Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts

Abstract The root microbiome includes fungal pathogens capable of colonizing multiple plant hosts, yet the underlying genetic determinants remain unknown. Here we report that Plectosphaerella cucumerina is a core member of the Arabidopsis thaliana root microbiota, which displays pathogenic potential across multiple hosts. Using a collection of 72 Plectosphaerella isolates and whole-genome sequencing, we observed subtle phenotypic and genotypic variation associated with fungal phylogeny but not host plant identity. Transcriptome profiling of a P. cucumerina isolate in roots of diverse plants revealed core and host-specific fungal responses, including induction of carbohydrate-active enzymes (CAZymes) involved in root cell wall deconstruction. A fungal gene encoding a candidate β-1,3-glucanase (GH64) was identified as a key genetic factor driving multihost infection. This gene is present across plant-colonizing fungi and functions as a disease determinant in both P. cucumerina and a Colletotrichum root pathogen. Our results indicate that host-induced CAZymes can couple fungal virulence with multihost compatibility.