sp. nov., isolated from a sediment sample Free

Abstract

An actinobacterial strain was isolated from a sediment sample from Chorao Island, in Goa province, India, and subjected to a taxonomic investigation. The isolate, designated NIO-1021, was a Gram-stain positive, aerobic, non-motile and coccoid. Strain NIO-1021 was identified as a member of the genus by a polyphasic approach. Strain NIO-1021 could be differentiated from other members of the genus on the basis of physiology and 16S rRNA gene sequence analysis. The 16S rRNA gene sequence similarity of strain NIO-1021 to the most closely related species, KCTC 9943, was 98.6 % with 19 nt differences). Furthermore, DNA–DNA hybridization analysis revealed that the novel strain had lower relatedness with the type strains of other members of the genus . The strain formed a monophyletic clade with with 100 % bootstrap values. The major phospholipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified lipids. The predominant menaquinone was MK-7(H). The major fatty acids were anteiso-C, iso-C and anteiso-C. The DNA GC content of strain NIO-1021 was 60.5 mol%. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification as representing a member of the genus . On the basis of phenotypic, chemotypic and molecular characteristics, strain NIO-1021 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed, with strain NIO-1021 ( = NCIM 5455 = DSM 25126 = CCTCC AA 209050) as the type strain.

Funding
This study was supported by the:
  • Council for Scientific and Industrial Research (CSIR)

Erratum

An erratum has been published for this content:
Corrigendum: sp. nov., isolated from a sediment sample
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2014-03-01
2024-03-29
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References

  1. Dong X. Z., Cai M. Y. ( 2001 ). Manual of Systematics and Identification of General Bacteria. Beijing:: Science Press;.
    [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, 224229. [View Article]
    [Google Scholar]
  3. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  4. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  5. Felsenstein J. ( 2002 ). phylip (phylogeny inference package), version 3.6a. Distributed by the author.. Department of Genome Sciences, University of Washington;, Seattle, USA:.
    [Google Scholar]
  6. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  7. Flügge C. ( 1886 ). Die Mikroorganismen. Part 2, , 3rd edn.. Leipzig:: F. C. W. Vogel;.
    [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, 5463. [View Article]
    [Google Scholar]
  9. Hasegawa T., Takizawa M., Tanida S. ( 1983 ). A rapid analysis for chemical grouping of aerobic actinomycetes. . J Gen Microbiol 29, 319322. [View Article]
    [Google Scholar]
  10. Kim S. B., Nedashkovskaya O. I., Mikhailov V. V., Han S. K., Kim K. O., Rhee M. S., Bae K. S. ( 2004 ). Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment. . Int J Syst Evol Microbiol 54, 16171620. [View Article] [PubMed]
    [Google Scholar]
  11. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  12. Kloos W. E., Tornabene T. G., Schleifer K. H. ( 1974 ). Isolation and characterization of micrococci from human skin, including two new species: Micrococcus lylae and Micrococcus kristinae . . Int J Syst Bacteriol 24, 79101. [View Article]
    [Google Scholar]
  13. Kovács G., Burghardt J., Pradella S., Schumann P., Stackebrandt E., Màrialigeti K. ( 1999 ). Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia). . Int J Syst Bacteriol 49, 167173. [View Article] [PubMed]
    [Google Scholar]
  14. Kroppenstedt R. M. ( 1982 ). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver-loaded ion exchanger. . J Liq Chromatogr 5, 23592367. [View Article]
    [Google Scholar]
  15. Leifson E. ( 1960 ). Atlas of Bacterial Flagellation. London:: Academic Press;.
    [Google Scholar]
  16. Li W. J., Zhang Y. Q., Schumann P., Chen H. H., Hozzein W. N., Tian X. P., Xu L. H., Jiang C. L. ( 2006 ). Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt. . Int J Syst Evol Microbiol 56, 733737. [View Article] [PubMed]
    [Google Scholar]
  17. Li W. J., Xu P., Schumann P., Zhang Y. Q., Pukall R., Xu L. H., Stackebrandt E., Jiang C. L. ( 2007 ). Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . . Int J Syst Evol Microbiol 57, 14241428. [View Article] [PubMed]
    [Google Scholar]
  18. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  19. Mayilraj S., Kroppenstedt R. M., Suresh K., Saini H. S. ( 2006 ). Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas. . Int J Syst Evol Microbiol 56, 19711975. [View Article] [PubMed]
    [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, 159167. [View Article]
    [Google Scholar]
  21. Migula W. ( 1900 ). System der Bakterien. Jena:: Gustav Fischer;.
    [Google Scholar]
  22. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal K., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  23. Park E.-J., Roh S. W., Kim M.-S., Jung M.-J., Shin K. S., Bae J.-W. ( 2010a ). Kocuria koreensis sp. nov., isolated from fermented seafood. . Int J Syst Evol Microbiol 60, 140143. [View Article] [PubMed]
    [Google Scholar]
  24. Park E.-J., Kim M.-S., Roh S. W., Jung M.-J., Bae J.-W. ( 2010b ). Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood. . Int J Syst Evol Microbiol 60, 914918. [View Article] [PubMed]
    [Google Scholar]
  25. Reddy G. S., Prakash J. S., Prabahar V., Matsumoto G. I., Stackebrandt E., Shivaji S. ( 2003 ). Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample. . Int J Syst Evol Microbiol 53, 183187. [View Article] [PubMed]
    [Google Scholar]
  26. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425. [PubMed]
    [Google Scholar]
  27. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20, 16.
    [Google Scholar]
  28. Seo Y. B., Kim D. E., Kim G. D., Kim H. W., Nam S. W., Kim Y. T., Lee J. H. ( 2009 ). Kocuria gwangalliensis sp. nov., an actinobacterium isolated from seawater. . Int J Syst Evol Microbiol 59, 27692772. [View Article] [PubMed]
    [Google Scholar]
  29. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  30. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  31. Stackebrandt E., Koch C., Gvozdiak O., Schumann P. ( 1995 ). Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.. Int J Syst Bacteriol 45, 682692. [View Article] [PubMed]
    [Google Scholar]
  32. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article] [PubMed]
    [Google Scholar]
  33. Tamura K., Dudley J., Nei M., Kumar S. ( 2007 ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24, 15961599. [View Article] [PubMed]
    [Google Scholar]
  34. Tang S. K., Wang Y., Lou K., Mao P. H., Xu L. H., Jiang C. L., Kim C. J., Li W. J. ( 2009 ). Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China. . Int J Syst Evol Microbiol 59, 13161320. [View Article] [PubMed]
    [Google Scholar]
  35. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  36. Tittsler R. P., Sandholzer L. A. ( 1936 ). The use of semi-solid agar for the detection of bacterial motility. . J Bacteriol 31, 575580. [PubMed]
    [Google Scholar]
  37. Tvrzová L., Schumann P., Sedláček I., Páčová Z., Spröer C., Verbarg S., Kroppenstedt R. M. ( 2005 ). Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.. Int J Syst Evol Microbiol 55, 139142. [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. Xu P., Li W. J., Tang S. K., Zhang Y. Q., Chen G. Z., Chen H. H., Xu L. H., Jiang C. L. ( 2005 ). Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. . Int J Syst Evol Microbiol 55, 11491153. [View Article] [PubMed]
    [Google Scholar]
  40. Yun J.-H., Roh S. W., Jung M.-J., Kim M.-S., Park E.-J., Shin K.-S., Nam Y.-D., Bae J.-W. ( 2011 ). Kocuria salsicia sp. nov., isolated from salt-fermented seafood. . Int J Syst Evol Microbiol 61, 286289. [View Article] [PubMed]
    [Google Scholar]
  41. Zhou G., Luo X., Tang Y., Zhang L., Yang Q., Qiu Y., Fang C. ( 2008 ). Kocuria flava sp. nov. and Kocuria turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China. . Int J Syst Evol Microbiol 58, 13041307. [View Article] [PubMed]
    [Google Scholar]
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