Abstract
In natural conditions, plants interact with a large diversity of microorganisms maintaining with them various types of interaction ranging from mutualism to pathogenesis. Whatever the type of interaction established, the plants are able to recognize conserved microbial molecular motifs which trigger a so-called “non-host” immune response when perceived. This basal immune response has been extensively studied in the case of interactions with mutualistic and pathogenic microorganisms. However, in the case of “associative symbiosis” with beneficial rhizobacteria or bacterial endophytes, grouped under the term Plant Growth-Promoting Rhizobacteria (PGPR), the immune and physiological responses of plants have been scarcely described. In this context, this thesis project aimed at describing the transcriptional regulations of the model monocotyledonous rice, in response to the interaction with beneficial -rhizospheric or endophytic- and pathogenic bacteria of the genus Burkholderia sensu lato (s.l.). This ubiquitous genus of beta-proteobacteria has the particularity of having been subdivided into two genera with distinct ecologies: the genus Paraburkholderia, which groups together environmental and plant-associated species, and the genus Burkholderia sensu stricto (s.s.), which groups together human opportunistic and pathogenic species but also phytobeneficial species such as B. vietnamiensis. RNA-Seq analysis of the transcriptomic response of rice to three endophytic strains, Paraburkholderia kururiensis M130, Burkholderia vietnamiensis TVV75 and Paraburkholderia phytofirmans PsJN, revealed contrasting physiological regulations depending on the inoculated strain; in addition, comparative analyses of root tissue colonization by these strains enabled to associate some of these regulations with different colonization patterns. Finally, the expression of genes involved in the immune response of plants, identified by the functional analysis of transcriptomes, was measured during interaction kinetics with a wider diversity of strains. For this, ten strains of Burkholderia s.l., comprising three pathogenic strains, as well as three model rice PGPR strains of the genera Azospirillum, Herbaspirillum and Pseudomonas were selected. This last approach highlighted transcriptional regulations associated with the types of colonization, rhizospheric and endophytic, or interaction, beneficial and deleterious.This work is part of the characterization of the molecular bases of plants’ response to beneficial microorganisms which represent an important potential for the development of sustainable agronomic solutions favoring nutrition and plant resistance to diseases.