Isolation and differentiation of methanogenic Archaea from mesophilic corn-fed on-farm biogas plants with special emphasis on the genus Methanobacterium

Applied Microbiology and Biotechnology

Volumn 98, Issue 12, 2014, Pages 5719-5735

  Stantscheff, R ^a   Kuever, J ^b   Rabenstein, A ^b   Seyfarth, K ^a   Droge S ^c   Konig H ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

^b UNIVERSITY OF BREMEN   (Germany)

^c Test and Research Institute Pirmasens eV   (Germany)

Author keywords

ARDRA; DGGE; Isolation and cultivation; MALDI TOF; Methanobacterium; On farm biogas plants; SAPD PCR

Indexed keywords

BIOGAS; CULTIVATION; ELECTROPHORESIS; MASS SPECTROMETRY; RNA;

ARDRA; BIOGAS PLANTS; DGGE; MALDI-TOF; METHANOBACTERIUM; SAPD-PCR;

POLYMERASE CHAIN REACTION;

BIOGAS; RNA 16S; RNA 23S; ARCHAEAL DNA; BIOFUEL; METHANE; RIBOSOME DNA;

BIOGAS; CATTLE; ELECTROKINESIS; GEL; METHANOGENIC BACTERIUM; PHYLOGENETICS; POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATION; CATTLE; DENATURING GRADIENT GEL ELECTROPHORESIS; GENE AMPLIFICATION; GENE LIBRARY; GENE SEQUENCE; GERMANY; MAIZE; MANURE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MESOPHILIC BACTERIUM; METHANOBACTERIUM; METHANOCULLEUS BOURGENSIS; METHANOCULLEUS CONCILII; METHANOCULLEUS FORMICICUM; METHANOCULLEUS MAZEI; METHANOGENIC ARCHAEON; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; SILAGE; ANIMAL; ARCHAEON; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; DOMESTIC ANIMAL; GENETICS; MATRIX-ASSISTED LASER DESORPTION-IONIZATION MASS SPECTROMETRY; METABOLISM; MOLECULAR GENETICS; MOLECULAR TYPING;

GERMANY; RHINELAND-PALATINATE;

BOS; METHANOBACTERIUM; METHANOBACTERIUM FORMICICUM; METHANOCULLEUS BOURGENSIS; METHANOSAETA CONCILII; METHANOSARCINA MAZEI; ZEA MAYS;

ANIMALS; ANIMALS, DOMESTIC; ARCHAEA; BIODIVERSITY; BIOFUELS; CLUSTER ANALYSIS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA, ARCHAEAL; DNA, RIBOSOMAL; GERMANY; METHANE; MOLECULAR SEQUENCE DATA; MOLECULAR TYPING; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84903815874     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5652-4     Document Type: Article

References (78)

1. Akarsubasi AT, Ince O, Oz NA, Kirdar B, Ince BK (2006) Evaluation of performance, acetoclastic methanogenic activity and archaeal composition of full-scale UASB reactors treating alcohol distillery wastewaters. Process Biochem 41:28-35 (Pubitemid 41785579)
2. Angenent LT, Karim K, Al-Dahhan MH, Wrenn BA, Domíguez-Espinosa R (2004) Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol 22:477-485 (Pubitemid 39141162)
3. Attebery HR, Finegold SM (1969) Combined screw-cap and rubberstopper closure for Hungate tubes (pre-reduced anaerobically sterilized roll tubes and liquid media). Appl Microbiol 18:558-561
4. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43:260-296 (Pubitemid 9231879)
5. Bauer C, Korthals M, Gronauer A, Lebuhn M (2008) Methanogens in biogas production from renewable resources-a novel molecular population analysis approach. Water Sci Technol 58:1433-1439
6. Bergmann I, Nettmann E, Mundt K, Klocke M (2010) Determination of methanogenic Archaea abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis. Can J Microbiol 56:440-444
7. Blättel V, Petri A, Rabenstein A, Kuever J, König H (2008) Differentiation of species of the genus Saccharomyces using biomolecular fingerprinting methods. Appl Microbiol Biotechnol 97:4597-4606
8. Böck A, Kandler O (1985) Antibiotic sensitivity of archaebacteria. In: Woese CR, Wolfe RS (eds) The Bacteria-a treatise on structure and function, vol VIII, Archaebacteria. Academic Press, New York, pp 525-544
9. Cheeseman P, Toms-Wood A, Wolfe RS (1972) Isolation and properties of a fluorescent compound, factor 420, from Methanobacterium strain M.o.H. J Bacteriol 112:527-531
10. Cherkaoui A, Hibbs J, Emonet S, Tangomo M, Girard M, Francois P, Schrenzel J (2010) Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J Clin Microbiol 47:1169-1175
11. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259-2261 (Pubitemid 350031697)
12. Collins G, Kavanagh S, McHugh S, Connaughton S, Kearney A, Rice O, Carrigg C, Scully C, Bhreathnach N, Mahony T, Madden P, Enright AM, O'Flaherty V (2006) Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments. J Environ Sci Health ATox Hazard Subst Environ Eng 41:897-922 (Pubitemid 43786033)
13. Doan NTL, Van Hoorde K, Cnockaert M, De Brandt E, Aerts M, Le Thanh B, Vandamme P (2012) Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam. Lett Appl Microbiol 55:265-273
14. DSMZ (2007a) Medium number 287: Methanogenium olentangyi medium. In: Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. List of recommended media for microorganisms. http://www.dsmz.de/microorganisms/ medium/pdf/DSMZ-Medium287.pdf. Accessed 27 July 2013
15. DSMZ (2007b)Mediumnumber 318: Methanosarcina (BCYT)medium. In: Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. List of recommended media for microorganisms. http://www.dsmz.de/microorganisms/ medium/pdf/DSMZ- Medium318.pdf. Accessed 27 July 2013
16. DSMZ (2007c) Medium number 334: Methanothrix medium. In: Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. List of recommended media for microorganisms. http://www.dsmz.de/microorganisms/medium/pdf/ DSMZ-Medium334.pdf. Accessed 27 July 2013
17. DSMZ (2007d) Medium number 332: Methanogenium bourgense medium. In: Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. List of recommended media for microorganisms http://www.dsmz.de/microorganisms /medium/pdf/DSMZ- Medium332.pdf. Accessed 27 July 2013
18. European Commission for Energy (2007) Communication from the commission to the council and the European parliament-renewable energy road map. Renewable energies in the 21st century: building a more sustainable future. Commissions of the European communities, Brussels 10.01.2007 COM(2006) 848 final, Belgium. Published online: http://eur-lex.europa.eu/LexUriServ/LexUriServ. do?uri=COM: 2006:0848:FIN:EN:PDF
19. Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci U S A 74:4537-4541 (Pubitemid 8225159)
20. Fröhlich J, Pfannebecker J (2007) Species-independent DNA fingerprint analysis with primers derived from the NotI identification sequence. Patent number: EP2027285 (A1)
21. Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R (1997) Molecular microbial diversity of an anaerobic digestor as determined by smallsubunit rDNA sequence analysis. Appl Environ Microbiol 63:2802-2813 (Pubitemid 27292879)
22. Hattori S (2008) Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ 23:118-127
23. Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y (2006) Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Appl Environ Microbiol 72:1623-1630 (Pubitemid 43271278)
24. Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, Jünemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Pühler A, Schlüter A, Goesmann A (2011) Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS ONE. doi:10.1371/0014519
25. Jetten MSM, Stams AJM, Zehnder AJB (1992) Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiol Lett 88:181-198
26. Karakashev D, Batstone DJ, Angelidaki I (2005) Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors. Appl Environ Microbiol 71:331-338 (Pubitemid 40116286)
27. Kaster AK, Moll J, Parey K, Thauer RK (2010) Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic Archaea. Proc Natl Acad Sci U S A 108:2981-2986
28. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716-721
29. Klocke M, Mähnert P, Mundt K, Souidi K, Linke B (2007) Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. System Appl Microbiol 30:139-151 (Pubitemid 46217841)
30. Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, Linke B (2008) Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass. System Appl Microbiol 31:190-205
31. König H (1993) Methanogens. In: Sahm H (ed) Biotechnology, vol 1, Biological fundamentals. Weinheim, Wiley, pp 249-264
32. König H (2009) Biology of methanogenic Archaea. In: Chauhan AK, Varma A (eds) A text book of molecular biotechnology, vol 1. I. K. International Publishing House Pvt. Ltd., New Delhi, pp 915-933
33. Krader P, Emerson D (2004) Identification of Archaea and some extremophilic bacteria using matrix-assisted laser desorption/ ionization time-of-flight (MALDI-TOF) mass spectrometry. Extremophiles 8:259-268 (Pubitemid 40882687)
34. Krakat N, Westphal A, Schmidt S, Scherer P (2010a) Anaerobic digestion of renewable biomass: thermophilic temperature governs methanogen population dynamics. Appl Environ Microbiol 76:1842-1850
35. Krakat N, Westphal A, Satke K, Schmidt S, Scherer P (2010b) The microcosm of a biogas fermenter: comparison of moderate hyperthermophilic (60 ° C) with thermophilic (55 ° C) conditions. Eng Life Sci 10:520-527
36. Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol 142:38-49
37. Laukenmann S, Polag D, Heuwinkel H, Greule M, Gronauer A, Lelieveld J, Keppler F (2010) Identification of methanogenic pathways in anaerobic digesters using stable carbon isotopes. Eng Life Sci 10:509-514
38. Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Ann N Y Acad Sci 1125: 171-189 (Pubitemid 351451164)
39. Marklein G, Josten M, Klanke U, Müller E, Horré R, Maier T, Wenzel T, Kostrzewa M, Bierbaum G, Hoerauf A, Sahl H-G (2009) Matrixassisted laser desorption ionization-time of flight mass spectrometry for fast reliable identification of clinical yeast isolates. J Clin Microbiol 47:2912-2917
40. Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A (2012) Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2T, isolated from a sewage sludge digester. J Bacteriol 194:5487-5488
41. Maus I, Wibberg D, Stantscheff R, Cibis K, Eikmeyer FG, König H, Pühler A, Schlüter A (2013) Complete genome sequence of the hydrogenotrophic archaeon Methanobacterium sp. Mb1, isolated from a production-scale biogas plant. J Biotechnol. doi:10.1016/j.jbiotec.2013.10.013
42. McMahon KD, Stroot PG, Mackie RI, Raskin L (2001) Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions - II: microbial population dynamics. Water Res 35:1817-1827 (Pubitemid 32201491)
43. Meher KK, Ranade DR (1993) Isolation of propionate degrading bacterium in co-culture with a methanogen from a cattle dung biogas plant. J Biosci 18:271-277
44. Meher KK, Kadam P, Ranade DR (1996) Short communication: butyratedegrading syntrophic culture from an anaerobic digester treating cattle waste. World J Microbiol Biotechnol 12:105-106
45. Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I, Iwen P, Dunn J, Hall G, Wilson D, Lasala P, Kostrzewa M, Harmsen D (2008) Evaluation of matrix-assisted laser desorption ionization-time- of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol 46:1946-1954 (Pubitemid 351831825)
46. Miller LT, Wolin MJ (1974) Serum bottle modification of the Hungate technique for cultivating obligate anaerobes. Appl Microbiol 27:985-987
47. Munk B, Bauer C, Gronauer A, Lebuhn M (2010) Population dynamics of methanogens during acidification of biogas fermenters fed with maize silage. Eng Life Sci 10:496-508
48. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturating gradient gel electrophoresis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700 (Pubitemid 23072343)
49. Nettmann E, Bergmann I, Mundt K, Linke B, Klocke M (2008) Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis. J Appl Microbiol 105:1835-1850
50. Nettmann E, Bergmann I, Pramschüfer S, Mundt K, Plogsties V, Herrmann C, Klocke M (2010) Polyphasic analyses ofmethanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 76:2540-2548
51. Park MJ, Job JH, Park D, Lee DS, Park JM (2010) Comprehensive study on a two-stage anaerobic digestion process for the sequential production of hydrogen and methane from cost-effectivemolasses. Int J Hydrogen Energy 35:6194-6202
52. Petri A, Pfannebecker J, Fröhlich J, König H (2013) Fast identification of wine related lactic acid bacteria by multiplex PCR. Food Microbiol 33:48-54
53. Pfannebecker J, Fröhlich J (2008) Use of a species-specific multiplex PCR for the identification of pediococci. Int J Food Microbiol 128:288-296
54. 13C carbon isotopes. Isotopes Environ Health Stud 49:365-377
55. 2 emissions from fuel combustion. Energy Policy 35: 5938-5952
56. Ranade DR, Gore JA, Godbole SH (1980) Methanogenic organisms from fermenting slurry of the Gobar gas plant. Curr Sci 49:395-397
57. Rouvière PE, Wolfe RS (1988) Novel biochemistry of methanogenesis. J Biol Chem 263:7913-7916
58. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
59. Sawayama S, Tsukahara K, Yagishita T (2006) Phylogenetic description of immobilized methanogenic community using real-time PCR in a fixed-bed anaerobic digester. Bioresour Technol 97:69-76 (Pubitemid 41265790)
60. Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61:262-280
61. Schnürer A, Zellner G, Svensson BH (1999) Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors. FEMS Microbiol Ecol 29:249-261 (Pubitemid 29313312)
62. Sebastian P, Herr P, Fischer U, König H (2011) Molecular identification of lactic acid bacteria occurring in must and wine. S Afr J Enol Vitic 32:300-309
63. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849 (Pubitemid 24315169)
64. Steinhaus B, Garcia ML, Shen AQ, Angenent LT (2007) A portable anaerobic microbioreactor reveals optimum growth conditions for the methanogen Methanosaeta concilii. Appl Environ Microbiol 73:1653-1658 (Pubitemid 46417892)
65. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030-11035 (Pubitemid 38989579)
66. 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 28:2731-2739
67. Tatsuoka N, Mohammed N, Mitsumori M, Tajima K, Hara K, Kurihara M, Itabashi H (2007) Analysis of methanogens in the bovine rumen by polymerase chain reaction single-strand conformation polymorphism. Animal Sci J 78:512-518 (Pubitemid 47373586)
68. Thauer RK (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144:2377-2406
69. Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R (2008) Methanogenic Archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6:579-591
70. Tilche A, Galatola M (2008) The potential of bio-methane as bio-fuel/bioenergy for reducing greenhouse gas emissions; a qualitative assessment for Europe in a life cycle perspective. Water Sci Technol 57:1683-1692 (Pubitemid 351999478)
71. Westerholm M, Dolfing J, Sherry A, Gray ND, Head IM, Schnürer A (2011) Quantification of syntrophic acetate-oxidizing microbial communities in biogas processes. Environ Microbiol Rep 3:500-505
72. Wirth R, Kovács E, Maróti G, Bagi Z, Rákhely G, Kovács KL (2012) Characterization of a biogas-producing microbial community by shortread next generation DNA sequencing. Biotechnol Biofuels 5:41
73. Wright ADG, Pimm C (2003) Improved strategy for presumptive identification of methanogens using 16S riboprinting. J Microbiol Methods 55:337-349
74. Wu W, Jain MK, Zeikus JG (1996) Formation of fatty acid-degrading, anaerobic granules by defined species. Appl Environ Microbiol 62:2037-2044 (Pubitemid 26168998)
75. Yang Y, Tada C, Miah MS, Tsukahara K, Yagishita T, Sawayama S (2004) Influence of bed materials on methanogenic characteristics and immobilized microbes in anaerobic digester. Mater Sci Eng C Mater Biol Appl 24:413-419 (Pubitemid 38464323)
76. Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative realtime polymerase chain reaction. Biotechnol Bioeng 89:670-679 (Pubitemid 40470355)
77. Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158:248-258
78. Zverlov VV, Hiegl W, Köck DE, Kellermann J, Köllmeier T, Schwarz WH (2010) Hydrolytic bacteria in mesophilic and thermophilic degradation of plant biomass. Eng Life Sci 10:528-536