Summary Early mutualistic interactions between host plants and their rhizosphere microbes have the potential to provide soil‐borne disease resistance. However, it remains unclear how the early rhizosphere microbiome protects against viral diseases such as wheat yellow mosaic virus, which is a major threat to global wheat production. We combined field trials with microbiome transplantation experiments to investigate the role of early rhizosphere microbiomes in suppressing wheat yellow mosaic disease. To uncover the underlying mechanisms, we further performed integrated multi‐omics analyses of microbial communities, functional genes, and metabolic profiles. Disease‐resistant wheat cultivars were consistently associated with distinct seedling rhizosphere microbiome assembly, including a lower Polymyxa graminis abundance, lower community compositional variation, and enrichment of beneficial taxa such as Bacillus , Pseudomonas , and Trichoderma . Resistant cultivars also exhibited distinct rhizosphere metabolite profiles, including higher levels of glyceraldehyde and N‐acetyltryptophan, which were positively associated with keystone microbial taxa and stimulated representative isolates in vitro . Isolate‐based and synthetic community validation further supported the functional relevance of these taxa, while microbial inoculation was associated with reduced vector abundance, lower virus accumulation, and activation of host defense‐related pathways. Our findings showed that early cultivar‐dependent rhizosphere microbiome assembly was closely linked to resistance against soil‐borne viral disease in wheat.
Wu et al. (2026) studied this question.