1887

Abstract

A taxonomic study was carried out on strain R8-12, which was isolated from deep-sea water of the Indian Ocean during the screening of oil-degrading bacteria. The isolate was Gram-stain-negative, oxidase and catalase-positive. Growth was observed at salinities from 0.5 to 15 % (optimum 3 %), at pH from 6–10 (optimum 7–8) and at temperatures from 10 to 42 °C (optimum 28 °C). On the basis of 16S rRNA gene sequence similarity, strain R8-12 was shown to belong to the genus and to be related to DSM 13974 (97.2 %), B-5 (95.0 %), MACL04 (94.6 %), A-11-3 (94.3 %), T9 (93.8 %), SK2 (93.7 %) and W11-5 (93.7 %). The sequence similarities between R8-12 and other species of the genus ranged from 77.9 % to 86.9 %. The major fatty acids were C (31.8 %), Cω7 (20.3 %), Cω8 cyclo (15.8 %) and summed feature 3 (Cω6 and/or Cω7) (8.9 %). The polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two aminolipids (AL1–AL2) and two phospholipids (PL1–PL2). Three alkane hydroxylase () genes were identified in the genome. The G+C content of the chromosomal DNA was 66.1 mol%. DNA–DNA hybridization showed that strain R8-12 and DSM 13974 had a DNA–DNA relatedness of 63±3 %. According to its phenotypic features and fatty acid composition as well as the 16S rRNA and gene sequences, the novel strain represents a member of the genus , but could be easily distinguished from all other known species of the genus described to date. The name sp. nov. is proposed, with the type strain R8-12 ( = MCCC 1A00382 = LMG 24621 = CCTCC AB 208234).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.049957-0
2013-12-01
2020-01-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/12/4428.html?itemId=/content/journal/ijsem/10.1099/ijs.0.049957-0&mimeType=html&fmt=ahah

References

  1. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K.. (editors) ( 1995;). Short Protocols in Molecular Biology: a Compendium of Methods from Current Protocols in Molecular Biology, , 3rd edn.. New York:: Wiley;.
    [Google Scholar]
  2. Bruns A., Berthe-Corti L.. ( 1999;). Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment. . Int J Syst Bacteriol 49:, 441–448. [CrossRef][PubMed]
    [Google Scholar]
  3. Dong X.-Z., Cai M.-Y.. ( 2001;). Determinative Manual for Routine Bacteriology. (English translation). Beijing:: Scientific Press;.
    [Google Scholar]
  4. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  5. Fernández-Martínez J., Pujalte M. J., García-Martínez J., Mata M., Garay E., Rodríguez-Valeral F.. ( 2003;). Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax. . Int J Syst Evol Microbiol 53:, 331–338. [CrossRef][PubMed]
    [Google Scholar]
  6. 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:, 716–721. [CrossRef][PubMed]
    [Google Scholar]
  7. Lai Q., Shao Z.. ( 2012a;). Genome sequence of an alkane-degrading bacterium, Alcanivorax pacificus type strain W11-5, isolated from deep sea sediment. . J Bacteriol 194:, 6936. [CrossRef][PubMed]
    [Google Scholar]
  8. Lai Q., Shao Z.. ( 2012b;). Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3. . J Bacteriol 194:, 6972. [CrossRef][PubMed]
    [Google Scholar]
  9. Lai Q., Yuan J., Wang B., Sun F., Qiao N., Zheng T., Shao Z.. ( 2009;). Bowmanella pacifica sp. nov., isolated from a pyrene-degrading consortium. . Int J Syst Evol Microbiol 59:, 1579–1582. [CrossRef][PubMed]
    [Google Scholar]
  10. Lai Q., Wang L., Liu Y., Fu Y., Zhong H., Wang B., Chen L., Wang J., Sun F., Shao Z.. ( 2011;). Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium. . Int J Syst Evol Microbiol 61:, 1370–1374. [CrossRef][PubMed]
    [Google Scholar]
  11. Lai Q., Li W., Shao Z.. ( 2012;). Complete genome sequence of Alcanivorax dieselolei type strain B5. . J Bacteriol 194:, 6674. [CrossRef][PubMed]
    [Google Scholar]
  12. Liu C., Shao Z.. ( 2005a;). Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. . Int J Syst Evol Microbiol 55:, 1181–1186. [CrossRef][PubMed]
    [Google Scholar]
  13. Liu C., Shao Z.. ( 2005b;). Isolation and characterization of oil-degrading marine microorganisms. . Acta Oceanol Sin 27:, 114–120.
    [Google Scholar]
  14. Rivas R., García-Fraile P., Peix A., Mateos P. F., Martínez-Molina E., Velázquez E.. ( 2007;). Alcanivorax balearicus sp. nov., isolated from Lake Martel. . Int J Syst Evol Microbiol 57:, 1331–1335. [CrossRef][PubMed]
    [Google Scholar]
  15. Rzhetsky A., Nei M.. ( 1992;). A simple method for estimating and testing minimum evolution trees. . Mol Biol Evol 9:, 945–967.
    [Google Scholar]
  16. Rzhetsky A., Nei M.. ( 1993;). Theoretical foundation of the minimum-evolution method of phylogenetic inference. . Mol Biol Evol 10:, 1073–1095.[PubMed]
    [Google Scholar]
  17. Saitou N., Nei M.. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  18. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE:: MIDI;.
    [Google Scholar]
  19. Schneiker S., Martins dos Santos V. A., Bartels D., Bekel T., Brecht M., Buhrmester J., Chernikova T. N., Denaro R., Ferrer M.. & other authors ( 2006;). Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. . Nat Biotechnol 24:, 997–1004. [CrossRef][PubMed]
    [Google Scholar]
  20. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  21. Venkateswaran K., Moser D. P., Dollhopf M. E., Lies D. P., Saffarini D. A., MacGregor B. J., Ringelberg D. B., White D. C., Nishijima M.. & other authors ( 1999;). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.. Int J Syst Bacteriol 49:, 705–724. [CrossRef][PubMed]
    [Google Scholar]
  22. 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;). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  23. Wu Y., Lai Q., Zhou Z., Qiao N., Liu C., Shao Z.. ( 2009;). Alcanivorax hongdengensis sp. nov., an alkane-degrading bacterium isolated from surface seawater of the straits of Malacca and Singapore, producing a lipopeptide as its biosurfactant. . Int J Syst Evol Microbiol 59:, 1474–1479. [CrossRef][PubMed]
    [Google Scholar]
  24. Yakimov M. M., Golyshin P. N., Lang S., Moore E. R. B., Abraham W. R., Lünsdorf H., Timmis K. N.. ( 1998;). Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. . Int J Syst Bacteriol 48:, 339–348. [CrossRef][PubMed]
    [Google Scholar]
  25. Yamamoto S., Kasai H., Arnold D. L., Jackson R. W., Vivian A., Harayama S.. ( 2000;). Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. . Microbiology 146:, 2385–2394.[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.049957-0
Loading
/content/journal/ijsem/10.1099/ijs.0.049957-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most cited articles

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