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A report of 21 unreported bacterial species in Korea, belonging to the Betaproteobacteria

Journal of Species Research / Journal of Species Research, (E)2713-8615
2016, v.5 no.1, pp.179-187
KIM PIL SOO
Bae Jin-Woo
Cha Chang Jun
JANGCHEON CHO
Chun, Jongsik
Im Wan-Taek
Kwang-Yeop Jahng
Che Ok Jeon
Joh Ki Seong
Seung Bum Kim
Chi-Nam Seong
YOON, JUNG HOON

Abstract

As a subset investigation to discover indigenous prokaryotic species in Korea, a total of 21 bacterial strains assigned to the class Betaproteobacteria were isolated from a wide range of environmental samples which collected from fresh water, roots of plants, mineral water and soil from ginseng farm. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 21 isolated strains were most closely related to the class Betaproteobacteria, with high 16S rRNA gene sequence similarity (>99.1%) and constructed a robust phylogenetic clade with the closest species in the class Betaproteobacteria. These isolated species have no previous report or publication in Korea; therefore 17 species in 14 genera of 6 families in the order Burkholderiales, 1 species in the order Methylophilales, 2 species in 2 genera of 1 family in the order Neisseriales are reported for betaproteobacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section and as an image.

keywords
Betaproteobacteria, unreported bacterial species, bacterial divesity

Reference

1.

Ash, C., J.A. Farrow, M. Dorsch, E. Stackebrandt and M.D. Collins. 1991. Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. International Journal of Systematic Bacteriology 41(3):343-346.

2.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17(6):368-376.

3.

Garrity, G.M., J.A. Bell and T. Lilburn. 2005. Class II. Betaproteobacteria class. nov. Bergey’s manual® of systematic bacteriology, Springer. pp. 575-922.

4.

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.

5.

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. Int. J. Syst. Evol. Microbiol. 62(Pt 3):716-721.

6.

Kluge, A.G. and F.S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18:1-32.

7.

Lagier, J.C., F. Armougom, M. Million, P. Hugon, I. Pagnier, C. Robert, F. Bittar, G. Fournous, G. Gimenez and M. Maraninchi. 2012. Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection 18(12):1185-1193.

8.

Lane, D.J. 1991. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics. E. Stackebrandt and M. Goodfellow. New York, Wiley. pp. 115-175.

9.

Liu, Z., C. Lozupone, M. Hamady, F.D. Bushman and R. Knight. 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Research 35(18):e120.

10.

Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4):406-425.

11.

Shigematsu, T., M. Hayashi, I. Kikuchi, S. Ueno, H. Masaki community structure analysis based on liquid cultivation and its application to a marine environment. FEMS Microbiology Letters 293(2):240-247.

12.

Sogin, M.L., H.G. Morrison, J.A. Huber, D.M. Welch, S.M. Huse, P.R. Neal, J.M. Arrieta and G.J. Herndl. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proceedings of the National Academy of Sciences 103(32):12115-12120.

13.

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(12):2725-2729.

14.

Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLU STAL 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.

15.

Turnbaugh, P.J., R.E. Ley, M. Hamady, C. Fraser-Liggett, R. Knight and J.I. Gordon. 2007. The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature 449(7164):804.

16.

Whitman, W.B., D.C. Coleman and W.J. Wiebe. 1998. Prokaryotes: the unseen majority. Proceedings of the National Academy of Sciences 95(12):6578-6583.

Journal of Species Research