Journal of Species Research

  • 제6권2호
  • /
  • Pages.141-153
  • /
  • 2017
  • /
  • 2234-7909(pISSN)
  • /
  • 2713-8615(eISSN)
국립생물자원관 (The National Institute of Biological Resources)
권호 표지
DOI QR코드

DOI QR Code

Description of 39 unrecorded bacterial species in Korea, belonging to the class Alphaproteobacteria

  • Siddiqi, Muhammad Zubair (Department of Biotechnology, Hankyong National University) ;
  • Kim, Seung-Bum (Department of Microbiology, Chungnam National University) ;
  • Cho, Jang-Cheon (Department of Biological Sciences, Inha University) ;
  • Yoon, Jung-Hoon (Department of Food Science and Biotechnology, Sungkyunkwan University) ;
  • Joh, Ki-seong (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies) ;
  • Seong, Chi-Nam (Department of Biology, Sunchon National University) ;
  • Bae, Jin-Woo (Department of Biology, Kyung Hee University) ;
  • Jahng, Kwang-Yeop (Department of Life Sciences, Chonbuk National University) ;
  • Jeon, Che-Ok (Department of Life Science, Chung-Ang University) ;
  • Im, Wan-Taek (Department of Biotechnology, Hankyong National University)
  • 투고 : 2016.10.04
  • 심사 : 2017.06.14
  • 발행 : 2017.06.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

During an investigation of the biodiversity of bacterial species in Korea, we discovered many indigenous prokaryotic species. A total of 39 bacterial strains in the class Alphaproteobacteria were isolated from various environmental samples collected from marine organisms, sea water, fresh water, tap water, mud flats, activated sludge, mineral water, tidal flats, soil and decayed plants. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of robust phylogenetic clades with the most closely related species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that any of these 39 Alphaproteobacteria species have been described in Korea. Specifically, 18 species in 11 genera in the order Sphingomonadales, 11 species in 10 genera in the order Rhizobiales, two species in two genera in the order Caulobacterales, six species in six genera in the order Rhodobacterales and two species in two genera in the order Rhodospirillales were found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

키워드

참고문헌

  1. Bazylinski, D.A., T.J. Williams, C.T. Lefevre, R.J. Berg, C.L. Zhang, S.S. Bowser, A.J. Dean and T.J. Beveridge. 2012. Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov.; Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int. J. Syst. Evol. Microbiol. 63:801-808.
  2. Bowers, L.M., E.B. Shapland and K.R. Ryan. 2008. Who's in charge here? Regulating cell cycle regulators. Curr. Opin. Microbiol. 11:547-552. 10.1016/j.mib.2008.09.019
  3. Brenner, D.J., N.R. Krieg and J.T. Staley. 2005. George M. Garrity, ed. The Proteobacteria. Bergey's Manual of Systematic Bacteriology 2C (2nd ed.) p. 1388. ISBN 978-0-387-24145-6. New York: Springer British Library no. GBA561951.
  4. Chilton, M.D., M.H. Drummond, D.J. Merio, D. Sciaky, A.L. Montoya, M.P. Gordon and E.W. Nester. 1977. Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis, Cell. Jun;11(2):263-271. https://doi.org/10.1016/0092-8674(77)90043-5
  5. Esser, C., N. Ahmadinejad, C. Wiegand, C. Rotte, F. Sebastiani, G. Gelius-Dietrich, K. Henze, E. Kretschmann, E. Richly, D. Leister, D. Bryant, M.A. Steel, P.J. Lockhart, D. Penny and W. Martin. 2004. A genome phylogeny for mitochondria among alpha-proteobacteria and a predom-inantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21:1643-1660. https://doi.org/10.1093/molbev/msh160
  6. Euzeby, J.P. 2011. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN).
  7. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  8. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416. https://doi.org/10.2307/2412116
  9. Fitzpatrick, D.A., C.J. Creevey and J.O. McInerney. 2006. Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol. 23:74-85. https://doi.org/10.1093/molbev/msj009
  10. 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.
  11. Kim, O.S., Y.J. Cho, K. Lee, S.H. Yoon, M. Kim, H. Na, S.C. Park, Y.S. Jeon, J.H. Lee, H. Yi, S. Won and J. Chun. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology 62(3):716-721. https://doi.org/10.1099/ijs.0.038075-0
  12. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press, Cambridge, New York.
  13. Matteo, P., J. Ferla, T. Cameron, J. Stephen and M. Wayne. Patrick. 2013. New rRNA Gene-Based Phylogenies of the Alphaproteobacteria provide perspective on major Groups, mitochondrial ancestry and mhylogenetic Instability. PLoS One 8(12):e83383. https://doi.org/10.1371/journal.pone.0083383
  14. Oren, A. and G.M. Garrity. 2014. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie van Leeuwenhoek 106(1):43-56. https://doi.org/10.1007/s10482-013-0084-1
  15. Parte, A.C. 2014. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic acids research 42 (Database issue):D613-616. https://doi.org/10.1093/nar/gkt1111
  16. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.
  17. Skerker, J.M. and M.T. Laub. 2004. Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus. Nat Rev Microbiol 2:325-337. https://doi.org/10.1038/nrmicro864
  18. Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725-2729. https://doi.org/10.1093/molbev/mst197
  19. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin and D.G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882. https://doi.org/10.1093/nar/25.24.4876
  20. Viollier, P.H. and L. Shapiro. 2004. Spatial complexity of mechanisms controlling a bacterial cell cycle. Curr Opin Microbiol 7:572-578. https://doi.org/10.1016/j.mib.2004.10.005
  21. Williams, K.P., B.W. Sobral and A.W. Dickerman. 2007. A robust species tree for the Alphaproteobacteria. Journal of Bacteriology 189(13):4578-4586. https://doi.org/10.1128/JB.00269-07
  22. Wu, M., L.V. Sun, J. Vamathevan, M. Riegler, R. Deboy, J.C. Brownlie, E.A. McGraw, W. Martin, C. Esser, N. Ahmadinejad, C. Wiegand, R. Madupu, M.J. Beanan, L.M. Brinkac, S.C. Daugherty, A.S. Durkin, J.F. Kolonay, W.C. Nelson, Y. Mohamoud, P. Lee, K. Berry, M.B. Young, T. Utterback, J. Weidman, W.C. Nierman, I.T. Paulsen, K.E. Nelson, H. Tettelin, S.L. O'Neill and J.A. Eisen. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2:E69. https://doi.org/10.1371/journal.pbio.0020069