Genotype-Specific Root Morphology and Metabolic Traits Shape Bacterial Communities and Tolerance to Fusarium Root Rot in Wheat

Plant genotype plays a critical role in shaping root-associated microbial communities and in modulating plant tolerance to soilborne diseases such as Fusarium root rot (FRR). In this study, we investigated how four wheat ( Triticum aestivum ) varieties, whose tolerance to FRR differs, influence the composition and structure of bacterial communities in the rhizosphere and root endosphere. We evaluated root traits that may contribute to the genotype-specific assembly of bacterial communities across the four wheat genotypes. The variety Concret exhibited the highest FRR tolerance, whereas Pilier was the most susceptible. Analyses of root morphology revealed significant genotype-dependent differences in root length and volume, which were positively correlated with the abundance of some rhizosphere bacteria affiliated with Bacillus, Lysobacter, and Sphingomonas . Untargeted metabolomics identified 879 features, with 20 key metabolites distinguishing the wheat genotypes, including alkaloids and benzoate- and benzoxazinoid-derived compounds. Correlation analysis revealed significant relationships between these root metabolites and key bacterial taxa. Our findings demonstrate that wheat genotypes influence the assembly of the root microbiota through genotype-based morphological and metabolic traits, providing valuable insights into traits that modulate the plant microbiome to improve wheat resistance to FRR.