A new genomovar of Pseudomonas cichorii, a causal agent of tomato pith necrosis

European Journal of Plant Pathology

Volumn 137, Issue 3, 2013, Pages 477-493

  Trantas, Emmanouil A ^a   Sarris, Panagiotis F ^a,b   Mpalantinaki, Evaggelia E ^a   Pentari, Marianna G ^a   Ververidis, Filippos N ^a   Goumas, Dimitrios E ^a  

^a TECHNOLOGICAL EDUCATIONAL INSTITUTE OF CRETE   (Greece)

^b SAINSBURY LABORATORY   (United Kingdom)

Author keywords

gyrB; MLSA; Pathogenicity; phylogenetic analysis; Pith necrosis; Pseudomonas cichorii; rep PCR; rpoB; rpoD

Indexed keywords

DISEASE; DNA; EMERGENCE; HETEROGENEITY; MORPHOTYPE; PATHOGEN; PATHOGENICITY; PLANT; POLYMERASE CHAIN REACTION;

APIUM GRAVEOLENS VAR. DULCE; CHRYSANTHEMUM; LACTUCA; LYCOPERSICON ESCULENTUM; PSEUDOMONAS; PSEUDOMONAS CICHORII;

EID: 84884987918     PISSN: 09291873     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10658-013-0258-8     Document Type: Article

References (60)

1. Ait Tayeb, L., Ageron, E., Grimont, F., & Grimont, P. A. (2005). Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Research in Microbiology, 156, 763-773.
2. Alippi, A., Dal Bo, E., Ronco, L., López, M., López, A., & Aguilar, O. (2003). Pseudomonas populations causing pith necrosis of tomato and pepper in Argentina are highly diverse. Plant Pathology, 52, 287-302.
3. Alivizatos, A. S. (1984). Etiology of tomato pith necrosis in Greece. Paper presented at the Proceedings of the 2nd working group Pseudomonas syringae pathovar organized by the Hellenic Phytopathological Society, Sounion, Greece.
4. Alivizatos, A. S. (1985). Bacterial wilt of tomato in Greece caused by Erwinia chrysanthemi. Plant Pathology, 34, 638-639.
5. Alivizatos, A. S. (1986). Tomato pith necrosis caused by Pseudomonas viridiflava. Annales de l'Institut phytopathologique Benaki, 15, 41-47.
6. Braun-Kiewnick, A., & Sands, D. C. (2001). Pseudomonas. In N. W. Schaad, J. B. Jones, & W. Chun (Eds.), Laboratory guide for identification of plant pathogenic bacteria (pp. 84-120). APS Press.
7. Buell, C. R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I. T., Gwinn, M. L., et al. (2003). The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America 100, 10181-10186.
8. Buonaurio, R., Karofilakis, A., & Scortichini, M. (1993). Occurrence of Pseudomonas corrugate Roberts et Scarlett on tomato plants in Crete. Phytopathologia Mediterranea, 32, 245-246.
9. Chase, A. R. (1987). Leaf and petiole rot of Ficus lyrata cv. Compacta caused by Pseudomonas cichorii. Plant Pathology, 36, 219-221.
10. Cladera, A. M., Sepulveda-Torres Ldel, C., Valens-Vadell, M., Meyer, J. M., Lalucat, J., & Garcia-Valdes, E. (2006). A detailed phenotypic and genotypic description of Pseudomonas strain OX1. Systematic and Applied Microbiology, 29, 422-430.
11. Cottyn, B., Heylen, K., Heyrman, J., Vanhouteghem, K., Pauwelyn, E., Bleyaert, P., van Vaerenbergh, J., Höfte, M., De Vos, P., & Maes, M. (2009). Pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in Flanders. Systematic and Applied Microbiology, 32, 211-225.
12. Dawson, S. L., Fry, J. C., & Dancer, B. N. (2002). A comparative evaluation of five typing techniques for determining the diversity of fluorescent pseudomonads. Journal of Microbiological Methods, 50, 9-22.
13. De Vos, D., Bouton, C., Sarniguet, A., De Vos, P., Vauterin, M., & Cornelis, P. (1998). Sequence diversity of the oprI gene, coding for major outer membrane lipoprotein I, among rRNA group I pseudomonads. Journal of Bacteriology, 180, 6551-6556.
14. Feil, H., Feil, W. S., Chain, P., Larimer, F., DiBartolo, G., Copeland, A., et al. (2005). Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America 102, 11064-11069.
15. Felsenstein, J. (1985). Confidence-limits on phylogenies - an approach using the bootstrap. Evolution, 39, 783-791.
16. Garibaldi, A., Bertetti, D., Scortichini, M., & Gullino, M. L. (2005). First report of bacterial leaf spot caused by Pseudomonas cichorii on Phlox paniculata in Italy. Plant Disease, 89, 912.
17. Goumas, D. E., Malathrakis, N. E., & Chatzaki, A. K. (1999). Characterization of Pseudomonas viridiflava associated with a new symptom on tomato fruit. European Journal of Plant Pathology, 105, 927-932.
18. Joardar, V., Lindeberg, M., Jackson, R. W., Selengut, J., Dodson, R., Brinkac, L. M., et al. (2005). Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. Journal of Bacteriology, 187, 6488-6498.
19. Jones, J. B., & Engelhard, A. W. (1983). Outbreak of a stem necrosis on chrysanthemum incited by Pseudomonas cichorii in Florida. Plant Disease, 67, 431-433.
20. King, E. O., Ward, M. K., & Raney, D. E. (1954). Two simple media for the demonstration of pyocyanine and fluorescin. Journal of Laboratory and Clinical Medicine, 44, 301-307.
21. Lelliott, R. A., Billing, E., & Hayward, A. C. (1966). A determinative scheme for the fluorescent plant pathogenic Pseudomonads. Journal of Applied Microbiology, 29, 470-489.
22. Liu, W. T., Marsh, T. L., Cheng, H., & Forney, L. J. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology, 63, 4516-4522.
23. Louws, F. J., Fulbright, D. W., Stephens, C. T., & de Bruijn, F. J. (1994). Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Applied and Environmental Microbiology, 60, 2286-2295.
24. Malathrakis, N. E., & Goumas, D. E. (1987). Bacterial soft rot of tomato in plastic greenhouses in Crete. Annals of Applied Biology, 111, 115-123.
25. Martin, B., Humbert, O., Camara, M., Guenzi, E., Walker, J., Mitchell, T., Andrew, P., Prudhomme, M., Alloing, G., Hakenbeck, R., et al. (1992). A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Research, 20, 3479-3483.
26. Mavrodi, D. V., Peever, T. L., Mavrodi, O. V., Parejko, J. A., Raaijmakers, J. M., Lemanceau, P., et al. (2010). Diversity and evolution of the phenazine biosynthesis pathway. Applied and Environmental Microbiology 76, 866-879.
27. Meyer, J. B., Frapolli, M., Keel, C., & Maurhofer, M. (2011). Pyrroloquinoline quinone biosynthesis gene pqqC, a novel molecular marker for studying the phylogeny and diversity of phosphate-solubilizing pseudomonads. Applied and Environmental Microbiology, 77, 7345-7354.
28. Mirik, M., Aysan, Y., & Sahin, F. (2011). Characterization of Pseudomonas cichorii isolated from different hosts in Turkey. International Journal of Agriculture and Biology, 13, 203-209.
29. Mollet, C., Drancourt, M., & Raoult, D. (1997). rpoB sequence analysis as a novel basis for bacterial identification. Molecular Microbiology, 26, 1005-1011.
30. Mulet, M., Bennasar, A., Lalucat, J., & Garcia-Valdes, E. (2009). An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Molecular and Cellular Probes, 23, 140-147.
31. Mulet, M., Lalucat, J., & García-Valdés, E. (2010). DNA sequence-based analysis of the Pseudomonas species. Environmental Microbiology, 12, 1513-1530.
32. Murillo, J., Bardaji, L., Navarro de la Fuente, L., Fuhrer, M. E., Aguilera, S., & Alvarez-Morales, A. (2011). Variation in conservation of the cluster for biosynthesis of the phytotoxin phaseolotoxin in Pseudomonas syringae suggests at least two events of horizontal acquisition. Research in Microbiology, 162, 253-261.
33. Nameth, S. T., Daughtrey, M. L., Moorman, G. W., & Sulzinski, M. A. (1999). Bacterial blight of Geranium: a history of diagnostic challenges. Plant Disease, 83, 204-212.
34. Palacio-Bielsa, A., Cambra, M. A., & Lopez, M. M. (2009). PCR detection and identification of plant-pathogenic bacteria: updated review of protocols (1989-2007). Journal of Plant Pathology, 91, 249-297.
35. Palleroni, N. J. (1984). Pseudomonads. In N. R. Krieg (Ed.), Bergey's manual of systematic bacteriology (pp. 141-199). Baltimore: Williams and Wilkins.
36. Parkinson, N., Bryant, R., Bew, J., & Elphinstone, J. (2011). Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus. Plant Pathology, 60, 338-344.
37. Paulsen, I. T., Press, C. M., Ravel, J., Kobayashi, D. Y., Myers, G. S., Mavrodi, D. V., et al. (2005). Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnology, 23, 873-878.
38. Pentari, M. G., Mpalantinaki, E. E., Sarris, P. F., Trantas, E. A., Ververidis, F. N., & Goumas, D. E. (2012). Characterization of bacterial isolates from pith necrosis disease of tomato. Paper presented at the 16th conference national conference organized by the Hellenic Phytopathological Society, Thessaloniki, Greece.
39. Pernezny, K., Datnoff, L., & Sommerfeld, M. L. (1994). Brown stem of celery caused by Pseudomonas cichorii. Plant Disease, 78, 917-919.
40. Piening, L. J., & MacPherson, D. J. (1985). Stem melanosis, a disease of spring wheat caused by Pseudomonas cichorii. Canadian Journal of Plant Pathology, 7, 168-172.
41. Rumbou, A., & Gessler, C. (2006). Particular structure of Plasmopara viticola populations evolved under Greek island conditions. Phytopathology, 96, 501-509.
42. Santos, S. R., & Ochman, H. (2004). Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environmental Microbiology, 6, 754-759.
43. Sarris, P., Abdelhalim, M., Kitner, M., Skandalis, N., Panopoulos, N., Doulis, A., & Lebeda, A. (2009). Molecular polymorphisms between populations of Pseudoperonospora cubensis from Greece and the Czech Republic and the phytopathological and phylogenetic implications. Plant Pathology, 58, 933-943.
44. Sarris, P. F., Karri, I. V., Goumas, D. E. (2010). First report of Pseudomonas syringae pv. alisalensis causing bacterial blight of arugula (Eruca vesicaria subsp. sativa) in Greece. New Disease Reports 22.
45. Sarris, P. F., Trantas, E. A., Mpalantinaki, E., Ververidis, F., & Goumas, D. E. (2012). Pseudomonas viridiflava, a multi host plant pathogen with significant genetic variation at the molecular level. PLoS ONE, 7, e36090.
46. Sneath, P. H. A., & Sokal, R. R. (1973). Numerical taxonomy: The principles and practice of numerical classification. San Francisco: W. H Freeman and Company.
47. Sokal, R. R., & Michener, C. D. (1958). A statistical method for evaluating systematic relationships. The University of Kansas science bulletin, 38, 1409-1438.
48. Soler, L., Yáñez, M. A., Chacon, M. R., Aguilera-Arreola, M. G., Catalán, V., Figueras, M. J., & Martínez-Murcia, A. J. (2004). Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes. International Journal of Systematic and Evolutionary Microbiology, 54, 1511-1519.
49. Stapp, C. (1928). Schizomycetes (Spaltpilze oder Bakterien). In P. Sorauer (Ed.), Handbuch der Pflanzenkrankheiten (pp. 1-295). Berlin: Paul Parey.
50. Stead, D. E., Simpkins, S. A., Weller, S. A., Hennessy, J., Aspin, A., Stanford, H., Smith, N. C., & Elphinstone, J. G. (2003). Classification and identification of plant pathogenic Pseudomonas species by REP-PCR derived genetic fingerprints. In N. S. Iacobellis, A. Collmer, S. W. Hutcheson, et al. (Eds.), Pseudomonas syringae and related pathogens: Biology and genetic (pp. 411-421). Dordrechts: Kluwer Academic Publishers.
51. Swingle, D. B. (1925). Center rot of French endive or wilt of chicory (Cichorium intybus L.). Phytopathology, 15, 730.
52. Tamura, K., Nei, M., & Kumar, S. (2004). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences of the United States of America, 101, 11030-11035.
53. 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. Molecular Biology and Evolution, 28, 2731-2739.
54. Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). Clustal-W - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
55. Trantas, E. A., Sarris, P. F., Pentari, M. G., Mpalantinaki, E. E., Ververidis, F. N., Goumas, D. E. (2012). Pseudomonas cichorii the causal agent of tomato pith necrosis in Crete. Paper presented at the 16th conference national conference organized by the Hellenic Phytopathological Society, Thessaloniki, Greece.
56. Vaneechoutte, M., De Beenhouwer, H., Claeys, G., Verschraegen, G., De Rouck, A., Paepe, N., Elaichouni, A., & Portaels, F. (1993). Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. Journal of Clinical Microbiology, 31, 2061-2065.
57. Wilkie, P., & Dye, D. W. (1974). Pseudomonas cichorii causing tomato and celery diseases in New Zealand. New Zealand Journal of Agricultural Research, 17, 123-130.
58. Yamamoto, S., Bouvet, P. J. M., & Harayama, S. (1999). Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. International Journal of Systematic Bacteriology, 49, 87-95.
59. Yamamoto, S., Kasai, H., Arnold, D. L., Jackson, R. W., Vivian, A., & Harayama, S. (2000). Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology-Uk, 146, 2385-2394.
60. Zuckerkandl, E., & Pauling, L. (1965). Evolutionary divergence and convergence in proteins. In V. Bryson & H. J. Vogel (Eds.), Evolving genes and proteins (pp. 97-166). New York: Academic.