1887

Abstract

Strain 12-3 was isolated from seawater of the Guanyinshan Coast, Xiamen, Fujian Province, PR China. The bacterium was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative. Growth of strain 12-3 occurred at 10–37 °C (optimum, 20–30 °C), at pH 5.0–11.0 (optimum, pH 7.0–8.0) and at a salinity range of 0–10 % (optimum, 3–5 %). The results of phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 12-3 belonged to the genus and had the highest sequence similarity to HDM-25 (97.4 %), followed by SW-3 (96.9 %), MJ17 (96.9 %), F14 (96.8 %) and other species in the genus (95.3–96.5 %). The average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) values between strain 12-3 and HDM-25 were 76.1 and 17.0 %, respectively. ANI and DDH values between strain 12-3 and SW-3 were 78.9 and 18.2 %, respectively. The principal fatty acid of strain 12-3 was summed feature 8 (C 6/7) and C. The respiratory quinone of strain 12-3 was Q10. The polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The G+C content of the chromosomal DNA was 63.9 mol%. The combination of the results of the phylogenetic, phenotypic and chemotaxonomic analyses, and its low ANI and DDH values indicate that strain 12-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 12-3 (=MCCC 1A16381=KCTC 72687).

Funding
This study was supported by the:
  • Zongze Shao , Instituto Nacional de Ciência e Tecnologia Centro de Estudos das Adaptações da Biota Aquática da Amazônia (BR) , (Award NIMR-2019-9)
  • Zongze Shao , Xiamen Ocean Economic Innovation and Development Demonstration Project , (Award 16PZP001SF16)
  • Zhiqiang Yu , Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (CAS) , (Award QYZDJ-SSW-DQC018-02)
  • Zhiqiang Yu , Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program , (Award 2017BT01Z134)
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2020-06-24
2020-10-20
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References

  1. Davis DH, Doudoroff M, Stanier RY, Mandel M. Proposal to reject the genus Hydrogenomonas: Taxonomic implications. Int J Syst Bacteriol 1969; 19:375–390 [CrossRef]
    [Google Scholar]
  2. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [CrossRef][PubMed]
    [Google Scholar]
  3. Kim B-Y, Weon H-Y, Yoo S-H, Kwon S-W, Cho Y-H et al. Paracoccus homiensis sp. nov., isolated from a sea-sand sample. Int J Syst Evol Microbiol 2006; 56:2387–2390 [CrossRef][PubMed]
    [Google Scholar]
  4. Zhang G, Yang Y, Yin X, Wang S. Paracoccus pacificus sp. nov., isolated from the Western Pacific Ocean. Antonie van Leeuwenhoek 2014; 106:725–731 [CrossRef][PubMed]
    [Google Scholar]
  5. Lin D, Zhu S, Chen Y, Huang Y, Yang J et al. Paracoccus indicus sp. nov., isolated from surface seawater in the Indian Ocean. Antonie van Leeuwenhoek 2019; 112:927–933 [CrossRef][PubMed]
    [Google Scholar]
  6. Xue H, Piao C-G, Guo M-W, Wang L-F, Li Y. Paracoccus aerius sp. nov., isolated from air. Int J Syst Evol Microbiol 2017; 67:2586–2591 [CrossRef][PubMed]
    [Google Scholar]
  7. Dong X, Zhang G, Xiong Q, Liu D, Wang D et al. Paracoccus salipaludis sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2018; 68:3812–3817 [CrossRef][PubMed]
    [Google Scholar]
  8. Sun X, Luo P, Li M. Paracoccus angustae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:3469–3475 [CrossRef][PubMed]
    [Google Scholar]
  9. Rai A, N S, G S, A S, G D et al. Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa . Int J Syst Evol Microbiol 2020; 70:1720–1728 [CrossRef][PubMed]
    [Google Scholar]
  10. Lin P, Yan Z-F, Won K-H, Yang J-E, Li C-T et al. Paracoccus hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Int J Syst Evol Microbiol 2017; 67:2452–2458 [CrossRef][PubMed]
    [Google Scholar]
  11. Lee M-J, Lee S-S. Paracoccus limosus sp. nov., isolated from activated sludge in a sewage treatment plant. Int J Syst Evol Microbiol 2013; 63:1311–1316 [CrossRef][PubMed]
    [Google Scholar]
  12. Liu X-Y, Wang B-J, Jiang C-Y, Liu S-J. Paracoccus sulfuroxidans sp. nov., a sulfur oxidizer from activated sludge. Int J Syst Evol Microbiol 2006; 56:2693–2695 [CrossRef][PubMed]
    [Google Scholar]
  13. Wei Y, Cao J, Yao H, Mao H, Zhu K et al. Paracoccus sediminilitoris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2019; 69:1035–1040 [CrossRef][PubMed]
    [Google Scholar]
  14. Yoon J, Maharjan S, Choi H. Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment. FEMS Microbiol Lett 2019; 366:fnz184 [CrossRef][PubMed]
    [Google Scholar]
  15. Zhang G, Jiao K, Xie F, Pei S, Jiang L. Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1472–1476 [CrossRef][PubMed]
    [Google Scholar]
  16. Kämpfer P, Irgang R, Poblete-Morales M, Fernández-Negrete G, Glaeser SP et al. Paracoccus nototheniae sp. nov., isolated from a black rock cod fish (Notothenia coriiceps) from the Chilean Antarctic. Int J Syst Evol Microbiol 2019; 69:2794–2800 [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. Chun J, Lee J-H, Jung Y, Kim M, Kim S et al. Eztaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [CrossRef][PubMed]
    [Google Scholar]
  19. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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 [CrossRef][PubMed]
    [Google Scholar]
  20. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  27. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  28. Jung Y-T, Park S, Lee J-S, Yoon J-H. Paracoccus lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2763–2769 [CrossRef][PubMed]
    [Google Scholar]
  29. Chen M-H, Sheu S-Y, Chen CA, Wang J-T, Chen W-M. Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera. Int J Syst Evol Microbiol 2011; 61:1138–1143 [CrossRef][PubMed]
    [Google Scholar]
  30. Yoon S-H, Ha S-M, 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]
  31. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  33. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [CrossRef][PubMed]
    [Google Scholar]
  34. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  35. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
  36. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
    [Google Scholar]
  37. MIDI Sherlock Microbial Identification System Operating Manual,Version 3.0 Newark, DE: MIDI, Inc; 1999
    [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  39. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [CrossRef]
    [Google Scholar]
  40. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [CrossRef]
    [Google Scholar]
  41. Kates M. Lipid Extraction Procedures Amsterdam: Techniques of lipidology Elsevier; 1986 pp 100–111
    [Google Scholar]
  42. Chen W-M, Li Y-S, Young C-C, Sheu S-Y. Paracoccus mangrovi sp. nov., isolated from a mangrove. Int J Syst Evol Microbiol 2017; 67:2689–2695 [CrossRef][PubMed]
    [Google Scholar]
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