1887

Abstract

A taxonomic study was carried out on strain 19-m-6, which was isolated from deep sea sediment of the South China Sea during the screening of alkane-degrading bacteria. The isolate was Gram-reaction-negative, and oxidase- and catalase- positive. On the basis of 16S rRNA gene sequence similarity, strain 19-m-6 was shown to belong to the genus , related to T9 (97.5 %), A-11-3 (97.3  %), SK2 (96.6 %) and seven other species of the genus (93.9–95.4 %). Average nucleotide identity values between strain 19-m-6 and T9, A-11-3 and SK2 were 85.12, 85.87 and 84.35 %, respectively. The estimated DNA–DNA hybridization values between strain 19-m-6 and these three type strains were 22.0, 22.6 and 21.2 %, respectively. Four alkane hydroxylase () genes were obtained from the draft genome sequence. The G+C content of the chromosomal DNA was 56.44 mol%. The major fatty acids were C, C 7 and summed feature 3 (C 6 and/or C 7). The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, one aminolipid, three phospholipids, two glycolipids and two aminophospholipids. According to its phenotypic features, fatty acid composition and 16S rRNA gene sequence, the novel strain fitted well into the genus , but could be clearly distinguished from all other known species described to date. The name sp. nov. is thus proposed, with 19-m-6 (=MCCC 1A05629=KCTC 52137) as the type strain.

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2016-09-01
2019-12-13
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References

  1. Auch A. F., Klenk H. P., Göker M.. 2010a; Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci2:142–148 [CrossRef][PubMed]
    [Google Scholar]
  2. Auch A. F., von Jan M., Klenk H. P., Göker M.. 2010b; Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  3. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J., Smith J. A., Struhl K.. 2002; Short Protocols in Molecular Biology: A Compendium of Methods From Current Protocols in Molecular Biology, 5th edn. New York: Wiley;
    [Google Scholar]
  4. Dong X., Cai M.. 2001; Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation);
    [Google Scholar]
  5. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 1 21 78T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax. Int J Syst Evol Microbiol53:331–338 [CrossRef][PubMed]
    [Google Scholar]
  7. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  8. Kyoung Kwon K., Hye Oh J., Yang S. H., Seo H. S., Lee J. H.. 2015; Alcanivorax gelatiniphagus sp. nov., a marine bacterium isolated from tidal flat sediments enriched with crude oil. Int J Syst Evol Microbiol65:2204–2208 [CrossRef][PubMed]
    [Google Scholar]
  9. Lai Q., Shao Z.. 2012a; Genome sequence of an alkane-degrading bacterium, Alcanivorax pacificus type strain W11-5, isolated from deep sea sediment. J Bacteriol194:6936 [CrossRef][PubMed]
    [Google Scholar]
  10. Lai Q., Shao Z.. 2012b; Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3. J Bacteriol194:6972 [CrossRef][PubMed]
    [Google Scholar]
  11. Lai Q., Yuan J., Gu L., Shao Z.. 2009; Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol59:1278–1281 [CrossRef][PubMed]
    [Google Scholar]
  12. 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 Microbiol61:1370–1374 [CrossRef][PubMed]
    [Google Scholar]
  13. Lai Q., Li W., Shao Z.. 2012; Complete genome sequence of Alcanivorax dieselolei type strain B5. J Bacteriol194:6674 [CrossRef][PubMed]
    [Google Scholar]
  14. Lai Q., Wang J., Gu L., Zheng T., Shao Z.. 2013; Alcanivorax marinus sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol63:4428–4432 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 Microbiol55:1181–1186[CrossRef]
    [Google Scholar]
  16. Liu C., Shao Z.. 2005b; Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol55:1181–1186[CrossRef]
    [Google Scholar]
  17. Luo R., Liu B., Xie Y., Li Z., Huang W., Yuan J., He G., Chen Y., Pan Q. et al. 2012; SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience1:18 [CrossRef][PubMed]
    [Google Scholar]
  18. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M.. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics14:60 [CrossRef][PubMed]
    [Google Scholar]
  19. Rahul K., Sasikala C., Tushar L., Debadrita R., Ramana C., Ramana C.. 2014; Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond. Int J Syst Evol Microbiol64:3553–3558 [CrossRef][PubMed]
    [Google Scholar]
  20. Richter M., Rosselló-Móra R.. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 Microbiol57:1331–1335 [CrossRef][PubMed]
    [Google Scholar]
  22. Rzhetsky A., Nei M.. 1993; Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol10:1073–1095[PubMed]
    [Google Scholar]
  23. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  24. Sasser M.. 1990; Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI;
    [Google Scholar]
  25. Schneiker S., Martins dos Santos V. A., Bartels D., Bekel T., Brecht M., Buhrmester J., Chernikova T. N., Denaro R., Ferrer M. et al. 2006; Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol24:997–1004 [CrossRef][PubMed]
    [Google Scholar]
  26. 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 Evol28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  27. 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. et al. 1999; Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol49:705–724 [CrossRef][PubMed]
    [Google Scholar]
  28. Wayne L. G., Brenner D., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L., Moore W. E. C., Murray R. G. E., Stackebrandt E.. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37:463–464[CrossRef]
    [Google Scholar]
  29. 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 Microbiol59:1474–1479 [CrossRef][PubMed]
    [Google Scholar]
  30. Yakimov M. M., Golyshin P. N., Lang S., Moore E. R., 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 Bacteriol48:339–348 [CrossRef][PubMed]
    [Google Scholar]
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