Abstract
The burkholderia group is composed of multiple bacterial genera (including Burkholderia and Paraburkholderia). Some species indulge in diverse interactions with eukaryotic hosts that range from pathogenicity to symbiosis. Many burkholderia species dwell in association with rice, making this host and ideal model for burkholderia/plant interactions. The taxonomy of burkholderia delineates a frontier between the Burkholderia genus, grouping the majority of pathogenic species, and the Paraburkholderia genus, mainly phytobeneficial and environmental species. This thesis project strived to characterize the genetic frontiers between species of both genera that share the capacity to interact with rice. First, we explored the taxonomic diversity for 124 rice-isolates using dedicated markers (16S and recA), and went into a more detailed analysis for a subset of 12 supposedly different species suing whole genome sequencing. We developed the intraspecific diversity of B. cenocepacia strains which we had found to be rice associated This was unexpected for this human pathogen and led us to describe a new species, with improved plant interaction abilities (which we propose to name B. servocepacia). We then explored the genetic bases regulating plant-adaptation of Burkholderia and Paraburkholderia species using two complementary approaches. We first undertook a transcriptomic profiling of the reaction to root exudates for six rice-isolates belonging to either genus. We thus demonstrated a strain specific response of the early plant-sensing, independent of the strain’s taxonomic attribution. We also listed the principal functions involved in exudate sensing. Our second approach focused on the rice endophyte models B. vietnamiensis LMG10929 (Bv) and P. kururiensis M130 (Pk) for which we undertook a high-throughput genetic screening of insertion mutant libraries (Tn-seq), during the root surface colonization step of two rice cultivars belonging to Oryza sativa ssp. japonica and Oryza sativa ssp. indica. We noticed a strong disparity in the adaptation for rice colonization between Bv and Pk as the display genetic requisites that differ in nature and number. Furthermore, we demonstrated a host-dependent adaptation for root colonization from both strains. Finally, we investigated on the distribution of type III secretion systems (T3SS) within burkholderia. We describe two novel T3SS types and in one instance, demonstrate its role in plant colonization for Bv. The thesis is concluded by a general discussion, summarizing the results of this project and situating them in the context of adaptative frontiers for plant interactions between Burkholderia and Paraburkholderia.