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Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China

  • Applied genetics and molecular biotechnology
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Abstract

Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0 % for 16S rRNA gene clones and 64.3 % for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54 % of the total volatile fatty acids and methane was 57.20 % of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

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References

  • Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, Sieprawska-Lupa M, Dharmarajan L, Goltsman E, Lapidus A, Saunders E, Han C, Land M, Lucas S, Mukhopadhyay B, Whitman WB, Woese C, Bristow J, Kyrpides N (2009a) Genomic characterization of Methanomicrobiales reveals three classes of methanogens. PLoS One 4(6):e5797. doi:10.1371/journal.pone.0005797

    Article  PubMed  Google Scholar 

  • Anderson IJ, Sieprawska-Lupa M, Goltsman E, Lapidus A, Copeland A, Glavina Del Rio T, Tice H, Dalin E, Barry K, Pitluck S, Hauser L, Land M, Lucas S, Richardson P, Whitman WB, Kyrpides NC (2009b) Complete genome sequence of Methanocorpusculum labreanum type strain Z. Stand Genomic Sci 1(2):197–203. doi:10.4056/sigs.35575

    Article  PubMed  Google Scholar 

  • Anderson I, Djao OD, Misra M, Chertkov O, Nolan M, Lucas S, Lapidus A, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Sikorski J, Spring S, Rohde M, Eichinger K, Huber H, Wirth R, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC (2010) Complete genome sequence of Methanothermus fervidus type strain (V24S). Stand Genomic Sci 3(3):315–324. doi:10.4056/sigs.1283367

    Article  PubMed  Google Scholar 

  • Bapteste E, Brochier C, Boucher Y (2005) Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1(5):353–363

    Article  PubMed  CAS  Google Scholar 

  • Boone D, Whitman W, Rouvière P (1993) Diversity and taxonomy of methanogens. In: Ferry J (ed) Methanogenesis. Chapman & Hall, New York, pp 35–80

    Chapter  Google Scholar 

  • Briones A, Raskin L (2003) Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr Opin Biotechnol 14(3):270–276

    Article  PubMed  CAS  Google Scholar 

  • Chao A, Shen T-J (2010) Program SPADE (Species Prediction and Diversity Estimation). Program and User's Guide. Available from http://chao.stat.nthu.edu.tw

  • Chao A, Chazdon RL, Colwell RK, Shen T-J (2005) A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol Lett 8(2):148–159. doi:10.1111/j.1461-0248.2004.00707.x

    Article  Google Scholar 

  • Conrad R, Erkel C, Liesack W (2006) Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 17(3):262–267. doi:10.1016/j.copbio.2006.04.002

    Article  PubMed  CAS  Google Scholar 

  • De Vrieze J, Hennebel T, Boon N, Verstraete W (2012) Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. Bioresour Technol 112:1–9. doi:10.1016/j.biortech.2012.02.079

    Article  PubMed  Google Scholar 

  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89(12):5685–5689

    Article  PubMed  CAS  Google Scholar 

  • Demirel B, Scherer P (2008) The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review. Rev Environ Sci Biotechnol 7(2):173–190. doi:10.1007/s11157-008-9131-1

    Article  CAS  Google Scholar 

  • Denman SE, Tomkins NW, McSweeney CS (2007) Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol Ecol 62(3):313–322. doi:10.1111/j.1574-6941.2007.00394.x

    Article  PubMed  CAS  Google Scholar 

  • Deppenmeier U (2002) The unique biochemistry of methanogenesis. Prog Nucleic Acid Res Mol Biol 71:223–283

    Article  PubMed  CAS  Google Scholar 

  • Dhillon A, Lever M, Lloyd KG, Albert DB, Sogin ML, Teske A (2005) Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Appl Environ Microbiol 71(8):4592–4601. doi:10.1128/AEM.71.8.4592-4601.2005

    Article  PubMed  CAS  Google Scholar 

  • Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M (2009) High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4(9):e7063. doi:10.1371/journal.pone.0007063

    Article  PubMed  Google Scholar 

  • Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638. doi:10.1126/science.1110591

    Article  PubMed  Google Scholar 

  • Elberson MA, Sowers KR (1997) Isolation of an aceticlastic strain of Methanosarcina siciliae from marine canyon sediments and emendation of the species description for Methanosarcina siciliae. Int J Syst Bacteriol 47(4):1258–1261

    Article  PubMed  CAS  Google Scholar 

  • Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK (1997) Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278(5342):1457–1462

    Article  PubMed  CAS  Google Scholar 

  • Ferry JG (1992) Biochemistry of methanogenesis. Crit Rev Biochem Mol Biol 27(6):473–503. doi:10.3109/10409239209082570

    Article  PubMed  CAS  Google Scholar 

  • Gagnon N, Barret M, Topp E, Kalmokoff M, Masse D, Masse L, Talbot G (2011) A novel fingerprint method to assess the diversity of methanogens in microbial systems. FEMS Microbiol Lett 325(2):115–122. doi:10.1111/j.1574-6968.2011.02418.x

    Article  PubMed  CAS  Google Scholar 

  • Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ (2007) Part 1—The "Archaea", Phyla "Crenarchaeota" and "Euryarchaeota". Taxonomic Outline of the Bacteria and Archaea. Release 7.7.: 6–31

  • Holm-Nielsen JB, Al Seadi T, Oleskowicz-Popiel P (2009) The future of anaerobic digestion and biogas utilization. Bioresour Technol 100(22):5478–5484. doi:10.1016/j.biortech.2008.12.046

    Article  PubMed  CAS  Google Scholar 

  • Imachi H, Sakai S, Nagai H, Yamaguchi T, Takai K (2009) Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field. Int J Syst Evol Microbiol 59(Pt 4):800–805. doi:10.1099/ijs.0.003731-0

    Article  PubMed  CAS  Google Scholar 

  • Jalalzadeh-Azar AA, National Renewable Energy Laboratory (U.S.) (2010) A technoeconomic analysis of biomethane production from biogas and pipeline delivery. NREL/PR 5600-49629

  • Jiang X, Sommer SG, Christensen KV (2011) A review of the biogas industry in China. Energy Policy 39(10):6073–6081. doi:10.1016/j.enpol.2011.07.007

    Article  Google Scholar 

  • Klieve AV, Ouwerkerk D, Maguire AJ (2012) Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations. J Appl Microbiol 113(5):1065–1075. doi:10.1111/j.1365-2672.2012.05428.x

    Article  PubMed  CAS  Google Scholar 

  • Kotsyurbenko OR, Chin KJ, Glagolev MV, Stubner S, Simankova MV, Nozhevnikova AN, Conrad R (2004) Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog. Environ Microbiol 6(11):1159–1173. doi:10.1111/j.1462-2920.2004.00634.x

    Article  PubMed  CAS  Google Scholar 

  • Lang H, Yang H, Zhang Y (2010) Methanogenic diversity in an anaerobic digester with chicken feces. Microbiol China 37(4):508–512

    CAS  Google Scholar 

  • Larson JA, National Agricultural Library (U.S.) (1988) Biogas from biomass, 1985–1987: 467 citations. U.S. Dept. of Agriculture, National Agricultural Library, Beltsville

  • Liu Y (2010) Taxonomy of Methanogens. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 547–558

    Chapter  Google Scholar 

  • Liu FH, Wang SB, Zhang JS, Zhang J, Yan X, Zhou HK, Zhao GP, Zhou ZH (2009) The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis. J Appl Microbiol 106(3):952–966. doi:10.1111/j.1365-2672.2008.04064.x

    Article  PubMed  CAS  Google Scholar 

  • Lueders T, Chin KJ, Conrad R, Friedrich M (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3(3):194–204

    Article  PubMed  CAS  Google Scholar 

  • Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148(Pt 11):3521–3530

    PubMed  CAS  Google Scholar 

  • Lwin KO, Matsui H, Ban-Tokuda T, Kondo M, Lapitan RM, Herrera JR, Del-Barrio AN, Fujihara T (2012) Comparative analysis of methanogen diversity in the rumen of crossbred buffalo and cattle in the Philippines by using the functional gene mcrA. Mol Biol Rep 39(12):10769–10774. doi:10.1007/s11033-012-1969-1

    Article  PubMed  CAS  Google Scholar 

  • Magurran AE (1988) Ecological diversity and its measurement. Princeton University Press, Princeton, NJ

    Book  Google Scholar 

  • Marchaim U (1992) Biogas processes for sustainable development. Food and Agriculture Organization of the United Nations, Italy

  • McOrist S, Khampee K, Guo A (2011) Modern pig farming in the People's Republic of China: growth and veterinary challenges. Rev Sci Tech 30(3):961–968

    PubMed  CAS  Google Scholar 

  • Nakagawa CH, Honquilada QL, Peace Corps (U.S.) (1985) Chinese biogas digester: a potential model for small-scale, rural applications: a manual for construction and operation. Peace Corps Information Collection and Exchange, Washington, DC

  • Narihiro T, Sekiguchi Y (2011) Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea. Microb Biotechnol 4(5):585–602. doi:10.1111/j.1751-7915.2010.00239.x

    Article  PubMed  CAS  Google Scholar 

  • Nettmann E, Bergmann I, Pramschufer S, Mundt K, Plogsties V, Herrmann C, Klocke M (2010) Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 76(8):2540–2548. doi:10.1128/AEM.01423-09

    Article  PubMed  CAS  Google Scholar 

  • Pender S, Toomey M, Carton M, Eardly D, Patching JW, Colleran E, O'Flaherty V (2004) Long-term effects of operating temperature and sulphate addition on the methanogenic community structure of anaerobic hybrid reactors. Water Res 38(3):619–630. doi:10.1016/j.watres.2003.10.055

    Article  PubMed  CAS  Google Scholar 

  • Rajendran K, Aslanzadeh S, Taherzadeh MJ (2012) Household biogas digesters—a review. Energies 5(8):2911–2942

    Article  CAS  Google Scholar 

  • Sakai S, Imachi H, Hanada S, Ohashi A, Harada H, Kamagata Y (2008) Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov. Int J Syst Evol Microbiol 58(Pt 4):929–936. doi:10.1099/ijs.0.65571-0

    Article  PubMed  Google Scholar 

  • Sharma PK, Capalash N, Kaur J (2007) An improved method for single step purification of metagenomic DNA. Mol Biotechnol 36(1):61–63

    Article  PubMed  CAS  Google Scholar 

  • Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV, Kozyavkin SA (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci USA 99(7):4644–4649. doi:10.1073/pnas.032671499

    Article  PubMed  CAS  Google Scholar 

  • Springer E, Sachs MS, Woese CR, Boone DR (1995) Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int J Syst Bacteriol 45(3):554–559

    Article  PubMed  CAS  Google Scholar 

  • Steinberg LM, Regan JM (2008) Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Appl Environ Microbiol 74(21):6663–6671. doi:10.1128/AEM.00553-08

    Article  PubMed  CAS  Google Scholar 

  • Strapoc D, Picardal FW, Turich C, Schaperdoth I, Macalady JL, Lipp JS, Lin YS, Ertefai TF, Schubotz F, Hinrichs KU, Mastalerz M, Schimmelmann A (2008) Methane-producing microbial community in a coal bed of the Illinois basin. Appl Environ Microbiol 74(8):2424–2432. doi:10.1128/AEM.02341-07

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. doi:10.1093/molbev/msr121

    Article  PubMed  CAS  Google Scholar 

  • Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6(8):579–591. doi:10.1038/nrmicro1931

    Article  PubMed  CAS  Google Scholar 

  • Ufnar JA, Ufnar DF, Wang SY, Ellender RD (2007) Development of a swine-specific fecal pollution marker based on host differences in methanogen mcrA genes. Appl Environ Microbiol 73(16):5209–5217. doi:10.1128/AEM.00319-07

    Article  PubMed  CAS  Google Scholar 

  • Waldron PJ, Petsch ST, Martini AM, Nusslein K (2007) Salinity constraints on subsurface archaeal diversity and methanogenesis in sedimentary rock rich in organic matter. Appl Environ Microbiol 73(13):4171–4179. doi:10.1128/AEM.02810-06

    Article  PubMed  CAS  Google Scholar 

  • Weiss DS, Thauer RK (1993) Methanogenesis and the unity of biochemistry. Cell 72(6):819–822

    Article  PubMed  CAS  Google Scholar 

  • Whitehead TR, Cotta MA (1999) Phylogenetic diversity of methanogenic archaea in swine waste storage pits. FEMS Microbiol Lett 179(2):223–226

    Article  PubMed  CAS  Google Scholar 

  • Yang Y, Zhang P, Li G (2012) Regional differentiation of biogas industrial development in China. Renew Sustain Energy Rev 16(9):6686–6693. doi:10.1016/j.rser.2012.07.016

    Article  Google Scholar 

  • Yasui H, Komatsu K, Goel R, Matsuhashi R, Ohashi A, Harada H (2005) Minimization of greenhouse gas emission by application of anaerobic digestion process with biogas utilization. Water Sci Technol 52(1–2):545–552

    PubMed  CAS  Google Scholar 

  • Zhang J, Madden TL (1997) PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res 7(6):649–656

    PubMed  CAS  Google Scholar 

  • Zhang J, Wei Y, Xiao W, Zhou Z, Yan X (2011) Performance and spatial community succession of an anaerobic baffled reactor treating acetone-butanol-ethanol fermentation wastewater. Bioresour Technol 102(16):7407–7414. doi:10.1016/j.biortech.2011.05.035

    Article  PubMed  CAS  Google Scholar 

  • Zhao Y, Boone DR, Mah RA, Boone JE, Xun L (1989) Isolation and Characterization of Methanocorpusculum labreanum sp. nov. from the LaBrea Tar Pits. Int J Syst Bacteriol 39(1):10–13. doi:10.1099/00207713-39-1-10

    Article  Google Scholar 

  • Zhu C, Zhang J, Tang Y, Zhengkai X, Song R (2011) Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis. Microbiol Res 166(1):27–35. doi:10.1016/j.micres.2010.01.004

    Article  PubMed  CAS  Google Scholar 

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Acknowledgment

This work was partly supported by The National Key Technology R&D Program of China (grant No. 2011BAC11B05).

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Authors and Affiliations

  1. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China

    Huibin Qin, Huihua Lang & Hongjiang Yang

  2. Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China

    Huibin Qin

  3. Xingtai Institute for Food and Drug Control, Xingtai, 054001, China

    Huihua Lang

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  1. Huibin Qin
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Qin, H., Lang, H. & Yang, H. Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China. Appl Microbiol Biotechnol 97, 8163–8171 (2013). https://doi.org/10.1007/s00253-013-4957-z

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