Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.


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Literature Cited

  1. Agrios GN. 1.  2005. Plant Pathology. Boston, MA: Academic, 5th ed.. [Google Scholar]
  2. Almeida NF, Yan S, Cai R, Clarke CR, Morris CE. 2.  et al. 2010. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 100:208–15 [Google Scholar]
  3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 3.  1990. Basic local alignment search tool. J. Mol. Biol. 215:403–10 [Google Scholar]
  4. Alvarez AM. 4.  2004. Integrated approaches for detection of plant pathogenic bacteria and diagnosis of bacterial diseases. Annu. Rev. Phytopathol. 42:339–66 [Google Scholar]
  5. Amaral GRS, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME. 5.  et al. 2014. Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int. J. Syst. Evol. Microbiol 64:357–65 [Google Scholar]
  6. Auch AF, Klenk H-P, Goker M. 6.  2010. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand. Genomic Sci. 2:142–48 [Google Scholar]
  7. Barraclough TG, Balbi KJ, Ellis RJ. 7.  2012. Evolving concepts of bacterial species. Evol. Biol. 39:148–57 [Google Scholar]
  8. Berge O, Monteil CL, Bartoli C, Chandeysson C, Guilbaud C. 8.  et al. 2014. A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PLOS ONE 9:e105547 [Google Scholar]
  9. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. 9.  1923. Bergey's Manual of Determinative Bacteriology Baltimore, MD: Williams and Wilkins [Google Scholar]
  10. Boero F. 10.  2001. Light after dark: the partnership for enhancing expertise in taxonomy. Trends Ecol. Evol. 16:266 [Google Scholar]
  11. Bradbury JF, Saddler GS. 11.  2002. A Guide to Plant Pathogenic Bacteria Wallingford, UK: Oxford Univ. Press, 2nd ed.. [Google Scholar]
  12. Bull CT, Clarke CR, Cai R, Vinatzer BA, Jardini TM, Koike ST. 12.  2011. Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley. Phytopathology 101:847–58 [Google Scholar]
  13. Bull CT, Coutinho TA, Denny TP, Firrao G, Fischer-Le Saux M. 13.  et al. 2014. List of new names of plant pathogenic bacteria (2011–2012). J. Plant Pathol. 96:223–26 [Google Scholar]
  14. Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M. 14.  et al. 2008. Demystifying the nomenclature of bacterial plant pathogens. J. Plant Pathol. 90:403–17 [Google Scholar]
  15. Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M. 15.  et al. 2010. Comprehensive list of names of plant pathogenic bacteria (1980–2007). J. Plant Pathol. 92:551–92 [Google Scholar]
  16. Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M. 16.  et al. 2012. List of new names of plant pathogenic bacteria (2008–2010). J. Plant Pathol. 94:21–27 [Google Scholar]
  17. Bull CT, Gebben SJ, Goldman PH, Trent MT, Hayes RJ. 17.  2015. Host genotype and hypersensitive reaction influence population levels of Xanthomonas campestris pv. vitians in lettuce. Phytopathology 105:316–24 [Google Scholar]
  18. Bull CT, Goldman PH, Cintas NA, Koike ST. 18.  2003. Identification of Pseudomonas species from a variety of hosts in the Salinas Valley of California. Pseudomonas syringae and Related Pathogens, ed. N Iacobellis, A Collmer, S Hutcheson, J Mansfield, C Morris, et al. 607–15 Netherlands: Springer [Google Scholar]
  19. Bull CT, Goldman PH, Hayes R, Madden LV, Koike ST, Ryder E. 19.  2007. Genetic diversity of lettuce for resistance to bacterial leaf spot caused by Xanthomonas campestris pv. vitians. Plant Health Prog. doi:10.1094/PHP-2007-0917-02-RS [Google Scholar]
  20. Bull CT, Goldman P, Koike ST. 20.  2004. Bacterial blight on arugula, a new disease caused by Pseudomonas syringae pv. alisalensis in California. Plant Dis. 88:1384 [Google Scholar]
  21. Bull CT, Goldman PH, Martin KJ. 21.  2014. Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ. Mol. Cell. Probes 28:211–17 [Google Scholar]
  22. Bull CT, Huerta AI, Koike ST. 22.  2009. First report of blossom blight of strawberry (Fragaria × ananassa) caused by Pseudomonas marginalis. Plant Dis. 93:1350 [Google Scholar]
  23. Bull CT, Koike ST, Huerta AI, Jardini TM, Mauzey SJ. 23.  et al. 2015. Plant pathogenic prokaryotes. Plant Pathology Concepts and Laboratory Exercises RN Trigiano, BH Ownley Boca Raton, FL: Taylor and Francis [Google Scholar]
  24. Bull CT, Manceau C, Lydon J, Kong H, Vinatzer BA, Fischer-Le Saux M. 24.  2010. Pseudomonas cannabina pv. cannabina pv. nov., and Pseudomonas cannabina pv. alisalensis (Cintas Koike and Bull, 2000) comb. nov., are members of the emended species Pseudomonas cannabina (ex Sutic & Dowson 1959) Gardan, Shafik, Belouin, Brosch, Grimont & Grimont 1999. Syst. Appl. Microbiol. 33:105–15 [Google Scholar]
  25. Bull CT, Mauzey SJ, Koike ST. 25.  2010. First report of bacterial blight of brussels sprouts (Brassica oleracea var. gemmifera) caused by Pseudomonas cannabina pv. alisalensis in California. Plant Dis. 94:1375 [Google Scholar]
  26. Bull CT, Rubio I. 26.  2011. First report of bacterial blight of crucifers caused by Pseudomonas cannabina pv. alisalensis in Australia. Plant Dis. 95:1027 [Google Scholar]
  27. Cai R, Yan S, Liu H, Leman S, Vinatzer BA. 27.  2011. Reconstructing host range evolution of bacterial plant pathogens using Pseudomonas syringae pv. tomato and its close relatives as a model. Infect. Genet. Evol. 11:1738–51 [Google Scholar]
  28. Cantino PD. 28.  1998. Binomials, hyphenated uninomials, and phylogenetic nomenclature. Taxon 47:425 [Google Scholar]
  29. Cerkauskas RF, Koike ST, Azad HR, Lowery DT, Stobbs LW. 29.  2006. Diseases, pests, and abiotic disorders of greenhouse-grown water spinach (Ipomoea aquatica) in Ontario and California. Can. J. Plant Pathol. 28:63–70 [Google Scholar]
  30. Chun J, Rainey FA. 30.  2014. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int. J. Syst. Evol. Microbiol. 64:316–24 [Google Scholar]
  31. Cintas NA, Bull CT, Koike ST, Bouzar H. 31.  2001. A new bacterial leaf spot disease of broccolini, caused by Pseudomonas syringae pathovar maculicola, in California. Plant Dis. 85:1207 [Google Scholar]
  32. Cintas NA, Koike ST, Bull CT. 32.  2002. A new pathovar, Pseudomonas syringae pv. alisalensis pv. nov., proposed for the causal agent of bacterial blight of broccoli and broccoli raab. Plant Dis. 86:992–98 [Google Scholar]
  33. Cintas NA, Koike ST, Bunch RA, Bull CT. 33.  2006. Holdover inoculum of Pseudomonas syringae pv. alisalensis from broccoli raab causes disease in subsequent plantings. Plant Dis. 90:1077–84 [Google Scholar]
  34. Coenye T, Gevers D, De Peer YV, Vandamme P, Swings J. 34.  2005. Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29:147–67 [Google Scholar]
  35. Cooksey DA, Azad HR, Paulus AO, Koike ST. 35.  1991. Leaf spot of cilantro in California caused by a nonfluorescent Pseudomonas syringae. Plant Dis. 75:101D [Google Scholar]
  36. Cooksey DA, Koike ST. 36.  1990. A new foliar blight of impatiens caused by Pseudomonas syringae. Plant Dis. 74:180 [Google Scholar]
  37. Cother EJ, Noble DH. 37.  2009. Identification of blossom blight in stock (Matthiola incana) caused by Pseudomonas syringae pv. maculicola. Australas. Plant Pathol. 38:242–46 [Google Scholar]
  38. Deloger M, El Karoui M, Petit M-A. 38.  2009. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J. Bacteriol. 191:91–99 [Google Scholar]
  39. Dowson WJ. 39.  1957. Plant Diseases Due to Bacteria Cambridge, UK: Cambridge Univ. Press, 2nd ed.. [Google Scholar]
  40. Dye DW. 40.  1980. International standards for naming pathovars of phytopathogenic bacteria and a list of pathovar names and pathotype strains. Rev. Plant Pathol. 59:153–68 [Google Scholar]
  41. Fournier P-E, Drancourt M, Colson P, Rolain J-M, Scola BL, Raoult D. 41.  2013. Modern clinical microbiology: new challenges and solutions. Nat. Rev. Microbiol. 11:574–85 [Google Scholar]
  42. Fox GE, Pechman KR, Woese CR. 42.  1977. Comparative cataloging of 16s ribosomal ribonucleic acid: molecular approach to procaryotic systematics. Int. J. Syst. Bacteriol. 27:44–57 [Google Scholar]
  43. Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J. 43.  et al. 1980. The phylogeny of prokaryotes. Science 209:457–63 [Google Scholar]
  44. Gardan L, Shafik H, Belouin S, Broch R, Grimont F, Grimont PAD. 44.  1999. DNA relatedness among the pathovars of Pseudomonas syringae and description of Pseudomonas tremae sp. nov. and Pseudomonas cannabina sp. nov. (ex Sutic and Dowson 1959). Int. J. Syst. Bacteriol. 49:469–78 [Google Scholar]
  45. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T. 45.  et al. 2005. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3:733–39 [Google Scholar]
  46. Gironde S, Manceau C. 46.  2012. Housekeeping gene sequencing and multilocus variable-number tandem-repeat analysis to identify subpopulations within Pseudomonas syringae pv. maculicola and Pseudomonas syringae pv. tomato that correlate with host specificity. Appl. Environ. Microbiol. 78:3266–79 [Google Scholar]
  47. Gordon RE. 47.  1978. A species definition. Int. J. Syst. Bacteriol. 28:605–7 [Google Scholar]
  48. Gürtler V, Mayall BC. 48.  2001. Genomic approaches to typing, taxonomy and evolution of bacterial isolates. Int. J. Syst. Evol. Microbiol. 51:3–16 [Google Scholar]
  49. Hajri A, Brin C, Hunault G, Lardeux F, Lemaire C. 49.  et al. 2009. A “repertoire for repertoire” hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas. PLOS ONE 4:8e6632 [Google Scholar]
  50. Hajri A, Pothier JF, Fischer-Le Saux M, Bonneau S, Poussier S. 50.  et al. 2012. Type three effector gene distribution and sequence analysis provide new insights into the pathogenicity of plant-pathogenic Xanthomonas arboricola. Appl. Environ. Microbiol. 78:371–84 [Google Scholar]
  51. Hayes RJ, Trent MA, Mou B, Simko I, Gebben SJ, Bull CT. 51.  2014. Baby leaf lettuce germplasm enhancement: developing diverse populations with resistance to bacterial leaf spot caused by Xanthomonas campestris pv. vitians. HortScience 49:18–24 [Google Scholar]
  52. Hwang MSH, Morgan RL, Sarkar SF, Wang PW, Guttman DS. 52.  2005. Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae. Appl. Environ. Microbiol. 71:5182–91 [Google Scholar]
  53. Ishiyama Y, Yamagishi N, Ogiso H, Fujinaga M, Takikawa Y. 53.  2012. Pseudomonas syringae pv. alisalensis isolated from the brown necrotic lesion on oat for green manure (black oat, Avena storigosa Schereb.). Jpn. J. Phytopathol. 78:239 [Google Scholar]
  54. Jardini TM, Koike ST, Bull CT. 54.  2011. First report of bacterial streak of fennel (Foeniculum vulgare) in California caused by Pseudomonas syringae pv. apii. Plant Dis. 96:285 [Google Scholar]
  55. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C. 55.  et al. 2012. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiol. 158:1005–15 [Google Scholar]
  56. Jones L, Saha S, Collmer A, Smart CD, Lindeberg M. 56.  2015. Genome assisted development of a diagnostic protocol for distinguishing high virulence Pseudomonas syringae pv. tomato strains. Plant Dis. 99:527–34 [Google Scholar]
  57. Kämpfer P. 57.  2012. Systematics of prokaryotes: the state of the art. Antonie Van Leeuwenhoek 101:3–11 [Google Scholar]
  58. Keinath AP, Wechter WP, Smith JP. 58.  2006. First report of bacterial leaf spot on leafy brassica greens caused by Pseudomonas syringae pv. maculicola in South Carolina. Plant Dis. 90:683 [Google Scholar]
  59. Kim M, Oh H-S, Park S-C, Chun J. 59.  2014. Towards a taxonomic coherence between average nucleotide identity and 16s rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64:346–51 [Google Scholar]
  60. Klenk H-P, Göker M. 60.  2010. En route to a genome-based classification of archaea and bacteria?. Syst. Appl. Microbiol. 33:175–82 [Google Scholar]
  61. Knapp S, Lamas G, Lughadha EN, Novarino G. 61.  2004. Stability or stasis in the names of organisms: the evolving codes of nomenclature. Philos. Trans. R. Soc. Lond. B. 359:611–22 [Google Scholar]
  62. Koike ST. 62.  1996. A new bacterial disease of arugula in California. Plant Dis. 80:464 [Google Scholar]
  63. Koike ST, Azad HR. 63.  2003. First report of bacterial blight of four o'clock (Mirabilis jalapa), caused by Xanthomonas campestris in California. Plant Dis. 87:874 [Google Scholar]
  64. Koike ST, Azad HR, Cooksey DA. 64.  2001. Xanthomonas leaf spot of catnip: a new disease caused by a pathovar of Xanthomonas campestris. Plant Dis. 85:1157–59 [Google Scholar]
  65. Koike ST, Azad HR, Cooksey DC. 65.  2002. First report of bacterial leaf spot of spinach caused by a Pseudomonas syringae pathovar in California. Plant Dis. 86:921 [Google Scholar]
  66. Koike ST, Barak JD, Henderson DM, Gilbertson RL. 66.  1999. Bacterial blight of leek: a new disease in California caused by Pseudomonas syringae. Plant Dis. 83:165–70 [Google Scholar]
  67. Koike ST, Bolda MP, Bull CT. 67.  2014. Pseudomonas blight caused by Pseudomonas syringae on raspberry in California. Plant Dis. 98:1151 [Google Scholar]
  68. Koike ST, Bull CT. 68.  2006. First report of bacterial leaf spot of Italian dandelion (Cichorium intybus) caused by a Pseudomonas syringae pathovar in California. Plant Dis. 90:245 [Google Scholar]
  69. Koike ST, Cintas NA, Bull CT. 69.  2000. Bacterial blight, a new disease of broccoli caused by Pseudomonas syringae in California. Plant Dis. 84:370 [Google Scholar]
  70. Koike ST, Gladders P, Paulus AO. 70.  2007. Vegetable Diseases: A Color Handbook Houston, TX: Gulf Prof. Publ. [Google Scholar]
  71. Koike ST, Henderson DM, Azad HR, Cooksey DA, Little EL. 71.  1998. Bacterial blight of broccoli raab: a new disease caused by a pathovar of Pseudomonas syringae. Plant Dis. 82:727–31 [Google Scholar]
  72. Koike ST, Henderson DM, Bull CT, Goldman PH, Lewellen RT. 72.  2003. First report of bacterial leaf spot of Swiss chard caused by Pseudomonas syringae pv. aptata in California. Plant Dis. 87:1397 [Google Scholar]
  73. Koike ST, Kammeijer K, Bull CT, O'Brien D. 73.  2006. First report of bacterial blight of Romanesco cauliflower (Brassica oleracea var. botrytis) caused by Pseudomonas syringae pv. alisalensis in California. Plant Dis. 90:1551 [Google Scholar]
  74. Koike ST, Kammeijer K, Bull CT, O'Brien D. 74.  2007. First report of bacterial blight of rutabaga (Brassica napus var. napobrassica) caused by Pseudomonas syringae pv. alisalensis in California. Plant Dis. 91:112 [Google Scholar]
  75. Koike ST, Tjosvold SA, Cooksey DA, Azad HR. 75.  1995. A bacterial leaf disease of lavender caused by Xanthomonas campestris. Plant Dis. 79:859 [Google Scholar]
  76. Konstantinidis KT, Tiedje JM. 76.  2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102:2567–72 [Google Scholar]
  77. Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM. 77.  et al. 2012. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLOS Pathog. 8:e1002824 [Google Scholar]
  78. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M. 78.  et al. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLOS Biol. 12:e1001920 [Google Scholar]
  79. Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG. 79.  et al. 2014. Genomic encyclopedia of type strains, Phase I: the one thousand microbial genomes (KMG-I) project. Stand. Genomic Sci. 9:1278–84 [Google Scholar]
  80. Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA. 80.  1992. International Code of Nomenclature of Bacteria Bacteriological Code, 1990 Revision Washington, DC: ASM Press [Google Scholar]
  81. Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R. 81.  et al. 1993. The ribosomal database project. Nucleic Acids Res. 21:3021–23 [Google Scholar]
  82. Lauritzen E. 82.  2013. Monterey County Crop Report Salinas, CA: Cty. Monterey Agric. Comm http://ag.co.monterey.ca.us/resources/category/crop-reports [Google Scholar]
  83. Lelliott RA, Billing E, Hayward AC. 83.  1966. A determinative scheme for the fluorescent plant pathogenic pseudomonads. J. Appl. Bacteriol. 29:470–89 [Google Scholar]
  84. Lindstedt B-A. 84.  2005. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26:2567–82 [Google Scholar]
  85. Little EL, Gilberston RL, Koike ST. 85.  1994. First report of Pseudomonas viridiflava causing a leaf necrosis on basil. Plant Dis. 78:831D [Google Scholar]
  86. Little EL, Koike ST, Gilbertson RL. 86.  1997. Bacterial leaf spot of celery in California: etiology, epidemiology, and role of contaminated seed. Plant Dis. 81:892–96 [Google Scholar]
  87. Louws F, Rademaker J, de Bruijn F. 87.  1999. The three Ds of PCR-based genomic analysis of phytobacteria: diversity, detection, and disease diagnosis. Annu. Rev. Phytopathol. 37:81–125 [Google Scholar]
  88. Maiden MCJ. 88.  2006. Multilocus sequence typing of bacteria. Annu. Rev. Microbiol. 60:561–88 [Google Scholar]
  89. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE. 89.  et al. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. 95:3140–45 [Google Scholar]
  90. Maiden MCJ, van Rensburg MJJ, Bray JE, Earle SG, Ford SA. 90.  et al. 2013. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol. 11:728–36 [Google Scholar]
  91. Marakeby H, Badr E, Torkey H, Song Y, Leman S. 91.  et al. 2014. A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature. PLOS ONE 9:e89142 [Google Scholar]
  92. Marcelletti S, Scortichini M. 92.  2014. Definition of plant pathogenic Pseudomonas genomospecies of the Pseudomonas syringae complex through multiple comparative approaches. Phytopathology 104:1274–82 [Google Scholar]
  93. Mauzey SJ, Davis CD, Martins OM, Koike ST, Bull CT. 93.  2011. A new disease of parsley (Petroselinum crispum) in California caused by a fluorescent pseudomonad related to Pseudomonas viridiflava. Phytopathology 101:S116 [Google Scholar]
  94. Mauzey SJ, Koike ST, Bull CT. 94.  2010. First report of bacterial blight of cabbage (Brassica oleracea var. capitata) caused by Pseudomonas cannabina pv. alisalensis in California. Plant Dis. 95:71 [Google Scholar]
  95. McCulloch L. 95.  1911. A spot disease of cauliflower. US Dept. Agric. Bur. Plant Ind. Bull. 225:7–15 [Google Scholar]
  96. McGinnis S, Madden TL. 96.  2004. Blast: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32:W20–25 [Google Scholar]
  97. Miller SA, Martin RR. 97.  1988. Molecular diagnosis of plant disease. Annu. Rev. Phytopathol. 26:409–32 [Google Scholar]
  98. Mulet M, Lalucat J, García-Valdés E. 98.  2010. DNA sequence–based analysis of the Pseudomonas species. Environ. Microbiol. 12:1513–30 [Google Scholar]
  99. Oren A. 99.  2004. Prokaryote diversity and taxonomy: current status and future challenges. Philos. Trans. R. Soc. B 359:623–38 [Google Scholar]
  100. Oren A, Garrity GM. 100.  2014. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie Van Leeuwenhoek 106:43–56 [Google Scholar]
  101. Pearson DL, Hamilton AL, Erwin TL. 101.  2011. Recovery plan for the endangered taxonomy profession. BioScience 61:58–63 [Google Scholar]
  102. Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA. 102.  2013. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect. Genet. Evol. 16:38–53 [Google Scholar]
  103. Peters BJ, Ash GJ, Cother EJ, Hailstones DL, Noble DH, Urwin NAR. 103.  2004. Pseudomonas syringae pv. maculicola in Australia: pathogenic, phenotypic and genetic diversity. Plant Pathol. 53:73–79 [Google Scholar]
  104. Popović T, Ivanović Ž, Ignjatov M, Milošević D. 104.  2015. First report of Pseudomonas syringae pv. coriandricola causing bacterial leaf spot on carrot, parsley and parsnip in Serbia. Plant Dis. 99:416 [Google Scholar]
  105. Rademaker JLW, Louws FJ, Versalovic J, de Bruijn FJ. 105.  2004. Characterization of the diversity of ecologically important microbes by rep-PCR genomic fingerprinting. Mol. Microb. Ecol. Man. 3.4.3:1–27 [Google Scholar]
  106. Ramasamy D, Mishra AK, Lagier J-C, Padhmanabhan R, Rossi M. 106.  et al. 2014. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int. J. Syst. Evol. Microbiol. 64:384–91 [Google Scholar]
  107. Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C. 107.  2014. Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. New Microbiol. 37:1–15 [Google Scholar]
  108. Richter M, Rossello-Mora R. 108.  2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106:19126–31 [Google Scholar]
  109. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ. 109.  et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–37 [Google Scholar]
  110. Rosselló-Mora R, Amann R. 110.  2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25:39–67 [Google Scholar]
  111. Rubio I, Bouzar H, Jardini TM, Koike ST, Bull CT. 111.  2012. Novel Pseudomonas syringae strains associated with leaf spot diseases on watermelon (Citrullus lanatus) and squash (Cucurbita pepo) in California. Phytopathology 102:103 [Google Scholar]
  112. Sarethy IP, Pan S, Danquah MK. 112.  2014. Modern taxonomy for microbial diversity. Biodiversity: The Dynamic Balance of the Planet O Grillo 51–68 Rijeka, Croatia: InTech [Google Scholar]
  113. Schaad NW, Jones JB, Chun W. 113.  2000. Laboratory Guide for Identification of Plant Pathogenic Bacteria St. Paul, MN: Am. Phytopathol. Soc, 3d ed.. [Google Scholar]
  114. Sentausa E, Fournier P-E. 114.  2013. Advantages and limitations of genomics in prokaryotic taxonomy. Clin. Microbiol. Infect. 19:790–95 [Google Scholar]
  115. Shariat N, Dudley EG. 115.  2014. CRISPRs: molecular signatures used for pathogen subtyping. Appl. Environ. Microbiol. 80:430–39 [Google Scholar]
  116. Skerman VBD, McGowan V, Sneath PHA. 116.  1980. Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30:225–420 [Google Scholar]
  117. Smith D, McCluskey K, Stackebrandt E. 117.  2014. Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres. SpringerPlus 3:81 [Google Scholar]
  118. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P. 118.  et al. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol 52:1043–47 [Google Scholar]
  119. Stackebrandt E, Goebel BM. 119.  1994. Taxonomic note: a place for DNA-DNA reassociation and 16s rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846–49 [Google Scholar]
  120. Starr MP. 120.  1959. Bacteria as plant pathogens. Annu. Rev. Microbiol. 13:211–38 [Google Scholar]
  121. Stolp H, Starr MP, Baigent NL. 121.  1965. Problems in speciation of phytopathogenic pseudomonads and xanthomonads. Annu. Rev. Phytopathol. 3:231–64 [Google Scholar]
  122. Sutcliffe IC, Trujillo ME, Goodfellow M. 122.  2012. A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 101:13–20 [Google Scholar]
  123. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. 123.  2003. A plea for DNA taxonomy. Trends Ecol. Evol. 18:70–74 [Google Scholar]
  124. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL. 124.  2013. Microbial genomic taxonomy. BMC Genomics 14:913 [Google Scholar]
  125. Tindall BJ. 125.  1999. Note: misunderstanding the bacteriological code. Int. J. Syst. Bacteriol. 49:1313–16 [Google Scholar]
  126. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. 126.  2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60:249–66 [Google Scholar]
  127. Toben H-M, Rudoph K. 127.  1996. Pseudomonas syringae pv. coriandricola, incitant of bacterial umbel blight and seed decay of coriander (Coriandrum sativum L.) in Germany. J. Phytopathol. 144:169–78 [Google Scholar]
  128. Van Belkum A, Struelens M, de Visser A, Verbrugh H, Tibayrenc M. 128.  2001. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin. Microbiol. Rev. 14:547–60 [Google Scholar]
  129. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. 129.  1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407–38 [Google Scholar]
  130. Vaneechoutte M. 130.  1996. DNA fingerprinting techniques for microorganisms. Mol. Biotechnol. 6:115–42 [Google Scholar]
  131. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K. 131.  et al. 2015. Microbial species delineation using whole genome sequences. Nucl. Acids Res. submitted [Google Scholar]
  132. Vauterin L, Hoste B, Kersters K, Swings J. 132.  1995. Reclassification of Xanthomonas. Int. J. Syst. Bacteriol. 45:472–89 [Google Scholar]
  133. Vinatzer BA, Bull CT. 133.  2009. The impact of genomic approaches on our understanding of diversity and taxonomy of plant pathogenic bacteria. Plant Pathogenic Bacteria: Genomics and Molecular Biology RW Jackson 37–61 Norfolk, UK: Caister Acad. Press [Google Scholar]
  134. Vincelli P, Tisserat N. 134.  2008. Nucleic acid–based pathogen detection in applied plant pathology. Plant Dis. 92:660–69 [Google Scholar]
  135. Watson DRW, Young JM. 135.  2007. Proposals that the international committee on systematics of prokaryotes establish a public database of validly published names and that the bacteriological code be amended to change the prescription for citation of validly published names. Int. J. Syst. Evol. Microbiol. 57:1167–68 [Google Scholar]
  136. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. 136.  et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463–64 [Google Scholar]
  137. Williams PH, Keen NT. 137.  1966. Bacterial blight of radish. Plant Dis. 50:192–95 [Google Scholar]
  138. Woese CR, Fox GE. 138.  1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:5088–90 [Google Scholar]
  139. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E. 139.  et al. 2009. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462:1056–60 [Google Scholar]
  140. Young JM. 140.  2000. Recent developments in systematics and their implications for plant pathogenic bacteria. Applied Microbial Systematics FG Priest, M Goodfellow 135–63 Dordrecht, Neth: Springer [Google Scholar]
  141. Young JM, Bull CT, De Boer SH, Firrao G, Gardan L. 141.  et al. 2001. Classification, nomenclature, and plant pathogenic bacteria: a clarification. Phytopathology 91:617–20 [Google Scholar]
  142. Young JM, Bull CT, De Boer SH, Firrao G, Gardan L. 142.  et al. 2001. International standards for naming pathovars of phytopathogenic bacteria. http://www.isppweb.org/about_tppb_naming.asp
  143. Young JM, Park D-C, Shearman HM, Fargier E. 143.  2008. A multilocus sequence analysis of the genus Xanthomonas. Syst. Appl. Microbiol. 31:366–77 [Google Scholar]
  144. Young JM, Takikawa Y, Gardan L, Stead DE. 144.  1992. Changing concepts in the taxonomy of plant pathogenic bacteria. Annu. Rev. Phytopathol. 30:67–105 [Google Scholar]
  145. Young JM, Wilkie JP, Park D-C, Watson DRW. 145.  2010. New Zealand strains of plant pathogenic bacteria classified by multi-locus sequence analysis; proposal of Xanthomonas dyei sp. nov. Plant Pathol. 59:270–81 [Google Scholar]
  146. Zacaroni AB, Koike ST, de Souza RM, Bull CT. 146.  2012. Bacterial leaf spot of radicchio (Cichorium intybus) is caused by Xanthomonas hortorum. Plant Dis. 96:1820–20 [Google Scholar]
  147. Zhao Y, Damicone JP, Demezas DH, Rangaswamy V, Bender CL. 147.  2000. Bacterial leaf spot of leafy crucifers in Oklahoma caused by Pseudomonas syringae pv. maculicola. Plant Dis. 84:1015–20 [Google Scholar]
  148. Zhi X-Y, Zhao W, Li W-J, Zhao G-P. 148.  2012. Prokaryotic systematics in the genomics era. Antonie Van Leeuwenhoek 101:21–34 [Google Scholar]

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