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Deinococcus swuensis sp. nov., a gamma-radiation-resistant bacterium isolated from soil

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
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Abstract

Strain DY59T, a Gram-positive non-motile bacterium, was isolated from soil in South Korea, and was characterized to determine its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence of strain DY59T revealed that the strain DY59T belonged to the family Deinococcaceae in the class Deinococci. The highest degree of sequence similarities of strain DY59T were found with Deinococcus radiopugnans KACC 11999T (99.0%), Deinococcus marmoris KACC 12218T (97.9%), Deinococcus saxicola KACC 12240T (97.0%), Deinococcus aerolatus KACC 12745T (96.2%), and Deinococcus frigens KACC 12220T (96.1%). Chemotaxonomic data revealed that the predominant fatty acids were iso-C15:0 (19.0%), C16:1 ω7c (17.7%), C15:1 ω6c (12.6%), iso-C17:0 (10.3%), and iso-C17:1 ω9c (10.3%). A complex polar lipid profile consisted of a major unknown phosphoglycolipid. The predominant respiratory quinone is MK-8. The cell wall peptidoglycan contained D-alanine, L-glutamic acid, glycine, and L-ornithine (di-amino acid). The novel strain showed resistance to gamma radiation, with a D10 value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 5 kGy. Based on the phylogenetic, chemotaxonomic, and phenotypic data, strain DY59T (=KCTC 33033T =JCM 18581T) should be classified as a type strain of a novel species, for which the name Deinococcus swuensis sp. nov. is proposed.

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References

  • Brooks, B.W. and 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.19, 353–360.

    Article  Google Scholar 

  • Brown, A.E. 2008. Benson’s microbiological applications: laboratory manual in general microbiology, complete version, 10th Edition. McGraw-Hill.

    Google Scholar 

  • Collins, M.D. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev.45, 316–354.

    PubMed  CAS  Google Scholar 

  • Ezaki, T., Hashimoto, Y., and 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.

    Article  Google Scholar 

  • Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution39, 783–791.

    Article  Google Scholar 

  • Ferreira, A.C., Nobre, M.F., Rainey, F.A., Silva, T.M.T., Wait, R., Burghardt, J., Chung, A.P., and Costa, M.S.D. 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.

    Article  PubMed  CAS  Google Scholar 

  • Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. 1994. Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C., USA.

    Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Hirsch, P., Gallikowski, C.A., Siebert, J., Peissl, K., Kroppenstedt, R., Schumann, P., Stackebrandt, E., and 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.

    Article  PubMed  CAS  Google Scholar 

  • Im, W.-T., Jung, H.-M., Ten, L.N., Kim, M.K., Bora, N., Goodfellow, M., Lim, S., Jung, J., and 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.

    Article  PubMed  CAS  Google Scholar 

  • Kämpfer, P., Lodders, N., Huber, B., Falsen, E., and Busse, H.-J. 2008. Deinococcus aquatilis sp. nov., isolated from water. Int. J. Syst. Evol. Microbiol.58, 2803–2806.

    Article  PubMed  Google Scholar 

  • 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., and 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.

    Article  PubMed  CAS  Google Scholar 

  • Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.

    Book  Google Scholar 

  • Komagata, K. and Suzuki, K. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol.19, 161–207.

    Article  CAS  Google Scholar 

  • Lai, W.-A., Kämpfer, P., Arun, A.B., Shen, F.-T., Huber, B., Rekha, P.D., and Young, C.-C. 2006. Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L. Int. J. Syst. Evol. Microbiol.56, 787–791.

    Article  PubMed  CAS  Google Scholar 

  • Lim, S., Song, D., Joe, M., and Kim, D. 2012. Development of a qualitative dose indicator for gamma radiation using lyophilized Deinococcus. J. Microbiol. Biotechnol.22, 1296–1300.

    Article  PubMed  CAS  Google Scholar 

  • Lim, S., Yoon, H., Ryu, S., Jung, J., Lee, M., and Kim, D. 2006. A comparative evaluation of radiation-induced DNA damage using real-time PCR: influence of base composition. Radiat. Res.165, 430–437.

    Article  PubMed  CAS  Google Scholar 

  • Mesbah, M., Premachandran, U., and 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.

    Article  CAS  Google Scholar 

  • Minnikin, D.E., O’Donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J.H. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods2, 233–241.

    Article  CAS  Google Scholar 

  • Oyaizu, H., Stackebrandt, E., Schleifer, K.H., Ludwig, W., Pohla, H., Ito, H., Hirata, A., Oyaizu, Y., and 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.

    Article  CAS  Google Scholar 

  • Rainey, F.A., Ray, K., Ferreira, M., Gatz, B.Z., Nobre, M.F., Bagaley, D., Rash, B.A., Park, M.-J., Earl, A.M., Shank, N.C., andet al. 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.

    Article  PubMed  CAS  Google Scholar 

  • Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425.

    PubMed  CAS  Google Scholar 

  • Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark, DE, USA.

    Google Scholar 

  • Shin, Y.K., Lee, J.S., Chun, C.O., Kim, H.J., and Park, Y.H. 1996. Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T. J. Microbiol. Biotechnol.6, 68–69.

    CAS  Google Scholar 

  • Srinivasan, S., Kim, M.K., Lim, S., Joe, M., and Lee, M. 2012a. Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int. J. Syst. Evol. Microbiol.62, 1265–1270.

    Article  PubMed  CAS  Google Scholar 

  • Srinivasan, S., Lee, J.J., Lim, S., Joe, M., and Kim, M.K. 2012b. Deinococcus humi sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol.62, 2844–2850.

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt, E. and Goebel, B.M. 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.

    Article  CAS  Google Scholar 

  • Tamaoka, J. and Komagata, K. 1984. Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol. Lett.25, 125–128.

    Article  CAS  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol.28, 2731–2739.

    Article  PubMed  CAS  Google Scholar 

  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res.24, 4876–4882.

    Article  Google Scholar 

  • Wang, W., Mao, J., Zhang, Z., Tang, Q., Xie, Y., Zhu, J., Zhang, L., Liu, Z., Shi, Y., and Goodfellow, M. 2010. Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil. Int. J. Syst. Evol. Microbiol.60, 2006–2010.

    Article  PubMed  CAS  Google Scholar 

  • 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., Stackebrandt, E., andet 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.

    Article  Google Scholar 

  • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol.173, 697–703.

    PubMed  CAS  Google Scholar 

  • White, O., Eisen, J.A., Heidelberg, J.F., Hickey, E.K., Peterson, J.D., Dodson, R.J., Haft, D.H., Gwinn, M.L., Nelson, W.C., Richardson, D.L., andet al. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science286, 1571–1577.

    Article  PubMed  CAS  Google Scholar 

  • Yoo, S.-H., Weon, H.-Y., Kim, S.-J., Kim, Y.-S., Kim, B.-Y., and 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.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, 139-774, Republic of Korea

    Jae-Jin Lee & Myung Kyum Kim

  2. Honor’s Class, Seoul Women’s University, Seoul, 139-774, Republic of Korea

    Hyun Ji Lee, Gi Seon Jang, Ja Myoung Yu, Ji Yoon Cha, Su Jeong Kim & Eun Bit Lee

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  1. Jae-Jin Lee
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Lee, JJ., Lee, H.J., Jang, G.S. et al. Deinococcus swuensis sp. nov., a gamma-radiation-resistant bacterium isolated from soil. J Microbiol. 51, 305–311 (2013). https://doi.org/10.1007/s12275-013-3023-y

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  • DOI: https://doi.org/10.1007/s12275-013-3023-y

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