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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 63, Issue Pt_1

sp. nov., an actinomycete isolated from tidal flat sediment Free

Abstract

A Gram-stain-positive, non-motile, aerobic actinobacterium, designated strain CJ10, was isolated from tidal flat sediment from the Yellow Sea in South Korea. Strain CJ10 grew on tryptic soy agar in the presence of 0–4 % (w/v) NaCl (optimum growth in the absence of NaCl) and at pH 6–11 (optimum pH 9). On the basis of 16S rRNA gene sequence analysis, strain CJ10 belonged to the genus and showed the highest sequence similarity to DSM 44140 (97.9 %) and DSM 44015 (97.6 %). DNA–DNA relatedness levels of strain CJ10 were 47.4 % (CJ10 as probe) and 42.2 % ( DSM 44140 as probe) to DSM 44140 and 8.6 % (CJ10 as probe) and 9.3 % ( DSM 44015 as probe) to DSM 44015. The major isoprenoid quinone was MK-9(H). The polar lipid profile of strain CJ10 consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were Cω9 (38.0 %), C (30.1 %) and summed feature 3 (Cω6 and/or Cω7; 17.4 %). The DNA G+C content was 67.7 mol%. Therefore, the results from our polyphasic taxonomic study suggest that strain CJ10 represents a novel species in the genus , for which the name sp. nov. is proposed; the type strain is CJ10 ( = KACC 16561  = JCM 18077).

  • Published Online:
Funding
This study was supported by the:
  • Korea Research Foundation (Award KRF-331-C00248)
  • Korean Government (MOEHRD)
  • National Institute of Biological Resources (NIBR)
© 2013 IUMS
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2013-01-01
2024-04-25
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References

  1. Atlas R. M. ( 1993 ). Handbook of Microbiology Media. Edited by Parks L. C. . Boca Raton, FL:: CRC Press;.
     [Google Scholar]
  2. Bendinger B., Rainey F. A., Kroppenstedt R. M., Moormann M., Klatte S. ( 1995 ). Gordona hydrophobica sp. nov., isolated from biofilters for waste gas treatment. . Int J Syst Bacteriol 45, 544–548. [View Article]
    [Google Scholar]
  3. Collins M. D. ( 1985 ). Analysis of isoprenoid quinones. . Methods Microbiol 18, 329–366. [View Article]
    [Google Scholar]
  4. Drzyzga O., Navarro Llorens J. M., Fernández de Las Heras L., García Fernández E., Perera J. ( 2009 ). Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge. . Int J Syst Evol Microbiol 59, 1011–1015. [View Article] [PubMed]
    [Google Scholar]
  5. 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]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [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. Felsenstein, J. (2005). phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  9. Jeon Y. S., Chung H., Park S., Hur I., Lee J. H., Chun J. ( 2005 ). jphydit: a java-based integrated environment for molecular phylogeny of ribosomal RNA sequences. . Bioinformatics 21, 3171–3173. [View Article] [PubMed]
    [Google Scholar]
  10. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by Munro H. N. . New York:: Academic Press;.
     [Google Scholar]
  11. Kämpfer P., Young C. C., Chu J. N., Frischmann A., Busse H. J., Arun A. B., Shen F. T., Rekha P. D. ( 2011 ). Gordonia humi sp. nov., isolated from soil. . Int J Syst Evol Microbiol 61, 65–70. [View Article] [PubMed]
    [Google Scholar]
  12. Kim S. B., Brown R., Oldfield C., Gilbert S. C., Goodfellow M. ( 1999 ). Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete. . Int J Syst Bacteriol 49, 1845–1851. [View Article] [PubMed]
    [Google Scholar]
  13. Kim S. B., Brown R., Oldfield C., Gilbert S. C., Iliarionov S., Goodfellow M. ( 2000 ). Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. . Int J Syst Evol Microbiol 50, 2031–2036. [View Article] [PubMed]
    [Google Scholar]
  14. Kim K. K., Lee K. C., Klenk H. P., Oh H. M., Lee J. S. ( 2009 ). Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream. . Int J Syst Evol Microbiol 59, 1992–1996. [View Article] [PubMed]
    [Google Scholar]
  15. 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, 716–721. [View Article] [PubMed]
    [Google Scholar]
  16. Klatte S., Kroppenstedt R. M., Schumann P., Altendorf K., Rainey F. A. ( 1996 ). Gordona hirsuta sp. nov.. Int J Syst Bacteriol 46, 876–880. [View Article] [PubMed]
    [Google Scholar]
  17. Kutchma A. J., Roberts M. A., Knaebel D. B., Crawford D. L. ( 1998 ). Small-scale isolation of genomic DNA from Streptomyces mycelia or spores. . Biotechniques 24, 452–456.[PubMed]
    [Google Scholar]
  18. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
     [Google Scholar]
  19. le Roes M., Goodwin C. M., Meyers P. R. ( 2008 ). Gordonia lacunae sp. nov., isolated from an estuary. . Syst Appl Microbiol 31, 17–23. [View Article] [PubMed]
    [Google Scholar]
  20. Linos A., Berekaa M. M., Steinbüchel A., Kim K. K., Spröer C., Kroppenstedt R. M. ( 2002 ). Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete. . Int J Syst Evol Microbiol 52, 1133–1139. [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Minnikin D. E., Alshamaony L., Goodfellow M. ( 1975 ). Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. . J Gen Microbiol 88, 200–204. [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. Park S., Kang S. J., Kim W., Yoon J. H. ( 2009 ). Gordonia hankookensis sp. nov., isolated from soil. . Int J Syst Evol Microbiol 59, 3172–3175. [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. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
     [Google Scholar]
  27. Soddell J. A., Stainsby F. M., Eales K. L., Seviour R. J., Goodfellow M. ( 2006 ). Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam. . Int J Syst Evol Microbiol 56, 2265–2269. [View Article] [PubMed]
    [Google Scholar]
  28. Stackebrandt E. ( 1988 ). Phylogenetic relationships vs. phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria. . Can J Microbiol 34, 552–556. [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Teather R. M., Wood P. J. ( 1982 ). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. . Appl Environ Microbiol 43, 777–780.[PubMed]
    [Google Scholar]
  31. Tindall B. J. ( 1990a ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128–130. [View Article]
    [Google Scholar]
  32. Tindall B. J. ( 1990b ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199–202. [View Article]
    [Google Scholar]
  33. Tsukamura M. ( 1971 ). Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. . J Gen Microbiol 68, 15–26. [View Article] [PubMed]
    [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. & 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, 463–464. [View Article]
    [Google Scholar]
  35. Yoon J. H., Lee J. J., Kang S. S., Takeuchi M., Shin Y. K., Lee S. T., Kang K. H., Park Y. H. ( 2000 ). Gordonia nitida sp. nov., a bacterium that degrades 3-ethylpyridine and 3-methylpyridine. . Int J Syst Evol Microbiol 50, 1203–1210. [View Article] [PubMed]
    [Google Scholar]
  36. Zhi X.-Y., Li W.-J., Stackebrandt E. ( 2009 ). An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. . Int J Syst Evol Microbiol 59, 589–608. [View Article] [PubMed]
    [Google Scholar]
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Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment
Int J Syst Evol Microbiol 63, 327 (2013); https://doi.org/10.1099/ijs.0.039289-0
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