Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지

Nocardioides tritolerans sp. nov., Isolated from Soil in Bigeum Island, Korea

  • Published : 2008.07.31
Download PDF
⟨ Previous Next ⟩

Abstract

A Gram-positive strain designated as MSL-$14^T$ isolated from a soil sample collected from Bigeum Island, Korea, was subjected to polyphasic taxonomy. The isolate was strictly aerobic. Cells were short rods and motile. Optimum growth temperature and pH was 28$^{\circ}C$ and 7.0, respectively. It was characterized chemotaxonomically as having a cell-wall peptidoglycan type based on LL-2,6-diaminopimelic acid and MK-$8(H_4)$ as the predominant menaquinone. The major fatty acids were iso-$C_{16:0}$, $C_{17:1}$ omega8c, and $C_{18:1}$ omega9c. The G+C content was 67.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain MSL-$14^T$ is affiliated to the genus Nocardioides and formed a distinct lineage within the genus. MSL-$14^T$ showed highest sequence similarity to Nocardioides aestuarii JCM $12125^T$, having a similarity of 96.5%. Based on the 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain MSL-$14^T$ should be classified as representing a novel member of the genus Nocardioides, for which we propose the name Nocardioides tritolerans sp. novo The type strain is strain MSL-$14^T$ (=KCTC $19289^T$=DSM $19320^T$).

Keywords

References

  1. Bakermans, C. and E. L. Madsen. 2002. Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tarwaste-contaminated aquifer waters. Microb. Ecol. 44: 95-106
  2. Chun, J., J.-H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim, and Y. W. Lim. 2007. EzTaxon: A Web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequence. Int. J. Syst. Evol. Microbiol. 57: 2259-2261 https://doi.org/10.1099/ijs.0.64915-0
  3. Felsenstein, J. 1981. Evolutionary tree from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376 https://doi.org/10.1007/BF01734359
  4. Felsenstein, J. 1985. Confidence limits on phylogenetics: An approach using the bootstrap. Evolution 39: 783-791 https://doi.org/10.2307/2408678
  5. Felsenstein, J. 2002. PHYLIP (phylogeny inference package), version 3.6a. Distributed by the author. Department of Genetics, University of Washington, Seattle, U.S.A
  6. Hopwood, D. A., M. J. Bibb, K. F. Chater, T. Kieser, C. J. Bruton, H. M. Kieser, et al. 1985. Genetic Manipulation of Streptomyces - A Laboratory Manual. The John Innes Foundation, Norwich
  7. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J. Mol. Evol. 16: 111-120 https://doi.org/10.1007/BF01731581
  8. Kluge, A. G. and F. S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1-32 https://doi.org/10.2307/2412407
  9. Komagata, K. and K. Suzuki. 1987. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol. 19: 161-206
  10. Kubota, M., K. Kawahara, K. Sekiya, T. Uchida, Y. Hattori, H. Futamata, and A. Hiraishi. 2005. Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst. Appl. Microbiol. 28: 165-174 https://doi.org/10.1016/j.syapm.2004.10.002
  11. Lanyi, B. 1987. Classical and rapid identification methods for medically important bacteria. Methods Microbiol. 19: 1-67
  12. Lechevalier, M. P. and H. Lechevalier. 1970. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int. J. Syst. Bacteriol. 20: 435-443 https://doi.org/10.1099/00207713-20-4-435
  13. Leifson, E. 1963. Determination of carbohydrate metabolism of marine bacteria. J. Bacteriol. 85: 1183-1184
  14. Marmur, J. and P. Doty. 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 5: 109-118 https://doi.org/10.1016/S0022-2836(62)80066-7
  15. Mesbah, M., U. Premachandran, and W. B. Whitman. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int. J. Syst. Bacteriol. 39: 159-167 https://doi.org/10.1099/00207713-39-2-159
  16. Prauser, H. 1976. Nocardioides, a new genus of the order Actinomycetales. Int. J. Syst. Bacteriol. 26: 58-65 https://doi.org/10.1099/00207713-26-1-58
  17. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic tree. Mol. Biol. Evol. 4: 406-425
  18. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett. 20: 1-6
  19. Stackebrandt, E. and B. M. Goebel. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol 44: 846-849 https://doi.org/10.1099/00207713-44-4-846
  20. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The Clustal X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876-4888
  21. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, et al. 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 https://doi.org/10.1099/00207713-37-4-463
  22. Xu, P., W. J. Li, L. H. Xu, and C. L. Jiang. 2003. A microwave based method for genomic DNA extraction from actinomycetes. Microbiology 30: 82-84
  23. Yi, H. and J. Chun. 2004. Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 54: 2151-2154 https://doi.org/10.1099/ijs.0.63192-0
  24. Yoon, J.-H. and Y.-H. Park. 2006. The genus Nocardioides. pp. 1099-1113. In M. Dworkin, S. Falkow, E. Rosenberg, K.- H. Schleifer, and E. Stackebrandt (eds.), The Prokaryotes. A Handbook on the Biology of Bacteria. 3rd Ed. Springer
  25. Yoon, J.-H., Y.-G. Cho, S. T. Lee, K.-I. Suzuki, T. Nakase, and Y.-H. Park. 1999. Nocardioides nitrophenolicus sp. nov., a pnitrophenol-degrading bacterium. Int. J. Syst. Bacteriol. 49: 675-680 https://doi.org/10.1099/00207713-49-2-675
  26. Yoon, J.-H., J.-K. Lee, S.-Y. Jung, J.-A. Kim, H.-K. Kim, and T.-K. Oh. 2006. Nocardioides kongjuensis sp. nov., an Nacylhomoserine lactone-degrading bacterium. Int. J. Syst. Evol. Microbiol. 56: 1783-1787 https://doi.org/10.1099/ijs.0.64120-0