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Background Soybean-corn intercropping is widely practised by farmers in Southwest China. Although rhizosphere microorganisms are important in nutrient cycling processes, the differences in rhizosphere microbial communities between intercropped soybean and corn and their monoculture are poorly known. Additionally, the effects of cadmium (Cd) pollution on these differences have not been examined. Therefore, a field experiment was conducted in Cd-polluted soil to determine the effects of monocultures and soybean–corn intercropping systems on Cd concentrations in plants, on rhizosphere bacterial communities, soil nutrients and Cd availability. Plants and soils were examined five times in the growing season, and Illumina sequencing of 16S rRNA genes was used to analyze the rhizosphere bacterial communities. Results Intercropping did not alter Cd concentrations in corn and soybean, but changed soil available Cd (ACd) concentrations and caused different effects in the rhizosphere soils of the two crop species. However, there was little difference in bacterial community diversity for the same crop species under the two planting modes.  Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria  and  Firmicutes  were the dominant phyla in the soybean and corn rhizospheres. In ecological networks of bacterial communities, intercropping soybean (IS) had more module hubs and connectors, whereas intercropped corn (IC) had fewer module hubs and connectors than those of corresponding monoculture crops. Soil organic matter (SOM) was the key factor affecting soybean rhizosphere bacterial communities, whereas available nutrients (N, P, K) were the key factors affecting those in corn rhizosphere. During the cropping season, the concentration of soil available phosphorus (AP) in the intercropped soybean–corn was significantly higher than that in corresponding monocultures. In addition, the soil available potassium (AK) concentration was higher in intercropped soybean than that in monocropped soybean. Conclusions Intercropped soybean–corn lead to an increase in the AP concentration during the growing season, and although crop absorption of Cd was not affected in the Cd-contaminated soil, soil ACd concentration was affected. Intercropped soybean–corn also affected the soil physicochemical properties and rhizosphere bacterial community structure. Thus, intercropped soybean–corn was a key factor in determining changes in microbial community composition and networks. These results provide a basic ecological framework for soil microbial function in Cd-contaminated soil.

Dynamic changes of rhizosphere soil bacterial community and nutrients in cadmium polluted soils with soybean-corn intercropping