Domain gain or loss in a fungal chitinase enables specialization towards antagonism or immune suppression

Effector proteins orchestrate interactions that determine host compatibility and microbial competition. Among these are microbial chitinases, widespread enzymes involved in nutrient acquisition, fungal cell-wall remodelling, and antagonism, yet how their functions diversify across ecological roles remains unclear. Here, we show that modular domain variation within a conserved GH18 chitinase family enables specialization between microbial antagonism and host immune suppression in the beneficial root endophyte Serendipita indica. The chitinase SiCHIT, bearing a C-terminal CBM5 domain, is induced during fungal confrontation and inhibits growth of the phytopathogen Bipolaris sorokiniana, thereby protecting host roots. Deleting CBM5 abolishes this antagonistic activity, whereas grafting CBM5 onto its paralog SiCHIT2, which lacks this domain, confers antifungal function. In contrast, SiCHIT2 is induced during root colonization and suppresses chitin-triggered immunity, promoting host compatibility. These results show how domain loss and regulatory divergence can reprogram antimicrobial enzymes into immune-suppressive effectors in beneficial plant-associated fungi.