1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 58, Issue 7

gen. nov., sp. nov., a marine bacterium in the family Free

Abstract

A Gram-negative, rod-shaped, strictly aerobic micro-organism, designated strain CL-GR60, was isolated from coastal seawater from the East Sea, Korea. A 16S rRNA gene sequence analysis revealed a clear affiliation with the family . Phylogenetic analyses showed that strain CL-GR60 formed a robust cluster with the species of the genus at sequence similarity levels of 91.1–93.1 %; no other species in the family shared more than 90 % sequence similarity with strain CL-GR60. The strain grew optimally in the presence of 3–4 % sea salts at 30–35 °C and pH 7. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. The strain contained C 7 (54.7 %), 11-methyl C 7 (19.3 %), C (14.4 %) as the predominant fatty acids. Ubiquinone-10 was the major quinone. The DNA G+C content was 62.9 mol%. On the basis of physiological data, fatty acid composition and results of phylogenetic analysis of the 16S rRNA gene sequence, strain CL-GR60 represents a novel genus and species within the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is CL-GR60 (=KCCM 90027 =DSM 18995).

  • Published Online:
© SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65587-0
2008-07-01
2023-06-10
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/58/7/1591.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65587-0&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J.(1990). Basic local alignment search tool. J Mol Biol 215, 403–410.[CrossRef] [Google Scholar]
  2. Bauer, A. W., Kirby, W. M. M., Sherris, J. C. & Turck, M.(1966). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45, 493–496. [Google Scholar]
  3. Baumann, P. & Baumann, L.(1981). The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In The Prokaryotes, pp. 1302–1330. Edited by M. P. Starr, H. Stolp, H. G. Trüper, A. Balows & H. G. Schlegel. Berlin: Springer.
  4. Brodie, E. L., DeSantis, T. Z., Joyner, D. C., Baek, S. M., Larsen, J. T., Andersen, G. L., Hazen, T. C., Richardson, P. M., Herman, D. J. & other authors(2006). Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72, 6288–6298.[CrossRef] [Google Scholar]
  5. Cole, J. R., Chai, B., Marsh, T. L., Farris, R. J., Wang, Q., Kulam, S. A., Chandra, S., McGarrell, D. M., Schmidt, T. M. & other authors(2003). The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31, 442–443.[CrossRef] [Google Scholar]
  6. Collins, M. D.(1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 329–366. [Google Scholar]
  7. Englen, M. D. & Kelley, L. C.(2000). A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Lett Appl Microbiol 31, 421–426.[CrossRef] [Google Scholar]
  8. Felsenstein, J.(1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef] [Google Scholar]
  9. Fitch, W. M.(1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef] [Google Scholar]
  10. Garrity, G. M., Bell, J. A. & Lilburn, T.(2005). Family VIII. Hyphomicrobiaceae Babudieri 1950, 589. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, The Proteobacteria, part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, p. 476. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  11. Gliesche, C., Fesefeldt, A. & Hirsch, P.(2005). Genus I. Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, The Proteobacteria, part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, pp. 476–494. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  12. Hansen, G. H. & Sørheim, R.(1991). Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13, 231–241.[CrossRef] [Google Scholar]
  13. Imhoff, J. F.(2005). Genus XVI. Rhodomicrobium Duchow and Douglas 1949, 415AL emend. Imhoff, Trüper and Pfennig 1984, 341. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, The Proteobacteria, part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, pp. 543–545. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  14. Jenkins, C., Stanley, P. M. & Staley, J. T.(2005). Genus II. Ancalomicrobium Staley 1968, 1940AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, The Proteobacteria, part C, The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, pp. 494–497. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  15. Jeon, Y.-S., Chung, H., Park, S., Hur, I., Lee, J.-H. & Chun, J.(2005). jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21, 3171–3173.[CrossRef] [Google Scholar]
  16. Jukes, T. H. & Cantor, C. R.(1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  17. Komagata, K. & Suzuki, K.(1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207. [Google Scholar]
  18. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  19. 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.
  20. Lee, K.-B., Liu, C.-T., Anzai, Y., Kim, H., Aono, T. & Oyaizu, H.(2005). The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 55, 1907–1919.[CrossRef] [Google Scholar]
  21. Lemos, M. L., Toranzo, A. E. & Barja, J. L.(1985). Modified medium for the oxidation-fermentation test in the identification of marine bacteria. Appl Environ Microbiol 49, 1541–1543. [Google Scholar]
  22. Lyman, J. & Fleming, R. H.(1940). Composition of sea water. J Mar Res 3, 134–146. [Google Scholar]
  23. Marmur, J.(1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef] [Google Scholar]
  24. Martens, T., Heidorn, T., Pukall, R., Simon, M., Tindall, B. J. & Brinkhoff, T.(2006). Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera. Int J Syst Evol Microbiol 56, 1293–1304.[CrossRef] [Google Scholar]
  25. Mesbah, M., Premachandran, U. & Whitman, W. B.(1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.[CrossRef] [Google Scholar]
  26. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H.(1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef] [Google Scholar]
  27. Nakagawa, Y., Sakane, T. & Yokota, A.(1996). Transfer of “Pseudomonas riboflavina” (Foster 1944), a Gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 39, 159–167. [Google Scholar]
  28. Posada, D. & Crandall, K. A.(1998).modeltest: testing the model of DNA substitution. Bioinformatics 14, 817–818.[CrossRef] [Google Scholar]
  29. Rivas, R., Willems, A., Subba-Rao, N. S., Mateos, P. F., Dazzo, F. B., Kroppenstedt, R. M., Martínez-Molina, E., Gillis, M. & Velázquez, E.(2003). Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst Appl Microbiol 26, 47–53.[CrossRef] [Google Scholar]
  30. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  31. Smibert, R. M. & Krieg, N. R.(1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  32. Staley, J. T.(1968).Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 95, 1921–1942. [Google Scholar]
  33. Suzuki, M., Nakagawa, Y., Harayama, S. & Yamamoto, S.(2001). Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 51, 1639–1652.[CrossRef] [Google Scholar]
  34. Swofford, D. L.(1998).paup: phylogenetic analysis using parsimony, version 4. Sunderland, MA: Sinauer Associates.
  35. Urakami, T. & Komagata, K.(1987a). Cellular fatty acid composition with special reference to the existence of hydroxy fatty acids in Gram-negative methanol-, methane-, and methylamine-utilizing bacteria. J Gen Appl Microbiol 33, 135–165.[CrossRef] [Google Scholar]
  36. Urakami, T. & Komagata, K.(1987b). Characterization and identification of methanol-utilizing Hyphomicrobium strains and a comparison with species of Hyphomonas and Rhodomicrobium. J Gen Appl Microbiol 33, 521–542.[CrossRef] [Google Scholar]
  37. Yoo, S.-H., Weon, H.-Y., Kim, B.-Y., Hong, S.-B., Kwon, S.-W., Cho, Y.-H., Go, S.-J. & Stackebrandt, E.(2006).Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 56, 2689–2692.[CrossRef] [Google Scholar]
  38. Yoon, J.-H., Kang, S.-J., Park, S. & Oh, T.-K.(2007).Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int J Syst Evol Microbiol 57, 1310–1314.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65587-0
Loading
Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae
Int J Syst Evol Microbiol 58, 1591 (2008); https://doi.org/10.1099/ijs.0.65587-0
/content/journal/ijsem/10.1099/ijs.0.65587-0
/content/journal/ijsem/10.1099/ijs.0.65587-0
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error