<?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%">Mackelprang, Rachel</style></author><author><style face="normal" font="default" size="100%">Waldrop, Mark P</style></author><author><style face="normal" font="default" size="100%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">David, Maude M</style></author><author><style face="normal" font="default" size="100%">Chavarria, Krystle L</style></author><author><style face="normal" font="default" size="100%">Blazewicz, Steven J</style></author><author><style face="normal" font="default" size="100%">Rubin, Edward M</style></author><author><style face="normal" font="default" size="100%">Jansson, Janet K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.</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%">Alaska</style></keyword><keyword><style  face="normal" font="default" size="100%">Arctic Regions</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacteria</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon</style></keyword><keyword><style  face="normal" font="default" size="100%">Carbon Cycle</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Freezing</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, rRNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Metagenome</style></keyword><keyword><style  face="normal" font="default" size="100%">Metagenomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Methane</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Nitrogen Cycle</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%">Soil</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Time Factors</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 Dec 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">480</style></volume><pages><style face="normal" font="default" size="100%">368-71</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.</style></abstract><issue><style face="normal" font="default" size="100%">7377</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22056985?dopt=Abstract</style></custom1></record><record><source-app 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%">Wu, Cindy H</style></author><author><style face="normal" font="default" size="100%">Beller, Harry R</style></author><author><style face="normal" font="default" size="100%">Brodie, Eoin L</style></author><author><style face="normal" font="default" size="100%">Chakraborty, Romy</style></author><author><style face="normal" font="default" size="100%">DeSantis, Todd Z</style></author><author><style face="normal" font="default" size="100%">Fortney, Julian L</style></author><author><style face="normal" font="default" size="100%">Hazen, Terry C</style></author><author><style face="normal" font="default" size="100%">Osman, Shariff R</style></author><author><style face="normal" font="default" size="100%">Singer, Mary E</style></author><author><style face="normal" font="default" size="100%">Tom, Lauren M</style></author><author><style face="normal" font="default" size="100%">Andersen, Gary L</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.</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%">Biodiversity</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA, Complementary</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Metagenomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Microarray Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Sensitivity and Specificity</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%">6313-22</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Environmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.</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/21764955?dopt=Abstract</style></custom1></record></records></xml>