A beneficial root endophyte buffers natural variation in pathogen susceptibility across Arabidopsis accessions

Summary Host genetic diversity shapes pathogen susceptibility within plant populations, raising the question of whether beneficial root microbes can buffer these differences. The fungal root endophyte Serendipita indica ( Si ) promotes plant growth and can mitigate disease caused by the pathogen Bipolaris sorokiniana ( Bs ). Here, we assessed how natural host genetic variation influences Si ‐mediated protection against Bs in Arabidopsis thaliana . We screened 47 A. thaliana accessions for susceptibility to Bs with and without Si colonization and performed phenotypic, transcriptomic, and comparative genomic analyses of two genetically and geographically proximate Swedish accessions, T510 and T530, that differed strongly in Bs colonization. Si conferred consistent protection against Bs across all accessions, despite variation in baseline susceptibility and immune‐gene content. T510 and T530 differed in Bs colonization, disease symptoms, transcriptional responses, and immune‐gene repertoires, including presence–absence variation of the TIR‐NLR gene ISI . T530 lacks ISI , and mutation of ISI in Col‐0 increased Bs susceptibility, demonstrating that ISI contributes to root immunity. However, Si ‐mediated protection was retained in the absence of ISI , demonstrating that ISI is not required for this protective effect. Beneficial fungal endophytes can thus buffer phenotypic consequences of natural variation in pathogen susceptibility, stabilizing disease outcomes across genetically diverse plant populations.