Continuous Wheat/Soybean Cropping Influences Soybean Yield and Rhizosphere Microbial Community Structure and Function

Wheat/soybean rotation is an important double-cropping system in the Huang-Huai-Hai plain of China. Continuous soybean cropping could cause soil quality deterioration and plant growth inhibition. However, the effects of continuous wheat/soybean cropping on soybean rhizosphere microbes remain largely unknown. In this study, we compared the soybean yield and rhizosphere soil microbial community between continuous winter wheat/summer soybean (W/S) with two harvests in one year and winter wheat/summer soybean-winter wheat/summer maize (W/S-W/M) with four harvests in two years. The results showed that the soybean yield in the W/S group significantly (p < 0.05) declined within the first two years. The W/S-W/M showed higher soybean yield and soil fertility index than the W/S group. The sequencing results revealed that cropping rotation had a higher impact on the fungal community than the bacterial community. The W/S group showed 22.08–23.01% higher alpha diversity of the fungal community, but the alpha diversity of the bacterial group did not vary significantly in this group. The fungal community composition in the W/S and W/S-W/M groups differed significantly. In the W/S-W/M group, a higher relative abundance of plant growth-promoting fungi (e.g., Mortierella), nematophagous fungi (e.g., Plectosphaerella), and biological control fungi (e.g., Coniothyrium) was observed. In the W/S group, a higher relative abundance of lignocellulose-degrading fungi (e.g., Trechispora, Myceliophthora, Botryotrichum, and Coniochaeta) and pathogenic fungi (e.g., Pyrenochaetopsis and Cyphellophora) was observed. LEfSe analysis demonstrated that Mortierella, Myceliophthora, and Trechispora could serve as crucial biomarkers. Mortierella was positively associated with available P levels and negatively associated with NO3−-N levels and pH while Trechispora showed the opposite trend. The findings of this study could enhance the current understanding of the mechanisms associated with the continuous wheat/soybean cropping obstacles and ensure the sustainability of agricultural production.