Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
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Description of unrecorded bacterial species belonging to the phylum Actinobacteria in Korea

  • Kim, Mi-Sun (Department of Biology, Sunchon National University) ;
  • Kim, Seung-Bum (Department of Microbiology, Chungnam National University) ;
  • Cha, Chang-Jun (Department of Biotechnology, Chung-Ang University) ;
  • Im, Wan-Taek (Department of Biotechnology, Hankyong National University) ;
  • Kim, Won-Yong (Department of Microbiology, College of Medicine, Chung-Ang University) ;
  • Kim, Myung-Kyum (Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women's University) ;
  • Jeon, Che-Ok (Department of Life Science, Chung-Ang University) ;
  • Yi, Hana (School of Biosystem and Biomedical Science, Korea University) ;
  • Yoon, Jung-Hoon (Department of Food Science and Biotechnology, Sungkyunkwan University) ;
  • Kim, Hyung-Rak (Department of Laboratory Medicine, Saint Garlo Medical Center) ;
  • Seong, Chi-Nam (Department of Biology, Sunchon National University)
  • Received : 2020.11.06
  • Accepted : 2021.01.22
  • Published : 2021.02.28
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Abstract

For the collection of indigenous prokaryotic species in Korea, 77 strains within the phylum Actinobacteria were isolated from various environmental samples, fermented foods, animals and clinical specimens in 2019. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust phylogenetic clade with actinobacterial species that were already defined and validated with nomenclature. There is no official description of these 77 bacterial species in Korea. The isolates were assigned to 77 species, 31 genera, 18 families, 14 orders and 2 classes of the phylum Actinobacteria. All the strains except one Coriobacteriia strain were affiliated within the class Actinomycetia. Among them, the orders Streptomycetales and Microbacteriales were predominant. A number of strains were isolated from forest soils, riverside soils, and ginseng cultivated soils. Twenty-nine strains were isolated from 'Protected Ecosystem and Scenery Areas'. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

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. Bae, K.S., M.S. Kim, J.H. Lee, J.W. Kang, D.I. Kim, J.H. Lee and C.N. Seong. 2016. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J Microbiol 54(12):789-795. https://doi.org/10.1007/s12275-016-6446-4
  2. Choi, J.H., J.H. Cha, J.W. Bae, J.C. Cho, J. Chun and others. 2016. Report on 31 unrecorded bacterial species in Korea that belong to the phylum Actinobacteria. J Sp Res 5(1):1-13. https://doi.org/10.12651/JSR.2016.5.1.001
  3. Chun, J. and M. Goodfellow. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45(2):240-245. https://doi.org/10.1099/00207713-45-2-240
  4. Dangel, A., A. Berger, R. Konrad and A. Sing. 2019. NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission. BMC Microbiol 19(1):28. https://doi.org/10.1186/s12866-019-1402-1
  5. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368-376. https://doi.org/10.1007/BF01734359
  6. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39(4):783-791. https://doi.org/10.2307/2408678
  7. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20(4):406-416. https://doi.org/10.2307/2412116
  8. Goodfellow, M. 2012. Phylum XXVI. Actinobacteria phyl. nov. In: Goodfellow, M., P. Kampfer, H.-J. Busse, M.E. Trujillo, K. Suzuki, W. Ludwig, Whitman, W.B. (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 5, Springer, New York. pp. 33-34.
  9. Goodfellow, M. and S.T. Williams. 1983. Ecology of Actinomycetes. Annu Rev Microbiol 37:189-216. https://doi.org/10.1146/annurev.mi.37.100183.001201
  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. Hwang, I.S., E.J. Oh, H.B. Lee and C.S. Oh. 2019. Functional Characterization of Two Cellulase Genes in the Gram-Positive Pathogenic Bacterium Clavibacter michiganensis for Wilting in Tomato. Mol Plant Microbe Interact 32(4):491-501. https://doi.org/10.1094/MPMI-08-18-0227-R
  12. Jukes, T.H. and C.R. Cantor. 1969. Evolution of protein molecules. In: Munro, H.N. (eds.), Mammalian Protein Metabolism. Academic Press, New York. pp. 21-132.
  13. Kim, M.S., J.H. Lee, J.W. Kang, S.B. Kim, J. C. Cho and others. 2016. A report of 38 unrecorded bacterial species in Korea, belonging to the phylum Actinobacteria. J Sp Res 5(2):223-234. https://doi.org/10.12651/JSR.2016.5.2.223
  14. Kim, M.S., J.H. Lee, S.B. Kim, J.C. Cho, S.D. Lee and others. 2017. Unrecorded bacterial species belonging to the phylum Actinobacteria originated from Republic of Korea. J Sp Res 6(1):25-41. https://doi.org/10.12651/JSR.2017.6.1.025
  15. Kim, M.S., S.H. Jeong, J.W. Kang, S.B. Kim, J.C. Cho and others. 2019. Unrecorded prokaryotic species belonging to the class Actinobacteria in Korea. J Sp Res 8(1): 97-108. https://doi.org/10.12651/JSR.2019.8.1.097
  16. Ko, K.S., C.J. Cha, W.T. Im, S.B. Kim, C.N. Seong and others. 2017. A report of 34 unrecorded bacterial species in Korea, belonging to the Actinobacteria. J Sp Res 6(1):1-14. https://doi.org/10.12651/JSR.2017.6.1.001
  17. Lee, N.Y., C.J. Cha, W.T. Im, S.B. Kim, C.N. Seong and others. 2018. A report of 42 unrecorded actinobacterial species in Korea. J Sp Res 7(1):36-49. https://doi.org/10.12651/JSR.2018.7.1.036
  18. Qin, S., K. Xing, J.H. Jiang, L.H. Xu and W.J. Li. 2011. Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 89(3):457-473. https://doi.org/10.1007/s00253-010-2923-6
  19. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406-425.
  20. Salam, N., J.Y. Jiao, X.T. Zhang and W.J. Li. 2020. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 70(2):1331-1355. https://doi.org/10.1099/ijsem.0.003920
  21. Servin, J.A., C.W. Herbold, R.G. Skophammer and J.A. Lake. 2008. Evidence excluding the root of the tree of life from the actinobacteria. Mol Biol Evol 25(1):1-4. https://doi.org/10.1093/molbev/msm249
  22. Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30(12):2725-2729. https://doi.org/10.1093/molbev/mst197
  23. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673-4680. https://doi.org/10.1093/nar/22.22.4673
  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 whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613-1617. https://doi.org/10.1099/ijsem.0.001755