Antonie van Leeuwenhoek

, Volume 83, Issue 1, pp 75–80 | Cite as

Gordonia sinesedis sp. nov., a novel soil isolate

  • Luis A. Maldonado
  • Fiona M. Stainsby
  • Alan C. Ward
  • Michael Goodfellow
Article

Abstract

The taxonomic position of an actinomycete isolated from soil was evaluated using a polyphasic approach. The organism, strain J72, was found to have chemical and morphological properties consistent with its assignment to the genus Gordonia. A nearly complete 16S rDNA sequence of the strain was determined by direct sequencing of the amplified gene. The tested strain formed a distinct phylogenetic line within the evolutionary radiation occupied by the genus Gordonia and was most closely related to G. polyisoprenivorans DSM 44302T. The phenotypic profile of strain 372 readily distinguishes it from representatives of the validly described species of Gordonia. The combined genotypic and phenotypic data show that strain J72 merits recognition as a new species of Gordonia. The name proposed for the new species is Gordonia sinesedis; the type strain is J72T (= DSM 44455T = NCIMB 13802T).

16S rDNA sequencing Gordonia Mycolic acids Polyphasic taxonomy 

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References

  1. Colquhoun J.A., Mexson J., Goodfellow M., Ward A.C., Horikoshi K. and Bull A.T. 1998. Novel rhodococci and other mycolate actinomycetes from the deep sea. Antonie van Leeuwenhoek 74: 27–40.PubMedCrossRefGoogle Scholar
  2. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368–376.PubMedCrossRefGoogle Scholar
  3. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.CrossRefGoogle Scholar
  4. Felsenstein J. 1993. PHYLIP (Phylogenetic Inference Package), version 3.5c. Department of Genetics, University of Washington, Seattle, USA.Google Scholar
  5. Fitch W.M. and Margoliash E. 1967. Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155: 279–284.PubMedGoogle Scholar
  6. Goodfellow M., Mordarski M., Szyba K. and Pulverer G. 1978. Relationship among rhodococci based on deoxyribonucleic acid reasociation. In: Freerksen E., Tárnok I. and Thumim J.H. (eds), Genetics of Actinomycetales. Gustav Fischer Verlag, Stuttgart, pp. 231–234.Google Scholar
  7. Goodfellow M., Davenport R., Stainsby F.M. and Curtis T.P. 1996. Actinomycete diversity associated with foaming in activated sludge plants. J. Ind. Microbiol. 17: 268–280.CrossRefGoogle Scholar
  8. Goodfellow M., Alderson G. and Chun J. 1998a. Rhodococcal systematics: problems and developments. Antonie van Leeuwenhoek 74: 1–12.CrossRefGoogle Scholar
  9. Goodfellow M., Stainsby F.M., Davenport R., Chun J. and Curtis T. 1998b. Activated sludge foaming: the true extent of actinomycete diversity. Wat. Sci. Tech. 137: 511–519.CrossRefGoogle Scholar
  10. Goodfellow M., Isik K. and Yates E. 1999. Actinomycete systematics: an unfinished synthesis. Nova Acta Leopoldina 312 NF80: 47–82.Google Scholar
  11. Goodfellow M., Chun J., Stackebrandt E. and Kroppenstedt R.M. 2001. Transfer of Tsukamurella wratislaviensis Goodfellow (1991) to the genus Rhodococcus as Rhodococcus wratislaviensis comb. nov. Int. J. Syst. Evol. Microbiol. 52: 749–755.CrossRefGoogle Scholar
  12. Gordon R.E. and Mihm J.M. 1962. Identification of Nocardia caviae (Erikson) nov.comb. Ann. N.Y. Acad. Sci. 98: 628–636.Google Scholar
  13. Jukes T.H. and Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N. (ed.), Mammalian Protein Metabolism Vol. 3. Academic Press, New York, pp. 21–132.Google Scholar
  14. Kim S.B., Falconer C., Williams E. and Goodfellow M. 1998. Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int. J. Syst. Bacteriol. 48: 59–68.PubMedGoogle Scholar
  15. Kim S.B., Brown R., Oldfield C., Gilbert S.C. and Goodfellow M. 1999. Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete. Int. J. Syst. Bacteriol. 49: 1845–1851.PubMedGoogle Scholar
  16. Kim S.B., Brown R., Oldfield C., Gilbert S.C., Iliarionov S. and Goodfellow M. 2000. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int. J. Syst. Bacteriol. 50: 2031–2036.Google Scholar
  17. Klatte S., Rainey F.A. and Kroppenstedt R.M. 1994. Transfer of Rhodococcus aichiensis Tsukamura (1982) and Nocardia reviamarae Lechevalier and Lechevalier (1974) to the genus Gordona as Gordona aichiensis comb. nov. and Gordona amarae comb. nov. Int. J. Syst. Bacteriol. 44: 769–773.PubMedGoogle Scholar
  18. Kluge A.G. and Farris F.S. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1–32.CrossRefGoogle Scholar
  19. Kummer C., Schumann P. and Stackebrandt E. 1999. Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int. J. Syst. Bacteriol. 49: 1513–1522.PubMedGoogle Scholar
  20. Lechevalier H.A. and Lechevalier M.P. 1970. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int. J. Syst. Bacteriol. 24: 278–288.Google Scholar
  21. Linos A., Steinbüchel A., Spröer C. and Kroppenstedt R.M. 1999. Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from an automobile tyre. Int. J. Syst. Bacteriol. 49: 1785–1791.PubMedGoogle Scholar
  22. Orchard V.A., Goodfellow M. and Williams S.T. 1977. Selective isolation and occurrence of nocardiae in soil. Soil Biol. Biochem. 9: 233–238.CrossRefGoogle Scholar
  23. Saitou N. and Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.PubMedGoogle Scholar
  24. Schaal K.P. 1985. Laboratory diagnosis of actinomycete diseases. In: Goodfellow M. and Minnikin D.E. (eds), Chemical Methods in Bacterial Systematics. Academic Press, London (pp 359–381).Google Scholar
  25. Stackebrandt E., Smida J. and Collins M.D. 1988. Evidence of phylogenetic heterogeneity within the genus Rhodococcus: revival of the genus Gordona (Tsukamura). J. Gen. Appl. Microbiol. 34: 341–348.Google Scholar
  26. Stackebrandt E., Rainey F.A. and Ward-Rainey N.-L. 1997. Proposal for a new hierarchic classification system,Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47: 479–491.CrossRefGoogle Scholar
  27. Takeuchi M. and Hatano K. 1998. Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere. Int. J. Syst. Bacteriol. 48: 907–912.PubMedGoogle Scholar
  28. 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.PubMedGoogle Scholar
  29. Uchida K., Kudo T., Suzuki K. and Nakano T. 1999. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J. Gen. Appl Microbiol. 45: 49–56.PubMedCrossRefGoogle Scholar
  30. Wayne L.G., Brenner D.J. and Colwell R.R., and nine 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.Google Scholar
  31. Yoon J.H., Lee J.J., Kang S.S., Takeuchi M., Shin Y.K., Lee S.T. et al. 2000. Gordonia nitida sp. nov., a bacterium that degrades 3-ethylpyridine and 3-methylpyridine. Int. J. Syst. Evol. Microbiol. 50: 1203–1210.PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Luis A. Maldonado
    • 1
  • Fiona M. Stainsby
    • 1
  • Alan C. Ward
    • 1
  • Michael Goodfellow
    • 1
  1. 1.Department of Agricultural and Environmental ScienceUniversity of NewcastleNewcastle upon TyneUnited Kingdom

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