Fungal infection triggers a community-wide dysbiosis and recruits a bacterial pathobiome in the Chinese celery rhizosphere
Soil-borne fungal pathogens threaten global crop security, but their impact on the entire rhizosphere microbiome, particularly cross-kingdom interactions, remains poorly elucidated. The pathobiome concept suggests that disease is a state of community-wide dysbiosis rather than the result of a single pathogen. Here, we investigated this by profiling the bacterial (16S rRNA) and fungal (ITS2) communities in the rhizosphere of healthy and Fusarium-infected Chinese celery across two farms and two growth stages. Our results reveal that fungal infection profoundly restructured the entire microbiome. In infected plants, fungal diversity and evenness plummeted, driven by an overwhelming dominance of the pathogen Fusarium (up to 98.9% relative abundance), which displaced key resident genera like Pyrenochaetopsis. Concurrently, infection facilitated the assembly of a context-dependent bacterial pathobiome. LEfSe analysis identified specific bacterial biomarkers of disease, including Tumebacillus, Ralstonia, and members of the Enterobacteriaceae, which replaced beneficial taxa like Lysobacter and Rhizobiaceae found in healthy rhizospheres. Notably, severe disease at one farm was associated with significant community instability (heterogeneous dispersion), preceding the diversity collapse. Our findings demonstrate that fungal disease is an ecological cascade, where a primary pathogen destabilizes the community, leading to the recruitment of a secondary bacterial pathobiome. This provides a systems-level understanding of plant disease and highlights microbiome stability as a key target for developing novel, sustainable disease management strategies.