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Abstract

During a study on biodiversity of bacteria inhabiting rhizospheric soil of rockrose ( L.), we isolated a strain coded RD25 in a soil from Northern Spain. The 16S rRNA gene sequence showed 99.5 % identity with respect to the closest related species DSM15294, and 99.4 % with respect to WS4672. The following related species showed 99.3 % or less identity, and therefore RD25 was classified within genus . The phylogenetic analysis of 16S rRNA and the housekeeping genes , and suggested that this strain could be a novel species. The strain RD25 has several polar-subpolar flagella. It can grow at 36 °C, at 0–6 % NaCl concentration and a range of pH 5–9. Positive for arginine dihydrolase and urease production, and negative for reduction of nitrate. The strain is catalase and oxidase positive. Major fatty acids are C ω7 / C ω6 in summed feature 3, C, and C ω7 / C ω6 in summed feature 8. The respiratory ubiquinone is Q9. The DNA G+C content was 59.9 mol%. The digital DNA–DNA hybridisation average values (dDDH) ranged between 30–61.2 % relatedness and the ANIb values ranged between 93.9–80.5 % with respect to the type strains of the closely related species. Therefore, the genotypic, genomic, phenotypic and chemotaxonomic data support the classification of strain RD25 as a novel species of genus , for which the name sp. nov. is proposed. The type strain is RD25 (=LMG 30152=CECT 9373).

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2019-10-01
2019-10-21
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References

  1. Peix A, Ramírez-Bahena MH, Velázquez E. Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect Genet Evol 2009;9:1132–1147 [CrossRef][PubMed]
    [Google Scholar]
  2. Peix A, Ramírez-Bahena MH, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: an update. Infect Genet Evol 2018;57:106–116 [CrossRef][PubMed]
    [Google Scholar]
  3. Doetsch RN. Determinative methods of light microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. (editors) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981; pp.21–33
    [Google Scholar]
  4. Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E. Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera. Lett Appl Microbiol 2007;44:181–187 [CrossRef][PubMed]
    [Google Scholar]
  5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403–410 [CrossRef][PubMed]
    [Google Scholar]
  6. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  7. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  10. Rogers JS, Swofford DL. A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst Biol 1998;47:77–89 [CrossRef][PubMed]
    [Google Scholar]
  11. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  12. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821–829 [CrossRef][PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Baïda N, Yazourh A, Singer E, Izard D. Pseudomonas brenneri sp. nov., a new species isolated from natural mineral waters. Res Microbiol 2001;152:493–502 [CrossRef][PubMed]
    [Google Scholar]
  16. von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M et al. Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk. Int J Syst Evol Microbiol 2017;67:1656–1664 [CrossRef][PubMed]
    [Google Scholar]
  17. Iizuka H, Komagata K. New species of Pseudomonas belonged to fluorescent group (Studies on the microorganisms of cereal grains. J Agric Chem Soc Jpn 1963;37:137–141
    [Google Scholar]
  18. Behrendt U, Ulrich A, Schumann P. Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov. Int J Syst Evol Microbiol 2003;53:1461–1469 [CrossRef][PubMed]
    [Google Scholar]
  19. Reddy GS, Matsumoto GI, Schumann P, Stackebrandt E, Shivaji S. Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov. Int J Syst Evol Microbiol 2004;54:713–719 [CrossRef][PubMed]
    [Google Scholar]
  20. Tambong JT, Xu R, Bromfield ESP. Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization. Int J Syst Evol Microbiol 2017;67:889–895 [CrossRef][PubMed]
    [Google Scholar]
  21. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010;12:1513–1530 [CrossRef][PubMed]
    [Google Scholar]
  22. Ait Tayeb L, Ageron E, Grimont F, Grimont PA. Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 2005;156:763–773 [CrossRef][PubMed]
    [Google Scholar]
  23. García-Valdés E, Lalucat J. In Kahlon RS. (editor) Pseudomonas: Molecular Phylogeny and Current Taxonomy Pseudomonas: Molecular and Applied Biology Switzerland: Springer International Publishing; 2016; pp.1–23
    [Google Scholar]
  24. Ramírez-Bahena MH, Cuesta MJ, Tejedor C, Igual JM, Fernández-Pascual M et al. Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain. Int J Syst Evol Microbiol 2015;65:2110–2117 [CrossRef][PubMed]
    [Google Scholar]
  25. 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][PubMed]
    [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  27. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  28. Palleroni NJ. Pseudomonas. Bergey's manual of systematics of archaea and bacteria. 1. Migula 1894, 237AL (Nom. Cons., Opin. 5 of the Jud. Comm. 1952, 121). Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust. 2015
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  30. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
    [Google Scholar]
  31. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986;123:31–36 [CrossRef][PubMed]
    [Google Scholar]
  32. Collins MD. Analysis of isoprenoid quinones. In Gottschalk G. (editor) Methods in Microbiologyvol. 18 London: Academic Press; 1981; pp.329–366
    [Google Scholar]
  33. Peix A, Berge O, Rivas R, Abril A, Velázquez E. Pseudomonas argentinensis sp. nov., a novel yellow pigment-producing bacterial species, isolated from rhizospheric soil in Cordoba, Argentina. Int J Syst Evol Microbiol 2005;55:1107–1112 [CrossRef][PubMed]
    [Google Scholar]
  34. Xiao YP, Hui W, Wang Q, Roh SW, Shi XQ et al. Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. Int J Syst Evol Microbiol 2009;59:2594–2598 [CrossRef][PubMed]
    [Google Scholar]
  35. Palleroni NJ, Genus I. Pseudomonas Migula 1894, 237AL (Nom. Cons., Opin. 5 of the Jud. Comm. 1952, 121). In Boone DR, Brenner DJ, Castenholz RW, Garrity GM, Krieg NR et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 2 New York: Springer; pp.323–379
    [Google Scholar]
  36. Clark LL, Dajcs JJ, Mclean CH, Bartell JG, Stroman DW. Pseudomonas otitidis sp. nov., isolated from patients with otic infections. Int J Syst Evol Microbiol 2006;56:709–714 [CrossRef][PubMed]
    [Google Scholar]
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