Agroecosystem Biodiversity through Crop Rotation: Yield, Soil Carbon, and Nitrogen Loss Trade-offs Between Continuous Corn and Soybean–Corn Systems in the Midwest

Crop rotation is a key component of agricultural biodiversity, yet its ecosystem and economic benefits remain incompletely quantified across intensive grain-production regions. Using the ecosys agroecosystem model, we evaluated how a soybean–corn (S–C) rotation—one of the most widespread forms of biodiversity in U.S. Midwestern agriculture—modifies crop productivity, soil carbon dynamics, and nitrogen losses relative to continuous corn (C–C). Simulations across ten Illinois sites reproduced observed nitrogen (N) fertilizer–yield relationships and CO₂ fluxes, enabling a robust comparison of system responses. We found that rotational biodiversity in the S–C system alters residue quality and seasonal biogeochemical dynamics: soybean residues provided less carbon but more N than corn residues, increasing early-spring soil temperature, accelerating N mineralization, and enhancing corn yields, particularly under moderate N fertilizer rates. However, this residue-driven acceleration of decomposition also reduced soil organic carbon (SOC) compared with C–C, illustrating a trade-off between short-term productivity and long-term soil carbon conservation. At the same time, S–C reduced N₂O and NH₃ emissions under typical N rates, although effects on N leaching differed between soybean and corn years. Economic analyses showed that biodiversity introduced through S–C rotations improved net returns at low N fertilizer levels but lost this advantage as N rates and fertilizer costs increased. Overall, our results demonstrate that agricultural biodiversity in the form of crop rotation reshapes the balance among yield, greenhouse gas emissions, nutrient losses, and soil carbon storage, and that N fertilizer rate is a critical factor governing these trade-offs in Midwestern cropping systems.