Sufflavibacter maritimus gen. nov., sp. nov., Novel Flavobacteriaceae Bacteria Isolated from Marine Environments

  • Kwon, Kae-Kyoung (Marine Biotechnology Research Center, Korea Ocean Research & Development Institute) ;
  • Yang, Seung-Jo (Division of Biology and Ocean Sciences, Inha University) ;
  • Lee, Hee-Soon (Marine Biotechnology Research Center, Korea Ocean Research & Development Institute) ;
  • Cho, Jang-Cheon (Division of Biology and Ocean Sciences, Inha University) ;
  • Kim, Sang-Jin (Marine Biotechnology Research Center, Korea Ocean Research & Development Institute)
  • Published : 2007.08.30

Abstract

Four Gram-negative, chemoheterotrophic, non-motile, yellow-colored strains were isolated from the East Sea or from deep-sea sediments of Nankai Trough by standard dilution plating. Characterization by polyphasic approaches indicated that the four strains are members of the same species. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The dominant cellular fatty acids were i-C15:0, 3-OH i-C17:0, and 2-OH i-C15:0 and/or C16:1 ${\omega}7c$. Predominance of 2-OH i-C15:0 and/or C16:1 ${\omega}7c$ clearly differentiated the strains from closely related members. The DNA G+C contents ranged 35.1-36.2 mol%. It is proposed, from the polyphasic evidence, that the strains should be placed into a novel genus and species named Sufflavibacter maritimus gen. nov., sp. nov., with strain $IMCC1001^T(=KCCM\;42359^T=NBRC\;102039^T)$ as the type strain.

Keywords

References

  1. Bae, S. S., K. K. Kwon, S. H. Yang, H.-S. Lee, S.-J. Kim, and J.-H. Lee. 2007. Flagellimonas eckloniae gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from the rhizosphere of Ecklonia kurome. Int. J. Syst. Evol. Microbiol. 57: 1050-1054 https://doi.org/10.1099/ijs.0.64565-0
  2. Bauer, M., M. Kube, H. Teeling, M. Richter, T. Lombardot, E. Allers, C. A. Würdemann, C. Quast, H. Kuhl, F. Knaust, D. Woebken, K. Bischof, M. Mussmann, J. V. Choudhuri, F. Meyer, R. Reinhardt, R. I. Amann, and F. O. Glöckner. 2006. Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8: 2201-2213 https://doi.org/10.1111/j.1462-2920.2006.01152.x
  3. Bernardet, J.-F., Y. Nakagawa, and B. Holmes. 2002. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int. J. Syst. Evol. Microbiol. 52: 1049-1070 https://doi.org/10.1099/ijs.0.02136-0
  4. Cho, J.-C. and S. J. Giovannoni. 2003. Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae. Syst. Appl. Microbiol. 26: 76-83 https://doi.org/10.1078/072320203322337344
  5. Cho, J.-C. and S. J. Giovannoni. 2003. Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the $\alpha$-Proteobacteria. Int. J. Syst. Evol. Microbiol. 53: 1031-1036 https://doi.org/10.1099/ijs.0.02566-0
  6. Cho, W., E.-H. Lee, E.-H. Shim, J. Kim, H. W. Ryu, and K.-S. Cho. 2005. Bacterial communities of biofilms sampled from seepage groundwater contaminated with petroleum oil. J. Microbiol. Biotechnol. 15: 952-964
  7. Chun, J. and M. Goodfellow. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 45: 240-245 https://doi.org/10.1099/00207713-45-2-240
  8. Collins, M. D. 1985. Isoprenoid quinone analysis in bacterial classification and identification, pp. 267-287. In M. Goodfellow and D. E. Minikin (eds.), Chemical Methods in Bacterial Systematics. Academic Press, London
  9. Cottrell, M. T. and D. L. Kirchman. 2000. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and highmolecular- weight dissolved organic matter. Appl. Environ. Microbiol. 66: 1692-1697 https://doi.org/10.1128/AEM.66.4.1692-1697.2000
  10. Eilers, H., J. Pernthaler, F. O. Glöckner, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66: 3044-3051 https://doi.org/10.1128/AEM.66.7.3044-3051.2000
  11. Fautz, E. and H. Reichenbach. 1980. A simple test for flexirubin-type pigments. FEMS Microbiol. Lett. 8: 87-91 https://doi.org/10.1111/j.1574-6968.1980.tb05056.x
  12. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791 https://doi.org/10.2307/2408678
  13. Fritz, I. 2000. Das Bakterioplankton im Westlichen Mittelmeer. Analyse der taxonomischen Struktur freilebender und partikelgebundener bakterieller Lebensgemeinschaften mit mikrobiologischen und molekularbiologischen Methoden. Ph. D. Thesis. Gemeinsame Naturwissenschaftliche Fakultaet, Technische Universitaet Carolo-Wilhelmina Braunschweig, Braunschweig, Germany
  14. Garrity, G. M. and J. G. Holt. 2001. The road map to the Manual, pp. 119-166. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (eds.), Bergey's Manual of Systematic Bacteriology, 2nd Ed. Vol. 1. Springer, New York
  15. Giuliano, L., M. De Domenico, E. De Domenico, M. G. Höfle, and M. M. Yakimov. 1999. Identification of culturable oligotrophic bacteria within naturally occuring bacterioplankton communities of the Ligurian Sea by 16S rRNA sequencing and probing. Microb. Ecol. 37: 77-85 https://doi.org/10.1007/s002489900132
  16. Glockner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: A first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65: 3721-3726
  17. Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58: 10-26
  18. Heijs, S. K., J. S. Sinninghe Damste, and L. J. Forney. 2005. Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea. FEMS Microbiol. Ecol. 54: 47-56 https://doi.org/10.1016/j.femsec.2005.02.007
  19. Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F. S. Colwell, K. H. Nealson, K. Horikoshi, S. D'hondt, and B. B. Jorgensen. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA 103: 2815-2820
  20. Ivanova, E. P., J. P. Bowman, R. Christen, N. V. Zhukova, A. M. Lysenko, N. M. Gorshkova, N. Mitik-Dineva, A. F. Sergeev, and V. V. Mikhailov. 2006. Salegentibacter flavus sp. nov. Int. J. Syst. Evol. Microbiol. 56: 583-586 https://doi.org/10.1099/ijs.0.64087-0
  21. Jukes, T. H. and C. R. Cantor. 1969. Evolution of protein molecules, pp. 21-132. In H. N. Munro (ed.), Mammalian Protein Metabolism. Academic Press, New York
  22. Kim, B. S., H.-Y. Oh, H. Kang, S.-S. Park, and J. Chun. 2004. Remarkable bacterial diversity in the tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. Biotechnol. 14: 205-211
  23. Kormas, K. Ar., D. C. Smith, V. Edgcomb, and A. Teske. 2003. Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol. Ecol. 45: 115-125 https://doi.org/10.1016/S0168-6496(03)00128-4
  24. Kwon, K. K., H.-S. Lee, S. H. Yang, and S-J. Kim. 2005. Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the 'Alphaproteobacteria'. Int. J. Syst. Evol. Microbiol. 55: 2033-2037 https://doi.org/10.1099/ijs.0.63684-0
  25. Lau, S. C. K., M. M. Y. Tsoi, X. Li, I. Plakhotnikova, S. Dobretsov, P.-K. Wong, and P.-Y. Qian. 2005. Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 55: 2497-2500 https://doi.org/10.1099/ijs.0.63824-0
  26. Madrid, V. M., J. Y. Aller, R. C. Aller, and A. Y. Chistoserdov. 2001. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: Identification of two new bacterial candidate divisions. FEMS Microbiol. Ecol. 37: 197-209 https://doi.org/10.1111/j.1574-6941.2001.tb00867.x
  27. McCammon, S. A. and J. P. Bowman. 2000. Taxonomy of Antarctic Flavobacterium species: Description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov. and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 50: 1055-1063 https://doi.org/10.1099/00207713-50-3-1055
  28. Nedashkovskaya, O. I., S. B. Kim, S. K. Han, A. M. Lysenko, M. Rohde, N. V. Zhukova, E. Falsen, G. M. Frolova, V. V. Mikhailov, and K. S. Bae. 2003. Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm. Int. J. Syst. Evol. Microbiol. 53: 1967-1971 https://doi.org/10.1099/ijs.0.02626-0
  29. Nedashkovskaya, O. I., M. Suzuki, M. Vancanneyt, I. Cleenwerck, N. V. Zhukova, M. V. Vysotskii, V. V. Mikhailov, and J. Swing. 2004. Salegentibacter holothuriorum sp. nov., isolated from the edible holothurian Apostichopus japonicus. Int. J. Syst. Evol. Microbiol. 54: 1107-1110 https://doi.org/10.1099/ijs.0.02987-0
  30. Nedashkovskaya, O. I., S. B. Kim, A. M. Lysenko, G. M. Frolova, V. V. Mikhailov, K. S. Bae, D. H. Lee, and I. S. Kim. 2005. Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. Int. J. Syst. Evol. Microbiol. 55: 391-394 https://doi.org/10.1099/ijs.0.63314-0
  31. Nedashkovskaya, O. I., S. B. Kim, A. M. Lysenko, V. V. Mikhailov, K. S. Bae, and I. S. Kim. 2005. Salegentibacter mishustinae sp. nov., isolated from the sea urchin Strongylocentrotus intermedius. Int. J. Syst. Evol. Microbiol. 55: 235-238 https://doi.org/10.1099/ijs.0.63297-0
  32. Nedashkovskaya, O. I., S. B. Kim, M. Vancanneyt, D. S. Shin, A. M. Lysenko, L. S., Shevchenko, V. B. Krasokhin, V. V. Mikhailov, J. Swings, and K. S. Bae. 2006. Salegentibacter agarivorans sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the sponge Artemisina sp. Int. J. Syst. Evol. Microbiol. 56: 883- 887 https://doi.org/10.1099/ijs.0.64167-0
  33. Nedashkovskaya, O. I., S. B. Kim, N. V. Zhukova, J. Kwak, V. V. Mikhailov, and S. B. Bae. 2006. Mesonia mobilis sp. nov., isolated from seawater, and emended description of the genus Mesonia. Int. J. Syst. Evol. Microbiol. 56: 2433-2436 https://doi.org/10.1099/ijs.0.64376-0
  34. Park, S.-J., C.-H. Kang, and S.-K. Lee. 2006. Characterization of the microbial diversity in a Korean solar saltern by 16S rRNA gene analysis. J. Microbiol. Biotechnol. 16: 1640- 1645
  35. Penn, K., D. Wu, J. A. Eisen, and N. Ward. 2006. Characterization of bacterial communities associated with deep-sea corals on gulf of Alaska seamounts. Appl. Environ. Microbiol. 72: 1680-1683 https://doi.org/10.1128/AEM.72.2.1680-1683.2006
  36. Reichenbach, H. 1989. Order I. Cytophagales Leadbetter 1974, $99^{AL}$, pp. 2011-2013. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (eds.), Bergey's Manual of Systematic Bacteriology, Vol. 3. Williams & Wilkins, Baltimore
  37. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
  38. Shuang, J. L., C. H. Liu, S. Q. An, Y. Xing, G. Q. Zheng, and Y. F. Shen. 2006. Some universal characteristics of intertidal bacterial diversity as revealed by 16S rRNA gene-based PCR clone analysis. J. Microbiol. Biotechnol. 16: 1882-1889
  39. Song, J., S.-J. Yang, and J.-C. Cho. 2007. 'Bring to Lab' of 19 novel species among 60 isolates retrieved from a freshwater pond. J. Microbiol. Biotechnol. 17: 168-175
  40. Stackebrandt, E. and W. Liesack. 1993. Nucleic acids and classification, pp. 158-160. In M. Goodfellow and A. G. O'Donnell (eds.), Handbook of New Bacterial Systematics. Academic Press, London