Taxonomic and functional diversity of the soil microbiome recruited from alternative crops in a rotation system

Intensive cropping is considered to contribute to negative effects both on soil physiochemical properties and on long‐term grain yield, which can be alleviated by appropriate crop rotations. The soil microbial community can vary with different crop rotations, which in turn affect soil quality and grain yield. Therefore, it is of great significance to elucidate the response of the soil microbial community to crop rotation. In this study, the structural and functional changes of microbial community in different crop rotations were analyzed using high‐throughput sequencing and metagenomics analysis in a field experiment. The continuous winter wheat‐summer maize cropping system was the control, and three crop rotations were established in October 2016 as follows: (1) spring peanut→winter wheat‐summer maize, (2) winter wheat‐summer peanut→winter wheat‐summer maize and (3) spring sweet potato→winter wheat‐summer maize. Soil samples were collected in September 2021 for soil microbial assessment. The results showed that the relative abundance of Actinobacteriota in the soil of spring sweet potato→winter wheat‐summer maize was significantly higher (15.2%) than that in the control. The relative abundance of Ascomycota was significantly higher (19.8%–23.2%) in the soil following crop rotation compared with the control. Compared with the control, spring peanut→winter wheat‐summer maize enriched energy metabolism genes, and spring sweet potato→winter wheat‐summer maize reduced the genes related to plant–pathogen interaction. Compared with the control, crop rotation significantly decreased the relative abundance of the inorganic phosphorus solubilization gene ( gcd ) and the phosphorus transport gene ( upgE ) and increased the abundance of organic phosphorus mineralization genes ( phoA and phyA ). Based on these results, we concluded that the composition of the soil microbial community and functional genes can be altered by crop rotation, and spring peanut→winter wheat‐summer maize and spring sweet potato→winter wheat‐summer maize had more significant effects. This study provided a reference for the selection of crop rotations in the North China Plain based on the soil microbial community and its function.