Skip to main content

Advertisement

SpringerLink
Log in

Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A novel Paracoccus-related strain, designated YLB-12T, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10–37 °C and pH 5.0–9.0 in the presence of 0–12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11T (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588T (97.4%), Paracoccus rhizosphaerae LMG 26205T (97.2%), Paracoccus beibuensis CGMCC 1.7295T (97.1%) and Paracoccus halotolerans CFH 90064T (97.0%). The DNA‒DNA hybridization values between strain YLB-12T and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12T was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12T also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (C18: 1ω6c /C18: 1ω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12T represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12T (= MCCC 1A17213T = KCTC 82197T).

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
Fig. 2

Similar content being viewed by others

Abbreviations

MCCC:

Marine Culture Collection of China

KCTC:

Korean Collection for Type Cultures

DDH:

DNA–DNA hybridization

ANI:

Average nucleotide identity

References

  1. Davis DH, Doudoroff M, Stanier RY et al (1969) Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Evol Microbiol 19(4):375–390. https://doi.org/10.1099/00207713-19-4-375

    Article  Google Scholar 

  2. Göker M (2022) Filling the gaps: missing taxon names at the ranks of class, order and family. Int J Syst Evol Microbiol 72(12):005638. https://doi.org/10.1099/ijsem.0.005638

    Article  Google Scholar 

  3. Parte AC, Carbasse JS, Meier-Kolthoff JP et al (2020) List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612

    Article  PubMed  PubMed Central  Google Scholar 

  4. van Spanning RJM, Stouthamer AH, Baker SC et al (2015) Paracoccus. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M and Chun J (eds) Bergey’s manual of systematics of archaea and bacteria, pp 1–14

  5. Chen W, Li Y, Young C et al (2017) Paracoccus mangrovi sp. nov., isolated from a mangrove. Int J Syst Evol Microbiol 67:2689–2695

    Article  CAS  PubMed  Google Scholar 

  6. Xue H, Piao C, Guo M et al (2017) Paracoccus aerius sp. nov., isolated from air. Int J Syst Evol Microbiol 67:2586–2591

    Article  CAS  PubMed  Google Scholar 

  7. Dong X, Zhang G, Xiong Q et al (2018) Paracoccus salipaludis sp. nov., isolated from saline–alkaline soil. Int J Syst Evol Microbiol 68:3812–3817

    Article  CAS  PubMed  Google Scholar 

  8. Sheu S, Hsieh T, Young C et al (2018) Paracoccus fontiphilus sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 68:2054–2060

    Article  CAS  PubMed  Google Scholar 

  9. Park S, Yoon S, Ha M et al (2017) Polaribacter litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 66:2036–2042

    Article  Google Scholar 

  10. Jung Y, Park S, Lee J et al (2014) Paracoccus lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 64:2763–2769

    Article  CAS  PubMed  Google Scholar 

  11. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci 89(12):5685–5689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Yoon SH, Ha SM, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617. https://doi.org/10.1099/ijsem.0.001755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  15. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376

    Article  CAS  PubMed  Google Scholar 

  16. Rzhetsky A, Nei M (1992) Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 35(4):367–375

    Article  CAS  PubMed  Google Scholar 

  17. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791

    Article  PubMed  Google Scholar 

  18. Parks D, Imelfort M, Skennerton C et al (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Meier-Kolthoff J, Auch A, Klenk H et al (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  20. Goris J, Konstantinidis K, Klappenbach J et al (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57(1):81–91

    Article  CAS  PubMed  Google Scholar 

  21. Na SI, Kim YO, Yoon SH et al (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285

    Article  CAS  PubMed  Google Scholar 

  22. Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428(4):726–731

    Article  CAS  PubMed  Google Scholar 

  23. Skerman V (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams & Wilkins, Baltimore

    Google Scholar 

  24. Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Scientific Press (English translation), Beijing

    Google Scholar 

  25. Sasser M (1990) Identification of bacteria through fatty acid analysis. Methods Phytobacteriol 565

  26. Tindall B (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    Article  CAS  Google Scholar 

  27. Komagata K, Susuki K (1987) Lipid and cell-wall systematics in bacterial systematics. Method Microbiol 19:161–207

    Article  CAS  Google Scholar 

  28. Wayne L, Brenner D, Colwell R et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37(4):463–464

    Article  Google Scholar 

  29. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106(45):19126–19131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors would like to acknowledge the opinions of Marine Culture Collection of China (MCCC) experts for the nomenclature of this strain.

Funding

This work was supported by the fund of the National Natural Science Foundation of China (No.42206101); Scientific Research Foundation of Third Institute of Oceanography, MNR (No. 2023003); National Microbial Resource Center (No. NMRC-2022-9) and National Science and Technology Fundamental Resources Investigation Program of China (2021FY100900).

Author information

Authors and Affiliations

  1. Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China

    Libo Yu, Guangxin Xu, Qiliang Lai & Zongze Shao

  2. School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China

    Shiping Wei

Authors
  1. Libo Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guangxin Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shiping Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qiliang Lai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zongze Shao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceive and design the experiments: Libo Yu, Shiping Wei and Zongze Shao; Perform the experiments:Libo Yu and Guangxin Xu; Data curation: Libo Yu and Qiliang Lai; Writing the paper: Libo Yu; All authors approved the final manuscript.

Corresponding author

Correspondence to Zongze Shao.

Ethics declarations

Conflict of interest

The authors declare that there is no conflict of interest.

Additional information

Publisher's Note

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

The GenBank accession number for the 16S rRNA gene sequence of Paracoccus maritimus YLB-12T is ON139213. The draft genome accession number for strain YLB-12T is JANAVZ000000000. The transmission electron micrographs of the cells and polar lipids of strain YLB-12T, maximum-likelihood tree and minimum evolution tree are available as supplementary figures in the CMIC online.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 939 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yu, L., Xu, G., Wei, S. et al. Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment. Curr Microbiol 81, 134 (2024). https://doi.org/10.1007/s00284-024-03637-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00284-024-03637-5

Search

Navigation