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Abstract

Nine agar-degrading strains, designated JAMB A3, JAMB A7, JAMB A24, JAMB A33, JAMB A94, JAMM 0654, JAMM 0793, JAMM 1327 and JAMM 1340, were isolated from deep-sea sediment in Suruga Bay and Sagami Bay and off Kagoshima, Japan. On the basis of 16S rRNA gene sequence analysis, the strains were found to be closely affiliated with members of the genera and . The hybridization values for DNA–DNA relatedness between two of these strains and reference strains were significantly lower than that accepted as the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, six of the isolated strains represent two novel species of the genus , for which the names sp. nov. (type strain JAMB A3 =JCM 14708 =DSM 19200) and sp. nov. (type strain JAMB A94 =JCM 14709 =DSM 19189) are proposed.

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2008-05-01
2024-04-18
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References

  1. Barrow, G. I. & Feltham, R. K. A.(1993).Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. New York: Cambridge University Press.
  2. Baumann, L., Baumann, P., Mandel, M. & Allen, R. D.(1972). Taxonomy of aerobic marine eubacteria. J Bacteriol 110, 402–429. [Google Scholar]
  3. Ezaki, T., Hashimoto, Y. & Yabuuchi, E.(1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.[CrossRef] [Google Scholar]
  4. Ferrer, M., Golyshina, O. V., Chernikova, T. N., Khachane, A. N., Martins Dos Santos, V. A., Yakimov, M. M., Timmis, K. N. & Golyshin, P. N.(2005). Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12, 895–904.[CrossRef] [Google Scholar]
  5. Gonzalez, J. M., Mayer, F., Moran, M. A., Hodson, R. E. & Whitman, W. B.(1997).Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 47, 369–376.[CrossRef] [Google Scholar]
  6. Groudieva, T., Kambourova, M., Yusef, H., Royter, M., Grote, R., Trinks, H. & Antranikian, G.(2004). Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen. Extremophiles 8, 475–488.[CrossRef] [Google Scholar]
  7. Hugh, R. & Leifson, E.(1953). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram negative bacteria. J Bacteriol 66, 22–26. [Google Scholar]
  8. Hung, V. S., Hatada, Y., Goda, S., Lu, J., Hidaka, Y., Li, Z., Akita, M., Ohta, Y., Watanabe, K. & other authors(2005).α-Glucosidase from a strain of deep-sea Geobacillus: a potential enzyme for the biosynthesis of complex carbohydrates. Appl Microbiol Biotechnol 68, 757–765.[CrossRef] [Google Scholar]
  9. Jean, W. D., Shieh, W. Y. & Liu, T. Y.(2006).Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas. Int J Syst Evol Microbiol 56, 1245–1250.[CrossRef] [Google Scholar]
  10. Kimura, M.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef] [Google Scholar]
  11. Kobayashi, R., Takisada, M., Suzuki, T., Kirimura, K. & Usami, S.(1997). Neoagarobiose as a novel moisturizer with whitening effect. Biosci Biotechnol Biochem 61, 162–163.[CrossRef] [Google Scholar]
  12. Kurahashi, M. & Yokota, A.(2004).Agarivorans albus gen. nov., sp. nov., a γ-proteobacterium isolated from marine animals. Int J Syst Evol Microbiol 54, 693–697.[CrossRef] [Google Scholar]
  13. Lane, D. J.(1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
  14. Macián, M. C., Ludwig, W., Schleifer, K. H., Garay, E. & Pujalte, M. J.(2001).Thalassomonas viridans gen. nov., sp. nov., a novel marine γ-proteobacterium. Int J Syst Evol Microbiol 51, 1283–1289. [Google Scholar]
  15. Miyazaki, M., Nogi, Y., Usami, R. & Horikoshi, K.(2006).Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan. Int J Syst Evol Microbiol 56, 1607–1613.[CrossRef] [Google Scholar]
  16. Nedashkovskaya, O. I., Suzuki, M., Vancanneyt, M., Cleenwerck, I., Lysenko, A. M., Mikhailov, V. V. & Swings, J.(2004).Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol 54, 1643–1648.[CrossRef] [Google Scholar]
  17. Ohta, Y., Hatada, Y., Nogi, Y., Li, Z., Zhang, H.-M., Ito, S. & Horikoshi, K.(2004a). Thermostable β-agarase from a deep-sea Microbulbifer isolate. J Appl Glycosci 51, 203–210.[CrossRef] [Google Scholar]
  18. Ohta, Y., Hatada, Y., Nogi, Y., Miyazaki, M., Li, Z., Akita, M., Hidaka, Y., Goda, S., Ito, S. & Horikoshi, K.(2004b). Enzymatic properties and nucleotide and amino acid sequences of a thermostable β-agarase from a novel species of deep-sea Microbulbifer. Appl Microbiol Biotechnol 64, 505–514.[CrossRef] [Google Scholar]
  19. Ohta, Y., Nogi, Y., Miyazaki, M., Li, Z., Hatada, Y., Ito, S. & Horikoshi, K.(2004c). Enzymatic properties and nucleotide and amino acid sequences of a thermostable β-agarase from the novel marine isolate, JAMB-A94. Biosci Biotechnol Biochem 68, 1073–1081.[CrossRef] [Google Scholar]
  20. Ohta, Y., Hatada, Y., Miyazaki, M., Nogi, Y., Ito, S. & Horikoshi, K.(2005). Purification and characterization of a novel alpha-agarase from a Thalassomonas sp. Curr Microbiol 50, 212–216.[CrossRef] [Google Scholar]
  21. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  22. Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef] [Google Scholar]
  23. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors(2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef] [Google Scholar]
  24. Tamaoka, J. & Komagata, K.(1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef] [Google Scholar]
  25. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.(1997). The clustal_x Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef] [Google Scholar]
  26. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors(1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef] [Google Scholar]
  27. Yoon, J. H., Kim, I. G., Shin, D. Y., Kang, K. H. & Park, Y. H.(2003a).Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh. Int J Syst Evol Microbiol 53, 53–57.[CrossRef] [Google Scholar]
  28. Yoon, J. H., Kim, H., Kang, K. H., Oh, T. K. & Park, Y. H.(2003b). Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov. Int J Syst Evol Microbiol 53, 1357–1361.[CrossRef] [Google Scholar]
  29. Yoon, J. H., Kim, I. G., Oh, T. K. & Park, Y. H.(2004).Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea. Int J Syst Evol Microbiol 54, 1111–1116.[CrossRef] [Google Scholar]
  30. Yoshizawa, Y., Ametani, A., Tsunehiro, J., Nomura, K., Itoh, M., Fukui, F. & Kaminogawa, S.(1995). Macrophage stimulation activity of the polysaccharide fraction from a marine alga (Porphyra yezoensis): structure-function relationships and improved solubility. Biosci Biotechnol Biochem 59, 1933–1937.[CrossRef] [Google Scholar]
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vol. , part 5, pp. 1128 - 1133

Fatty acid compositions of strains JAMB A3 and JAMB A94 and strains. [PDF](19 KB)



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