Organic Fertilizer Combined with Microbial Inoculant Alleviates Saline–Alkali Stress in Wheat: A Multi-Tissue Analysis

Soil salinization constrains global wheat production, but how organic–microbial amendments alleviate saline–alkali stress across plant tissues remains poorly characterized. In a single-season field trial, we compared three treatments—a non-saline control (CK), a saline–alkali control (SCK), and an organic fertilizer combined with a microbial inoculant applied to saline–alkali soil (SDM)—to evaluate effects on soil properties, the rhizosphere microbiome structure, leaf antioxidant defense, and grain quality. SDM improved soil nutrient availability: available phosphorus and potassium increased by 96.0% and 51.8%, respectively, relative to SCK, and rhizosphere microbiome shifts favored copiotrophic taxa (Flavobacterium, Devosia, Mortierella) over halotolerant genera (Arthrobacter, Filobasidium). In leaves, SDM induced a controlled antioxidant activation—peroxidase (POD) functioned as a key mediator of oxidative homeostasis, with activities exceeding CK yet remaining below extreme SCK levels—producing the lowest malondialdehyde content (−48.4% vs. SCK). At moderate concentrations, reactive oxygen species participated in developmental signaling rather than causing pathological damage, enabling grain soluble sugars and total starch to be restored to CK levels. These results reveal a coordinated soil–microbiome–plant response in which organic–microbial amendment enhances nutrient cycling, redirects community assembly toward nutrient-cycling functional guilds, and achieves oxidative homeostasis and grain quality restoration. Our findings offer a conceptual basis for the microbiome-informed management of saline–alkali wheat production.