Skip to main content
SpringerLink
Log in

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

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

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).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • 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 53:231–238

    Article  CAS  PubMed  Google Scholar 

  • 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 68:461–466

    Article  PubMed  Google Scholar 

  • 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:e02136

    Google Scholar 

  • da Costa MS, Albuquerque L, Nobre MF, Wait R (2011) The identification of polar lipids in prokaryotes. Methods Microbiol 38:165–181

    Article  CAS  Google Scholar 

  • 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 529–530

    Google Scholar 

  • Davis DH, Doudoroff M, Stanier RY, Mandel M (1969) Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Bacteriol 19:375–390

    Article  Google Scholar 

  • 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 66:2265–2270

    Article  CAS  PubMed  Google Scholar 

  • Gomori G (1955) Preparation of buffers for use in enzyme studies. Methods Enzymol 1:138–146

    Article  CAS  Google Scholar 

  • 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 56:2387–2390

    Article  CAS  PubMed  Google Scholar 

  • Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lane DJ (1991) 16S, 23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • 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 64:352–356

    Article  CAS  PubMed  Google Scholar 

  • 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 53:443–447

    Article  CAS  PubMed  Google Scholar 

  • Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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 607–654

    Google Scholar 

  • 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 266:34–38

    Article  CAS  PubMed  Google Scholar 

  • Wang YS, Yan ZF, Lin P, Gao W, Yi TH (2018b) Paracoccus pueri sp. nov., isolated from Pu’er tea. Antonie Van Leeuwenhoek 111:1535–1542

    Article  CAS  PubMed  Google Scholar 

  • 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 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

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 information

Authors and Affiliations

  1. College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, People’s Republic of China

    Danqiu Lin, Sidong Zhu, Yong Chen, Yizhe Huang, Jifang Yang & Jigang Chen

Authors
  1. Danqiu Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sidong Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yong Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yizhe Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jifang Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jigang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Corresponding authors

Correspondence to Jifang Yang or Jigang Chen.

Ethics declarations

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.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 530 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lin, D., Zhu, S., Chen, Y. et al. Paracoccus indicus sp. nov., isolated from surface seawater in the Indian Ocean. Antonie van Leeuwenhoek 112, 927–933 (2019). https://doi.org/10.1007/s10482-019-01226-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-019-01226-2

Keywords

Search

Navigation