1887

Abstract

Strain 11-3 was isolated from the surface seawater along the coast of Xiamen Island, China. Cells were Gram-stain-negative, oxidase- and catalase-positive, short and rod-shaped, nonmotile, 0.5-1.0 μm in width and 1.0-2.0 μm in length. Growth of strain 11-3 was at temperature of 15–37°C (optimum 28–35°C), at pH of 5.0-11.0 (optimum 7.0-9.0) and at salinity range of 0-10 (optimum 0.5–1). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 11-3 belonged to the genus and had the highest similarity with MJ17 (98.1 %), followed by 12-3 (97.1 %), ATCC 21588 (97.1 %), DSM 19484 (97.0 %), 2251 (97.0 %), KCTC 22803 (97.0 %) and other species of the genus (95.2–96.8 %). The DNA-DNA hybridization values between strain 11-3 and the selected strains ( MJ17, 12-3, ATCC 21588, DSM 19484 and 2251) were 19.4, 19.5, 21.6, 19.3 and 19.8 %, respectively. Corresponding, their ANI values were 77.53, 75.61, 75.36, 75.73 and 75.33 %, respectively. The major fatty acid was summed feature 8 (C 6/7). The major respiratory quinone was Q10. The polar lipids included phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentified glycolipid (GL) and unidentified aminolipid (AL). The DNA G+C content of strain 11-3 was 60.1 %. Based on results of the phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain 11-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 11-3 (=MCCC 1A16380=KCTC 72689).

Funding
This study was supported by the:
  • ZongzeShao , National Infrastructure of Natural Resources for Science and Technology Program of China , (Award NIMR-2020-9)
  • ZhiqiangYu , Key Research Program of Frontier Sciences of the Chinese Academy of Sciences , (Award QYZDJ-SSW-DQC018-02)
  • ZhiqiangYu , Guangdong Pearl River Talents Program , (Award 2017BT01Z134)
  • ZongzeShao , Xiamen Ocean Economic Innovation and Development Demonstration Project , (Award 16PZP001SF16)
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2021-03-02
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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. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Lee M, Woo S-G, Park G, Kim MK. Paracoccus caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 2011; 61: 1968 1972 [CrossRef] [PubMed]
    [Google Scholar]
  17. Lyu L, Zhi B, Lai Q, Shao Z, Yu Z. Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen. Int J Syst Evol Microbiol 2020; 70: 4285 4290 [CrossRef] [PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368 376 [CrossRef] [PubMed]
    [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783 791 [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. 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 2010a; 2: 142 148 [CrossRef] [PubMed]
    [Google Scholar]
  29. 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 2010b; 2: 117 134 [CrossRef] [PubMed]
    [Google Scholar]
  30. 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]
  31. 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]
  32. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9: 75 [CrossRef] [PubMed]
    [Google Scholar]
  33. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42: D206 D214 [CrossRef] [PubMed]
    [Google Scholar]
  34. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5: 8365 [CrossRef] [PubMed]
    [Google Scholar]
  35. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, SI N 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]
  36. 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]
  37. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64: 352 356 [CrossRef] [PubMed]
    [Google Scholar]
  38. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR 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]
  39. 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]
  40. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: a Laboratory Manual , 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
    [Google Scholar]
  41. MIDI Sherlock Microbial Identification System Operating Manual, Version 3.0 Newark, DE: MIDI, Inc; 1999
    [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids , MIDI Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  43. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990a; 13: 128 130 [CrossRef]
    [Google Scholar]
  44. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990b; 66: 199 202 [CrossRef]
    [Google Scholar]
  45. Kates M. Lipid Extraction Procedures. Techniques of Lipidology Amsterdam: Elsevier; 1986 pp 100 111
    [Google Scholar]
  46. Sheu S-Y, Hsieh T-Y, Young C-C, Chen W-M. Paracoccus fontiphilus sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 2018; 68: 2054 2060 [CrossRef] [PubMed]
    [Google Scholar]
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