sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Jean 2013 Free

Abstract

A Gram-stain-negative heterotrophic bacterium, designated GSD6, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6 was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6 contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising Cω7 and/or iso-C 2-OH), C, Cω7, C 10-methyl and Cω8 as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6 formed a phylogenetic lineage with members of the genus . Strain GSD6 was most closely related to E3 with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is GSD6 ( = KACC 18129 = JCM 30133). An emended description of the genus is also proposed.

Funding
This study was supported by the:
  • National Institute of Biological Resources (Award 2014-02-001 and 2014-02-066)
  • Chung-Ang Univ. Research Scholarship Grant
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2015-05-01
2024-03-28
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References

  1. Chen L. P., Xu H. Y., Fu S. Z., Fan H. X., Liu Y. H., Liu S. J., Liu Z. P. ( 2009 ). Glaciecola lipolytica sp. nov., isolated from seawater near Tianjin city, China. . Int J Syst Evol Microbiol 59, 7376. [View Article] [PubMed]
    [Google Scholar]
  2. Felsenstein, J. (2002). phylip (phylogeny inference package) version 3.6a. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  3. Gomori G. ( 1955 ). Preparation of buffers for use in enzyme studies. . Methods Enzymol, 1, 138146. [View Article]
    [Google Scholar]
  4. Gonzalez J. M., Saiz-Jimenez C. ( 2002 ). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. . Environ Microbiol 4, 770773. [View Article] [PubMed]
    [Google Scholar]
  5. Jean W. D., Hsu C. Y., Huang S.-P., Chen J.-S., Lin S., Su M.-H., Shieh W. Y. ( 2013 ). Reclassification of [Glaciecola] lipolytica and [Aestuariibacter] litoralis in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively. . Int J Syst Evol Microbiol 63, 28592864. [View Article] [PubMed]
    [Google Scholar]
  6. Jin H. M., Kim J. M., Lee H. J., Madsen E. L., Jeon C. O. ( 2012 ). Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil-contaminated coastal sediment. . Environ Sci Technol 46, 77317740. [View Article] [PubMed]
    [Google Scholar]
  7. Jin H. M., Choi E. J., Jeon C. O. ( 2013 ). Isolation of a BTEX-degrading bacterium, Janibacter sp. SB2, from a sea-tidal flat and optimization of biodegradation conditions. . Bioresour Technol 145, 5764. [View Article] [PubMed]
    [Google Scholar]
  8. 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 Microbiol 62, 716721.[PubMed] [CrossRef]
    [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. Lányí B. ( 1987 ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19, 167. [View Article]
    [Google Scholar]
  11. Lee S. H., Shim J. K., Kim J. M., Choi H.-K., Jeon C. O. ( 2011 ). Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella . . Int J Syst Evol Microbiol 61, 722727. [View Article] [PubMed]
    [Google Scholar]
  12. Lo N., Kang H. J., Jeon C. O. ( 2014 ). Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov.. Int J Syst Evol Microbiol 64, 37683774. [View Article] [PubMed]
    [Google Scholar]
  13. Math R. K., Jin H. M., Kim J. M., Hahn Y., Park W., Madsen E. L., Jeon C. O. ( 2012 ). Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism. . PLoS ONE 7, e35784. [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. Nawrocki E. P., Eddy S. R. ( 2007 ). Query-dependent banding (QDB) for faster RNA similarity searches. . PLOS Comput Biol 3, e56. [View Article] [PubMed]
    [Google Scholar]
  16. Park S., Yoon J. H. ( 2013 ). Glaciecola aquimarina sp. nov., a gammaproteobacterium isolated from coastal seawater. . Antonie van Leeuwenhoek 103, 11411148. [View Article] [PubMed]
    [Google Scholar]
  17. Ryu S. H., Nguyen T. T. H., Park W., Kim C. J., Jeon C. O. ( 2006 ). Runella limosa sp. nov., isolated from activated sludge. . Int J Syst Evol Microbiol 56, 27572760. [View Article] [PubMed]
    [Google Scholar]
  18. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  19. Shivaji S., Reddy G. S. ( 2014 ). Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean. . Int J Syst Evol Microbiol 64, 32643275. [View Article] [PubMed]
    [Google Scholar]
  20. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  21. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. et al. ( 2002 ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52, 10431047. [View Article] [PubMed]
    [Google Scholar]
  22. Stamatakis A., Ott M., Ludwig T. ( 2005 ). RAxML-OMP: an efficient program for phylogenetic inference on SMPs. . In Parallel Computing Technologies, Proceedings of 8th International Conference (PaCT2005) (Lecture Notes in Computer Science vol. 3606), pp. 288302. Edited by Malyshkin V. . Berlin:: Springer;. [View Article]
    [Google Scholar]
  23. Tanaka N., Romanenko L. A., Frolova G. M., Mikhailov V. V. ( 2010 ). Aestuariibacter litoralis sp. nov., isolated from a sandy sediment of the Sea of Japan. . Int J Syst Evol Microbiol 60, 317320. [View Article] [PubMed]
    [Google Scholar]
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