sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from sea sediment Free

Abstract

A rod-shaped, Gram-stain-negative, slightly halotolerant bacterium, designated strain D15-8P, was isolated from a sediment sample from the South China Sea. The strain could grow in NaCl concentrations ranging from 0.5 % to 10 % (w/v) (optimum 0.5–1.5 %), and could be cultivated at 10–40 °C (optimum 25 °C) and pH 5.5–9.5 (optimum pH 7.0–8.0). The strain was positive for catalase, oxidase, and hydrolysis of Tween 80, but negative for hydrolysis of DNA and gelatin, nitrite reduction, indole production, Voges–Proskauer reaction, and methyl red test. Strain D15-8P could biodegrade naphthalene, phenanthrene, and anthracene. The major respiratory quinone was Q-9. The main cellular fatty acids were C (11.5 %), C 3-methyl (22.0 %), C (19.2 %), Cω9 (22.9 %), and Cω9 (6.7 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified phospholipid. The DNA G+C content was 56.8 mol%. Phylogenetic analyses based on 16S rRNA genes showed that strain D15-8P was most closely related to JCM 12521 (98.5 % 16S rRNA gene sequence similarity), CGMCC 1.10835 (98.1 %), DSM 15157 (97.1 %), and CECT 7243 (97.0 %). Results of the gene analysis and DNA–DNA hybridization were both less than the cut-off values (90 % for gene sequence similarity and 70 % for DNA–DNA hybridization). On the basis of this taxonomic study using a polyphasic approach, strain D15-8P represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is D15-8P ( = CGMCC 1.11015 = KCTC 23781).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000722
2016-01-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/1/353.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000722&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 215:403–410 [View Article][PubMed]
    [Google Scholar]
  2. Collins M. D. 1985; Isoprenoid quinone analysis in bacterial classification and identification. In In Chemical Methods in Bacterial Systematics pp 267–287Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
    [Google Scholar]
  3. Collins M. D., Jones D. 1980; Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470 [View Article]
    [Google Scholar]
  4. Dong X. Z., Cai M. Y. 2001 Determinative Manual for Routine Bacteriology Beijing: Scientific Press;
    [Google Scholar]
  5. Dyksterhouse S. E., Gray J. P., Herwig R. P., Lara J. C., Staley J. T. 1995; Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 45:116–123 [View Article][PubMed]
    [Google Scholar]
  6. Euzéby J. P. 2015 List of bacterial names with standing in nomenclature: a folder available on the Internet. [Last full update 5 May 2015]. www.bacterio.net
  7. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  8. Gao W., Cui Z., Li Q., Xu G., Jia X., Zheng L. 2013; Marinobacter nanhaiticus sp. nov., polycyclic aromatic hydrocarbon-degrading bacterium isolated from the sediment of the South China Sea. Antonie van Leeuwenhoek 103:485–491 [View Article][PubMed]
    [Google Scholar]
  9. Gauthier M. J., Lafay B., Christen R., Fernandez L., Acquaviva M., Bonin P., Bertrand J. C. 1992; Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Bacteriol 42:568–576 [View Article][PubMed]
    [Google Scholar]
  10. Green D. H., Bowman J. P., Smith E. A., Gutierrez T., Christopher J. B. S. 2006; Marinobacter algicola sp. nov., isolated from laboratory cultures of paralytic shellfish toxin-producing dinoflagellates. Int J Syst Evol Microbiol 56:523–527 [CrossRef]
    [Google Scholar]
  11. Huu N. B., Denner E. B. M., Ha D. T. C., Wanner G., Stan-Lotter H. 1999; Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well. Int J Syst Evol Microbiol 49:367–375
    [Google Scholar]
  12. Kato S., Watanabe K. 2009; Analysis of gene transcripts in a crude oil-degrading marine microbial community. Biosci Biotechnol Biochem 73:1665–1668 [View Article][PubMed]
    [Google Scholar]
  13. Kim B. Y., Weon H. Y., Yoo S. H., Kim J. S., Kwon S. W., Stackebrandt E., Go S. J. 2006; Marinobacter koreensis sp. nov., isolated from sea sand in Korea. Int J Syst Evol Microbiol 56:2653–2656 [View Article][PubMed]
    [Google Scholar]
  14. 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 [View Article][PubMed]
    [Google Scholar]
  15. Komagata K., Suzuki K. 1987; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [View Article]
    [Google Scholar]
  16. Liu C., Shao Z. 2005; 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 [View Article][PubMed]
    [Google Scholar]
  17. Liu C., Chen C. X., Zhang X. Y., Yu Y., Liu A., Li G. W., Chen X. L., Chen B., Zhou B. C., Zhang Y. Z. 2012; Marinobacter antarcticus sp. nov., a halotolerant bacterium isolated from Antarctic intertidal sandy sediment. Int J Syst Evol Microbiol 62:1838–1844 [CrossRef]
    [Google Scholar]
  18. Lu X. Y., Zhang T., Fang H.H.-P., Leung K. M. Y., Zhang G. 2011; Biodegradation of naphthalene by enriched marine denitrifying bacteria. International Biodeterioration & Biodegradation 65:204–211 [View Article]
    [Google Scholar]
  19. Márquez M. C., Ventosa A. 2005; Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 and Marinobacter aquaeolei Nguyen et al. 1999 are heterotypic synonyms. Int J Syst Evol Microbiol 55:1349–1351 [CrossRef]
    [Google Scholar]
  20. Martín S., Márquez M. C., Sánchez-Porro C., Mellado E., Arahal D. R., Ventosa A. 2003; Marinobacter lipolyticus sp. nov., a novel moderate halophile with lipolytic activity. Int J Syst Evol Microbiol 53:1383–1387 [CrossRef]
    [Google Scholar]
  21. Mesbah M., Whitman W. B. 1989; Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr A 479:297–306 [View Article][PubMed]
    [Google Scholar]
  22. Montes M. J., Bozal N., Mercade E. 2008; Marinobacter guineae sp. nov., a novel moderately halophilic bacterium from an Antarctic environment. Int J Syst Evol Microbiol 58:1346–1349 [CrossRef]
    [Google Scholar]
  23. Rontani J. F., Gilewicz M. J., Michotey V. D., Zheng T. L., Bonin P. C., Bertrand J. C. 1997; Aerobic and anaerobic metabolism of 6,10,14-trimethylpentadecan-2-one by a denitrifying bacterium isolated from marine sediments. Appl Environ Microbiol 63:2636–2643
    [Google Scholar]
  24. 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]
  25. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  26. Shieh W. Y., Jean W. D., Lin Y. T., Tseng M. 2003; Marinobacter lutaoensis sp. nov., a thermotolerant marine bacterium isolated from a coastal hot spring in Lutao, Taiwan. Can J Microbiol 49:244–252 [View Article][PubMed]
    [Google Scholar]
  27. Shivaji S., Gupta P., Chaturvedi P., Suresh K., Delille D. 2005; Marinobacter maritimus sp. nov., a psychrotolerant strain isolated from sea water off the subantarctic Kerguelen islands. Int J Syst Evol Microbiol 55:1453–1456 [View Article][PubMed]
    [Google Scholar]
  28. 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 44:846–849 [View Article]
    [Google Scholar]
  29. Tamura K., Nei M. 1993; Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526[PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. 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 37:463–464 [View Article]
    [Google Scholar]
  32. 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 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000722
Loading
/content/journal/ijsem/10.1099/ijsem.0.000722
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited Most Cited RSS feed