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Abstract

An actinomycete strain, designated IR27-S3, was isolated from a forest soil sample collected from Iriomote Island, Okinawa, Japan. Cells of the isolate were Gram-stain-positive, aerobic, non-sporulating, non-motile coccoids or short rods. The strain grew in the presence of 0–7 % (w/v) NaCl, at pH 6–8 and at 12–37 °C, with optimum growth at 30 °C. Chemotaxonomically, the strain contained -diaminopimelic acid as the diagnostic diamino acid and MK-8(H) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids were iso-C, C -9, C and iso-C. The DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain IR27-S3 was closely related to MSL-22 (98.1 % 16S rRNA gene sequence similarity), MSL-05 (97.2 %) and DSM 20641 (96.5 %). On the basis of fatty acid analysis, phylogenetic analysis and phenotypic data, the isolate should be classified in a novel species of the genus , for which the name sp. nov. is proposed. The type strain is IR27-S3 ( = NBRC 105384  = KACC 14926).

Funding
This study was supported by the:
  • Institute for Fermentation, Osaka (IFO)
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2011-09-01
2024-12-12
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References

  1. Cho C. H., Lee J.-S., An D.-S., Whon T. W., Kim S.-G. 2010; Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field. Int J Syst Evol Microbiol 60:387–392 [View Article][PubMed]
    [Google Scholar]
  2. 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 [View Article][PubMed]
    [Google Scholar]
  3. Dastager S. G., Lee J.-C., Ju Y.-J., Park D.-J., Kim C.-J. 2008; Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae . Int J Syst Evol Microbiol 58:1060–1063 [View Article][PubMed]
    [Google Scholar]
  4. Dastager S. G., Lee J.-C., Ju Y.-J., Park D.-J., Kim C.-J. 2009; Nocardioides sediminis sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol 59:280–284 [View Article][PubMed]
    [Google Scholar]
  5. Dastager S. G., Lee J.-C., Pandey A., Kim C.-J. 2010; Nocardioides mesophilus sp. nov., isolated from soil. Int J Syst Evol Microbiol 60:2288–2292 [View Article][PubMed]
    [Google Scholar]
  6. Euzéby J. P. 1997; List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592 [View Article][PubMed]
    [Google Scholar]
  7. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  8. Gerhardt P. 1981 Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  9. Gordon R. E., Mihm J. M. 1962; Identification of Nocardia caviae (Erikson) nov. comb.. Ann N Y Acad Sci 98:628–636 [View Article]
    [Google Scholar]
  10. Guindon S., Lethiec F., Duroux P., Gascuel O. 2005; PHYML Online – a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557–W559 [View Article][PubMed]
    [Google Scholar]
  11. Hasegawa T., Takizawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322 [View Article]
    [Google Scholar]
  12. Hatano K., Nishii T., Kasai H. 2003; Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA–DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev.. Int J Syst Evol Microbiol 53:1519–1529 [View Article][PubMed]
    [Google Scholar]
  13. Hayakawa M., Nonomura H. 1987; Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509 [View Article]
    [Google Scholar]
  14. Kim K.-H., Roh S. W., Chang H.-W., Nam Y.-D., Yoon J.-H., Jeon C. O., Oh H.-M., Bae J.-W. 2009; Nocardioides basaltis sp. nov., isolated from black beach sand. Int J Syst Evol Microbiol 59:42–47 [View Article][PubMed]
    [Google Scholar]
  15. Kusunoki S., Ezaki T., Tamesada M., Hatanaka Y., Asano K., Hashimoto Y., Yabuuchi E. 1991; Application of colorimetric microdilution plate hybridization for rapid genetic identification of 22 Mycobacterium species. J Clin Microbiol 29:1596–1603[PubMed]
    [Google Scholar]
  16. Lechevalier M. P., Lechevalier H. A. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443 [View Article]
    [Google Scholar]
  17. Lechevalier M. P., De Bièvre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260 [View Article]
    [Google Scholar]
  18. Matson J. A., Bush J. A. 1989; Sandramycin, a novel antitumor antibiotic produced by a Nocardioides sp. Production, isolation, characterization and biological properties. J Antibiot (Tokyo) 42:1763–1767[PubMed] [CrossRef]
    [Google Scholar]
  19. 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]
  20. 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 quinines and polar lipids. J Microbiol Methods 2:233–241 [View Article]
    [Google Scholar]
  21. Nesterenko O. A., Kvasnikov E. I., Nogina T. M. 1985; Nocardioidaceae fam. nov., a new family of the order Actinomycetales Buchanan 1917. Mikrobiol Zh 47:3–12
    [Google Scholar]
  22. Park S. C., Baik K. S., Kim M. S., Chun J., Seong C. N. 2008; Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment. Int J Syst Evol Microbiol 58:2619–2623 [View Article][PubMed]
    [Google Scholar]
  23. Prauser H. 1976; Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 26:58–65 [View Article]
    [Google Scholar]
  24. Saito H., Miura K. I. 1963; Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72:619–629 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  27. Schaal K. P. 1985; Identification of clinically significant actinomycetes and related bacteria using chemical techniques. In Chemical Methods in Bacterial Systematics pp. 359–381 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
    [Google Scholar]
  28. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
    [Google Scholar]
  29. Sierra G. 1957; A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 23:15–22 [View Article][PubMed]
    [Google Scholar]
  30. Takahashi K., Nei M. 2000; Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258[PubMed] [CrossRef]
    [Google Scholar]
  31. Tamura T., Hatano K. 2001; Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and ‘Actinoplanes aurantiacus’ to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov.. Int J Syst Evol Microbiol 51:2119–2125 [View Article][PubMed]
    [Google Scholar]
  32. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
    [Google Scholar]
  33. 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]
  34. Urzì C., Salamone P., Schumann P., Stackebrandt E. 2000; Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50:529–536 [View Article][PubMed]
    [Google Scholar]
  35. 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 systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  36. Williams S. T., Goodfellow M., Alderson G., Wellington E. M. H., Sneath P. H. A., Sackin M. J. 1983; Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813[PubMed]
    [Google Scholar]
  37. Yoon J.-H., Park Y.-H. 2006; The genus Nocardioides . In The Prokaryotes, 3rd edn. vol. 3 pp. 1099–1113 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackebrandt E. New York: Springer; [View Article]
    [Google Scholar]
  38. Yoon J.-H., Kang S.-J., Park S., Kim W., Oh T.-K. 2009; Nocardioides caeni sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 59:2794–2797 [View Article][PubMed]
    [Google Scholar]
  39. Yoon J.-H., Park S., Kang S.-J., Lee J.-S., Lee K. C., Oh T.-K. 2010; Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil. Int J Syst Evol Microbiol 60:1334–1338 [View Article][PubMed]
    [Google Scholar]
  40. Zhang J. Y., Liu X.-Y., Liu S.-J. 2009; Nocardioides terrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 59:2444–2448 [View Article][PubMed]
    [Google Scholar]
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