Effects of different rotation crops on soil physicochemical properties and microbial community structure in continuous cotton fields

Cotton monoculture is widespread in the oasis cotton-growing region of Xinjiang. Long-term continuous cropping has led to declines in soil fertility and imbalances in microbial communities, constraining sustainable, green production. Crop rotation is an effective agronomic practice to mitigate the deleterious effects of continuous cropping; however, the selection of rotation crops and the regulatory mechanisms by which rotation reshapes the soil micro-ecology require systematic clarification. Using continuous cotton (CK) cropping as the control, we combined high-throughput amplicon sequencing with soil physicochemical analyses to evaluate the effects of four previous-crop schemes—cotton → peanut (CPC), cotton → soybean (CSC), cotton → rapeseed (CRC), and cotton → maize (CMC)—on soil properties and the microbial community structure. Relative to CK, the CPC, CSC, and CRC treatments led to significantly reductions in yield and gross output value ranging from 38.72 to 62.23% and 34.54 to 55.35%, respectively. Although the net profit under CPC treatment decreased by 36.27% relative to CK, the benefit–cost ratio showed no significant difference. CPC significantly increased soil organic matter, available phosphorus, NH4 + –N, and NO3 − –N, while decreasing the pH and electrical conductivity, demonstrating the best overall improvement in soil fertility. In the fungal community, under CPC, Basidiomycota and Mortierellomycota significantly increased by 17.15 and 52.37%, respectively, whereas Basidiomycota significantly increased under CSC and CRC (by 17.15 and 20.58%). Functional guild analysis indicated that all four rotation schemes significantly reduced the relative abundance of plant pathogen fungi, with the greatest decrease under CPC (36.80%), with statistically significant differences. In the bacterial community, CPC significantly increased Actinobacteriota, Gemmatimonadota, and Firmicutes by 16.20, 15.75, and 29.73%, respectively, while CRC rose substantially Bacteroidota by 28.58%. Bacterial metabolism constituted the major predicted functional category (79.27–79.68%), no significant differences between treatments. Redundancy analysis identified soil moisture and the N/P ratio as key drivers of the variation in the fungal community, while bacterial communities were regulated by N/P, pH, and organic matter. Overall, rotation alleviated continuous-cropping constraints by optimizing soil properties and the soil microbial structure. The results provide an empirical basis for improving soil microbiomes and designing sustainable planting strategies in oasis cotton systems.