Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants

Applied and Environmental Microbiology

Volumn 76, Issue 8, 2010, Pages 2540-2548

  Nettmann, E ^a,b   Bergmann, I ^a,b   Pramschufer S ^a,c   Mundt, K ^a   Plogsties, V ^a   Herrmann, C ^a,d   Klocke, M ^a  

^a LEIBNIZ INSTITUTE FOR AGRICULTURAL ENGINEERING AND BIOECONOMY ATB   (Germany)

^b TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^c BEUTH UNIVERSITY OF APPLIED SCIENCES   (Germany)

^d HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ARCHAEAL; ARCHAEAL CELLS; AVERAGE VALUES; BIOGAS PLANTS; BIOGAS REACTOR; FISH ANALYSIS; FLUORESCENCE IN SITU HYBRIDIZATION; HIGH CONCENTRATION; LIQUID MANURE; METHANE FORMATION; METHANOGENESIS; METHANOGENIC ARCHAEA; METHANOSAETACEAE; MICROBIAL CONSORTIA; NUCLEOTIDE SEQUENCES; POLYPHASIC; QUANTITATIVE REAL TIME PCR; RENEWABLE RAW MATERIALS; RRNA GENES;

FISH; FLUORESCENCE MICROSCOPY; MANURES; MEATS; METHANATION; METHANE; RENEWABLE ENERGY RESOURCES; RNA;

BIOGAS;

AMMONIA; ARCHAEAL DNA; ARCHAEAL RNA; BIOFUEL; HYDROGEN; METHANE; RIBOSOME DNA; RNA 16S;

AMMONIA; BIOGAS; BIOREACTOR; FLUORESCENCE; GENETIC ANALYSIS; HYBRIDIZATION; MANURE; MICROBIAL COMMUNITY; PROKARYOTE; RENEWABLE RESOURCE; SUBSTRATE;

ARCHAEBACTERIUM; ARTICLE; BIOREACTOR; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA GENE; SEQUENCE HOMOLOGY;

AMMONIA; ARCHAEA; BIOFUELS; BIOREACTORS; DNA, ARCHAEAL; DNA, RIBOSOMAL; GENES, RRNA; HYDROGEN; IN SITU HYBRIDIZATION, FLUORESCENCE; METHANE; MOLECULAR SEQUENCE DATA; RNA, ARCHAEAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARCHAEA; METHANOCULLEUS; METHANOMICROBIALES; METHANOSAETACEAE;

EID: 77950562179     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01423-09     Document Type: Article

References (65)

1. Ahring, B. K. 2003. Perspectives for anaerobic digestion. Adv. Biochem. Eng. Biotechnol. 81:1-30.
2. Amann, R. L, B. J. Binder, R. J. Olson, S. W. Chrishalm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
3. Angelidaki, I., and B. K. Ahring. 1993. Thermophilic anaerobic digestion of livestock waste: the effect of ammonia. Appl. Microbiol. Biotechnol. 38:560-564.
4. Anthonisen, A. C, R. C. Loehr, T. B. S. Prakasam, and E. G. Srinath. 1976. Inhibition of nitrification by ammonia and nitrous acid. J. Water Pollut. Control Fed. 48:835-852.
5. Balk, M., J. Weijma, and A. J. M. Stams. 2002. Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilick anaerobic reactor. Int. J. Syst. Evol. Microbiol. 52:1361-1368.
6. Batstone, D. J., J. Keller, I. Angelidaki, S. V. Kalyuzhnyi, S. G. Pavlostathis, A. Rozzi, W. T. M. Sanders, H. Siegrist, and V. A. Vavilin. 2002. Anaerobic digestion model no. 1, p.1-77. IWA scientific and technical report no. 13. IWA Publishing, London, United Kingdom.
7. Bauer, C, M. Korthals, A. Gronauer, and M. Lebuhn. 2008. Methanogens in biogas production from renewable resources-a novel molecular population analysis approach. Water Sci. Technol. 58:1433-1439.
8. Böckelmann, U., U. Szewzyk, and E. Grohmann. 2003. A new enzymatic method for the detachment of particle associated soil bacteria. J. Microbiol. Methods 55:201-211.
9. Bundesforschungsanstalt für Landwirtschaft (FAL). 2005. Ergebnisse des Biogas-Messprogramms. Fachagentur für Nachwachsende Rohstoffe e. V. (FNR), Gülzow, Germany.
10. Chan, O. C, P. Claus, P. Casper, A. Ulrich, T. Lueders, and R. Conrad. 2005. Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment. Environ. Microbiol. 7:1139-1149.
11. 11. Chao, A. 1987. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43:783-791. (Pubitemid 18016764)
12. Chao, A., R. L. Chazdon, R. K. Colwell, and T. Shen. 2005. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8:148-159.
13. Chouari, R., D. Le Paslier, P. Daegelen, P. Ginestet, J. Weissenbach, and A. Sghir. 2005. Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ. Microbiol. 7:1104-1115.
14. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443.
15. Collins, G., S. Kavanagh, S. McHugh, S. Connaughton, A. Kearney, O. Rice, C. Carrigg, C. Scully, N. Bhreathnach, T. Mahony, P. Madden, A. Enright, and V. O'Flaherty. 2006. Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments. J. Environ. Sci. Health A Tox. Hazard Subst. Environ. Eng. 41:897-922.
16. Conrad, R. 1999. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiol. Ecol. 28:193-202.
17. Conrad, R., and M. Klose. 2006. Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw. Eur. J. Soil Sci. 57:476-484.
18. Crocetti, G., M. Murto, and L. Bjornsson. 2006. An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescence in situ, hybridisation (FISH). J. Microbiol. Methods 65:194-201.
19. Daims, H., K. Stoecker, and Wagner, M. 2005. Fluorescence in situ hybridisation for the detection of prokaryotes. p. 213-239. In A. M. Osborn and C. J. Smith (ed.), Advanced methods in molecular microbial ecology. BiosGarland, Abingdon, United Kingdom.
20. Denhardt, D. T. 1966. A membran-filter technique for the detection of complementary DNA. Biochem. Biophys. Res. Commun. 23:641-646.
21. Fernandez, A. S., S. Huang, S. Seston, J. Xing, R. F. Hickey, C. S. Criddle, and J. M. Tiedje. 1999. How stable is stable? Function versus community composition. Appl. Environ. Microbiol. 65:3697-3704.
22. Gallert, C, and J. Winter. 1997. Mesophilic and thermophilic anaerobic digestion of source-sorted organic wastes: effect of ammonia on glucose degradation and methane production. Appl. Microbiol. Biotechnol. 48:405-410.
23. Garrity, G. M., and J. G. Holt 2001. Phylum AII. Euryarchaeota, p. 211-345. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol.1. Springer, New York, NY.
24. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
25. Godon, J.-J., E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta. 1997. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63:2802-2813.
26. Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264.
27. Hattori, S. 2008. Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ. 23:118-127.
28. Hofman-Bang, J., D. Zhang, P. Westermann, B. K. Ahring, and L. Raskin. 2003. Molecular ecology of anaerobic reactor systems. Adv. Biochem. Eng. Biotechnol. 81:151-203.
29. Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. M. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
30. Kadam, P. C., and D. R. Boone. 1996. Influence of pH on ammonia accumulation and toxicity in halophilic, methylotrophic methanogens. Appl. Environ. Microbiol. 62:4486-4492.
31. Kamagata, Y., and E. Mikami. 1989. Diversity of acetotrophic methanogens in anaerobic digestion, p. 459-464. In T. Hattori, Y. Ishida, Y. Maruyana, R. Y. Morita, and A. Uccida (ed.), Recent advances in microbial ecology. Japan Scientific Societies Press, Tokyo, Japan.
32. Karakashev, D., D. J. Batstone, and I. Angelidaki. 2005. Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors. Appl. Environ. Microbiol. 71:331-338.
33. Karakashev, D., D. J. Batstone, E. Trably, and I. Angelidaki. 2006. Acetate oxidation is the dominant methanogenic pathway from acetate in the absence of Methanosaetaceae. Appl. Environ. Microbiol. 72:5138-5141.
34. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
35. Klocke, M., E. Nettmann, I. Bergmann, K. Mundt, K. Souidi, J. Mumme, and B. Linke. 2008. Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass. Syst. Appl. Microbiol. 31:190-205.
36. Koster, I. W. 1986. Characteristics of the pH-influenced adaptation of methanogenic sludge to ammonium toxicity. J. Chem. Technol. Biotechnol. 36:445-455.
37. Krause, L., N. N. Diaz, R. A. Edwards, K.-H. Gartemann, H. Krömeke, H. Neuweger, A. Pühler, K. J. Runte, A. Schlüter, J. Stoye, R. Szczepanowski, A. Tauch, A. Goesmann, N. N. Diaz, and R. A. Edwards. 2008. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J. Biotechnol. 136:91-101.
38. Leclerc, M., J.-P. Delgenes, and J.-J. Godon. 2004. Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environ. Microbiol. 6:809-819.
39. 2. Appl. Environ. Microbiol. 54:124-129.
40. Lovley, D. R., and M. J. Klug. 1983. Methanogenesis from methanol and methylamines and acetogenesis from hydrogen and carbon dioxide in the sediments of a eutrophic lake. Appl. Environ. Microbiol. 45:1310-1315.
41. Loy, A., M. Horn, and M. Wagner. 2003. probeBase: an online resource for rRNA-targeted oligonucleotides probes. Nucleic Acids Res. 31:514-516.
42. 2 to methanogenesis in cattle waste at 40 and 60°C. Appl. Environ. Microbiol. 41:1363-1373.
43. McHugh, S., M. Carton, T. Mahony, and V. O'Flaherty. 2003. Methanogenic population structure in a variety of anaerobic bioreactors. FEMS Microbiol. Lett. 219:297-304.
44. 44. Moreira, D. 1998. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acids Res. 26:3309-3310. (Pubitemid 28288935)
45. Nettmann, E., I. Bergmann, K. Mundt, B. Linke, and M. Klocke. 2008. Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis. J. Appl. Microbiol. 105:1835-1850.
46. Oude Elferink, S. J. W. H., R. van Lis, H. G. H. J. Heilig, A. D. L. Akkermans, and A. J. M. Stams. 1998. Detection and quantification of microorganisms in anaerobic bioreactors. Biodegradation 9:169-177.
47. Pielou, E. C. 1966. The measurement of diversity in different types of biological colledions. J. Theor. Biol. 13:131-144.
48. Poggi-Varaldo, H. M., R. Rodríguez-Vázquez, G. Fernánez-Villagómez, and F. Esparza-Gracia. 1997. Inhibition of mesophilic solid-substrate anaerobic digestion by ammonia nitrogen. Appl. Microbiol. Biotechnol. 47:284-291.
49. Raizada, N. 2004. Application of molecular-biological method for optimization of anaerobic reactors. In Berichte aus Wassergüte- und Abfallwirtschaft. Technische Universität München, Garching, Germany.
50. Raskin, L., J. M. Stromley, B. E. Rittmann, and D. Stahl. 1994. Groupspecific 16S ribosomal-RNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
51. Saitou, N., and M. Nei. 1987. The Neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
52. Schnürer, A., and A. Nordberg. 2008. Ammonia, a selective agent for methane production by syntrophic acetate oxidation at mesophilic temperature. Water Sci. Technol. 57:735-740.
53. Schnürer, A., B. Schink, and B. H. Svensson. 1996. Clostridium ultunense sp. nov., a mesophilic bacterium oxidizing acetate in syntrophic association with a hydrogenotrophlc methanogenic bacterium. Int. J. Syst. Bacteriol. 46:1145-1152.
54. Schnürer, A., G. Zellner, and B. H. Svensson. 1999. Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors. FEMS Microbiol. Ecol. 29:249-261.
55. Shannon, C. E., and W. Weaver. 1963. The mathematical theory of communication. University of Illinois Press, Urbana, IL.
56. Solera, R., L. I. Romero, and D. Sales. 2001. Analysis of the methane production in thermophilic anaerobic reactors: use of autofluorescence microscopy. Biotechnol. Lett. 23:1889-1892.
57. Souidi, K., J. Mumme, K. Mundt, E. Nettmann, I. Bergmann, B. Linke, and M. Klocke. 2007. Microbial diversity in a biogas-producing co-fermentation of maize silage and bovine manure. Agrartechnische Forsch. 13:197-205.
58. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics, John Wiley & Sons Ltd., Chichester, England.
59. Stams, A. J., S. J. Oude Elferink, and P. Westermann. 2003. Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria. Adv. Biochem. Eng. Biotechnol. 81:31-56.
60. Steinhaus, B., M. L. Garcia, A. Q. Shen, and L. T. Angenent. 2007. A portable anaerobic microbioreactor reveals optimum growth conditions for the methanogen Methanosaeta concilii. Appl. Environ. Microbiol. 73:1653-1658.
61. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (Mega) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
62. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
63. Winter, J. U., and R. S. Wolfe. 1980. Methane formation from fructose by syntrophic associations of Acetobacterium woodii and different strains of methanogens. Arch. Microbiol. 124:73-79.
64. Yu, Y., J. Kim, and S. Hwang. 2006. Use of real-time FCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol. Bioeng. 93:424-433.
65. Yu, Y., C. Lee, J. Kim, and S. Hwang. 2005. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol. Bioeng. 89:670-679.