1887

Abstract

Three isolates obtained from symptomatic nectarine trees ( var. ) cultivated in Murcia, Spain, which showed yellow and mucoid colonies similar to pv. , were negative after serological and real-time PCR analyses for this pathogen. For that reason, these isolates were characterized following a polyphasic approach that included both phenotypic and genomic methods. By sequence analysis of the 16S rRNA gene, these novel strains were identified as members of the genus and by multilocus sequence analysis (MLSA) they were clustered together in a distinct group that showed similarity values below 95 % with the rest of the species of this genus. Whole-genome comparisons of the average nucleotide identity (ANI) of genomes of the strains showed less than 91 % average nucleotide identity with all other species of the genus . Additionally, phenotypic characterization based on API 20 NE, API 50 CH and BIOLOG tests differentiated the strains from the species of the genus described previously. Moreover, the three strains were confirmed to be pathogenic on peach (), causing necrotic lesions on leaves. On the basis of these results, the novel strains represent a novel species of the genus , for which the name is proposed. The type strain is CFBP 8353 (=CECT 9404=IVIA 3287.1).

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2018-06-01
2019-12-14
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References

  1. Jacques MA, Arlat M, Boulanger A, Boureau T, Carrère S et al. Using ecology, physiology, and genomics to understand host specificity in Xanthomonas. Annu Rev Phytopathol 2016;54:163–187 [CrossRef][PubMed]
    [Google Scholar]
  2. Burkholder WH, Starr MP. The generic and specific characters of phytopathogenic species of Pseudomonas and Xanthomonas. Phytopathology 1948;38:494–502
    [Google Scholar]
  3. Vauterin L, Rademaker J, Swings J. Synopsis on the taxonomy of the genus Xanthomonas. Phytopathology 2000;90:677–682 [CrossRef][PubMed]
    [Google Scholar]
  4. Dye DW, Lelliott RA. Genus II. Xanthomonas. In Buchanan RE, Gibbons NE. (editors) Bergey’s Manual of Determinative Bacteriology, 8th ed. Baltimore, MD: Williams and Wilkins; 1974; pp.243–249
    [Google Scholar]
  5. Young JM, Dye DW, Bradbury JF, Panagopoulos CG, Robbs CF. A proposed nomenclature and classification for plant pathogenic bacteria. New Z J Agric Res 1978;21:153–177 [CrossRef]
    [Google Scholar]
  6. Dye DW, Bradbury JF, Goto M, Hayward AC, Lelliott RA et al. International standards for naming pathovars of phytopathogenic bacteria and a list of pathovar names and pathotypes. Rev Pl Pathol 1980;59:153–168
    [Google Scholar]
  7. 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]
  8. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002;52:1043–1047 [CrossRef][PubMed]
    [Google Scholar]
  9. Van den Mooter M, Swings J. Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Bacteriol 1990;40:348–369 [CrossRef][PubMed]
    [Google Scholar]
  10. Berthier Y, Verdier V, Guesdon JL, Chevrier D, Denis JB et al. Characterization of Xanthomonas campestris pathovars by rRNA gene restriction patterns. Appl Environ Microbiol 1993;59:851–859[PubMed]
    [Google Scholar]
  11. Yang P, Vauterin L, Vancanneyt M, Swings J, Kersters K. Application of fatty acid methyl esters for the taxonomic analysis of the genus Xanthomonas. Syst Appl Microbiol 1993;16:47–71 [CrossRef]
    [Google Scholar]
  12. Vauterin L, Swings J, Kersters K. Grouping of Xanthomonas campestris pathovars by SDS-PAGE of proteins. J Gen Microbiol 1991;137:1677–1687 [CrossRef]
    [Google Scholar]
  13. Lazo GR, Gabriel DW. Conservation of plasmid DNA sequences and pathovar identification of strains of Xanthomonas campestris. Phytopathology 1987;77:448–453 [CrossRef]
    [Google Scholar]
  14. Rademaker JL, Hoste B, Louws FJ, Kersters K, Swings J et al. Comparison of AFLP and rep-PCR genomic fingerprinting with DNA–DNA homology studies: Xanthomonas as a model system. Int J Syst Evol Microbiol 2000;50:665–677 [CrossRef][PubMed]
    [Google Scholar]
  15. Vauterin L, Hoste B, Kersters K, Swings J. Reclassification of Xanthomonas. Int J Syst Bacteriol 1995;45:472–489 [CrossRef]
    [Google Scholar]
  16. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846–849 [CrossRef]
    [Google Scholar]
  17. 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]
  18. Young JM, Park DC, Shearman HM, Fargier E. A multilocus sequence analysis of the genus Xanthomonas. Syst Appl Microbiol 2008;31:366–377 [CrossRef][PubMed]
    [Google Scholar]
  19. 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]
  20. Trébaol G, Gardan L, Manceau C, Tanguy JL, Tirilly Y et al. Genomic and phenotypic characterization of Xanthomonas cynarae sp. nov., a new species that causes bacterial bract spot of artichoke (Cynara scolymus L.). Int J Syst Evol Microbiol 2000;50:1471–1478 [CrossRef][PubMed]
    [Google Scholar]
  21. Jones JB, Lacy GH, Bouzar H, Stall RE, Schaad NW. Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 2004;27:755–762 [CrossRef][PubMed]
    [Google Scholar]
  22. Schaad NW, Postnikova E, Lacey GH, Sechler A, Agarkova I et al. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2007;57:893–897[Crossref]
    [Google Scholar]
  23. Young JM, Wilkie JP, Park D-C, Watson DRW. New Zealand strains of plant pathogenic bacteria classified by multi-locus sequence analysis; proposal of Xanthomonas dyei sp. nov. Plant Pathol 2010;59:270–281 [CrossRef]
    [Google Scholar]
  24. Triplett LR, Verdier V, Campillo T, van Malderghem C, Cleenwerck I et al. Characterization of a novel clade of Xanthomonas isolated from rice leaves in Mali and proposal of Xanthomonas maliensis sp. nov. Antonie van Leeuwenhoek 2015;107:869–881 [CrossRef][PubMed]
    [Google Scholar]
  25. Vicente JG, Rothwell S, Holub EB, Studholme DJ. Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. Int J Syst Evol Microbiol 2017;67:3645–3654 [CrossRef][PubMed]
    [Google Scholar]
  26. Randhawa PS. A detached-leaf bioassay for Xanthomonas campestris pv. pruni. Phytopathology 1985;75:1060–1063 [CrossRef]
    [Google Scholar]
  27. Schaad NW, Stall RE. Xanthomonas. In Schaad NW. (editor) Laboratory Guide For identification of Plant Pathogenic Bacteria, 2nd ed. St. Paul, MN: APS Press; 1988; pp.81–91
    [Google Scholar]
  28. European and Mediterranean Plant Protection Organization (EPPO) Standards PM 7/64. Diagnostics Xanthomonas arboricola pv. pruni. EPPO Bulletin 2006;36:129–133[Crossref]
    [Google Scholar]
  29. López-Soriano P, Noguera P, Gorris MT, Puchades R, Maquieira Á et al. Lateral flow immunoassay for on-site detection of Xanthomonas arboricola pv. pruni in symptomatic field samples. PLoS One 2017;12:e0176201 [CrossRef][PubMed]
    [Google Scholar]
  30. Llop P, Caruso P, Cubero J, Morente C, López MM. A simple extraction procedure for efficient routine detection of pathogenic bacteria in plant material by polymerase chain reaction. J Microbiol Methods 1999;37:23–31 [CrossRef][PubMed]
    [Google Scholar]
  31. Palacio-Bielsa A, Cubero J, Cambra MA, Collados R, Berruete IM et al. Development of an efficient real-time quantitative PCR protocol for detection of Xanthomonas arboricola pv. pruni in Prunus species. Appl Environ Microbiol 2011;77:89–97 [CrossRef][PubMed]
    [Google Scholar]
  32. Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J. Pan-genomic analysis permits differentiation of virulent and non-virulent strains of Xanthomonas arboricola that cohabit Prunus spp. and elucidate bacterial virulence factors. Front Microbiol 2017;8:573 [CrossRef][PubMed]
    [Google Scholar]
  33. 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]
  34. Merda D, Briand M, Bosis E, Rousseau C, Portier P et al. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens. Mol Ecol 2017;26:5939–5952 [CrossRef][PubMed]
    [Google Scholar]
  35. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  36. Hall T. BioEdit: an important software for molecular biology. GERF Bull Biosci 2011;2:60–61
    [Google Scholar]
  37. Goujon M, McWilliam H, Li W, Valentin F, Squizzato S et al. A new bioinformatics analysis tools framework at EMBL–EBI. Nucleic Acids Res 2010;38:W695–W699 [CrossRef][PubMed]
    [Google Scholar]
  38. Posada D, Buckley TR. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 2004;53:793–808 [CrossRef][PubMed]
    [Google Scholar]
  39. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–272 [CrossRef][PubMed]
    [Google Scholar]
  40. 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]
  41. Sallet E, Gouzy J, Schiex T. EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes. Bioinformatics 2014;30:2659–2661 [CrossRef][PubMed]
    [Google Scholar]
  42. Roselló M, Peñalver J, Llop P, Gorris MT, Cambra M et al. Identification of an Erwinia sp. different from Erwinia amylovora and responsible for necrosis on pear blossoms. Can J Plant Pathol 2006;28:30–41 [CrossRef]
    [Google Scholar]
  43. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolf K, Sands DC. (editors) Methods in Phytobacteriology Budapest, Hungary: Akadémiai Kiadó; 1990; pp.199–204
    [Google Scholar]
  44. Saddler GS, Bradbury JF. Genus I. Xanthomonas Dowson 1939, 187AL emend. Vauterin, Hoste, Kersters and Swings, 483. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 2 part B New York, NY: Springer; 1995; pp.63–90
    [Google Scholar]
  45. Dye DW. A taxonomic study of the genus Erwinia.1. The “Amylovora” group. New Zeal J Sci 1968;11:590–607
    [Google Scholar]
  46. Verniere C, Pruvost O, Civerolo EL, Gambin O, Jacquemoud-Collet JP et al. Evaluation of the biolog substrate utilization system to identify and assess metabolic variation among strains of Xanthomonas campestris pv. citri. Appl Environ Microbiol 1993;59:243–249[PubMed]
    [Google Scholar]
  47. Garita-Cambronero J, Palacio-Bielsa A, López MM, Cubero J. Comparative genomic and phenotypic characterization of pathogenic and non-pathogenic strains of Xanthomonas arboricola reveals insights into the infection process of bacterial spot disease of stone fruits. PLoS One 2016;11:e0161977 [CrossRef][PubMed]
    [Google Scholar]
  48. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M et al. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 2007;8:460 [CrossRef][PubMed]
    [Google Scholar]
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