1887

Abstract

A novel mesophilic marine actinobacterial strain, designated as SCSIO 08198, was isolated from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-positive, rod-shaped and salmon pink in colour. Good growth occurred on marine agar with 1–5 % (w/v) NaCl and incubation at 28 °C for more than a fortnight. Sensitive to short ultraviolet radiation. Analysis of 16S rRNA gene sequences revealed that strain SCSIO 08198 had the highest similarity of 97.2 % to Rubrobacter radiotolerans DSM 5868, and loosely related (<94.2 %) to all other species in the genus Rubrobacter . Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the novel isolate shared a lineage with members of the genus Rubrobacter . The total cellular fatty acid profile was dominated by C16 : 0 12-methyl. MK-8 was the main menaquinone. The peptidoglycan type was A3α (l-Lys-l-Ala). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. Based on the whole genome sequence analysis, the genome size is 3 078 689 bp with DNA G+C value of 63.8 mol%, including one circular chromosome and two plasmids. Based on these polyphasic data, a new species, Rubrobacter indicoceani sp. nov., is proposed, with the type strain SCSIO 08198 (=DSM 105148=CGMCC 1.16398).

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2018-10-09
2019-10-21
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References

  1. Kamjam M, Sivalingam P, Deng Z, Hong K. Deep sea actinomycetes and their secondary metabolites. Front Microbiol 2017;8:760 [CrossRef][PubMed]
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Evol Microbiol 1997;47:479–491
    [Google Scholar]
  3. Suzuki K-I, Collins MD, Iijima E, Komagata K. Chemotaxonomic characterization of a radiotolerant bacterium, Arthrobacter radiotolerans : description of Rubrobacter radiotolerans gen. nov., comb. nov. FEMS Microbiol Lett 1988;52:33–39
    [Google Scholar]
  4. Norman JS, King GM, Friesen ML. Rubrobacter spartanus sp. nov., a moderately thermophilic oligotrophic bacterium isolated from volcanic soil. Int J Syst Evol Microbiol 2017;67:3597–3602 [CrossRef][PubMed]
    [Google Scholar]
  5. Yoshinaka T, Yano K, Yamaguchi H. Isolation of highly radioresistant bacterium, Arthrobacter radiotolerans nov. sp. Agric Biol Chem 1973;37:2269–2275 [CrossRef]
    [Google Scholar]
  6. Gremion F, Chatzinotas A, Harms H. Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ Microbiol 2003;5:896–907 [CrossRef][PubMed]
    [Google Scholar]
  7. Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006;72:1719–1728 [CrossRef][PubMed]
    [Google Scholar]
  8. Kämpfer P, Glaeser SP, Busse HJ, Abdelmohsen UR, Hentschel U. Rubrobacter aplysinae sp. nov., isolated from the marine sponge Aplysina aerophoba. Int J Syst Evol Microbiol 2014;64:705–709 [CrossRef][PubMed]
    [Google Scholar]
  9. Jurado V, Miller AZ, Alias-Villegas C, Laiz L, Saiz-Jimenez C. Rubrobacter bracarensis sp. nov., a novel member of the genus Rubrobacter isolated from a biodeteriorated monument. Syst Appl Microbiol 2012;35:306–309 [CrossRef][PubMed]
    [Google Scholar]
  10. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 1994; pp.611–654
    [Google Scholar]
  11. Xu XW, Ren PG, Liu SJ, Wu M, Zhou PJ. Natrinema altunense sp. nov., an extremely halophilic archaeon isolated from a salt lake in Altun Mountain in Xinjiang, China. Int J Syst Evol Microbiol 2005;55:1311–1314 [CrossRef][PubMed]
    [Google Scholar]
  12. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007;57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  13. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007; pp.330–393
    [Google Scholar]
  14. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  15. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Bacteriol 1980;48:277–282 [CrossRef][PubMed]
    [Google Scholar]
  16. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982;5:2359–2367 [CrossRef]
    [Google Scholar]
  17. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990;20:1–6
    [Google Scholar]
  18. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW, Arlington VA. (editors) Actinomycete Taxonomy Society for Industrial Microbiology; 1980; pp.227–291
    [Google Scholar]
  19. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Microbiol 1979;47:87–95
    [Google Scholar]
  20. Albuquerque L, Johnson MM, Schumann P, Rainey FA, da Costa MS. Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis. Syst Appl Microbiol 2014;37:235–243 [CrossRef][PubMed]
    [Google Scholar]
  21. Albuquerque L, França L, Rainey FA, Schumann P, Nobre MF et al. Gaiella occulta gen. nov., sp. nov., a novel representative of a deep branching phylogenetic lineage within the class Actinobacteria and proposal of Gaiellaceae fam. nov. and Gaiellales ord. nov. Syst Appl Microbiol 2011;34:595–599 [CrossRef][PubMed]
    [Google Scholar]
  22. Carreto L, Moore E, Nobre MF, Wait R, Riley PW et al. Rubrobacter xylanophilus sp. nov., a new thermophilic species isolated from a thermally polluted effluent. Int J Syst Evol Microbiol 1996;46:460–465
    [Google Scholar]
  23. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Evol Microbiol 1989;39:159–167
    [Google Scholar]
  24. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Evol Microbiol 1996;46:1088–1092
    [Google Scholar]
  25. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  26. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  27. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  28. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  29. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: University Press; 1983
    [Google Scholar]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  31. Stackebrandt E. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  32. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002;52:1043–1047 [CrossRef][PubMed]
    [Google Scholar]
  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
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