Development of protection tools targetingDickeya species is an important issue in the potato production. Here, we present the identification and the characterization of novel biocontrol agents. Successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several Dickeya sp. and/or Pectobacterium sp. pathogens. Most of them belonged to the Pseudomonas and Bacillus genera. In vitro assays revealed a fitness decrease of the tested Dickeya sp. and Pectobacterium sp. pathogens in the presence of the biocontrol agents. In addition, four independent greenhouse assays performed to evaluate the biocontrol bacteria effect on potato plants artificially contaminated with Dickeya dianthicola revealed that a mix of three biocontrol agents, namely, Pseudomonas putida PA14H7 and Pseudomonas fluorescens PA3G8 and PA4C2, repeatedly decreased the severity of blackleg symptoms as well as the transmission of D. dianthicola to the tuber progeny. This work highlights the use of a combination of biocontrol strains as a potential strategy to limit the soft rot and blackleg diseases caused by D. dianthicola on potato plants and tubers. The Pectobacterium and Dickeya pectinolytic bacteria are phytopathogens responsible for several macerating diseases on a wide range of crop and ornamental plants (1-3). The damage caused by these pathogens remains an important issue in many countries worldwide. In Europe, the pectinolytic pathogens on potato crops include Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum, Dickeya dianthicola, and Dickeya solani (4-8). Recently, new Pectobacterium taxa, i.e., P. wasabiae and P. carotovorum subsp. brasiliense, have been characterized (2, 9, 10). Pectobacterium sp. populations are qualified as endemic, as their presence has been observed for almost a century in Europe, while the presence of Dickeya spp. as a cause of the symptoms in potato fields was sporadic until the 2000s and the Dickeya sp. damages were probably exclusively due to the species D. dianthicola. In contrast, D. solani seems to have emerged in the 2000s (3).Pectobacterium and Dickeya potato pathogens induce blackleg on stems and soft rot on tubers (11,12). A polyphyletic pathogen population may be isolated from a single sample of symptomatic plant tissues (13). The pathogens penetrate in host plants through natural pores or wounds (i.e., the lenticels, the elongation zones of roots, or insect wounds) as well as mechanical wounds. Insects can act as vectors; surface water and aerosols may also contribute to the dissemination of the pathogens (12, 14-21). Once the pathogens have infected the plant, they may propagate throughout the whole plant and son tubers by the vascular vessels. Losses due to Pectobacterium and Dickeya, related to stem and tuber rot, are major causes for downgrading and rejection of potatoes during seed potato certification. The certification is based on visual inspections in fields or on lots, ranging in Europe from 0 to 4% blackl...

Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive ability against the closely related resident D. dianthicola species. Epidemiological records over one decade in France revealed the establishment of D. solani and the maintenance of the resident D. dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D. dianthicola caused a higher symptom incidence on aerial parts of potato plants than D. solani, while D. solani was more aggressive on tubers (i.e. with more severe symptoms). In co-infection assays, D. dianthicola outcompeted D. solani in aerial parts, while the two species co-existed in tubers. A comparison of 76 D. solani genomes (56 of which have been sequenced here) revealed balanced frequencies of two previously uncharacterized alleles, VfmB Pro and VfmB Ser , at the vfmB virulence gene. Experimental inoculations showed that the VfmB Ser population was more aggressive on tubers, while the VfmB Pro population outcompeted the VfmB Ser population in stem lesions, suggesting an important role of the vfmB virulence gene in the ecology of the pathogens. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why the endemic D. dianthicola nevertheless persisted.

Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive ability against the closely-related resident D. dianthicola species. Epidemiological records over one decade in France revealed the establishment of D. solani and the maintenance of the resident D. dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D. dianthicola caused a higher symptom incidence on aerial parts of potato plants than D. solani, while D. solani was more aggressive on tubers (i.e. with more severe symptoms). In co-infection assays, D. dianthicola outcompeted D. solani in aerial parts, while the two species co-existed in tubers. A comparison of 76 D. solani genomes (56 of which having been sequenced here) revealed balanced frequencies of two previously uncharacterized alleles, VfmBPro and VfmBSer, at the vfmB virulence gene. Experimental inoculations showed that the VfmBSer population was more aggressive on tubers while the VfmBPro population outcompeted the VfmBSer population in stem lesions, suggesting an important role of the vfmB virulence gene in the ecology of the pathogens. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why the endemic D.dianthicola nevertheless persisted.

Dickeya and Pectobacterium species are necrotrophic pathogens that macerate stems (blackleg disease) and tubers (soft rot disease) of Solanum tuberosum. They proliferate by exploiting plant cell remains. They also colonize roots, even if no symptoms are observed. The genes involved in pre-symptomatic root colonization are poorly understood. Here, transposon-sequencing (Tn-seq) analysis of Dickeya solani living in macerated tissues revealed 126 genes important for competitive colonization of tuber lesions and 207 for stem lesions, including 96 genes common to both conditions. Common genes included acr genes involved in the detoxification of plant defense phytoalexins and kduD, kduI, eda (=kdgA), gudD, garK, garL, and garR genes involved in the assimilation of pectin and galactarate. In root colonization, Tn-seq highlighted 83 genes, all different from those in stem and tuber lesion conditions. They encode the exploitation of organic and mineral nutrients (dpp, ddp, dctA, and pst) including glucuronate (kdgK and yeiQ) and synthesis of metabolites: cellulose (celY and bcs), aryl polyene (ape), and oocydin (ooc). We constructed in-frame deletion mutants of bcsA, ddpA, apeH, and pstA genes. All mutants were virulent in stem infection assays, but they were impaired in the competitive colonization of roots. In addition, the ΔpstA mutant was impaired in its capacity to colonize progeny tubers. Overall, this work distinguished two metabolic networks supporting either an oligotrophic lifestyle on roots or a copiotrophic lifestyle in lesions. This work revealed novel traits and pathways important for understanding how the D. solani pathogen efficiently survives on roots, persists in the environment, and colonizes progeny tubers.

Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive advantages or disadvantages against the closely-related resident D.dianthicola species. Epidemiological records over one decade in France revealed the establishment of D.solani and the maintenance of the resident D.dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D.dianthicola was more aggressive than D.solani on aerial parts, while D.solani was more aggressive on tubers. In co-infection assays, D.dianthicola outcompeted D.solani in aerial parts, while D.solani and D.dianthicola co-existed in tubers. A comparison of 76 D.solani genomes (56 of which having been sequenced here) revealed balanced frequencies of two uncharacterized alleles, VfmBPro and VfmBSer, at the vfmB virulence gene. Experimental inoculations showed that the VfmBSer population was more aggressive on tubers, while VfmBPro and VfmBSer populations exhibited a similar aggressiveness on stems. In stem co-infections, the VfmBPro population outcompeted the VfmBSer population, while they co-existed in tubers. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why D.dianthicola nevertheless persisted. More broadly, this study contributes to our understanding the ecological determinants of pathogen invasion and of the conditions for the maintenance of endemic competitors.