Fungal network and plant metabolites drive the assembly of the peanut root microbiome

Root-associated microbiome, especially the core taxa, profoundly affect host fitness. Previous studies have shown that the fungal probiotic Phomopsis liquidambaris caused the reassembly of the peanut root core microbiome, promoting plant growth and disease resistance. However, the assembly mechanism of the root core microbiome remains largely unknown.

The rhizosphere bacterial communities and the dynamic changes of core microbes were analyzed throughout the growing season with high-throughput sequencing. High-Performance Liquid Chromatography was carried out to determine the influence of Ph. liquidambaris colonization on the metabolic profiles of peanut root exudates. Based on correlation analysis, bacterial growth, biofilm formation, and chemotaxis experiments were carried out to verify the effect of Ph. liquidambaris-induced root exudates on colonization behavior of core microbes. The nested plate assay was used to analyze the interaction between fungal networks and core microbes.

Here, we demonstrated that the process from bulk soil to rhizosphere is a key step in the peanut root microbiome reassembly. In vitro and in vivo experiments revealed that Ph. liquidambaris-induced changes in root exudates mediated the reassembly process by promoting the colonization of Bacillus sp. HB1, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Further, we found that the Ph. liquidambaris hyphal network selectively promotes bacterial dispersal and collaborates with root exudates to encourage the enrichment of core microbes.

Our results revealed that the additive effect of plant chemistry and physical network supports the fungal probiotics caused peanut root microbiome reassembly, mediating plant fitness to monocropping obstacles.