Soil organic carbon (SOC) plays a pivotal role in the global carbon cycle, impacting climate dynamics and necessitating accurate estimation for sustainable land and agricultural management. While traditional methods of SOC estimation face resolution and accuracy challenges, recent technological solutions harness remote sensing, machine learning, and high-resolution satellite mapping. Graph Neural Networks (GNNs), especially when integrated with positional encoders, can capture complex relationships between soil and climate. Using the LUCAS database, this study compared four GNN operators in the positional encoder framework. Results revealed that the PESAGE and PETransformer models outperformed others in SOC estimation, indicating their potential in capturing the complex relationship between SOC and climate features. Our findings confirm the feasibility of applications of GNN architectures in SOC prediction, establishing a framework for future explorations of this topic with more advanced GNN models.

Measuring and monitoring soil organic carbon is critical for agricultural productivity and for addressing critical environmental problems. Soil organic carbon not only enriches nutrition in soil, but also has a gamut of co-benefits such as improving water storage and limiting physical erosion. Despite a litany of work in soil organic carbon estimation, current approaches do not generalize well across soil conditions and management practices. We empirically show that explicit modeling of cause-and-effect relationships among the soil processes improves the out-of-distribution generalizability of prediction models. We provide a comparative analysis of soil organic carbon estimation models where the skeleton is estimated using causal discovery methods. Our framework provide an average improvement of 81% in test mean squared error and 52% in test mean absolute error.