Root microbiome assembly and functional differentiation drive salt tolerance variation in wheat

Soil salinization severely constrains wheat production, with seedling-stage stress significantly impacting yield. However, the mechanisms underlying how the seedling rhizosphere microbiome contributes to salt tolerance differences among varieties remain unclear. This study utilized the salt-tolerant wheat variety Jimaij60 (JM60) and the salt-sensitive variety Guomaij301 (GM301), cultivated in native saline-alkali soil. By integrating 16S rRNA gene amplicon sequencing, metagenomic sequencing, and soil physicochemical analysis, we systematically compared the assembly, interaction networks, and functional characteristics of the root-associated microbiomes during the seedling stage between the two varieties. Results indicate that although planting reduced rhizosphere bacterial diversity, the salt-tolerant variety JM60 assembled a unique microbial community significantly enriched in Bacteroidetes, particularly with Sphingobacterium serving as a core hub in its co-occurrence network. In contrast, the rhizosphere network of the salt-sensitive variety GM301 centered on Zobellella and exhibited a higher proportion of negatively correlated interactions. Metagenomic analysis revealed enrichment of hydrogen peroxide synthase (katE), pyruvate dehydrogenase (pdhD), and histidine utilization protein (hutF) genes in the JM60 rhizosphere microbiome, suggesting enhanced potential for antioxidant stress resistance, rhizosphere pH regulation, and ion homeostasis maintenance. These functional traits correlate with elevated antioxidant enzyme activity in JM60 leaves and altered root-zone nutrient availability. This study uncovers an ecological mechanism whereby salt-tolerant wheat varieties actively shape root-zone microbiomes during seedling stages. These microbiomes, anchored by specific core communities and enriched with multiple stress-response genes, synergistically enhance salt tolerance. This provides theoretical foundations and direction for improving crop stress resistance through microbiome engineering.