Spatial niche differentiation and bacillin 20 mediated modulation shape fungal community diversity and network structure in roots and rhizospheres of corn and wheat

Background The phytomicrobiome plays a crucial role in nutrient cycling, plant growth promotion, and stress resilience in cereals. However, how spatial niche differentiation (root vs. rhizosphere), host genotype and microbial biocontrol agents jointly shape fungal community structure and function remains poorly understood. Results Using ITS-based amplicon sequencing, we examined the effects of compartmental identity, host species ( Zea mays and Triticum aestivum ) and a Bacillus thuringiensis -derived bacteriocin (bacillin 20) on fungal community diversity, composition and co-occurrence networks. Alpha and beta diversity analyses revealed strong compartmental segregation, with rhizosphere communities exhibiting greater richness and taxonomic heterogeneity than roots, which harbored more even and host-filtered assemblages. Setophoma , Myrmecridium , Periconia , and Talaromyces as dominant root taxa, while Fusarium , Chaetomium , Alternaria , and Exophiala were enriched in rhizospheres. Bacillin 20 treatments, particularly at higher concentrations, enhanced the abundance of saprotrophic guilds and increased network complexity in rhizosphere communities. In contrast, root-associated networks were more compact and modular, reflecting stronger host-mediated ecological filtering. Functional annotation using FUNGuild revealed that saprotrophic fungi predominated in corn, whereas symbiotrophic guilds dominated wheat, highlighting host-specific functional partitioning. Conclusion Our findings demonstrated that spatial compartmentalization is the primary driver of fungal community assembly in cereals, with host genotype and Bacillus -mediated modulation exerting secondary but significant effects on composition and trophic function. Bacillin 20 acted as an ecological modulator, promoting saprotrophic activity and metabolic flexibility in rhizospheres while maintaining stable, symbiotic networks within roots. This study establishes a hierarchical model of cereal mycobiome organization, providing a framework for phytomicrobiome-informed biocontrol and sustainable crop management strategies.