Rhizosphere microbiome assembly and functional enrichment drive salt tolerance in wheat.

Soil salinization is a major constraint on wheat production, as seedling-stage stress strongly constrains early growth and potential yield. However, the mechanisms by which the rhizosphere microbiome mediates varietal differences in salt tolerance remain poorly understood. Here, we compared a salt-tolerant wheat cultivar (Jimai60, JM60) and a salt-sensitive cultivar (Guomai301, GM301) grown in saline-alkali soil. Integrating soil physicochemical, enzymatic analyses and 16S rRNA gene and shotgun metagenomic sequencing, we investigated rhizosphere microbiome assembly, network structure, and functional potential at the seedling stage. JM60 assembled a distinct rhizosphere microbiome enriched in Bacteroidota, with Sphingobacterium acting as a keystone taxon in a more stable co-occurrence network. In contrast, GM301 was dominated by Zobellella and exhibited increased negative microbial interactions, indicating a reduced network that is structurally more cooperative. Metagenomic analyses showed enrichment in JM60-associated microbiomes of genes linked to oxidative stress resistance (katE), central carbon metabolism (pdhD), and nitrogen utilization (hutF), suggesting enhanced redox homeostasis, nutrient cycling, and ion balance regulation. These functional traits aligned with higher leaf antioxidant enzyme activity and altered rhizosphere nutrient profiles in JM60. Our findings demonstrate that wheat salt tolerance is linked to assembly of a functionally enriched rhizosphere microbiome, highlighting microbiome-driven mechanisms for improving crop resilience in saline soils.