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).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000451
2015-10-01
2019-12-07
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/10/3527.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000451&mimeType=html&fmt=ahah

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: 493–503 [CrossRef] [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. 248–270. Edited by Brenner D. J. , Krieg N. R. , Staley J. T. . New York: Springer; [CrossRef].
    [Google Scholar]
  3. Bowman J.P. . ( 2011;). Approaches for the characterization and description of novel methanotrophic bacteria. Methods Enzymol 495: 45–62.[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: 735–753 [CrossRef].
    [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: 1551–1558 [CrossRef] [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: 1125–1131.[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: 5066–5074 [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: 2384–2396 [CrossRef].
    [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: 278–287 [CrossRef] [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: 448–456 [CrossRef] [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: 393–404 [CrossRef].
    [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: 2568–2572 [CrossRef] [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: 2646–2653 [CrossRef] [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: 1073–1082 [CrossRef] [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: 989–999 [CrossRef] [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: 2100–2107 [CrossRef] [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: 203–208 [CrossRef] [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: 111–120 [CrossRef] [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: 3169–3172 [CrossRef].
    [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: 716–721.[CrossRef]
    [Google Scholar]
  21. Krema C. , Lidstrom M.E. . ( 1990;). Hydroxypyruvate reductase from Methylobacterium extorquens AM1. Methods Enzymol 188: 373–378 [CrossRef].
    [Google Scholar]
  22. Leadbetter E.R. , Foster J.W. . ( 1958;). Studies on some methane-utilizing bacteria. Arch Mikrobiol 30: 91–118 [CrossRef] [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: 31656–31662 [CrossRef] [PubMed].
    [Google Scholar]
  24. Marmur J. . ( 1961;). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3: 208–218 [CrossRef].
    [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: 233–241 [CrossRef].
    [Google Scholar]
  26. Nash T. . ( 1953;). The colorimetric estimation of formaldehyde by means of the Hantzsch reaction. Biochem J 55: 416–421 [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: 49–55 [CrossRef].
    [Google Scholar]
  28. Schlegel H.G. , Lafferty R. , Krauss I. . ( 1970;). The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71: 283–294 [CrossRef] [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: 125–128 [CrossRef].
    [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: 251–259 [CrossRef] [PubMed].
    [Google Scholar]
  31. Vela G.R. , Wyss O. . ( 1964;). Improved stain for visualization of Azotobacter encystment. J Bacteriol 87: 476–477 [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: 697–703 [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: 219–226 [CrossRef] [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: 205–218 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000451
Loading
/content/journal/ijsem/10.1099/ijsem.0.000451
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error