In Situ Detection, Isolation, and Physiological Properties of a Thin Filamentous Microorganism Abundant in Methanogenic Granular Sludges: A Novel Isolate Affiliated with a Clone Cluster, the Green Non-Sulfur Bacteria, Subdivision I

Applied and Environmental Microbiology

Volumn 67, Issue 12, 2001, Pages 5740-5749

  Sekiguchi, Yuji ^a,b   Takahashi, Hiroki ^a   Kamagata, Yoichi ^b   Ohashi, Akiyoshi ^a   Harada, Hideki ^a  

^a NAGAOKA UNIVERSITY OF TECHNOLOGY   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RNA 16S;

ANAEROBIC BACTERIUM; ANIMAL; ARTICLE; BIOREACTOR; CHLOROBIUM; CLASSIFICATION; CULTURE MEDIUM; DNA SEQUENCE; GENETICS; IN SITU HYBRIDIZATION; ISOLATION AND PURIFICATION; METABOLISM; METHANOBACTERIALES; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGY; SCANNING ELECTRON MICROSCOPY; SEA URCHIN; SEWAGE;

ANIMAL; BACTERIA, ANAEROBIC; BASE SEQUENCE; BIOREACTORS; CULTURE MEDIA; DNA, RIBOSOMAL; GREEN SULFUR BACTERIA; IN SITU HYBRIDIZATION; METHANOGENS; MICROSCOPY, ELECTRON, SCANNING; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEA URCHINS; SEQUENCE ANALYSIS, DNA; SEWAGE; SUPPORT, NON-U.S. GOV'T; WASTE DISPOSAL, FLUID;

EID: 0035651020     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.12.5740-5749.2001     Document Type: Article

References (58)

1. Alphenaar, P. A. 1994. Anaerobic granular sludge: characterization and factors affecting its functioning, Ph.D. thesis. Wageningen Agricultural University, Wageningen, The Netherlands.
2. Amann, R. I., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
3. Chandler, D. P., F. J. Brockman, T. J. Bailey, and J. K. Fredrickson. 1998. Phylogenetic diversity of Archaea and Bacteria in a deep subsurface pleosol. Microb. Ecol. 36:37-50.
4. Daffonchio, D. D., J. Thaveesri, and W. Verstraete. 1995. Contact angle measurement and cell hydrophobicity of granular sludge from upflow anaerobic sludge bed reactors. Appl. Environ. Microbiol. 61:3676-3680.
5. Daims, H., A. Breul, R. Amann, K.-H. Schleifer, and M. Wagner. 1999 The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22:434-444.
6. Delbes, C., R. Moletta, and J. J. Godon. 2000. Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction-single-strand conformation polymorphism analysis. Environ. Microbiol. 2:506-515.
7. Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
8. Dubourguier, H. C., G. Prensier, and G. Albagnac. 1987. Structure and microbial activities of granular anaerobic sludge, p. 18-41. In G. Lettinga, A. J. B. Zehnder, J. T. C. Grotenhuis, and L. W. Hulshoff Pol (ed.), Granular anaerobic sludge; microbiology and technology. Centre for Agricultural Publishing and Documentation, Wageningen, The Netherlands.
9. Endo, G., and Y. Tohya. 1988. Ecological study on anaerobic sludge bulking caused by filamentous bacterial growth in an anaerobic contact process. Water Sci. Technol. 20:205-211.
10. Felsenstein, J. 1985. Confidence limits of phylogenies: an approach using the bootstrap. Evolution 39:783-791.
11. Grotenhuis, J. T. C., C. M. Plugge, A. J. M. Stams, and A. J. B. Zehnder. 1992. Hydrophobicities and electrophoretic mobilities of anaerobic bacterial isolates from methanogenic granular sludge. Appl. Environ. Microbiol. 58: 1054-1056.
12. Grotenhuis, J. T. C., M. Smit, C. M. Plugge, X. Yuansheng, A. A. M. van Lammeren, A. J. M. Stams, and A. J. B. Zehnder. 1991. Bacteriological composition and structure of granular sludge adapted to different substrate. Appl. Environ. Microbiol. 57:1942-1949.
13. Hiraishi, A. 1992. Direct automated sequencing of 16S rDNA amplitied by polymerase chain reaction from bacterial cultures without DNA purification. Lett. Appl. Microbiol. 15:210-213.
14. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
15. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellow-stone hot spring. J. Bacteriol. 180:366-376.
16. Hulshoff Pol, L. W., K. Heijnekamp, and G. Lettinga. 1988. The selection pressure as a driving force behind the granulation of anaerobic sludge, p. 153. In G. Lettinga, A. J. B. Zehnder, J. T. C. Grotenhuis, and L. W. Hulshoff Pol (ed.), Granular anaerobic sludge; microbiology and technology. Centre for Agricultural Publishing and Documentation, Wageningen, The Netherlands.
17. lmachi, H., Y. Sekiguchi, Y. Kamagata, A. Ohashi, and H. Harada. 2000. Cultivation and in situ detection of a thermophilic bacterium capable of oxidizing propionate in syntrophic association with hydrogenotrophic methanogens in a thermophilic methanogenic granular sludge. Appl. Environ. Microbiol. 66:3608-3615.
18. Kamagata, Y., H. Kawasaki, H. Oyaizu, K. Nakamura, E. Mikami, G. Endo, Y. Koga, and K. Yamasato. 1992. Characterization of three thermophilic strains of Methanothrix ("Methanosaeta") thermophila sp. nov. and rejection of Methanothrix ("Methanosaete") thermoacetophila. Int. J. Syst. Bactcriol. 42:463-468.
19. Kamagata, Y., and E. Mikami. 1991. Isolation and characterization of a novel thermophilic Methanosaeta strain. Int. J. Syst. Bacteriol. 41:191-196.
20. Kamagata, Y., and E. Mikami. 1990. Some characteristics of 2 morphotypes of Methanothrix sochngenii from mesophilic anaerobic digesters. J. Ferment. Bioeng. 70:272-274.
21. Krumholz, L. R., and M. P. Bryant. 1986. Syntrophococcus sucromutans sp. nov. gen. nov. uses carbohydrates as electron donors and formate, methoxymonobenzoids or Methanobrevibacter as electron acceptor systems. Arch. Microbiol. 143:313-318.
22. Lettinga, G. 1995. Anaerobic digestion and wastewater treatment systems. Antonie van Leeuwenhoek 67:3-28.
23. Macario, A. J. L., F. A. Visser, J. B. van Lier, and E. Conway de Macario. 1991. Topography of methanogenic subpopulations in a microbial consortium adapting to thermophilic conditions. J. Gen. Microbiol. 137:2179-2189.
24. MacLeod, F., S. R. Guiot, and J. W. Costerton. 1990. Layered structure of bacterial aggregates produced in an upflow anaerobic sludge bed and filter reactor. Appl. Environ. Microbiol. 56:1598-1607.
25. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denatured gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
26. Phelps, C. D., L. J. Kerkhof, and L. Y. Young. 1998. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol. Ecol. 27:269-279.
27. Raskin, L., J. M. Stromley, B. E. Rittmann, and D. A. Stahl. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
28. Saito, N., and M. Nei. 1987. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
29. Schlötelburg, C., F. von Wintzingerode, R. Hauck, W. Hegemann, and U. B. Göbel. 2000. Bacteria of an anaerobic 1,2-dichloropropane-dechlorinating mixed culture are phylogenetically related to those of other anaerobic dechlorinating consortia. Int. J. Syst. Evol. Microbiol. 50:1505-1511.
30. Schmidt, J. E., and B. K. Ahring. 1996. Granular sludge formation in upflow anaerobic sludge blanket (UASB) reactors. Biotech. Bioeng. 49:229-246.
31. Sekiguchi, Y., Y. Kamagata, and H. Harada. 2001. Recent advances in methane fermentation technology. Curr. Opin. Biotechnol. 12:277-282.
32. Sekiguchi, Y., Y. Kamagata, K. Nakamura, A. Ohashi, and H. Harada. 1999. Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl. Environ. Microbiol. 65: 1280-1288.
33. Sekiguchi, Y., Y. Kamagata, K. Nakamura, A. Ohashi, and H. Harada. 2000. Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int. J. Syst. Evol. Microbiol. 50:771-779.
34. Sekiguchi, Y., Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura. 1998. Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144: 2655-2665.
35. Snaidr, J., R. Amann, I. Huber, W. Ludwig, and K.-H. Schleifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63:2884-2896.
36. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
37. Syutsubo, K., H. Harada, A. Ohashi, and H. Suzuki. 1997. An effective start-up of thermophilic UASB reactor by seeding mesophilically-grown granular sludge. Water Sci. Technol. 36:391-398.
38. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 24:4876-4882.
39. Uemura, S., and H. Harada. 1995. Inorganic composition and microbial characteristics of methanogenic granular sludge grown in a thermophilic upflow anaerobic sludge blanket reactor. Appl. Microbiol. Biotechnol. 43: 358-364.
40. Uemura, S., and H. Harada. 1993. Microbial characteristics of methanogenic sludge consortia developed in thermophilic UASB reactors. Appl. Microbiol. Biotechnol. 39:654-660.
41. Urbach, E., K. L. Vergin, L. Young, A. Morse, G. L. Larson, and S. J. Giovannoni. 2001. Unusual bacterioplankton community structure in ultraoligotrophic Crater Lake. Lininol. Oceanogr. 46:557-572.
42. van Lier, J. B. 1996. Limitations of thermophilic anaerobic wastewater treatment and the consequences for process design. Antonie van Leeuwenhoek 69:1-14.
43. van Lier, J. B., F. Boersma, M. M. W. H. Debets, and G. Lettinga. 1994. High-rate thermophilic anaerobic wastewater treatment in compartmentalized uplfow reactors. Water Sci. Technol. 30:251-261.
44. van Lier, J. B., N. Groeneveld, and G. Lettinga. 1996. Development of thermophilic methanogenic sludge in compartmentalized upflow reactors. Biotech. Bioeng. 50:115-124.
45. van Lier, J. B., K. C. F. Grolle, A. J. M. Stams, E. C. de Macario, and G. Lettinga. 1992. Start-up a thermophilic upflow anaerobic sludge bed (UASB) reactor with mesophilic granular sludge. Appl. Microbiol. Biotechnol. 37: 130-135.
46. Veiga, M. C., M. K. Jain, W.-M. Wu, R. I. Hollingsworth, and J. G. Zeikus. 1997. Composition and role of extracellular polymers in methanogenic granules. Appl. Environ. Microbiol. 63:403-407.
47. von Wintzingerode, K., O. Landt, A. Ehrlich, and U. B. Göbel. 2000 Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Appl. Environ. Microbiol. 66:549-557.
48. von Wintzingerode, K., B. Selent, W. Hegemann, and U. B. Gobel. 1999 Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl. Environ. Microhiol. 65:283-286.
49. Wasserfallen, A., J. Nöling, P. Pfister, J. Reeve, and E. Coway de Maeario. 2000. Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen., nov., and to reclassify several isolates in three species, Methanothermobacter thermoautotrophicus comb, nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov. Int. J. Syst. Evol. Microbiol. 50:43-53.
50. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
51. Wiegant, W. M. 1986. Thermophilic anaerobic digestion for waste and wastewater treatment. Ph.D. thesis. Wageningen Agricultural University, Wageningen, The Netherlands.
52. Wiegant, W. M., and A. W. A. de Man. 1986. Granulation of biomass in thermophilic upflow anaerobic sludge blanket reactors treating acidified wastewaters. Biotechnol. Bioeng. 28:718-727.
53. Wiegant, W. W. 1987. The "spaghetti theory" on anaerobic granular sludge formation, or the inevitability of granulation, p. 146-152. In G. Lettinga, A. J. B. Zehnder, J. T. C. Grotenhuis, and L. W. Hulshoff Pol (ed.), Granular anaerobic sludge: microbiology and technology. Centre for Agricultural Publishing and Documentation. Wageningen, The Netherlands.
54. Wiegant, W. W., and G. Lettinga. 1985. Thermophilic anaerobic digestion of sugers in upflow anaerobic sludge blanket reactors. Biotechnol. Bioeng. 28:718-727.
55. Wise, M. G., J. V. McArthur, and L. J. Shimkets. 1997. Bacterial diversity of a Carolina bay as determined by 16S rRNA gene analysis: confirmation of novel taxa. Appl. Environ. Microbiol. 63:1505-1514.
56. Wu, J.-H., W.-T. Liu, I.-C. Tseng, and S.-S. Cheng. 2001. Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system. Microbiology 147:373-382.
57. Wu, W.-M., J. H. Thiele, H. S. Pankratz, R. F. Hickey, and J. G. Zeikus. 1993. Comparison of rod- versus filament-type methanogenic granules: microbial population and reactor performance. Appl. Microbiol. Biotechnol. 39:795-803.
58. Yu, Z., and W. W. Mohn. 2001. Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing. Appl. Environ. Microbiol. 67:1565-1574.