Rice-crayfish farming systems improve soil carbon stocks and ecosystems services

Soil aggregates are central to soil ecological functioning, regulating both carbon sequestration and nutrient retention. The rice–crayfish (RC) farming system has been widely promoted as a diversification strategy for rice monoculture, yet its capacity to stabilize soil organic carbon (SOC) has largely been inferred from bulk soil measurements, leaving underlying aggregate-scale mechanisms unresolved. Here, using an eight-year field experiment on the Jianghan Plain, China, we provide the first long-term, depth-resolved evidence that RC enhances SOC sequestration through aggregate-mediated carbon protection rather than changes in aggregate size distribution alone. Across surface (0–20 cm) and subsurface (20–40 cm) soils, SOC stocks were strongly and negatively coupled to aggregate-level carbon mineralization. Large macroaggregates—comprising more than 60% of total aggregate mass—exhibited the lowest mineralization quotients, revealing a previously unquantified stabilization efficiency within RC systems. RC farming increased SOC concentrations within large macroaggregates by 45% in surface soils and 38% in subsurface soils, resulting in an 8% increase in SOC stocks across the 0–40 cm profile. Crucially, this increase occurred despite elevated absolute mineralization potential, demonstrating a decoupling between carbon input and decomposition intensity that has not previously been documented in rice–aquaculture systems. In parallel, RC enhanced soil ecosystem multifunctionality by 18-fold in surface soils, linking aggregate-scale carbon persistence to broader gains in nutrient cycling and soil function. By explicitly connecting soil structural hierarchy, mineralization efficiency, and multifunctionality, this study identifies a mechanistic pathway through which integrated rice–aquaculture systems can simultaneously enhance carbon sequestration and agroecosystem performance—advancing RC farming from a productivity-based practice to a quantifiable, process-driven climate mitigation strategy.