Detection and identification of Dickeya genomic species. Erwinia Workshop. St Denis, Reunion, France. 5-6 June 2010

Potato blackleg in Europe is caused by pectinolytic Pectobacterium atrosepticum (syn. Erwinia carotovora subsp. atroseptica), P. carotovorum subsp. carotovororum (syn. E. c. subsp. carotovora) and Dickeya spp. (syn. E. chrysanthemi). In the past, the blackleg pathogens equally contributed to the occurrence of blackleg, but in the last five years Dickeya spp. predominate in different European countries. Dickeya spp. has been distributed recently among six genomic species, largely coinciding with seven biochemically distinct groups (biovars). In potato in Europe, before 2000 D. dianthicola (biovar 1 and 7) was almost exclusively found, a species more adapted to temperate climates. Since 2000, a biovar 3 Dickeya sp. was isolated from potatoes grown in Israel, Finland, Poland and the Netherlands, which could not be classified. Results from dnaX and 16S rDNA sequence analysis, rep-PCR and biochemical assays indicate that strains belong to a new species, preliminary called “D. solani”. To study the incidence and epidemiology of the Dickeya species complex, seven TaqMan PCR assays specific for the different Dickeya spp. were developed, based on dnaX sequences. The assays were evaluated with potato tuber samples derived from field experiments. For detection of low densities of Dickeya in plant material a procedure was evaluated to enrich Dickeya and Pectobacterium in a pectate broth medium (PEB) under low oxygen conditions, prior to detection with TaqMan PCR or ELISA. Bacteria antagonizing growth of Dickeya and Pectobacterium were isolated from the PEB and characterized by 16S rDNA sequencing. To improve the selectivity of the enrichment, an antibiotic (sulfomethoxazole) was selected that reduces growth of many of the antagonists without affecting growth of Dickeya and Pectobacterium.