Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
권호 표지
DOI QR코드

DOI QR Code

A report of 23 unrecorded bacterial species 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, Kiseong (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)
  • Received : 2018.01.08
  • Accepted : 2018.05.15
  • Published : 2021.08.31
Download PDF
⟨ Previous Next ⟩

Abstract

To study the biodiversity of bacterial species, here we report indigenous prokaryotic species of Korea. A total of 23 bacterial strains affiliated to the class Alphaproteobacteria were isolated from various environmental sources including seaweeds, seawater, fresh water, wetland/marsh, tidal sediment, plant roots, sewage and soil. Considering higher than 98.8% 16S rRNA gene sequence similarities and formation of a well-defined phylogenetic clade with named species, it was confirmed that each strain belonged to the predefined bacterial species of the class Alphaproteobacteria. There is no official report of these 23 species in Korea; 20 species of 16 genera (Mameliella, Yangia, Paracoccus, Ruegeria, Loktanella, Phaeobacter, Dinoroseobacter, Tropicimonas, Lutimaribacter, Litoreibacter, Sulfitobacter, Roseivivax, Labrenzia, Hyphomonas, Maricaulis, Thalassospira) in the order Rhodobacterales and 3 species of a single genus (Brevundimonas) in the order Caulobacterales. Gram-staining, cell morphology, basic biochemical characteristics, isolation sources, optimum temperature, growth media, and strain IDs are detailed in the species description as well as Table 1.

Keywords

Acknowledgement

This study was supported by the research grant "The Survey of Korean Indigenous Species" from the National Institute of Biological Resources of the Ministry of Environment in Korea.

References

  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. International Journal of Systematic and Evolutionary Microbiology 63:801-808. https://doi.org/10.1099/ijs.0.038927-0
  2. 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.
  3. DeLong, E.F., C.M. Preston, T. Mincer, V. Rich, S.J. Hallam, N.U. Frigaard, A. Martinez, M.B. Sullivan, R. Edwards, B.R. Brito, S.W. Chisholm and D.M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503. https://doi.org/10.1126/science.1120250
  4. 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 predominantly eubacterial ancestry of yeast nuclear genes. Molecular Biology and Evolution 21:1643-1660. https://doi.org/10.1093/molbev/msh160
  5. Euzeby, J.P. 2011. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN).
  6. 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
  7. Ferla, M.P., J.C. Thrash, S.J. Giovannoni and W.M. Patrick. 2013. New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS One 8(12):e83383. https://doi.org/10.1371/journal.pone.0083383
  8. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 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. Molecular Biology and Evolution 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 Symposium Series 41:95-98.
  11. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press, Cambridge, New York.
  12. Krom, M.D., N. Kress, S. Brenner and L.I. Gordon. 1991. Phosphorus limitation of primary productivity in the eastern Mediterranean Sea. Limnology and Oceanography 36:424-432. https://doi.org/10.4319/lo.1991.36.3.0424
  13. 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
  14. 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
  15. Pitta, P., N. Stambler, T. Tanaka, T. Zohary, A. Tselepides and F. Rassoulzadegan. 2005. Biological response to P addition in the Eastern Mediterranean Sea. The microbial race against time. Deep Sea Research. Part II: Topical Studies in Oceanography 52:2961-2974. https://doi.org/10.1016/j.dsr2.2005.08.012
  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. Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30:2725-2729. https://doi.org/10.1093/molbev/mst197
  18. 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 Research 25:4876-4882. https://doi.org/10.1093/nar/25.24.4876
  19. Thompson, L.R., C. Field, T. Romanuk, D.K. Ngugi, R. Siam, H.E. Dorry and U. Stingl. 2013. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments. Ecology and Evolution 3(6):1780-1797. https://doi.org/10.1002/ece3.593
  20. Viollier, P.H. and L. Shapiro. 2004. Spatial complexity of mechanisms controlling a bacterial cell cycle. Current Opinion in Microbiology 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. Woese, C.R. 1987. Bacterial Evolution. Microbiological Review 51(2):221-271. https://doi.org/10.1128/mr.51.2.221-271.1987
  23. 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 and others. 2004. Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biolgy 2:E69. https://doi.org/10.1371/journal.pbio.0020069
  24. Yoon, S.H., S.M. Ha, S. Kwon, J. Lim, Y. Kim, H. Seo and J. Chun. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and wholegenome assemblies. International Journal of Systematic and Evolutionary Microbiology 67:1613-1617. https://doi.org/10.1099/ijsem.0.001755