Sequence Diversity in the Dickeya fliC Gene: Phylogeny of the Dickeya Genus and TaqMan® PCR for 'D. solani', New Biovar 3 Variant on Potato in Europe

Abstract

Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large diversity of crops and ornamental plants. Strains affecting potato are mainly found in D. dadantii, D. dianthicola and D. zeae, which appear to have a marked geographical distribution. Furthermore, a few Dickeya isolates from potato are attributed to D. chrysanthemi and D. dieffenbachiae. In Europe, isolates of Erwinia chrysanthemi biovar 1 and biovar 7 from potato are now classified in D. dianthicola. However, in the past few years, a new Dickeya biovar 3 variant, tentatively named ‘Dickeya solani’, has emerged as a common major threat, in particular in seed potatoes. Sequences of a fliC gene fragment were used to generate a phylogeny of Dickeya reference strains from culture collections and with this reference backbone, to classify pectinolytic isolates, i.e. Dickeya spp. from potato and ornamental plants. The reference strains of the currently recognized Dickeya species and ‘D. solani’ were unambiguously delineated in the fliC phylogram. D. dadantii, D. dianthicola and ‘D. solani’ displayed unbranched clades, while D. chrysanthemi, D. zeae and D. dieffenbachiae branched into subclades and lineages. Moreover, Dickeya isolates from diagnostic samples, in particular biovar 3 isolates from greenhouse ornamentals, formed several new lineages. Most of these isolates were positioned between the clade of ‘D. solani’ and D. dadantii as transition variants. New lineages also appeared in D. dieffenbachiae and in D. zeae. The strains and isolates of D. dianthicola and ‘D. solani’ were differentiated by a fliC sequence useful for barcode identification. A fliC TaqMan®real-time PCR was developed for ‘D. solani’ and the assay was provisionally evaluated in direct analysis of diagnostic potato samples. This molecular tool can support the efforts to control this particular phytopathogen in seed potato certification.

Genomic and metabolic comparison with Dickeya dadantii 3937 reveals the emerging Dickeya solani potato pathogen to display distinctive metabolic activities and T5SS/T6SS-related toxin repertoire

“…Aside the current effort on the taxonomic description of D. solani , questions arose about the origin, adaptation, ecology and, in an applied issue, the control of this emerging plant pathogen on potato cultures. Even if only a few genetic markers were analysed in several D. solani isolates from different countries, their high similarities suggested a clonal origin of D. solani populations affecting the potato plant host [4-6,8]. Remarkably, under greenhouse conditions at a high temperature (28°C), when the two bacterial species D. solani and D. dianthicola are coinoculated, D. solani isolates outcompete those of the other Dickeya species, revealing a high efficiency for colonizing potato roots and stems [9,10].…”

Putative new species of the genus Dickeya as major soft rot pathogens in Phalaenopsis orchid production

“…Based on the variability in the fliC nucleotide sequence, these isolates were divided into two groups, namely UDL‐3 and UDL‐4, as described in Van Vaerenbergh et al . (), which clustered together with similar Dickeya isolates from ornamental plants.…”

“…strains was observed in indigoidine production on NGM medium (Table ), as previously observed (Czajkowski et al ., ). Based on partial sequencing of 16S rDNA and fliC (Edwards et al ., ; Coenye et al ., ; Van Vaerenbergh et al ., ), all 14 isolates were confirmed to belong to the Dickeya genus. Again, some variability was observed in the partial fli C sequence, with most isolates corresponding to sequevars 13 (10/14 isolates) and 15 (4/14 isolates).…”

“…(). Overall, the data indicated that the group of isolates are indeed a distinct genetic lineage within the genus Dickeya and might be more widespread than previously thought (Van Vaerenbergh et al ., ; Suharjo et al ., ).…”

“…Real‐time PCR assays were designed to target the region of fli C specific for UDL‐3 and UDL‐4 of the Dickeya genus (Van Vaerenbergh et al ., ) and the gyrB regions specific for P. cypripedii . Publicly available target sequences from GenBank and sequence data produced in this study were aligned using CLC main workbench v. 6.8.2.…”