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Volume 66, Issue 8

sp. nov. and sp. nov., isolated from reared clams () Free

Abstract

Three Gram-negative bacterial strains (Cmf 17.2, Rd 20.33 and Cmf 18.22) isolated from reared clams in Galicia were subjected to a taxonomic study, based on genetic and phenotypic characterization. Analysis of the 16S rRNA gene allowed the identification of the strains as members of the genus , sharing the highest similarity with CECT 5080 (97.8 %–98.5 % 16S rRNA gene sequence similarity). Phylogenetic analysis of the sequences showed that the three isolates formed two different groups distantly related to their closest relative, . DNA–DNA hybridizations were performed to confirm the taxonomic position and the results were below the recommended threshold for species delimitation, specifically 44.5 % (Cmf 17.2 with CECT 5080) and 55 % (Cmf 18.22with CECT 5080). Furthermore, the average nucleotide identity (ANIb, ANIm and OrthoANI) and estimated DNA–DNA reassociation values among Cmf 17.2, Cmf 18.22 and CECT 5080 were in all cases below the respective threshold for species differentiation. The estimated G+C content of the genomic DNA was found to be 45.3 % (Cmf 17.2) and 44.6 % (Cmf 18.22). The principal fatty acids of the strains were found to be summed feature 3 (C ω7/Cω6), summed feature 8 (Cω7/Cω6), C, C and C 3-OH. The results obtained on the characterization of the clam isolates indicate that they represent two novel species of the genus , for which the names sp. nov. (type strain Cmf 17.2=CECT 9049=LMG 29243) and sp. nov. (type strain Cmf 18.22=CECT 9050=LMG 29244) are proposed.

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Keyword(s): Marinomonas atlanticasp. nov. , Marinomonas gallaicasp. nov. , Oceanospirillaceae and reared clams
© 2016 IUMS
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2016-08-01
2024-04-19
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References

  1. Auch A. F., von Jan M., Klenk H.-P., Göker M. 2010a; Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134 [View Article]
     [Google Scholar]
  2. Auch A. F., Klenk H.-P., Göker M. 2010b; Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2:142–148 [View Article]
     [Google Scholar]
  3. Baumann P., Baumann L. 1981; The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes . In The Prokaryotes pp. 1302–1331 Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schleger H. G. Berlin, Germany: Springer-Verlag;
     [Google Scholar]
  4. Bolger A. M., Lohse M., Usadel B. 2014; Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120 [View Article][PubMed]
     [Google Scholar]
  5. Chimetto L. A., Cleenwerck I., Brocchi M., Willems A., De Vos P., Thompson F. L. 2011; Marinomonas brasilensis sp. nov., isolated from the coral Mussismilia hispida, and reclassification of Marinomonas basaltis as a later heterotypic synonym of Marinomonas communis . Int J Syst Evol 61:1170–1175 [CrossRef]
     [Google Scholar]
  6. Espinosa E., Marco-Noales E., Gómez D., Lucas-Elío P., Ordax M., Garcías-Bonet N., Duarte C. M., Sanchez-Amat A. 2010; Taxonomic study of Marinomonas strains isolated from the seagrass Posidonia oceanica, with descriptions of Marinomonas balearica sp. nov. and Marinomonas pollencensis sp. nov. Int J Syst Evol Microbiol 60:93–98 [View Article][PubMed]
     [Google Scholar]
  7. Goris J., Suzuki K., de Vos P., Nakase T., Kersters K. 1998; Evaluation of a microplate DNA–DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:1148–1153 [CrossRef]
     [Google Scholar]
  8. Ivanova E. P., Onyshchenko O. M., Christen R., Lysenko A. M., Zhukova N. V., Shevchenko L. S., Kiprianova E. A. 2005; Marinomonas pontica sp. nov., isolated from the Black Sea. Int J Syst Evol Microbiol 55:275–279 [View Article][PubMed]
     [Google Scholar]
  9. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
     [Google Scholar]
  10. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. 2007; clustal w and clustal x version 2.0. Bioinformatics 23:2947–2948 [View Article][PubMed]
     [Google Scholar]
  11. Lee I., Kim Y. W., Park S. C., Chun J. 2015; OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol in press doi: [View Article]
     [Google Scholar]
  12. Macián M. C., Arahal D. R., Garay E., Pujalte M. J. 2005; Marinomonas aquamarina sp. nov., isolated from oysters and seawater. Syst Appl Microbiol 28:145–150 [View Article][PubMed]
     [Google Scholar]
  13. MacFaddin J. F. 1993; Pruebas bioquímicas para la identificación de bacterias de importancia clínica (translation by Médica Panamericana SA). Baltimore: Williams & Wilkins (in Spanish);
  14. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60 [View Article][PubMed]
     [Google Scholar]
  15. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelsky A., Pyshkin A., Sirotkin A. et al. 2013; Assembling genomes and Mmni-metagenomes from highly chimeric reads. Lect N Bioinformat 7821:158–170
     [Google Scholar]
  16. Richter M., Rosselló-Móra R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  17. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc;
     [Google Scholar]
  18. Solano F., Sanchez-Amat A. 1999; Studies on the phylogenetic relationships of melanogenic marine bacteria: proposal of Marinomonas mediterranea sp. nov. Int J Syst Bacteriol 49:1241–1246 [View Article][PubMed]
     [Google Scholar]
  19. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  20. Van Landschoot A., De Ley J. 1983; Intra- and Intergeneric Similarities of the rRNA Cistrons of Alteromonas, Marinomonas (gen. nov.) and Some Other Gram-negative Bacteria. J Gen Microbiol 129:3057–3074 [View Article]
     [Google Scholar]
  21. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K.-H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article][PubMed]
     [Google Scholar]
  22. Yarza P., Yilmaz P., Pruesse E., Glöckner F. O., Ludwig W., Schleifer K.-H., Whitman W. B., Euzéby J., Amann R. et al. 2014; Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645 [View Article]
     [Google Scholar]
  23. Zhang D. C., Li H. R., Xin Y. H., Liu H. C., Chen B., Chi Z. M., Zhou P. J., Yu Y. 2008; Marinomonas arctica sp. nov., a psychrotolerant bacterium isolated from the Arctic. Int J Syst Evol Microbiol 58:1715–1718 [View Article][PubMed]
     [Google Scholar]
  24. Ziemke F., Höfle M. G., Lalucat J., Rosselló-Mora R. 1998; Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48:179–186 [View Article][PubMed]
     [Google Scholar]
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Marinomonas gallaica sp. nov. and Marinomonas atlantica sp. nov., isolated from reared clams (Ruditapes decussatus)
Int J Syst Evol Microbiol 66, 3183 (2016); https://doi.org/10.1099/ijsem.0.001170
/content/journal/ijsem/10.1099/ijsem.0.001170
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