1887

Abstract

A Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, curved rod-shaped bacterium, strain N384, was isolated from a marine sponge (; phylum Porifera) collected from a depth of 795 feet (242 m) off the west coast of Curaçao. On the basis of 16S rRNA gene sequencing, strain N384 was shown to belong to the genus , most closely related to LMG 20546 (98.8 % similarity), ATCC 27043 (98.5 %), ATCC 19109 (98.6 %) and DSM 21326 (98.2 %). The DNA G+C content of strain N384 was 41.6 mol%. An analysis of concatenated sequences of five genes (, , , and ; 4068 bp) demonstrated a clear separation between strain N384 and its closest neighbours and clustered strain N384 into the ‘Orientalis’ clade of vibrios. Phenotypically, the novel species belonged to the arginine dihydrolase-positive, lysine decarboxylase- and ornithine decarboxylase-negative (A+/L−/O−) cluster. The novel species was also differentiated on the basis of fatty acid composition, specifically that the proportions of iso-C, iso-C, C, iso-C, C, iso-C, Cω8 and C were significantly different from those found in and . The results of DNA–DNA hybridization, average nucleotide identity and physiological and biochemical tests further allowed differentiation of this strain from other described species of the genus . Collectively, these findings confirm that strain N384 represents a novel species, for which the name sp. nov. is proposed, with the type strain N384 ( = ATCC BAA-2122 = DSM 23640).

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2012-08-01
2019-10-19
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References

  1. Ahn J. , Park J. W. , McConnell J. A. , Ahn Y. B. , Häggblom M. M. . ( 2011; ). Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the marine sponge Chondrilla nucula . . Int J Syst Evol Microbiol 61:, 961–964. [CrossRef] [PubMed]
    [Google Scholar]
  2. Allard M. W. , Farris J. S. , Carpenter J. M. . ( 1999; ). Congruence among mammalian mitochondrial genes. . Cladistics 15:, 75–84. [CrossRef]
    [Google Scholar]
  3. Baumann P. , Baumann L. . ( 1981; ). The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes . . In The Prokaryotes, vol. 2, pp. 1302–1330. Edited by Starr M. P. , Stolp H. , Trüper H. G. , Balows A. , Schlegel H. G. . . Berlin:: Springer;.
    [Google Scholar]
  4. Baumann P. , Furniss A. L. , Lee J. V. . ( 1984; ). Genus I. Vibrio Pacini 1854, 411AL . . In Bergey’s Manual Systematic Bacteriology, vol. 1, pp. 518–538. Edited by Krieg N. R. , Holt J. G. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  5. Brown E. W. , LeClerc J. E. , Kotewicz M. L. , Cebula T. A. . ( 2001; ). Three R’s of bacterial evolution: how replication, repair, and recombination frame the origin of species. . Environ Mol Mutagen 38:, 248–260. [CrossRef] [PubMed]
    [Google Scholar]
  6. Brown E. W. , Kotewicz M. L. , Cebula T. A. . ( 2002; ). Detection of recombination among Salmonella enterica strains using the incongruence length difference test. . Mol Phylogenet Evol 24:, 102–120. [CrossRef] [PubMed]
    [Google Scholar]
  7. Buck J. D. . ( 1982; ). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. . Appl Environ Microbiol 44:, 992–993.[PubMed]
    [Google Scholar]
  8. Bull J. J. , Huelsenbeck J. P. , Cunningham C. W. , Swofford D. L. , Waddell P. J. . ( 1993; ). Partitioning and combining data in phylogenetic analysis. . Syst Biol 42:, 384–397.[CrossRef]
    [Google Scholar]
  9. Cashion P. , Holder-Franklin M. A. , McCully J. , Franklin M. . ( 1977; ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81:, 461–466. [CrossRef] [PubMed]
    [Google Scholar]
  10. Chimetto L. A. , Cleenwerck I. , Alves N. Jr , Silva B. S. , Brocchi M. , Willems A. , De Vos P. , Thompson F. L. . ( 2011; ). Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei . . Int J Syst Evol Microbiol 61:, 362–368. [CrossRef] [PubMed]
    [Google Scholar]
  11. CLSI ( 2006; ). Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria, Approved Standard M45-A, vol. 26, no. 19. Wayne, PA: Clinical and Laboratory Standards Institute.
  12. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef] [PubMed]
    [Google Scholar]
  13. Dykhuizen D. E. , Green L. . ( 1991; ). Recombination in Escherichia coli and the definition of biological species. . J Bacteriol 173:, 7257–7268.[PubMed]
    [Google Scholar]
  14. Farmer J. J. , Janda J. M. , Brenner F. W. , Cameron D. N. , Birkhead K. M. . ( 2005; ). Genus I. Vibrio Pacini 1854, 411AL . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2B, pp. 494–546. Edited by Garrity G. M. , Brenner D. J. , Krieg N. R. , Staley J. R. . . New York:: Springer;.
    [Google Scholar]
  15. Farris J. S. , Kallersjo M. , Kluge A. G. , Bult C. . ( 1994; ). Testing significance of incongruence. . Cladistics 10:, 315–319. [CrossRef]
    [Google Scholar]
  16. FDA ( 2004; ). Bacteriological Analytical Manual. Chapter 9. Vibrio. Washington, DC: US Food and Drug Administration. http://www.fda.gov/Food/ScienceResearch/LaboratoryMethods/BacteriologicalAnalyticalManualBAM/UCM070830
  17. Frati F. , Simon C. , Sullivan J. , Swofford D. L. . ( 1997; ). Evolution of the mitochondrial cytochrome oxidase II gene in collembola. . J Mol Evol 44:, 145–158. [CrossRef] [PubMed]
    [Google Scholar]
  18. Goris J. , Konstantinidis K. T. , Klappenbach J. A. , Coenye T. , Vandamme P. , Tiedje J. M. . ( 2007; ). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. . Int J Syst Evol Microbiol 57:, 81–91. [CrossRef] [PubMed]
    [Google Scholar]
  19. Hallin P. F. , Binnewies T. T. , Ussery D. W. . ( 2008; ). The genome BLASTatlas – a GeneWiz extension for visualization of whole-genome homology. . Mol Biosyst 4:, 363–371. [CrossRef] [PubMed]
    [Google Scholar]
  20. Hoffmann M. , Fischer M. , Ottesen A. , McCarthy P. J. , Lopez J. V. , Brown E. W. , Monday S. R. . ( 2010a; ). Population dynamics of Vibrio spp. associated with marine sponge microcosms. . ISME J 4:, 1608–1612. [CrossRef] [PubMed]
    [Google Scholar]
  21. Hoffmann M. , Fischer M. , Whittaker P. . ( 2010b; ). Evaluating the use of fatty acid profiles to identify deep-sea Vibrio isolates. . Food Chem 122:, 943–950. [CrossRef]
    [Google Scholar]
  22. Hoffmann M. , Brown E. W. , Feng P. C. , Keys C. E. , Fischer M. , Monday S. R. . ( 2010c; ). PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species. . BMC Microbiol 10:, 90. [CrossRef] [PubMed]
    [Google Scholar]
  23. Huelsenbeck J. P. , Ronquist F. . ( 2001; ). mrbayes: Bayesian inference of phylogenetic trees. . Bioinformatics 17:, 754–755. [CrossRef] [PubMed]
    [Google Scholar]
  24. Hülsmann A. , Rosche T. M. , Kong I.-S. , Hassan H. M. , Beam D. M. , Oliver J. D. . ( 2003; ). RpoS-dependent stress response exoenzyme production in Vibrio vulnificus . . Appl Environ Microbiol 69:, 6114–6120. [CrossRef] [PubMed]
    [Google Scholar]
  25. Huß V. A. R. , Festl H. , Schleifer K. H. . ( 1983; ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4:, 184–192. [CrossRef]
    [Google Scholar]
  26. Katoh K. , Misawa K. , Kuma K. , Miyata T. . ( 2002; ). mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform. . Nucleic Acids Res 30:, 3059–3066. [CrossRef] [PubMed]
    [Google Scholar]
  27. Kilburn J. O. , O’Donnell K. F. , Silcox V. A. , David H. L. . ( 1973; ). Preparation of a stable mycobacterial tween hydrolysis test substrate. . Appl Microbiol 26:, 826.[PubMed]
    [Google Scholar]
  28. Konstantinidis K. T. , Tiedje J. M. . ( 2005; ). Genomic insights that advance the species definition for prokaryotes. . Proc Natl Acad Sci U S A 102:, 2567–2572. [CrossRef] [PubMed]
    [Google Scholar]
  29. Lecointre G. , Rachdi L. , Darlu P. , Denamur E. . ( 1998; ). Escherichia coli molecular phylogeny using the incongruence length difference test. . Mol Biol Evol 15:, 1685–1695. [CrossRef] [PubMed]
    [Google Scholar]
  30. Noguerola I. , Blanch A. R. . ( 2008; ). Identification of Vibrio spp. with a set of dichotomous keys. . J Appl Microbiol 105:, 175–185. [CrossRef] [PubMed]
    [Google Scholar]
  31. Oliver J. D. , Wear J. E. , Thomas M. B. , Warner M. , Linder K. . ( 1986; ). Production of extracellular enzymes and cytotoxicity by Vibrio vulnificus . . Diagn Microbiol Infect Dis 5:, 99–111. [CrossRef] [PubMed]
    [Google Scholar]
  32. Olson J. B. , Harmody D. K. , Bej A. K. , McCarthy P. J. . ( 2007; ). Tsukamurella spongiae sp. nov., a novel actinomycete isolated from a deep-water marine sponge. . Int J Syst Evol Microbiol 57:, 1478–1481. [CrossRef] [PubMed]
    [Google Scholar]
  33. Patel P. H. , Loeb L. A. . ( 2000; ). DNA polymerase active site is highly mutable: evolutionary consequences. . Proc Natl Acad Sci U S A 97:, 5095–5100. [CrossRef] [PubMed]
    [Google Scholar]
  34. Sawabe T. , Kita-Tsukamoto K. , Thompson F. L. . ( 2007; ). Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. . J Bacteriol 189:, 7932–7936. [CrossRef] [PubMed]
    [Google Scholar]
  35. Sfanos K. , Harmody D. , Dang P. , Ledger A. , Pomponi S. , McCarthy P. , Lopez J. . ( 2005; ). A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates. . Syst Appl Microbiol 28:, 242–264. [CrossRef] [PubMed]
    [Google Scholar]
  36. Snedecor G. W. , Cochran W. G. . ( 1980; ). Statistical Methods, , 7th edn.. Ames, IA:: Iowa State University Press;.
    [Google Scholar]
  37. Sullivan J. , Markert J. A. , Kilpatrick C. W. . ( 1997; ). Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. . Syst Biol 46:, 426–440. [CrossRef] [PubMed]
    [Google Scholar]
  38. Swofford D. L. . ( 2002; ). paup*: Phylogenetic analysis using parsimony (and other methods), version 4. . Sunderland, MA:: Sinauer Associates;.
  39. Swofford D. L. , Olsen G. J. , Wadell P. J. , Hillis D. M. . ( 1996; ). Phylogenetic Inference Molecular Systematics, , 2nd edn.. Sunderland, MA:: Sinauer Associates;.
    [Google Scholar]
  40. Tamura K. , Dudley J. , Nei M. , Kumar S. . ( 2007; ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24:, 1596–1599. [CrossRef] [PubMed]
    [Google Scholar]
  41. Taylor M. W. , Radax R. , Steger D. , Wagner M. . ( 2007; ). Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. . Microbiol Mol Biol Rev 71:, 295–347. [CrossRef] [PubMed]
    [Google Scholar]
  42. Thompson F. L. , Iida T. , Swings J. . ( 2004; ). Biodiversity of vibrios. . Microbiol Mol Biol Rev 68:, 403–431. [CrossRef] [PubMed]
    [Google Scholar]
  43. Thompson F. L. , Gevers D. , Thompson C. C. , Dawyndt P. , Naser S. , Hoste B. , Munn C. B. , Swings J. . ( 2005; ). Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. . Appl Environ Microbiol 71:, 5107–5115. [CrossRef] [PubMed]
    [Google Scholar]
  44. Thompson C. C. , Vicente A. C. , Souza R. C. , Vasconcelos A. T. , Vesth T. , Alves N. Jr , Ussery D. W. , Iida T. , Thompson F. L. . ( 2009; ). Genomic taxonomy of vibrios. . BMC Evol Biol 9:, 258. [CrossRef] [PubMed]
    [Google Scholar]
  45. Van Soest R. W. M. , Boury-Esnault N. , Hooper J. N. A. , Rützler K. , de Voogd N. J. , Alvarez de Glasby B. , Hajdu E. , Pisera A. B. , Manconi R. , . & other authors ( 2008; ). World Porifera database. Accessed 9 October 2010. http://www.marinespecies.org/porifera
  46. Wayne L. G. , Brenner D. J. , Colwell R. R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. . & other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  47. Yoon B. J. , You H. S. , Lee D. H. , Oh D. C. . ( 2011; ). Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro . . Int J Syst Evol Microbiol 61:, 417–421. [CrossRef] [PubMed]
    [Google Scholar]
  48. Zwickl D. . (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis, University of Texas, Austin, TX, USA.
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