Early Emergence of Dickeya solani Revealed by Analysis of Dickeya Diversity of Potato Blackleg and Soft Rot Causing Pathogens in Switzerland

Abstract

Blackleg and soft rot in potato caused by Pectobacterium and Dickeya enterobacteral genera are among the most destructive bacterial diseases in this crop worldwide. In Europe, over the last century, Pectobacterium spp. were the predominant causal agents of these diseases. As for Dickeya, before the large outbreak caused by D. solani in the 2000s, only D. dianthicola was isolated in Europe. The population dynamics of potato blackleg causing soft rot Pectobacteriaceae was, however, different in Switzerland as compared to that in other European countries with a high incidence (60 up to 90%) of Dickeya species (at the time called Erwinia chrysanthemi) already in the 1980s. To pinpoint what may underlie this Swiss peculiarity, we analysed the diversity present in the E. chrysanthemi Agroscope collection gathering potato isolates from 1985 to 2000s. Like elsewhere in Europe during this period, the majority of Swiss isolates belonged to D. dianthicola. However, we also identified a few isolates, such as D. chrysanthemi and D. oryzeae, two species that have not yet been reported in potatoes in Europe. Interestingly, this study allowed the characterisation of two “early” D. solani isolated in the 1990s. Genomic comparison between these early D. solani strains and strains isolated later during the large outbreak in the 2000s in Europe revealed only a few SNP and gene content differences, none of them affecting genes known to be important for virulence.

The Broad Host Range Plant Pathogen Dickeya dianthicola Shows a High Genetic Diversity

“…Previous studies of D. dianthicola genomic diversity [ 12 , 19 , 21 ] focused on strains isolated from potato. They highlighted the high relatedness of the strains that shared ANI values higher than 99% and even the clonality of most strains isolated during the outbreak that have ravaged the US since 2015.…”

“…Although reports of D. dianthicola (at the time grouped with all Dickeya under the name Erwinia chrysanthemi ) on potato in Europe date back to the 1970s, losses caused by this pathogen have been generally low and sporadic in most countries [ 10 ]. An exception is Switzerland and the Netherlands, where D. dianthicola has been one of the dominant agents of blackleg and soft rot in potato since the 1980s until 2000, after which D. solani became prevalent; since 2014, P. brasiliense dominates [ 3 , 11 , 12 ]. In the past decade, potato blackleg caused by D. dianthicola has been reported in several locations worldwide.…”

“…MLSA analyses based on housekeeping gene sequences showed that little sequence diversity was found in D. dianthicola strains [ 8 , 12 , 16 , 18 , 19 , 20 ]. This high relatedness was confirmed by whole-genome analyses [ 19 , 20 , 21 ].…”

Biocontrol Activity of Aspergillus terreus ANU-301 against Two Distinct Plant Diseases, Tomato Fusarium Wilt and Potato Soft Rot

“…Fusarium wilt is strongly related with tomato production loss in field conditions ( Chakraborty and Acharya, 2017 ). Blackleg and soft rot in potato, both caused by D. chrysanthemi , are among the most damaging bacterial diseases plaguing this world’s fourth most important food crop ( Pédron et al, 2021 ). The potentials of Aspergillus spp., particularly A. terreus , are currently underutilized ( Galeano et al, 2021 ; Vassileva et al, 2020 ).…”

Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity

“…In addition to the above-mentioned fungi and oomycetes, the present study also examined the effect of the three selected Streptomyces strains on two bacterial pathogens, Dickeya solani, and Pectobacterium carotovorum, responsible for inducing blackleg disease and soft rot of potato tubers (Mansfield et al, 2012;Pédron et al, 2021;Toth et al, 2011).…”