<?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%">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%">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%">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%">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></records></xml>