1887

Abstract

The taxonomic position of strain SD29, isolated from soil, was clarified using a polyphasic taxonomic approach. The organism produced an elementary branching mycelium which fragmented into rod/coccus-shaped elements and it possessed -diaminopimelic acid, arabinose, galactose as diagnostic diamino acid and sugars, MK-9(H) as predominant menaquinone, phospholipids of type PII and mycolic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SD29 was most closely related to DSM 44015 and DSM 44576, forming a distinct but loosely related branch in the phylogenetic tree. A number of physiological properties readily separated the isolate from its nearest neighbours. It is evident from genotypic and phenotypic data that strain SD29 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SD29 (=CGMCC 4.3492=JCM 13907).

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2007-03-01
2020-01-23
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References

  1. Chun, J. & Goodfellow, M. ( 1995; ). A phylogenetic analysis of genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.[CrossRef]
    [Google Scholar]
  2. Collins, M. D. ( 1985; ). Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  3. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  4. Fitch, W. M. ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef]
    [Google Scholar]
  5. Goodfellow, M., Isik, K. & Yates, E. ( 1999; ). Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold 312 (NF80), 47–82.
    [Google Scholar]
  6. Gordon, R. E. ( 1967; ). The taxonomy of soil bacteria. In The Ecology of Soil Bacteria, pp. 293–321. Edited by T. R. G. Gray & D. Parkinson. Liverpool: Liverpool University Press.
  7. Gordon, R. E. & Mihm, J. M. ( 1957; ). A comparative study of some strains received as nocardiae. J Bacteriol 73, 15–27.
    [Google Scholar]
  8. Hasegawa, T., Takizawa, M. & Tanida, S. ( 1983; ). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29, 319–322.[CrossRef]
    [Google Scholar]
  9. Huang, Y., Qi, W., Lu, Z., Liu, Z. & Goodfellow, M. ( 2001; ). Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil. Int J Syst Evol Microbiol 51, 1093–1097.[CrossRef]
    [Google Scholar]
  10. Iida, S., Taniguchi, H., Kageyama, A., Yazawa, K., Chibana, H., Murata, S., Nomura, F., Kroppenstedt, R. M. & Mikami, Y. ( 2005; ). Gordonia otitidis sp. nov., isolated from a patient with external otitis. Int J Syst Evol Microbiol 55, 1871–1876.[CrossRef]
    [Google Scholar]
  11. Kageyama, A., Iida, S., Yazawa, K., Kudo, T., Suzuki, S., Koga, T., Saito, H., Inagawa, H., Wada, A. & other authors ( 2006; ). Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan. Int J Syst Evol Microbiol 56, 1817–1821.[CrossRef]
    [Google Scholar]
  12. Kämpfer, M. & Kroppenstedt, R. M. ( 1996; ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989–1005.[CrossRef]
    [Google Scholar]
  13. 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.[CrossRef]
    [Google Scholar]
  14. Kim, K. K., Lee, C. S., Kroppenstedt, R. M., Stackebrandt, E. & Lee, S. T. ( 2003; ). Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor. Int J Syst Evol Microbiol 53, 1427–1433.[CrossRef]
    [Google Scholar]
  15. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  16. Klatte, S., Rainey, F. A. & Kroppenstedt, R. M. ( 1994; ). Transfer of Rhodococcus aichiensis Tsukamura 1982 and Nocardia amarae 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.[CrossRef]
    [Google Scholar]
  17. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  18. Kummer, C., Schumann, P. & Stackebrandt, E. ( 1999; ). Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int J Syst Bacteriol 49, 1513–1522.[CrossRef]
    [Google Scholar]
  19. Lechevalier, H. A. & Lechevalier, M. P. ( 1980; ). The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy (Special Publication no. 6), pp. 277–284. Edited by A. Dietz & D. W. Thayer. Arlington, VA: Society of Industrial Microbiology.
  20. Lechevalier, M. P. & Lechevalier, H. A. ( 1970; ). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20, 435–443.[CrossRef]
    [Google Scholar]
  21. Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A. ( 1977; ). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5, 249–260.[CrossRef]
    [Google Scholar]
  22. Linos, A., Steinbüchel, A., Spröer, C. & Kroppenstedt, R. M. ( 1999; ). Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from an automobile tyre. Int J Syst Bacteriol 49, 1785–1791.[CrossRef]
    [Google Scholar]
  23. Maldonado, L. A., Stainsby, F. M., Ward, A. C. & Goodfellow, M. ( 2003; ). Gordonia sinesedis sp. nov., a novel soil isolate. Antonie van Leeuwenhoek 83, 75–80.[CrossRef]
    [Google Scholar]
  24. 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.[CrossRef]
    [Google Scholar]
  25. 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 isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
    [Google Scholar]
  26. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  27. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101. Newark, DE: MIDI Inc.
  28. Shen, F.-T., Goodfellow, M., Jones, A. L., Chen, Y.-P., Arun, A. B., Lai, W.-A., Rekha, P. D. & Young, C.-C. ( 2006; ). Gordonia soli sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 56, 2597–2601.[CrossRef]
    [Google Scholar]
  29. Shirling, E. B. & Gottlieb, D. ( 1966; ). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]
    [Google Scholar]
  30. 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.[CrossRef]
    [Google Scholar]
  31. Stackebrandt, E., Smida, J. & 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.[CrossRef]
    [Google Scholar]
  32. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. ( 1997; ). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479–491.[CrossRef]
    [Google Scholar]
  33. Takeuchi, M. & Hatano, K. ( 1998; ). Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere. Int J Syst Bacteriol 48, 907–912.[CrossRef]
    [Google Scholar]
  34. 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.[CrossRef]
    [Google Scholar]
  35. Wu, C., Lu, X., Qin, M., Wang, Y. & Ruan, J. ( 1989; ). Analysis of menaquinone compound in microbial cells by HPLC. Microbiology (Beijing) 16, 176–178 (in Chinese).
    [Google Scholar]
  36. Xue, Y., Sun, X., Zhou, P., Liu, R., Liang, F. & Ma, Y. ( 2003; ). Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well. Int J Syst Evol Microbiol 53, 1643–1646.[CrossRef]
    [Google Scholar]
  37. 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-ethylpyridene and 3-methylpyridine. Int J Syst Evol Microbiol 50, 1203–1210.[CrossRef]
    [Google Scholar]
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