<?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%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">D'haeseleer, Patrik</style></author><author><style face="normal" font="default" size="100%">Chivian, Dylan</style></author><author><style face="normal" font="default" size="100%">Simmons, Blake</style></author><author><style face="normal" font="default" size="100%">Arkin, Adam P</style></author><author><style face="normal" font="default" size="100%">Mavromatis, Konstantinos</style></author><author><style face="normal" font="default" size="100%">Malfatti, Stephanie</style></author><author><style face="normal" font="default" size="100%">Tringe, Susannah</style></author><author><style face="normal" font="default" size="100%">Hazen, Terry C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.</style></title><secondary-title><style face="normal" font="default" size="100%">Stand Genomic Sci</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stand Genomic Sci</style></alt-title></titles><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%">7</style></volume><pages><style face="normal" font="default" size="100%">382-98</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates for improving biofuel production. To investigate how iron availability affects decomposition, we cultivated feedstock-adapted consortia (FACs) derived from iron-rich tropical forest soils accustomed to experiencing frequent episodes of anaerobic conditions and frequently fluctuating redox. One consortium was propagated under fermenting conditions, with switchgrass as the sole carbon source in minimal media (SG only FACs), and the other consortium was treated the same way but received poorly crystalline iron as an additional terminal electron acceptor (SG + Fe FACs). We sequenced the metagenomes of both consortia to a depth of about 150 Mb each, resulting in a coverage of 26&amp;times; for the more diverse SG + Fe FACs, and 81&amp;times; for the relatively less diverse SG only FACs. Both consortia were able to quickly grow on switchgrass, and the iron-amended consortium exhibited significantly higher microbial diversity than the unamended consortium. We found evidence of higher stress in the unamended FACs and increased sugar transport and utilization in the iron-amended FACs. This work provides metagenomic evidence that supplementation of alternative TEAs may improve feedstock deconstruction in biofuel production.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Borglin, Sharon</style></author><author><style face="normal" font="default" size="100%">Joyner, Dominique</style></author><author><style face="normal" font="default" size="100%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">Khudyakov, Jane</style></author><author><style face="normal" font="default" size="100%">D'haeseleer, Patrik</style></author><author><style face="normal" font="default" size="100%">Joachimiak, Marcin P</style></author><author><style face="normal" font="default" size="100%">Hazen, Terry</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Application of phenotypic microarrays to environmental microbiology.</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><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%">23</style></volume><pages><style face="normal" font="default" size="100%">41-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. This review describes applications of phenotype arrays to anaerobic and thermophilic microorganisms, use of the plates in stress response studies, in development of culture media for newly discovered strains, and for assessment of phenotype of environmental communities. Also discussed are considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting.</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/22217654?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Khudyakov, Jane I</style></author><author><style face="normal" font="default" size="100%">D'haeseleer, Patrik</style></author><author><style face="normal" font="default" size="100%">Borglin, Sharon E</style></author><author><style face="normal" font="default" size="100%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">Woo, Hannah</style></author><author><style face="normal" font="default" size="100%">Lindquist, Erika A</style></author><author><style face="normal" font="default" size="100%">Hazen, Terry C</style></author><author><style face="normal" font="default" size="100%">Simmons, Blake A</style></author><author><style face="normal" font="default" size="100%">Thelen, Michael P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.</style></title><secondary-title><style face="normal" font="default" size="100%">Proc Natl Acad Sci U S A</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</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 Aug 7</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">109</style></volume><pages><style face="normal" font="default" size="100%">E2173-82</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.</style></abstract><issue><style face="normal" font="default" size="100%">32</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22586090?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">D'haeseleer, Patrik</style></author><author><style face="normal" font="default" size="100%">Chivian, Dylan</style></author><author><style face="normal" font="default" size="100%">Fortney, Julian L</style></author><author><style face="normal" font="default" size="100%">Khudyakov, Jane</style></author><author><style face="normal" font="default" size="100%">Simmons, Blake</style></author><author><style face="normal" font="default" size="100%">Woo, Hannah</style></author><author><style face="normal" font="default" size="100%">Arkin, Adam P</style></author><author><style face="normal" font="default" size="100%">Davenport, Karen Walston</style></author><author><style face="normal" font="default" size="100%">Goodwin, Lynne</style></author><author><style face="normal" font="default" size="100%">Chen, Amy</style></author><author><style face="normal" font="default" size="100%">Ivanova, Natalia</style></author><author><style face="normal" font="default" size="100%">Kyrpides, Nikos C</style></author><author><style face="normal" font="default" size="100%">Mavromatis, Konstantinos</style></author><author><style face="normal" font="default" size="100%">Woyke, Tanja</style></author><author><style face="normal" font="default" size="100%">Hazen, Terry C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Complete genome sequence of &quot;Enterobacter lignolyticus&quot; SCF1.</style></title><secondary-title><style face="normal" font="default" size="100%">Stand Genomic Sci</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Stand Genomic Sci</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Oct 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">5</style></volume><pages><style face="normal" font="default" size="100%">69-85</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated &quot;Enterobacter lignolyticus&quot; SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of &quot;E. lignolyticus&quot; SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.</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/22180812?dopt=Abstract</style></custom1></record></records></xml>