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Volume 70, Issue 2

sp. nov., isolated from a marine invertebrate from the South China Sea Free

Abstract

A novel bacterial strain, XY-99, was isolated from the epidermis of a marine invertebrate of the genus from seawater of the South China Sea. The cells of the strain were aerobic, Gram-stain-negative, non-motile, and oval-shaped (0.8–1.0 µm wide and 1.0–1.5 µm long) without a flagellum. The strain grew at temperatures of 15–37 °C (optimum, 35–37 °C), at pH 5.5–9.5 (optimum 7.5), and at NaCl concentrations of 0–12.0 % (w/v) (optimum 1.5–3.0 %). The major fatty acids (>10 %) were summed feature 8 (comprising Cω7 and/or Cω6), C and 11-methyl Cω7. The predominant polar lipid was diphosphatidylglycerol. The respiratory quinone was Q-10. The closet phylogenetic neighbours were DY470 and JLT1210, showing 97.5 and 97.3 % of 16 s rRNA gene sequence similarity. The genome size of XY-99 was 3 673 499 bp, with 64.5 % DNA G+C content. The average nucleotide identity and digital DNA–DNA hybridization values between XY-99 and DY470 were 72.8 and 14.0 %, respectively, while they were 79.3 and 22.3 % between XY-99 and JLT1210. Characterization based on phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that XY-99 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is XY-99 (=KCTC 72211=MCCC 1K03607).

  • Received:
  • Accepted:
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Keyword(s): Dapeng Nature Reserve , marine invertebrate , Pseudooceanicola onchidii and taxonomy
Funding
This study was supported by the:
  • Shenzhen science and technology application demonstration project (Award KJYY20180201180253571)
    • Principle Award Recipient: Ying Xu
  • the Scientific and Technical Innovation Council of Shenzhen (Award KQJSCX20170727101743831)
    • Principle Award Recipient: Ying Xu
  • the 62st-class General Financial Grant from the China Postdoctoral Science Foundation (Award No. 2017M622754)
    • Principle Award Recipient: Qi Yin
© 2020 The Authors
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2019-11-28
2024-04-26
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References

  1. Zhang W, Ding W, Li YX, Tam C, Bougouffa S et al. Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nat Commun 2019; 10:517 [View Article]
     [Google Scholar]
  2. Lai Q, Li G, Liu X, Du Y, Sun F et al. Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov. Antonie van Leeuwenhoek 2015; 107:1065–1074 [View Article]
     [Google Scholar]
  3. Huang MM, Guo LL, Wu YH, Lai QL, Shao ZZ et al. Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola . Int J Syst Evol Microbiol 2018; 68:409–415 [View Article]
     [Google Scholar]
  4. Huo YY, Li ZY, You H, Wang CS, Post AF et al. Oceanicola antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater. Int J Syst Evol Microbiol 2014; 64:2975–2979 [View Article]
     [Google Scholar]
  5. Cho JC, Giovannoni SJ. Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-β-hydroxybutyrate-producing marine bacteria in the order 'Rhodobacterales' . Int J Syst Evol Microbiol 2004; 54:1129–1136 [View Article]
     [Google Scholar]
  6. Lin KY, Sheu SY, Chang PS, Cho JC, Chen WM. Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan. Int J Syst Evol Microbiol 2007; 57:1625–1629 [View Article]
     [Google Scholar]
  7. Zheng Q, Chen C, Wang YN, Jiao N. Oceanicola nitratireducens sp. nov., a marine alphaproteobacterium isolated from the South China Sea. Int J Syst Evol Microbiol 2010; 60:1655–1659 [View Article]
     [Google Scholar]
  8. Gu J, Guo B, Wang YN, Yu SL, Inamori R et al. Oceanicola nanhaiensis sp. nov., isolated from sediments of the South China Sea. Int J Syst Evol Microbiol 2007; 57:157–160 [View Article]
     [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley & Sons; 1991 pp 115–175
     [Google Scholar]
  10. 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 [View Article]
     [Google Scholar]
  11. 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 [View Article]
     [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  14. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article]
     [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  17. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article]
     [Google Scholar]
  18. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article]
     [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article]
     [Google Scholar]
  20. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992; 8:275–282 [View Article]
     [Google Scholar]
  21. Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008; 9:R151 [View Article]
     [Google Scholar]
  22. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  24. Xu Y, Li Q, Tian R, Lai Q, Zhang Y. Pseudovibrio hongkongensis sp. nov., isolated from a marine flatworm. Antonie van Leeuwenhoek 2015; 108:127–132 [View Article]
     [Google Scholar]
  25. Liang X, Lin H, Wang K, Liao Y, Lai Q et al. Altererythrobacter salegens sp. nov., a slightly halophilic bacterium isolated from surface sediment. Int J Syst Evol Microbiol 2017; 67:909–913 [View Article]
     [Google Scholar]
  26. Gerhardt PMR, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  27. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC, USA: American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  28. Rashid MH, Kornberg A. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa . Proc Natl Acad Sci USA 2000; 97:4885–4890 [View Article]
     [Google Scholar]
  29. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  30. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  31. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article]
     [Google Scholar]
  32. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  33. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
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Pseudooceanicola onchidii sp. nov., isolated from a marine invertebrate from the South China Sea
Int J Syst Evol Microbiol 70, 1224 (2020); https://doi.org/10.1099/ijsem.0.003905
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