Article: Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing
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| Title | Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing |
|---|---|
| Authors | Ye, L1 Zhang, T1 |
| Keywords | Chemistry Biotechnology Microbiology Microbial Genetics and Genomics |
| Issue Date | 2012 |
| Publisher | Springer Berlin / Heidelberg |
| Citation | Applied Microbiology and Biotechnology, 2012 [Epub ahead of print] [How to Cite?] DOI: http://dx.doi.org/10.1007/s00253-012-4082-4 |
| ISSN | 0175-7598 2011 Impact Factor: 3.425 2011 SCImago Journal Rankings: 0.180 |
| DOI | http://dx.doi.org/10.1007/s00253-012-4082-4 |
| References | Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410 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 Ferris M, Muyzer G, Ward D (1996) Denaturing gradient gel electrophoresis profiles of 16 S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62(2):340–346 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 Heuer H, Krsek M, Baker P, Smalla K, Wellington E (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16 S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63(8):3233–3241 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 Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774 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 Kim T, Kim H, Kwon S, Park H (2011) Nitrifying bacterial community structure of a full-scale integrated fixed-film activated sludge process as investigated by pyrosequencing. J Microbiol Biotechnol 21(3):293–298 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 Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63(11):4516–4522 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 Muyzer G, De Waal E, Uitterlinden A (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695–700 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 Roesch L, Fulthorpe R, Riva A, Casella G, Hadwin A, Kent A, Daroub S, Camargo F, Farmerie W, Triplett E (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290 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 Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63(7):2884–2896 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, Zhang T (2011) Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ Sci Technol 45(17):7173–7179 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 Cracraft J, Donoghue MJ (2004) Assembling the tree of life. Oxford University Press, Oxford Kwon S, Kim T, Yu G, Jung J, Park H (2010) Bacterial community composition and diversity of a full-scale integrated fixed-film activated sludge system as investigated by pyrosequencing. J Microbiol Biotechnol 20(12):1717–1723 |
| dc.contributor.author | Ye, L |
|---|---|
| dc.contributor.author | Zhang, T |
| dc.date.accessioned | 2012-05-28T08:20:50Z |
| dc.date.available | 2012-05-28T08:20:50Z |
| dc.date.issued | 2012 |
| dc.description.nature | published_or_final_version |
| dc.description.other | Springer Open Choice, 28 May 2012 |
| dc.identifier.citation | Applied Microbiology and Biotechnology, 2012 [Epub ahead of print] [How to Cite?] DOI: http://dx.doi.org/10.1007/s00253-012-4082-4 |
| dc.identifier.citeulike | 10657784 |
| dc.identifier.doi | http://dx.doi.org/10.1007/s00253-012-4082-4 |
| dc.identifier.eissn | 1432-0614 |
| dc.identifier.epage | 10 |
| dc.identifier.hkuros | 208078 |
| dc.identifier.issn | 0175-7598 2011 Impact Factor: 3.425 2011 SCImago Journal Rankings: 0.180 |
| dc.identifier.openurl | |
| dc.identifier.scopus | eid_2-s2.0-84860575036 |
| dc.identifier.spage | 1 |
| dc.identifier.uri | http://hdl.handle.net/10722/147138 |
| dc.language | Eng |
| dc.publisher | Springer Berlin / Heidelberg |
| dc.relation.ispartof | Applied Microbiology and Biotechnology |
| dc.relation.references | Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Ferris M, Muyzer G, Ward D (1996) Denaturing gradient gel electrophoresis profiles of 16 S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62(2):340–346 |
| dc.relation.references | Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso sea bacterioplankton. Nature 345:60–63. doi: 10.1038/345060a0 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Heuer H, Krsek M, Baker P, Smalla K, Wellington E (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16 S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63(8):3233–3241 |
| dc.relation.references | 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 |
| dc.relation.references | Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Kim T, Kim H, Kwon S, Park H (2011) Nitrifying bacterial community structure of a full-scale integrated fixed-film activated sludge process as investigated by pyrosequencing. J Microbiol Biotechnol 21(3):293–298 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63(11):4516–4522 |
| dc.relation.references | 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 |
| dc.relation.references | Muyzer G, De Waal E, Uitterlinden A (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695–700 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Roesch L, Fulthorpe R, Riva A, Casella G, Hadwin A, Kent A, Daroub S, Camargo F, Farmerie W, Triplett E (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63(7):2884–2896 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | 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 |
| dc.relation.references | Ye L, Zhang T (2011) Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ Sci Technol 45(17):7173–7179 |
| dc.relation.references | 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 |
| dc.relation.references | Cracraft J, Donoghue MJ (2004) Assembling the tree of life. Oxford University Press, Oxford |
| dc.relation.references | Kwon S, Kim T, Yu G, Jung J, Park H (2010) Bacterial community composition and diversity of a full-scale integrated fixed-film activated sludge system as investigated by pyrosequencing. J Microbiol Biotechnol 20(12):1717–1723 |
| dc.rights | The Author(s) |
| dc.rights | Creative Commons: Attribution 3.0 Hong Kong License |
| dc.subject | Chemistry |
| dc.subject | Biotechnology |
| dc.subject | Microbiology |
| dc.subject | Microbial Genetics and Genomics |
| dc.title | Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing |
| dc.type | Article |
Author Affiliations
- The University of Hong Kong