1887

Abstract

A marine bacterium, designated IMCC2115, was isolated from coastal seawater (Yellow Sea, Korea) using a high throughput cultivation method based on dilution-to-extinction, and taxonomically investigated. Cells of the strain formed tiny, beige to off-white colonies and were Gram-stain-negative, obligately aerobic, chemoheterotrophic, non-motile cocci. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to the genera (92.0–92.4 %) and (91.6–92.8 %), but phylogenetic trees showed that the strain formed a distinct phyletic line in the class adjacent to the OM60 and SAR92 clades. The DNA G+C content of the strain was 47.8 mol% and the predominant cellular fatty acids were anteiso-C (67.6 %), anteiso-C (14.4 %) and C (6.9 %). The 16S rRNA gene sequence analyses and phenotypic and chemotaxonomic tests allowed the differentiation of IMCC2115 from other related genera in the class . Therefore, strain IMCC2115 (=KCCM 42369 =NBRC 102686) is proposed as the representative of a new genus and species, for which the name gen. nov., sp. nov. is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.013938-0
2010-04-01
2019-12-11
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/4/727.html?itemId=/content/journal/ijsem/10.1099/ijs.0.013938-0&mimeType=html&fmt=ahah

References

  1. Béjà, O., Aravind, L., Koonin, E. V., Suzuki,M. T., Hadd, A., Nguyen, L. P., Jovanovich, S. B., Gates, C. M., Feldman,R. A. & other authors ( 2000; ). Bacterial rhodopsin:evidence for a new type of phototrophy in the sea. Science 289, 1902–1906.[CrossRef]
    [Google Scholar]
  2. Béjà, O., Suzuki, M. T., Heidelberg, J. F., Nelson,W. C., Preston, C. M., Hamada, T., Eisen, J. A., Fraser, C. M. & DeLong,E. F. ( 2002; ). Unsuspected diversity among marine aerobicanoxygenic phototrophs. Nature 415, 630–633.[CrossRef]
    [Google Scholar]
  3. Cho, J.-C. & Giovannoni, S. J. ( 2003; ). Parvularcula bermudensis gen. nov., sp. nov., a marine bacteriumthat forms a deep branch in the α-Proteobacteria. Int J Syst Evol Microbiol 53, 1031–1036.[CrossRef]
    [Google Scholar]
  4. Cho, J. C. & Giovannoni, S. J. ( 2004; ). Cultivation and growth characteristics of a diverse group of oligotrophicmarine Gammaproteobacteria. Appl Environ Microbiol 70, 432–440.[CrossRef]
    [Google Scholar]
  5. Cho, J. C. & Giovannoni, S. J. ( 2006; ). Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacteriumwithin the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 56, 855–859.[CrossRef]
    [Google Scholar]
  6. Cho, J. C., Stapels, M. D., Morris, R. M., Vergin, K. L., Schwalbach,M. S., Givan, S. A., Barofsky, D. F. & Giovannoni, S. J. ( 2007; ). Polyphyletic photosynthetic reaction centre genes in oligotrophicmarine Gammaproteobacteria. Environ Microbiol 9, 1456–1463.[CrossRef]
    [Google Scholar]
  7. Choi, D. H., Cho, J.-C., Lanoil, B. D., Giovannoni, S. J. &Cho, B. C. ( 2007; ). Maribius salinus gen.nov., sp. nov., isolated from a solar saltern and Maribius pelagiussp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade. Int J Syst Evol Microbiol 57, 270–275.[CrossRef]
    [Google Scholar]
  8. Choo, Y. J., Lee, K., Song, J. & Cho, J. C. ( 2007; ). Puniceicoccus vermicola gen. nov., sp. nov., anovel marine bacterium, and description of Puniceicoccaceae fam.nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. Int J Syst Evol Microbiol 57, 532–537.[CrossRef]
    [Google Scholar]
  9. Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. &Lim, Y. W. ( 2007; ). EzTaxon: a web-based tool for theidentification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259–2261.[CrossRef]
    [Google Scholar]
  10. de la Torre, J. R., Christianson, L. M., Béjà,O., Suzuki, M. T., Karl, D. M., Heidelberg, J. & DeLong, E. F. ( 2003; ). Proteorhodopsin genes are distributed among divergentmarine bacterial taxa. Proc Natl Acad Sci U S A 100, 12830–12835.[CrossRef]
    [Google Scholar]
  11. Distel, D. L., Morrill, W., MacLaren-Toussaint, N., Franks,D. & Waterbury, J. ( 2002; ). Teredinibacterturnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic γ-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia:Teredinidae). Int J Syst Evol Microbiol 52, 2261–2269.[CrossRef]
    [Google Scholar]
  12. Eilers, H., Pernthaler, J., Peplies, J., Glöckner, F. O.,Gerdts, G. & Amann, R. ( 2001; ). Isolation of novelpelagic bacteria from the German Bight and their seasonal contributions tosurface picoplankton. Appl Environ Microbiol 67, 5134–5142.[CrossRef]
    [Google Scholar]
  13. Felsenstein, J. ( 1981; ). Evolutionarytrees from DNA sequences: a maximum likelihood approach. J MolEvol 17, 368–376.
    [Google Scholar]
  14. Felsenstein, J. ( 1985; ). Confidence limitson phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  15. Fitch, W. M. ( 1971; ). Toward definingthe course of evolution: minimum change for a specific tree topology. Syst Zool 27, 401–410.
    [Google Scholar]
  16. Giovannoni, S. J., Bibbs, L., Cho, J. C., Stapels, M. D., Desiderio,R., Vergin, K. L., Rappé, M. S., Laney, S., Wilhelm, L. J. & otherauthors ( 2005; ). Proteorhodopsin in the ubiquitousmarine bacterium SAR11. Nature 438, 82–85.[CrossRef]
    [Google Scholar]
  17. Glatz, R. E., Lepp, P. W., Ward, B. B. & Francis, C. A. ( 2006; ). Planktonic microbial community compositionacross steep physical/chemical gradients in permanently ice-covered LakeBonney, Antarctica. Geobiology 4, 53–67.[CrossRef]
    [Google Scholar]
  18. González, J. M. & Weiner, R. M. ( 2000; ). Phylogenetic characterization of marine bacterium strain 2-40,a degrader of complex polysaccharides. Int J Syst Evol Microbiol 50, 831–834.[CrossRef]
    [Google Scholar]
  19. González, J. M., Mayer, F., Moran, M. A., Hodson, R.E. & Whitman, W. B. ( 1997; ). Microbulbiferhydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp millwaste enrichment community. Int J Syst Evol Microbiol 47, 369–376.
    [Google Scholar]
  20. Graeber, I., Kaesler, I., Borchert, M. S., Dieckmann, R., Pape,T., Lurz, R., Nielsen, P., von Döhren, H., Michaelis, W. & Szewzyk,U. ( 2008; ). Spongiibacter marinus gen. nov.,sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1. Int J Syst Evol Microbiol 58, 585–590.[CrossRef]
    [Google Scholar]
  21. Humphry, D. R., Black, G. W. & Cummings, S. P. ( 2003; ). Reclassification of ‘Pseudomonas fluorescenssubsp. cellulosa' NCIMB 10462 (Ueda et al. 1952)as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. Int J Syst Evol Microbiol 53, 393–400.[CrossRef]
    [Google Scholar]
  22. Jorgensen, J. H., Turnidge, J. D. & Washington, J. A. ( 1999; ). Antibacterial susceptibility tests: dilution anddisk diffusion methods. In Manual of Clinical Microbiology, pp. 1526–1543.Edited by P. R. Murray, E. J. Baron, M. A. Pfaller, F. C. Tenover & R.H. Yolken. Washington, DC: American Society for Microbiology.
  23. Kim, M. K., Schubert, K., Im, W.-T., Kim, K.-H., Lee, S.-T. &Overmann, J. ( 2007; ). Sphingomonas kaistensissp. nov., a novel alphaproteobacterium containing pufLM genes. Int J Syst Evol Microbiol 57, 1527–1534.[CrossRef]
    [Google Scholar]
  24. Lee, Y. K., Hong, S. G., Cho, H. H., Cho, K. H. & Lee, H.K. ( 2007; ). Dasania marina gen. nov., sp.nov., of the order Pseudomonadales, isolated from Arctic marine sediment. J Microbiol 45, 505–509.
    [Google Scholar]
  25. Lim, G. E. & Haygood, M. G. ( 2004; ).Candidatus Endobugula glebosa,’ a specific bacterialsymbiont of the marine bryozoan Bugula simplex. Appl EnvironMicrobiol 70, 4921–4929.
    [Google Scholar]
  26. Lim, J.-M., Jeon, C. O., Lee, J.-C., Song, S.-M., Kim, K.-Y. &Kim, C.-J. ( 2006; ). Marinimicrobium koreensegen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novelmoderately halotolerant bacteria isolated from tidal flat sediment in Korea. Int J Syst Evol Microbiol 56, 653–657.[CrossRef]
    [Google Scholar]
  27. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H.,Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors ( 2004; ). arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef]
    [Google Scholar]
  28. Mesbah, M., Premachandran, U. & Whitman, W. B. ( 1989; ). Precise measurement of the G+C content of deoxyribonucleicacid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.[CrossRef]
    [Google Scholar]
  29. Miyazaki, M., Nogi, Y., Ohta, Y., Hatada, Y., Fujiwara, Y.,Ito, S. & Horikoshi, K. ( 2008; ). Microbulbiferagarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov.,agar-degrading bacteria isolated from deep-sea sediment. Int JSyst Evol Microbiol 58, 1128–1133.
    [Google Scholar]
  30. Nagashima, K. V. P., Hiraishi, A., Shimada, K. & Matsuura,K. ( 1997; ). Horizontal transfer of genes coding forthe photosynthetic reaction centers of purple bacteria. J Mol Evol 45, 131–136.[CrossRef]
    [Google Scholar]
  31. Sabehi, G., Massana, R., Bielawski, J. P., Rosenberg, M., Delong,E. F. & Béjà, O. ( 2003; ). Novel proteorhodopsinvariants from the Mediterranean and Red Seas. Environ Microbiol 5, 842–849.[CrossRef]
    [Google Scholar]
  32. Sabehi, G., Loy, A., Jung, K. H., Partha, R., Spudich, J. L.,Isaacson, T., Hirschberg, J., Wagner, M. & Béjà, O. ( 2005; ). New insights into metabolic properties of marinebacteria encoding proteorhodopsins. PLoS Biol 3, e273 [CrossRef]
    [Google Scholar]
  33. Saitou, N. & Nei, M. ( 1987; ). Theneighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  34. Shieh, W. Y., Liu, T. Y., Lin, S. Y., Jean, W. D. & Chen,J.-S. ( 2008; ). Simiduia agarivorans gen. nov.,sp. nov., a marine, agarolytic bacterium isolated from shallow coastal waterfrom Keelung, Taiwan. Int J Syst Evol Microbiol 58, 895–900.[CrossRef]
    [Google Scholar]
  35. Smibert, R. M. & Krieg, N. R. ( 1994; ). Phenotypic characterization. In Methods for General and MolecularMicrobiology, pp. 611–654. Edited by P. Gerhardt, R. G. E. Murray,W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  36. Stingl, U., Desiderio, R. A., Cho, J. C., Vergin, K. L. &Giovannoni, S. J. ( 2007; ). The SAR92 clade: an abundantcoastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol 73, 2290–2296.[CrossRef]
    [Google Scholar]
  37. Swofford, D. L. ( 2002; ). paup*:Phylogenetic analysis using parsimony (and other methods), version4. Sunderland, MA: Sinauer Associates.
  38. Tanaka, T., Yan, L. & Burgess, J. G. ( 2003; ). Microbulbifer arenaceous sp. nov., a new endolithicbacterium isolated from the inside of red sandstone. Curr Microbiol 47, 412–416.
    [Google Scholar]
  39. Urios, L., Intertaglia, L., Lesongeur, F. & Lebaron, P. ( 2008; ). Haliea salexigens gen. nov., sp.nov., a member of the Gammaproteobacteria from the MediterraneanSea. Int J Syst Evol Microbiol 58, 1233–1237.[CrossRef]
    [Google Scholar]
  40. Yoon, J.-H., Kim, H., Kang, K. H., Oh, T.-K. & Park, Y.-H. ( 2003a; ). Transfer of Pseudomonas elongataHumm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov. Int J Syst Evol Microbiol 53, 1357–1361.[CrossRef]
    [Google Scholar]
  41. Yoon, J.-H., Kim, I.-G., Shin, D.-Y., Kang, K. H. & Park,Y.-H. ( 2003b; ). Microbulbifer salipaludissp. nov., a moderate halophile isolated from a Korean salt marsh. Int J Syst Evol Microbiol 53, 53–57.[CrossRef]
    [Google Scholar]
  42. Yoon, J.-H., Kim, I.-G., Oh, T.-K. & Park, Y.-H. ( 2004; ). Microbulbifer maritimus sp. nov., isolatedfrom an intertidal sediment from the Yellow Sea, Korea. Int J SystEvol Microbiol 54, 1111–1116.
    [Google Scholar]
  43. Yoon, J.-H., Jung, S.-Y., Kang, S.-J. & Oh, T.-K. ( 2007; ). Microbulbifer celer sp. nov., isolated froma marine solar saltern of the Yellow Sea in Korea. Int J Syst EvolMicrobiol 57, 2365–2369.
    [Google Scholar]
  44. Zeng, R., Zhao, J., Zhang, R. & Lin, N. ( 2005; ). Bacterial community in sediment from the Western Pacific ‘WarmPool’ and its relationship to environment. Sci China SerD Earth Sci 48, 282–290.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.013938-0
Loading
/content/journal/ijsem/10.1099/ijs.0.013938-0
Loading

Data & Media loading...

Supplements

Transmission electron micrograph of cells of strain IMCC2115 . Bar, 0.2 µm.

IMAGE

Cellular fatty acid profiles of strain IMCC2115 and previously reported related taxa. [ PDF] (69 KB)

PDF

Most Cited This Month

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