Considerable attention has been paid to the establishment of an appropriate cropping patterns for the restoration of saline-alkali lands. This study’s goal was to explore changes in nitrogen-cycling (N-cycling) gene (nitrogen fixation: nifH; nitrification: AOA, AOB, and nxrB; denitrification: narG, norB, and nosZ) abundance of three cropping patterns at two soil depths in saline-alkali soils. Results showed that rotation and mixture promoted soil nutrients. N-cycling functional genes were significantly influenced by soil depths and cropping patterns. Compared with monoculture, rotation decreased the abundance of nifH, AOA, narG, and nosZ and increased the abundance of AOB; mixture decreased the abundance of AOA, narG, and nosZ and increased the abundance of AOB and nxrB in the 0–15 cm soil depth. Rotation increased all genes abundance; mixture increased nosZ abundance and decreased nxrB abundance in 15–30 cm soil depth. Soil protease, cellulase, nitrate reductase, pH, AK (available potassium), and AP (available phosphorus) were important factors influencing N-cycling gene abundance. In conclusion, rotation and mixture not only reduced soil salinity but also improved soil fertility and nitrogen cycling. These findings can provide some theories for the sustainable development of N-cycling during the restoration of saline-alkali soils.

Soil salinization remains a major global challenge, and rice cultivation has been widely practiced in saline–alkali soils of the black soil region in Northeast China as an effective strategy for soil improvement. However, this practice is often slow to produce benefits and is prone to secondary salinization, limiting rapid gains in soil fertility and crop productivity. To address these limitations, this study evaluated the effects of four soil amendment strategies (microbial inoculant, organic fertilizer, biochar, and their combined application) on bacterial and fungal communities, as assessed by high-throughput sequencing of the 16S rRNA gene and the ITS region, respectively. The application of microbial inoculants significantly increased bacterial diversity and richness, while all amendment treatments promoted the enrichment of key microbial groups. Organic inputs strongly influenced microbial community assembly, with microbial inoculant and combined treatments shifting assembly toward more deterministic processes. In addition, the amendments altered microbial interaction networks, leading to widespread cooperative relationships dominated by positive associations and strong interactions across taxonomic groups. Notably, the combined treatment reshaped bacterial functional profiles and reduced the predicted abundance of pathogenic fungi. Overall, these results demonstrate that organic amelioration strategies can improve the ecological functioning of saline–alkali soils by regulating microbial community assembly and interactions. This study provides a robust theoretical framework and scalable practical solutions for the integrated management and sustainable development of saline–alkali agriculture.