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A report of 39 unrecorded bacterial species in Korea, belonging to the Betaproteobacteria and Gammaproteobacteria

  • Choi, Ahyoung (Department of Biological Sciences, Inha University) ;
  • Bae, Jin-Woo (Department of Biology, Kyung Hee University) ;
  • Cha, Chang-Jun (Department of Biotechnology, Chung-Ang University) ;
  • Chun, Jongsik (School of Biological Sciences, Seoul National University) ;
  • Im, Wan-Taek (Department of Biotechnology, Hankyong National University) ;
  • Jahng, Kwang Yeop (Department of Life Sciences, Chonbuk National University) ;
  • Jeon, Che Ok (Department of Life Science, Chung-Ang University) ;
  • Joh, Kiseong (Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies) ;
  • Kim, Seung Bum (Department of Microbiology, Chungnam National University) ;
  • Seong, Chi Nam (Department of Biology, Sunchon National University) ;
  • Yoon, Jung-Hoon (Department of Food Science and Biotechnology, Sungkyunkwan University) ;
  • Cho, Jang-Cheon (Department of Biological Sciences, Inha University)
  • Received : 2015.05.15
  • Accepted : 2015.07.27
  • Published : 2015.08.30

Abstract

As a subset study to discover indigenous prokaryotic species in Korea, a total of 39 bacterial strains assigned to the classes Betaproteobacteria and Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, seaweed, wetland, plant roots, guts of insects, and fermented foods. From the high 16S rRNA gene sequence similarity (>99.1%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 39 species have been described in Korea; therefore 4 species of 4 genera in the order Burkholderiales and 1 species in the order Neisseriales within the class Betaproteobacteria, and 10 species of 6 genera in the order Alteromonadales, 11 species of 3 genera in the order Pseudomonadales, 4 species of 4 genera in the order Enterobacteriales, 2 species of 2 genera in the order Vibrionales, 1 species in the order Aeromonadales, 3 species of 3 genera in the order Oceanospirillales, 2 species of 2 genera in the order Xanthomonadales, and 1 species in the order Chromatiales within the Gammaproteobacteia are reported for proteobacterial 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.

Keywords

References

  1. Arahal, D.R., M.T. Garcia, W. Ludwig, K.H. Schleifer and A. Ventosa. 2001. Transfer of Halomonas canadensis and Halomonas israelensis to the genus Chromohalobacter as Chromohalobacter canadensis comb. nov. and Chromohalobacter israelensis comb. nov. International Journal of Systematic and Evolutionary Microbiology 51(4):1443-1448. https://doi.org/10.1099/00207713-51-4-1443
  2. Borrego, J.J., D. Castro, A. Luque, C. Paillard, P. Maes, M.T. Garcia and A. Ventosa. 1996. Vibrio tapetis sp. nov., the causative agent of the brown ring disease affecting cultured clams. International Journal of Systematic and Evolutionary Microbiology 46(2):480-484.
  3. Bouvet, P.J.M. and P.A.D. Grimont. 1986. Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov. and emended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii. International Journal of Systematic Bacteriology 36(2):228-240. https://doi.org/10.1099/00207713-36-2-228
  4. Bozal, N., M.J. Montes and E. Mercade. 2007. Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment. International Journal of Systematic and Evolutionary Microbiology 57(11):2609-2612. https://doi.org/10.1099/ijs.0.65141-0
  5. Bozal, N., M.J. Montes, E. Tudela and J. Guinea. 2003. Characterization of several Psychrobacter strains isolated from Antarctic environments and description of Psychrobacter luti sp. nov. and Psychrobacter fozii sp. nov. International Journal of Systematic and Evolutionary Microbiology 53(4):1093-1100. https://doi.org/10.1099/ijs.0.02457-0
  6. Brady, C., S. Denman, S. Kirk, S. Venter, P. Rodriguez-Palenzuela and T. Coutinho. 2010. Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline. Systematic and Applied Microbiology 33(8):444-450. https://doi.org/10.1016/j.syapm.2010.08.006
  7. Brady, C.L., S.N. Venter, I. Cleenwerck, K. Engelbeen, M. Vancanneyt, J. Swings and T.A. Coutinho. 2009. Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov. International Journal of Systematic and Evolutionary Microbiology 59(9):2339-2345. https://doi.org/10.1099/ijs.0.009241-0
  8. Cho, J.C. and S.J. Giovannoni. 2004. Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Applied and Environmental Microbiology 70(1):432-440. https://doi.org/10.1128/AEM.70.1.432-440.2004
  9. 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(3):367-393. https://doi.org/10.1099/00207713-28-3-367
  10. Chun, J., H.D. Youn, Y.I. Yim, H. Lee, M.Y. Kim, Y.C. Hah and S.O. Kang. 1997. Streptomyces seoulensis sp. nov. International Journal of Systematic Bacteriology 47(2):492-498. https://doi.org/10.1099/00207713-47-2-492
  11. Connon, S.A. and S.J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Applied and Environmental Microbiology 68:3878-3885. https://doi.org/10.1128/AEM.68.8.3878-3885.2002
  12. Coroler, L., M. Elomari, B. Hoste, M. Gillis, D. Izard and H. Leclerc. 1996. Pseudomonas rhodesiae sp. nov., a new species isolated from natural mineral waters. Systematic and Applied Microbiology 19(4):600-607. https://doi.org/10.1016/S0723-2020(96)80032-4
  13. Coyne, V., C. Pillidge, D. Sledjeski, H. Hori, B. Ortiz-Conde, D. Muir, R. Weiner and R. Colwell. 1989. Reclassification of Alteromonas colwelliana to the genus Shewanella by DNA-DNA hybridization, serology and 5S ribosomal RNA sequence data. Systematic and Applied Microbiology 12(3):275-279. https://doi.org/10.1016/S0723-2020(89)80074-8
  14. Delong, E.F., G.S. Wickham and N.R. Pace. 1989. Phylogenetic stains: Ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363. https://doi.org/10.1126/science.2466341
  15. Donachie, S.P., S. Hou, T.S. Gregory, A. Malahoff and M. Alam. 2003. Idiomarina loihiensis sp. nov., a halophilic $\gamma$-Proteobacterium from the Loihi submarine volcano, Hawaii. International Journal of Systematic and Evolutionary Microbiology 53(6):1873-1879. https://doi.org/10.1099/ijs.0.02701-0
  16. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17(6):368-376. https://doi.org/10.1007/BF01734359
  17. Gauthier, G., M. Gauthier and R. Christen. 1995. Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations. International Journal of Systematic Bacteriology 45(4):755-761. https://doi.org/10.1099/00207713-45-4-755
  18. Giovannoni, S.J., T.B. Britschgi, C.L. Moyer and K.G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63. https://doi.org/10.1038/345060a0
  19. Giovannoni, S.J., D.H. Hayakawa, H.J. Tripp, U. Stingl, S.A. Givan, J.C. Cho, H.M. Oh, J.B. Kitner, K.L. Vergin and M.S. Rappe. 2008. The small genome of an abundant coastal ocean methylotroph. Environmental Microbiology 10:1771-1782. https://doi.org/10.1111/j.1462-2920.2008.01598.x
  20. Hauser, E., P. Kampfer and H.-J. Busse. 2004. Pseudomonas psychrotolerans sp. nov. International Journal of Systematic and Evolutionary Microbiology 54(5):1633-1637. https://doi.org/10.1099/ijs.0.03024-0
  21. Heuchert, A., F.O. Glockner, R. Amann and U. Fischer. 2004. Psychrobacter nivimaris sp. nov., a heterotrophic bacterium attached to organic particles Isolated from the South Atlantic (Antarctica). Systematic and Applied Microbiology 27(4):399-406. https://doi.org/10.1078/0723202041438455
  22. Hickman-Brenner, F.W., K.L. MacDonald, A.G. Steigerwalt, G.R. Fanning, D.J. Brenner and J.J. Farmer. 1987. Aeromonas veronii, a new ornithine decarboxylase-positive species that may cause diarrhea. Journal of Clinical Microbiology 25(5):900-906.
  23. Hoffmann, H., S. Stindl, A. Stumpf, A. Mehlen, D. Monget, J. Heesemann, K.H. Schleifer and A. Roggenkamp. 2005. Description of Enterobacter ludwigii sp. nov., a nove Enterobacter species of clinical relevance. Systematic and Applied Microbiology 28(3):206-212. https://doi.org/10.1016/j.syapm.2004.12.009
  24. Hoppener-Ogawa, S., W. de Boer, J. Leveau, J. Van Veen, E. De Brandt, E. Vanlaere, H. Sutton, D.J. Dare and P. Vandamme. 2008. Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-) natural grassland soils. International Journal of Systematic and Evolutionary Microbiology 58(2):414-419. https://doi.org/10.1099/ijs.0.65375-0
  25. Jung, S.-Y., T.-K. Oh and J.-H. Yoon. 2006. Colwellia aestuarii sp. nov., isolated from a tidal flat sediment in Korea. International Journal of Systematic and Evolutionary Microbiology 56(1):33-37. https://doi.org/10.1099/ijs.0.63920-0
  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(3):716-721. https://doi.org/10.1099/ijs.0.038075-0
  27. Kurilenko, V.V., R. Christen, N.V. Zhukova, N.I. Kalinovskaya, V.V. Mikhailov, R.J. Crawford and E.P. Ivanova. 2010. Granulosicoccus coccoides sp. nov., isolated from leaves of seagrass (Zostera marina). International Journal of Systematic and Evolutionary Microbiology 60(4):972-976. https://doi.org/10.1099/ijs.0.013516-0
  28. Lang, E., B. Griese, C. Sproer, P. Schumann, M. Steffen and S. Verbarg. 2007. Characterization of 'Pseudomonas azelaica' DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Lizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym. International Journal of Systematic and Evolutionary Microbiology 57(4):878-882. https://doi.org/10.1099/ijs.0.64849-0
  29. Lee, H.-W., N.-R. Shin, J. Lee, S.W. Roh, T.W. Whon and J.-W. Bae. 2012. Neptunomonas concharum sp. nov., isolated from a dead ark clam, and emended description of the genus Neptunomonas. International Journal of Systematic and Evolutionary Microbiology 62(Pt 11):2657-2661. https://doi.org/10.1099/ijs.0.037473-0
  30. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A.W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode and K.H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Research 32(4):1363-1371. https://doi.org/10.1093/nar/gkh293
  31. Makkar, N. and L. Casida. 1987. Cupriavidus necator gen. nov., sp. nov.; a nonobligate bacterial predator of bacteria in soil. International Journal of Systematic Bacteriology 37(4):323-326. https://doi.org/10.1099/00207713-37-4-323
  32. Martinez-Canovas, M.J., V. Bejar, F. Martinez-Checa, R. Paez and E. Quesada. 2004. Idiomarina fontislapidosi sp. nov. and Idiomarina ramblicola sp. nov., isolated from inland hypersaline habitats in Spain. International Journal of Systematic and Evolutionary Microbiology 54(5):1793-1797. https://doi.org/10.1099/ijs.0.63172-0
  33. Nalin, R., P. Simonet, T.M. Vogel and P. Normand. 1999. Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. International Journal of Systematic Bacteriology 49(1):19-23. https://doi.org/10.1099/00207713-49-1-19
  34. Nam, Y.-D., H.-W. Chang, J.R. Park, H.-Y. Kwon, Z.-X. Quan, Y.-H. Park, J.-S. Lee, J.-H. Yoon and J.-W. Bae. 2007. Pseudoalteromonas marina sp. nov., a marine bacterium isolated from tidal flats of the Yellow Sea, and reclassification of Pseudoalteromonas sagamiensis as Algicola sagamiensis comb. nov. International Journal of Systematic and Evolutionary Microbiology 57(1):12-18. https://doi.org/10.1099/ijs.0.64523-0
  35. 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
  36. Palleroni, N.J., M. Doudoroff, R.Y. Stanier, R.E. Solanes, and M. Mandel. 1970. Taxonomy of the aerobic Pseudomonads: the properties of the Pseudomonas stutzeri group. Journal of General Microbiology 60(2):215-231. https://doi.org/10.1099/00221287-60-2-215
  37. 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
  38. Pedros-Alio, C. 2006. Marine microbial diversity: can it be determined? Trends in Microbiology 14(6):257-263. https://doi.org/10.1016/j.tim.2006.04.007
  39. Pruesse, E., J. Peplies and F.O. Glockner. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28(14):1823-1829. https://doi.org/10.1093/bioinformatics/bts252
  40. Romanenko, L.A., M. Uchino, B.M. Tebo, N. Tanaka, G.M. Frolova and V.V. Mikhailov. 2008. Pseudomonas marincola sp. nov., isolated from marine environments. International Journal of Systematic and Evolutionary Microbiology 58(3):706-710. https://doi.org/10.1099/ijs.0.65406-0
  41. Romanenko, L.A., N.V. Zhukova, M. Rohde, A.M. Lysenko, V.V. Mikhailov and E. Stackebrandt. 2003. Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium. International Journal of Systematic and Evolutionary Microbiology 53(3):647-651. https://doi.org/10.1099/ijs.0.02469-0
  42. 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.
  43. Sanchez-Porro, C., R.R. de la Haba, N. Soto-Ramirez, M.C. Marquez, R. Montalvo-Rodriguez and A. Ventosa. 2009. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. International Journal of Systematic and Evolutionary Microbiology 59(2):397-405. https://doi.org/10.1099/ijs.0.001461-0
  44. Sawabe, T., R. Tanaka, M.M. Iqbal, K. Tajima, Y. Ezura, E.P. Ivanova and R. Christen. 2000. Assignment of Alteromonas elyakovii KMM 162T and five strains isolated from spot-wounded fronds of Laminaria japonica to Pseudoalteromonas elyakovii comb. nov. and the extended description of the species. International Journal of Systematic and Evolutionary Microbiology 50(1):265-271. https://doi.org/10.1099/00207713-50-1-265
  45. Schaad, N.W., E. Postnikova, A. Sechler, L.E. Claflin, A.K. Vidaver, J.B. Jones, I. Agarkova, A. Ignatov, E. Dickstein and B.A. Ramundo. 2008. Reclassification of subspecies of Acidovorax avenae as A. Avenae (Manns 1905) emend., A. cattleyae (Pavarino, 1911) comb. nov., A. citrulli (Schaad et al., 1978) comb. nov., and proposal of A. oryzae sp. nov. Systematic and Applied Microbiology 31(6):434-446. https://doi.org/10.1016/j.syapm.2008.09.003
  46. Sipkema, D., K. Schippers, W.J. Maalcke, Y. Yang, S. Salim and H.W. Blanch. 2011. Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp. Applied and Environmental Microbiology 77(6):2130-2140. https://doi.org/10.1128/AEM.01203-10
  47. 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. https://doi.org/10.1093/molbev/mst197
  48. Thompson, F.L., B. Hoste, C.C. Thompson, J. Goris, B. Gomez-Gil, L. Huys, P. De Vos and J. Swings. 2002. Enterovibrio norvegicus gen. nov., sp. nov., isolated from the gut of turbot (Scophthalmus maximus) larvae: a new member of the family Vibrionaceae. International Journal of Systematic and Evolutionary Microbiology 52(6):2015-2022. https://doi.org/10.1099/ijs.0.02315-0
  49. Vandamme, P., E. Mahenthiralingam, B. Holmes, T. Coenye, B. Hoste, P. De Vos, D. Henry and D. Speert. 2000. Identification and population structure of Burkholderia stabilis sp. nov. (formerly Burkholderia cepacia Genomovar IV). Journal of Clinical Microbiology 38(3):1042-1047.
  50. Vanparys, B., K. Heylen, L. Lebbe and P. De Vos. 2006. Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum. International Journal of Systematic and Evolutionary Microbiology 56(8):1875-1881. https://doi.org/10.1099/ijs.0.64224-0
  51. Watanabe, K., N. Komatsu, Y. Ishii and M. Negishi. 2009. Effective isolation of bacterioplankton genus Polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter. FEMS Microbiology Ecology 67(1):57-68. https://doi.org/10.1111/j.1574-6941.2008.00606.x
  52. Whitman, W.B., D.C. Coleman and W.J. Wiebe. 1998. Prokaryotes: the unseen majority. Proceedings of National Academy of Sciences USA. 95:6578-6583. https://doi.org/10.1073/pnas.95.12.6578
  53. Xiao, Y.-P., W. Hui, Q. Wang, S.W. Roh, X.-Q. Shi, J.-H. Shi and Z.-X. Quan. 2009. Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. International Journal of Systematic and Evolutionary Microbiology 59(10):2594-2598.
  54. Yoon, J.-H., K.H. Kang, T.-K. Oh and Y.-H. Park. 2004. Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea. International Journal of Systematic and Evolutionary Microbiology 54(2):487-491. https://doi.org/10.1099/ijs.0.02731-0
  55. Yoon, J.H., S.K. Rhee, J.S. Lee, Y.H. Park and S.T. Lee. 1997. Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. International Journal of Systematic Bacteriology 47(4):933-938. https://doi.org/10.1099/00207713-47-4-933
  56. Young, C.-C., A.B. Arun, W.-A. Lai, W.-M. Chen, J.-H. Chao, F.-T. Shen, P.D. Rekha and P. Kampfer. 2008. Chromobacterium aquaticum sp. nov., isolated from spring water samples. International Journal of Systematic and Evolutionary Microbiology 58(4):877-880. https://doi.org/10.1099/ijs.0.65573-0
  57. Zhang, D.-C., H.-R. Li, Y.-H. Xin, Z.-M. Chi, P.-J. Zhou and Y. Yu. 2008. Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic. International Journal of Systematic and Evolutionary Microbiology 58(6):1463-1466. https://doi.org/10.1099/ijs.0.65690-0