Tobacco pathogen-microbiome dynamics reveal dual-functional microbial resources for disease control and growth promotion

Mixed infections trigger rhizosphere microbiome disruption and diversity collapse. New amplicon-qPCR method quantifies pathogens and microbiome shifts. B. orbicola ZY288 combats pathogens and boosts tobacco growth. Tobacco bacterial wilt and black shank, caused by Ralstonia solanacearum and Phytophthora nicotianae , respectively, severely threaten global tobacco production. Although the rhizosphere microbiome has emerged as a key factor in disease suppression, limited knowledge is available regarding how mixed infections by these pathogens reshapes microbial communities or affects soil health. Most existing studies focus on single-pathogen interactions, leaving a critical gap in understanding the complex microbiome responses to dual infections. Here, we investigated rhizosphere microbiome dynamics under single and mixed infections with these pathogens to identify microbial resources for disease suppression and growth enhancement. Using an amplicon-qPCR combined method, we demonstrated the restructuring of the microbiome. Healthy soils exhibited higher diversity and enrichment of beneficial taxa, including Sphingomonas and Rhizobium , whereas diseased soils were dominated by pathogens such as Ralstonia , with intensified diversity losses in mixed infected samples. Network analyses revealed collapsed microbial connectivity in diseased soils, indicating destabilized community resilience. Among the 2,048 rhizosphere isolates, Burkholderia orbicola ZY288 was identified as a potent biocontrol agent that suppressed pathogens and provided control effect by 53%–57% in greenhouse trials. Strain ZY288 also promoted plant growth via phosphate solubilization, protease activity, and ammonia synthesis, significantly increasing tobacco biomass and height. Phylogenetic and amplicon data linked strain ZY288 to disease-suppressive rhizosphere taxa, validating its ecological niche. Our findings highlight pathogen-driven microbiome shifts in tobacco soils and suggest that strain ZY288 is a sustainable biocontrol agent with plant-protective and growth-promoting capacities. This study advances microbiome-guided strategies for managing soil-borne diseases and promotes the integration of microbial ecology into agriculture.