Enzyme-substrate reactions and kinetic theory in biogeochemical cycling in soils: What we know and what we don't know

Soil enzymes produced by microbes play a central role in ecosystem functioning by mediating the decomposition of soil organic matter (SOM) and nutrient mineralization. This perspective examines how enzyme kinetics may improve our understanding of these processes and enhance their representation in biogeochemical models. We synthesize current knowledge of enzyme–substrate interactions and evaluate recent advances in both experimental and modeling approaches. We identified that, despite significant progress in experimental and modeling studies, in-situ characterization of soil enzyme activity and its explicit integration into ecosystem models remain challenging. These challenges are largely attributed to the difficulties in scaling enzyme-mediated processes across spatial and temporal domains coupled with uncertainties in microbial functional redundancy, incomplete understanding of enzyme responses to global change, and constraints related to substrate accessibility and physicochemical stabilization. As a result, enzyme-mediated processes—regulated by multiple interacting biotic and abiotic factors—are often oversimplified in existing models. We further identify key knowledge gaps, particularly in linking microscale enzyme dynamics to large-scale ecosystem processes. We conclude that integrating mechanistic representations of enzyme kinetics across multiple scales is critical for improving predictions of soil carbon and nutrient dynamics under global change. Future research should therefore prioritize multiscale, process-based approaches to better incorporate enzyme-mediated processes into ecosystem and Earth system models.