Cross-kingdom sRNA Ta_sRNA1 silences PRIM2 to fine-tune Arabidopsis immunity during symbiosis with Trichoderma atroviride.

Beneficial root-colonizing fungi such as Trichoderma promote plant growth and immunity, yet the contribution of fungal small RNAs (sRNAs) to these interactions remains poorly understood. Here, we identified Ta_sRNA1, a highly abundant Trichoderma atroviride sRNA that accumulates in Arabidopsis root cells and associates with ARGONAUTE 1 and 2 (AGO1/2) complexes to modulate host gene expression. Using stem-loop reverse transcription quantitative polymerase chain reaction, AGO immunoprecipitation, transgenic lines and a fungal overexpression strain, we examined the function of Ta_sRNA1 and identified PRIM2, encoding the large subunit of DNA primase, as a host target associated with Ta_sRNA1 activity. Ta_sRNA1-mediated repression of PRIM2 restricts fungal overcolonization and enhances resistance to Botrytis cinerea. This regulation is associated with systemic immune priming, increased reactive oxygen species (ROS) accumulation and maintenance of plant growth. By contrast, PRIM2 overexpression suppresses ROS and increases pathogen susceptibility. These findings indicate that a Trichoderma-derived cross-kingdom sRNA modulates plant immunity by targeting the susceptibility-associated gene PRIM2. This mechanism fine-tunes the balance between beneficial colonization and defense responses, highlighting fungal sRNAs as regulators of plant immune homeostasis during beneficial plant-microbe interactions.