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

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Beneficial interactions between plants and microorganisms strongly influence plant health and productivity, androot exudates play a central role in shaping these associations. In this study, we analyzed the transcriptional responses of thebacterial endophytes Enterobacter asburiae RCA24 and Kosakonia sacchari RCA25 to root exudates from two commercialItalian 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. Differentiallyexpressed genes were mainly associated with central metabolism, stress response, and signal transduction, suggesting distinctpatterns of bacterial adaptation to the different exudate profiles. Transcriptome analysis of inoculated rice further indicatedbroader transcriptional changes in plants colonized by RCA24 than in those colonized by RCA25. Differentially expressedgenes, particularly in shoots, were associated with defense responses, hormone-mediated signaling pathways, and ribosomebiogenesis, consistent with genotype-dependent plant responses to different bacterial strains. Overall, these findings indicatethat wild and cultivated rice accessions differ in their interaction with beneficial bacterial endophytes at the transcriptionallevel. 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 cultivatedrice.

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