Microbiome Analysis Reveals Biocontrol of Aspergillus and Mycotoxin Mitigation in Maize by the Growth-Promoting Fungal Endophyte Colletotrichum tofieldiae Ct0861

Maize (<i>Zea mays</i> L.) is a globally critical crop that faces numerous challenges, including contamination by mycotoxigenic fungi such as <i>Aspergillus</i> spp. The use of fungal endophytes as bioinoculants offers a sustainable strategy to improve plant resilience against biotic and abiotic stresses. Here, we evaluate the potential of <i>Colletotrichum tofieldiae</i> strain Ct0861 as a bioinoculant and its impact on maize-associated bacterial and fungal microbiomes. Field trials demonstrated that Ct0861 enhanced biomass and yield compared to controls, regardless of the application method (seed or foliar). Microbiome profiling showed that Ct0861 induced subtle, compartment-specific changes in microbial diversity and composition, while preserving the stability of core microbiome assemblages. Both microbiome data and qPCR quantification confirmed a significant reduction in <i>Aspergillus</i> spp. abundance in Ct0861-treated plants. Greenhouse assays corroborated these results: Ct0861 reduced <i>A. flavus</i> biomass by up to 90% and significantly lowered aflatoxin levels in infected grains. Dual-culture assays and the absence of Ct0861 in grain samples suggest an indirect biocontrol mechanism, potentially mediated by plant-induced resistance. This study provides the first evidence that Ct0861 acts as a biocontrol agent against mycotoxigenic <i>Aspergillus</i> spp. in maize. Beyond promoting plant growth, Ct0861 enhances food safety by reducing mycotoxin accumulation without disrupting the native microbiome, supporting its potential as a tool for sustainable crop protection.