Maize Kernel-Associated Metagenomes Reveal Potential Microbe-Microbe Interactions that Underlie Fusarium Ear Rot Disease

Abstract

As an alternative to host resistance, transgenic expression of entomocidal and antimicrobial proteins from Bacillus thuringiensis (Bt) in maize can mitigate Fusarium ear rot (FER). This study evaluates FER in Bt and conventional maize; and the role of microbes in the kernel-associated metagenome using quantitative reduced representation sequencing (qRRS). Our results revealed significant differences in FER severity across environments and varieties, and between inoculation treatments. The lower FER scores of conventional maize Spectrum-6416 relative to other varieties highlight resistant alleles in maize germplasm, while strong correlations indicate FER-induced yield loss. Mitigation of FER by the transgenes was validated by about 3-fold enrichment of Fusarium verticillioides (Fv) post-inoculation, compared to non-significant Fv enrichment in conventional maize. While the major causal pathogen of FER, Fv, was the most abundant species in the metagenomes, similar degree of correlations was observed between FER and several Fusarium spp. (0.2-0.56; Fv: 0.41-0.49). The potential FER-suppressing properties of Talaromyces stipitatus and Ustilago maydis were indicated by negative correlations with FER (-0.22 to -0.42), Fv and some Fusarium spp. The more FER resistant varieties consistently enriched for the potential FER-suppressing Burkholderia cenocepacia (negatively correlated with Fv). This suggests host genetic background-dependent recruitment of beneficial microbes that suppress pathogens and that microbe-microbe interactions play a role in FER severity. Quantitative and species/strain-level metagenomic profiles hold promise for identifying robust disease-suppressing microbes, microbes that act in synergy with pathogens, and for developing a holobiont-aware breeding strategies that accounts for host-microbiome coevolution and host genotype, microbiome/metagenome, and environment (GxGxE) interactions.