Phylogenetic diversity and UV resistance analysis of radiation-resistant bacteria isolated from the water in Han River

한강물로부터 분리된 방사선 내성 세균들의 계통학적 다양성 및 UV 내성 분석

  • Lee, Jae-Jin (Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University) ;
  • Joo, Eun Sun (Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University) ;
  • Lee, Do Hee (Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University) ;
  • Jung, Hee-Young (College of Agricultural and Life Sciences, Kyungpook National University) ;
  • Kim, Myung Kyum (Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University)
  • 이재진 (서울여자대학교 자연과학대학 생명환경공학과) ;
  • 주은선 (서울여자대학교 자연과학대학 생명환경공학과) ;
  • 이도희 (서울여자대학교 자연과학대학 생명환경공학과) ;
  • 정희영 (경북대학교 농업생명과학대학 응용생명과학부) ;
  • 김명겸 (서울여자대학교 자연과학대학 생명환경공학과)
  • Received : 2016.03.04
  • Accepted : 2016.03.22
  • Published : 2016.03.31


The aim of this study was to investigate the UV-resistance of radiation-resistant bacteria isolated from the water of Han River, South Korea. The water sample was irradiated with 3 kGy gamma radiation prior to isolation. Radiation-resistant bacterial strains were isolated by standard serial dilution method on R2A and 1/10 diluted R2A agar. The resulting purely isolated 60 cultures of bacteria were analysed for UV resistance and used in further studies. Based on the comparative analyses of 16S rRNA gene sequences, the bacterial isolates were divided into 3 phyla (4 genera): the phylum Deinococcus-Thermus (the genus Deinococcus) was 61.7%, Bacteroidetes (Hymenobacter and Spirosoma) was 23.4%, and Firmicutes (Exiguobacterium) was 15%. The results suggested that twenty-nine isolates are candidates new species belonging to Deinococcus, Hymenobacter, and Spirosoma, or other new genera. Nine bacterial strains were selected among the novel candidates and the UV-resistance analysis was conducted. All the candidate bacterial strains showed high UV resistance, similar to that of D. radiodurans R1.


16S rDNA;Han River;phylogenetic tree;radiation-resistant bacteria;UV resistance analysis;water


Supported by : 서울여자대학교


  1. 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.
  2. 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., et al. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286, 1571-1577.
  3. Woo, P.C., Lau, S.K., Teng, J.L., and Yuen, K.Y. 2008. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin. Microbiol. Infect. 14, 908-909.
  4. 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.
  5. Yu, L.Z., Luo, X.S., Liu, M., and Huang, Q. 2015. Diversity of ionizing radiation-resistant bacteria obtained from the Taklimakan Desert. J. Basic Microbiol. 55, 135-140.
  6. Yuan, M., Zhang, W., Dai, S., Wu, J., Wang, Y., Tao, T., Chen, M., and Lin, M. 2009. Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium. Int. J. Syst. Evol. Microbiol. 59, 1513-1517.
  7. 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 Spirosoma obtained from a single soil sample. Appl. Environ. Microbiol. 71, 5225-5235.
  8. Rodrigues, D.F., Goris, J., Vishnivetskaya, T., Gilichinsky, D., Thomashow, M.F., and Tiedje, J.M. 2006. Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. Extremophiles 10, 285-294
  9. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  10. Servinsky, M.D. and Julin, D.A. 2007. Effect of a recD mutation on DNA damage resistance and transformation in Deinococcus radiodurans. J. Bacteriol. 189, 5101-5107.
  11. 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.
  12. 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.
  13. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: molecular evolutionary genetics 298 analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739.
  14. 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.
  15. Kampfer, 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.
  16. Klassen, J.L. and Foght, J.M. 2011. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 15, 45-57.
  17. Kwon, J.Y. and 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.
  18. Lai, W.A., Kampfer, 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.
  19. Lee, J.J., Kang, M.S., Joo, E.S., Kim, M.K., and Srinivasan, S. 2015. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. J. Microbiol. 53, 429-434.
  20. Lee, J.J., Srinivasan, S., Lim, S., Joe, M., Im, S., Bae, S.I., Park, K.R., Han, J.H., Park, S.H., Joo, B.M., et al. 2014. Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil. Cur. Microbiol. 69, 286-291.
  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.
  22. Park, S.J., Choi, J.H., and Cha, C.J. 2013. Chryseobacterium rigui sp. nov., isolated from an estuarine wetland. Int. J. Syst. Evol. Microbiol. 63, 1062-1067.
  23. Asker, D., Awad, T.S., Beppu, T., and Ueda, K. 2009. Deinococcus aquiradiocola sp. nov., isolated from a radioactive site in Japan. Int. J. Syst. Evol. Microbiol. 59, 144-149.
  24. Asker, D., Awad, T.S., McLandsborough, L., Beppu, T., and Ueda, K. 2011. Deinococcus depolymerans sp. nov., a gamma and UV-radiation-resistant bacterium, isolated from a naturally radioactive site. Int. J. Syst. Evol. Microbiol. 61, 1448-1453.
  25. Bae, J.Y., Kim, K.Y., Kim, J.H., Lee, K., Cho, J.C., and Cha, C.J. 2010. Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland. Int. J. Syst. Evol. Microbiol. 60, 644-647.
  26. Baik, K.S., Kim, M.S., Park, S.C., Lee, D.W., Lee, S.D., Ka, J.O., Choi, S.K., and Seong, C.N. 2007. Spirosoma rigui sp. nov., isolated from fresh water. Int. J. Syst. Evol. Microbiol. 57, 2870-2873.
  27. 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.
  28. Cha, S., Srinivasan, S., Seo, T., and Kim, M.K. 2014. Deinococcus radiotolerans sp. nov., a gamma-radiation resistant bacterium isolated from gamma ray-irradiated soil. Antonie van Leeuwenhoek 105, 229-235.
  29. Choi, M.J., Bae, J.Y., Kim, K.Y., Kang, H., and Cha, C.J. 2010. Brevibacillus fluminis sp. nov., isolated from sediment of estuarine wetland. Int. J. Syst. Evol. Microbiol. 60, 1595-1599.
  30. Cox, M.M. and Battista, J.R. 2005. Deinococcus radiodurans - the consummate survivor. Nature Rev. Microbiol. 3, 882-892.
  31. de Groot, A., Chapon, V., Servant, P., Christen, R., Saux, M.F., Sommer, S., and 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.
  32. Gabani, P. and Singh, O.V. 2013. Radiation-resistant extremophiles and their potential in biotechnology and therapeutics. Appl. Microbiol. Biotechnol. 97, 993-1004.
  33. 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.
  34. 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 draughttolerating, UV-resistant bacteria from continental Antarctica. Syst. Appl. Microbiol. 27, 636-645.
  35. Hirsch, P., Ludwig, W., Hethke, C., Sittig, M., Hoffmann, B., and Gallikowski, C.A. 1998. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antarctic soils and sandstone: bacteria of the cytophaga/flavobacterium/bacteroides line of phylogenetic descent. Syst. Appl. Microbiol. 21, 374-383.
  36. 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.
  37. Zhang, Y.Q., Sun, C.H., Li, W.J., Yu, L.Y., Zhou, J.Q., Xu, L.H., and Jiang, C.L. 2007. Deinococcus yunweiensis sp. nov., a gamma- and UV radiation-resistant bacterium from China. Int. J. Syst. Evol. Microbiol. 57, 370-375.