Diversity in the Bacterial Genus Dickeya Grouping Plant Pathogens and Waterways Isolates

Abstract

Background: Genus Dickeya comprises aggressive soft rot plant pathogens with wide geographic distribution and host ranges. Ten Dickeya species were characterized. Seven of them (Dickeya chrysanthemi, D. dadantii, D. dianthicola, D. fangzhongdai, D. solani, D. paradisiaca, and D. zeae) group causative agents of maceration-associated diseases that impact a wide variety of crops or ornamentals as well as isolates from fresh water. The other three species (D. aquatica, D. lacustris, D. undicola) were recently isolated only from water sources, so far. Here, we analyzed the Dickeya genetic diversity in relation to species affiliation and habitats. Methods: We compared the genomes of 59 Dickeya strains isolated from various hosts and from different environments, determined their relatedness both at the genetic level (ANI) and their pan-genome content and carried out SiLix analysis to explore the occurrence of orthologous or species/strain-specific gene families. Results: Our study revealed significant conservation of virulence-associated genes in most Dickeya species (including “water-specific” ones). We also identified the genome-specific traits of the various species and highlighted the intra-species diversities. At the species level, we observed a contrasting diversity with some species grouping highly related strains while others were much more diverse or at the limit of subdivision in separate species. The diversity was not related to diversity in habitat or geographical origin neither in the extent of the species accessory genome nor in the number of strain-specific genes. Conclusions: The genus Dickeya pangenome analysis did not highlight strain clustering following host/environment of isolation. The different Dickeya species present few specific characteristics and fewer specific gene losses, which are frequently found in specialized human pathogens, reflecting the broad host range of this genus. No “water-specific” genes were identified that would indicate possible spread of Dickeya via waterways and implicate irrigation water as a potential threat for economically important crops.