Synergistic Application of Humic Acid and Microbial Fertilizers Improve Soil Quality, Reshape Microbial Network, and Enhance Wheat Yield in Coastal Saline–Alkali Soils

Coastal saline–alkali soils represent one of the most challenging agroecosystems due to coupled chemical, physical, and biological constraints. Although humic acid (HA) and microbial fertilizers (MFs) are recognized as effective amendments, the mechanisms linking soil improvements to yield gains remain unclear. Here, a 2-year field experiment was conducted in the Yellow River Delta to assess the effects of HA, applied alone or in combination with Bacillus subtilis and Trichoderma harzianum, on soil salinity, nutrient availability, aggregate stability, microbial communities, and wheat yields. Results showed that HA application alone reduced soil electrical conductivity (EC) and total soluble salts (TSS), and enhanced aggregate mean weight diameter (MWD), leading to 40.94–55.64% higher yields. Co-application with MFs further amplified these improvements, lowering EC and TSS up to 77.04% and 73.83%, enhancing MWD by 122.50%, and raising yields by 75.79%. Soil enzyme activities (e.g., catalase, β-glucosidase, urease, and alkaline phosphatase) and fungal diversity were substantially enhanced, whereas bacterial diversity showed no significant change. Co-occurrence network analysis demonstrated that application of HA with MFs (particularly with B. subtilis) reshaped microbial networks by enriching modules linked to nutrient provisioning, aggregate stability, and enzyme activity, while suppressing modules associated with salinity tolerance. Keystone species such as Lysobacter and Massilia were significantly enriched and closely associated with soil chemical and aggregate improvements. Structural equation modeling further revealed that yield gains were mainly explained by reduced salinity and enhanced aggregate stability rather than nutrient provisioning. These findings provide mechanistic evidence that HA improves soil quality and wheat productivity in coastal saline–alkali soils through integrated chemical, physical, and biological pathways, and that these benefits are strengthened when combined with microbial fertilizers.