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Volume 66, Issue 12

sp. nov., isolated from deep-sea sediments from the Carlsberg and Southwest Indian Ridges Free

Abstract

Three actinobacterial strains, FXJ8.128, FXJ8.269 and FXJ8.309, were isolated from deep-sea sediments collected from the Carlsberg Ridge and Southwest Indian Ridge at depths of 3690, 1800 and 2461 m, respectively. The three strains had highly similar 16S rRNA gene sequences (99.8–99.9 % identities) and formed a monophyletic clade within the 16S rRNA gene tree, showing 98.2–98.9 % 16S rRNA gene sequence identities with type strains NCIMB 702286, DSM 20626, DSM 20425, BBH7 and VKM Ac-2280. All three isolates showed activity towards the breakdown of pectin and fluoranthene. They contained MK-8(H) as the most predominant menaquinone, diphosphatidylglycerol, phosphatidylglycerol and a glycolipd as the main polar lipids, and anteiso-C and anteiso-C as the major cellular fatty acids. Moreover, the three isolates were distinguished readily from the phylogenetically related type strains by DNA–DNA hybridization values, by random amplified polymorphic DNA fingerprint profiles and by a range of physiological and biochemical characteristics. On the basis of the above polyphasic taxonomic data, strains FXJ8.128, FXJ8.269 and FXJ8.309 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FXJ8.269 (=CGMCC 1.15472=DSM 102229).

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  • Accepted:
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Keyword(s): Brevibacterium sediminis sp. nov. , Carlsberg Ridge , deep-sea sediment , polyphasic taxonomy and Southwest Indian ridge
© 2016 IUMS
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2016-12-01
2024-04-19
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References

  1. Augustine D., Jacob J. C., Ramya K., Philip R. 2013; Actinobacteria from sediment samples of Arabian Sea and Bay of Bengal: biochemical and physiological characterization. Int J Res Mar Sci 2:56–63
     [Google Scholar]
  2. Bhadra B., Raghukumar C., Pindi P. K., Shivaji S. 2008; Brevibacterium oceani sp. nov., isolated from deep-sea sediment of the Chagos Trench, Indian Ocean. Int J Syst Evol Microbiol 58:57–60 [View Article][PubMed]
     [Google Scholar]
  3. Breed R. 1953; The Brevibacteriaceae fam. nov. of order Eubacteriales . Rias Commun VI Congr Int Microbiol Roma 1:13–14
     [Google Scholar]
  4. Buck J. D. 1982; Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
     [Google Scholar]
  5. Chen P., Zhang L., Guo X., Dai X., Liu L., Xi L., Wang J., Song L., Wang Y. et al. 2016; Diversity, biogeography, and biodegradation potential of actinobacteria in the deep-sea sediments along the Southwest Indian Ridge. Front Microbiol 7:1340 [View Article][PubMed]
     [Google Scholar]
  6. Chun J., Goodfellow M. 1995; A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245 [View Article][PubMed]
     [Google Scholar]
  7. Collins M. D. 1985; Isoprenoid quinone analyses in bacterial classification and identification. In Chemical Methods in Bacterial Systematics pp. 267–287 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
     [Google Scholar]
  8. 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]
  9. Collins M. D., Jones D., Keddie R. M., Sneath P. H. A. 1980; Reclassification of Chromobacterium iodinum (Davis) in a redefined genus Brevibacterium (Breed) as Brevibacterium iodinum nom.rev.; comb. nov. Microbiology 120:1–10 [View Article]
     [Google Scholar]
  10. Cui Y., Kang M. S., Woo S. G., Jin L., Kim K. K., Park J., Lee M., Lee S. T. 2013; Brevibacterium daeguense sp. nov., a nitrate-reducing bacterium isolated from a 4-chlorophenol enrichment culture. Int J Syst Evol Microbiol 63:152–157 [View Article][PubMed]
     [Google Scholar]
  11. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
     [Google Scholar]
  12. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
     [Google Scholar]
  13. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
     [Google Scholar]
  14. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416 [View Article]
     [Google Scholar]
  15. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
     [Google Scholar]
  16. German C., Baker E., Mevel C., Tamaki K. 1998; Hydrothermal activity along the southwest Indian ridge. Nature 395:490–493 [CrossRef]
     [Google Scholar]
  17. Hasegawa T., Takizawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322 [View Article]
     [Google Scholar]
  18. Huss V. A., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article][PubMed]
     [Google Scholar]
  19. Iyer S. D., Mukhopadhyay R., Drolia R. K., Ray D. 2003; Mid-ocean ridges, InRidge and the future. Curr Sci 85:272–276
     [Google Scholar]
  20. Kiyohara H., Nagao K., Yana K. 1982; Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl Environ Microbiol 43:454–457[PubMed]
     [Google Scholar]
  21. Lane D. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp. 115–175 Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;
     [Google Scholar]
  22. Lee S. D. 2006; Brevibacterium samyangense sp. nov., an actinomycete isolated from a beach sediment. Int J Syst Evol Microbiol 56:1889–1892 [View Article][PubMed]
     [Google Scholar]
  23. Li W., Cowley A., Uludag M., Gur T., McWilliam H., Squizzato S., Park Y. M., Buso N., Lopez R. 2015; The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res 43:W580–W584 [View Article][PubMed]
     [Google Scholar]
  24. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [View Article]
     [Google Scholar]
  25. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 2:233–241 [View Article]
     [Google Scholar]
  26. Müller K., Schmid E. N., Kroppenstedt R. M. 1998; Improved identification of mycobacteria by using the microbial identification system in combination with additional trimethylsulfonium hydroxide pyrolysis. J Clin Microbiol 36:2477–2480[PubMed]
     [Google Scholar]
  27. Murton B., Taylor R. 2003; Spreading-ridge geometry, hydrothermal activity, and the influence of modern and ancient hotspots on the Carlsberg Ridge-northwestern Indian Ocean. In Cruise Report: CD149–RRS Charles Darwin 18th July to 6th August, 2003. Southampton Oceanography Centre UK: Southampton;
     [Google Scholar]
  28. Qiu D., Ruan J., Huang Y. 2008; Selective isolation and rapid identification of members of the genus Micromonospora . Appl Environ Microbiol 74:5593–5597 [View Article][PubMed]
     [Google Scholar]
  29. Roberts M. A., Crawford D. L. 2000; Use of randomly amplified polymorphic DNA as a means of developing genus- and strain-specific Streptomyces DNA probes. Appl Environ Microbiol 66:2555–2564 [View Article][PubMed]
     [Google Scholar]
  30. Rong X., Huang Y. 2012; Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 35:7–18 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Technical Note 101 Newark, DE: MIDI Inc;
     [Google Scholar]
  33. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156 [CrossRef]
     [Google Scholar]
  34. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477[PubMed]
     [Google Scholar]
  35. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
     [Google Scholar]
  36. 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 [View Article][PubMed]
     [Google Scholar]
  37. Trujillo M. E., Kroppenstedt R. M., Schumann P., Martínez-Molina E. 2006; Kribbella lupini sp. nov., isolated from the roots of Lupinus angustifolius . Int J Syst Evol Microbiol 56:407–411 [View Article][PubMed]
     [Google Scholar]
  38. Tunnicliffe V., Mary R. Fowler C. 1996; Influence of sea-floor spreading on the global hydrothermal vent fauna. Nature 379:531–533 [View Article]
     [Google Scholar]
  39. Veiga M., Esparis A., Fabregas J. 1983; Isolation of cellulolytic actinomycetes from marine sediments. Appl Environ Microbiol 46:286[PubMed]
     [Google Scholar]
  40. 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. et al. 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 [CrossRef]
     [Google Scholar]
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Brevibacterium sediminis sp. nov., isolated from deep-sea sediments from the Carlsberg and Southwest Indian Ridges
Int J Syst Evol Microbiol 66, 5268 (2016); https://doi.org/10.1099/ijsem.0.001506
/content/journal/ijsem/10.1099/ijsem.0.001506
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