Rhizosphere microbiome promotes wheat salt tolerance through root lignin biosynthesis

Salinity imposes strong selective pressure on plant roots, yet how rhizosphere microbiomes contribute to root structural adaptation under salt stress remains unclear. Using a plant–soil feedback framework across 100 wheat accessions, we show that salt-tolerant genotypes condition distinct rhizosphere microbiomes that enhance salt tolerance across host backgrounds. These microbiome effects are linked to activation of host phenylpropanoid biosynthesis and enhanced lignin deposition in roots. Metagenomic analyses reveal enrichment of microbial functions related to stress tolerance and carbon metabolism, while root transcriptomics identify coordinated induction of lignin biosynthetic genes. Isolation and reconstitution of core taxa identified a synthetic microbial community that promoted endodermal lignin deposition, enhanced Na⁺ efflux, restricted Na⁺ entry into the stele, and increased wheat yield in salinized field sites. Analyses using Arabidopsis lignin-deficient mutants further indicate that lignification is a key, though not exclusive, component of this response. Together, our results uncover an unappreciated microbiome-driven mechanism of root anatomical remodeling that contributes to plant salt tolerance.