Root core microbiome assembly by probiotic is associated with fungal network and plant metabolites

Root-associated microbiomes, especially the core microbiome, play critical roles in plant physiology and fitness. Previous studies have shown that the fungal probiotic Phomopsis liquidambaris induced a root core microbiome consisting of six endophytic bacteria which promotes plant growth and disease resistance, protecting peanuts from continuous monocropping obstacles. However, the assembly mechanism of the root core microbiome remains largely unknown. Here, we used pot and laboratory experiments to investigate the effect of fungal probiotics (Ph. liquidambaris) on the assembly process of the root core microbiome. By comparing the variation of the relative abundance of root core microbes in peanut rhizosphere through 16S rRNA gene analysis, we demonstrated that the process from bulk soil to rhizosphere is a key step in Ph. liquidambaris-induced reassembly of root core microbiome. In vitro and in vivo experiments revealed that Ph. liquidambaris-induced root exudates mediated the reassembly of the root core microbiome by specifically promoting the colonization of Bacillus sp., Streptomyces sp., and Bradyrhizobium sp. Further, we found that the Ph. liquidambaris hyphal network selectively promotes bacterial dispersal, such as Bacillus sp., Pseudomonas sp., Streptomyces sp., and Bradyrhizobium sp. The co-occurrence of fungal mycelium and root exudates significantly promoted this cooperation. Taken together, our results revealed that the additive effect of plant chemistry and physical network supports the fungal probiotics-induced root core microbiome reassembly, mediating plant fitness to agricultural obstacles.