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Abstract

An aerobic, Gram-stain-negative, oxidase-negative, catalase-positive, non-motile, non-spore-forming, rod-shaped, light pink-pigmented bacterium, designated strain R135, was isolated from soil in Hwaseong, South Korea. Flexirubin-type pigments were absent. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain R135 formed a lineage within the family of the phylum It was distinct from various species of the genus including DS-57 (98.13 % sequence similarity), NWER-II11 (97.76 %), 15-52 (97.71 %), KACC 16221 (97.37 %), CG-GP80 (97.24 %), 15-51 (97.23 %) and DS-27 (97.09 %). The major isoprenoid quinone was menaquinone-7 (MK-7), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C 7 and/or C 6), iso-C, iso-C3-OH and C. The DNA G+C content of strain R135 was 40.4 mol%. Levels of DNA–DNA hybridization similarities between strain R135and other members of the genus ranged from 25 % to 43 %. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R135 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is R135 (=KEMB 9005-332=KACC 18452=JCM 31010).

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2016-06-10
2024-03-28
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References

  1. Berznak J. A., Costilow R. N. 2007; Physicochemical factors in growth. In Methods for General and Molecular Bacteriology, 3rd edn. pp. 309–329 Edited by Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  2. Card G. L. 1973; Metabolism of phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin of Bacillus stearothermaphilus . J Bacteriol 114:1125–1137[PubMed]
    [Google Scholar]
  3. Chen L., Jiang F., Xiao M., Dai J., Kan W., Fang C., Peng F. 2013; Dyadobacter arcticus sp. nov., isolated from Arctic soil. Int J Syst Evol Microbiol 63:1616–1620 [View Article][PubMed]
    [Google Scholar]
  4. Dahal R. H., Kim J. 2016; Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 66:308–314 [View Article][PubMed]
    [Google Scholar]
  5. Doetsch R. N. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology pp. 21–33 Edited by Gerhardt P. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric DNA-DNA hybridization in microdilution wells as an alternative to member filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39:224–229
    [Google Scholar]
  7. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  9. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  10. Frank J. A., Reich C. I., Sharma S., Weisbaum J. S., Wilson B. A., Olsen G. J. 2008; Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  11. Gordon N. S., Valenzuela A., Adams S. M., Ramsey P. W., Pollock J. L., Holben W. E., Gannon J. E. 2009; Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 59:1720–1726 [View Article][PubMed]
    [Google Scholar]
  12. Hall T. A. 1999; BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
    [Google Scholar]
  13. Hwang C. Y., Choi D. H., Cho B. C. 2006; Pedobacter roseu sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter . Int J Syst Evol Microbiol 56:1831–1836 [View Article][PubMed]
    [Google Scholar]
  14. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 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 [View Article][PubMed]
    [Google Scholar]
  15. 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 [View Article][PubMed]
    [Google Scholar]
  16. Komagata K., Suzuki K. 1987; Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–203 [View Article]
    [Google Scholar]
  17. Kwon S. W., Kim B. Y., Lee K. H., Jang K. Y., Seok S. J., Kwon J. S., Kim W. G., Weon H. Y. 2007; Pedobacter suwonensissp. nov., isolated from the rhizosphere of the Chinese cabbage (Brassica campestris) . Int J Syst Evol Microbiol 53:1291–1296
    [Google Scholar]
  18. Kwon S. W., Son J. A., Kim S. J., Kim Y. S., Park I. C., Bok J. I., Weon H. Y. 2011; Pedobacter rhizosphaerae sp. nov. and Pedobacter solisp. nov., isolated from rhizosphere soil of chinese cabbage (Brassica campestris). Int J Syst Evol Microbiol 61:2874–2879 [View Article][PubMed]
    [Google Scholar]
  19. Macfaddin J. F. 1980 Bacterial Tests for Identification of Medical Bacteria, 2nd edn. pp 162–218 Baltimore, MD: Williams and Wilkins;
    [Google Scholar]
  20. 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 [View Article]
    [Google Scholar]
  21. 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 [View Article]
    [Google Scholar]
  22. Pham V. H., Kim J. 2012; Cultivation of unculturable soil bacteria. Trends Biotechnol 30:475–484 [View Article][PubMed]
    [Google Scholar]
  23. Reichenbach H. 1992; The order Cytophagales . In The Prokaryotes, 2nd edn. Vol. 4 pp. 3631–3675 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. New York: Springer; [CrossRef]
    [Google Scholar]
  24. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  25. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101. Newark, DE: MIDI Inc;
    [Google Scholar]
  26. Schaeffer A. B., Fulton M. 1933; A simplified method o staining endospores. Science 77:194 [View Article]
    [Google Scholar]
  27. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  28. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J. 1998; Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinuscomb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48:165–177 [View Article][PubMed]
    [Google Scholar]
  29. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  30. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  31. Tindall B. J, Sikorski J, Smibert R. A., Krieg N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. pp. 330–393 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, D.C.: ASM Press;
    [Google Scholar]
  32. Tittsler R. P., Sandholzer L. A. 1936; The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580[PubMed]
    [Google Scholar]
  33. Vaughn R. H., Mitchell N. B., Levine M. 1939; The Voges-Proskauer and methyl red reactions in the coli-aerogenes group. J Am Water Works Assoc 31:993–1001
    [Google Scholar]
  34. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  35. Wilson K. 1997; Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology pp. 241–245 Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. NY: John Wiley and Sons, Inc;
    [Google Scholar]
  36. Yang J. E., Shin J. Y., Park S. Y., Mavlonov G. T., Yi E. J., Lee E. H., Lee J. M., Yi T. H. 2012; Pedobacter kyungheensis sp. nov., with ginsenoside converting activity. J Gen Appl Microbiol 58:309–316[PubMed] [CrossRef]
    [Google Scholar]
  37. Yoon J. H., Kang S. J., Oh T. K. 2007; Pedobacter terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 57:2462–2466 [View Article][PubMed]
    [Google Scholar]
  38. Yoon J. H., Lee M. H., Kang S. J., Park S. Y., Oh T. K. 2006; Pedobacter sandarakinus sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:1273–1277 [View Article][PubMed]
    [Google Scholar]
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