Understanding Local Drivers of Soil Organic Carbon Stocks and Stability Using SHAP Analysis in an Agricultural Territory of Eastern France

Soil organic carbon (SOC) plays a key role in climate regulation and soil functioning. Although SOC stock and stability result from complex interactions between environmental, biological, and anthropogenic factors, the hierarchy of these drivers is strongly scale-dependent. At large spatial scales, climatic forcing often dominates SOC patterns, potentially masking the effects of land management. At local scales, where climatic variability is reduced, the relative influence of agricultural practices compared to landscape heterogeneity (e.g., topography and soil properties) remains poorly quantified, notably due to the scarcity of datasets combining soil properties and high-resolution management data. Clarifying this balance is essential for designing effective climate mitigation strategies in agricultural systems.

We investigated the drivers of SOC stock and stability within a 3,000 km² heterogeneous agricultural territory in Burgundy (France). The territory spans a diverse landscape, transitioning from western limestone plateaus to agricultural plains in the east. SOC measurements (0–20 cm) from 147 cropland sites were combined with 18 explanatory variables derived from in situ measurements, field survey, or satellite data and describing topography, climate, soil physico-chemical properties, vegetation dynamics, and contrasting agricultural management (diverse crop rotations, residue management, the use of cover crops, and organic amendments). SOC stable and active fractions were quantified using Rock-Eval® thermal analysis coupled with the PARTYsoc learning model. The SOC stocks averaged 41.7 ± 13.9 tC.ha^-1, with the active (C_a​) and stable (C_s) stocks representing 19.9 ± 8.3 tC.ha^-1 and 21.8 ± 6.1 tC.ha^-1, respectively. 

Random Forest models were used to capture non-linear relationships between SOC variables and their drivers, and SHAP (SHapley Additive exPlanations) values were applied to quantify the relative importance and direction of individual drivers. Model performance reached a coefficient of determination (R²) of 0.41 for SOC stocks, and 0.50 and 0.26 for C_a​ and C_s stocks respectively. The lower R² for C_s​ likely reflects missing explanatory variables related to historical land use or specific soil mineralogy.

SHAP analysis revealed that even at local scales (a few km), soil properties and climate remain the dominant drivers of SOC stock and stability in this study. Nevertheless, management-related factors, such as crop residue management and number of vegetation days during the intercrop periods, exert a stronger influence on SOC stock than topographic variables. Patterns differ among pools: active carbon is mainly influenced by CaCO₃, temperature, and precipitation, whereas clay content dominates the stable carbon fraction.

Our results demonstrate that while soil and climate largely control SOC stocks at local scales in the context of a highly heterogeneous terrain, agricultural management can meaningfully influence SOC dynamics and stability, highlighting opportunities for targeted strategies to enhance soil carbon sequestration.