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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 4

sp. nov. and sp. nov. two marine bacteria No Access

Abstract

Two Gram-stain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacteria, designated strains DBSS07 and ZSDZ65, were isolated from the surface sediments of the Bohai sea and Qingdao coastal seawater, respectively. Phylogenetic analysis based on 16S rRNA genes, multilocus sequence analysis (MLSA), phylogenomic analysis of single-copy gene families and whole-genome data placed DBSS07 and ZSDZ65 within the genus . DBSS07 was most closely related to M22, with 97.51 % sequence similarity, whereas ZSDZ65 was most closely related to R-40492 with 97.58 % sequence similarity. DBSS07 grew with 1–7 % (w/v) NaCl (optimum 3 %), at 16–37 °C (optimum 28 °C) and at pH 6.0–9.0 (optimum pH 7.0); whereas ZSDZ65 grew with 1–5 % (w/v) NaCl (optimum 2 %), at 16–32 °C (optimum 28 °C) and at pH 6.0–9.0 (optimum pH 8.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (Cω7 or/and Cω6), with different proportions. The DNA G+C contents of DBSS07 and ZSDZ65 were 44.7 and 44.3 %, respectively. On the basis of the results of polyphasic analysis, DBSS07 and ZSDZ65 are considered to represent novel species within the genus , for which the names sp. nov. (type strain, DBSS07 = KCTC 82896= MCCC 1K06284) and sp. nov. (type strain, ZSDZ65 = KCTC 82893 = MCCC 1K06289) are proposed, respectively.

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  • Accepted:
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Keyword(s): Bohai sea , Qingdao coastal seawater , surface sediment , Vibrio paucivorans sp. nov and Vibrio qingdaonensis sp. nov
Funding
This study was supported by the:
  • Fundamental Research Funds for the Central Universities (Award 202172002)
    • Principle Award Recipient: Xiao-HuaZhang
  • National Key Research and Development Program of China (Award 2018YFE0124100)
    • Principle Award Recipient: Xiao-HuaZhang
  • National Natural Science Foundation of China (Award 41730530 and 92251303)
    • Principle Award Recipient: Xiao-HuaZhang
© 2023 The Authors
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2023-04-11
2025-01-18
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References

  1. Farmer JJ, Brenner FW, Cameron DN, Birkhead KM et al. Genus I Vibrio Pacini 1854, 411AL. In Garrity GM. eds Bergey’s Manual of Systematic BacteriologyThe Proteobacteria, Part B, 2nd ed. vol 2 New York: Springer Press; 2005 pp 494–546
     [Google Scholar]
  2. Zhang X, Lin H, Wang X, Austin B. Significance of Vibrio species in the marine organic carbon cycle—a review. Sci China Earth Sci 2018; 61:1357–1368 [View Article]
     [Google Scholar]
  3. Geng YH, He XY, Li N, Li J, Gu TJ et al. Vibrio algicola sp. nov., isolated from the surface of coralline algae. Int J Syst Evol Microbiol 2020; 70:5149–5155 [View Article]
     [Google Scholar]
  4. Li B, Li Y, Liu R, Xue C, Zhu X et al. Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:172–179 [View Article]
     [Google Scholar]
  5. Li Y, Liang J, Liu R, Xue C-X, Zhou S et al. Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:889–896 [View Article] [PubMed]
     [Google Scholar]
  6. Tanaka M, Hongyu B, Jiang C, Mino S, Milet Meirelles P et al. Vibrio taketomensis sp. nov. by genome taxonomy. Syst Appl Microbiol 2020; 43:126048 [View Article]
     [Google Scholar]
  7. Wang X, Guo F, Tian P, Yu S, Xue CX et al. Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China). Int J Syst Evol Microbiol 2021; 71:71 [View Article]
     [Google Scholar]
  8. Huang WS, Wang LT, Chen JS, Chen YT, Wei ST et al. Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll. Antonie van Leeuwenhoek 2021; 114:933–945 [View Article]
     [Google Scholar]
  9. Moon YL, Park JS. Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus. Int J Syst Evol Microbiol 2021; 71:71 [View Article]
     [Google Scholar]
  10. Wu J, Qu W, Lai Q, Pei S, Zhang T et al. Vibrio ziniensis sp. nov., isolated from mangrove sediments. Int J Syst Evol Microbiol 2021; 71:71 [View Article]
     [Google Scholar]
  11. Islam MT, Nasreen T, Kirchberger PC, Liang KYH, Orata FD et al. Population analysis of Vibrio cholerae in aquatic reservoirs reveals a novel sister species (Vibrio paracholerae sp. nov.) with a history of association with humans. Appl Environ Microbiol 2021; 87:e0042221 [View Article]
     [Google Scholar]
  12. Muhammad N, Nguyen TTH, Lee YJ, Ko J, Avila F et al. Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster. Int J Syst Evol Microbiol 2022; 72:72 [View Article]
     [Google Scholar]
  13. Islam MT, Liang K, Orata FD, Im MS, Alam M et al. Vibrio tarriae sp. nov., a novel member of the Cholerae clade. Int J Syst Evol Microbiol 2022; 72:72 [View Article]
     [Google Scholar]
  14. Liu J, Zheng Y, Lin H, Wang X, Li M et al. Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. Microbiome 2019; 7:47 [View Article] [PubMed]
     [Google Scholar]
  15. Lucena T, Ruvira MA, Arahal DR, Macián MC, Pujalte MJ. Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. Syst Appl Microbiol 2012; 35:427–431 [View Article]
     [Google Scholar]
  16. Wang H, Liu J, Wang Y, Zhang XH. Vibrio marisflavi sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011; 61:568–573 [View Article]
     [Google Scholar]
  17. Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A et al. Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum. Int J Syst Evol Microbiol 2011; 61:3009–3015 [View Article]
     [Google Scholar]
  18. Ruimy R, Breittmayer V, Elbaze P, Lafay B, Boussemart O et al. Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences. Int J Syst Bacteriol 1994; 44:416–426 [View Article]
     [Google Scholar]
  19. Cerdà-Cuéllar M, Rosselló-Mora RA, Lalucat J, Jofre J, Blanch A. Vibrio scophthalmi sp. nov., a new species from turbot (Scophthalmus maximus). Int J Syst Bacteriol 1997; 47:58–61 [View Article]
     [Google Scholar]
  20. Moore ERB, Arnscheidt A, Krüger A, Strömpl C, Mau M. Simplified protocols for the preparation of genomic DNA from bacterial cultures. In Molecular Microbial Ecology Manual 1999 pp 1–15
     [Google Scholar]
  21. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article]
     [Google Scholar]
  22. Dai W, Sun W, Fu T, Jia C, Cui H et al. Marinifilum caeruleilacunae sp. nov., isolated from Yongle Blue Hole in the South China Sea. Int J Syst Evol Microbiol 2022; 72:005358 [View Article] [PubMed]
     [Google Scholar]
  23. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  24. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  27. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  28. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  29. 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 [View Article] [PubMed]
     [Google Scholar]
  30. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687 [View Article]
     [Google Scholar]
  31. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  32. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article]
     [Google Scholar]
  33. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article]
     [Google Scholar]
  36. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  37. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  38. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article]
     [Google Scholar]
  39. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
     [Google Scholar]
  40. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article]
     [Google Scholar]
  41. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
     [Google Scholar]
  42. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
     [Google Scholar]
  43. Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL et al. Vibrio Clade 3.0: new Vibrionaceae evolutionary units using genome-based approach. Curr Microbiol 2021; 79:10 [View Article]
     [Google Scholar]
  44. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  45. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. eds Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 19–33 [View Article]
     [Google Scholar]
  46. Lyman J, Fleming RH. Composition of sea water. J Mar Res 1940; 3:134–146
     [Google Scholar]
  47. Tindal BS, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. eds Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 330–393
     [Google Scholar]
  48. Teather RM, Wood PJ. Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 1982; 43:777–780 [View Article] [PubMed]
     [Google Scholar]
  49. Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article]
     [Google Scholar]
  50. Krichevsky M, Moore L, Moore W, Murray R, Stackebrandt E et al. International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J of Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  51. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 19901–6
     [Google Scholar]
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Vibrio paucivorans sp. nov. and Vibrio qingdaonensis sp. nov., two marine bacteria
Int J Syst Evol Microbiol 73, 005822 (2023); https://doi.org/10.1099/ijsem.0.005822
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