Partial Substitution of Chemical Fertilizer with Organic Materials Improves Soil Physicochemical Properties and Shapes Microbial Communities in Rainfed Farmland of Northwest China

Soil degradation and low productivity in dryland areas require sustainable measures to improve the resilience of agroecosystems. The experimental design was based on the principle of organic matter substitution. To evaluate the effects of the combined application of chemical fertilizer and organic amendments on soil quality and microbial communities in rainfed loessial farmland in southern Ningxia, a field experiment was conducted in 2021 with maize as the test crop. Five treatments were established: control with no fertilizer (CK); chemical fertilizer (N—240 kg/ha, P2O5—150 kg/ha, and K2O—120 kg/ha) (F); 50% F (N—120 kg/ha, P2O5—75 kg/ha, and K2O—60 kg/ha) combined with decomposed cow manure (18,000 kg/ha) (MF1); 50% F (N—120 kg/ha, P2O5—75 kg/ha, and K2O—60 kg/ha) combined with decomposed cow manure (30,000 kg/ha) (MF2); and 50% F (N—120 kg/ha, P2O5—75 kg/ha, and K2O—60 kg/ha) combined with straw (14,527 kg/ha), equal in carbon content to the decomposed cow manure applied with MF1) (SF). Regular methods and high-throughput sequencing techniques were used to determine the physical and chemical properties, soil water stability aggregates, and the diversity and community structure of the soil bacteria and fungi. The results showed that the MF2 treatment resulted in the highest soil organic matter (SOM), available phosphorus (AP), available potassium (AK), and total nitrogen (TN) contents. Compared with CK, MF2 significantly increased SOM, AP, AK, and TN by 5.84%, 112.16%, 52.13%, and 16.88%, respectively. The MF1 and MF2 treatments increased the soil fungal diversity and richness. The BG and ALP activities with the MF2 treatment increased by 95.32% and 22.38%, respectively, compared with the F treatment, while the NAG and CBH activities with the SF treatment increased by 44.10% and 17.18%, respectively, compared with the F treatment. The MF2 treatment increased the relative abundances of the soil bacteria Chloroflexi and Acidobacteria and the soil fungi Mortierellomycota and Basidiomycota. In soils amended with mature cow manure, the quantity of water-stable aggregates with a diameter greater than 0.25 mm (R0.25), soil organic matter (SOM), β-glucosidase (BG) activity, and alkaline phosphatase (ALP) activity were the primary factors influencing the soil bacterial Chao1 index and Shannon index, while R0.25 and ALP activity were the main factors affecting the fungal Observed species index. Overall, 50% chemical fertilizer combined with decomposed cow manure (MF2) is an effective strategy to improve the physicochemical properties and microbial function in soil of farmland. These findings provide a theoretical basis for rational fertilization and soil quality improvement in rainfed farmland in southern Ningxia.