Insight into biodiversity of the recently rearranged genus Dickeya

Abstract

The genus Dickeya includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of six species in 2005, this genus now includes 12 recognized species. Despite the description of several new species in recent years, the diversity of the genus Dickeya is not yet fully explored. Many strains have been analyzed for species causing diseases on economically important crops, such as for the potato pathogens D. dianthicola and D. solani. In contrast, only a few strains have been characterized for species of environmental origin or isolated from plants in understudied countries. To gain insights in the Dickeya diversity, recent extensive analyzes were performed on environmental isolates and poorly characterized strains from old collections. Phylogenetic and phenotypic analyzes led to the reclassification of D. paradisiaca (containing strains from tropical or subtropical regions) in the new genus, Musicola, the identification of three water species D. aquatica, D. lacustris and D. undicola, the description of a new species D. poaceaphila including Australian strains isolated from grasses, and the characterization of the new species D. oryzae and D. parazeae, resulting from the subdivision of the species D. zeae. Traits distinguishing each new species were identified from genomic and phenotypic comparisons. The high heterogeneity observed in some species, notably for D. zeae, indicates that additional species still need to be defined. The objective of this study was to clarify the present taxonomy of the genus Dickeya and to reassign the correct species to several Dickeya strains isolated before the current classification.

Bacterial pathogens dynamic during multi-species infections

“…parvum , we did not find discriminating strains in our collection (Table S2). This is probably due to the fact that these latter species are quite homogeneous (Hugouvieux-Cotte-Pattat et al 2023; Pasanen et al 2020). The bacterial media used were LB medium without NaCl (hereafter LB: per liter 10 g tryptone, 5 g yeast extract) and TSB (per liter: 1,7 g casein peptone, 0.3 g soya peptone, 0.3 g NaCl, 0.25 g K 2 HPO 4 , 0.25 g glucose).…”

“…Due to their collective large host spectrum, SRP plant infections lead to severe economic losses and are collectively recognized as one of the ten most important bacterial plant pathogens (Mansfield et al 2012; Ma et al 2007; Portier et al 2020). Among SRP species, some species like Pectobacterium brasiliense , Pectobacterium carotovorum or Pectobacterium versatile are described as broad range species isolated from a large number of plant species while other like Pectobacterium parmentieri , Pectobacterium atrosepticum or Dickeya solani have been mainly recorded on a single host (Ma et al 2007; Portier et al 2020; Hugouvieux-Cotte-Pattat et al 2023) . P. versatile is the most frequently isolated taxon among the SRP species, both on plants and in the environment, a characteristic that might be linked with its higher resistance to antibiotics than other Pectobacterium spp.…”

“…Some newly described species like Pectobacterium aquaticum or Pectobacterium quasiaquaticum have been isolated solely from river water and their potential host plants (if any) are currently unknown raising the possibility that these species act are merely saprophytes on plant debris or evolved toward hosts alternative to plant, for example as gut species of plant feeding insect or water microfauna (Pédron et al 2019; Ben Moussa et al 2022, 2023). Species belonging to the Dickeya genus are well known to infect ornamentals of high economical value but several species could also be observed on major crops such as maize ( Dickeya zeae ) rice ( Dickeya oryzae ) or potato ( Dickeya dianthicola or D. solani ) where they have been responsible of severe outbreaks (Hugouvieux-Cotte-Pattat et al 2023).…”

Bacterial pathogens dynamic during multi-species infections

“…Due to their collective large host spectrum, SRP plant infections lead to severe economic losses and are collectively recognized as one of the ten most important bacterial plant pathogens (Ma et al, 2007;Mansfield et al, 2012;Portier et al, 2020). Among SRP species, some species like Pectobacterium brasiliense, Pectobacterium carotovorum or Pectobacterium versatile are described as broad range species isolated from a large number of plant species while other like Pectobacterium parmentieri, Pectobacterium atrosepticum or Dickeya solani have been mainly recorded on a single host (Ma et al 2007;Portier et al 2020;Hugouvieux-Cotte-Pattat et al 2023). P. versatile is the most frequently isolated taxon among the SRP species, both on plants and in the environment, a characteristic that might be linked with its higher resistance to antibiotics than other Pectobacterium spp.…”

“…Some newly described species like Pectobacterium aquaticum or Pectobacterium quasiaquaticum have been isolated solely from river water and their potential host plants (if any) are currently unknown raising the possibility that these species act are merely saprophytes on plant debris or evolved toward hosts alternative to plant, for example as gut species of plant feeding insect or water microfauna Ben Moussa et al, 2022. Species belonging to the Dickeya genus are well known to infect ornamentals of high economical value but several species could also be observed on major crops such as maize (Dickeya zeae) rice (Dickeya oryzae) or potato (Dickeya dianthicola or D. solani) where they have been responsible of severe outbreaks (Hugouvieux-Cotte-Pattat et al, 2023).…”