Assessment of a biogas-generating microbial community in a pilot-scale anaerobic reactor

Journal of Bioscience and Bioengineering

Volumn 117, Issue 6, 2014, Pages 730-736

  Ziganshina, Elvira E ^a   Bagmanova, Alsu R ^a   Khilyas, Irina V ^a   Ziganshin, Ayrat M ^a  

^a KAZAN FEDERAL UNIVERSITY   (Russian Federation)

Author keywords

16S rRNA genes; Agricultural wastes; Biogas; McrA genes; Terminal restriction fragment length polymorphism

Indexed keywords

AGRICULTURAL WASTES; BIOGAS; RNA;

16S RRNA GENE; ANAEROBIC REACTOR; METHANOGENIC ARCHAEA; METHANOMICROBIALES (MMB); METHANOSARCINALES; MICROBIAL COMMUNITIES; PROTEOBACTERIA; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS;

GENES;

BIOGAS; RNA 16S; BIOFUEL;

AGRICULTURAL WASTE; ANAEROBIC METABOLISM; ANAEROTRUNCUS; ARTICLE; BACTEROIDALES; BACTEROIDETES; BIOREACTOR; CASTELLANIELLA; CLOSTRIDIA; CLOSTRIDIALES; DESULFOTOMACULUM; EURYARCHAEOTA; FIRMICUTES; FLEXIBACTER; METHANOBACTERIACEAE; METHANOBACTERIALES; METHANOCORPUSCULUM PARVUM; METHANOGENIC ARCHAEON; METHANOMICROBIALES; METHANOSARCINA BARKERI; METHANOSARCINA THERMOPHILA; MICROBIAL COMMUNITY; NONHUMAN; PROTEOBACTERIA; RUMEN MICROORGANISM; TISSIERELLA; ANAEROBIC GROWTH; ARCHAEAL GENE; BACTERIAL GENE; CLOSTRIDIUM; DNA SEQUENCE; GENETICS; METHANOSARCINALES; MICROFLORA; MOLECULAR TYPING; PILOT STUDY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ANAEROBIOSIS; BIOFUELS; BIOREACTORS; CLOSTRIDIUM; GENES, ARCHAEAL; GENES, BACTERIAL; METHANOMICROBIALES; METHANOSARCINALES; MICROBIOTA; MOLECULAR TYPING; PILOT PROJECTS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84899623618     PISSN: 13891723     EISSN: 13474421     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2013.11.013     Document Type: Article

References (47)

1. Antoni D., Zverlov V.V., Schwarz W.H. Biofuels from microbes. Appl. Microbiol. Biotechnol. 2007, 77:23-35.
2. Kröber M., Bekel T., Diaz N.N., Goesmann A., Jaenicke S., Krause L., Miller D., Runte K.J., Viehöver P., Pühler A., Schlüter A. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J.Biotechnol. 2009, 142:38-49.
3. El-Mashad H.M., Zhang R. Biogas production from co-digestion of dairy manure and food waste. Bioresour. Technol. 2010, 101:4021-4028.
4. Karakashev D., Batstone D.J., Angelidaki I. Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors. Appl. Environ. Microbiol. 2005, 71:331-338.
5. Goberna M., Insam H., Franke-Whittle I.H. Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor. Appl. Environ. Microbiol. 2009, 75:2566-2572.
6. Krause L., Diaz N.N., Edwards R.A., Gartemann K.H., Krömeke H., Neuweger H., Pühler A., Runte K.J., Schlüter A., Stoye J., other 3 authors Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J.Biotechnol. 2008, 136:91-101.
7. Karlsson A., Einarsson P., Schnürer A., Sundberg C., Ejlertsson J., Svensson B.H. Impact of trace element addition on degradation efficiency of volatile fatty acids, oleic acid and phenyl acetate and on microbial populations in a biogas digester. J.Biosci. Bioeng. 2012, 114:446-452.
8. Wirth R., Kovács E., Maróti G., Bagi Z., Rákhely G., Kovács K.L. Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnol. Biofuels 2012, 5:1-16.
9. Qiao J.T., Qiu Y.L., Yuan X.Z., Shi X.S., Xu X.H., Guo R.B. Molecular characterization of bacterial and archaeal communities in a full-scale anaerobic reactor treating corn straw. Bioresour. Technol. 2013, 143:512-518.
10. Ziganshin A.M., Liebetrau J., Pröter J., Kleinsteuber S. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl. Microbiol. Biotechnol. 2013, 97:5161-5174.
11. Luton P.E., Wayne J.M., Sharp R.J., Riley P.W. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 2002, 148:3521-3530.
12. Steinberg L.M., Regan J.M. Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Appl. Environ. Microbiol. 2008, 74:6663-6671.
13. Hunger S., Schmidt O., Hilgarth M., Horn M.A., Kolb S., Conrad R., Drake H.L. Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. Appl. Environ. Microbiol. 2011, 77:3773-3785.
14. Nikolausz M., Walter R.F., Sträuber H., Liebetrau J., Schmidt T., Kleinsteuber S., Bratfisch F., Günther U., Richnow H.H. Evaluation of stable isotope fingerprinting techniques for the assessment of the predominant methanogenic pathways in anaerobic digesters. Appl. Microbiol. Biotechnol. 2013, 97:2251-2262.
15. Shima S., Thauer R.K. Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic Archaea. Curr. Opin. Microbiol. 2005, 8:643-648.
16. Ziganshin A.M., Schmidt T., Scholwin F., Il'inskaya O.N., Harms H., Kleinsteuber S. Bacteria and archaea involved in anaerobic digestion of distillers grains with solubles. Appl. Microbiol. Biotechnol. 2011, 89:2039-2052.
17. Abdo Z., Schüette U.M., Bent S.J., Williams C.J., Forney L.J., Joyce P. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ. Microbiol. 2006, 8:929-938.
18. Tang Y.Q., Ji P., Hayashi J., Koike Y., Wu X.L., Kida K. Characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding. Appl. Microbiol. Biotechnol. 2011, 91:1447-1461.
19. Koch C., Fetzer I., Schmidt T., Harms H., Muller S. Monitoring functions in managed microbial systems by cytometric bar coding. Environ. Sci. Technol. 2013, 47:1753-1760.
20. Riviere D., Desvignes V., Pelletier E., Chaussonnerie S., Guermazi S., Weissenbach J., Li T., Camacho P., Sghir A. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J. 2009, 3:700-714.
21. Lawson P.A., Song Y., Liu C., Molitoris D.R., Vaisanen M.L., Collins M.D., Finegold S.M. Anaerotruncus colihominis gen. nov., sp. nov., from human faeces. Int. J. Syst. Evol. Microbiol. 2004, 54:413-417.
22. Liu F.H., Wang S.B., Zhang J.S., Zhang J., Yan X., Zhou H.K., Zhao G.P., Zhou Z.H. 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. 2009, 106:952-966.
23. Harms C., Schleicher A., Collins M.D., Andreesen J.R. Tissierella creatinophila sp. nov., a gram-positive, anaerobic, non-spore-forming, creatinine-fermenting organism. Int. J. Syst. Bacteriol. 1998, 48:983-993.
24. Chen S., Niu L., Zhang Y. Saccharofermentans acetigenes gen. nov., sp. nov., an anaerobic bacterium isolated from sludge treating brewery wastewater. Int. J. Syst. Evol. Microbiol. 2010, 60:2735-2738.
25. Lynd L.R., Weimer P.J., van Zyl W.H., Pretorius I.S. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 2002, 66:506-577.
26. Fontes C.M., Gilbert H.J. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu. Rev. Biochem. 2010, 79:655-681.
27. Zverlov V.V., Hiegl W., Köck D.E., Kellermann J., Köllmeier T., Schwarz W.H. Hydrolytic bacteria in mesophilic and thermophilic degradation of plant biomass. Eng. Life Sci. 2010, 10:528-536.
28. Liu J., Wu W., Chen C., Sun F., Chen Y. Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems. Appl. Microbiol. Biotechnol. 2011, 91:1659-1675.
29. Li H., Shen T.T., Wang X.L., Lin K.F., Liu Y.D., Lu S.G., Gu J.D., Wang P., Lu Q., Du X.M. Biodegradation of perchloroethylene and chlorophenol co-contamination and toxic effect on activated sludge performance. Bioresour. Technol. 2013, 137:286-293.
30. Li A., Chu Y., Wang X., Ren L., Yu J., Liu X., Yan J., Zhang L., Wu S., Li S. Apyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol. Biofuels 2013, 6:1-17.
31. Nunoura T., Oida H., Miyazaki J., Miyashita A., Imachi H., Takai K. Quantification of mcrA by fluorescent PCR in methanogenic and methanotrophic microbial communities. FEMS Microbiol. Ecol. 2008, 64:240-247.
32. Yamamoto N., Asano R., Yoshii H., Otawa K., Nakai Y. Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis. Appl. Microbiol. Biotechnol. 2011, 90:1501-1510.
33. Zinder S.H., Sowers K.R., Ferry J.G. Methanosarcina thermophila sp. nov., a thermophilic, acetotrophic, methane-producing bacterium. Int. J. Syst. Bacteriol. 1985, 35:522-523.
34. T and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-761T. Int. J. Syst. Bacteriol. 1991, 41:267-274.
35. Zhilina T.N., Zavarzin G.A. Methanosarcina vacuolata sp. nov. a vacuolated Methanosarcina. Int. J. Syst. Bacteriol. 1987, 37:281-283.
36. Simankova M.V., Parshina S.N., Tourova T.P., Kolganova T.V., Zehnder A.J., Nozhevnikova A.N. Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments. Syst. Appl. Microbiol. 2001, 24:362-367.
37. Elberson M.A., Sowers K.R. 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. 1997, 47:1258-1261.
38. Sowers K.R., Baron S.F., Ferry J.G. Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl. Environ. Microbiol. 1984, 47:971-978.
39. Zellner G., Messner P., Winter J., Stackebrandt E. Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in north-Sumatra, Indonesia. Int. J. Syst. Bacteriol. 1998, 48:1111-1117.
40. Romesser J.A., Wolfe R.S., Mayer F., Spiess E., Walther-Mauruschat A. Methanogenium, a new genus of marine methanogenic bacteria, and characterization of Methanogenium cariaci sp. nov. and Methanogenium marisnigri sp. nov. Arch. Microbiol. 1979, 121:147-153.
41. Kendall M.M., Wardlaw G.D., Tang C.F., Bonin A.S., Liu Y., Valentine D.L. Diversity of archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov. Appl. Environ. Microbiol. 2007, 73:407-414.
42. Roussel E.G., Sauvadet A.L., Allard J., Chaduteau C., Richard P., Cambon Bonavita M.A., Chaumillon E. Archaeal methane cycling communities associated with gassy subsurface sediments of Marennes-Oléron bay (France). Geomicrobiol. J. 2009, 26:31-43.
43. Newberry C.J., Webster G., Cragg B.A., Parkes R.J., Weightman A.J., Fry J.C. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 2004, 6:274-287.
44. Blotevogel K.H., Fischer U. Transfer of Methanococcus frisius to the genus Methanosarcina as Methanosarcina frisia comb. nov. Int. J. Syst. Bacteriol. 1989, 39:91-92.
45. Zellner G., Alten C., Stackebrandt E., Conway de Macario E., Winter J. Isolation and characterization of Methanocorpusculum parvum, gen. nov., spec. nov., a new tungsten requiring, coccoid methanogens. Arch. Microbiol. 1987, 147:13-20.
46. Denman S.E., Tomkins N.W., McSweeney C.S. Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol. Ecol. 2007, 62:313-322.
47. Miller T.L., Wolin M.J., de Macario E.C., Macario A.J.L. Isolation of Methanobrevibacter smithii from human feces. Appl. Environ. Microbiol. 1982, 43:227-232.