Effects of Microbial Fertilizer Application on Soil Ecology in Saline–Alkali Fields

Microbial fertilizer is an environment-friendly fertilizer that can effectively improve the microecological environment of soil, playing an important role in the remediation of saline–alkali soil and promoting sustainable agricultural development. In this study, we examined the impact of microbial fertilizer application on saline–alkali field improvement over two years. The results indicated that, compared to NS0 and NS2 (the initial sowing period without microbial fertilizer addition), the soil pH and electrical conductivity (EC) levels significantly decreased by 4.1% and 8.49% and 60.56% and 39.66% for NS1 (after the first harvest) and NS3 (after the second harvest), respectively. Compared to NS0, the concentrations of Na+ and Cl−, among the eight major ions in the soil, decreased significantly by 87.23% and 80.91% in the second year, while Ca2+ increased significantly in NS1 and NS3, being 5.27 times and 2.46 times higher than before sowing. Comparing NS3 to NS0, the sodium adsorption ratio decreased by 87.04%. The activities of soil urease, alkaline phosphatase, and invertase in NS3 increased significantly by 90.18%, 45.67%, and 82.31% compared to those in NS0. In contrast, the activity of catalase decreased by 2.79% (p < 0.05). Alpha diversity analysis demonstrated that the Ace, Chao1, and Sobs indices for both bacteria and fungi were significantly higher at NS3 than before sowing, indicating the highest species richness at this stage. The Shannon index exhibited an ascending trend, and the difference in the Simpson index was not significant. After applying microbial fertilizer in the saline–alkali field, the number of bacterial and fungal operational taxonomic units (OTUs) significantly increased. In the bacteria, the proportion of Proteobacteria rose, while Actinobacteriota exhibited a significant reduction. Among fungi, the proportion of Ascomycota decreased and Basidiomycota increased. Principal component analysis (PCA) revealed distinct separation among treatments, indicating significant differences in microbial communities. Redundancy analysis (RDA) identified that the key physicochemical factors influencing bacterial community structure were available phosphorus (AP), electrical conductivity (EC), and pH, whereas for fungi, they were AP, available potassium (AK), and dissolved organic carbon (DOC). This research presents the effects of microbial fertilizer application on the improvement in a saline–alkali field over two years. It provides a scientific basis for the remediation of the saline–alkali field via microbe-induced changes in soil physicochemical properties, enzyme activity, microbial diversity, and community structure at different periods.