@article {369,
	title = {Phylogenetic clustering of soil microbial communities by 16S rRNA but not 16S rRNA genes.},
	journal = {Appl Environ Microbiol},
	volume = {78},
	year = {2012},
	month = {2012 Apr},
	pages = {2459-61},
	abstract = {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.},
	keywords = {Archaea, Bacteria, Biodiversity, Cluster Analysis, Ecosystem, Genes, rRNA, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Trees, Tropical Climate},
	issn = {1098-5336},
	doi = {10.1128/AEM.07547-11},
	author = {Deangelis, Kristen M and Firestone, Mary K}
}
@article {374,
	title = {Effects of selected root exudate components on soil bacterial communities.},
	journal = {FEMS Microbiol Ecol},
	volume = {77},
	year = {2011},
	month = {2011 Sep},
	pages = {600-10},
	abstract = {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 (<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.},
	keywords = {Bacteria, DNA, Bacterial, Molecular Sequence Data, Organic Chemicals, Phylogeny, Pinus, Plant Exudates, Plant Roots, Rhizosphere, RNA, Ribosomal, 16S, Soil, Soil Microbiology},
	issn = {1574-6941},
	doi = {10.1111/j.1574-6941.2011.01150.x},
	author = {Shi, Shengjing and Richardson, Alan E and O{\textquoteright}Callaghan, Maureen and Deangelis, Kristen M and Jones, Eirian E and Stewart, Alison and Firestone, Mary K and Condron, Leo M}
}
@article {372,
	title = {Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.},
	journal = {Nature},
	volume = {480},
	year = {2011},
	month = {2011 Dec 15},
	pages = {368-71},
	abstract = {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 {\textdegree}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.},
	keywords = {Alaska, Arctic Regions, Bacteria, Carbon, Carbon Cycle, DNA, Freezing, Genes, rRNA, Metagenome, Metagenomics, Methane, Nitrogen, Nitrogen Cycle, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Soil, Soil Microbiology, Temperature, Time Factors},
	issn = {1476-4687},
	doi = {10.1038/nature10576},
	author = {Mackelprang, Rachel and Waldrop, Mark P and Deangelis, Kristen M and David, Maude M and Chavarria, Krystle L and Blazewicz, Steven J and Rubin, Edward M and Jansson, Janet K}
}
@article {376,
	title = {Microbial communities acclimate to recurring changes in soil redox potential status.},
	journal = {Environ Microbiol},
	volume = {12},
	year = {2010},
	month = {2010 Dec},
	pages = {3137-49},
	abstract = {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 CO$_{2}$ respiration, methanogenesis, N$_{2}$O 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.},
	keywords = {Acclimatization, Archaea, Bacteria, Carbon Dioxide, DNA, Archaeal, DNA, Bacterial, Iron, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, RNA, Archaeal, RNA, Bacterial, Soil, Soil Microbiology, Trees},
	issn = {1462-2920},
	doi = {10.1111/j.1462-2920.2010.02286.x},
	author = {Deangelis, Kristen M and Silver, Whendee L and Thompson, Andrew W and Firestone, Mary K}
}
@article {377,
	title = {Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing.},
	journal = {Appl Environ Microbiol},
	volume = {75},
	year = {2009},
	month = {2009 Mar},
	pages = {1566-74},
	abstract = {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. "Candidatus Liberibacter asiaticus" 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 "Candidatus Liberibacter asiaticus" in symptomatic leaves. These data implicate "Candidatus Liberibacter asiaticus" as the pathogen responsible for HLB disease.},
	keywords = {Bacteria, Biodiversity, Citrus, DNA, Bacterial, DNA, Ribosomal, Genes, rRNA, Microarray Analysis, Molecular Sequence Data, Phylogeny, Plant Diseases, Plant Leaves, Rhizobiaceae, RNA, Bacterial, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid},
	issn = {1098-5336},
	doi = {10.1128/AEM.02404-08},
	author = {Sagaram, Uma Shankar and Deangelis, Kristen M and Trivedi, Pankaj and Andersen, Gary L and Lu, Shi-En and Wang, Nian}
}
@article {378,
	title = {Selective progressive response of soil microbial community to wild oat roots.},
	journal = {ISME J},
	volume = {3},
	year = {2009},
	month = {2009 Feb},
	pages = {168-78},
	abstract = {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.},
	keywords = {Avena sativa, Bacteria, Biodiversity, Colony Count, Microbial, Microarray Analysis, Oligonucleotide Array Sequence Analysis, Plant Roots, Polymerase Chain Reaction, RNA, Bacterial, RNA, Ribosomal, 16S, Soil Microbiology},
	issn = {1751-7370},
	doi = {10.1038/ismej.2008.103},
	author = {Deangelis, Kristen M and Brodie, Eoin L and DeSantis, Todd Z and Andersen, Gary L and Lindow, Steven E and Firestone, Mary K}
}
