Interactions of fungal pathogens and antagonistic bacteria in the rhizosphere of Brassica napus

The rhizosphere is an active interface where plants and microorganisms (pathogenic, beneficial and neutral) establish a complex and varied molecular dialogue, however knowledge of the functional mechanisms mediating interactions is still limited. Plants invest a significant proportion of their photosynthetically fixed carbon in maintaining the rhizosphere microbiome via root exudation and in return beneficial microbes provide profitable functions to the plant. The potential of naturally occurring soil microorganisms to control phytopathogens and to promote plant growth is well documented, but the functional mechanisms governing the reciprocal signaling between microbial communities and plants are not well understood. The aim of the studies described in this thesis was to gain insight into the functional basis of interactions between the fungal root pathogen Rhizoctonia solani and root associated antagonistic bacteria of the genus Serratia in the rhizosphere of Brassica napus. \nTranscriptomic responses of the oilseed rape pathogen R. solani, to the plant-associated and pathogen- antagonistic bacteria Serratia proteamaculans S4 and S. plymuthica AS13, were studied using RNA-sequencing. The results demonstrate a major shift in the fungal gene expression with simultaneous alterations in primary metabolism, activation of defense and attack mechanisms and distortions in hyphal morphology. \nStable isotope probing coupled with high throughput sequencing allowed the description of the composition of bacterial and fungal communities in the rhizosphere soil and the roots of B. napus and the identification of active taxa capable of assimilating recently fixed plant carbon. Our results support the idea of active selection of microbial communities from the more diverse rhizosphere environment by the roots. Furthermore, the data confirm the potential of some active genera (Streptomyces, Rhizobium, Clonostachys and Fusarium) to be used as microbial inoculants for improved productivity and health of oilseed rape. \nPatterns of gene expression in B. napus exposed to factorial combinations of R. solani and S. proteamaculans S4 were examined in-vitro using RNA-sequencing. Plants inoculated with R. solani only were almost dead at 240h post-inoculation and massive transcriptional reprogramming was observed, whereas the presence of S4 modulated the transcriptional responses and resulted in healthy plants. With R. solani present, we observed an interplay between stress and defense involving salicylic acid, jasmonic acid, ethylene and abscisic acid as common regulators. Induced systemic resistance when S4 present potentially depends on jasmonic acid, auxin and salicylic acid. Downregulation of stress-related and upregulation of defense-related genes were associated with transcriptional responses suggesting floral induction and plant development.