1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 62, Issue Pt_12

sp. nov., isolated from soil Free

Abstract

A Gram-staining-positive, strictly aerobic, spherical, non-motile, red-pigmented bacterium, designated strain MK03, was isolated from a soil sample collected in South Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain MK03 was placed in a clade formed by members of the genus in the family and appeared to be most closely related to 5516T-9 (97.4 % sequence similarity), AA-63 (97.2 %), ATCC 19172 (97.2 %) and AA-1444 (96.9 %). The genomic DNA G+C content of the novel strain was 64.5 mol%. The chemotaxonomic characteristics of strain MK03 were typical of members of the genus : MK-8 was identified as the predominant respiratory quinine, the major fatty acids were Cω7, Cω6, C and Cornithine was found to be the diamino acid in the cell-wall peptidoglycan and the novel strain showed resistance to gamma radiation, with a D value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 9 kGy. In hybridization experiments, only low DNA–DNA relatedness values (11.6–34.5 %) were recorded between the novel strain and its closest relatives in the genus . Based on the phylogenetic, chemotaxonomic, phenotypic and DNA–DNA relatedness data, strain MK03 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MK03 ( = KCTC 13619  = JCM 17915).

  • Published Online:
Funding
This study was supported by the:
  • Seoul Women’s University
© 2012 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.037234-0
2012-12-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/12/2844.html?itemId=/content/journal/ijsem/10.1099/ijs.0.037234-0&mimeType=html&fmt=ahah

References

  1. 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[PubMed] [CrossRef]
     [Google Scholar]
  2. Buck J. D. 1982; Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
     [Google Scholar]
  3. Cappuccino J. G., Sherman N. 2002 Microbiology: a Laboratory Manual, 6th edn. San Francisco: Benjamin/Cummings;
     [Google Scholar]
  4. Cox M. M., Battista J. R. 2005; Deinococcus radiodurans – the consummate survivor. Nat Rev Microbiol 3:882–892 [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. 1985; Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
     [Google Scholar]
  7. 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 [View Article][PubMed]
     [Google Scholar]
  8. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
     [Google Scholar]
  9. 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]
  10. Hiraishi A., Ueda Y., Ishihara J., Mori T. 1996; Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469 [View Article]
     [Google Scholar]
  11. Im W. T., Jung H. M., Ten L. N., Kim M. K., Bora N., Goodfellow M., Lim S., Jung J., Lee S. T. 2008; Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 58:2348–2353 [View Article][PubMed]
     [Google Scholar]
  12. 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[PubMed]
     [Google Scholar]
  13. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H., Yi H., Won S., Chun J. 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]
  14. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
     [Google Scholar]
  15. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [View Article][PubMed]
     [Google Scholar]
  16. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
     [Google Scholar]
  17. Kwon J. Y., Seo Y. R. 2010; Genome-wide profiling induced by ionizing radiation (IR) in non-small cell lung cancer (NSCLC) grown as three-dimensional spheroid. Mol Cell Toxicol 6:229–237 [View Article]
     [Google Scholar]
  18. 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]
  19. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. 1977; Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117 [View Article]
     [Google Scholar]
  20. 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 [View Article]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.;
     [Google Scholar]
  24. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477[PubMed]
     [Google Scholar]
  25. Seong K. M., Kim C. S., Jeon H. Y., Oh S.-H., Nam S. Y., Yang K. H., Kim J.-Y., Jin Y.-W. 2010; Intrinsic radiosensitivity correlated with radiation-induced ROS and cell cycle regulation. Mol Cell Toxicol 6:1–7 [View Article]
     [Google Scholar]
  26. Servinsky M. D., Julin D. A. 2007; Effect of a recD mutation on DNA damage resistance and transformation in Deinococcus radiodurans . J Bacteriol 189:5101–5107 [View Article][PubMed]
     [Google Scholar]
  27. Srinivasan S., Kim M. K., Lim S., Joe M., Lee M. 2012; Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int J Syst Evol Microbiol 62:1265–1270[PubMed] [CrossRef]
     [Google Scholar]
  28. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
     [Google Scholar]
  29. 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 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. 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 [View Article][PubMed]
     [Google Scholar]
  32. Yang Y., Itoh T., Yokobori S., Itahashi S., Shimada H., Satoh K., Ohba H., Narumi I., Yamagishi A. 2009; Deinococcus aerius sp. nov., isolated from the high atmosphere. Int J Syst Evol Microbiol 59:1862–1866 [View Article][PubMed]
     [Google Scholar]
  33. Yang Y., Itoh T., Yokobori S., Shimada H., Itahashi S., Satoh K., Ohba H., Narumi I., Yamagishi A. 2010; Deinococcus aetherius sp. nov., isolated from the stratosphere. Int J Syst Evol Microbiol 60:776–779 [View Article][PubMed]
     [Google Scholar]
  34. Yoo S. H., Weon H. Y., Kim S. J., Kim Y. S., Kim B. Y., Kwon S. W. 2010; Deinococcus aerolatus sp. nov. and Deinococcus aerophilus sp. nov., isolated from air samples. Int J Syst Evol Microbiol 60:1191–1195 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.037234-0
Loading
Deinococcus humi sp. nov., isolated from soil
Int J Syst Evol Microbiol 62, 2844 (2012); https://doi.org/10.1099/ijs.0.037234-0
/content/journal/ijsem/10.1099/ijs.0.037234-0
/content/journal/ijsem/10.1099/ijs.0.037234-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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