Global evaluation of the fitness and virulence determinants in the phytopathogen Ralstonia solanacearum

[eng] Losses to plant pathogens pose a major threat to global agriculture and food security worldwide. In the context of globalisation and climate change, the emergence and dispersion of pathogens resistant to conventional management strategies causes destructive outbreaks. One of the most important bacterial phytopathogen is R. solanacearum, the causal agent of the bacterial wilt disease, infecting over 200 plant species. R. solanacearum colonises the vascular system of the plants and blocks the water flow by secreting exopolysaccharides, which causes the wilting symptoms. Moreover, it can persist and easily disperse through contaminated soil and waterways. Many different virulence factors have been studied to date but a comprehensive understanding of the transcriptional regulation during the life cycle of this pathogen is lacking. The huge genetic and phenotypic variability of this traditionally tropical pathogen has led to its spread and establishment in temperate regions. To prevent its dispersal and design efficient management strategies, inexistent to date, a thorough understanding of the pathogen infection and dispersion process is of paramount importance. In this thesis we set to characterise the transcriptomic landscape of R. solanacearum to unravel novel virulence and fitness determinants deployed by the pathogen throughout its life cycle. In the first two chapters, we studied the gene expression profile of the bacterium during in different stages of plant infection (Chapter 1 or C1) and the environmental soil and water stages (Chapter 2 or C2). Overall, we have identified a dynamic expression profile of different metabolism and virulence genes along the life cycle of the pathogen. Consistent with previous analysis, we identified that the Type III secretion system (T3SS) is also transcriptionally active at late stages of infection but also in water. Interestingly, we identified the alkali pH as a cue triggering T3SS expression in water, which links to the pH alkalinisation along infection inside the plant. Moreover, we validated the expression of different virulence factors in planta such as the flagellar or T4P motility along infection. In soil, we identified the expression of multiple metabolic pathways and stress-related genes that are required for the life of the bacterium in the soil. Among them, we described the induction of genes related to lignin degradation, and alternative metabolic pathways to synthetise carbon molecules related to str