1887

Abstract

A novel mesophilic, hydrogenotrophic methanogen, strain SANAE, was isolated from an anaerobic, propionate-degrading enrichment culture, which was originally established from rice paddy soil. The cells were non-motile, Gram-negative and rod-shaped (1.8–2.4 μm long by 0.3–0.6 μm wide). Growth of strain SANAE was observed at 25–40 °C, with an optimum temperature range for growth of 35–37 °C. The pH range for growth was 6.5–7.8, with an optimum at pH 7.0. The salinity range for growth was 0–1 g NaCl l (0–17 mM). The isolate was able to utilize H/CO and formate for growth and methane production. The G+C content of the genomic DNA was 56.6 mol%. Based on comparative 16S rRNA gene sequence analysis, strain SANAE was affiliated with a clone lineage of the , Rice Cluster I (RC-I), placing it between the orders and within the class ‘’. 16S rRNA gene sequence similarities between strain SANAE and members of were in the range 80.0–82.8 %, and those between the strain and members of ranged from 77.5 to 82.4 %. In addition to 16S rRNA gene analysis, sequence analysis of the gene (encoding the subunit of methyl-coenzyme M reductase, a key enzyme in the methane production pathway) also showed that strain SANAE was affiliated with the RC-I lineage. Here, we propose the name gen. nov., sp. nov. for the isolate, the first of the RC-I lineage. The type strain is SANAE (=JCM 13418=NBRC 101707=DSM 17711). In addition, we also propose the status of order for the RC-I lineage, for which we propose the name ord. nov.

Keyword(s): RC-I, Rice Cluster I
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2008-04-01
2019-12-15
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References

  1. Boone, D. R., Whitman, W. B. & Rouvière, P. ( 1993; ). Diversity and taxonomy of methanogens. In Methanogenesis, pp. 35–80. Edited by J. G. Ferry. New York: Chapman & Hall.
  2. Boone, D. R., Whitman, W. B. & Koga, Y. ( 2001a; ). Order II. Methanomicrobiales. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 246–267. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
  3. Boone, D. R., Whitman, W. B. & Koga, Y. ( 2001b; ). Order III. Methanosarcinales. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 248–293. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
  4. Chong, S. C., Liu, Y., Cummins, M., Valentine, D. L. & Boone, D. R. ( 2002; ). Methanogenium marinum sp. nov., a H2-using methanogen from Skan Bay, Alaska, and kinetics of H2 utilization. Antonie van Leeuwenhoek 81, 263–270.[CrossRef]
    [Google Scholar]
  5. Conrad, R., Erkel, C. & Liesack, W. ( 2006; ). Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 17, 262–267.[CrossRef]
    [Google Scholar]
  6. DeLong, E. F. ( 1992; ). Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89, 5685–5689.[CrossRef]
    [Google Scholar]
  7. Dentener, F., Derwent, R., Dlugokencky, E., Holland, E., Isaksen, I., Katima, J., Kirchhoff, V., Matson, P., Midgley, P. & Wang, M. ( 2001; ). Climate change 2001, the scientific basis. Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge: Cambridge University Press.
  8. Dianou, D., Miyaki, T., Asakawa, S., Morii, H., Nagaoka, K., Oyaizu, H. & Matsumoto, S. ( 2001; ). Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA–DNA hybridization among Methanoculleus species. Int J Syst Evol Microbiol 51, 1663–1669.[CrossRef]
    [Google Scholar]
  9. Doetsch, R. N. ( 1981; ). Determinative methods of light microscopy. In Manual of Methods for General Bacteriology, pp. 21–33. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. H. Phillips. Washington, DC: American Society for Microbiology.
  10. Erkel, C., Kemnitz, D., Kube, M., Ricke, P., Chin, K.-J., Dedysh, S., Reinhardt, R., Conrad, R. & Liesack, W. ( 2005; ). Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques. FEMS Microbiol Ecol 53, 187–204.[CrossRef]
    [Google Scholar]
  11. Erkel, C., Kube, M., Reinhardt, R. & Liesack, W. ( 2006; ). Genome of Rice Cluster I Archaea – the key methane producers in the rice rhizosphere. Science 313, 370–372.[CrossRef]
    [Google Scholar]
  12. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  13. Garrity, G. M., Bell, J. A. & Lilburn, T. G. ( 2003; ). Taxonomic outline of the Procaryotes. In Bergey's Manual of Systematic Bacteriology, 2nd edn, Release 4.0. New York: Springer. doi:10.1007/bergeysoutline200310
  14. Großkopf, R., Stubner, S. & Liesack, W. ( 1998; ). Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol 64, 4983–4989.
    [Google Scholar]
  15. Hales, B. A., Edwards, C., Ritchie, D. A., Hall, G., Pickup, R. W. & Saunders, J. R. ( 1996; ). Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl Environ Microbiol 62, 668–675.
    [Google Scholar]
  16. Imachi, H., Sekiguchi, Y., Kamagata, Y., Ohashi, A. & Harada, H. ( 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.[CrossRef]
    [Google Scholar]
  17. Imachi, H., Sekiguchi, Y., Kamagata, Y., Hanada, S., Ohashi, A. & Harada, H. ( 2002; ). Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. Int J Syst Evol Microbiol 52, 1729–1735.[CrossRef]
    [Google Scholar]
  18. Imachi, H., Sekiguchi, Y., Kamagata, Y., Loy, A., Qiu, Y.-L., Hugenholtz, P., Kimura, N., Wagner, M., Ohashi, A. & Harada, H. ( 2006; ). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl Environ Microbiol 72, 2080–2091.[CrossRef]
    [Google Scholar]
  19. Jiang, B., Parshina, S. N., van Doesburg, W., Lomans, B. P. & Stams, A. J. M. ( 2005; ). Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. Int J Syst Evol Microbiol 55, 2465–2470.[CrossRef]
    [Google Scholar]
  20. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  21. Kamagata, Y. & Mikami, E. ( 1991; ). Isolation and characterization a novel thermophilic Methanosaeta strain. Int J Syst Bacteriol 41, 191–196.[CrossRef]
    [Google Scholar]
  22. Lai, M.-C. & Chen, S.-C. ( 2001; ). Methanofollis aquaemaris sp. nov., a methanogen isolated from an aquaculture fish pond. Int J Syst Evol Microbiol 51, 1873–1880.[CrossRef]
    [Google Scholar]
  23. Lai, M.-C., Chen, S.-C., Shu, C.-M., Chiou, M.-S., Wang, C.-C., Chuang, M.-J., Hong, T.-Y., Liu, C.-C., Lai, L.-J. & Hua, J.-J. ( 2002; ). Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int J Syst Evol Microbiol 52, 1799–1806.[CrossRef]
    [Google Scholar]
  24. Lai, M.-C., Lin, C.-C., Yu, P.-H., Huang, Y.-F. & Chen, S.-C. ( 2004; ). Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int J Syst Evol Microbiol 54, 183–189.[CrossRef]
    [Google Scholar]
  25. Lehmann-Richter, S., Großkopf, R., Liesack, W., Frenzel, P. & Conrad, R. ( 1999; ). Methanogenic archaea and CO2-dependent methanogenesis on washed rice roots. Environ Microbiol 1, 159–166.[CrossRef]
    [Google Scholar]
  26. Lomans, B. P., Maas, R., Luderer, R., Op den Camp, H. J., Pol, A., van der Drift, C. & Vogels, G. D. ( 1999; ). Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microbiol 65, 3641–3650.
    [Google Scholar]
  27. Lu, Y. & Conrad, R. ( 2005; ). In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309, 1088–1090.[CrossRef]
    [Google Scholar]
  28. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors ( 2004; ). arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef]
    [Google Scholar]
  29. Lueders, T., Chin, K. J., Conrad, R. & Friedrich, M. ( 2001; ). Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3, 194–204.[CrossRef]
    [Google Scholar]
  30. Lyimo, T. J., Pol, A., Op den Camp, H. J. M., Harhangi, H. R. & Vogels, G. D. ( 2000; ). Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. Int J Syst Evol Microbiol 50, 171–178.[CrossRef]
    [Google Scholar]
  31. Ma, K., Liu, X. & Dong, X. ( 2006; ). Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor. Int J Syst Evol Microbiol 56, 127–131.[CrossRef]
    [Google Scholar]
  32. Mikucki, J. A., Liu, Y., Delwiche, M., Colwell, F. S. & Boone, D. R. ( 2003; ). Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. Appl Environ Microbiol 69, 3311–3316.[CrossRef]
    [Google Scholar]
  33. Mori, K., Yamamoto, H., Kamagata, Y., Hatsu, M. & Takamizawa, K. ( 2000; ). Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. Int J Syst Evol Microbiol 50, 1723–1729.
    [Google Scholar]
  34. Neue, H.-U. ( 1993; ). Methane emission from rice fields. Bioscience 43, 466–474.[CrossRef]
    [Google Scholar]
  35. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  36. Sakai, S., Imachi, H., Sekiguchi, Y., Ohashi, A., Harada, H. & Kamagata, Y. ( 2007; ). Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster Rice Cluster I. Appl Environ Microbiol 73, 4326–4331.[CrossRef]
    [Google Scholar]
  37. Sekiguchi, Y., Kamagata, Y., Syutsubo, K., Ohashi, A., Harada, H. & Nakamura, K. ( 1998; ). Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144, 2655–2665.[CrossRef]
    [Google Scholar]
  38. Sekiguchi, Y., Kamagata, Y., Nakamura, K., Ohashi, A. & Harada, H. ( 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.[CrossRef]
    [Google Scholar]
  39. Sekiguchi, Y., Yamada, T., Hanada, S., Ohashi, A., Harada, H. & Kamagata, Y. ( 2003; ). Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53, 1843–1851.[CrossRef]
    [Google Scholar]
  40. Sekiguchi, Y., Imachi, H., Susilorukmi, A., Muramatsu, M., Ohashi, A., Harada, H., Hanada, S. & Kamagata, Y. ( 2006; ). Tepidanaerobacter syntrophicus gen. nov., sp. nov., an anaerobic, moderately thermophilic, syntrophic alcohol- and lactate-degrading bacterium isolated from thermophilic digested sludges. Int J Syst Evol Microbiol 56, 1621–1629.[CrossRef]
    [Google Scholar]
  41. Simankova, M. V., Parshina, S. N., Tourova, T. P., Kolganova, T. V., Zehnder, A. J. & Nozhevnikova, A. N. ( 2001; ). Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments. Syst Appl Microbiol 24, 362–367.[CrossRef]
    [Google Scholar]
  42. Singh, N., Kendall, M. M., Liu, Y. & Boone, D. R. ( 2005; ). Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. Int J Syst Evol Microbiol 55, 2531–2538.[CrossRef]
    [Google Scholar]
  43. Sizova, M. V., Panikov, N. S., Tourova, T. P. & Flanagan, P. W. ( 2003; ). Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol Ecol 45, 301–315.[CrossRef]
    [Google Scholar]
  44. Sprenger, W. W., van Belzen, M. C., Rosenberg, J., Hackstein, J. H. P. & Keltjens, J. T. ( 2000; ). Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int J Syst Evol Microbiol 50, 1989–1999.[CrossRef]
    [Google Scholar]
  45. von Klein, D., Arab, H., Völker, H. & Thomm, M. ( 2002; ). Methanosarcina baltica, sp. nov., a novel methanogen isolated from the Gotland Deep of the Baltic Sea. Extremophiles 6, 103–110.[CrossRef]
    [Google Scholar]
  46. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. ( 1991; ). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697–703.
    [Google Scholar]
  47. Wu, S.-Y., Chen, S.-C. & Lai, M.-C. ( 2005; ). Methanofollis formosanus sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 55, 837–842.[CrossRef]
    [Google Scholar]
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