Comparative transcriptomic analysis reveals distinct responses of beneficial bacterial endophytes to wild and cultivated rice root exudates

Beneficial interactions between plants and microorganisms strongly influence plant health and productivity, and root exudates play a central role in shaping these associations. In this study, we analyzed the transcriptional responses of the bacterial endophytes Enterobacter asburiae RCA24 and Kosakonia sacchari RCA25 to root exudates from two commercial Italian rice accessions (Oryza sativa Baldo and Vialone Nano) and from an accession of the wild progenitor of tropical rice, Oryza rufipogon. Transcriptome analysis showed that RCA24 displayed distinct responses to the two O. sativa varieties, whereas RCA25 exhibited more extensive transcriptional changes in response to O. rufipogon root exudates. Differentially expressed genes were mainly associated with central metabolism, stress response, and signal transduction, suggesting distinct patterns of bacterial adaptation to the different exudate profiles. Transcriptome analysis of inoculated rice further indicated broader transcriptional changes in plants colonized by RCA24 than in those colonized by RCA25. Differentially expressed genes, particularly in shoots, were associated with defense responses, hormone-mediated signaling pathways, and ribosome biogenesis, consistent with genotype-dependent plant responses to different bacterial strains. Overall, these findings indicate that wild and cultivated rice accessions differ in their interaction with beneficial bacterial endophytes at the transcriptional level. Traits associated with plant–microbiota interactions in O. rufipogon, which are lost during domestication and diversification, may represent valuable targets for future studies aimed at enhancing beneficial microbial associations in cultivated rice.