One open question regarding plant–microbe interactions is how a plant interacts molecularly with both a beneficial microbe and a pathogenic fungus. This study used RNA-seq to investigate molecular responses in maize roots during a tripartite interaction with the fungal pathogen Fusarium verticillioides (Fv), which causes stalk, ear, and root rot, and the endophytic biocontrol agent Bacillus cereus sensu lato B25, known to suppress Fv and promote plant growth. Roots of seven-day-old maize inoculated with Fv (Zm-Fv), B25 (Zm-B25), and co-inoculated (Zm-Fv-B25) were compared to uninoculated control (Zm). Differential Gene Expression (DEG), Gene Ontology (GO) and KEGG analysis revealed distinct molecular responses. Fv suppressed plant pathways related to DNA and protein synthesis and impaired root development. In contrast, B25 triggered defense priming and growth-related responses. In the co-inoculation experiment (Zm-B25-Fv), upregulated DEGs were associated with both defense-related metabolic pathways, including jasmonic acid signaling and secondary metabolite biosynthesis, and genes involved in plant growth processes. Co-expression networks using Arabidopsis orthologs supported the induction of defense- and growth and development-related genes. This study is the first RNA-seq analysis of maize root molecular responses during the tripartite interaction with a fungal pathogen and its bacterial biocontrol agent, providing new directions for further research to understand the detailed molecular mechanisms underlying this interaction fully.

One open question regarding plant-microbe interactions is how a plant interacts molecularly with both a beneficial microbe and a pathogenic fungus. This study used RNA-seq to investigate molecular responses in maize roots during a tripartite interaction with the fungal pathogen Fusarium verticillioides (Fv), which causes stalk, ear, and root rot, and the endophytic biocontrol agent Bacillus cereus sensu lato B25, known to suppress Fv and promote plant growth. Roots of seven-day-old maize inoculated with Fv (Zm-Fv), B25 (Zm-B25), and co-inoculated (Zm-Fv-B25) were compared to uninoculated control (Zm). Differential Gene Expression (DEG), Gene Ontology (GO) and KEGG analysis revealed distinct molecular responses. Fv suppressed plant pathways related to DNA and protein synthesis and impaired root development. In contrast, B25 triggered defense preparedness and growth-related responses. In the co-inoculation (Zm-Fv-B25), upregulated DEGs were associated with defense-related metabolic pathways, including jasmonic acid signaling and secondary metabolite biosynthesis, while also promoting plant growth. Co-expression networks using Arabidopsis orthologs supported these findings. This study is the first RNA-seq analysis of maize root molecular responses during the tripartite interaction with a fungal pathogen and its bacterial biocontrol agent, providing new directions for further research to understand the detailed molecular mechanisms underlying this interaction fully.