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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 60, Issue 12

sp. nov., a hydrogenotrophic methanogen isolated from rice field soil Free

Abstract

A novel hydrogenotrophic methanogen, designated strain MRE50, was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3–2.8 μm long and 0.4–0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50 grew at 37–55 °C (optimally at 45 °C), at pH 6–7.8 (optimally at pH 7.0) and in the presence of 0–20 g NaCl l. The isolate utilized H/CO and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker gene showed that strain MRE50 is affiliated with the order , previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene and gene sequences, strain MRE50 was related most closely to SANAE. Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50 and SANAE represent different species within the genus . In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genus , strain MRE50 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MRE50 (=NBRC 105507 =DSM 22066).

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Keyword(s): FISH, fluorescence in situ hybridization and RC-I, rice cluster I
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2010-12-01
2024-04-24
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References

  1. Chin K. J., Rainey F. A., Janssen P. H., Conrad R. 1998; Methanogenic degradation of polysaccharides and the characterization of polysaccharolytic clostridia from anoxic rice field soil. Syst Appl Microbiol 21:185–200 [CrossRef]
     [Google Scholar]
  2. 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]
  3. 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]
  4. 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]
  5. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
     [Google Scholar]
  6. 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]
  7. Hatamoto M., Imachi H., Ohashi A., Harada H. 2007; Identification and cultivation of anaerobic, syntrophic long-chain fatty acid-degrading microbes from mesophilic and thermophilic methanogenic sludges. Appl Environ Microbiol 73:1332–1340 [CrossRef]
     [Google Scholar]
  8. 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]
  9. Imachi H., Sakai S., Sekiguchi Y., Hanada S., Kamagata Y., Ohashi A., Harada H. 2008; Methanolinea tarda gen. nov., sp. nov. a methane-producing archaeon isolated from a methanogenic digester sludge. Int J Syst Evol Microbiol 58:294–301 [CrossRef]
     [Google Scholar]
  10. 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]
  11. 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]
  12. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
     [Google Scholar]
  13. Lee Y. J., Romanek C. S., Mills G. L., Davis R. C., Whitman W. B., Wiegel G. 2006; Gracilibacter thermotolerans gen. nov., sp. nov. an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water. Int J Syst Evol Microbiol 56:2089–2093 [CrossRef]
     [Google Scholar]
  14. Lomans B. P., Maas R., Luderer R., Op den Camp H. J. M., 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]
  15. Lu Y., Conrad R. 2005; In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309:1088–1090 [CrossRef]
     [Google Scholar]
  16. 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]
  17. 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]
  18. Nakagawa S., Takai K., Horikoshi K., Sako Y. 2003; Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 53:863–869 [CrossRef]
     [Google Scholar]
  19. Ollivier B. M., Mah R. A., Garcia J. L., Boone D. R. 1986; Isolation and characterization of Methanogenium bourgense sp. nov. Int J Syst Bacteriol 36:297–301 [CrossRef]
     [Google Scholar]
  20. Ollivier B. M., Fardeau M. L., Cayol J. L., Magot M., Patel B. K. C., Prensier G., Garcia J. L. 1998; Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well. Int J Syst Bacteriol 48:821–828 [CrossRef]
     [Google Scholar]
  21. Rivard C. J., Smith P. H. 1982; Isolation and characterization of a thermophilic marine methanogenic bacterium, Methanogenium thermophilicum sp. nov. Int J Syst Bacteriol 32:430–436 [CrossRef]
     [Google Scholar]
  22. 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]
  23. Sakai S., Imachi H., Hanada S., Ohashi A., Harada H., Kamagata Y. 2008; Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov. Int J Syst Evol Microbiol 58:929–936 [CrossRef]
     [Google Scholar]
  24. Sekiguchi Y., Syutsubo K., Ohashi A., Harada H., Kamagata Y., Nakamura K. 1998; Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144:2655–2665 [CrossRef]
     [Google Scholar]
  25. 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]
  26. 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]
  27. Whitman W. B., Boone D. R., Koga Y., Keswani J. 2001; Taxonomy of methanogenic Archaea . In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol 1 pp 211–213 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
     [Google Scholar]
  28. Yashiro Y., Sakai S., Ehara M., Miyazaki M., Yamaguchi T., Imachi H. 2011; Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge. Int J Syst Evol Microbiol (in press). doi: [View Article]
     [Google Scholar]
  29. Zillig W., Holz I., Janekovic D., Klenk H. P., Imsel E., Trent J., Wunderl S., Forjaz V. H., Coutinho R., Ferreira T. 1990; Hyperthermus butylicus , a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. J Bacteriol 172:3959–3965
     [Google Scholar]
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Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil
Int J Syst Evol Microbiol 60, 2918 (2010); https://doi.org/10.1099/ijs.0.020883-0
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