Insights into the lifestyle of Kosakonia rice endophytes

Endophytes are microorganisms that live inside plants and are often beneficial for the host. Kosakonia is a novel bacterial genus which includes several species which are diazotrophic and plant-associated. In this thesis, plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed. Three experimental chapters are presented, the first includes comparative genomics, secretome profiling, in-planta tests and a field release trial. Secretomics revealed 80 putative secreted proteins including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizosphere and endosphere colonization ability. A field trial using rice seeds inoculated with Kosakonia sp. showed no effect on plant growth promotion upon nitrogen stress and its microbiome studies revealed that Kosakonia was significantly more present in the inoculated rice. Comparative genomics evidenced that several protein domains were enriched in Kosakonia plant-associated strains. The second experimental chapter presents an enrichment strategy for the isolation of endophytes and for the identification of Kosakonia bacterial co-inhabitants in rice root endosphere. The last experimental chapter is a study on two LuxR solos from Kosakonia KO348 which are involved in cell-cell signaling and discusses their possible involvement in bacterial interspecies and plant-bacteria interkingdom signaling. One of these LuxR solos designated as LoxR, responds to exogenously signals produced by bacterial neighbors whereas the other, designated as PsrR, is important for plant-bacteria signaling. This thesis highlights that Kosakonia is an important recently classified genus having strains that possess good root endosphere colonization ability and undergoing signaling in the microbiome and with the plant host.