1887

Abstract

A novel methane-oxidizing bacterium, strain Fw12E-Y, was isolated from floodwater of a rice paddy field in Japan. Cells of strain Fw12E-Y were Gram-negative, motile rods with a single polar flagellum and type I intracytoplasmic membrane arrangement. The strain grew only on methane or methanol as sole carbon and energy source. It was able to grow at 10–40 °C (optimum 30 °C), at pH 5.5–7.0 (optimum 6.5) and with 0–0.1 % (w/w) NaCl (no growth above 0.5 % NaCl). 16S rRNA gene sequence analysis showed that strain Fw12E-Y is related most closely to members of the genus , but at low levels of similarity (95.0–95.4 %). Phylogenetic analysis of and genes indicated that the strain belongs to the genus (97 and 92 % deduced amino acid sequence identities to S1, respectively). The DNA G+C content of strain Fw12E-Y was 57.1 mol%. Chemotaxonomic data regarding the major quinone (MQ-8) and major fatty acids (C and C) also supported its affiliation to the genus . Based on phenotypic, genomic and phylogenetic data, strain Fw12E-Y is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Fw12E-Y ( = JCM 16701 = NBRC 105905 = NCIMB 14606).

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2012-08-01
2020-01-22
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References

  1. Bowman J. P. . ( 2005; ). Order VII. Methylococcales ord. nov.. In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2B, pp. 248–270. Edited by Brenner D. J. , Krieg N. R. , Staley J. T. . . New York:: Springer;. [CrossRef]
    [Google Scholar]
  2. Bowman J. P. , Sly L. I. , Cox J. M. , Hayward A. C. . ( 1990; ). Methylomonas fodinarum sp. nov. and Methylomonas aurantiaca sp. nov.: two closely related type I obligate methanotrophs. . Syst Appl Microbiol 13:, 279–287. [CrossRef]
    [Google Scholar]
  3. Bowman J. P. , Skerratt J. H. , Nichols P. D. , Sly L. I. . ( 1991; ). Phospholipid fatty acid and lipopolysaccharide fatty acid signature lipids in methane-utilizing bacteria. . FEMS Microbiol Ecol 85:, 15–22. [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. Chun J. , Lee J.-H. , Jung Y. , Kim M. , Kim S. , Kim B. K. , Lim Y. W. . ( 2007; ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57:, 2259–2261. [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] [PubMed]
    [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. 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 (in press) [CrossRef] [PubMed]
    [Google Scholar]
  9. Eller G. , Stubner S. , Frenzel P. . ( 2001; ). Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation. . FEMS Microbiol Lett 198:, 91–97. [CrossRef] [PubMed]
    [Google Scholar]
  10. 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]
  11. 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]
  12. 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]
  13. Kalyuzhnaya M. G. , Khmelenina V. N. , Kotelnikova S. , Holmquist L. , Pedersen K. , Trotsenko Y. A. . ( 1999; ). Methylomonas scandinavica sp. nov., a new methanotrophic psychrotrophic bacterium isolated from deep igneous rock ground water of Sweden. . Syst Appl Microbiol 22:, 565–572. [CrossRef] [PubMed]
    [Google Scholar]
  14. 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]
  15. Leadbetter E. R. , Foster J. W. . ( 1958; ). Studies on some methane-utilizing bacteria. . Arch Mikrobiol 30:, 91–118. [CrossRef] [PubMed]
    [Google Scholar]
  16. McDonald I. R. , Kenna E. M. , Murrell J. C. . ( 1995; ). Detection of methanotrophic bacteria in environmental samples with the PCR. . Appl Environ Microbiol 61:, 116–121.[PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Pernthaler J. , Glöckner F. O. , Schönhuber W. , Amann R. . ( 2001; ). Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. . Methods Microbiol 30:, 207–226. [CrossRef]
    [Google Scholar]
  20. Sowers K. R. . ( 1995; ). Isolation of chromosomal and plasmid DNAs from methanogenic archaea. . In Archaea: A Laboratory Manual: Methanogens, pp. 369–378. Edited by Sowers K. R. , Schreier H. I. . . New York:: Cold Spring Harbor Laboratory Press;.
    [Google Scholar]
  21. 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]
  22. Vela G. R. , Wyss O. . ( 1964; ). Improved stain for visualization of Azotobacter encystment. . J Bacteriol 87:, 476–477.[PubMed]
    [Google Scholar]
  23. 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]
  24. Whittenbury R. , Krieg N. R. . ( 1984; ). Genus II. Methylomonas . . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 260–261. Edited by Krieg N. R. , Holt J. G. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  25. Whittenbury R. , Davies S. L. , Davey J. F. . ( 1970a; ). Exospores and cysts formed by methane-utilizing bacteria. . J Gen Microbiol 61:, 219–226.[PubMed] [CrossRef]
    [Google Scholar]
  26. Whittenbury R. , Phillips K. C. , Wilkinson J. F. . ( 1970b; ). Enrichment, isolation and some properties of methane-utilizing bacteria. . J Gen Microbiol 61:, 205–218.[PubMed] [CrossRef]
    [Google Scholar]
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