Objective The objective of this study was to clarify the effects of different organic materials application on the physical and chemical properties of soil and microbial community structure in plateau summer vegetables, so as to provide theoretical basis and technical support for improving soil quality in semi-arid plateau summer vegetable planting areas.

Methods Through field experiments, four fertilization treatments were included such as the bio-fertilizer + straw (BC), bio-fertilizer + cow manure + straw (BS), bio-fertilizer + cattle manure (BD), and single chemical fertilizer (CK). The physical and chemical properties of surface (0 - 20 cm) and sub-surface (20 - 40 cm) soil, soil aggregates and microbial community composition were determined. And the high-throughput sequencing method was used to determine the structure and composition of soil microbial communities.

Results Compared with the CK, BS treatment significantly decreased soil pH and total soluble salts in both soil layers, while increasing the contents of soil organic matter (SOM), available nitrogen (AN), and available phosphorus (AP) by 26.84%, 35.99%, and 39.38%, respectively. BC treatment demonstrated more pronounced effects on soil available potassium content in the sub-layer soil. The BS treatment resulted in a significant increase of 243.84% in the proportion of soil aggregates with a particle size of 0.25 - 0.50 mm in the topsoil, and increased the proportions of 0.25 - 0.50 mm and 2.00 - 5.00 mm aggregates in the subsoil by 73.73% and 20.90%, respectively. The BD treatment increased the proportion of 0.25 - 0.50 mm aggregates in the topsoil and 2.00 ~ 5.00 mm aggregates in the subsoil by 409.53% and 77.86%, respectively. All treatments except compound fertilizer showed significant increases in Acidobacteria relative abundance and decreases in Proteobacteria abundance across both soil layers. BS treatment exhibited 36 and 25 unique bacterial genera in the top layer and sublayer, respectively, associated with organic matter decomposition, nitrogen cycle regulation, and soil aggregation. Among the dominant fungal phyla, the relative abundance of Ascomycota in both the topsoil and subsoil under BC and BS treatments were significantly reduced by 24.45% ~ 63.63% and 30.96% ~ 53.49%, respectively, while the relative abundances of Mortierellomycota were significantly increased by 8.6% ~ 255.19% in the topsoil and 31.23% ~ 261.89% in the subsoil.

Conclusion Combination of bio-fertilizer with straw and cattle manure facilitates soil macroaggregate formation, significantly enhances soil nutrient contents and structural properties, while providing substantial carbon sources for microbial communities. This integrated approach demonstrates superior performance in optimizing microbial community architecture.