@article {413,
	title = {Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction.},
	journal = {Appl Environ Microbiol},
	volume = {78},
	year = {2012},
	month = {2012 Apr},
	pages = {2966-72},
	abstract = {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.},
	keywords = {Biodegradation, Environmental, Biota, Environmental Microbiology, Environmental Pollutants, Genetic Variation, Microarray Analysis, Oxidation-Reduction, Uranium},
	issn = {1098-5336},
	doi = {10.1128/AEM.06528-11},
	author = {Liang, Yuting and Van Nostrand, Joy D and N{\textquoteright}guessan, Lucie A and Peacock, Aaron D and Deng, Ye and Long, Philip E and Resch, C Tom and Wu, Liyou and He, Zhili and Li, Guanghe and Hazen, Terry C and Lovley, Derek R and Zhou, Jizhong}
}
@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}
}
