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. Reliable soil biogeochemical modeling is a prerequisitefor credible projections of climate change and associated ecosystemfeedbacks. This recognition has called for frameworks that can supportflexible and efficient development and application of new or alternativesoil biogeochemical modules in Earth system models (ESMs). The the Biogeochemical Transport and Reaction model version 1 (BeTR-v1) code(i.e., CLM4-BeTR) is one such framework designed to accelerate thedevelopment and integration of new soil biogeochemistry formulations intoESMs and to analyze structural uncertainty in ESM simulations. With ageneric reactive transport capability, BeTR-v1 can represent multiphase(e.g., gaseous, aqueous, and solid), multi-tracer (e.g., nitrate and organiccarbon), and multi-organism (e.g., plants, bacteria, and fungi) dynamics.Here, we describe the new version, Biogeochemical Transport and Reaction model version 2 (BeTR-v2), which adopts more robustnumerical solvers for multiphase diffusion and advection and couplingbetween biogeochemical reactions and improves code modularization overBeTR-v1. BeTR-v2 better supports different mathematical formulations in ahierarchical manner by allowing the resultant model be run for asingle topsoil layer or a vertically resolved soil column, and it allows the model to be fully coupledwith the land component of the Energy Exascale Earth System Model (E3SM). Wedemonstrate the capability of BeTR-v2 with benchmark cases and example soil biogeochemical (BGC)implementations. By taking advantage of BeTR-v2's generic structureintegrated in E3SM, we then found that calibration could not resolve biasesintroduced by different numerical coupling strategies of plant–soilbiogeochemistry. These results highlight the importance of numericallyrobust implementation of soil biogeochemistry and coupling with hydrology,thermal dynamics, and plants – capabilities that the open-source BeTR-v2provides. We contend that Earth system models should strive to minimize this uncertainty by applying better numerical solvers.

Supporting hierarchical soil biogeochemical modeling: version 2 of the Biogeochemical Transport and Reaction model (BeTR-v2)