DOI QR코드

DOI QR Code

A report of 22 unrecorded bacterial species in Korea in the phyla Bacteroidetes and Rhodothermaeota

  • Lee, Do-Hoon (Department of Systems Biotechnology, Chung-Ang University) ;
  • Jang, Ho-Jin (Department of Systems Biotechnology, Chung-Ang University) ;
  • Bae, Jin-Woo (Department of Biology, Kyung Hee University) ;
  • Cho, Jang-Cheon (Department of Biological Sciences, Inha University) ;
  • Jang, Kwang-Yeop (Department of Life Sciences, Chonbuk National University) ;
  • Joh, Ki-seong (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies) ;
  • Seong, Chi-Nam (Department of Biology, Sunchon National University) ;
  • Cha, Chang-Jun (Department of Systems Biotechnology, Chung-Ang University)
  • Received : 2018.02.05
  • Accepted : 2018.05.14
  • Published : 2018.05.31

Abstract

A total of 22 bacterial strains belonging to the phylum Bacteroidetes were isolated primarily from aquatic environments such as seawater, freshwater, lagoon and tidal flat. One of these 22 strains was isolated from ginseng soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 21 strains showed the high sequence similarities(${\geq}98.7%$) to the closest type strains and formed robust phylogenetic clades with closely related species in the phylum Bacteroidetes. One strain, which had been previously classified as Balneola vulgaris in the phylum Bacteroidetes, was identified as a member of the newly described phylum Rhodothermaeota. These strains had not been previously reported in Korea. Here, we report 21 species of 13 genera in the phylum Bacteroidetes and one species in the phylum Rhodothermaeota which were not reported in Korea. Morphological, biochemical, and physiological characteristics, isolation sources, and NIBR deposit numbers are described in the species descriptions.

Keywords

References

  1. Bernardet, J.­F., P. Segers, M. Vancanneyt, F. Berthe, K. Kersters and P. Vandamme. 1996. Cutting a Gordian Knot: Emended Classification and Description of the Genus Flavobacterium, Emended Description of the Family Flavobacteriaceae, and Proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). International Journal of Systematic and Evolutionary Microbiology 46:128-148.
  2. Cho, J.C. and S.J. Giovannoni. 2003. Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae. Systematic and Applied Microbiol­ogy 26:76­83.
  3. de Beer, H., C.J. Hugo, P.J. Jooste, M. Vancanneyt, T. Coenye and P. Vandamme. 2006. Chryseobacterium piscium sp. nov., isolated from fsh of the South Atlantic Ocean off South Africa. International Journal of Systematic and Evolutionary Microbiology 56:1317-1322. https://doi.org/10.1099/ijs.0.64014-0
  4. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368-376. https://doi.org/10.1007/BF01734359
  5. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  6. Gordon, N.S., A. Valenzuela, S.M. Adams, P.W. Ramsey, J.L. Pollock, W.E. Holben and J.E. Gannon. 2009. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana food-plain sediment and forest soil. International Journal of Systematic and Evolutionary Microbiology 59:1720-1726. https://doi.org/10.1099/ijs.0.000158-0
  7. Herzog, P., I. Winkler, D. Wolking, P. Kämpfer and A. Lipski. 2008. Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer­bottling plants. International Journal of Systematic and Evolutionary Microbiology 58:26-33. https://doi.org/10.1099/ijs.0.65362-0
  8. Holmes, B., A.G. Steigerwalt and A.C. Nicholson. 2013. DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole­producing non­fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov. International Journal of Systematic and Evolutionary Microbiology 63:4639-4662. https://doi.org/10.1099/ijs.0.054353-0
  9. Jackson, S.A., J. Kennedy, J.P. Morrissey, F. O'Gara and A.D.W. Dobson. 2015. Maribacter spongiicola sp. nov. and Maribacter vaceletii sp. nov., isolated from marine sponges, and emended description of the genus Maribacter. International Journal of Systematic and Evolutionary Microbiology 65:2097-2103. https://doi.org/10.1099/ijs.0.000224
  10. Jin, L., S.-Y. Shin, H.-G. Lee, C.-Y. Ahn and H.-M. Oh. 2013. Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir. International Journal of Systematic and Evolutionary Microbiology 63:4519-4523. https://doi.org/10.1099/ijs.0.053702-0
  11. Kampfer, P., H. Matthews, S.P. Glaeser, K. Martin, N. Lodders and I. Faye. 2011. Elizabethkingia anophelis sp. nov., isolated from the midgut of the mosquito Anopheles gambiae. International Journal of Systematic and Evolutionary Microbiology 61:2670-2675. https://doi.org/10.1099/ijs.0.026393-0
  12. Kampfer, P., K. Fallschissel and R. Avendano-Herrera. 2011. Chryseobacterium chaponense sp. nov., isolated from farmed Atlantic salmon (Salmo salar). International Journal of Systematic and Evolutionary Microbiology 61:497-501. https://doi.org/10.1099/ijs.0.022004-0
  13. Kampfer, P., N. Lodders, K. Martin and R. Avendano-Herrera. 2012. Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fsh. International Journal of Systematic and Evolutionary Microbiology 62:1402-1408. https://doi.org/10.1099/ijs.0.033431-0
  14. 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 62:716-721. https://doi.org/10.1099/ijs.0.038075-0
  15. Kim, Y.­J., N.­L. Nguyen, H.­Y. Weon and D.­C. Yang. 2013. Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng feld, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum. International Journal of Systematic and Evolutionary Microbiology 63:905-912. https://doi.org/10.1099/ijs.0.038554-0
  16. Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for big­ger datasets. Molecular Biology and Evolution 33:1870-1874. https://doi.org/10.1093/molbev/msw054
  17. Lee, D.H. and C.J. Cha. 2016. Flavihumibacter sediminis sp. nov., isolated from tidal fat sediment. International Journal of Systematic and Evolutionary Microbiology 66:1-5. https://doi.org/10.1099/ijsem.0.000737
  18. Liu, Y., H. Li, J.­T. Jiang, Y.­H. Liu, X.­F. Song, C.­J. Xu and Z.­P. Liu. 2009. Algoriphagus aquatilis sp. nov., isolated from a freshwater lake. International Journal of Systematic and Evolutionary Microbiology 59:1759-1763. https://doi.org/10.1099/ijs.0.005215-0
  19. Montero-Calasanz, M. d. C., M. Goker, M. Rohde, C. Sproer, P. Schumann, H.­J. Busse, M. Schmid, B.J. Tindall, H.­P. Klenk and M. Camacho. 2013. Chryseobacterium hispalense sp. nov., a plant­growth­promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defuvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. International Journal of Systematic and Evolutionary Microbiology 63:4386-4395. https://doi.org/10.1099/ijs.0.052456-0
  20. Munoz, R., R. Rossello-Mora and R. Amann. 2016. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology 39:281-296. https://doi.org/10.1016/j.syapm.2016.04.004
  21. O'Sullivan, L.A., J. Rinna, G. Humphreys, A.J. Weightman and J.C. Fry. 2006. Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology 56:169-180. https://doi.org/10.1099/ijs.0.63941-0
  22. Oh, H.-W., B.-C. Kim, D.-S. Park, W.-J. Jeong, H. Kim, K.H. Lee and S.U. Kim. 2013. Pedobacter luteus sp. nov., isolated from soil. International Journal of Systematic and Evolutionary Microbiology 63:1304-1310. https://doi.org/10.1099/ijs.0.033134-0
  23. Park, C.S., K. Han and T.­Y. Ahn. 2014. Mucilaginibacter koreensis sp. nov., isolated from leaf mould. International Journal of Systematic and Evolutionary Microbiology 64:2274-2279. https://doi.org/10.1099/ijs.0.058008-0
  24. Saitou, N. and M. Nei. 1987. The neighbor­joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
  25. Sheu, S.­Y., C.­S. Yang, M.­H. Chen, A.B. Arun, C.­C. Young and W.­M. Chen. 2010. Arcicella aurantiaca sp. nov., isolated from stream water. International Journal of Systematic and Evolutionary Microbiology 60:2979-2983. https://doi.org/10.1099/ijs.0.021527-0
  26. Sheu, S.­Y., C.­S. Yang and W.­M. Chen. 2013. Flavobacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond, and emended descriptions of Flavobacterium haoranii, Flavobacterium cauense, Flavobacterium terrae and Flavobacterium aquatile. International Journal of Systematic and Evolutionary Microbiology 63:2239-2247. https://doi.org/10.1099/ijs.0.046425-0
  27. Thomas, F., J.H. Hehemann, E. Rebuffet, M. Czjzek and G. Michel. 2011. Environmental and Gut Bacteroidetes: The Food Connection. Frontiers in Microbiology 2:93.
  28. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin and D.G. Higgins. 1997. The CLUSTAL_X windows interface: fexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25:4876-4882. https://doi.org/10.1093/nar/25.24.4876
  29. Urios, L., H. Agogue, F. Lesongeur, E. Stackebrandt and P. Lebaron. 2006. Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north­western Mediterranean Sea. International Journal of Systematic and Evolutionary Microbiology 56:1883-1887. https://doi.org/10.1099/ijs.0.64285-0
  30. Woese, C.R., D. Yang, L. Mandelco and K.O. Stetter. 1990. The flexibacter-flavobacter connection. Systematic and Applied Microbiology 13:161-165. https://doi.org/10.1016/S0723-2020(11)80163-3
  31. Xu, M., Y. Xin, J. Tian, K. Dong, Y. Yu, J. Zhang, H. Liu and Y. Zhou. 2011. Flavobacterium sinopsychrotolerans sp. nov., isolated from a glacier. International Journal of Systematic and Evolutionary Microbiology 61:20-24. https://doi.org/10.1099/ijs.0.014126-0
  32. Yoon, J.-H., S.-J. Kang, Y.-T. Jung and T.-K. Oh. 2008. Aestuariicola saemankumensis gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology 58:2126-2131. https://doi.org/10.1099/ijs.0.65717-0