Long-term integrated soil-crop management improves soil microbial community structure to reduce GHG emission and increase yield.

Integrated soil-crop management (ISCM) has been shown as an effective strategy to increase efficiency and yield while its soil microbial community structure and function remain unclear. We evaluated changes in soil physicochemical factors, bacterial community structure responses, and the contributions of soil properties and bacterial communities to summer maize-winter wheat yield and GHG emissions through an ISCM experiment [T1 (local smallholder farmers practice system), T2 (improved management system), T3 (high-yield production system), and T4 (optimized management system)], which could provide scientific guidance for sustainable development of soil in summer maize-winter wheat rotation system. The results showed that the optimized ISCM could improve the soil quality, which significantly changed the soil bacterial community structure to reduce GHG emissions and increase yield. The co-occurrence network density of T3 was increased significantly. The Acidobacteria (class) and OM190 (class) were enriched in T2 and T4. The Frankiales (order) and Gaiellales (order) were enriched in T3. However, the changes in different crop growth stages were different. At the wheat jointing stage and maize mature stage, T4 could enhance carbon-related functional groups, such as aromatic hydrocarbon degradation and hydrocarbon degradation, to increase the soil organic carbon content. And at the maize tasseling stage, T4 could enhance nitrogen-related functional groups. And soil bacteria structure and function indirectly affected annual yield and GHG emission. T2 and T4 exhibited a similar soil microbial community. However, the yield and nitrogen use efficiency of T2 were reduced compared to those of T4. The yield of T3 was the highest, but the GHG emission increased and soil pH and nitrogen use efficiency decreased significantly. Therefore, T4 was a suitable management system to improve soil quality and soil bacterial community structure and function to decrease GHG emissions and increase the yield of the summer maize-winter wheat rotation system.