Objective To explore the diversity of soil rhizosphere microorganisms and metabolic functions in cotton-peanut rotation systems.

Methods The composition of microbial communities and functional genes in the rhizosphere soil of cotton and peanut rotation (continuous cropping) were analyzed using metagenomic sequencing technology.

Results There were significant differences in operational taxonomic units (OTUs) between peanut-cotton rotation (HR), cotton-peanut rotation (MR), peanut continuous cropping (HC), and cotton continuous cropping (MC), with 83 OTUs being the same. Alpha and Beta diversity analyses revealed that the HR system had the highest species diversity. The Non-metric multidimensional scaling (NR) results showed that bacteria accounted for 90.95% of the microbiota, with Acidobacteria and Proteobacteria being the main core microbial communities. In the HR system, Actinobacteria and Nitrospiraehad covered higher proportions. In the HR system, the ratio of Firmicutes to Bacteroidetes was also high, and the soil was acidic, and the activity of membrane transport genes was high. The relative abundance of genes involved in carbon metabolism pathways was higher in the HR group than that in the control group; the relative abundance of carbohydrate active enzymes GH accounted for 33.4% of the total, and GT accounted for 41.0% of the total, with significant differences.

Conclusion Cotton and peanut rotation increase the richness of carbohydrate active enzymes in the rhizosphere soil microorganisms and genes of main metabolic pathways, change the soil environment, and effectively increase the diversity of soil microbial communities.