Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Yu, Ke ^a   Zhang, Tong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA MONOOXYGENASE; COMPLEMENTARY DNA; DNA; HYDROXYLAMINE OXIDASE; MESSENGER RNA; NITROGEN; RIBOSOME RNA; UNCLASSIFIED DRUG; UNSPECIFIC MONOOXYGENASE; ENZYME;

ACTINOBACTERIA; ACTIVATED SLUDGE; AMMONIA OXIDIZING BACTERIA; AMOA GENE; AMOB GENE; AMOC GENE; ARCHAEON; ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BACTEROIDETES; COMMUNITY STRUCTURE; DENITRIFICATION; DNA SEQUENCE; ENZYME SUBUNIT; FIRMICUTES; GENE EXPRESSION; GENE SEQUENCE; GENETIC DATABASE; GENOME SIZE; HONG KONG; METAGENOMICS; METATRANSCRIPTOMICS; MICROBIAL COMMUNITY; NITRIFICATION; NITROSOMONAS; NITROSOSPIRA; NONHUMAN; PROKARYOTES BY METABOLISM; PROTEOBACTERIA; SIGNAL TRANSDUCTION; TAXONOMY; TRANSCRIPTOMICS; VERRUCOMICROBIA; WASTE WATER TREATMENT PLANT; CLASSIFICATION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; SEWAGE; SPECIES DIFFERENCE;

ACTINOBACTERIA; BACTEROIDETES; FIRMICUTES; NITROSOMONADALES; NITROSOMONAS; NITROSOSPIRA; PROTEOBACTERIA; VERRUCOMICROBIA;

CLASSIFICATION; ENZYMES; GENE EXPRESSION PROFILING; METAGENOMICS; NITROGEN; RNA, MESSENGER; RNA, RIBOSOMAL; SEWAGE; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC; WASTE DISPOSAL, FLUID;

EID: 84861633828     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038183     Document Type: Article

References (29)

1. Gittel A, Mussmann M, Sass H, Cypionka H, Konneke M, (2008) Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environ Microbiol 10: 2645-2658.
2. Wittebolle L, Vervaeren H, Verstraete W, Boon N, (2008) Quantifying community dynamics of nitrifiers in functionally stable reactors. Appl Environ Microbiol 74: 286-293.
3. Zhang T, Fang HH, (2006) Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 70: 281-289.
4. Zhang T, Zhang M, Zhang X, Fang HH, (2009) Tetracycline resistance genes and tetracycline resistant lactose-fermenting Enterobacteriaceae in activated sludge of sewage treatment plants. Environ Sci Technol 43: 3455-3460.
5. Xia S, Duan L, Song Y, Li J, Piceno YM, et al. (2010) Bacterial community structure in geographically distributed biological wastewater treatment reactors. Environ Sci Technol 44: 7391-7396.
6. Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, et al. (2008) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. Isme Journal 2: 853-864.
7. Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.
8. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, et al. (2008) Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome. PLoS One 3.
9. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
10. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, et al. (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods 79: 266-271.
11. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 105: 3805-3810.
12. Shi Y, Tyson GW, Eppley JM, DeLong EF, (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. Isme Journal 5: 999-1013.
13. Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, et al. (2009) Molecular Diversity of a North Carolina Wastewater Treatment Plant as Revealed by Pyrosequencing. Applied and Environmental Microbiology 75: 1688-1696.
14. Zhang T, Shao MF, Ye L, (2011) 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. Isme Journal.
15. Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, et al. (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
16. Park HD, Wells GF, Bae H, Criddle CS, Francis CA, (2006) Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microbiol 72: 5643-5647.
17. Lucker S, Wagner M, Maixner F, Pelletier E, Koch H, et al. (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci U S A 107: 13479-13484.
18. Ye L, Shao MF, Zhang T, Tong AH, 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: 4390-4398.
19. Ye L, Zhang T, (2011) Ammonia-Oxidizing Bacteria Dominates Over Ammonia-Oxidizing Archaea in a Saline Nitrification Reactor Under Low DO and High Nitrogen Loading. Biotechnology and Bioengineering 108: 2544-2552.
20. Geets J, de Cooman M, Wittebolle L, Heylen K, Vanparys B, et al. (2007) Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge. Appl Microbiol Biotechnol 75: 211-221.
21. 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: 2884-2896.
22. McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML, (2010) Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12: 378-392.
23. Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA, (2011) Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. Isme Journal 5: 461-472.
24. Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, et al. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7: 1985-1995.
25. Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MSM, Klotz MG, (2011) A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environmental Microbiology Reports 3: 91-100.
26. Meyer F, Paarman D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
27. Huson DH, Auch AF, Qi J, Schuster SC, (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
28. Pfister CA, Meyer F, Antonopoulos DA, (2010) Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling. PLoS One 5: e10518.
29. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, et al. (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 108 (Suppl 1): 4578-4585.