1887

Abstract

Strain S658 was isolated from a nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and gene showed that this strain clustered within the genus The closest related species was, in both cases, PETP02 with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658 differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S658( = LMG 27289 = CECT 8230).

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2014-03-01
2019-10-22
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References

  1. Altschul S. F. , Gish W. , Miller W. , Myers E. W. , Lipman D. J. . ( 1990; ). Basic local alignment search tool. . J Mol Biol 215:, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Chun J. , Goodfellow M. . ( 1995; ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. . Int J Syst Bacteriol 45:, 240–245. [CrossRef] [PubMed]
    [Google Scholar]
  3. Díaz P. , Borsani O. , Monza J. . ( 2005; ). Lotus-related species and their agronomic importance. . In Lotus japonicus Handbook. pp. 25–37. Edited by Márquez A. J. , Stougaard J. , Udvardi M. , Parniske M. , Spaink H. , Saalbach G. , Webb J. , Chiurazzi M. . . Dordrecht:: Springer;. [CrossRef]
    [Google Scholar]
  4. Doetsch R. N. . ( 1981; ). Determinative methods of light microscopy. . In Manual of Methods for General Bacteriology, pp. 21–33. Edited by Gerdhardt P. , Murray R. G. E. , Costilow R. N. , Nester E. W. , Wood W. A. , Krieg N. R. , Phillips G. B. . . Washington:: American Society for Microbiology;.
    [Google Scholar]
  5. Ezaki T. , Hashimoto Y. , Yabuuchi E. . ( 1989; ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39:, 224–229. [CrossRef]
    [Google Scholar]
  6. Flores-Félix J. D. , Carro L. , Velázquez E. , Valverde A. , Cerda-Castillo E. , García-Fraile P. , Rivas R. . ( 2013; ). Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris . . Int J Syst Evol Microbiol 63:, 821–826. [CrossRef] [PubMed]
    [Google Scholar]
  7. Jurado V. , Laíz L. , González J. M. , Hernández-Marine M. , Valens M. , Saiz-Jimenez C. . ( 2005; ). Phyllobacterium catacumbae sp. nov., a member of the order ‘Rhizobiales’ isolated from Roman catacombs. . Int J Syst Evol Microbiol 55:, 1487–1490. [CrossRef] [PubMed]
    [Google Scholar]
  8. Kim O. S. , Cho Y. J. , Lee K. , Yoon S. H. , Kim M. , Na H. , Park S. C. , Jeon Y. S. , Lee J. H. . & other authors ( 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. [CrossRef] [PubMed]
    [Google Scholar]
  9. Kimura M. . ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef] [PubMed]
    [Google Scholar]
  10. Knösel D. H. . ( 1962; ). Prufung von Bakterien auf Fahigkeit zur Sternbildung. . Zentralbl Bakteriol Parasirtenkd Infektionskr Hyg II Abt 116:, 79–100.
    [Google Scholar]
  11. Knösel D. H. . ( 1984; ). Genus IV. Phyllobacterium (ex Knösel 1962) nom. rev.. In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 254–256. Edited by Krieg N. R. , Holt J. G. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  12. Laguerre G. , Nour S. M. , Macheret V. , Sanjuan J. , Drouin P. , Amarger N. . ( 2001; ). Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. . Microbiology 147:, 981–993.[PubMed]
    [Google Scholar]
  13. Mandel M. , Marmur J. . ( 1968; ). Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12B:, 195–206. [CrossRef]
    [Google Scholar]
  14. Mantelin S. , Saux M. F. , Zakhia F. , Béna G. , Bonneau S. , Jeder H. , de Lajudie P. , Cleyet-Marel J. C. . ( 2006; ). Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov.. Int J Syst Evol Microbiol 56:, 827–839. [CrossRef] [PubMed]
    [Google Scholar]
  15. Mergaert J. , Swings J. . ( 2005; ). Genus I. Phyllobacterium . . In The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2, pp. 394–396. Edited by Brenner D. J. , Krieg N. R. , Staley J. T. , Garrity G. M. . . New York:: Springer;. [CrossRef]
    [Google Scholar]
  16. Mergaert J. , Cnockaert M. C. , Swings J. . ( 2002; ). Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend. . Int J Syst Evol Microbiol 52:, 1821–1823. [CrossRef] [PubMed]
    [Google Scholar]
  17. Rivas R. , García-Fraile P. , Mateos P. F. , Martínez-Molina E. , Velázquez E. . ( 2007; ). Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera . . Lett Appl Microbiol 44:, 181–187. [CrossRef] [PubMed]
    [Google Scholar]
  18. Rogers J. S. , Swofford D. L. . ( 1998; ). A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. . Syst Biol 47:, 77–89. [CrossRef] [PubMed]
    [Google Scholar]
  19. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  20. Sasser M. . ( 1990; ). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
  21. Sotelo M. , Irisarri P. , Lorite M. J. , Casaretto E. , Rebuffo M. , Sanjuán J. , Monza J. . ( 2011; ). Diversity of rhizobia nodulating Lotus corniculatus grown in northern and southern regions of Uruguay. . Appl Soil Ecol 49:, 197–207. [CrossRef]
    [Google Scholar]
  22. 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. [CrossRef] [PubMed]
    [Google Scholar]
  23. Thompson J. D. , Gibson T. J. , Plewniak F. , Jeanmougin F. , Higgins D. G. . ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25:, 4876–4882. [CrossRef] [PubMed]
    [Google Scholar]
  24. Valverde A. , Velázquez E. , Fernández-Santos F. , Vizcaíno N. , Rivas R. , Mateos P. F. , Martínez-Molina E. , Igual J. M. , Willems A. . ( 2005; ). Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. . Int J Syst Evol Microbiol 55:, 1985–1989. [CrossRef] [PubMed]
    [Google Scholar]
  25. Vincent J. M. . ( 1970; ). The cultivation, isolation and maintenance of rhizobia. . In A Manual for the Practical Study of Root-Nodule, pp. 1–13. Edited by Vincent J. M. . . Oxford:: Blackwell Scientific Publications;.
    [Google Scholar]
  26. 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]
  27. Weir B. S. , Turner S. J. , Silvester W. B. , Park D. C. , Young J. M. . ( 2004; ). Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species. . Appl Environ Microbiol 70:, 5980–5987. [CrossRef] [PubMed]
    [Google Scholar]
  28. Willems A. , Doignon-Bourcier F. , Goris J. , Coopman R. , de Lajudie P. , De Vos P. , Gillis M. . ( 2001; ). DNA–DNA hybridization study of Bradyrhizobium strains. . Int J Syst Evol Microbiol 51:, 1315–1322.[PubMed]
    [Google Scholar]
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