Abstract Burkholderia vietnamiensis LMG10929 ( Bv ) and Paraburkholderia kururiensis M130 ( Pk ) are bacterial rice growth-promoting models. Besides this common ecological niche, species of the Burkholderia genus are also found as opportunistic human pathogens while Paraburkholderia are mostly environmental and plant-associated species. Here, we compared the genetic strategies used by Bv and Pk to colonize two subspecies of their common host, Oryza sativa ssp. japonica (cv. Nipponbare) and ssp. indica (cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes in Bv involved in rice roots colonization compared to Pk , including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towards Bv compared to Pk . For both strains, the bacterial fitness depends on a higher number of genes when colonizing indica rice compared to japonica . These divergences in host pressure on bacterial adaptation could be partly linked to the cultivar’s differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production in Bv and quorum sensing in Pk. The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays. Importance Burkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. However, the closely related Burkholderia genus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits in Burkholderia vietnamiensis and Paraburkholderia kururiensis that contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.

Differential genetic strategies ofBurkholderia vietnamiensisandParaburkholderia kururiensisfor root colonization ofOryza sativassp.japonicaand ssp.indica, as revealed by Tn-seq