Journal of Species Research

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

DOI QR Code

Report of 29 unrecorded bacterial species from the phylum Proteobacteria

  • Nam, Yoon-Jong (Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Beak, Kiwoon (Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Han, Ji-Hye (Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Park, Sanghwa (Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources(NNIBR)) ;
  • Lee, Mi-Hwa (Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources(NNIBR))
  • Received : 2017.11.17
  • Accepted : 2018.01.10
  • Published : 2018.02.28
Download PDF
⟨ Previous Next ⟩

Abstract

Our study aimed to discover indigenous prokaryotic species in Korea. A total of 29 bacterial species in the phylum Proteobacteria were isolated from freshwater and sediment of rivers and brackish zones in Korea. From the high 16S rRNA gene sequence similarity (${\geq}98.8%$) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to an independent and predefined bacterial species. To our knowledge, there is no official report or publication that has previously described these 29 species in Korea. Specifically, we identified 10, 12, and seven species of eight, 12, and seven genera that belong to classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, respectively; all are reported as previously unrecorded bacterial species in Korea. The Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs for each are also described.

Keywords

References

  1. Busse, H.j., E. Hauser and P. Kampfer. 2005. Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov. International Journal of Systematic and Evolutionary Microbiology 55:2565-2569. https://doi.org/10.1099/ijs.0.63872-0
  2. Chen, W.M., C.Y. Lin, C.C. Young and S.Y. Sheu. 2010. Rheinheimera aquatica sp. nov., an antimicrobial activity-producing bacterium isolated from freshwater culture pond. Journal of Microbiology and Biotechnology 20:1386-1392. https://doi.org/10.4014/jmb.1004.04048
  3. Chen, W.M., F.S. Sheu, C.C. Young and S.Y. Sheu. 2012. Inhella fonticola sp. nov., isolated from spring water, and emended description of the genus Inhella. International Journal of Systematic and Evolutionary Microbiology 62:1048-1054. https://doi.org/10.1099/ijs.0.034884-0
  4. Chern, L.L., E. Stackebrandt, S.F. Lee, F.L. Lee, J.K. Chen and H.M. Fu. 2004. Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan. International Journal of Systematic and Evolutionary Microbiology 54:1387-1391. https://doi.org/10.1099/ijs.0.02834-0
  5. Christensen, P. and F.D. Cook. 1978. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. International Journal of Systematic Bacteriology 28:367-393. https://doi.org/10.1099/00207713-28-3-367
  6. Chun, J. and M. Goodfellow. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. International Journal of Systematic Bacteriology 45:240-245. https://doi.org/10.1099/00207713-45-2-240
  7. Costello, E.K., C.L. Lauber, M. Hamady, N. Fierer, J.I. Gordon and R. Knight. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697. https://doi.org/10.1126/science.1177486
  8. De Meyer, S.E., A. Coorevits and A. Willems. 2012. Tardiphaga robiniae gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from Robinia pseudoacacia in Flanders (Belgium). Systematic and Applied Microbiology 35:205-214. https://doi.org/10.1016/j.syapm.2012.02.002
  9. Emerson, D., J.A. Rentz, T.G. Lilburn, R.E. Davis, H. Aldrich, C. Chan and C.L. Moyer. 2007. A novel lineage of Proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS One 2:e667. https://doi.org/10.1371/journal.pone.0000667
  10. Famintzin, A. 1892. Eine neue Bacterienform: Nevskia ramosa. Bulletin of the Academy of Science St. Petersbourg New Series 2 34:481-486.
  11. 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
  12. 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
  13. Fitch, W.M. 1971. Towards defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 20:406-416. https://doi.org/10.2307/2412116
  14. Garrity, G.M., J.A. Nell and T. Lilburn. 2005. Phylum XIV. Proteobacteria phyl. nov. Bergeys's Manual of Systematic Bacteriology, 2nd edn, pp. 1. Edited by D.J. Brenner, N.R. Krieg, J.T. Staley and G.M. Garrity. New York: Springer.
  15. Gomila, M., J. Pinhassi, E. Falsen, E.R.B. Moore and J. Lalucat. 2010. Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae. International Journal of Systematic and Evolutionary Microbiology 60:809-814. https://doi.org/10.1099/ijs.0.011478-0
  16. Goto, M. and H. Kuwata. 1988. Rhizobacter daucus gen. nov., sp. nov., the causal agent of carrot bacterial gall. International Journal of Systematic and Evolutionary Microbiology 38:233-239.
  17. Hahn, M.W., J. Schmidt, A. Pitt, S.J. Taipale and E. Lang. 2016. Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessaries. International Journal of Systematic and Evolutionary Microbiology 66:2883-2892. https://doi.org/10.1099/ijsem.0.001073
  18. Holmstrom, C., S. James, B.A. Neilan, D.C. Whote and S. Kjelleberg. 1998. Pseudoalteromonas tunicata sp. nov., a bacterium that produces antifouling agents. International Journal of Systematic Bacteriology 48:1205-1212. https://doi.org/10.1099/00207713-48-4-1205
  19. Hoppe, T., K. Peters and F. Schmidt. 2011. Methylobacterium bullatum sp. nov., a methylotrophic bacterium isolated from Funaria hygrometrica. Systematic and Applied Microbaiology 34:482-486. https://doi.org/10.1016/j.syapm.2010.12.005
  20. Huang, H.Y., J. Li, G.Z. Zhao, W.Y. Zhu, L.L. Yang, H.Y. Tang, L.H. Xu and W.J. Li. 2012. Sphingomonas endophytica sp. nov., isolated from Artemisia annua L. International Journal of Systematic and Evolutionary Microbiology 62:1576-1580. https://doi.org/10.1099/ijs.0.031484-0
  21. Janse, J.D., P. Rossi, L. Angelucci, M. Scortichini, J.H.J. Derks, A.D.L. Akkermans, R. De Vrijer and P.G. Psallidas. 1996. Reclassification of Pseudomonas syringae pv. avellanae as Pseudomonas avellanae (spec. nov.), the bacterium causing canker of hazelnut (Corylus avellana L.). Systematic and Applied Microbiology 19:589-595. https://doi.org/10.1016/S0723-2020(96)80030-0
  22. Joung, Y., H. Kim, B.I. Lee, H. Kang, K. Joh, S.H. Kim, H.J. Kwon, H.H. Lee, M.M. Rahman, J.H. Seok, J.H. Choi, J.H. Cha, C.N. Thawng, C.J. Cha, A. Choi, K. Baek and J.C. Cho. 2014. Report on 19 unrecorded bacterial species of the phylum Proteobacteria, isolated from Korea in 2011. Journal of Species Research 3:37-46.
  23. Jukes, T.H. and C.R. Cantor. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism. pp. 121-132. Edited by H.N. Munro. New York: Academic Press.
  24. Kampfer, P., R. Schulze, U. Jackel, K.A. Malik, R. Amann and S. Spring. 2005. Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. International Journal of Systematic and Evolutionary Microbiology 55:341-344. https://doi.org/10.1099/ijs.0.03041-0
  25. Kampfer, P., S.P. Glaeser, N. Lodders, H.J. Busse and E. Falsen. 2013. Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals. International Journal of Systematic and Evolutionary Microbiology 63:412-417. https://doi.org/10.1099/ijs.0.039073-0
  26. 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
  27. Lai, Q., G. Li, X. Liu, Y. Du, F. Sun and Z. Shao. 2015. Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov. Antonie van Leeuwenhoek 107:105-1074.
  28. La Scola, B., M.N. Mallet, P.A.D. Grimont and D. Raoult. 2002. Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A. International Journal of Systematic and Evolutionary Microbiology 52:1773-1782.
  29. Makk, J., Z.G. Homonnay, Z._Keki, K. Nemes-Barnas, K. Marialigeti, P. Schumann and E.M. Toth 2015. Arenimonas subflava sp. nov., isolated from a drinking water network, and emended description of the genus Arenimonas. International Journal of Systematic Bacteriology 65:1915-1921.
  30. Malmqvist, A., T. Welander, E. Moore, A. Ternstrom, G. Molin and I.M. Stenstrom. 1994. Ideonella dechloratans, gen. nov., sp. nov., a new bacterium capable of growing anaerobically with chlorate as an electron acceptor. Systematic and Applied Microbiology 17:58-64. https://doi.org/10.1016/S0723-2020(11)80032-9
  31. Mechichi, T., E. Stackebrandt, N. Gad'on and G. Fuchs. 2002. Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. Archives of Microbiology 178:26-35. https://doi.org/10.1007/s00203-002-0422-6
  32. Pascault, N., S. Roux, J. Artigas, S. Pesce, J. Leloup, R.D. Tadonleke, D. Debroas, A. Bouchez and J.F. Humbert. 2014. A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole. FEMS Microbiology Ecology 90:563-574. https://doi.org/10.1111/1574-6941.12416
  33. Pruesse, E., J. Peplies and F.O. Glockner. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829. https://doi.org/10.1093/bioinformatics/bts252
  34. Reddy, G.S.N., M. Nagy and F. Garcia-Pichel. 2006. Belnapia moabensis gen. nov., sp. nov., an alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA. International Journal of Systematic and Evolutionary Microbiology 56:51-58. https://doi.org/10.1099/ijs.0.63764-0
  35. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
  36. Spring, S., M. Wagner, P. Schu. 2005. Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov. International Journal of Systematic and Evolutionary Microbiology 55:621-629. https://doi.org/10.1099/ijs.0.63356-0
  37. Stackebrandt, E., R.G.E. Murray and H.G. Truper. 1988. Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives". International Journal of Systematic Bacteriology 38:321-325. https://doi.org/10.1099/00207713-38-3-321
  38. Stackebrandt, E., S. Verbarg, A. Fruhling, H.J. Busse and B.J. Tindall. 2009. Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium. International Journal of Systematic and Evolutionary Microbiology 59:2552-2560. https://doi.org/10.1099/ijs.0.008383-0
  39. 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
  40. Uchino, Y., T. Hamada and A. Yokota. 2002. Proposal of Pseudorhodobacter ferrugineus gen. nov., comb. nov., for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter. The Journal of General and Applied Microbiology 48:309-319. https://doi.org/10.2323/jgam.48.309
  41. Wang, L., S. Zheng, D. Wang, L. Wang and G. Wang. 2014. Thermomonas carbonis sp. nov., isolated from the soil of a coal mine. International Journal of Systematic Bacteriology 64:3631-3635.
  42. Wang, Y., H.F. Sheng, Y. He, J.Y. Wu, Y.X. Jiang, N.F.Y. Tam and H.W. Zhou. 2012. Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags. Applied and Environmental Microbiology 78:8264-8271. https://doi.org/10.1128/AEM.01821-12
  43. Wolterink, A., S. Kim, M. Muusse, I.S. Kim, P.J.M. Roholl, C.G. Van Ginkel, A.J.M. Stams and S.W.M. Kengen. 2005. Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1. International Journal of Systematic and Evolutionary Microbiology 55:2063-2068. https://doi.org/10.1099/ijs.0.63404-0
  44. Xiao, N., Y. Liu, X. Liu, Z. Gu, N. Jiao, H. Liu, Y. Zhou and L. Shen. 2015. Blastomonas aquatica sp. nov., a bacteriochlorophyll-containing bacterium isolated from lake water. International Journal of Systematic and Evolutionary Microbiology 65:1653-1658. https://doi.org/10.1099/ijs.0.000153
  45. Zhang, Y.Q., Y.G. Chen, W.J. Li, X.P. Tian, L.H. Xu and C.L. Jiang. 2005. Sphingomonas yunnanensis sp. nov., a novel Gram-negative bacterium from a contaminated plate. International Journal of Systematic and Evolutionary Microbiology 55:2361-2364. https://doi.org/10.1099/ijs.0.63697-0