Root rot induces a core assemblage of bacterial microbiome to prevent disease infection in Sanqi ginseng

Plants rely on rhizosphere microbes as the first line of defense against pathogen invasion and for maintaining the health of itself. Increasing evidence suggests that plants recruit beneficial microbes to the roots, strengthening their resistance to pathogens. However, the response of the rhizosphere core bacterial microbiome to root rot infection remains largely unclear. In this study, we investigated the rhizosphere and bulk soil core bacterial microbiome of healthy and root rot-diseased Sanqi ginseng in genuine production areas in China. We utilized 16S amplicon sequencing, co-occurrence network analysis, and strain culture approaches to explore whether root rot-induced plant rhizosphere alterations in the bacterial core microbiome could improve disease suppression. Root rot infection had a significant impact on the rhizosphere core bacterial microbiome of Sanqi ginseng. Root rot led to a reduction in the diversity and evenness of the core bacterial microbiome in the rhizosphere, while the variability of the core bacterial community in the rhizosphere increased. In response to fungal root rot pathogen infestation, Sanqi ginseng recruited potentially beneficial bacteria with disease-suppressive functions to the rhizosphere, such as Sphingobium, Pseudoxanthomonas, Pseudomonas, Stenotrophomonas, and Flavobacterium. Function prediction analysis demonstrated a remarkable enrichment of several functional genes involved in antibiotic biosynthesis in the rhizosphere that was infected with root rot. Strain isolation and pot addition experiments further confirmed the effectiveness of root rot rhizosphere-specific enrichment of Operational Taxonomic Units (OTUs) for controlling root rot. Furthermore, co-occurrence network analysis indicated that root rot activated the disease-suppressive functions of the rhizosphere core bacterial microbiome by enhancing complexity and connectivity at the expense of network stability. These findings expand our knowledge of plant-microbe interactions and provides new evidence supporting the "cry for help" strategy for rhizosphere responses to root rot.