Synthetic microbial seed coating reshapes rhizosphere microbiome assembly and enhances maize tolerance to saline-alkali stress

Saline-alkali soils severely constrain crop productivity by disrupting rhizosphere physicochemical conditions and microbial ecological processes. Although microbial inoculation has emerged as a promising strategy for improving plant stress tolerance, the ecological mechanisms by which early microbial colonization reshapes rhizosphere microbiome assembly under saline-alkali stress remain poorly understood. Here, we applied a synthetic microbial seed coating (MSC) to maize and investigated its effects on rhizosphere microbial communities, community assembly processes, cross-kingdom interaction networks, and plant performance under field saline-alkali conditions. MSC treatment significantly enhanced seed germination, seedling growth, agronomic traits, and grain yield, while reducing rhizosphere electrical conductivity (EC), indicating alleviation of saline-alkali stress. Amplicon sequencing and metagenomic analyses revealed that MSC selectively reshaped bacterial community composition and increased bacterial diversity, whereas fungal and protozoan communities showed comparatively weaker responses. Null-model analysis demonstrated that bacterial community assembly shifted from deterministic variable selection in the control to stochastic ecological drift under MSC treatment, accompanied by broader niche width, suggesting reduced environmental filtering in the rhizosphere. Co-occurrence network analysis further showed that MSC remodeled both single-kingdom and cross-kingdom microbial interaction networks, increasing the ecological contribution of protozoa and promoting a more balanced multi-kingdom microbiome structure. Metagenomic functional profiling further revealed that MSC reduced the abundance of stress-associated ion transport genes, indicating alleviated ionic stress pressure on the rhizosphere microbiome. Partial least squares path modeling (PLS-PM) revealed that MSC improved maize yield through both direct effects and indirect microbiome-mediated pathways involving rhizosphere environmental modification, bacterial community reassembly, and functional regulation. Collectively, our findings demonstrate that early inoculation via MSC represents an effective microbiome-centered strategy for enhancing crop resilience and productivity in saline-alkali soils.