1887

Abstract

The taxonomic positions of two environmental isolates from South Korea were established using a combination of genotypic and phenotypic data. The organisms, designated PB314 and Ho-08, were Gram-negative, rod-shaped and non-spore-forming and had chemotaxonomic properties consistent with their classification in the genus 16S rRNA gene tree, the highest sequence similarities being shown to the type strains of (96.3–96.7 %) and (96.3–96.4 %). The isolates shared relatively high 16S rRNA gene sequence similarity (98.1 %) but had a DNA–DNA relatedness value of only 22 %. Chemotaxonomic data revealed that both strains possess quinone system MK-8 as the predominant compound, C 7 and C as major fatty acids and ornithine as a diamino acid in the peptidoglycan structure, corroborating our assignment of the strains to the genus . The results of phylogenetic analyses based on 16S rRNA gene sequences, DNA–DNA relatedness values and physiological and biochemical tests clearly demonstrated that the two strains represent distinct species. On the basis of these data, two novel species, sp. nov. (type strain PB314 =KCTC 12552 =NBRC 101311) and sp. nov. (type strain Ho-08 =KCTC 12553 =NBRC 101312), are proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.64082-0
2008-10-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/58/10/2348.html?itemId=/content/journal/ijsem/10.1099/ijs.0.64082-0&mimeType=html&fmt=ahah

References

  1. Atlas, R. M.(1993).Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
  2. Battista, J. R. & Rainey, F. A.(2001). Order I. Deinococcales Rainey, Nobre, Schumann, Stackebrandt and da Costa 1997, 513VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, p. 395. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
  3. Battista, J. R., Earl, A. M. & Park, M.-J.(1999). Why is Deinococcus radiodurans so resistant to ionizing radiation? Trends Microbiol 7, 362–365.[CrossRef] [Google Scholar]
  4. Brooks, B. W. & Murray, R. G. E.(1981). Nomenclature for “Micrococcus radiodurans” and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Bacteriol 31, 353–360.[CrossRef] [Google Scholar]
  5. Buck, J. D.(1982). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992–993. [Google Scholar]
  6. Collins, M. D. & Jones, D.(1981). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45, 316–354. [Google Scholar]
  7. de Groot, A., Chapon, V., Servant, P., Christen, R., Fischer-Le Saux, M., Sommer, S. & Heulin, T.(2005).Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 55, 2441–2446.[CrossRef] [Google Scholar]
  8. 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.[CrossRef] [Google Scholar]
  9. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  10. Felsenstein, J.(1989).phylip – phylogeny inference package (version 3.2). Cladistics 5, 164–166. [Google Scholar]
  11. Ferreira, A. C., Nobre, M. F., Rainey, F. A., Silva, M. T., Wait, R., Burghardt, J., Chung, A. P. & da Costa, M. S.(1997).Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 47, 939–947.[CrossRef] [Google Scholar]
  12. 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]
  13. Hall, T. A.(1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98. [Google Scholar]
  14. Hirsch, P., Gallikowski, C. A., Siebert, J., Peissl, K., Kroppenstedt, R., Schumann, P., Stackebrandt, E. & Anderson, R.(2004).Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Syst Appl Microbiol 27, 636–645.[CrossRef] [Google Scholar]
  15. Im, W.-T., Kang, M.-S., Park, H.-Y., Kim, M.-K. & Lee, S.-T.(2003). Culturable bacterial strain's diversity of environmental samples. In Proceedings of the International Meeting of the Federation of Korean Microbiological Societies, abstract B4023, p. 165. Seoul: Federation of Korean Microbiological Societies.
  16. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T.(2005).Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43, 152–157. [Google Scholar]
  17. Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  18. Kouker, G. & Jaeger, K.-E.(1987). Specific and sensitive plate assay for bacterial lipase. Appl Environ Microbiol 53, 211–213. [Google Scholar]
  19. 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]
  20. Lai, W. A., Kämpfer, P., Arun, A. B., Shen, F. T., Huber, B., Rekha, P. D. & Young, C. C.(2006).Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. Int J Syst Evol Microbiol 56, 787–791.[CrossRef] [Google Scholar]
  21. Mattimore, V. & Battista, J. R.(1996). Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. J Bacteriol 178, 633–637. [Google Scholar]
  22. 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.[CrossRef] [Google Scholar]
  23. Oyaizu, H., Stackebrandt, E., Schleifer, K. H., Ludwig, W., Pohla, H., Ito, H., Hirata, A., Oyaizu, Y. & Komagata, K.(1987). A radiation-resistant rod-shaped bacterium, Deinobacter grandis gen. nov., sp. nov., with peptidoglycan containing ornithine. Int J Syst Bacteriol 37, 62–67.[CrossRef] [Google Scholar]
  24. Rainey, F. A., Nobre, M. F., Schumann, P., Stackebrandt, E. & da Costa, M. S.(1997). Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. Int J Syst Bacteriol 47, 510–514.[CrossRef] [Google Scholar]
  25. Rainey, F. A., Ray, K., Ferreira, M., Gatz, B. Z., Nobre, M. F., Bagaley, D., Rash, B. A., Park, M. J., Earl, A. M. & other authors(2005). Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl Environ Microbiol 71, 5225–5235.[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, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  28. Schleifer, K. H. & Kandler, O.(1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477. [Google Scholar]
  29. Shashidhar, R. & Bandekar, J. R.(2006).Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India. FEMS Microbiol Lett 254, 275–280.[CrossRef] [Google Scholar]
  30. Shin, Y. K., Lee, J.-S., Chun, C. O., Kim, H.-J. & Park, Y.-H.(1996). Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J Microbiol Biotechnol 6, 68–69. [Google Scholar]
  31. Staneck, J. L. & Roberts, G. D.(1974). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226–231. [Google Scholar]
  32. Suresh, K., Reddy, G. S., Sengupta, S. & Shivaji, S.(2004).Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India. Int J Syst Evol Microbiol 54, 457–461.[CrossRef] [Google Scholar]
  33. Ten, L. N., Im, W.-T., Kim, M.-K., Kang, M.-S. & Lee, S.-T.(2004). Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56, 375–382.[CrossRef] [Google Scholar]
  34. 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, 4876–4882.[CrossRef] [Google Scholar]
  35. 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.[CrossRef] [Google Scholar]
  36. Weon, H. Y., Kim, B. Y., Schumann, P., Son, J. A., Jang, J., Go, S. J. & Kwon, S. W.(2007).Deinococcus cellulosilyticus sp. nov., isolated from air. Int J Syst Evol Microbiol 57, 1685–1688.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.64082-0
Loading
/content/journal/ijsem/10.1099/ijs.0.64082-0
Loading

Data & Media loading...

Supplements

[PDF file of Supplementary Figs S1 and S2](108 KB)

PDF

Cellular fatty acid profiles of strains PB314 and Ho-08 and related species of genus . [PDF](133 KB)

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error