Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystem

Abstract Soil microbes play key roles in soil nutrient cycling and absorption by crops. Thus, shifts in soil microbial community structure affect the functioning and productivity of agricultural ecosystems. However, the complex impact of agricultural management methods, such as fertilization regime, crop rotation, and growth stage, on soil microbial communities are poorly understood. Here, we used a 33-year field experiment to examine soil bacterial and fungal communities at the seedling, flowering, and mature stages for winter wheat and soybean in a wheat-soybean rotation system under four fertilization regimes: no fertilization (NF), mineral fertilizer only (NPK), mineral fertilization with 7500 kg ha−1 of wheat straw (WS), and mineral fertilization with 30,000 kg ha−1 composted cow manure (CM). We used 16S rRNA and ITS amplicon sequencing to determine the taxonomic structure of the bacterial and fungal communities. Fertilization not only significantly improved crop productivity but also had a greater effect on soil bacterial and fungal community structure than crop rotation and growth stage. In the bacterial community, CM had a positive effect on the abundances of Deltaproteobacteria and Bacteroidetes, while the fungi Glomeromycota and Chytridiomycota were significantly impacted by crop rotation. Redundancy analysis further showed that manure application combined with chemical fertilizers could reduce the impact of environmental factors on bacterial community structure when compared to no fertilization, chemical fertilization alone, or wheat straw incorporation combined with chemical fertilization. Our results suggest that fertilization regime has a greater impact on soil microbe properties than crop rotation or growth stage and that the different responses of soil bacterial and fungal communities to agricultural practices might influence overall ecosystem functioning.