Fusarium Oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis Thaliana Roots

BackgroundAlthough it is well established that plant metabolomes mediate microbiome assembly, the question of how metabolome-microbiome interactions may prevent pathogen invasion remains to be answered. To address this question, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions, Columbia-0 (Col-0) and Landsberg erecta (Ler-0) with differential resistance profiles to the fungal pathogen Fusarium oxysporum f.sp. mathioli (FOM). We used amplicon sequencing to characterize bacterial (16S) and fungal (ITS2) communities, and we used targeted metabolite analysis across 5 stages of FOM host progression. ResultsWe found that microbiome and metabolome profiles were markedly altered in FOM-inoculated and non-inoculated samples of resistant Col-0 and susceptible Ler-0. Co-occurrence network analysis revealed robust microbial networks in the resistant Col-0 compared to the susceptible Ler-0, during FOM infection. Specific metabolites and microbial OTUs (including indicator and hub OTUs) correlated in both non-inoculated and inoculated Col-0 and Ler-0. The glucosinolates 4-hydroxyglucobrassicin, neoglucobrassicin and indole-3 carbinol, but also phenolic compounds were active in structuring the A. thaliana-microbiome. ConclusionsOur results highlight the interactive effects of host resistance and its associated microbiota on Fusarium infection and progression. These findings shed significant insights into plant inter-omics dynamics during pathogen invasion and could possibly facilitate the exploitation of microbiomes for plant disease control.