Genotype-Specific Interactions Between Wheat and Rhizosphere Microbiome Under Drought Stress

Drought severely limits global wheat production, and plants can mitigate this stress by recruiting beneficial rhizosphere microbiomes. However, the role of host genotype in shaping this recruitment and influencing microbial inoculant efficacy is poorly understood. Here, we aimed to elucidate the interplay among host genotype, drought stress, and inoculation with Trichoderma citrinoviride. A factorial pot experiment investigated the responses of two wheat genotypes (JN 14-95, constitutively drought-tolerant; JN 72, drought-responsive) to water regimes and inoculation with T. citrinoviride. Metagenomic analysis was performed to characterize rhizosphere bacterial community structure and functional potential. Host genotype was the primary driver of bacterial community structure (42.3% of variation), exceeding water stress (23.8%) and inoculation (11.5%). JN 14-95 adopted a "physiological autonomy" strategy with constitutive high root-to-shoot ratio and inferred enrichment of auxin and SOD biosynthesis genes. JN 72 employed a "microbial outsourcing" strategy, enriching beneficial bacteria (Pseudomonas, Bacillus, Streptomyces) and showing inferred enrichment of central carbon metabolism genes. T. citrinoviride amplified these genotype-specific responses, increasing the total dry matter by 21.3% in JN 14-95 and 30.3% in JN 72 under drought. Our findings suggest a need to move from uniform inoculation practices toward genotype-informed microbiome management. The two strategies provide a framework for leveraging host genetics in sustainable agriculture, highlighting that breeding and microbiome management should be integrated.