1887

Abstract

Strain CECT 5091, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria , in the family Rhodobacteraceae , with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae , Ruegeria atlantica and Ruegeria arenilitoris , respectively. Average nucleotide identities (ANI) and in silico DNA–DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091 with those of the type strains of 12 species of the genus Ruegeria : the values obtained were always below the thresholds (95–96 % ANI, 70 % in silico DDH) used to define genomic species, proving that CECT 5091 represents a novel species of the genus Ruegeria . The strain was slightly halophilic and mesophilic, with optimum growth at 26 °C, pH 7.0 and 3 % salinity, it required sodium and magnesium ions for growth and was able to reduce nitrate to dinitrogen. Carbon sources for growth include some carbohydrates (d-ribose, d-glucose, l-rhamnose, N-acetyl-d-glucosamine) and multiple organic acids and amino acids. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), representing 70 % of the total fatty acids. Carbon monoxide oxidation, cyanophycin synthetic ability and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine production are predicted from genome annotation, while bacteriochlorophyll a production was absent. The DNA G+C content of the genome was 56.7 mol%. We propose the name Ruegeria denitrificans sp. nov. and strain CECT 5091 (=5OM10=LMG 29896) as the type strain for the novel species.

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2018-06-26
2020-05-29
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References

  1. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC et al. The family Rhodobacteraceae. In Rosenberg E, DeLong EF, Stackebrandt E, Lory S, Thompson F et al. (editors) The Prokaryotes—Alphaproteobacteria and Betaproteobacteria, 4th ed. Berlin, Germany: Springer Verlag; 2014; pp.439–512
    [Google Scholar]
  2. Rüger HJ, Höfle MG. Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev. Int J Syst Bacteriol 1992;42:133–143 [CrossRef][PubMed]
    [Google Scholar]
  3. Uchino Y, Hirata A, Yokota A, Sugiyama J. Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 1998;44:201–210 [CrossRef][PubMed]
    [Google Scholar]
  4. Yi H, Lim YW, Chun J. Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int J Syst Evol Microbiol 2007;57:815–819 [CrossRef][PubMed]
    [Google Scholar]
  5. Muramatsu Y, Uchino Y, Kasai H, Suzuki K, Nakagawa Y. Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int J Syst Evol Microbiol 2007;57:1304–1309 [CrossRef][PubMed]
    [Google Scholar]
  6. Vandecandelaere I, Nercessian O, Segaert E, Achouak W, Faimali M et al. Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm. Int J Syst Evol Microbiol 2008;58:2726–2733 [CrossRef][PubMed]
    [Google Scholar]
  7. Huo YY, Xu XW, Li X, Liu C, Cui HL et al. Ruegeria marina sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011;61:347–350 [CrossRef][PubMed]
    [Google Scholar]
  8. Oh KH, Jung YT, Oh TK, Yoon JH. Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2011;61:1182–1188 [CrossRef][PubMed]
    [Google Scholar]
  9. Kim YO, Park S, Nam BH, Kang SJ, Hur YB et al. Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi. Int J Syst Evol Microbiol 2012;62:925–930 [CrossRef][PubMed]
    [Google Scholar]
  10. Park S, Yoon JH. Ruegeria arenilitoris sp. nov., isolated from the seashore sand around a seaweed farm. Antonie van Leeuwenhoek 2012;102:581–589 [CrossRef][PubMed]
    [Google Scholar]
  11. Lee J, Whon TW, Shin NR, Roh SW, Kim J et al. Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii. Int J Syst Evol Microbiol 2012;62:2851–2857 [CrossRef][PubMed]
    [Google Scholar]
  12. Kämpfer P, Arun AB, Rekha PD, Busse HJ, Young CC et al. Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. Int J Syst Evol Microbiol 2013;63:2538–2544 [CrossRef][PubMed]
    [Google Scholar]
  13. Kim YO, Park S, Nam BH, Jung YT, Kim DG et al. Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi. Antonie van Leeuwenhoek 2014;105:551–558 [CrossRef][PubMed]
    [Google Scholar]
  14. Zhang G, Haroon MF, Zhang R, Dong X, Wang D et al. Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea. Int J Syst Evol Microbiol 2017;67:4624–4631 [CrossRef][PubMed]
    [Google Scholar]
  15. Ortigosa M, Garay E, Pujalte MJ. Numerical taxonomy of aerobic, Gram-negative bacteria associated with oysters and surrounding seawater of the Mediterranean Coast. Syst Appl Microbiol 1994;17:216–225
    [Google Scholar]
  16. Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DR. Comparative genomics of Thalassobius including the description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. Front Microbiol 2018;8:2645 [CrossRef][PubMed]
    [Google Scholar]
  17. Spiekermann P, Rehm BH, Kalscheuer R, Baumeister D, Steinbüchel A. A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 1999;171:73–80 [CrossRef][PubMed]
    [Google Scholar]
  18. Farmer III JJ, Hickman-Brenner FW. The genera Vibrio and Photobacterium. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) The Prokaryotes, 3rd ed. New York: Springer; 2006; pp.508–563
    [Google Scholar]
  19. Baumann P, Baumann L. The marine gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas and Alcaligenes. In Starr MP, Stolp H, Trueper HG, Balows A, Schleger H et al. (editors) The Prokaryotesvol. 2 Berlin & Heidelberg: Springer; 1981; pp.1302–1331
    [Google Scholar]
  20. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: DE: MIDI Inc; 1990
    [Google Scholar]
  21. MIDI Sherlock Microbial Identification System Operating Manual, version 6.1 Newark, DE: MIDI Inc; 2008
    [Google Scholar]
  22. Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N et al. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics 2014;30:1928–1929 [CrossRef][PubMed]
    [Google Scholar]
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  24. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25:1043–1055 [CrossRef][PubMed]
    [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. 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][PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  31. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  32. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:281–285 [CrossRef][PubMed]
    [Google Scholar]
  33. 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 [CrossRef][PubMed]
    [Google Scholar]
  34. Arahal DR, Sánchez E, Macián MC, Garay E. Value of recN sequences for species identification and as a phylogenetic marker within the family "Leuconostocaceae". Int Microbiol 2008;11:33–39[PubMed]
    [Google Scholar]
  35. Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH et al. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010;33:291–299 [CrossRef][PubMed]
    [Google Scholar]
  36. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004;32:1363–1371 [CrossRef][PubMed]
    [Google Scholar]
  37. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ et al. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera. Int J Syst Evol Microbiol 2006;56:1293–1304 [CrossRef][PubMed]
    [Google Scholar]
  38. Füser G, Steinbüchel A. Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes. Macromol Biosci 2007;7:278–296 [CrossRef][PubMed]
    [Google Scholar]
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