1887

Abstract

Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233 and LJC006, were isolated from the East China Sea. On the basis of the results of 16S rRNA gene sequencing and multilocus sequence analysis, BEI233 and LJC006 should be assigned to the genus . The closest phylogenetic relatives of BEI233 are LMG 19158 (98.7 % 16S rRNA gene sequence pairwise similarity), DSM 14397 (98.5 %), KCTC 42287 (97.7 %), ATCC 35048 (97.3 %) and MD16 (96.5 %), whereas for LJC006 they were CAIM 518 (97.1 %), LMG 7894 (97.0%), JCM 16456 (96.9 %) and LMG 21346 (96.1 %). The growth of BEI233 occurred at 10–37 °C, pH 5.0–8.0 and with 1–7 % (w/v) NaCl, while the growth of LJC006 occurred at 10–37 °C, pH 6.0–9.0, and 0–8 % (w/v) NaCl. The predominant fatty acids (>10 %) were summed feature 3 (Cω7 or/and Cω6), C and summed feature 8 (Cω7 or/and Cω6), with different proportions. The DNA G+C contents of BEI233 and LJC006 are 42.41 mol% and 41.88 mol%, respectively. On the basis of the results of polyphasic analysis, BEI233 and LJC006 are considered to represent novel species of the genus for which the names sp. nov. and sp. nov. are proposed. The type strains are BEI233 (=JCM 32692=KCTC 62618) and LJC006 (=JCM 32693=KCTC 62620), respectively.

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2019-11-08
2019-11-21
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References

  1. Baumann P, Schubert RHW. Genus II. V ibrionaceae Veron 1965, 5245AL In Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology1 Baltimore: Williams & Wilkins; 1984; pp 516– 517
    [Google Scholar]
  2. Urbanczyk H, Ast JC, Higgins MJ, Carson J, Dunlap PV. Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Alii vibrio fischeri gen. nov., comb. nov., Alii vibrio logei comb. nov., Alii vibrio salmonicida comb. nov. and Alii vibrio wodanis comb. nov. Int J Syst Evol Microbiol 2007;57: 2823– 2829 [CrossRef]
    [Google Scholar]
  3. Thompson FL, Hoste B, Thompson CC, Goris J, Gomez-Gil B et al. Enterovibrio norvegicus gen. nov., sp. nov., isolated from the gut of turbot (Scophthalmus maximus) larvae: a new member of the family Vibrionaceae. Int J Syst Evol Microbiol 2002;52: 2015– 2022 [CrossRef]
    [Google Scholar]
  4. Thompson FL, Hoste B, Vandemeulebroecke K, Swings J. Reclassification of Vibrio hollisae as Grimontia hollisae gen. nov., comb. nov. Int J Syst Evol Microbiol 2003;53: 1615– 1617 [CrossRef]
    [Google Scholar]
  5. Huang Z, Dong C, Shao Z. Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater. Int J Syst Evol Microbiol 2016;66: 3050– 3056 [CrossRef]
    [Google Scholar]
  6. Baumann P. Baumann L. Genus II. Photobacterium Beijerinck 1889, 401AL In Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology1 Baltimore: Williams & Wilkins; 1984; pp 539– 545
    [Google Scholar]
  7. Mellado E, Moore ER, Nieto JJ, Ventosa A. Analysis of 16S rRNA gene sequences of Vibrio costicola strains: description of Salinivibrio costicola gen. nov., comb. nov. Int J Syst Bacteriol 1996;46: 817– 821 [CrossRef]
    [Google Scholar]
  8. Amin AKMR, Tanaka M, Al-Saari N, Feng G, Mino S et al. Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan. Syst Appl Microbiol 2017;40: 290– 296 [CrossRef]
    [Google Scholar]
  9. Parte AC. LPSN - List of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018;68: 1825– 1829 [CrossRef]
    [Google Scholar]
  10. Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S et al. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 2005;71: 5107– 5115 [CrossRef]
    [Google Scholar]
  11. Pascual J, Macián MC, Arahal DR, Garay E, Pujalte MJ. Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int J Syst Evol Microbiol 2010;60: 154– 165 [CrossRef]
    [Google Scholar]
  12. Machado H, Gram L. The fur gene as a new phylogenetic marker for Vibrionaceae species identification. Appl Environ Microbiol 2015;81: 2745– 2752 [CrossRef]
    [Google Scholar]
  13. 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 [CrossRef]
    [Google Scholar]
  14. 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 [CrossRef]
    [Google Scholar]
  15. Farmer JJ, Janda JM, Brenner FW, Cameron DN, Birkhead KM et al. Genus I. Vibrio Pacini 1854, 411AL Bergey’s Manual of Systematic Bacteriology 20052B, 2nd edn. 1854; pp 494– 546
    [Google Scholar]
  16. Thompson FL, Austin B, Swings J. The Biology of Vibrios Washington, DC: American Society for Microbiology; 2006
    [Google Scholar]
  17. 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 [CrossRef]
    [Google Scholar]
  18. Ishimaru K, Akagawa-matsushita M, Muroga K. Vibrio ichthyoenteri sp. nov., a pathogen of Japanese flounder (Paralichthys olivaceus) larvae. Int J Syst Bacteriol 1996;46: 155– 159 [CrossRef]
    [Google Scholar]
  19. Balcázar JL, Pintado J, Planas M. Vibrio hippocampi sp. nov., a new species isolated from wild seahorses (Hippocampus guttulatus). FEMS Microbiol Lett 2010;307: 30– 34 [CrossRef]
    [Google Scholar]
  20. Brenner DJ, Hickman-Brenner FW, Lee JV, Steigerwalt AG, Fanning GR et al. Vibrio furnissii (formerly aerogenic biogroup of Vibrio fluvialis), a new species isolated from human feces and the environment. J Clin Microbiol 1983;18: 816– 824
    [Google Scholar]
  21. Tomoo S, Yoshitoshi O. Updating the vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Frontiers in Microbiology 2013;4: [CrossRef]
    [Google Scholar]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68: 461– 466 [CrossRef]
    [Google Scholar]
  23. 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]
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. 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 [CrossRef]
    [Google Scholar]
  26. Zhang Z, Yu T, Xu T, Zhang X-H. Aquimarina pacifica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014;64: 1991– 1997 [CrossRef]
    [Google Scholar]
  27. Yoon SH, Ha S-M, 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 [CrossRef]
    [Google Scholar]
  28. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016;44: D279– D285 [CrossRef]
    [Google Scholar]
  29. Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 2010;11: 431 [CrossRef]
    [Google Scholar]
  30. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30: 2068– 2069 [CrossRef]
    [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef]
    [Google Scholar]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  33. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20: 406– 416 [CrossRef]
    [Google Scholar]
  34. 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]
    [Google Scholar]
  35. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013;79: 7696– 7701 [CrossRef]
    [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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  38. Nguyen L-T, 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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  40. Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, SV L. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology & Evolution 2017;35:
    [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 [CrossRef]
    [Google Scholar]
  42. 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]
    [Google Scholar]
  43. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy In Reddy CA, Beveridge TJ, Breznak TA, Marzluf G. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007; pp 19– 33
    [Google Scholar]
  44. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52: 1049– 1070 [CrossRef]
    [Google Scholar]
  45. Lyman J, Fleming RH. Composition of sea water. J Mar Res 1940;3: 134– 146
    [Google Scholar]
  46. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007; pp 330– 393
    [Google Scholar]
  47. 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
    [Google Scholar]
  48. Yoon JH, Park YH, Lee KC, Kim CJ, Kho YH et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002;52: 123– 130 [CrossRef]
    [Google Scholar]
  49. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990;20: 1– 6
    [Google Scholar]
  50. Xie CH, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003;49: 345– 349 [CrossRef]
    [Google Scholar]
  51. 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 [CrossRef]
    [Google Scholar]
  52. Wayne LG, Brenner DJ, Colwell RR. International committee on systematic bacteriology. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Bacteriol 1987;37: 463– 464
    [Google Scholar]
  53. Colwell RR. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 1970;104: 410– 433
    [Google Scholar]
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