sp. nov., a marine bacterium of the family isolated from Arctic sediment Free

Abstract

A novel Gram-negative, rod–coccus shaped, non-motile, strain, RS-3, was isolated from a sediment sample collected from the marine transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic. Colonies and broth cultures were yellowish in colour due to the presence of carotenoids. Strain RS-3 was positive for oxidase, aesculinase, caseinase, gelatinase and urease activities and negative for amylase, catalase, lipase, lysine decarboxylase, ornithine decarboxylase, DNase and β-galactosidase activities. The predominant fatty acids were iso-C (18.0), anteiso-C (16.8), iso-C G (14.2), anteiso-C A (6.0) and iso-C 3-OH (6.8). Strain RS-3 contained MK-6 (72.42 %) and MK-7 (27.58 %) as the major respiratory quinones and phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids make up the polar lipid composition. The DNA G+C content of strain RS-3 was 34.7±1.2 mol%. The 16S rRNA gene sequence analysis indicated that and are the most closely related species with sequence similarities to the type strains of these species of 98.5 and 97.7 %, respectively. However, DNA–DNA hybridization with KCTC 22997 and DSM 15363 showed a relatedness of 22 and 42.5 % with respect to strain RS-3. Based on the DNA–DNA hybridization values, phenotypic and chemotaxonomic characteristics and phylogenetic inference, strain RS-3 is proposed as a novel species of the genus , for which the name sp. nov. is proposed. The type strain of sp. nov. is RS-3 ( = CIP 110154 = NBRC 106169). An emended description of the genus is provided.

Funding
This study was supported by the:
  • Council of Scientific and Industrial Research (CSIR) (Award NWP0006)
  • CSIR
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.044669-0
2013-05-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/5/1646.html?itemId=/content/journal/ijsem/10.1099/ijs.0.044669-0&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, 403410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in Actinomycetes and Corynebacteria . . J Gen Microbiol 100, 221230.[PubMed] [CrossRef]
    [Google Scholar]
  3. Felsenstein J. ( 1993 ). phylip (phylogeny inference package) version 3.5.1. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  4. Groth I., Schumann P., Rainey F. A., Martin K., Schuetze B., Augsten K. ( 1997 ). Demetria terragena sp. nov., a new genus of Actinomycetes isolated from compost soil. . Int J Syst Bacteriol 47, 11291133. [View Article] [PubMed]
    [Google Scholar]
  5. Guindon S., Lethiec F., Duroux P., Gascuel O. ( 2005 ). PHYML Online–a web server for fast maximum likelihood-based phylogenetic inference. . Nucleic Acids Res 33 (Web Server issue), W557W559. [View Article] [PubMed]
    [Google Scholar]
  6. Ivanova E. P., Christen R., Gorshkova N. M., Zhukova N. V., Kurilenko V. V., Crawford R. J., Mikhailov V. V. ( 2010 ). Winogradskyella exilis sp. nov., isolated from the starfish Stellaster equestris, and emended description of the genus Winogradskyella . . Int J Syst Evol Microbiol 60, 15771580. [View Article] [PubMed]
    [Google Scholar]
  7. Kim S. B., Nedashkovskaya O. I. ( 2010 ). Winogradskyella pacifica sp. nov., a marine bacterium of the family Flavobacteriaceae . . Int J Syst Evol Microbiol 60, 19481951. [View Article] [PubMed]
    [Google Scholar]
  8. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  9. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  10. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Good Fellow M. . Chichester:: Wiley;.
    [Google Scholar]
  11. Lányí B. ( 1987 ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19, 167. [View Article]
    [Google Scholar]
  12. Lau S. C. K., Tsoi M. M. Y., Li X., Plakhotnikova I., Dobretsov S., Lau K. W. K., Wu M., Wong P. K., Pawlik J. R., Qian P. Y. ( 2005 ). Winogradskyella poriferorum sp. nov., a novel member of the family Flavobacteriaceae isolated from a sponge in the Bahamas. . Int J Syst Evol Microbiol 55, 15891592. [View Article] [PubMed]
    [Google Scholar]
  13. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  14. Nedashkovskaya O. I., Kim S. B., Han S. K., Snauwaert C., Vancanneyt M., Swings J., Kim K. O., Lysenko A. M., Rohde M. & other authors ( 2005 ). Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae . . Int J Syst Evol Microbiol 55, 4955. [View Article] [PubMed]
    [Google Scholar]
  15. Nedashkovskaya O. I., Vancanneyt M., Kim S. B., Zhukova N. V. ( 2009 ). Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius . . Int J Syst Evol Microbiol 59, 14651468. [View Article] [PubMed]
    [Google Scholar]
  16. Nedashkovskaya O. I., Kukhlevskiy A. D., Zhukova N. V. ( 2012 ). Winogradskyella ulvae sp. nov., a novel epiphyte of a Pacific seaweed and emended descriptions of the genus Winogradskyella and Winogradskyella thalassocola, Winogradskyella echinorum, Winogradskyella exilis and Winogradskyella eximia . . Int J Syst Evol Microbiol 62, 14501456. [View Article] [PubMed]
    [Google Scholar]
  17. Pinhassi J., Nedashkovskaya O. I., Hagström Å., Vancanneyt M. ( 2009 ). Winogradskyella rapida sp. nov., isolated from protein-enriched seawater. . Int J Syst Evol Microbiol 59, 21802184. [View Article] [PubMed]
    [Google Scholar]
  18. Reddy G. S. N., Aggarwal R. K., Matsumoto G. I., Shivaji S. ( 2000 ). Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. . Int J Syst Evol Microbiol 50, 15531561. [View Article] [PubMed]
    [Google Scholar]
  19. Romanenko L. A., Tanaka N., Frolova G. M., Mikhailov V. V. ( 2009 ). Winogradskyella arenosi sp. nov., a member of the family Flavobacteriaceae isolated from marine sediments from the Sea of Japan. . Int J Syst Evol Microbiol 59, 14431446. [View Article] [PubMed]
    [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. Shivaji S., Ray M. K., Shyamala Rao N., Saisree L., Jagannadham M. V., Seshu Kumar G., Reddy G. S. N., Bhargava P. M. ( 1992 ). Sphingobacterium antarcticus sp. nov.: a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. . Int J Syst Bacteriol 42, 102106. [View Article]
    [Google Scholar]
  22. Sly L. I., Blackall L. L., Kraat P. C., Tian-Shen T., Sangkhobol V. ( 1986 ). The use of second derivative plots for the determination of mol% guanine plus cytosine of DNA by the thermal denaturation method. . J Microbiol Methods 5, 139156. [View Article]
    [Google Scholar]
  23. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  24. Srinivas T. N. R., Nageswara Rao S. S. S., Vishnu Vardhan Reddy P., Pratibha M. S., Sailaja B., Kavya B., Hara Kishore K., Begum Z., Singh S. M., Shivaji S. ( 2009 ). Bacterial diversity and bioprospecting for cold-active lipases, amylases and proteases, from culturable bacteria of Kongsfjorden and Ny-alesund, Svalbard, Arctic. . Curr Microbiol 59, 537547. [View Article] [PubMed]
    [Google Scholar]
  25. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G., Higgins D. G. ( 1997 ). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25, 48764882. [View Article] [PubMed]
    [Google Scholar]
  26. Tourova T. P., Antonov A. S. ( 1988 ). Identification of microorganisms by rapid DNA–DNA hybridisation. . Methods Microbiol 19, 333355. [View Article]
    [Google Scholar]
  27. 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, 463464. [View Article]
    [Google Scholar]
  28. Yoon B. J., Byun H. D., Kim J. Y., Lee D. H., Kahng H. Y., Oh D. C. ( 2011 ). Winogradskyella lutea sp. nov., isolated from seawater, and emended description of the genus Winogradskyella . . Int J Syst Evol Microbiol 61, 15391543. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.044669-0
Loading
/content/journal/ijsem/10.1099/ijs.0.044669-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed