1887

Abstract

An aerobic, methane-oxidizing bacterium (strain RS11D-Pr) was isolated from rice rhizosphere. Cells of strain RS11D-Pr were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). and genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-Pr is related closely to the genera , , and in the family . The similarity was low (94.6 %) between strain RS11D-Pr and the most closely related type strain ( R-49797). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the gene and chemotaxonomic data regarding the major cellular fatty acids (Cω7, C and C) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-Pr to the clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-Pr is considered to represent a novel genus and species within the family , for which the name gen. nov., sp. nov. is proposed. The type strain is RS11D-Pr ( = JCM 18894 = NBRC 109438 = DSM 29768 = KCTC 4681).

Funding
This study was supported by the:
  • Japan Society for the Promotion of Sciences (Award 25292207)
  • ESPEC Foundation for Global Environment Research and Technology (Award 5331)
  • Chubu Science and Technology Center
  • Japan Science and Technology Agency
  • Japan Society for the Promotion of Science
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2015-10-01
2024-12-14
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References

  1. Bodrossy L., Holmes E.M., Holmes A.J., Kovács K.L., Murrell J.C. ( 1997;). Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov. Arch Microbiol 168 493503 [View Article] [PubMed].
    [Google Scholar]
  2. Bowman J.P. ( 2005;). Order VII. Methylococcales ord. nov. . In Bergey's Manual of Systematic Bacteriology, vol. 2B, , 2nd edn., pp. 248270. Edited by Brenner D. J., Krieg N. R., Staley J. T. New York: Springer; [View Article].
    [Google Scholar]
  3. Bowman J.P. ( 2011;). Approaches for the characterization and description of novel methanotrophic bacteria. Methods Enzymol 495 4562. [CrossRef]
    [Google Scholar]
  4. Bowman J.P., Sly L.I., Nichols P.D., Hayward A.C. ( 1993;). Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Bacteriol 43 735753 [View Article].
    [Google Scholar]
  5. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. ( 2002;). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52 15511558 [View Article] [PubMed].
    [Google Scholar]
  6. Collins M. D., Green P. N. . ( 1985;). Isolation and characterization of a novel coenzyme Q from some methane-oxidizing bacteria. Biochem Biophys Res Commun 133 11251131. [CrossRef]
    [Google Scholar]
  7. Costello A.M., Lidstrom M.E. ( 1999;). Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65 50665074 [PubMed].
    [Google Scholar]
  8. De Meyer S.E., van Hoorde K., Vekeman B., Braeckman T., Willems A. ( 2011;). Genetic diversity of rhizobia associated with indigenous legumes in different regions of Flanders (Belgium). Soil Biol Biochem 43 23842396 [View Article].
    [Google Scholar]
  9. Dianou D., Ueno C., Ogiso T., Kimura M., Asakawa S. ( 2012;). Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH). Microbes Environ 27 278287 [View Article] [PubMed].
    [Google Scholar]
  10. Eshinimaev B.Ts., Medvedkova K.A., Khmelenina V.N., Suzina N.E., Osipov G.A., Lysenko A.M., Trotsenko Yu.A. ( 2004;). New thermophilic methanotrophs of the genus Methylocaldum . Microbiology (English translation of Mikrobiologya) 73 448456 [View Article] [PubMed].
    [Google Scholar]
  11. Fujie K., Hu H.Y., Tanaka H., Urano K., Saitou K., Katayama A. ( 1998;). Analysis of respiratory quinones in soil for characterization of microbiota. Soil Sci Plant Nutr 44 393404 [View Article].
    [Google Scholar]
  12. Geymonat E., Ferrando L., Tarlera S.E. ( 2011;). Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. Int J Syst Evol Microbiol 61 25682572 [View Article] [PubMed].
    [Google Scholar]
  13. Hirayama H., Suzuki Y., Abe M., Miyazaki M., Makita H., Inagaki F., Uematsu K., Takai K. ( 2011;). Methylothermus subterraneus sp. nov., a moderately thermophilic methanotroph isolated from a terrestrial subsurface hot aquifer. Int J Syst Evol Microbiol 61 26462653 [View Article] [PubMed].
    [Google Scholar]
  14. Hirayama H., Fuse H., Abe M., Miyazaki M., Nakamura T., Nunoura T., Furushima Y., Yamamoto H., Takai K. ( 2013;). Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments. Int J Syst Evol Microbiol 63 10731082 [View Article] [PubMed].
    [Google Scholar]
  15. Hirayama H., Abe M., Miyazaki M., Nunoura T., Furushima Y., Yamamoto H., Takai K. ( 2014;). Methylomarinovum caldicuralii gen. nov., sp. nov., a moderately thermophilic methanotroph isolated from a shallow submarine hydrothermal system, and proposal of the family Methylothermaceae fam. nov. Int J Syst Evol Microbiol 64 989999 [View Article] [PubMed].
    [Google Scholar]
  16. Hoefman S., van der Ha D., Iguchi H., Yurimoto H., Sakai Y., Boon N., Vandamme P., Heylen K., De Vos P. ( 2014;). Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water. Int J Syst Evol Microbiol 64 21002107 [View Article] [PubMed].
    [Google Scholar]
  17. Holmes A.J., Costello A., Lidstrom M.E., Murrell J.C. ( 1995;). Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132 203208 [View Article] [PubMed].
    [Google Scholar]
  18. Hutchens E., Radajewski S., Dumont M.G., McDonald I.R., Murrell J.C. ( 2004;). Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ Microbiol 6 111120 [View Article] [PubMed].
    [Google Scholar]
  19. Katayama-Fujimura Y., Komatsu Y., Kuraishi H., Kaneko T. ( 1984;). Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. Agric Biol Chem 48 31693172 [View Article].
    [Google Scholar]
  20. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., 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 716721. [CrossRef]
    [Google Scholar]
  21. Krema C., Lidstrom M.E. ( 1990;). Hydroxypyruvate reductase from Methylobacterium extorquens AM1. Methods Enzymol 188 373378 [View Article].
    [Google Scholar]
  22. Leadbetter E.R., Foster J.W. ( 1958;). Studies on some methane-utilizing bacteria. Arch Mikrobiol 30 91118 [View Article] [PubMed].
    [Google Scholar]
  23. Maeda N., Kanai T., Atomi H., Imanaka T. ( 2002;). The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. J Biol Chem 277 3165631662 [View Article] [PubMed].
    [Google Scholar]
  24. Marmur J. ( 1961;). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3 208218 [View Article].
    [Google Scholar]
  25. Minnikin D.E., O'Donnell A.G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J.H. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2 233241 [View Article].
    [Google Scholar]
  26. Nash T. ( 1953;). The colorimetric estimation of formaldehyde by means of the Hantzsch reaction. Biochem J 55 416421 [PubMed]. [CrossRef]
    [Google Scholar]
  27. Nichols P.D., Guckert J.B., White D.C. ( 1986;). Determination of monounsaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulphide adducts. J Microbiol Methods 5 4955 [View Article].
    [Google Scholar]
  28. Schlegel H.G., Lafferty R., Krauss I. ( 1970;). The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71 283294 [View Article] [PubMed].
    [Google Scholar]
  29. Tamaoka J., Komagata K. ( 1984;). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25 125128 [View Article].
    [Google Scholar]
  30. Tavormina P.L., Hatzenpichler R., McGlynn S., Chadwick G., Dawson K.S., Connon S.A., Orphan V.J. ( 2015;). Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the ‘deep sea-1’ clade of marine methanotrophs. Int J Syst Evol Microbiol 65 251259 [View Article] [PubMed].
    [Google Scholar]
  31. Vela G.R., Wyss O. ( 1964;). Improved stain for visualization of Azotobacter encystment. J Bacteriol 87 476477 [PubMed].
    [Google Scholar]
  32. Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703 [PubMed].
    [Google Scholar]
  33. Whittenbury R., Davies S.L., Davey J.F. ( 1970a;). Exospores and cysts formed by methane-utilizing bacteria. J Gen Microbiol 61 219226 [View Article] [PubMed].
    [Google Scholar]
  34. Whittenbury R., Phillips K.C., Wilkinson J.F. ( 1970b;). Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61 205218 [View Article] [PubMed].
    [Google Scholar]
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