Soil type and growth stage‐dependent rhizosphere bacteriome of alfalfa under challenge by the fungal pathogen Rhizoctonia solani

BACKGROUND: Alfalfa (Medicago sativa) is the most important forage legume crop in China, but its productivity is severely threatened by root rot caused by Rhizoctonia solani. The use of resistant varieties is regarded as the most effective and sustainable strategy for disease management. However, the interaction between the host genotypes of alfalfa and R. solani in shaping the rhizosphere microbiome, and the role of these microbial assemblages in host resistance, remains poorly understood. This study investigated the rhizosphere bacteriome of alfalfa varieties with contrasting resistance to R. solani across different soil types and growth stages. Disease severity, plant biomass, and antioxidant enzyme activities were also evaluated. RESULTS: Significant changes were observed in the composition and diversity of the bacterial community under infection by R. solani. The resistant variety exhibited higher activities of superoxide dismutase, peroxidase, and catalase. Pathogen inoculation was associated with a more complex and positively interconnected microbial network, indicating shifts in potential microbial associations. Notable shifts in α-diversity, Bray-Curtis β-diversity, and growth-stage-specific bacterial genera were observed between 8 and 16 weeks. In contrast, differences between soil types were less pronounced, which shows that the growth stage strongly influenced rhizosphere bacteriome structure. CONCLUSION: These findings advance understanding of host-microbiome-pathogen interactions and provide a basis for microbiome-assisted strategies in sustainable management of root rot in alfalfa cultivation. © 2026 Society of Chemical Industry.