Core microbiota recruited by Salvia miltiorrhiza enhance resistance against Fusarium root rot disease

Abstract Fusarium root rot, caused by the soilborne pathogen Fusarium oxysporum , leads to substantial yield losses across multiple agriculturally crucial crops. While rhizosphere microbiota have been extensively studied in model species, a deeper understanding of the rhizosphere microbiome assembly associated with herb health is still needed. Given its economic importance in traditional medicine, we used Salvia miltiorrhiza and Fusarium root rot as a model to elucidate the rhizosphere microbiome assembly associated with plant health. Here, we employed 16S rRNA amplicon sequencing to profile the soil microbiome across three geographically distinct cultivation regions. Comparative analysis revealed marked divergence in bacterial community structures between healthy and diseased plants, identifying Lysobacter spp. as keystone bacterial taxa within the core microbiome enriched in healthy rhizospheres. Functional validation demonstrated potent antifungal activity of isolated Lysobacter strains against F. oxysporum , with Lysobacter enzymogenes strain Ly-1 exhibiting consistent biocontrol efficacy in both greenhouse and field experiments. Genomic and transcriptomic analyses further revealed that Ly-1 encodes specialized iron acquisition systems, including siderophore synthesis and transport machinery, with its antifungal activity being significantly amplified under iron-limited conditions, consistent with a model where iron competition cooperates with other biocontrol traits. Collectively, this study establishes a novel biocontrol paradigm and highlights the translational potential of core rhizobacterial enrichment for sustainable management of soilborne diseases in medicinal plants.