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Volume 64, Issue Pt_10

sp. nov., isolated from rhizospheric soil of L. Free

Abstract

The taxonomic status of a rhizospheric soil actinomycete, designated R8-39, was established using a polyphasic approach. The organism had phenotypic and morphological characteristics consistent with its classification in the genus . Phylogenetic analysis based on an almost complete 16S rRNA gene sequence showed that the strain formed a monophyletic clade with the type strains of members of the genus . Strain R8-39 displayed the highest levels of 16S rRNA gene sequence similarity to DSM 44149 (98.8 %) and YIM 120521 (98.3 %). However, the DNA–DNA hybridization values between strain R8-39 and and were clearly below the 70 % threshold. The organism was found to have chemical characteristics consistent with its classification in the genus . Whole-cell hydrolysates contained -diaminopimelic acid, arabinose, galactose, glucose, mannose, rhamnose and ribose. The main menaquinone was MK-9(H). No mycolic acid was detected. The G+C content of the genomic DNA was 71.8 mol%. In addition, strain R8-39 had a phenotypic profile that readily distinguished it from recognized representatives of the genus . It is evident from the combined genotypic and phenotypic properties that strain R8-39 represents a novel species of the genus . The proposed name for this species is sp. nov.; the type strain is R8-39 ( = BCC 60399 = NBRC 109649).

  • Published Online:
Funding
This study was supported by the:
  • Kasetsart University Research and Development Institute (KURDI)
  • Thailand, Office of the Higher Education Commission
  • Kitasato Institute for Life Sciences, Kitasato University
  • Faculty of Science, Kasetsart University
  • Kasetsart University
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2014-10-01
2024-04-25
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References

  1. Becker B., Lechevalier M. P., Lechevalier H. A. ( 1965 ). Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. . Appl Microbiol 13, 236–243.[PubMed]
    [Google Scholar]
  2. Cao Y. R., Chen X., Jiang Y., Wang L. S., Jiang C. L. ( 2013 ). Allokutzneria multivorans sp. nov., an actinomycete isolated from soil. . Int J Syst Evol Microbiol 63, 4254–4258. [View Article] [PubMed]
    [Google Scholar]
  3. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221–230. [View Article] [PubMed]
    [Google Scholar]
  4. 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. [View Article]
    [Google Scholar]
  5. Felsenstein J. ( 1993 ). phylip (phylogenetic inference package) version 3.5c. Distributed by the author. . Department of Genome Sciences, University of Washington, Seattle, USA .
  6. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimal change for a specific tree topology. . Syst Zool 20, 406–416. [CrossRef]
    [Google Scholar]
  7. Gordon R. E., Mihm J. M. ( 1957 ). A comparative study of some strains received as nocardiae. . J Bacteriol 73, 15–27.[PubMed]
    [Google Scholar]
  8. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. ( 1974 ). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. . Int J Syst Bacteriol 24, 54–63. [View Article]
    [Google Scholar]
  9. 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]
  10. Jacobson E., Grauville W. C., Fogs C. E. ( 1958 ). Color Harmony Manual, , 4th edn.. Chicago:: Container Corporation of America;.
     [Google Scholar]
  11. Kieser T., Bibb M. J., Buttner M. J., Chater K. F., Hopwood D. A. ( 2000 ). Practical Streptomyces Genetics. Norwich:: John Innes Foundation;.
     [Google Scholar]
  12. 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]
  13. Küster E., Williams S. T. ( 1964 ). Selection of media for isolation of Streptomycetes . . Nature 202, 928–929. [View Article] [PubMed]
    [Google Scholar]
  14. Labeda D. P., Kroppenstedt R. M. ( 2008 ). Proposal for the new genus Allokutzneria gen. nov. within the suborder Pseudonocardineae and transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov.. Int J Syst Evol Microbiol 58, 1472–1475. [View Article] [PubMed]
    [Google Scholar]
  15. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–148. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
     [Google Scholar]
  16. Mingma R., Pathom-aree W., Trakulnaleamsai S., Thamchaipenet A., Duangmal K. ( 2014 ). Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine . . World J Microbiol Biotechnol 30, 271–280. [View Article] [PubMed]
    [Google Scholar]
  17. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. ( 1977 ). Polar lipid composition in the classification of Nocardia and related bacteria. . Int J Syst Bacteriol 27, 104–117. [View Article]
    [Google Scholar]
  18. 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]
  19. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
     [Google Scholar]
  20. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313–340. [View Article]
    [Google Scholar]
  21. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152–155.
     [Google Scholar]
  22. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125–128. [View Article]
    [Google Scholar]
  23. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 2731–2739. [View Article] [PubMed]
    [Google Scholar]
  24. Tomita K., Hoshino Y., Miyaki T. ( 1993 ). Kibdelosporangium albatum sp. nov., producer of the antiviral antibiotics cycloviracins. . Int J Syst Bacteriol 43, 297–301. [View Article] [PubMed]
    [Google Scholar]
  25. Tomiyasu I. ( 1982 ). Mycolic acid composition and thermally adaptative changes in Nocardia asteroides . . J Bacteriol 151, 828–837.[PubMed]
    [Google Scholar]
  26. Uchida K., Aida K. ( 1984 ). An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. . J Gen Appl Microbiol 30, 131–134. [View Article]
    [Google Scholar]
  27. 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 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
  28. 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]
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Allokutzneria oryzae sp. nov., isolated from rhizospheric soil of Oryza sativa L.
Int J Syst Evol Microbiol 64, 3559 (2014); https://doi.org/10.1099/ijs.0.065169-0
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