Journal of Microbiology

, Volume 54, Issue 8, pp 537–542 | Cite as

Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea

  • Jae-Jin Lee
  • Yeon-Hee Lee
  • Su-Jin Park
  • Sangyong Lim
  • Sun-Wook Jeong
  • Seung-Yeol Lee
  • Young-Je Cho
  • Myung Kyum Kim
  • Hee-Young JungEmail author
Microbial Systematics and Evolutionary Microbiology


Strain 16F1ET was isolated from a 3-kGy-irradiated sediment sample collected at Han River in Seoul, Republic of Korea. Cells of this strain were observed to be Gram-positive, pililike structure, and short rod shape, and colonies were red in color. The strain showed the highest degree of 16S rRNA gene sequence similarity to Deinococcus aquaticus PB314T (98.8%), Deinococcus depolymerans TDMA-24T (98.1%), Deinococcus caeni Ho-08T (98.0%), and Deinococcus grandis DSM 3963T (97.0%). 16S rRNA gene sequence analysis identified this strain as a member of the genus Deinococcus (Family: Deinococcaceae). The genomic DNA G+C content of strain 16F1ET was 66.9 mol%. The low levels of DNA-DNA hybridization (< 56.2%) with the species mentioned above identified strain 16F1ET as a novel Deinococcus species. Its oxidase and catalase activities as well as the production of acid from glucose were positive. Growth of the strain was observed at 10–37°C (optimum: 20–30°C) and pH 4–10 (optimum: pH 7–8). The cells tolerated less than 5% NaCl and had low resistance to gamma radiation (D10 < 4 kGy). Strain 16F1ET possessed the following chemotaxonomic characteristics: C16:0, C15:1 ω6c, and C16:1 ω7c as the major fatty acids; phosphoglycolipid as the predominant polar lipid; and menaquinone-8 as the predominant respiratory isoprenoid quinone. Based on the polyphasic evidence, as well as the phylogenetic, genotypic, phenotypic, and chemotaxonomic characterization results, strain 16F1ET (=KCTC 33793T =JCM 31404T) is proposed to represent the type strain of a novel species, Deinococcus seoulensis sp. nov.


Deinococcus polyphasic taxonomy gamma-radiation resistance 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

12275_2016_6253_MOESM1_ESM.pdf (888 kb)
Supplementary material, approximately 891 KB.


  1. Ahmed, I., Abbas, S., Kudo, T., Iqbal, M., Fujiwara, T., and Ohkuma, M. 2014. Deinococcus citri sp. nov., isolated from citrus leaf canker lesions. Int. J. Syst. Evol. Microbiol. 64, 4134–4140.CrossRefPubMedGoogle Scholar
  2. Asker, D., Awad, T.S., McLandsborough, L., Beppu, T., and Ueda, K. 2011. Deinococcus depolymerans sp. nov., a gamma- and UVradiation- resistant bacterium, isolated from a naturally radioactive site. Int. J. Syst. Evol. Microbiol. 61, 1448–1453.CrossRefPubMedGoogle Scholar
  3. Bernardet, J.F., Nakagawa, Y., Holmes, B., and Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 2002. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int. J. Syst. Evol. Microbiol. 52, 1049–1070.PubMedGoogle Scholar
  4. 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. Evol. Microbiol. 31, 353–360.Google Scholar
  5. Buck, J.D. 1982. Non-staining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44, 992–993.PubMedPubMedCentralGoogle Scholar
  6. Cha, S., Srinivasan, S., Seo, T., and Kim, M.K. 2014. Deinococcus soli sp. nov., a gamma-radiation-resistant bacterium isolated from rice field soil. Antonie van Leeuwenhoek 105, 229–235.CrossRefPubMedGoogle Scholar
  7. Daly, M.J. 2012. Death by protein damage in irradiated cells. DNA Repair 11, 12–21.CrossRefPubMedGoogle Scholar
  8. 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.CrossRefGoogle Scholar
  9. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.CrossRefGoogle Scholar
  10. 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, DC, USA.Google Scholar
  11. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41, 95–98.Google Scholar
  12. Hiraishi, A., Ueda, Y., Ishihara, J., and 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.CrossRefGoogle Scholar
  13. 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.CrossRefPubMedGoogle Scholar
  14. Im, S., Song, D., Joe, M., Kim, D., Park, D.H., and Lim, S. 2013. Comparative survival analysis of 12 histidine kinase mutants of Deinococcus radiodurans after exposure to DNA-damaging agents. Bioprocess Biosyst. Eng. 36, 781–789.CrossRefPubMedGoogle Scholar
  15. Jukes, T.H. and Cantor, C.R. 1969). Evolution of protein molecules. In Munro, H.N. (ed.), Mammalian Protein Metabolism, pp. 21–132. Academic Press, New York, USA.CrossRefGoogle Scholar
  16. Kisker, C., Kuper, J., and Van Houten, B. 2013. Prokaryotic nucleotide excision repair. Cold Spring Harb. Perspect. Biol. 5, a012591.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Komagata, K. and Suzuki, K. 1988. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–207.CrossRefGoogle Scholar
  18. Lai, W.A., Kä mpfer, 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.CrossRefPubMedGoogle Scholar
  19. Lee, J.J., Lee, H.J., Jang, G.S., Yu, J.M., Cha, J.Y., Kim, S.J., Lee, E.B., and Kim, M.K. 2013. Deinococcus swuensis sp. nov., a gammaradiation-resistant bacterium isolated from soil. J. Microbiol. 51, 305–311.CrossRefPubMedGoogle Scholar
  20. Marmur, J. 1961. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J. Mol. Biol. 3, 208–218.CrossRefGoogle Scholar
  21. Mattimore, V. and 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.PubMedPubMedCentralGoogle Scholar
  22. 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.CrossRefGoogle Scholar
  23. 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. Methods 2, 233–241.CrossRefGoogle Scholar
  24. Minnikin, D.E., Patel, P.V., Alshamaony, L., and Goodfellow, M. 1977. Polar lipid composition in the classification of Nocardia and related bacteria. Int. J. Syst. Bacteriol. 27, 104–117.CrossRefGoogle Scholar
  25. 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.CrossRefGoogle Scholar
  26. 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., et 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.CrossRefPubMedPubMedCentralGoogle Scholar
  27. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.PubMedGoogle Scholar
  28. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark, DE, USA.Google Scholar
  29. Scharer, O.D. 2013. Nucleotide excision repair in eukaryotes. Cold Spring Harb. Perspect. Biol. 5, a012609.CrossRefPubMedPubMedCentralGoogle Scholar
  30. Shashidhar, R. and Bandekar, J.R. 2009. Deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish. Int. J. Syst. Evol. Microbiol. 59, 2714–2717.CrossRefPubMedGoogle Scholar
  31. Srinivasan, S., Kim, M.K., Lim, S., Joe, M., and Lee, M. 2012. Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant. Int. J. Syst. Evol. Microbiol. 62, 1265–1270.CrossRefPubMedGoogle Scholar
  32. 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.CrossRefGoogle Scholar
  33. Suresh, K., Reddy, G.S.N., Sengupta, S., and 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.CrossRefPubMedGoogle Scholar
  34. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 30, 2725–2729.CrossRefPubMedPubMedCentralGoogle Scholar
  35. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876–4882.CrossRefGoogle Scholar
  36. Tittsler, R.P. and Sandholzer, L.A. 1936. The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575–580.PubMedPubMedCentralGoogle Scholar
  37. 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., 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.CrossRefGoogle Scholar
  38. Weisburg, W.G., Barns, S.M., Pellerier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703.PubMedPubMedCentralGoogle Scholar
  39. Weon, H.Y., Kim, B.Y., Schumann, P., Son, J.A., Jang, J., Go, S.J., and Kwon, S.W. 2007. Deinococcus cellulosilyticus sp. nov., isolated from air. Int. J. Syst. Evol. Microbiol. 57, 1685–1688.CrossRefPubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Jae-Jin Lee
    • 1
  • Yeon-Hee Lee
    • 1
  • Su-Jin Park
    • 1
  • Sangyong Lim
    • 2
  • Sun-Wook Jeong
    • 2
  • Seung-Yeol Lee
    • 1
  • Young-Je Cho
    • 3
  • Myung Kyum Kim
    • 4
  • Hee-Young Jung
    • 1
    • 5
    Email author
  1. 1.School of Applied BiosciencesKyungpook National UniversityDaeguRepublic of Korea
  2. 2.Radiation Research Division for BiotechnologyKorea Atomic Energy Research InstituteJeongeupRepublic of Korea
  3. 3.School of Food Science and Biotechnology/Food and Bio-Industry Research InstituteKyungpook National UniversityDaeguRepublic of Korea
  4. 4.Department of Bio and Environmental TechnologySeoul Women’s UniversitySeoulRepublic of Korea
  5. 5.Institute of Plant MedicineKyungpook National UniversityDaeguRepublic of Korea

Personalised recommendations