@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 {373,
	title = {PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.},
	journal = {Appl Environ Microbiol},
	volume = {77},
	year = {2011},
	month = {2011 Sep},
	pages = {6313-22},
	abstract = {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.},
	keywords = {Biodiversity, DNA, Complementary, Environmental Microbiology, Metagenomics, Microarray Analysis, Oligonucleotide Array Sequence Analysis, RNA, Ribosomal, 16S, Sensitivity and Specificity},
	issn = {1098-5336},
	doi = {10.1128/AEM.05262-11},
	author = {Deangelis, Kristen M and Wu, Cindy H and Beller, Harry R and Brodie, Eoin L and Chakraborty, Romy and DeSantis, Todd Z and Fortney, Julian L and Hazen, Terry C and Osman, Shariff R and Singer, Mary E and Tom, Lauren M and Andersen, Gary L}
}
