Maize recruits beneficial microorganisms via rhizosphere metabolites as signals to construct a functional network for saline–alkaline stress resistance

Introduction Carbonate-type saline–alkaline stress severely constrains maize production; however, the synergistic response mechanisms between rhizosphere microorganisms and metabolites remain unclear. Methods Through field experiments along with the integration of soil chemical factor analysis, microbial high-throughput sequencing, and non-targeted metabolomics, we systematically investigated the response mechanisms of the rhizosphere microecosystem to saline–alkaline stress in maize fields in the carbonate chernozem region of the Songnen Plain, Northeast China. Results and discussion Saline–alkaline stress significantly increased soil pH and electrical conductivity (EC) and decreased soil organic matter (SOM), total nitrogen (TN), and total phosphorus (TP) content. However, the rhizosphere exhibited buffering capacity and maintained a high cation exchange capacity (CEC). Microbial community analysis revealed that bacterial alpha diversity increased under stressful conditions. Contrarily, fungal diversity significantly decreased, and the community structure shifted towards a pathogen-dominated community, primarily within Ascomycota, particularly in the genus Fusarium . This indicates differential stress tolerance between the bacterial and fungal communities. Co-occurrence network analysis further indicated that saline–alkaline conditions enhanced bacterial network complexity and connectivity, whereas they resulted in the contraction and structural simplification of fungal networks. Metabolite analysis showed that saline–alkaline stress induced significant reprogramming of the rhizosphere metabolic profile. Organophosphorus compounds, nucleotides, and their analogs were significantly enriched, whereas defensive secondary metabolites, such as cajanol, specifically accumulated in the saline–alkaline rhizosphere. Pathway analysis indicated the activation of stress resistance and oxidative stress-mitigation-related pathways, including betalain biosynthesis, flavonoid biosynthesis, tryptophan metabolism, and arginine metabolism. Multi-omics integration analysis identified soil EC and total potassium (TK) as key environmental factors driving the differentiation of microbial and metabolite communities. Key differential metabolites showed significant positive correlations with saline–alkaline-enriched microbial taxa ( Sphingomonas ), revealing a metabolite-mediated microbial recruitment mechanism. Using multi-omics analysis, this study revealed that the maize rhizosphere responds to saline–alkaline stress through metabolic reprogramming (enriching defensive metabolites such as cajanol) to directionally recruit beneficial bacteria such as Sphingomonas and maintain a higher bacterial network complexity, while also leading to the pathologization of the fungal community. Our findings highlight that maize recruits beneficial microbes through rhizosphere metabolic reprogramming, providing a mechanistic basis for microbiome-assisted saline–alkaline soil remediation.