1887

Abstract

A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, designated Hp12, was isolated from a marine sponge in the intertidal zone off the coast of Seltjarnarnes (64° 16′ N 22° 00′ W), Iceland. Strain Hp12 grew optimally at 20–22 °C, at pH 7–8 and in the presence of 1–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed strain Hp12 in the class Gammaproteobacteria , related to members of the genus Alcanivorax in the order Oceanospirillales with 90.3–88.5 % sequence similarity. The strain had a draft genome size of 4.99 Mbp with a DNA G+C content of 43.0 mol%. Cellular fatty acids were dominated by C16 : 1 ω7c, C18 : 1 ω7c and C16 : 0. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The major respiratory lipoquinones were ubiquinone Q8 and menaquinone MK8. From the taxonomic information and phenotypic properties obtained in this study, it is proposed that strain Hp12 be placed into a novel genus and species named Pelagibaculum spongiae gen. nov., sp. nov. The type strain of Pelagibaculum spongiae is Hp12 (=DSM 104963=CECT 9367).

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2019-05-23
2019-09-20
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References

  1. Taylor MW, Radax R, Steger D, Wagner M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 2007;71:295–347 [CrossRef][PubMed]
    [Google Scholar]
  2. Leinonen R, Sugawara H, Shumway M.. International Nucleotide Sequence Database Collaboration The sequence read archive. Nucleic Acids Res 2011;39:D19–D21 [CrossRef][PubMed]
    [Google Scholar]
  3. Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M et al. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep 2016;6:33721 [CrossRef][PubMed]
    [Google Scholar]
  4. Cowan ST, Steel KJ. Cowan and Steel’s Manual for the Identification of Medical Bacteria Cambridge university press; 2004
    [Google Scholar]
  5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  6. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  7. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017;110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  8. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403–410 [CrossRef][PubMed]
    [Google Scholar]
  10. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Ostell J et al. GenBank. Nucleic Acids Res 2018;46:D41–D47 [CrossRef][PubMed]
    [Google Scholar]
  11. 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]
  12. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28:1823–1829 [CrossRef][PubMed]
    [Google Scholar]
  13. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res 2014;42:D643–D648 [CrossRef][PubMed]
    [Google Scholar]
  14. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004;32:1363–1371 [CrossRef][PubMed]
    [Google Scholar]
  15. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. 2004;http://www.evolution.gs.washington.edu/phylip.html. http://ci.nii.ac.jp/naid/10027221536/en/ Accessed 23 January 2019
  16. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52:696–704 [CrossRef][PubMed]
    [Google Scholar]
  17. Liu C, Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005;55:1181–1186 [CrossRef][PubMed]
    [Google Scholar]
  18. Rahul K, Sasikala C, Tushar L, Debadrita R, Ramana CV. Alcanivorax xenomutans sp. nov., a hydrocarbonoclastic bacterium isolated from a shrimp cultivation pond. Int J Syst Evol Microbiol 2014;64:3553–3558 [CrossRef][PubMed]
    [Google Scholar]
  19. Lai Q, Wang J, Gu L, Zheng T, Shao Z. Alcanivorax marinus sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2013;63:4428–4432 [CrossRef][PubMed]
    [Google Scholar]
  20. Yoon JH, Oh TK, Park YH. Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004;54:1829–1835 [CrossRef][PubMed]
    [Google Scholar]
  21. Vreeland RH, Litchfield CD, Martin EL, Elliot E. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. Int J Syst Bacteriol 1980;30:485–495 [CrossRef]
    [Google Scholar]
  22. Giordano A, Vella FM, Romano I, Gambacorta A. Structural elucidation of a novel phosphoglycolipid isolated from six species of Halomonas. J Lipid Res 2007;48:1825–1831 [CrossRef][PubMed]
    [Google Scholar]
  23. Miao C, Jia F, Wan Y, Zhang W, Lin M et al. Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. Int J Syst Evol Microbiol 2014;64:915–920 [CrossRef][PubMed]
    [Google Scholar]
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