1887

Abstract

Three strains isolated from the soil of a garden in Tokyo, Japan, were characterized physiologically, biochemically and in terms of fatty acid profile, DNA–DNA relatedness and 16S rRNA gene sequence. The isolates were Gram-negative, aerobic, rod-shaped cells with polar flagellation. According to DNA–DNA similarity, the strains belonged to the same species. The bacteria grew at temperatures from 10 to 37 °C, with an optimum around 25–30 °C. Growth was observed at pH values from 5·6 to 8·0. The DNA G+C content ranged from 63·4 to 64·0 mol%. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation with members of the family ‘’. The closest relationship was seen with and , but, in terms of physiology and fatty acid profile, the bacteria described were rather distant from and . On the basis of phenotypic and phylogenetic distinctness, it is proposed that the isolates represent a novel species in a novel genus, namely gen. nov., sp. nov. The type strain is XD53 (=IAM 15069=DSM 16301=ATCC BAA-939).

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2005-03-01
2024-12-13
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References

  1. Entani E., Ohmori S., Masai H., Suzuki K. 1985; Acetobacter polyoxogenes sp. nov., a new species of an acetic acid bacterium useful for producing vinegar with high acidity. J Gen Appl Microbiol 31:475–490 [CrossRef]
    [Google Scholar]
  2. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [CrossRef]
    [Google Scholar]
  3. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  4. Felsenstein J. 1989; phylip – phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  5. Gillis M., Vandamme P., De Vos P., Swings J., Kersters K. 2001; Polyphasic taxonomy. In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 1 pp  43–48 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
    [Google Scholar]
  6. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
    [Google Scholar]
  7. Lisdiyanti P., Yamada Y., Uchimura T., Komagata K. 2003; Identification of Frateuria aurantia strains isolated from Indonesian sources. Microbiol Cult Coll 19:81–90
    [Google Scholar]
  8. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218 [CrossRef]
    [Google Scholar]
  9. Mergaert J., Cnockaert M. C., Swings J. 2002; Fulvimonas soli gen. nov. sp. nov. a γ -proteobacterium isolated from soil after enrichment on acetylated starch plastic. Int J Syst Evol Microbiol 521285–1289 [CrossRef]
    [Google Scholar]
  10. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [CrossRef]
    [Google Scholar]
  11. Nalin R., Simonet P., Vogel T. M., Normand P. 1999; Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 49:19–23 [CrossRef]
    [Google Scholar]
  12. Oyaizu-Masuchi Y., Komagata K. 1988; Isolation of free-living nitrogen-fixing bacteria from the rhizosphere of rice. J Gen Appl Microbiol 34:127–164 [CrossRef]
    [Google Scholar]
  13. Poly F., Monrozier L. J., Bally R. 2001; Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152:95–103 [CrossRef]
    [Google Scholar]
  14. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  15. Swings J., De Ley J., Gillis M. 1984; Genus III. Frateuria Swings, Gillis, Kersters, De Vos, Gosselé and De Ley, 1980, 547VP . In Bergey's Manual of Systematic Bacteriology vol 1 pp  210–211 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  16. Swofford D. L. 1998 paup* version 4. Phylogenetic Analysis Using Parsimony (*and Other Methods) Sunderland, MA: Sinauer;
    [Google Scholar]
  17. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  18. Xie C. H., Yokota A. 2003; Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49:345–349 [CrossRef]
    [Google Scholar]
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