Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

Journal of Biotechnology

Volumn 136, Issue 1-2, 2008, Pages 91-101

  Krause, Lutz ^a,b   Diaz, Naryttza N ^a   Edwards, Robert A ^c,d,e   Gartemann, Karl Heinz ^a   Krömeke, Holger ^a   Neuweger, Heiko ^a   Pühler, Alfred ^a   Runte, Kai J ^a   Schlüter, Andreas ^a   Stoye, Jens ^a   Szczepanowski, Rafael ^a   Tauch, Andreas ^a   Goesmann, Alexander ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b NESTLÉ RESEARCH CENTER   (Switzerland)

^c Center for Microbial Sciences   (United States)

^d San Diego State University   (United States)

^e ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Anaerobic food chain; Biofuel; Biogas reactor; Environmental sample; Maize silage; Metagenome; Methane production; Pyrosequencing

Indexed keywords

MANURES; METHANE; NUCLEIC ACIDS; ORGANIC ACIDS;

ANAEROBIC FOOD CHAIN; ARCHAEA; BIOFUEL; BIOGAS REACTOR; CHICKEN MANURE; ENVIRONMENTAL SAMPLE; FIRMICUTES; GENE CONTENT; GREEN RYE; MAIZE SILAGE; METAGENOME; METHANE PRODUCTION; METHANOGENIC ARCHAEA; MICROBIAL COMMUNITIES; OPERATIONAL TAXONOMIC UNITS; PYROSEQUENCING; TAXONOMIC COMPOSITION;

BIOGAS;

BIOGAS; CARBON DIOXIDE; DEUTERIUM; GLYCOSIDASE;

ARTICLE; BACTERIUM ISOLATION; CLOSTRIDIALES; CONTROLLED STUDY; DNA SEQUENCE; FIRMICUTES; GENETIC ANALYSIS; METHANOMICROBIALES; MICROBIAL COMMUNITY; MICROBIAL GENETICS; NONHUMAN; PRIORITY JOURNAL; REACTOR; TAXONOMY;

ARCHAEA; BASE SEQUENCE; BIOREACTORS; CHROMOSOME MAPPING; GENOME, ARCHAEAL; METHANE; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

CLOSTRIDIA; CLOSTRIDIALES; FIRMICUTES; METHANOCULLEUS; METHANOMICROBIALES; OTUS; SECALE CEREALE; ZEA MAYS;

EID: 49949089661     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2008.06.003     Document Type: Article

References (31)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman J.D. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S., Eppig J.T., Harris M.A., Hill D.P., Kasarskis L.I.-T.A., Lewis S., Matese J.C., Ringwald J.E.R.M., Rubin G.M., and Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 (2000) 25-29
3. Bagi Z., Acs N., Bálint B., Horváth L., Dobó K., Perei K.R., Rákhely G., and Kovács K.L. Biotechnological intensification of biogas production. Appl. Microbiol. Biotechnol. 76 (2007) 473-482
4. Chao A. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11 (1984) 265-270
5. Drake H.L., and Daniel S.L. Physiology of the thermophilic acetogen Moorella thermoacetica. Res. Microbiol. 155 (2004) 869-883
6. Finn R.D., Tate J., Mistry J., Coggill P.C., Sammut S.J., Hotz H.-R., Ceric G., Forslund K., Eddy S.R., Sonnhammer E.L.L., and Bateman A. The Pfam protein families database. Nucleic Acids Res. 36 (2008) D281-D288
7. Gold N.D., and Martin V.J.J. Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis. J. Bacteriol. 189 (2007) 6787-6795
8. Hughes J.B., Hellmann J.J., Ricketts T.H., and Bohannan B.J. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67 (2001) 4399-4406
9. Klocke M., Mähnert P., Mundt K., Souidi K., and Linke B. Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. Syst. Appl. Microbiol. 30 (2007) 139-151
10. Kosaka T., Uchiyama T., Ishii S.-i., Enoki M., Imachi H., Kamagata Y., Ohashi A., Harada H., Ikenaga H., and Watanabe K. Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. J. Bacteriol. 188 (2006) 202-210
11. Krause L., Diaz N.N., Goesmann A., Kelley S., Nattkemper T.W., Rohwer F., Edwards R.A., and Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 36 (2008) 2230-2239
12. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar B.A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüssmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., and Schleifer K.H. ARB: a software environment for sequence data. Nucleic Acids Res. 32 (2004) 1363-1371
13. Lynd L.R., Weimer P.J., van Zyl W.H., and Pretorius I.S. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 66 (2002) 506-577
14. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L.I., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
15. McInerney M.J., Bryant M.P., Hespell R.B., and Costerton J.W. Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl. Environ. Microbiol. 41 (1981) 1029-1039
16. Nielsen H.B., Mladenovska Z., and Ahring B.K. Bioaugmentation of a two-stage thermophilic (68 degrees C/55 degrees C) anaerobic digestion concept for improvement of the methane yield from cattle manure. Biotechnol. Bioeng. 97 (2007) 1638-1643
17. Petitdemange E., Caillet F., Giallo J., and Gaudin C. Clostridium cellulolyticum sp. nov., a cellulolytic mesophilic species from decayed grass. Int. J. Syst. Bacteriol. 34 (1984) 155-159
18. Rastogi G., Ranade D.R., Yeole T.Y., Patole M.S., and Shouche Y.S. Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes. Bioresour. Technol. 99 (2008) 5317-5326
19. Schink B. Syntrophic associations in methanogenic degradation. Prog. Mol. Subcell. Biol. 41 (2006) 1-19
20. Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61 (1997) 262-280
21. Schlüter A., Bekel T., Diaz N.N., Dondrup M., Eichenlaub R., Gartemann K.-H., Krahn I., Krause L., Krömeke H., Kruse O., Mussgnug J.H., Neuweger H., Niehaus K., Pühler A., Runte K.J., Szczepanowski R., Tauch A., Tilker A., Viehöver P., and Goesmann A. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J. Biotechnol. 136 (2008) 77-90
22. Seedorf H., Fricke W.F., Veith B., Brüggemann H., Liesegang H., Strittmatter A., Miethke M., Buckel W., Hinderberger J., Li F., Hagemeier C., Thauer R.K., and Gottschalk G. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 2128-2133
23. Shimizu T., Ohtani K., Hirakawa H., Ohshima K., Yamashita A., Shiba T., Ogasawara N., Hattori M., Kuhara S., and Hayashi H. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 996-1001
24. Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse S.M., Neal P.R., Arrieta J.M., and Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". PNAS 103 (2006) 12115-12120
25. Sokolova T.G., González J.M., Kostrikina N.A., Chernyh N.A., Slepova T.V., Bonch-Osmolovskaya E.A., and Robb F.T. Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park. Int. J. Syst. Evol. Microbiol. 54 (2004) 2353-2359
26. Thauer R.K. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. Microbiology 144 Pt 9 (1998) 2377-2406
27. Tatusov R.L., Koonin E.V., and Lipman D.J. A genomic perspective on protein families. Science 278 (1997) 631-637
28. Wang Q., Garrity G.M., Tiedje J.M., and Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73 (2007) 5261-5267
29. Warnick T.A., Methé B.A., and Leschine S.B. Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. Int. J. Syst. Evol. Microbiol. 52 (2002) 1155-1160
30. Wiegel J., Mothershed C.P., and Puls J. Differences in xylan degradation by various noncellulolytic thermophilic anaerobes and Clostridium thermocellum. Appl. Environ. Microbiol. 49 (1985) 656-659
31. Wu M., Ren Q., Durkin A.S., Daugherty S.C., Brinkac L.M., Dodson R.J., Madupu R., Sullivan S.A., Kolonay J.F., Haft D.H., Nelson W.C., Tallon L.J., Jones K.M., Ulrich L.E., Gonzalez J.M., Zhulin I.B., Robb F.T., and Eisen J.A. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. 1 (2005) e65