1887

Abstract

A novel actinomycete, strain DS3030, was isolated from a deep sediment sample, collected from the southern Black Sea coast, Turkey, and was examined using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain DS3030 was shown to belong to the genus and to be related most closely to XMU15 (99.6 % similarity). Sequence similarities with other strains of the genus were lower than 97.0 %. The organism had chemical and morphological features typical of the genus . The cell wall of the novel strain contained -diaminopimelic acid, arabinose and galactose as diagnostic sugars. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone was MK-9(H). Major fatty acids were iso-C, iso-C 2-OH and C 9. Phenotypic data clearly distinguished the new isolate from its closest relative, XMU15. The combined genotypic and phenotypic data and low DNA–DNA relatedness with its closest related strain reveal that strain DS3030 represents a novel species of the genus, for which the name sp. nov. is proposed. The type strain is DS3030 ( = DSM 45685 = KCTC 29069 = NRRL B-24885).

Funding
This study was supported by the:
  • Ondokuz Mayis University (Award PYO. FEN. 1901.09.003)
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2013-10-01
2024-04-25
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References

  1. Al-Zarban S. S., Al-Musallam A. A., Abbas I., Stackebrandt E., Kroppenstedt R. M. ( 2002 ). Saccharomonospora halophila sp. nov., a novel halophilic actinomycete isolated from marsh soil in Kuwait. . Int J Syst Evol Microbiol 52, 555558.[PubMed]
    [Google Scholar]
  2. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461466. [View Article] [PubMed]
    [Google Scholar]
  3. Chun J., Goodfellow M. ( 1995 ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. . Int J Syst Bacteriol 45, 240245. [View Article] [PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 143153.[PubMed] [CrossRef]
    [Google Scholar]
  5. Embley T. M., Goodfellow M., O'Donnell A. G., Rose D., Minnikin D. E. ( 1985 ). Chemical criteria in the classification of the mycolateless wall chemotype IV actinomycetes. . In Biological, Biochemical and Biomedical Aspects of Actinomycetes, pp. 553556. Edited by Szabo G., Biro S., Goodfellow M. . Budapest:: Academica Kiado;.
    [Google Scholar]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1985 ). Confidence limits on phylogeny: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  8. Gonzalez J. M., Saiz-Jimenez C. ( 2005 ). A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. . Extremophiles 9, 7579. [View Article] [PubMed]
    [Google Scholar]
  9. Gordon R. E., Mihm J. M. ( 1957 ). A comparative study of some strains received as nocardiae. . J Bacteriol 73, 1527.[PubMed]
    [Google Scholar]
  10. 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, 5463. [View Article]
    [Google Scholar]
  11. Greiner-Mai E., Kroppenstedt R. M., Korn-Wendisch F., Kutzner H. J. ( 1987 ). Morphological and biochemical characterization and emended descriptions of thermophilic actinomycetes species. . Syst Appl Microbiol 9, 97109. [View Article]
    [Google Scholar]
  12. Huss V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [View Article] [PubMed]
    [Google Scholar]
  13. Jones K. L. ( 1949 ). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. . J Bacteriol 57, 141145.[PubMed]
    [Google Scholar]
  14. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21132. Edited by Munro H. N. . New York:: Academic Press;.
    [Google Scholar]
  15. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 9891005. [View Article]
    [Google Scholar]
  16. Kim O. S., Cho Y.-J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  17. Kluge A. G., Farris F. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 132. [View Article]
    [Google Scholar]
  18. Kroppenstedt R. M. ( 1985 ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . Soc Appl Bacteriol Tech Ser 20, 173197.
    [Google Scholar]
  19. Lechevalier M. P., Lechevalier H. ( 1970 ). Chemical composition as a criterion in the classification of aerobic actinomycetes. . Int J Syst Bacteriol 20, 435443. [View Article]
    [Google Scholar]
  20. Li W. J., Tang S. K., Stackebrandt E., Kroppenstedt R. M., Schumann P., Xu L. H., Jiang C. L. ( 2003 ). Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China. . Int J Syst Evol Microbiol 53, 15911594. [View Article] [PubMed]
    [Google Scholar]
  21. Liu Z., Li Y., Zheng L. Q., Huang Y. J., Li W. J. ( 2010 ). Saccharomonospora marina sp. nov., isolated from an ocean sediment of the East China Sea. . Int J Syst Evol Microbiol 60, 18541857. [View Article] [PubMed]
    [Google Scholar]
  22. Nonomura H., Ohara Y. ( 1971 ). Distribution of actinomycetes in soil. New genus and species of monosporic actinomycetes. . J Ferment Technol 49, 895903.
    [Google Scholar]
  23. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  24. Sasser M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. , Technical Note 101. Newark, DE:: MIDI Inc.;
    [Google Scholar]
  25. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  26. Staneck J. L., Roberts G. D. ( 1974 ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28, 226231.[PubMed]
    [Google Scholar]
  27. Syed D. G., Tang S. K., Cai M., Zhi X. Y., Agasar D., Lee J. C., Kim C. J., Jiang C. L., Xu L. H., Li W. J. ( 2008 ). Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil. . Int J Syst Evol Microbiol 58, 570573. [View Article] [PubMed]
    [Google Scholar]
  28. 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, 27312739. [View Article] [PubMed]
    [Google Scholar]
  29. Tan G. Y. A., Ward A. C., Goodfellow M. ( 2006 ). Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. . Syst Appl Microbiol 29, 557569. [View Article] [PubMed]
    [Google Scholar]
  30. Tindall B. J. ( 1990a ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  31. Tindall B. J. ( 1990b ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  32. 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. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  33. 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, 17431813.[PubMed]
    [Google Scholar]
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