DOI QR코드

DOI QR Code

A report on 14 unrecorded bacterial species isolated from the Nakdong River, South Korea

  • Cho, Ja Young (Microbial Research Department, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Baek, Kiwoon (Bioresources Collection & Bioinformation Department, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Kim, Eui-Jin (Microbial Research Department, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Han, Ji-Hye (Microbial Research Department, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Hwang, Seoni (Microbial Research Department, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Choi, Ahyoung (Strategic Planning Department, Nakdonggang National Institute of Biological Resources(NNIBR))
  • Received : 2019.12.27
  • Accepted : 2020.03.03
  • Published : 2020.05.31

Abstract

As a part of the research project "Survey of freshwater organisms and specimen collection," freshwater samples were collected from the Nakdong River. Among the bacterial isolates, we selected strains that showed higher than 98.7% 16S rRNA gene sequence similarity with confirmed bacterial species previously unreported in South Korea. The 14 new records to South Korea were phylogenetically diverse and belonged to four phyla, six classes, 11 orders, and 14 genera. At the genus level, these species were found to be affiliated with Reyranella, Ferrovibrio, Brevundimonas, and Aquidulcibacter of the class Alphaproteobacteria; Pseudomonas, Cellvibrio, and Photobacterium of the class Gammaproteobacteria; Paenibacillus and Bacillus of the phylum Firmicutes; Chryseobacterium, Flavobacterium, Pedobacter of the phylum Bacteroidetes; and Actinomadura and Leifsonia of the phylum Actinobacteria. These species were further characterized by examining their Gram reaction, colony and cell morphologies, biochemical properties, and phylogenetic positions. The detailed descriptions of these 14 previously unreported species are provided.

References

  1. Chun, S.J., Y. Cui, C.S. Lee, A.R. Cho, K. Baek, A. Choi, S.R. Ko, H.G. Lee, S. Hwang, H.M. Oh and C.Y. Ahn. 2019. Characterization of Distinct CyanoHABs-Related Modules in Microbial Recurrent Association Network. Frontiers in Microbiology 10:1637. https://doi.org/10.3389/fmicb.2019.01637
  2. Edwards, R.A., B. Rodriguez-Brito, L. Wegley, M. Haynes, M. Breitbart, D.M. Peterson, M.O. Saar, S. Alexander, E.C. Jr Alexander and F. Rohwer. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57. https://doi.org/10.1186/1471-2164-7-57
  3. Falkowski, P.G., T. Fenchel and E.F. DeLong. 2008. The microbial engines that drive earth's biogeochemical cycles. Science 320:1034-1039. https://doi.org/10.1126/science.1153213
  4. 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
  5. Huse, S.M., L. Dethlefsen, J.A. Huber, D.M. Welch, D.A. Relman and M.L. Sogin. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics 4:e1000255. https://doi.org/10.1371/journal.pgen.1000255
  6. Jeon, Y.S., K. Lee, S.C. Park, B.S. Kim, Y.J. Cho, S.M. Ha and J. Chun. 2014. EzEditor: a versatile sequence alignment editor for both rRNA-and protein-coding genes. International Journal of Systematic and Evolutionary Microbiology 64:689-691. https://doi.org/10.1099/ijs.0.059360-0
  7. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120. https://doi.org/10.1007/BF01731581
  8. 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
  9. Miettinen, I.T., T. Vartiainen and P.J. Martikainen. 1997. Phosphorus and bacterial growth in drinking water. Applied and Environmental Microbiology 63:324-3245. https://doi.org/10.1128/AEM.63.1.324-328.1997
  10. Newton, R.J., S.E. Jones, A. Eiler, K.D. Mcmahon and S. Bertilsson. 2011. A guide to the natural history of freshwater lake bacteria. Microbiology and Molecular Biology Reviews 75:14-49. https://doi.org/10.1128/MMBR.00028-10
  11. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
  12. Sin, Y., C. Lee, K. Cho and E. Song. 2005. Trends of phytoplankton community and water quality and implications for management in estuarine river systems. Korean Journal of Ecology and Environment 38:160-180.
  13. Weisburg, W.G., S.M. Barns, D.A. Pelletier and D.J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697-703. https://doi.org/10.1128/JB.173.2.697-703.1991
  14. Williamson, N., T. Kobayashi, D. Outhet and L.C. Bowling. 2018. Survival of cyanobacteria in rivers following their release in water from large headwater reservoirs. Harmful Algae 75:1-15. https://doi.org/10.1016/j.hal.2018.04.004
  15. 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
  16. Zhou, S., T. Huang, H. Zhang, M. Zeng, F. Liu, S. Bai, J. Shi, X. Qiu and X. Yang. 2016. Nitrogen removal characteristics of enhanced in situ indigenous aerobic denitrification bacteria for micro-polluted reservoir source water. Bioresource Technology 201:195-207. https://doi.org/10.1016/j.biortech.2015.11.041