Bibby K, Viau E, Peccia J (2010) Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids. Water Res 44(14):4252–4260 doi: 10.1016/j.watres.2010.05.039

Claesson M, O'Sullivan O, Wang Q, Nikkila J, Marchesi J, Smidt H, De Vos W, Ross R, O'Toole P (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4(8):e6669 doi: 10.1371/journal.pone.0006669

Cole J, Wang Q, Cardenas E, Fish J, Chai B, Farris R, Kulam-Syed-Mohideen A, McGarrell D, Marsh T, Garrity G (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(suppl 1):D141–D145 doi: 10.1093/nar/gkn879

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072 doi: 10.1128/AEM.03006-05

DiPippo JL, Nesbo CL, Dahle H, Doolittle WF, Birkland NK, Noll KM (2009) Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J Syst Evol Microbiol 59(12):2991–3000 doi: 10.1099/ijs.0.008045-0

Droege M, Hill B (2008) The Genome Sequencer FLX (TM) System—longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol 136(1–2):3–10 doi: 10.1016/j.jbiotec.2008.03.021

Erhart R, Bradford D, Seviour R, Amann R, Blackall L (1997) Development and use of fluorescent in situ hybridization probes for the detection and identification of Microthrix parvicella in activated sludge. Syst Appl Microbiol 20(2):310–318 doi: 10.1016/S0723-2020(97)80078-1

Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso sea bacterioplankton. Nature 345:60–63 doi: 10.1038/345060a0

Glenn TC (2011) Field guide to next generation DNA sequencers. Mol Ecol Resour 15:759–769 doi: 10.1111/j.1755-0998.2011.03024.x

Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E (2011) Chimeric 16 S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21(3):494–504 doi: 10.1101/gr.112730.110

Huber R, Woese CR, Langworthy TA, Kristjansson JK, Stetter KO (1990) Fervidobacterium islandicum sp. nov., a new extremely thermophilic eubacterium belonging to the “Thermotogales”. Arch Microbiol 154(2):105–111 doi: 10.1007/BF00423318

Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12(7):1889–1898 doi: 10.1111/j.1462-2920.2010.02193.x

Huson D, Auch A, Qi J, Schuster S (2007) MEGAN analysis of metagenomic data. Genome Res 17(3):377–386 doi: 10.1101/gr.5969107

Klappenbach J, Saxman P, Cole J, Schmidt T (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29(1):181–184 doi: 10.1093/nar/29.1.181

Lee Z, Bussema C III, Schmidt T (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37:D489–D493 doi: 10.1093/nar/gkn689

McLellan S, Huse S, Mueller Spitz S, Andreishcheva E, Sogin M (2010) Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12(2):378–392 doi: 10.1111/j.1462-2920.2009.02075.x

Neilson A (1978) The occurrence of aeromonads in activated sludge: isolation of Aeromonas sobria and its possible confusion with Escherichia coli. J Appl Microbiol 44(2):259–264 doi: 10.1111/j.1365-2672.1978.tb00798.x

Nunoura T, Hirai M, Imachi H, Miyazaki M, Makita H, Hirayama H, Furushima Y, Yamamoto H, Takai K (2010) Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov., and emended description of the genus Kosmotoga. Arch Microbiol 192:811–819 doi: 10.1007/s00203-010-0611-7

Park S, Park B, Rhee S (2008) Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremophiles 12(4):605–615 doi: 10.1007/s00792-008-0165-7

Qian P, Wang Y, Lee O, Lau S, Yang J, Lafi F, Al-Suwailem A, Wong T (2010) Vertical stratification of microbial communities in the Red Sea revealed by 16 S rDNA pyrosequencing. ISME J 5:507–518 doi: 10.1038/ismej.2010.112

Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5:1595–1608 doi: 10.1038/ismej.2011.38

Sasaki D, Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y (2010) Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste. J Biosci Bioeng 111(1):41–46 doi: 10.1016/j.jbiosc.2010.08.011

Schuppler M, Mertens F, Schön G, Göbel UB (1995) Molecular characterization of nocardioform actinomycetes in activated sludge by 16S rRNA analysis. Microbiology 141(2):513–521 doi: 10.1099/13500872-141-2-513

Urich T, Lanzén A, Qi J, Huson D, Schleper C, Schuster S (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 3(6):e2527 doi: 10.1371/journal.pone.0002527

Wagner M, Loy A, Nogueira R, Purkhold U, Lee N, Daims H (2002) Microbial community composition and function in wastewater treatment plants. Antonie Van Leeuwenhoek 81(1):665–680 doi: 10.1023/A:1020586312170

Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261–5267 doi: 10.1128/AEM.00062-07

Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95(12):6578–6583 doi: 10.1073/pnas.95.12.6578

Ye L, Zhang T (2010) Estimation of nitrifier abundances in a partial nitrification reactor treating ammonium-rich saline wastewater using DGGE. T-RFLP and mathematical modeling. Appl Microbiol Biotechnol 88(6):1403–1412 doi: 10.1007/s00253-010-2837-3

Ye L, Shao MF, Zhang T, Tong AHY, Lok S (2011) Analysis of the bacterial community in a laboratory-scale nitrification reactor and a wastewater treatment plant by 454-pyrosequencing. Water Res 45(15):4390–4398 doi: 10.1016/j.watres.2011.05.028