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

详细信息    查看全文

• 作者：Jianhua Guo (1) (2)
  Yongzhen Peng (1)
  Bing-Jie Ni (2)
  Xiaoyu Han (1) (3)
  Lu Fan (2)
  Zhiguo Yuan (2)
  
  1. Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering ; Engineering Research Center of Beijing ; Beijing University of Technology ; Beijing ; 100124 ; Peoples鈥?Republic of China
  2. Advanced Water Management Centre (AWMC) ; The University of Queensland ; St Lucia ; Brisbane ; QLD ; 4072 ; Australia
  3. Beijing Drainage Group Co. ; Ltd ; Beijing ; 100022 ; Peoples鈥?Republic of China
  
• 关键词：Waste activated sludge ; Anaerobic digestion ; Metagenomic sequencing ; Microbial community ; Methanogenesis pathway ; Biological wastewater treatment
• 刊名：Microbial Cell Factories
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：14
• 期：1
• 全文大小：1,697 KB
• 参考文献：1. van Loosdrecht, MCM, Brdjanovic, D (2014) Anticipating the next century of wastewater treatment. Science 344: pp. 1452-3 CrossRef
  2. Guo, J, Peng, Y, Wang, S, Ma, B, Ge, S, Wang, Z (2013) Pathways and organisms involved in ammonia oxidation and nitrous oxide emission. Crit Rev Env Sci Tec 43: pp. 2213-96 CrossRef
  3. Canales, A, Pareilleux, A, Rols, JL, Goma, G, Huyard, A (1994) Decreased sludge production strategy for domestic wastewater treatment. Water Sci Technol 30: pp. 97-106
  4. Appels, L, Baeyens, J, Degreve, J, Dewil, R (2008) Principles and potential of the anaerobic digestion of waste-activated sludge. Prog Energ Combust 34: pp. 755-81 CrossRef
  5. Amani, T, Nosrati, M, Sreekrishnan, TR (2010) Anaerobic digestion from the viewpoint of microbiological, chemical, and operational aspects - a review. Environ Rev 18: pp. 255-78 CrossRef
  6. Vanwonterghem, I, Jensen, PD, Ho, DP, Batstone, DJ, Tyson, GW (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotech 27: pp. 55-64 CrossRef
  7. Ye, L, Zhang, T, Wang, TT, Fang, ZW (2012) Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing. Environ Sci Technol 46: pp. 13244-52 CrossRef
  8. Aird, D, Ross, MG, Chen, W-S, Danielsson, M, Fennell, T, Russ, C (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12: pp. R18 CrossRef
  9. Bragg, L, Tyson, GW Metagenomics Using Next-Generation Sequencing. In: Paulsen, IT, Holmes, AJ eds. (2014) Environmental Microbiology: Methods and Protocols. Humana Press, New York City, pp. 183-201 CrossRef
  10. Albertsen, M, Hugenholtz, P, Skarshewski, A, Nielsen, KL, Tyson, GW, Nielsen, PH (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: pp. 533-8 CrossRef
  11. Wong, MT, Zhang, D, Li, J, Hui, RKH, Tun, HM, Brar, MS (2013) Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH聽10 pretreatment. Biotechnol Biofuels 6: pp. 38 CrossRef
  12. Li, A, Chu, Y, Wang, X, Ren, L, Yu, J, Liu, X (2013) A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol Biofuels 6: pp. 3 CrossRef
  13. Sundberg, C, Al-Soud, WA, Larsson, M, Alm, E, Yekta, SS, Svensson, BH (2013) 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. FEMS Microbiol Ecol 85: pp. 612-26 CrossRef
  14. Mardis, ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: pp. 133-41 CrossRef
  15. Glenn, TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11: pp. 759-69 CrossRef
  16. Mackelprang, R, Waldrop, MP, DeAngelis, KM, David, MM, Chavarria, KL, Blazewicz, SJ (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480: pp. 368-U120 CrossRef
  17. Mason, OU, Scott, NM, Gonzalez, A, Robbins-Pianka, A, Baelum, J, Kimbrel, J (2014) Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 8: pp. 1464-75 CrossRef
  18. Qin, J, Li, R, Raes, J, Arumugam, M, Burgdorf, KS, Manichanh, C (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: pp. 59-U70 CrossRef
  19. Albertsen, M, Hansen, LBS, Saunders, AM, Nielsen, PH, Nielsen, KL (2012) A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J 6: pp. 1094-106 CrossRef
  20. Ju, F, Guo, F, Ye, L, Xia, Y, Zhang, T (2014) Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4聽years. Environ Microbiol Rep 6: pp. 80-9 CrossRef
  21. Yang, Y, Yu, K, Xia, Y, Lau, FTK, Tang, DTW, Fung, WC (2014) Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biot 98: pp. 5709-18 CrossRef
  22. Ariesyady, HD, Ito, T, Okabe, S (2007) Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Res 41: pp. 1554-68 CrossRef
  23. Garcia-Pe帽a, EI, Parameswaran, P, Kang, DW, Canul-Chan, M, Krajmalnik-Brown, R (2011) Anaerobic digestion and co-digestion processes of vegetable and fruit residues: Process and microbial ecology. Bioresour Technol 102: pp. 9447-55 CrossRef
  24. Traversi, D, Villa, S, Lorenzi, E, Degan, R, Gilli, G (2012) 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 111: pp. 173-7 CrossRef
  25. Pelletier, E, Kreimeyer, A, Bocs, S, Rouy, Z, Gyapay, G, Chouari, R (2008) 鈥淐andidatus Cloacamonas acidaminovorans鈥? Genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol 190: pp. 2572-9 CrossRef
  26. Nelson, MC, Morrison, M, Yu, Z (2011) A meta-analysis of the microbial diversity observed in anaerobic digesters. Bioresour Technol 102: pp. 3730-9 CrossRef
  27. Ziganshin, AM, Liebetrau, J, Proeter, J, Kleinsteuber, S (2013) Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biot 97: pp. 5161-74 CrossRef
  28. Regueiro, L, Veiga, P, Figueroa, M, Alonso-Gutierrez, J, Stams, AJM, Lema, JM (2012) Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters. Microbiol Res 167: pp. 581-9 CrossRef
  29. Vanwonterghem, I, Jensen, PD, Dennis, PG, Hugenholtz, P, Rabaey, K, Tyson, GW (2014) Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME J 8: pp. 2015-2028 CrossRef
  30. Ramsay, IR, Pullammanappallil, PC (2001) Protein degradation during anaerobic wastewater treatment: derivation of stoichiometry. Biodegradation 12: pp. 247-57 CrossRef
  31. Papagianni, M (2012) Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact 11: pp. 50 CrossRef
  32. Noor, E, Eden, E, Milo, R, Alon, U (2010) Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol Cell 39: pp. 809-20 CrossRef
  33. Ferry, JG (1999) Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol Rev 23: pp. 13-38 CrossRef
  34. Sandoval Lozano, CJ, Vergara Mendoza, M, Carreno De Arango, M, Castillo Monroy, EF (2009) Microbiological characterization and specific methanogenic activity of anaerobe sludges used in urban solid waste treatment. Waste Manage 29: pp. 704-11 CrossRef
  35. Ragsdale, SW, Pierce, E (2008) Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochimica Et Biophysica Acta-Proteins and Proteomics 1784: pp. 1873-98 CrossRef
  36. Liu, Y, Whitman, WB In: Wiegel, J, Maier, RJ, Adams, MWW eds. (2008) Incredible Anaerobes: From Physiology to Genomics to Fuels. HighWire Press, Blackwell Publishing, New York, pp. 171-189
  37. Yu, Y, Lee, C, Hwang, S (2005) Analysis of community structures in anaerobic processes using a quantitative real-time PCR method. Water Sci Technol 52: pp. 85-91
  38. Meyer, F, Paarmann, D, D鈥橲ouza, M, Olson, R, Glass, EM, Kubal, M (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: pp. 386 CrossRef
  39. Jung, JY, Lee, SH, Kim, JM, Park, MS, Bae, J-W, Hahn, Y (2011) Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl Environ Microb 77: pp. 2264-74 CrossRef
  40. Kanehisa, M, Goto, S, Hattori, M, Aoki-Kinoshita, KF, Itoh, M, Kawashima, S (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: pp. D354-7 CrossRef
  41. Tatusov, RL, Galperin, MY, Natale, DA, Koonin, EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: pp. 33-6 CrossRef
  42. Mitra, S, Rupek, P, Richter, DC, Urich, T, Gilbert, JA, Meyer, F (2011) Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 12: pp. S21 CrossRef
  43. Huson, D, Mitra, S, Ruscheweyh, H, Weber, N, Schuster, S (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21: pp. 1552-60 CrossRef
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Biotechnology
  Applied Microbiology
  Environmental Engineering/Biotechnology
  
• 出版者：BioMed Central
• ISSN：1475-2859

文摘

Background Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion. Results In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester. Conclusions In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.