Endophytic signaling networks orchestrate microbiome-mediated disease suppression

Plant-associated microbial communities form complex interaction networks that underpin host health and disease resistance, yet current microbiome engineering strategies largely emphasize direct antagonism by introduced microbes while overlooking indirect, signal-mediated mechanisms that regulate community-wide functions. Using the Ralstonia solanacearum-tomato pathosystem, we combined long-term field experiments, controlled microcosm assays, multi-omics profiling, and culture-based analyses to disentangle the relative contributions of rhizosphere and endophytic microbiomes to disease suppression and to elucidate the mechanisms governing their assembly and function. We show that continuous application of a bio-organic fertilizer containing Bacillus amyloliquefaciens T-5 establishes a persistently disease-suppressive state that is driven primarily by the root endosphere rather than the rhizosphere. This effect is not mediated by direct antagonism but by plant-mediated metabolic reprogramming that selectively enriches keystone endophytic taxa, particularly Devosia. Bio-agent application induced the accumulation of plant secondary metabolites, including riboflavin, which promoted Devosia proliferation within roots. Functional Devosia strains did not directly inhibit the pathogen; instead, they secreted a specific tripeptide, Ile-Asp-Ile, that activated stress-response pathways and secondary metabolism across diverse resident microbial taxa. This signal-mediated activation reconstructed microbial metabolic networks into a self-reinforcing, pathogen-excluding community while concurrently shifting host transcriptional programs toward growth rather than defense. Together, our findings redefine microbiome-mediated disease suppression as a hierarchical signaling process operating across plant-microbe-microbe interactions and establish signal-driven amplification of indigenous microbiome function as a fundamental principle of holobiont immunity. This framework provides a scalable alternative to conventional microbial replacement strategies by leveraging endogenous microbiome potential for durable and sustainable disease control.