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