<?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%">Firestone, Mary K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic clustering of soil microbial communities by 16S rRNA but not 16S rRNA genes.</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%">Biodiversity</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Ecosystem</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, rRNA</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%">RNA, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Trees</style></keyword><keyword><style  face="normal" font="default" size="100%">Tropical Climate</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%">2459-61</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.</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/22286992?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Shi, Shengjing</style></author><author><style face="normal" font="default" size="100%">Richardson, Alan E</style></author><author><style face="normal" font="default" size="100%">O'Callaghan, Maureen</style></author><author><style face="normal" font="default" size="100%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">Jones, Eirian E</style></author><author><style face="normal" font="default" size="100%">Stewart, Alison</style></author><author><style face="normal" font="default" size="100%">Firestone, Mary K</style></author><author><style face="normal" font="default" size="100%">Condron, Leo M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Effects of selected root exudate components on soil bacterial communities.</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%">Bacteria</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%">Organic Chemicals</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Pinus</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Exudates</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Roots</style></keyword><keyword><style  face="normal" font="default" size="100%">Rhizosphere</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></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%">600-10</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (&lt;24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth.</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/21658090?dopt=Abstract</style></custom1></record><record><source-app 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%">Silver, Whendee L</style></author><author><style face="normal" font="default" size="100%">Thompson, Andrew W</style></author><author><style face="normal" font="default" size="100%">Firestone, Mary K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Microbial communities acclimate to recurring changes in soil redox potential status.</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%">Acclimatization</style></keyword><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%">Carbon Dioxide</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%">Iron</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, Archaeal</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Bacterial</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%">Trees</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</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">3137-49</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA-based) and active (RNA-based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO₂ respiration, methanogenesis, N₂O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4-day redox potential fluctuations did not. Using RNA:DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbial community adapted to fluctuating redox potential.</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/20629704?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sagaram, Uma Shankar</style></author><author><style face="normal" font="default" size="100%">Deangelis, Kristen M</style></author><author><style face="normal" font="default" size="100%">Trivedi, Pankaj</style></author><author><style face="normal" font="default" size="100%">Andersen, Gary L</style></author><author><style face="normal" font="default" size="100%">Lu, Shi-En</style></author><author><style face="normal" font="default" size="100%">Wang, Nian</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing.</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%">Biodiversity</style></keyword><keyword><style  face="normal" font="default" size="100%">Citrus</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%">Genes, rRNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Microarray Analysis</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%">Plant Diseases</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Leaves</style></keyword><keyword><style  face="normal" font="default" size="100%">Rhizobiaceae</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><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Nucleic Acid</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%">75</style></volume><pages><style face="normal" font="default" size="100%">1566-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. &quot;Candidatus Liberibacter asiaticus&quot; was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of &quot;Candidatus Liberibacter asiaticus&quot; in symptomatic leaves. These data implicate &quot;Candidatus Liberibacter asiaticus&quot; as the pathogen responsible for HLB disease.</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/19151177?dopt=Abstract</style></custom1></record><record><source-app 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%">Brodie, Eoin L</style></author><author><style face="normal" font="default" size="100%">DeSantis, Todd Z</style></author><author><style face="normal" font="default" size="100%">Andersen, Gary L</style></author><author><style face="normal" font="default" size="100%">Lindow, Steven E</style></author><author><style face="normal" font="default" size="100%">Firestone, Mary K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Selective progressive response of soil microbial community to wild oat roots.</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%">Avena sativa</style></keyword><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%">Colony Count, Microbial</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%">Plant Roots</style></keyword><keyword><style  face="normal" font="default" size="100%">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, Ribosomal, 16S</style></keyword><keyword><style  face="normal" font="default" size="100%">Soil Microbiology</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%">168-78</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.</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/19005498?dopt=Abstract</style></custom1></record></records></xml>