The rice sheath rot pathogen Pseudomonas fuscovaginae; microbiome and cell-cell signalling studies

Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. In this thesis the bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Three experimental work chapters are presented; the first concerns the pathobiome and microbiome performed on rice plant samples collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. The results have showed that in symptomatic samples the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in symptomatic samples in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is a very useful approach in determining the microorganisms involved in a plant disease. The second experimental chapter presents the culturable microbiome on rice sheath asymptomatic samples from highland where P. fuscovaginae was predominant. This work also includes the purification and characterization of a set of bacterial isolates making up a culture collection. Some phenotypes assays including antibacterial activity against P. fuscovaginae have been performed and a bacterial isolate belonging to Alcaligenes genus displayed a strong antagonistic activity against the pathogen. The last chapter presents the cell-cell signaling studies of P. fuscovaginae since it has been evidenced in the previous chapters that a complex microbial community in the pathobiome is associated with the disease. Previous studies have shown that quorum sensing signalling in P. fuscovaginae is inactive in vitro but it is active in planta and plays a role in virulence. The aim of the final experimental chapter was to shed light on the molecular switching-on system of the quorumsensing cascade. Genetics screening on P. fuscovaginae Tn5 mutant bank identified a transcriptional repressor that increases quorum sensing signal production and also regulates an RND efflux pump. This thesis highlights that pathobiome/microbiome studies are instrumental in identifying plant pathogens and that plant microbiome interactions can play a role in the disease process.