Abstract
Soil and plant‐associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top‐down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil–plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra‐ and inter‐kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti‐predator responses than healthy plants, but also contained a greater abundance of metagenome‐assembled genomes with functional traits involved in this response. The increased microbial inter‐kingdom associations between bacteria and protists, coupled with the notable bacterial anti‐predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top‐down forces under pathogenic stress.