geobacteraceae is a phylogenetically coherent family within the delta-subclass of the Proteobacteria that is composed of three distinct phylogenetic clusters: Geobacter, Desulfuromonas and Desulfuromusa. The sequence data provided here will make it possible to discriminate better between physiologically distinct members of the Geobacteraceae, such as Pelobacter propionicus and Geobacter species, in geobacteraceae-dominated microbial communities and greatly expands the potential to identify geobacteraceae sequences in libraries of environmental genomic DNA.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15388715?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Yan, Bin</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Krushkal, Julia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae.</style></title><secondary-title><style face="normal" font="default" size="100%">J Theor Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Theor. Biol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Conserved Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Footprinting</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Regulator</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Sep 7</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">230</style></volume><pages><style face="normal" font="default" size="100%">133-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction. In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements. We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens. Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria. The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction. Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites. We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites. These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15276006?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chin, Kuk-Jeong</style></author><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Direct correlation between rates of anaerobic respiration and levels of mRNA for key respiratory genes in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Primers</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxygen Consumption</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">5183-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The predominance of Geobacter species in environments in which Fe(III) reduction is important has suggested that Fe(III) reduction rates might be estimated in Geobacter-dominated environments by assessing in situ activity with molecular techniques. To determine whether mRNA levels of key respiratory genes might be correlated with respiration rates in Geobacter sulfurreducens, studies were conducted with fumarate as the electron acceptor and acetate as the limiting electron donor in anaerobic continuous cultures. Levels of mRNA for a fumarate reductase gene, frdA, quantified by real-time reverse transcription-PCR were directly correlated with fumarate reduction rates. In similar studies with Fe(III) as the electron acceptor, mRNA levels for omcB, a gene for an outer membrane c-type cytochrome involved in Fe(III) reduction, were positively correlated with Fe(III) reduction rates. Levels of mRNA for frdA and omcB were also positively correlated with fumarate and Fe(III) reduction rates, respectively, when growth was limited by the availability of fumarate or Fe(III), but mRNA levels were higher than in acetate-limited cultures. Levels of mRNA for omcC, which encodes a c-type cytochrome highly similar to OmcB but not necessary for Fe(III) reduction, followed patterns different than those of omcB. This agrees with the previous finding that OmcC is not involved in Fe(III) reduction and suggests that changes in mRNA levels of omcB are related to its role in Fe(III) reduction. These results demonstrate that mRNA levels for respiratory genes might be used to estimate in situ Fe(III) reduction rates in Geobacter-dominated environments but suggest that information on environmental conditions and/or the metabolic state of Geobacter species is also required for accurate rate estimates.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15345398?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dissimilatory Fe(III) and Mn(IV) reduction.</style></title><secondary-title><style face="normal" font="default" size="100%">Adv Microb Physiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Adv. Microb. Physiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Manganese</style></keyword><keyword><style  face="normal" font="default" size="100%">Manganese Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword><keyword><style  face="normal" font="default" size="100%">Shewanella</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Pollutants</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">49</style></volume><pages><style face="normal" font="default" size="100%">219-86</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble. Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor. Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction. Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them. In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells. Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different. In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions. The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments. In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15518832?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electron transfer by Desulfobulbus propionicus to Fe(III) and graphite electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Pyruvic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">1234-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Desulfobulbus propionicus was able to grow with Fe(III), the humic acids analog anthraquinone-2,6-disulfonate (AQDS), or a graphite electrode as an electron acceptor. These results provide an explanation for the enrichment of Desulfobulbaceae species on the surface of electrodes harvesting electricity from anaerobic marine sediments and further expand the diversity of microorganisms known to have the ability to use both sulfate and Fe(III) as an electron acceptor.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14766612?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gregory, Kelvin B</style></author><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Graphite electrodes as electron donors for anaerobic respiration.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Graphite</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Scanning</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrates</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">596-604</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It has been demonstrated previously that Geobacter species can transfer electrons directly to electrodes. In order to determine whether electrodes could serve as electron donors for microbial respiration, enrichment cultures were established from a sediment inoculum with a potentiostat-poised graphite electrode as the sole electron donor and nitrate as the electron acceptor. Nitrate was reduced to nitrite with the consumption of electrical current. The stoichiometry of electron and nitrate consumption and nitrite accumulation were consistent with the electrode serving as the sole electron donor for nitrate reduction. Analysis of 16 rRNA gene sequences demonstrated that the electrodes supplied with current were specifically enriched in microorganisms with sequences most closely related to the sequences of known Geobacter species. A pure culture of Geobacter metallireducens was shown to reduce nitrate to nitrite with the electrode as the sole electron donor with the expected stoichiometry of electron consumption. Cells attached to the electrode appeared to be responsible for the nitrate reduction. Attached cells of Geobacter sulfurreducens reduced fumarate to succinate with the electrode as an electron donor. These results demonstrate for the first time that electrodes may serve as a direct electron donor for anaerobic respiration. This finding has implications for the harvesting of electricity from anaerobic sediments and the bioremediation of oxidized contaminants.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15142248?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anthraquinones</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Operon</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidoreductases</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">186</style></volume><pages><style face="normal" font="default" size="100%">3022-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the G. sulfurreducens genome revealed two operons, hya and hyb, which appeared to encode periplasmically oriented respiratory uptake hydrogenases. In order to assess the roles of these two enzymes in hydrogen-dependent growth, Hya- and Hyb-deficient mutants were generated by gene replacement. Hyb was found to be required for hydrogen-dependent reduction of Fe(III), anthraquinone-2,6-disulfonate, and fumarate by resting cell suspensions and to be essential for growth with hydrogen and these three electron acceptors. Hya, in contrast, was not. These findings suggest that Hyb is an essential respiratory hydrogenase in G. sulfurreducens.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15126463?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">In situ expression of nifD in Geobacteraceae in subsurface sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogenase</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Quaternary Ammonium Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Rec A Recombinases</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">7251-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 microM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15574924?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shelobolina, Evgenya S</style></author><author><style face="normal" font="default" size="100%">Sullivan, Sara A</style></author><author><style face="normal" font="default" size="100%">O'Neill, Kathleen R</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant Bacterium from Low-pH, nitrate- and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrates</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Salmonella</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollution, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">2959-65</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A facultatively anaerobic, acid-resistant bacterium, designated strain FRCl, was isolated from a low-pH, nitrate- and U(VI)-contaminated subsurface sediment at site FW-024 at the Natural and Accelerated Bioremediation Research Field Research Center in Oak Ridge, Tenn. Strain FRCl was enriched at pH 4.5 in minimal medium with nitrate as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Clones with 16S ribosomal DNA (rDNA) sequences identical to the sequence of strain FRCl were also detected in a U(VI)-reducing enrichment culture derived from the same sediment. Cells of strain FRCl were gram-negative motile regular rods 2.0 to 3.4 micro m long and 0.7 to 0.9 microm in diameter. Strain FRCl was positive for indole production, by the methyl red test, and for ornithine decarboxylase; it was negative by the Voges-Proskauer test (for acetylmethylcarbinol production), for urea hydrolysis, for arginine dihydrolase, for lysine decarboxylase, for phenylalanine deaminase, for H(2)S production, and for gelatin hydrolysis. Strain FRCl was capable of using O(2), NO(3)(-), S(2)O(3)(2-), fumarate, and malate as terminal electron acceptors and of reducing U(VI) in the cell suspension. Analysis of the 16S rDNA sequence of the isolate indicated that this strain was 96.4% similar to Salmonella bongori and 96.3% similar to Enterobacter cloacae. Physiological and phylogenetic analyses suggested that strain FRCl belongs to the genus Salmonella and represents a new species, Salmonella subterranea sp. nov.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15128557?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Butler, Jessica E</style></author><author><style face="normal" font="default" size="100%">Kaufmann, Franz</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">MacA, a diheme c-type cytochrome involved in Fe(III) reduction by Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Deletion</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">186</style></volume><pages><style face="normal" font="default" size="100%">4042-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A 36-kDa diheme c-type cytochrome abundant in Fe(III)-respiring Geobacter sulfurreducens, designated MacA, was more highly expressed during growth with Fe(III) as the electron acceptor than with fumarate. Although MacA has homology to proteins with in vitro peroxidase activity, deletion of macA had no impact on response to oxidative stress. However, the capacity for Fe(III) reduction was greatly diminished, indicating that MacA, which is predicted to be localized in the periplasm, is a key intermediate in electron transfer to Fe(III).</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15175321?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Nicoll, Julie S</style></author><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Potential role of a novel psychrotolerant member of the family Geobacteraceae, Geopsychrobacter electrodiphilus gen. nov., sp. nov., in electricity production by a marine sediment fuel cell.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Temperature</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">6023-30</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have shown that members of the family Geobacteraceae that attach to the anodes of sediment fuel cells are directly involved in harvesting electricity by oxidizing organic compounds to carbon dioxide and transferring the electrons to the anode. In order to learn more about this process, microorganisms from the anode surface of a marine sediment fuel cell were enriched and isolated with Fe(III) oxide. Two unique marine isolates were recovered, strains A1(T) and A2. They are gram-negative, nonmotile rods, with abundant c-type cytochromes. Phylogenetic analysis of the 16S rRNA, recA, gyrB, fusA, rpoB, and nifD genes indicated that strains A1(T) and A2 represent a unique phylogenetic cluster within the Geobacteraceae. Both strains were able to grow with an electrode serving as the sole electron acceptor and transferred ca. 90% of the electrons available in their organic electron donors to the electrodes. These organisms are the first psychrotolerant members of the Geobacteraceae reported thus far and can grow at temperatures between 4 and 30 degrees C, with an optimum temperature of 22 degrees C. Strains A1(T) and A2 can utilize a wide range of traditional electron acceptors, including all forms of soluble and insoluble Fe(III) tested, anthraquinone 2,6-disulfonate, and S(0). In addition to acetate, both strains can utilize a number of other organic acids, amino acids, long-chain fatty acids, and aromatic compounds to support growth with Fe(III) nitrilotriacetic acid as an electron acceptor. The metabolism of these organisms differs in that only strain A1(T) can use acetoin, ethanol, and hydrogen as electron donors, whereas only strain A2 can use lactate, propionate, and butyrate. The name Geopsychrobacter electrodiphilus gen. nov., sp. nov., is proposed for strains A1(T) and A2, with strain A1(T) (ATCC BAA-880(T); DSM 16401(T); JCM 12469) as the type strain. Strains A1(T) and A2 (ATCC BAA-770; JCM 12470) represent the first organisms recovered from anodes that can effectively couple the oxidation of organic compounds to an electrode. Thus, they may serve as important model organisms for further elucidation of the mechanisms of microbe-electrode electron transfer in sediment fuel cells.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15466546?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Esteve-Núñez, Abraham</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Preferential reduction of FeIII over fumarate by Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Fumarates</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Succinate Dehydrogenase</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">186</style></volume><pages><style face="normal" font="default" size="100%">2897-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The presence of Fe(III), but not that of Fe(II), resulted in ca. 20-fold-lower levels of mRNA for fumarate reductase, inhibiting fumarate reduction and favoring utilization of fumarate as an electron donor in chemostat cultures of Geobacter sulfurreducens, despite the fact that growth yield with fumarate was 3-fold higher than with Fe(III).</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15090532?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ortiz-Bernad, Irene</style></author><author><style face="normal" font="default" size="100%">Anderson, Robert T</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Resistance of solid-phase U(VI) to microbial reduction during in situ bioremediation of uranium-contaminated groundwater.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Radioactive</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">7558-60</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Speciation of solid-phase uranium in uranium-contaminated subsurface sediments undergoing uranium bioremediation demonstrated that although microbial reduction of soluble U(VI) readily immobilized uranium as U(IV), a substantial portion of the U(VI) in the aquifer was strongly associated with the sediments and was not microbially reducible. These results have important implications for in situ uranium bioremediation strategies.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15574961?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Adams, Lorrie</style></author><author><style face="normal" font="default" size="100%">Childers, Susan</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adaptation, Physiological</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidative Stress</style></keyword><keyword><style  face="normal" font="default" size="100%">Sigma Factor</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Initiation Site</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">186</style></volume><pages><style face="normal" font="default" size="100%">5543-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Geobacter sulfurreducens RpoS sigma factor was shown to contribute to survival in stationary phase and upon oxygen exposure. Furthermore, a mutation in rpoS decreased the rate of reduction of insoluble Fe(III) but not of soluble forms of iron. This study suggests that RpoS plays a role in regulating metabolism of Geobacter under suboptimal conditions in subsurface environments.</style></abstract><issue><style face="normal" font="default" size="100%">16</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15292160?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Vinogradov, Evgeny</style></author><author><style face="normal" font="default" size="100%">Korenevsky, Anton</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Beveridge, Terry J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The structure of the core region of the lipopolysaccharide from Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Carbohydr Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Carbohydr. Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Carbohydrate Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Lipopolysaccharides</style></keyword><keyword><style  face="normal" font="default" size="100%">Magnetic Resonance Spectroscopy</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligosaccharides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Dec 27</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">339</style></volume><pages><style face="normal" font="default" size="100%">2901-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The structure of the core part of the LPS from Geobacter sulfurreducens was analysed. The LPS contained no O-specific polysaccharide (O-side chain) and upon mild hydrolysis gave a core oligosaccharide, which was isolated by gel chromatography. It was studied by chemical methods, NMR and mass spectrometry, and the following structure was proposed. [carbohydrate structure: see text] where Q = 3-O-Me-alpha-L-QuiNAc-(1--&gt;or H (approximately 3:2).</style></abstract><issue><style face="normal" font="default" size="100%">18</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15582618?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ortiz-Bernad, Irene</style></author><author><style face="normal" font="default" size="100%">Anderson, Robert T</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Mining</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Vanadium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollution, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">70</style></volume><pages><style face="normal" font="default" size="100%">3091-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that G. metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15128571?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lloyd, Jon R</style></author><author><style face="normal" font="default" size="100%">Leang, Ching</style></author><author><style face="normal" font="default" size="100%">Hodges Myerson, Allison L</style></author><author><style face="normal" font="default" size="100%">Coppi, Maddalena V</style></author><author><style face="normal" font="default" size="100%">Cuifo, Stacey</style></author><author><style face="normal" font="default" size="100%">Methe, Barb</style></author><author><style face="normal" font="default" size="100%">Sandler, Steven J</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens.</style></title><secondary-title><style face="normal" font="default" size="100%">Biochem J</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biochem. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochrome c Group</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Periplasm</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Amino Acid</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Jan 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">369</style></volume><pages><style face="normal" font="default" size="100%">153-61</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A 9.6 kDa periplasmic c -type cytochrome, designated PpcA, was purified from the Fe(III)-reducing bacterium Geobacter sulfurreducens and characterized. The purified protein is basic (pI 9.5), contains three haems and has an N-terminal amino acid sequence closely related to those of the previously described trihaem c (7) cytochromes of Geobacter metallireducens and Desulfuromonas acetoxidans. The gene encoding PpcA was identified from the G. sulfurreducens genome using the N-terminal sequence, and encodes a protein of 71 amino acids (molecular mass 9.58 kDa) with 49% identity to the c (7) cytochrome of D. acetoxidans. In order to determine the physiological role of PpcA, a knockout mutant was prepared with a single-step recombination method. Acetate-dependent Fe(III) reduction was significantly inhibited in both growing cultures and cell suspensions of the mutant. When ppcA was expressed in trans, the full capacity for Fe(III) reduction with acetate was restored. The transfer of electrons from acetate to anthraquinone 2,6-disulphonate (AQDS; a humic acid analogue) and to U(VI) was also compromised in the mutant, but acetate-dependent reduction of fumarate was not altered. The rates of reduction of Fe(III), AQDS, U(VI) and fumarate were also the same in the wild type and ppcA mutant when hydrogen was supplied as the electron donor. When taken together with previous studies on other electron transport proteins in G. sulfurreducens, these results suggest that PpcA serves as an intermediary electron carrier from acetate to terminal Fe(III) reductases in the outer membrane, and is also involved in the transfer of electrons from acetate to U(VI) and humics.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12356333?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lloyd, Jonathan R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Macaskie, Lynne E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Biotechnological application of metal-reducing microorganisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Adv Appl Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Adv. Appl. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioreactors</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Gram-Negative Anaerobic Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals, Heavy</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">53</style></volume><pages><style face="normal" font="default" size="100%">85-128</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14696317?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Cleaning up with genomics: applying molecular biology to bioremediation.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Rev Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Rev. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Physiological Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecology</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Fungi</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Vectors</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Fungal</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Biology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1</style></volume><pages><style face="normal" font="default" size="100%">35-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Bioremediation has the potential to restore contaminated environments inexpensively yet effectively, but a lack of information about the factors controlling the growth and metabolism of microorganisms in polluted environments often limits its implementation. However, rapid advances in the understanding of bioremediation are on the horizon. Researchers now have the ability to culture microorganisms that are important in bioremediation and can evaluate their physiology using a combination of genome-enabled experimental and modelling techniques. In addition, new environmental genomic techniques offer the possibility for similar studies on as-yet-uncultured organisms. Combining models that can predict the activity of microorganisms that are involved in bioremediation with existing geochemical and hydrological models should transform bioremediation from a largely empirical practice into a science.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15040178?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chaudhuri, Swades K</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electricity generation by direct oxidation of glucose in mediatorless microbial fuel cells.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Biotechnol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioreactors</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Comamonadaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Transfer</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Design</style></keyword><keyword><style  face="normal" font="default" size="100%">Equipment Failure Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Glucose</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">1229-32</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Abundant energy, stored primarily in the form of carbohydrates, can be found in waste biomass from agricultural, municipal and industrial sources as well as in dedicated energy crops, such as corn and other grains. Potential strategies for deriving useful forms of energy from carbohydrates include production of ethanol and conversion to hydrogen, but these approaches face technical and economic hurdles. An alternative strategy is direct conversion of sugars to electrical power. Existing transition metal-catalyzed fuel cells cannot be used to generate electric power from carbohydrates. Alternatively, biofuel cells in which whole cells or isolated redox enzymes catalyze the oxidation of the sugar have been developed, but their applicability has been limited by several factors, including (i) the need to add electron-shuttling compounds that mediate electron transfer from the cell to the anode, (ii) incomplete oxidation of the sugars and (iii) lack of long-term stability of the fuel cells. Here we report on a novel microorganism, Rhodoferax ferrireducens, that can oxidize glucose to CO(2) and quantitatively transfer electrons to graphite electrodes without the need for an electron-shuttling mediator. Growth is supported by energy derived from the electron transfer process itself and results in stable, long-term power production.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12960964?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electricity production by Geobacter sulfurreducens attached to electrodes.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron, Scanning</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">1548-55</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have suggested that members of the Geobacteraceae can use electrodes as electron acceptors for anaerobic respiration. In order to better understand this electron transfer process for energy production, Geobacter sulfurreducens was inoculated into chambers in which a graphite electrode served as the sole electron acceptor and acetate or hydrogen was the electron donor. The electron-accepting electrodes were maintained at oxidizing potentials by connecting them to similar electrodes in oxygenated medium (fuel cells) or to potentiostats that poised electrodes at +0.2 V versus an Ag/AgCl reference electrode (poised potential). When a small inoculum of G. sulfurreducens was introduced into electrode-containing chambers, electrical current production was dependent upon oxidation of acetate to carbon dioxide and increased exponentially, indicating for the first time that electrode reduction supported the growth of this organism. When the medium was replaced with an anaerobic buffer lacking nutrients required for growth, acetate-dependent electrical current production was unaffected and cells attached to these electrodes continued to generate electrical current for weeks. This represents the first report of microbial electricity production solely by cells attached to an electrode. Electrode-attached cells completely oxidized acetate to levels below detection (&lt;10 micro M), and hydrogen was metabolized to a threshold of 3 Pa. The rates of electron transfer to electrodes (0.21 to 1.2 micro mol of electrons/mg of protein/min) were similar to those observed for respiration with Fe(III) citrate as the electron acceptor (E(o)' =+0.37 V). The production of current in microbial fuel cell (65 mA/m(2) of electrode surface) or poised-potential (163 to 1,143 mA/m(2)) mode was greater than what has been reported for other microbial systems, even those that employed higher cell densities and electron-shuttling compounds. Since acetate was completely oxidized, the efficiency of conversion of organic electron donor to electricity was significantly higher than in previously described microbial fuel cells. These results suggest that the effectiveness of microbial fuel cells can be increased with organisms such as G. sulfurreducens that can attach to electrodes and remain viable for long periods of time while completely oxidizing organic substrates with quantitative transfer of electrons to an electrode.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12620842?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kashefi, Kazem</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extending the upper temperature limit for life.</style></title><secondary-title><style face="normal" font="default" size="100%">Science</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Science</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Pacific Ocean</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Aug 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">301</style></volume><pages><style face="normal" font="default" size="100%">934</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">5635</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12920290?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jara, Mónica</style></author><author><style face="normal" font="default" size="100%">Núñez, Cinthia</style></author><author><style face="normal" font="default" size="100%">Campoy, Susana</style></author><author><style face="normal" font="default" size="100%">Fernández de Henestrosa, Antonio R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Barbé, Jordi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter sulfurreducens has two autoregulated lexA genes whose products do not bind the recA promoter: differing responses of lexA and recA to DNA damage.</style></title><secondary-title><style face="normal" font="default" size="100%">J Bacteriol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Bacteriol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Consensus Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Damage</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Polymerase beta</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Repair</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrophoretic Mobility Shift Assay</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Promoter Regions, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Rec A Recombinases</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Serine Endopeptidases</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">185</style></volume><pages><style face="normal" font="default" size="100%">2493-502</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Escherichia coli LexA protein was used as a query sequence in TBLASTN searches to identify the lexA gene of the delta-proteobacterium Geobacter sulfurreducens from its genome sequence. The results of the search indicated that G. sulfurreducens has two independent lexA genes designated lexA1 and lexA2. A copy of a dinB gene homologue, which in E. coli encodes DNA polymerase IV, is present downstream of each lexA gene. Reverse transcription-PCR analyses demonstrated that, in both cases, lexA and dinB constitute a single transcriptional unit. Electrophoretic mobility shift assays with purified LexA1 and LexA2 proteins have shown that both proteins bind the imperfect palindrome GGTTN(2)CN(4)GN(3)ACC found in the promoter region of both lexA1 and lexA2. This sequence is also present upstream of the Geobacter metallireducens lexA gene, indicating that it is the LexA box of this bacterial genus. This palindrome is not found upstream of either the G. sulfurreducens or the G. metallireducens recA genes. Furthermore, DNA damage induces expression of the lexA-dinB transcriptional unit but not that of the recA gene. However, the basal level of recA gene expression is dramatically higher than that of the lexA gene. Likewise, the promoters of the G. sulfurreducens recN, ruvAB, ssb, umuDC, uvrA, and uvrB genes do not contain the LexA box and are not likely to bind to the LexA1 or LexA2 proteins. G. sulfurreducens is the first bacterial species harboring a lexA gene for which a constitutive expression of its recA gene has been described.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12670973?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tor, Jason M</style></author><author><style face="normal" font="default" size="100%">Amend, Jan P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria, Anaerobic</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzoates</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Glucose</style></keyword><keyword><style  face="normal" font="default" size="100%">Glutamic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Italy</style></keyword><keyword><style  face="normal" font="default" size="100%">Molybdenum</style></keyword><keyword><style  face="normal" font="default" size="100%">Organic Chemicals</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Palmitates</style></keyword><keyword><style  face="normal" font="default" size="100%">Seawater</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">583-91</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies of hot (&gt;80 degrees C) microbial ecosystems have primarily relied on the study of pure cultures or analysis of 16S rDNA sequences. In order to gain more information on anaerobic metabolism by natural communities in hot environments, sediments were collected from a shallow marine hydrothermal vent system in Baia di Levante, Vulcano, Italy and incubated under strict anaerobic conditions at 90 degrees C. Sulphate reduction was the predominant terminal electron-accepting process in the sediments. The addition of molybdate inhibited sulphate reduction in the sediments and resulted in a linear accumulation of acetate and hydrogen over time. [U-14C]- acetate was completely oxidized to 14CO2, and the addition of molybdate inhibited 14CO2 production by 60%. [U-14C]-glucose was oxidized to 14CO2, and this was inhibited when molybdate was added. When the pool sizes of short-chain fatty acids were artificially increased, radiolabel from [U-14C]-glucose accumulated in the acetate pool. L-[U-14C]-glutamate, [ring-14C]-benzoate and [U-14C]-palmitate were also anaerobically oxidized to 14CO2 in the sediments, but molybdate had little effect on the oxidation of these compounds. These results demonstrate that natural microbial communities living in a hot, microbial ecosystem can oxidize acetate and a range of other organic electron donors under sulphate-reducing conditions and suggest that acetate is an important extracellular intermediate in the anaerobic degradation of organic matter in hot microbial ecosystems.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12823190?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Finneran, Kevin T</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microorganisms associated with uranium bioremediation in a high-salinity subsurface sediment.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptococcaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">Pseudomonas</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sodium Chloride</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollution</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">3672-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Although stimulation of dissimilatory metal reduction to promote the reductive precipitation of uranium has been shown to successfully remove uranium from some aquifer sediments, the organisms in the family Geobacteraceae that have been found to be associated with metal reduction in previous studies are not known to grow at the high salinities found in some uranium-contaminated groundwaters. Studies with a highly saline uranium-contaminated aquifer sediment demonstrated that the addition of acetate could stimulate the removal of U(VI) from the groundwater. This removal was associated with an enrichment in microorganisms most closely related to Pseudomonas and Desulfosporosinus species.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12788780?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Finneran, Kevin T</style></author><author><style face="normal" font="default" size="100%">Johnsen, Claudia V</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III).</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Typing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Betaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Cold Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">53</style></volume><pages><style face="normal" font="default" size="100%">669-73</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">To further investigate the diversity of micro-organisms capable of conserving energy to support growth from dissimilatory Fe(III) reduction, Fe(III)-reducing micro-organisms were enriched and isolated from subsurface sediments collected in Oyster Bay, VA, USA. A novel isolate, designated T118(T), was recovered in a medium with lactate as the sole electron donor and Fe(III) as the sole electron acceptor. Cells of T1 18(T) were Gram-negative, motile, short rods with a single polar flagellum. Strain T1 18(T) grew between pH 6.7 and 7.1, with a temperature range of 4-30 degrees C. The optimal growth temperature was 25 degrees C. Electron donors utilized by strain T1 18(T) with Fe(III) as the sole electron acceptor included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds tested was fermented. Electron acceptors utilized with either acetate or lactate as the electron donor included Fe(III)-NTA (nitrilotriacetic acid), Mn(IV) oxide, nitrate, fumarate and oxygen. Phylogenetic analysis demonstrated that strain T1 18(T) is most closely related to the genus Rhodoferax. Unlike other species in this genus, strain T1 18(T) is not a phototroph and does not ferment fructose. However, phototrophic genes may be present but not expressed under the experimental conditions tested. No Rhodoferax species have been reported to grow via dissimilatory Fe(III) reduction. Based on these physiological and phylogenetic differences, strain T1 18(T) (=ATCC BAA-621(T) = DSM 15236(T)) is proposed as a novel species, Rhodoferax ferrireducens sp. nov.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12807184?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Anderson, Robert T</style></author><author><style face="normal" font="default" size="100%">Vrionis, Helen A</style></author><author><style face="normal" font="default" size="100%">Ortiz-Bernad, Irene</style></author><author><style face="normal" font="default" size="100%">Resch, Charles T</style></author><author><style face="normal" font="default" size="100%">Long, Philip E</style></author><author><style face="normal" font="default" size="100%">Dayvault, Richard</style></author><author><style face="normal" font="default" size="100%">Karp, Ken</style></author><author><style face="normal" font="default" size="100%">Marutzky, Sam</style></author><author><style face="normal" font="default" size="100%">Metzler, Donald R</style></author><author><style face="normal" font="default" size="100%">Peacock, Aaron</style></author><author><style face="normal" font="default" size="100%">White, David C</style></author><author><style face="normal" font="default" size="100%">Lowe, Mary</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acetates</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Fatty Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geobacter</style></keyword><keyword><style  face="normal" font="default" size="100%">Mining</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phospholipids</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollution, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">5884-91</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 micro M in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14532040?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kashefi, Kazem</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Baross, John A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Thermophily in the Geobacteraceae: Geothermobacter ehrlichii gen. nov., sp. nov., a novel thermophilic member of the Geobacteraceae from the &quot;Bag City&quot; hydrothermal vent.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Base Composition</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytochromes</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Drug Resistance, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen-Ion Concentration</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Pacific Ocean</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Seawater</style></keyword><keyword><style  face="normal" font="default" size="100%">Sodium Chloride</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">2985-93</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Little is known about the microbiology of the &quot;Bag City&quot; hydrothermal vent, which is part of a new eruption site on the Juan de Fuca Ridge and which is notable for its accumulation of polysaccharide on the sediment surface. A pure culture, designated strain SS015, was recovered from a vent fluid sample from the Bag City site through serial dilution in liquid medium with malate as the electron donor and Fe(III) oxide as the electron acceptor and then isolation of single colonies on solid Fe(III) oxide medium. The cells were gram-negative rods, about 0.5 micro m by 1.2 to 1.5 micro m, and motile and contained c-type cytochromes. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain SS015 placed it in the family Geobacteraceae in the delta subclass of the Proteobacteria. Unlike previously described members of the Geobacteraceae, which are mesophiles, strain SS015 was a thermophile and grew at temperatures of between 35 and 65 degrees C, with an optimum temperature of 55 degrees C. Like many previously described members of the Geobacteraceae, strain SS015 grew with organic acids as the electron donors and Fe(III) or nitrate as the electron acceptor, with nitrate being reduced to ammonia. Strain SS015 was unique among the Geobacteraceae in its ability to use sugars, starch, or amino acids as electron donors for Fe(III) reduction. Under stress conditions, strain SS015 produced copious quantities of extracellular polysaccharide, providing a model for the microbial production of the polysaccharide accumulation at the Bag City site. The 16S rDNA sequence of strain SS015 was less than 94% similar to the sequences of previously described members of the Geobacteraceae; this fact, coupled with its unique physiological properties, suggests that strain SS015 represents a new genus in the family Geobacteraceae. The name Geothermobacter ehrlichii gen. nov., sp. nov., is proposed (ATCC BAA-635 and DSM 15274). Although strains of Geobacteraceae are known to be the predominant Fe(III)-reducing microorganisms in a variety of Fe(III)-reducing environments at moderate temperatures, strain SS015 represents the first described thermophilic member of the Geobacteraceae and thus extends the known environmental range of this family to hydrothermal environments.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12732575?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rothermich, Mary M</style></author><author><style face="normal" font="default" size="100%">Hayes, Lory A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Anaerobic, sulfate-dependent degradation of polycyclic aromatic hydrocarbons in petroleum-contaminated harbor sediment.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria, Anaerobic</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Monitoring</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Weight</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Polycyclic Hydrocarbons, Aromatic</style></keyword><keyword><style  face="normal" font="default" size="100%">Ships</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur-Reducing Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Transportation</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Nov 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">4811-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It has previously been demonstrated that [14C]-labeled polycyclic aromatic hydrocarbons (PAHs) can be oxidized to 14CO2 in anoxic, PAH-contaminated, marine harbor sediments in which sulfate reduction is the terminal electron-accepting process. However, it has not previously been determined whether this degradation of [14C]-PAHs accurately reflects the degradation of the in situ pools of contaminant PAHs. In coal tar-contaminated sediments from Boston Harbor, [14C]-naphthalene was readily oxidized to 14CO2, but, after 95 d of incubation under anaerobic conditions, there was no significant decrease in the detectable pool of in situ naphthalene in these sediments. Therefore, to better evaluate the anaerobic biodegradation of the in situ PAH pools, the concentrations of these contaminants were monitored for ca. 1 year during which the sediments were incubated under conditions that mimicked those found in situ. There was loss of all of the PAHs that were monitored (2-5 ring congeners), including high molecular weight PAHs, such as benzo[a]pyrene, that have not previously been shown to be degraded under anaerobic conditions. There was no significant change in the PAH levels in the sediments amended with molybdate to inhibit sulfate-reducing bacteria or in sediments in which all microorganisms had been killed with glutaraldehyde. In some instances, over half of the detectable pools of in situ 2-3 ring PAHs were degraded. In general, the smaller PAHs were degraded more rapidly than the larger PAHs. A distinct exception in the Boston Harbor sediment was naphthalene which was degraded very slowly at a rate comparable to the larger PAHs. In a similar in situ-like study of fuel-contaminated sediments from Liepaja Harbor, Latvia, there was no decline in PAH levels in samples that were sulfate-depleted. However, when the Latvia sediments were supplemented with sufficient sodium sulfate or gypsum to elevate pore water levels of sulfate to approximately 14-25 mM there was a 90% decline in the naphthalene and a 60% decline in the 2-methylnaphthalene pool within 90 days. These studies demonstrate for the first time that degradation by anaerobic microorganisms can significantly impact the in situ pools of PAHs in petroleum-contaminated, anoxic, sulfate-reducing harbor sediments and suggest that the self-purification capacity of contaminated harbor sediments is greater than previously considered.</style></abstract><issue><style face="normal" font="default" size="100%">22</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12487304?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter.</style></title><secondary-title><style face="normal" font="default" size="100%">OMICS</style></secondary-title><alt-title><style face="normal" font="default" size="100%">OMICS</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Theoretical</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">331-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The proposed research will investigate two microbial communities that are of direct relevance to Department of Energy interests. One is the microbial community associated with the in situ bioremediation of uranium-contaminated groundwater. The second is a microbial community that harvests energy from waste organic matter in the form of electricity. These studies will address DOE needs for (1) remediation of metals and radionuclides at DOE sites and (2) the development of cleaner forms of energy and biomass conversion to energy. Our previous studies have demonstrated that the microbial communities involved in uranium bioremediation and energy harvesting are both dominated by microorganisms in the family Geobacteraceae and that the organisms in this family are responsible for uranium bioremediation and electron transfer to electrodes. The initial objectives of this study are to (1) describe the genetic potential of the Geobacteraceae that predominate in the environments of interest; (2) identify conserved patterns of gene expression within the Geobacteraceae family in response to a range of environmental conditions; (3) begin to identify mechanisms controlling the expression of key genes related to survival, growth, and activity in subsurface environments and on electrodes; and (4) use the results from subobjectives 1-3 to develop a conceptual model for predicting gene expression of Geobacteraceae in the environments of interest. This will serve as the basis for a subsequent simulation model of the growth and activity of Geobacteraceae in the subsurface and on electrodes.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12626092?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Finneran, Kevin T</style></author><author><style face="normal" font="default" size="100%">Forbush, Heather M</style></author><author><style face="normal" font="default" size="100%">VanPraagh, Catherine V Gaw</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Desulfitobacterium metallireducens sp. nov., an anaerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Humic Substances</style></keyword><keyword><style  face="normal" font="default" size="100%">Metals</style></keyword><keyword><style  face="normal" font="default" size="100%">Microscopy, Electron</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Peptococcaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">52</style></volume><pages><style face="normal" font="default" size="100%">1929-35</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Strain 853-15A(T) was enriched and isolated from uranium-contaminated aquifer sediment by its ability to grow under anaerobic conditions via the oxidation of lactate coupled to the reduction of anthraquinone-2,6-disulfonate (AQDS) to anthrahydroquinone-2,6-disulfonate (AHQDS). Lactate was oxidized incompletely to acetate and carbon dioxide according to the reaction CH3CHOHCOO(-)+ 2AQDS+H2O --&gt; CH3COO(-)+ 2AHQDS+CO2. Additional electron donors utilized included formate, ethanol, butanol, butyrate, malate and pyruvate. Lactate also supported growth with Fe(III) citrate, Mn(IV) oxide, humic substances, elemental sulfur, 3-chloro-4-hydroxyphenylacetate, trichloroethylene or tetrachloroethylene serving as the electron acceptor. Growth was not observed with sulfate, sulfite, nitrate or fumarate as the terminal electron acceptor. The temperature optimum for growth was 30 degrees C, but growth was also observed at 20 and 37 degrees C. The pH optimum was approximately 7.0. The 16S rDNA sequence of strain 853-15A(T) suggested that it was most closely related to Desulfitobacterium dehalogenans and closely related to Desulfitobacterium chlororespirans and Desulfitobacterium frappieri. The phylogenetic and physiological properties exhibited by strain 853-15A(T) (= ATCC BAA-636(T)) place it within the genus Desulfitobacterium as the type strain of a novel species, Desulfitobacterium metallireducens sp. nov.</style></abstract><issue><style face="normal" font="default" size="100%">Pt 6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12508850?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Tender, Leonard M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrode-reducing microorganisms that harvest energy from marine sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Science</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Science</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Aerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Anthraquinones</style></keyword><keyword><style  face="normal" font="default" size="100%">Benzoates</style></keyword><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Dioxide</style></keyword><keyword><style  face="normal" font="default" size="100%">Colony Count, Microbial</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Energy Metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Seawater</style></keyword><keyword><style  face="normal" font="default" size="100%">Sodium Acetate</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Jan 18</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">295</style></volume><pages><style face="normal" font="default" size="100%">483-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Energy in the form of electricity can be harvested from marine sediments by placing a graphite electrode (the anode) in the anoxic zone and connecting it to a graphite cathode in the overlying aerobic water. We report a specific enrichment of microorganisms of the family Geobacteraceae on energy-harvesting anodes, and we show that these microorganisms can conserve energy to support their growth by oxidizing organic compounds with an electrode serving as the sole electron acceptor. This finding not only provides a method for extracting energy from organic matter, but also suggests a strategy for promoting the bioremediation of organic contaminants in subsurface environments.</style></abstract><issue><style face="normal" font="default" size="100%">5554</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11799240?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Finneran, Kevin T</style></author><author><style face="normal" font="default" size="100%">O'Neil, Regina A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Gene Library</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">68</style></volume><pages><style face="normal" font="default" size="100%">2300-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11976101?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Klapper, Lisa</style></author><author><style face="normal" font="default" size="100%">McKnight, Diane M</style></author><author><style face="normal" font="default" size="100%">Fulton, J Robin</style></author><author><style face="normal" font="default" size="100%">Blunt-Harris, Elizabeth L</style></author><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">Hatcher, Patrick G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Fulvic acid oxidation state detection using fluorescence spectroscopy.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Sci Technol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Sci. Technol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Benzopyrans</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Monitoring</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Spectrometry, Fluorescence</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Jul 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">3170-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Humic substances are a heterogeneous class of moderate molecular weight, yellow-colored biomolecules present in all soils, sediments, and natural waters. Although humic substances are generally resistant to microbial degradation under anaerobic conditions, some microorganisms in soils and sediments can use quinone moieties in humic substances as electron acceptors. Laboratory experiments have shown that humic substances can act as electron shuttles in the microbial reduction of ferric iron. Field studies of electron shuttling processes have been constrained by the lack of methods to characterize the oxidation state of quinone moieties in humic substances at natural concentrations. All humic substances have fluorescent properties, and fluorescence spectroscopy can indicate differences in precursor organic source of humic substances. Here we show that the quinone moieties responsible for electron transfer reactions contribute significantly to the fluorescence of humic substances. Further we use fluorescence spectroscopy to elucidate the oxidation state of quinone moieties in humic substances at natural concentrations found in sediment interstitial waters.</style></abstract><issue><style face="normal" font="default" size="100%">14</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12141500?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Childers, Susan E</style></author><author><style face="normal" font="default" size="100%">Ciufo, Stacy</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Chemotaxis</style></keyword><keyword><style  face="normal" font="default" size="100%">Deltaproteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferrous Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fimbriae, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Flagella</style></keyword><keyword><style  face="normal" font="default" size="100%">Manganese Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Movement</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxides</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Apr 18</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">416</style></volume><pages><style face="normal" font="default" size="100%">767-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Microorganisms that use insoluble Fe(III) oxide as an electron acceptor can have an important function in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater. Although Fe(III) oxides are often abundant, Fe(III)-reducing microbes are faced with the problem of how to access effectively an electron acceptor that can not diffuse to the cell. Fe(III)-reducing microorganisms in the genus Shewanella have resolved this problem by releasing soluble quinones that can carry electrons from the cell surface to Fe(III) oxide that is at a distance from the cell. Here we report that another Fe(III)-reducer, Geobacter metallireducens, has an alternative strategy for accessing Fe(III) oxides. Geobacter metallireducens specifically expresses flagella and pili only when grown on insoluble Fe(III) or Mn(IV) oxide, and is chemotactic towards Fe(II) and Mn(II) under these conditions. These results suggest that G. metallireducens senses when soluble electron acceptors are depleted and then synthesizes the appropriate appendages to permit it to search for, and establish contact with, insoluble Fe(III) or Mn(IV) oxide. This approach to the use of an insoluble electron acceptor may explain why Geobacter species predominate over other Fe(III) oxide-reducing microorganisms in a wide variety of sedimentary environments.</style></abstract><issue><style face="normal" font="default" size="100%">6882</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11961561?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kashefi, Kazem</style></author><author><style face="normal" font="default" size="100%">Tor, Jason M</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Gaw Van Praagh, Catherine V</style></author><author><style face="normal" font="default" size="100%">Reysenbach, Anna-Louise</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Syst Evol Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int. J. Syst. Evol. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anaerobiosis</style></keyword><keyword><style  face="normal" font="default" size="100%">Archaea</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial Typing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Fatty Acids</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">52</style></volume><pages><style face="normal" font="default" size="100%">719-28</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A novel, regular to irregular, coccoid-shaped, anaerobic, Fe(III)-reducing microorganism was isolated from the Guaymas Basin hydrothermal system at a depth of 2000 m. Isolation was carried out with a new technique using Fe(III) oxide as the electron acceptor for the recovery of colonies on solid medium. The isolate, designated strain 234T, was strictly anaerobic and exhibited a tumbling motility. The cells had a single flagellum. Strain 234T grew at temperatures between 65 and 90 degrees C, with an optimum at about 88 degrees C. The optimal salt concentration for growth was around 19 g l(-1). The isolate was capable of growth with H2 as the sole electron donor coupled to the reduction of Fe(III) without the need for an organic carbon source. This is the first example of a dissimilatory Fe(III)-reducing micro-organism capable of growing autotrophically on hydrogen. In addition to molecular hydrogen, strain 234T oxidizes pyruvate, acetate, malate, succinate, peptone, formate, fumarate, yeast extract, glycerol, isoleucine, arginine, serine, glutamine, asparagine, stearate, palmitate, valerate, butyrate and propionate with the reduction of Fe(III). This isolate is the first example of a hyperthermophile capable of oxidizing long-chain fatty acids anaerobically. Isolate 234T grew exclusively with Fe(III) as the sole electron acceptor. The G+C content was 58.7 mol%. Based on detailed analysis of its 16S rDNA sequence, G+C content, distinguishing physiological features and metabolism, strain 234T is proposed to represent a novel genus within the Archaeoglobales. The name proposed for strain 234T is Geoglobus ahangari gen. nov., sp. nov..</style></abstract><issue><style face="normal" font="default" size="100%">Pt 3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12054231?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tender, Leonard M</style></author><author><style face="normal" font="default" size="100%">Reimers, Clare E</style></author><author><style face="normal" font="default" size="100%">Stecher, Hilmar A</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lowy, Daniel A</style></author><author><style face="normal" font="default" size="100%">Pilobello, Kanoelani</style></author><author><style face="normal" font="default" size="100%">Fertig, Stephanie J</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Harnessing microbially generated power on the seafloor.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Biotechnol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Biotechnol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Bioelectric Energy Sources</style></keyword><keyword><style  face="normal" font="default" size="100%">Biotechnology</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Conservation of Energy Resources</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electricity</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">New Jersey</style></keyword><keyword><style  face="normal" font="default" size="100%">Oceans and Seas</style></keyword><keyword><style  face="normal" font="default" size="100%">Oregon</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfides</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">821-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In many marine environments, a voltage gradient exists across the water sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12091916?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chapelle, Francis H</style></author><author><style face="normal" font="default" size="100%">O'Neill, Kathleen</style></author><author><style face="normal" font="default" size="100%">Bradley, Paul M</style></author><author><style face="normal" font="default" size="100%">Methé, Barbara A</style></author><author><style face="normal" font="default" size="100%">Ciufo, Stacy A</style></author><author><style face="normal" font="default" size="100%">Knobel, LeRoy L</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A hydrogen-based subsurface microbial community dominated by methanogens.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Archaeal</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Euryarchaeota</style></keyword><keyword><style  face="normal" font="default" size="100%">Exobiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Hydrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Microbiology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Jan 17</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">415</style></volume><pages><style face="normal" font="default" size="100%">312-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.</style></abstract><issue><style face="normal" font="default" size="100%">6869</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11797006?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nevin, Kelly P</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Electrons</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron Chelating Agents</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">68</style></volume><pages><style face="normal" font="default" size="100%">2294-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Mechanisms for Fe(III) oxide reduction were investigated in Geothrix fermentans, a dissimilatory Fe(III)-reducing microorganism found within the Fe(III) reduction zone of subsurface environments. Culture filtrates of G. fermentans stimulated the reduction of poorly crystalline Fe(III) oxide by washed cell suspensions, suggesting that G. fermentans released one or more extracellular compounds that promoted Fe(III) oxide reduction. In order to determine if G. fermentans released electron-shuttling compounds, poorly crystalline Fe(III) oxide was incorporated into microporous alginate beads, which prevented contact between G. fermentans and the Fe(III) oxide. G. fermentans reduced the Fe(III) within the beads, suggesting that one of the compounds that G. fermentans releases is an electron-shuttling compound that can transfer electrons from the cell to Fe(III) oxide that is not in contact with the organism. Analysis of culture filtrates by thin-layer chromatography suggested that the electron shuttle has characteristics similar to those of a water-soluble quinone. Analysis of filtrates by ion chromatography demonstrated that there was as much as 250 microM dissolved Fe(III) in cultures of G. fermentans growing with Fe(III) oxide as the electron acceptor, suggesting that G. fermentans released one or more compounds capable of chelating and solubilizing Fe(III). Solubilizing Fe(III) is another strategy for alleviating the need for contact between cells and Fe(III) oxide for Fe(III) reduction. This is the first demonstration of a microorganism that, in defined medium without added electron shuttles or chelators, can reduce Fe(III) derived from Fe(III) oxide without directly contacting the Fe(III) oxide. These results are in marked contrast to those with Geobacter metallireducens, which does not produce electron shuttles or Fe(III) chelators. These results demonstrate that phylogenetically distinct Fe(III)-reducing microorganisms may use significantly different strategies for Fe(III) reduction. Thus, it is important to know which Fe(III)-reducing microorganisms predominate in a given environment in order to understand the mechanisms for Fe(III) reduction in the environment of interest.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11976100?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Finneran, Kevin T</style></author><author><style face="normal" font="default" size="100%">Housewright, Meghan E</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferrous Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrates</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteobacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword><keyword><style  face="normal" font="default" size="100%">Uranium</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">510-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Microbiological reduction of soluble U(VI) to insoluble U(IV) has been proposed as a remediation strategy for uranium-contaminated groundwater. Nitrate is a common co-contaminant with uranium. Nitrate inhibited U(VI) reduction in acetate-amended aquifer sediments collected from a uranium-contaminated site in New Mexico. Once nitrate was depleted, both U(VI) and Fe(III) were reduced concurrently. When nitrate was added to sediments in which U(VI) had been reduced, U(VI) reappeared in solution. Parallel studies with the dissimilatory Fe(III)-, U(VI)- and nitrate-reducing microorganism, Geobacter metallireducens, demonstrated that nitrate inhibited reduction of Fe(III) and U(VI) in cell suspensions of cells that had been grown with nitrate as the electron acceptor, but not in Fe(III)-grown cells. Suspensions of nitrate-grown G. metallireducens oxidized Fe(II) and U(IV) with nitrate as the electron acceptor. U(IV) oxidation was accelerated when Fe(II) was also added, presumably due to the Fe(III) being formed abiotically oxidizing U(IV). These studies demonstrate that although the presence of nitrate is not likely to be an impediment to the bioremediation of uranium contamination with microbial U(VI) reduction, it is necessary to reduce nitrate before U(VI) can be reduced. These results also suggest that anaerobic oxidation of U(IV) to U(VI) with nitrate serving as the electron acceptor may provide a novel strategy for solubilizing and extracting microbial U(IV) precipitates from the subsurface.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12220407?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Chapelle, Francis H</style></author><author><style face="normal" font="default" size="100%">Bradley, Paul M</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author><author><style face="normal" font="default" size="100%">O'Neill, Kathleen</style></author><author><style face="normal" font="default" size="100%">Landmeyer, James E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Rapid evolution of redox processes in a petroleum hydrocarbon-contaminated aquifer.</style></title><secondary-title><style face="normal" font="default" size="100%">Ground Water</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Ground Water</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Hydrocarbons</style></keyword><keyword><style  face="normal" font="default" size="100%">Iron</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Petroleum</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Solubility</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfates</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Supply</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Jul-Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">40</style></volume><pages><style face="normal" font="default" size="100%">353-60</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Ground water chemistry data collected over a six-year period show that the distribution of contaminants and redox processes in a shallow petroleum hydrocarbon-contaminated aquifer has changed rapidly over time. Shortly after a gasoline release occurred in 1990, high concentrations of benzene were present near the contaminant source area. In this contaminated zone, dissolved oxygen in ground water was depleted, and by 1994 Fe(III) reduction and sulfate reduction were the predominant terminal electron accepting processes. Significantly, dissolved methane was below measurable levels in 1994, indicating the absence of significant methanogenesis. By 1996, however, depletion of solid-phase Fe(III)-oxyhydrox ides in aquifer sediments and depletion of dissolved sulfate in ground water resulted in the onset of methanogenesis. Between 1996 and 2000, water-chemistry data indicated that methanogenic metabolism became increasingly prevalent. Molecular analysis of 16S-rDNA extracted from sediments shows the presence of a more diverse methanogenic community inside as opposed to outside the plume core, and is consistent with water-chemistry data indicating a shift toward methanogenesis over time. This rapid evolution of redox processes reflects several factors including the large amounts of contaminants, relatively rapid ground water flow (approximately 0.3 m/day [approximately foot/day]), and low concentrations of microbially reducible Fe(III) oxyhydroxides ( approximately 1 micromol/g) initially present in aquifer sediments. These results illustrate that, under certain hydrologic conditions, redox conditions in petroleum hydrocarbon-contaminated aquifers can change rapidly in time and space, and that the availability of solid-phase Fe(III)-oxyhydroxides affects this rate of change.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12113353?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bond, Daniel R</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reduction of Fe(III) oxide by methanogens in the presence and absence of extracellular quinones.</style></title><secondary-title><style face="normal" font="default" size="100%">Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Anthraquinones</style></keyword><keyword><style  face="normal" font="default" size="100%">Euryarchaeota</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Humic Substances</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Species Specificity</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">115-24</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Five methanogens (Methanosarcina barkeri MS, Methanosphaera cuniculi 1R7, Methanobacterium palustre F, Methanococcus voltaei A3 and Methanolobus vulcani PL-12/M) were investigated for their ability to reduce Fe(III) oxide and the soluble quinone anthraquinone-2,6-disulphonate (AQDS). Two species (M. barkeri and M. voltaei) reduced significant amounts of Fe(III) oxide using hydrogen as the electron donor, and 0.1 mM AQDS greatly accelerated Fe(III) reduction by these organisms. Although Fe(III) appeared to inhibit growth and methanogenesis of some strains, hydrogen partial pressures under donor-limited conditions were much lower (&lt;0.5 Pa) in the presence of Fe(III) than in normal media (1-10 Pa) for all species except for M. vulcani. These results demonstrate that electrons were transferred to Fe(III) by hydrogen-utilizing methanogens even when growth and methanogenesis were inhibited. All species except the obligate methylotroph M. vulcani were able to reduce AQDS when their growth substrates were present as electron donors, and rates were highest when organisms used hydrogen as the electron donor. Purified soil humic acids could also be reduced by the AQDS-reducing methanogens. The ability of methanogens to interact with extracellular quinones, humic acids and Fe(III) oxides raises the possibility that this functional group of organ-isms contributes to Fe(III) and humic acid reduction under certain conditions in the environment and provides an alternative explanation for the inhibition of methanogenesis in some Fe(III)-containing ecosystems.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11972621?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hayes, L A</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Specific 16S rDNA sequences associated with naphthalene degradation under sulfate-reducing conditions in harbor sediments.</style></title><secondary-title><style face="normal" font="default" size="100%">Microb Ecol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Microb. Ecol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biodegradation, Environmental</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Primers</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Naphthalenes</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxidation-Reduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymerase Chain Reaction</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Sulfur-Reducing Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Water Pollutants, Chemical</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">43</style></volume><pages><style face="normal" font="default" size="100%">134-45</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Previous studies have demonstrated that naphthalene and other polycyclic aromatic hydrocarbons (PAHs) can be anaerobically oxidized with the reduction of sulfate in PAH-contaminated marine harbor sediments, including those in San Diego Bay. In order to learn more about the microorganisms that might be involved in anaerobic naphthalene degradation, the microorganisms associated with naphthalene degradation in San Diego Bay sediments were evaluated. A dilution-to-extinction enrichment culture strategy, designed to recover the most numerous culturable naphthalene-degrading sulfate reducers, resulted in the enrichment of microorganisms with 16S rDNA sequences in the d-Proteobacteria, which were closely related to a previously described pure culture of a naphthalene-degrading sulfate reducer, NaphS2, isolated from sediments in Germany. A more traditional enrichment culture approach, expected to enrich for the fastest-growing naphthalene-degrading sulfate reducers, yielded 16S rDNA sequences closely related to those found in the dilution-to-extinction enrichments and NaphS2. Analysis of 16S rDNA sequences in sediments from two sites in San Diego Bay that had been adapted for rapid naphthalene degradation by continual amendment with low levels of naphthalene suggested that the microbial community composition in the amended sediments differed from that present in the unamended sediments from the same sites. Most significantly, 6-8% of the sequences recovered from 100 clones of each of the naphthalene-amended sediments were closely related to the 16S rDNA sequences in the enrichment cultures as well as the sequence of the pure culture, NaphS2. No sequences in this NaphS2 phylotype were recovered from the sediments that were not continually exposed to naphthalene. A PCR primer, which was designed based on these phylotype sequences, was used to amplify additional 16S rDNA sequences belonging to the NaphS2 phylotype from PAH-degrading sediments from Island End River (Boston), MA, and Liepaja Harbor, Latvia. Closely related sequences were also recovered from highly contaminated sediment from Tampa Bay, FL. These results suggest that microorganisms closely related to NaphS2 might be involved in naphthalene degradation in harbor sediments. This finding contrasts with the frequent observation that the environmentally relevant microorganisms cannot be readily recovered in pure culture and suggests that further study of the physiology of NaphS2 may provide insights into factors controlling the rate and extent of naphthalene degradation in marine harbor sediments.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11984635?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kashefi, Kazem</style></author><author><style face="normal" font="default" size="100%">Holmes, Dawn E</style></author><author><style face="normal" font="default" size="100%">Reysenbach, Anna-Louise</style></author><author><style face="normal" font="default" size="100%">Lovley, Derek R</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov.</style></title><secondary-title><style face="normal" font="default" size="100%">Appl Environ Microbiol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Appl. Environ. Microbiol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Typing Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Culture Media</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Ribosomal</style></keyword><keyword><style  face="normal" font="default" size="100%">Electron Transport</style></keyword><keyword><style  face="normal" font="default" size="100%">Ferric Compounds</style></keyword><keyword><style  face="normal" font="default" size="100%">Fresh Water</style></keyword><keyword><style  face="normal" font="default" size="100%">Geologic Sediments</style></keyword><keyword><style  face="normal" font="default" size="100%">Gram-Negative Anaerobic Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">68</style></volume><pages><style face="normal" font="default" size="100%">1735-42</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 microm by 1.0 to 1.2 microm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100 degrees C with an optimum of 85 to 90 degrees C. To our knowledge this is the highest temperature optimum of any organism in the Bacteria. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the Bacteria, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms from hydrothermal environments and illustrate that caution must be used in inferring the physiological characteristics of at least some thermophilic microorganisms solely from 16S rDNA sequences. Based on both its 16S rDNA sequence and physiological characteristics, strain FW-1a represents a new genus among the Bacteria. The name Geothermobacterium ferrireducens gen. nov., sp. nov., is proposed (ATCC BAA-426).</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11916691?dopt=Abstract</style></custom1></record></records></xml>