sp. nov., isolated from a tidal flat sediment Free

Abstract

A Gram-stain-negative, non-motile, coccoid- or oval-shaped bacterial strain, designated S-5, belonging to the class , was isolated from a tidal flat sediment of the Yellow Sea, Korea and was subjected to a polyphasic taxonomic study. Strain S-5 grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining analysis based on 16S rRNA gene sequences showed that strain S-5 fell within the clade comprising the species of the genus , clustering with the type strains of , and with which it exhibited the highest 16S rRNA gene sequence similarity (96.0–96.7 %). The DNA G+C content was 66.0 mol%. Strain S-5 contained Q-10 as the predominant ubiquinone and summed feature 8 (Cω7 and/or Cω6) and Cω6 as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-5 is distinguishable from other species of the genus . On the basis of the data presented, strain S-5 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S-5 ( = KCTC 42109 = CECT 8624).

Funding
This study was supported by the:
  • National Institute of Biological Resources (NIBR)
  • Ministry of Environment (MOE)
  • Ministry of Science, ICT & Future Planning (MSIP) of the Republic of Korea
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.067728-0
2014-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/12/4184.html?itemId=/content/journal/ijsem/10.1099/ijs.0.067728-0&mimeType=html&fmt=ahah

References

  1. Barrow G. I., Feltham R. K. A. (editors) ( 1993 ). Cowan and Steel’s Manual for the Identification of Medical Bacteria, , 3rd edn.. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  2. Baumann P., Baumann L. ( 1981 ). The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes . . In The Prokaryotes, pp. 13021331. Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. . Berlin:: Springer;.
    [Google Scholar]
  3. Bruns A., Rohde M., Berthe-Corti L. ( 2001 ). Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. . Int J Syst Evol Microbiol 51, 19972006. [View Article] [PubMed]
    [Google Scholar]
  4. Cohen-Bazire G., Sistrom W. R., Stanier R. Y. ( 1957 ). Kinetic studies of pigment synthesis by nonsulfur purple bacteria. . J Cell Comp Physiol 49, 2568. [View Article]
    [Google Scholar]
  5. Denner E. B. M., Vybiral D., Koblízek M., Kämpfer P., Busse H.-J., Velimirov B. ( 2002 ). Erythrobacter citreus sp. nov., a yellow-pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea. . Int J Syst Evol Microbiol 52, 16551661. [View Article] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1993 ). phylip (phylogeny inference package) version 3.5. . Distributed by the author. Department of Genome Sciences, University of Washington;, Seattle, USA:.
    [Google Scholar]
  8. Ivanova E. P., Bowman J. P., Lysenko A. M., Zhukova N. V., Gorshkova N. M., Kuznetsova T. A., Kalinovskaya N. I., Shevchenko L. S., Mikhailov V. V. ( 2005 ). Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates. . Syst Appl Microbiol 28, 123130. [View Article] [PubMed]
    [Google Scholar]
  9. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21132. Edited by Munro H. N. . New York:: Academic Press;. [View Article]
    [Google Scholar]
  10. Jung Y.-T., Park S., Oh T.-K., Yoon J.-H. ( 2012 ). Erythrobacter marinus sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 62, 20502055. [View Article] [PubMed]
    [Google Scholar]
  11. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  12. Kluge A. G., Farris J. S. ( 1969 ). Quantitative phyletics and the evolution of anurans. . Syst Zool 18, 132. [View Article]
    [Google Scholar]
  13. Komagata K., Suzuki K. ( 1987 ). Lipids and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  14. Kwon K. K., Woo J. H., Yang S. H., Kang J. H., Kang S. G., Kim S. J., Sato T., Kato C. ( 2007 ). Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov.. Int J Syst Evol Microbiol 57, 22072211. [View Article] [PubMed]
    [Google Scholar]
  15. Lányí B. ( 1987 ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19, 167. [View Article]
    [Google Scholar]
  16. Lee Y. S., Lee D. H., Kahng H. Y., Kim E. M., Jung J. S. ( 2010 ). Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater. . Int J Syst Evol Microbiol 60, 14131417. [View Article] [PubMed]
    [Google Scholar]
  17. Leifson E. ( 1963 ). Determination of carbohydrate metabolism of marine bacteria. . J Bacteriol 85, 11831184.[PubMed]
    [Google Scholar]
  18. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. ( 1977 ). Polar lipid composition in the classification of Nocardia and related bacteria. . Int J Syst Bacteriol 27, 104117. [View Article]
    [Google Scholar]
  19. 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, 233241. [View Article]
    [Google Scholar]
  20. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  21. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
    [Google Scholar]
  22. Shiba T., Simidu U. ( 1982 ). Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a . . Int J Syst Bacteriol 32, 211217. [View Article]
    [Google Scholar]
  23. 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, 846849. [View Article]
    [Google Scholar]
  24. Staley J. T. ( 1968 ). Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. . J Bacteriol 95, 19211942.[PubMed]
    [Google Scholar]
  25. Subhash Y., Tushar L., Sasikala Ch., Ramana Ch. V. ( 2013 ). Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. . Int J Syst Evol Microbiol 63, 45244532. [View Article] [PubMed]
    [Google Scholar]
  26. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [View Article]
    [Google Scholar]
  27. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 46734680. [View Article] [PubMed]
    [Google Scholar]
  28. Wu H.-X., Lai P. Y., Lee O. O., Zhou X.-J., Miao L., Wang H., Qian P.-Y. ( 2012 ). Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea. . Int J Syst Evol Microbiol 62, 13481353. [View Article] [PubMed]
    [Google Scholar]
  29. Xu M., Xin Y., Yu Y., Zhang J., Zhou Y., Liu H., Tian J., Li Y. ( 2010 ). Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. . Int J Syst Evol Microbiol 60, 22152220. [View Article] [PubMed]
    [Google Scholar]
  30. Yoon J.-H., Kim H., Kim S.-B., Kim H.-J., Kim W. Y., Lee S. T., Goodfellow M., Park Y.-H. ( 1996 ). Identification of Saccharomonospora strains by the use of genomic DNA fragments and rRNA gene probes. . Int J Syst Bacteriol 46, 502505. [View Article]
    [Google Scholar]
  31. Yoon J.-H., Lee S. T., Park Y.-H. ( 1998 ). Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. . Int J Syst Bacteriol 48, 187194. [View Article] [PubMed]
    [Google Scholar]
  32. Yoon J.-H., Kang K. H., Park Y.-H. ( 2003a ). Psychrobacter jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. . Int J Syst Evol Microbiol 53, 449454. [View Article] [PubMed]
    [Google Scholar]
  33. Yoon J.-H., Kim H., Kim I. G., Kang K. H., Park Y.-H. ( 2003b ). Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. . Int J Syst Evol Microbiol 53, 11691174. [View Article] [PubMed]
    [Google Scholar]
  34. Yoon J.-H., Kang K. H., Oh T.-K., Park Y.-H. ( 2004 ). Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 54, 19811985. [View Article] [PubMed]
    [Google Scholar]
  35. Yoon J.-H., Oh T. K., Park Y.-H. ( 2005a ). Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 55, 7175. [View Article] [PubMed]
    [Google Scholar]
  36. Yoon J.-H., Kang K. H., Yeo S. H., Oh T. K. ( 2005b ). Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. . Int J Syst Evol Microbiol 55, 11671170. [View Article] [PubMed]
    [Google Scholar]
  37. Yoon B.-J., Lee D.-H., Oh D.-C. ( 2013 ). Erythrobacter jejuensis sp. nov., isolated from seawater. . Int J Syst Evol Microbiol 63, 14211426. [View Article] [PubMed]
    [Google Scholar]
  38. Yurkov V., Stackebrandt E., Holmes A., Fuerst J. A., Hugenholtz P., Golecki J., Gad’on N., Gorlenko V. M., Kompantseva E. I., Drews G. ( 1994 ). Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov.. Int J Syst Bacteriol 44, 427434. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.067728-0
Loading
/content/journal/ijsem/10.1099/ijs.0.067728-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed