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Paracoccus indicus sp. nov., isolated from surface seawater in the Indian Ocean

  • Danqiu Lin
  • Sidong Zhu
  • Yong Chen
  • Yizhe Huang
  • Jifang YangEmail author
  • Jigang ChenEmail author
Original Paper
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Abstract

Strain IO390502T, isolated from surface seawater in the Indian Ocean, was characterised using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain IO390502T belongs to the genus Paracoccus and is closely related to Paracoccus seriniphilus DSM 14827T (97.6%), followed by P. zeaxanthinifaciens JCM 21774T (97.5%), P. homiensis DSM 17862T (97.3%), P. marcusii DSM 11574T (97.2%), P. haeundaensis BC 74171T (97.0%) and P. carotinifaciens E-396T (97.0%). Cells are Gram-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile, rod-shaped, and forms creamy-white colonies. Optimal growth occurred at 25–30 °C, pH 5–8, and in the presence of 3–8% NaCl. The genome of strain IO390502T has a G+C content of 64.9 mol% and a 3.5 Mb chromosome. The in silico DNA–DNA hybridisation and average nucleotide identity values between strain IO390502T and the three closely related taxa, P. seriniphilus DSM 14827T, P. zeaxanthinifaciens JCM 21774T and P. homiensis DSM 17862T, are 19.6%, 21.9% and 20.6%, and 76.0%, 79.9% and 77.8%, respectively. Phosphatidylglycerol is the major lipid present, ubiquinone-10 (Q-10) is the sole isoprenoid quinone, and the major cellular fatty acid is C18:1ω7c. Based on data from phenotypic tests and genotypic differences between strain IO390502T and its close phylogenetic relatives, strain IO390502T represents a new species belonging to the genus Paracoccus, for which the name Paracoccus indicus sp. nov. is proposed. The type strain is IO390502T (= JCM 32637T = CCTCC AB 2018071T).

Keywords

Paracoccus Surface seawater Indian Ocean Phylogenetic analysis Cell morphology Classification 
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Notes

Acknowledgements

This work was funded by the China Ocean Mineral Resources R&D Association (CPMRA) Foundation (Grant No. DY125-15-R-03), the Zhejiang Provincial Top Key Discipline of Biological Engineering (Grant No. CX2017020), and the Key Science and Technology Program of Ningbo City, Zhejiang Province, China (Grant No. 2012C10038).

Author contributions

Conceived and designed the experiments: Danqiu Lin, Jigang Chen, Jifang Yang. Performed the experiments: Danqiu Lin, Sidong Zhu, Yong Chen, Yizhe Huang. Analyzed the data: Danqiu Lin, Jigang Chen. Contributed reagents/materials: Jifang Yang. Wrote the paper: Danqiu Lin, Jigang Chen.

Compliance with ethical standards

Conflict of interest

All authors discussed and approved the final manuscript, and declare no competing interests.

Ethical statement

This article does not contain any studies with animals performed by any of the authors.

Supplementary material

10482_2019_1226_MOESM1_ESM.pdf (531 kb)
Supplementary material 1 (PDF 530 kb)

References

  1. Berry A, Janssens D, Hümbelin M, Jore JP, Hoste B, Cleenwerck I, Vancanneyt M, Bretzel W, Mayer AF, Lopez-Ulibarri R, Shanmugam B, Swings J, Pasamontes L (2003) Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium. Int J Syst Evol Microbiol 53:231–238CrossRefGoogle Scholar
  2. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466CrossRefGoogle Scholar
  3. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J (2014) Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio 185:e02136Google Scholar
  4. da Costa MS, Albuquerque L, Nobre MF, Wait R (2011) The identification of polar lipids in prokaryotes. Methods Microbiol 38:165–181CrossRefGoogle Scholar
  5. Daniels L, Hanson RS, Phillips JA (1994) Poly-β-hydroxybutyrate. In: Gerhardt P, Murray RGE, Wood WA, Kreig NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 529–530Google Scholar
  6. Davis DH, Doudoroff M, Stanier RY, Mandel M (1969) Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Bacteriol 19:375–390CrossRefGoogle Scholar
  7. Dominguez-Moñino I, Jurado V, Hermosin B, Saiz-Jimenez C (2016) Paracoccus cavernae sp. nov., isolated from a show cave. Int J Syst Evol Microbiol 66:2265–2270CrossRefGoogle Scholar
  8. Gomori G (1955) Preparation of buffers for use in enzyme studies. Methods Enzymol 1:138–146CrossRefGoogle Scholar
  9. Kim BY, Weon HY, Yoo SH, Kwon SW, Cho YH, Stackebrandt E, Go SJ (2006) Paracoccus homiensis sp. nov., isolated from a sea-sand sample. Int J Syst Evol Microbiol 56:2387–2390CrossRefGoogle Scholar
  10. Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207CrossRefGoogle Scholar
  11. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  12. Lane DJ (1991) 16S, 23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175Google Scholar
  13. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  14. Meier-Kolthoff JP, Klenk HP, Göker M (2014) Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356CrossRefGoogle Scholar
  15. Pukall R, Laroche M, Kroppenstedt RM, Schumann P, Stackebrandt E, Ulber R (2003) Paracoccus seriniphilus sp. nov., an l-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa. Int J Syst Evol Microbiol 53:443–447CrossRefGoogle Scholar
  16. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefGoogle Scholar
  17. Sheu SY, Hsieh TY, Young CC, Chen WM (2018) Paracoccus fontiphilus sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 68:2054-2060.CrossRefGoogle Scholar
  18. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654Google Scholar
  19. Wang X, Lin D, Jing X, Zhu S, Yang J, Chen J (2018a) Complete genome sequence of the highly Mn(II) tolerant Staphylococcus sp. AntiMn-1 isolated from deep-sea sediment in the Clarion-Clipperton Zone. J Biotechnol 266:34–38CrossRefGoogle Scholar
  20. Wang YS, Yan ZF, Lin P, Gao W, Yi TH (2018b) Paracoccus pueri sp. nov., isolated from Pu’er tea. Antonie Van Leeuwenhoek 111:1535–1542CrossRefGoogle Scholar
  21. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.College of Biological and Environmental SciencesZhejiang Wanli UniversityNingboPeople’s Republic of China

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