1887

Abstract

Two gamma- and UVC-resistant bacterial strains, designated JSH3-1 and 9-2-2, were isolated from garden soil in South Korea. Cells were Gram-stain-positive, aerobic, non-motile and spherical. A polyphasic approach was used to study the taxonomic properties of strains JSH3-1 and 9-2-2. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences of strains JSH3-1 and 9-2-2 indicated highest similarity with Deinococcus radiomollis PO-04-20-132 (94.7 and 94.9 %, respectively); levels of sequence similarity with the type strains of other Deinococcus species were less than 94.0 %. Strains JSH3-1 and 9-2-2 shared relatively high 16S rRNA gene sequence similarity (98.7 %) and had a high DNA reassociation value of 81±0.5 %. Meanwhile, they showed low levels of DNA reassociation (<25 %) with other closely related species of the genus Deinococcus . The two strains showed chemotaxonomic features typical of the genus Deinococcus , with the presence of menaquinone 8 as the respiratory quinone. The predominant fatty acids were iso-C17 : 0, iso-C13 : 0 and anteiso-C13 : 0. The polar lipids comprised phosphoglycolipid, aminophospholipid, glycolipid and unknown aminolipids. The DNA G+C contents of strains JSH3-1 and 9-2-2 were 62.0 and 61.9 mol%, respectively. On the basis of their phenotypic and genotypic characteristics, and phylogenetic distinction, strains JSH3-1 (=KCTC 33790=JCM 31311) and 9-2-2 (=KCTC 33789=JCM 31310) should be classified within a novel species of the genus Deinococcus , for which the name Deinococcus ruber sp. nov. is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001567
2017-02-20
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/1/72.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001567&mimeType=html&fmt=ahah

References

  1. Brooks BW, Murray RGE. Nomenclature for “Micrococcus radiodurans” and other radiation-resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Evol Microbiol 1981;31:353–360
    [Google Scholar]
  2. Cha SH, Srinivasan S, Seo TG, Kim MK. Deinococcus soli sp. nov., a gamma-radiation-resistant bacterium isolated from rice field soil. Curr Microbiol 2014;68:777–783 [CrossRef][PubMed]
    [Google Scholar]
  3. Srinivasan S, Lee JJ, Lim SY, Joe MH, Im SH et al. Deinococcus radioresistens sp. nov., a UV and gamma radiation-resistant bacterium isolated from mountain soil. Antonie van Leeuwenhoek 2015;107:539–545 [CrossRef][PubMed]
    [Google Scholar]
  4. Lee S, Yoon H, Bae H, Ha J, Pak H et al. Implication of ultraviolet B radiation exposure for non-melanoma skin cancer in Korea. Mol Cell Toxicol 2014;10:91–94 [CrossRef]
    [Google Scholar]
  5. Kisker C, Kuper J, van Houten B. Prokaryotic nucleotide excision repair. Cold Spring Harb Perspect Biol 2013;5:a012591 [CrossRef][PubMed]
    [Google Scholar]
  6. Joo ES, Kim EB, Jeon SH, Srinivasan S. Complete genome sequence of Deinococcus soli N5T, a gamma-radiation- resistant bacterium isolated from rice field in South Korea. J Biotechnol 2015;211:115–116 [CrossRef][PubMed]
    [Google Scholar]
  7. Kim MK, Back C-G, Jung H-Y, Srinivasan S. Complete genome sequence of Spirosoma radiotolerans, a gamma-radiation-resistant bacterium isolated from rice field in South Korea. J Biotechnol 2015;208:11–12 [CrossRef][PubMed]
    [Google Scholar]
  8. Kim MK, Srinivasan S, Back C-G, Joo ES, Lee S-Y et al. Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity. Mol Cell Toxicol 2015;11:315–321 [CrossRef]
    [Google Scholar]
  9. Michael MC, John RB. Deinococcus radiodurans– the consummate survivor. Nature Rev Microbiol 2005;3:882–892 [CrossRef][PubMed]
    [Google Scholar]
  10. Bolhuis H, Stal LJ. Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. ISME J 2011;5:1701–1712 [CrossRef][PubMed]
    [Google Scholar]
  11. Rainey FA, Ray K, Ferreira M, Gatz BZ, Nobre MF et al. 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 2005;71:5225–5235 [CrossRef][PubMed]
    [Google Scholar]
  12. Oyaizu H, Stackebrandt E, Schleifer KH, Ludwig W, Pohla H et al. A radiation-resistant rod-shaped bacterium, Deinobacter grandis gen. nov., sp. nov., with peptidoglycan containing ornithine. Int J Syst Evol Microbiol 1987;37:62–67
    [Google Scholar]
  13. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  14. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999;41:95–98
    [Google Scholar]
  15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  16. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  17. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983;[CrossRef]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  19. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  21. Doetsch R. Determinative methods of light microscopy. In Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. et al. (editors) Manual Methods General Bacteriol Washington, DC: American Society for Microbiology; 1981; pp.21–33
    [Google Scholar]
  22. Im WT, Jung HM, Ten LN, Kim MK, Bora N et al. Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2008;58:2348–2353 [CrossRef][PubMed]
    [Google Scholar]
  23. Lee JJ, Srinivasan S, Lim S, Joe M, Im S et al. Deinococcus puniceus sp. nov., a bacterium isolated from soil irradiated with gamma radiation. Curr Microbiol 2015;70:464–469 [CrossRef][PubMed]
    [Google Scholar]
  24. Im S, Song D, Joe M, Kim D, Park DH et al. Comparative survival analysis of 12 histidine kinase mutants of Deinococcus radiodurans after exposure to DNA-damaging agents. Bioprocess Biosyst Eng 2013;36:781–789 [CrossRef][PubMed]
    [Google Scholar]
  25. Selvam K, Duncan JR, Tanaka M, Battista JR. DdrA, DdrD, and PprA: components of UV and mitomycin C resistance in Deinococcus radiodurans R1. PLoS One 2013;8:e69007 [CrossRef][PubMed]
    [Google Scholar]
  26. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988;38:358–361 [CrossRef]
    [Google Scholar]
  27. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  28. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
    [Google Scholar]
  29. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241 [CrossRef]
    [Google Scholar]
  30. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  31. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric DNA–DNA reassociation in microdilution wells as an alternative to membrane filter reassociation in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 1989;39:224–229
    [Google Scholar]
  32. Battista JR. Deinococcus-Thermus group. In: eLS Chichester: John Wiley & Sons, Ltd; 2016
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001567
Loading
/content/journal/ijsem/10.1099/ijsem.0.001567
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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