Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing

Microbial Cell Factories

Volumn 14, Issue 1, 2015, Pages

  Guo, Jianhua ^a,b   Peng, Yongzhen ^a   Ni, Bing Jie ^b   Han, Xiaoyu ^a,c   Fan, Lu ^b   Yuan, Zhiguo ^b  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c Beijing Drainage Group Co Ltd   (China)

Author keywords

Anaerobic digestion; Biological wastewater treatment; Metagenomic sequencing; Methanogenesis pathway; Microbial community; Waste activated sludge

Indexed keywords

ACETATE KINASE; ACETYL COENZYME A SYNTHETASE; PHOSPHATE ACETYLTRANSFERASE; ARCHAEAL DNA; ARCHAEAL PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; METHANE; SEWAGE; WASTE WATER;

ACTINOBACTERIA; ACTIVATED SLUDGE; ANAEROBIC DIGESTION; ANAEROBIC REACTOR; ARCHAEON; ARTICLE; BACTERIA; BACTEROIDETES; COMMUNITY STRUCTURE; DNA SEQUENCE; EUKARYOTE; FIRMICUTES; GENE FUNCTION; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; METHANOGENESIS; METHANOSAETA; METHANOSARCINA; MICROBIAL COMMUNITY; NONHUMAN; PROTEOBACTERIA; SLUDGE DIGESTION; TAXONOMY; VIRUS; WASTE WATER MANAGEMENT; ANAEROBIC GROWTH; BACTERIUM; BIOREACTOR; BIOSYNTHESIS; CHEMISTRY; CLASSIFICATION; GENETICS; METABOLISM; METAGENOME; METHANOSARCINALES; MICROBIAL CONSORTIUM; MICROBIOLOGY; PROCEDURES; SEWAGE; WASTE WATER;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; FIRMICUTES; METHANOSAETA; METHANOSARCINA; PROTEOBACTERIA;

ANAEROBIOSIS; ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; BIOREACTORS; BIOSYNTHETIC PATHWAYS; DNA, ARCHAEAL; DNA, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; METAGENOMICS; METHANE; METHANOSARCINA; METHANOSARCINALES; MICROBIAL CONSORTIA; SEWAGE; WASTE DISPOSAL, FLUID; WASTE WATER;

EID: 84925873422     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-015-0218-4     Document Type: Article

References (43)

1. van Loosdrecht MCM, Brdjanovic D. Anticipating the next century of wastewater treatment. Science. 2014;344:1452-3.
2. Guo J, Peng Y, Wang S, Ma B, Ge S, Wang Z, et al. Pathways and organisms involved in ammonia oxidation and nitrous oxide emission. Crit Rev Env Sci Tec. 2013;43:2213-96.
3. Canales A, Pareilleux A, Rols JL, Goma G, Huyard A. Decreased sludge production strategy for domestic wastewater treatment. Water Sci Technol. 1994;30:97-106.
4. Appels L, Baeyens J, Degreve J, Dewil R. Principles and potential of the anaerobic digestion of waste-activated sludge. Prog Energ Combust. 2008;34:755-81.
5. Amani T, Nosrati M, Sreekrishnan TR. Anaerobic digestion from the viewpoint of microbiological, chemical, and operational aspects - a review. Environ Rev. 2010;18:255-78.
6. Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW. Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotech. 2014;27:55-64.
7. Ye L, Zhang T, Wang TT, Fang ZW. Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing. Environ Sci Technol. 2012;46:13244-52.
8. Aird D, Ross MG, Chen W-S, Danielsson M, Fennell T, Russ C, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12:R18.
9. Bragg L, Tyson GW. Metagenomics Using Next-Generation Sequencing. In: Paulsen IT, Holmes AJ, editors. Environmental Microbiology: Methods and Protocols, vol. 1096. 2nd ed. New York City: Humana Press; 2014. p. 183-201. Methods in Molecular Biology.
10. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533-8.
11. Wong MT, Zhang D, Li J, Hui RKH, Tun HM, Brar MS, et al. Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment. Biotechnol Biofuels. 2013;6:38.
12. Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, et al. A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol Biofuels. 2013;6:3.
13. Sundberg C, Al-Soud WA, Larsson M, Alm E, Yekta SS, Svensson BH, et al. 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. FEMS Microbiol Ecol. 2013;85:612-26.
14. Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008;24:133-41.
15. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour. 2011;11:759-69.
16. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature. 2011;480:368-U120.
17. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Baelum J, Kimbrel J, et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 2014;8:1464-75.
18. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-U70.
19. Albertsen M, Hansen LBS, Saunders AM, Nielsen PH, Nielsen KL. A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J. 2012;6:1094-106.
20. Ju F, Guo F, Ye L, Xia Y, Zhang T. Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4 years. Environ Microbiol Rep. 2014;6:80-9.
21. Yang Y, Yu K, Xia Y, Lau FTK, Tang DTW, Fung WC, et al. Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biot. 2014;98:5709-18.
22. Ariesyady HD, Ito T, Okabe S. Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Res. 2007;41:1554-68.
23. Garcia-Peña EI, Parameswaran P, Kang DW, Canul-Chan M, Krajmalnik-Brown R. Anaerobic digestion and co-digestion processes of vegetable and fruit residues: Process and microbial ecology. Bioresour Technol. 2011;102:9447-55.
24. Traversi D, Villa S, Lorenzi E, Degan R, Gilli G. Application of a real-time qPCR method to measure the methanogen concentration during anaerobic digestion as an indicator of biogas production capacity. J Environ Manage. 2012;111:173-7.
25. Pelletier E, Kreimeyer A, Bocs S, Rouy Z, Gyapay G, Chouari R, et al. "Candidatus Cloacamonas acidaminovorans": Genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol. 2008;190:2572-9.
26. Nelson MC, Morrison M, Yu Z. A meta-analysis of the microbial diversity observed in anaerobic digesters. Bioresour Technol. 2011;102:3730-9.
27. Ziganshin AM, Liebetrau J, Proeter J, Kleinsteuber S. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biot. 2013;97:5161-74.
28. Regueiro L, Veiga P, Figueroa M, Alonso-Gutierrez J, Stams AJM, Lema JM, et al. Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters. Microbiol Res. 2012;167:581-9.
29. Vanwonterghem I, Jensen PD, Dennis PG, Hugenholtz P, Rabaey K, Tyson GW. Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME J. 2014;8:2015-28.
30. Ramsay IR, Pullammanappallil PC. Protein degradation during anaerobic wastewater treatment: derivation of stoichiometry. Biodegradation. 2001;12:247-57.
31. Papagianni M. Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact. 2012;11:50.
32. Noor E, Eden E, Milo R, Alon U. Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol Cell. 2010;39:809-20.
33. Ferry JG. Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol Rev. 1999;23:13-38.
34. Sandoval Lozano CJ, Vergara Mendoza M, Carreno De Arango M, Castillo Monroy EF. Microbiological characterization and specific methanogenic activity of anaerobe sludges used in urban solid waste treatment. Waste Manage. 2009;29:704-11.
35. Ragsdale SW, Pierce E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2008;1784:1873-98.
36. Liu Y, Whitman WB. In: Wiegel J, Maier RJ, Adams MWW, editors. Incredible Anaerobes: From Physiology to Genomics to Fuels, vol. 1125. New York: HighWire Press, Blackwell Publishing; 2008. p. 171-89. Annals of the New York Academy of Sciences.
37. Yu Y, Lee C, Hwang S. Analysis of community structures in anaerobic processes using a quantitative real-time PCR method. Water Sci Technol. 2005;52:85-91.
38. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
39. Jung JY, Lee SH, Kim JM, Park MS, Bae J-W, Hahn Y, et al. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl Environ Microb. 2011;77:2264-74.
40. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34:D354-7.
41. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33-6.
42. Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, et al. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics. 2011;12:S21.
43. Huson D, Mitra S, Ruscheweyh H, Weber N, Schuster S. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011;21:1552-60.