Terrestrial plants assimilate anthropogenic CO₂ through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in ESMs. We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland ¹⁵ N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the ¹⁵ N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition.

Reliable soil biogeochemical modeling is a prerequisite for credible projections of climate change and associated ecosystem feedbacks. This recognition has called for frameworks that can support flexible and efficient development and application of new or alternative soil 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 the development and integration of new soil biogeochemistry formulations into ESMs and to analyze structural uncertainty in ESM simulations. With a generic reactive transport capability, BeTR-v1 can represent multiphase (e.g., gaseous, aqueous, and solid), multi-tracer (e.g., nitrate and organic carbon), 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 robust numerical solvers for multiphase diffusion and advection and coupling between biogeochemical reactions and improves code modularization over BeTR-v1. BeTR-v2 better supports different mathematical formulations in a hierarchical manner by allowing the resultant model be run for a single topsoil layer or a vertically resolved soil column, and it allows the model to be fully coupled with the land component of the Energy Exascale Earth System Model (E3SM). We demonstrate the capability of BeTR-v2 with benchmark cases and example soil biogeochemical (BGC) implementations. By taking advantage of BeTR-v2's generic structure integrated in E3SM, we then found that calibration could not resolve biases introduced by different numerical coupling strategies of plant-soil biogeochemistry. These results highlight the importance of numerically robust implementation of soil biogeochemistry and coupling with hydrology, thermal dynamics, and plants - capabilities that the open-source BeTR-v2 provides. We contend that Earth system models should strive to minimize this uncertainty by applying better numerical solvers. Copyright:

Permafrost stability is significantly influenced by the thermal buffering effects of snow and active-layer peat soils. In the warm season, peat soils act as a barrier to downward heat transfer mainly due to their low thermal conductivity. In the cold season, the snowpack serves as a thermal insulator, retarding the release of heat from the soil to the atmosphere. Currently, many global land models overestimate permafrost soil temperature and active layer thickness (ALT), partially due to inaccurate representations of soil organic matter (SOM) density profiles and snow thermal insulation. In this study, we evaluated the impacts of SOM and snow schemes on ALT simulations at pan-Arctic permafrost sites using the Energy Exascale Earth System Model (E3SM) land model (ELM). We conducted simulations at the Circumpolar Active Layer Monitoring (CALM) sites across the pan-Arctic domain. We improved ELM-simulated site-level ALT using a knowledge-based hierarchical optimization procedure and examined the effects of precipitation-phase partitioning methods (PPMs), snow compaction schemes, and snow thermal conductivity schemes on simulated snow depth, soil temperature, ALT, and CO2 fluxes. Results showed that the optimized ELM significantly improved agreement with observed ALT (e.g. RMSE decreased from 0.83 m to 0.15 m). Our sensitivity analysis revealed that snow-related schemes significantly impact simulated snow thermal insulation levels, soil temperature, and ALT. For example, one of the commonly used snow thermal conductivity schemes (quadratic Sturm or SturmQua) generally produced warmer soil temperatures and larger ALT compared to the other two tested schemes. The SturmQua scheme also amplified the model’s sensitivity to PPMs and predicted deeper ALTs than the other two snow schemes under both current and future climates. The study highlights the importance of accurately representing snow-related processes and peat soils in land models to enhance permafrost dynamics simulations.

Methane (CH4) is globally the second most critical greenhouse gas after carbon dioxide, contributing to 16%–25% of the observed atmospheric warming. Wetlands are the primary natural source of methane emissions globally. However, wetland methane emission estimates from biogeochemistry models contain considerable uncertainty. One of the main sources of this uncertainty arises from the numerous uncertain model parameters within various physical, biological, and chemical processes that influence methane production, oxidation, and transport. Sensitivity Analysis (SA) can help identify critical parameters for methane emission and achieve reduced biases and uncertainties in future projections. This study performs SA for 19 selected parameters responsible for critical biogeochemical processes in the methane module of the Energy Exascale Earth System Model (E3SM) land model (ELM). The impact of these parameters on various CH4 fluxes is examined at 14 FLUXNET- CH4 sites with diverse vegetation types. Given the extensive number of model simulations needed for global variance-based SA, we employ a machine learning (ML) algorithm to emulate the complex behavior of ELM methane biogeochemistry. We found that parameters linked to CH4 production and diffusion generally present the highest sensitivities despite apparent seasonal variation. Comparing simulated emissions from perturbed parameter sets against FLUXNET-CH4 observations revealed that better performances can be achieved at each site compared to the default parameter values. This presents a scope for further improving simulated emissions using parameter calibration with advanced optimization techniques.

Arctic warming has increased vegetation growth and soil respiration during recent decades. The rate of Arctic warming will likely amplify over the 21st century. Previous studies have revealed that the most severe Arctic warming occurred during the cold season (September to May). The cold-season warming has posited significant CO2 emissions to the atmosphere via respiration, possibly offsetting warm-season (June to August) net CO2 uptake. However, prevailing Earth system land models poorly represent cold-season CO2 emissions, making estimates of Arctic tundra annual CO2 budgets highly uncertain. Here, we demonstrate that an improved version of the energy exascale Earth system model (E3SM) land model (ELMv1-ECA) captures the large amount of cold-season CO2 emissions over Alaskan Arctic tundra as reported by two independent, observationally-constrained datasets. We found that the recent seven-decades warming trend of cold-season soil temperature is three times that of the warm-season. The climate sensitivity of warm-season net CO2 uptake, however, is threefold higher than for the cold-season net CO2 loss, mainly due to stronger plant resilience than microbial resilience to hydroclimatic extremes. Consequently, the modeled warm-season net CO2 uptake has a larger positive trend (0.74 ± 0.14 gC m-2 yr-1) than that of cold-season CO2 emissions (0.64 ± 0.11 gC m-2 yr-1) from 1950 to 2017, supported by enhanced plant nutrient uptake and increased light- and water-use efficiency. With continued warming and elevated CO2 concentrations under the representative concentration pathway (RCP) 8.5 scenario, the increasing rate of warm-season net CO2 uptake is more than twice the rate of cold-season emissions (1.33 ± 0.32 gC m-2 yr-1 vs 0.50 ± 0.12 gC m-2 yr-1), making the modeled Alaskan Arctic tundra ecosystem a net CO2 sink by 2100. However, other geomorphological and ecological disturbances (e.g. abrupt permafrost thaw, thermokarst development, landscape-scale hydrological changes, wildfire, and insects) that are not considered here might alter our conclusion.

Field measurements have shown that cold-season methane (CH4) and carbon dioxide (CO2) emissions contribute a substantial portion to the annual net carbon emissions in permafrost regions. However, most earth system land models do not accurately reproduce cold-season CH4 and CO2 emissions, especially over the shoulder (i.e., thawing and freezing) seasons. Here we use the Energy Exascale Earth System Model (E3SM) land model version 1 (ELMv1-ECA) to tackle this challenge and fill the knowledge gap of how cold-season CH4 and CO2 emissions contribute to the annual totals at Alaska Arctic tundra sites. Specifically, we improved the ELMv1-ECA soil water phase-change scheme, environmental controls on microbial activity, and the methane module. Results demonstrate that both soil temperature and the duration of zero-curtain periods (i.e., the fall period when soil temperatures linger around 0°C) simulated by the updated ELMv1-ECA were greatly improved; e.g., the mean absolute error (MAE) in zero-curtain durations at 12 cm depth was reduced by 62 % on average. Furthermore, the MAEs of simulated cold-season carbon emissions at three tundra sites were improved by 72 % and 70 % on average for CH4 and CO2, respectively. Overall, CH4 emitted during the early cold season (September and October), which often includes most of the zero-curtain period in Arctic tundra, accounted for more than 50 % of the total emissions throughout the entire cold season (September to May) in the model, compared with around 49.4 % (43 %-58 %) in observations. From 1950 to 2017, both CO2 emissions during the zero-curtain period and during the entire cold season showed increasing trends, for example, of 0.17 and 0.36 gC m-2 yr-1 at Atqasuk. This study highlights the importance of zero-curtain periods in facilitating cold-season CH4 and CO2 emissions from tundra ecosystems.

Evapotranspiration (ET) plays an important role in land-atmosphere coupling of energy, water, and carbon cycles. Following deforestation, ET is typically observed to decrease substantially as a consequence of decreases in leaf area and roots and increases in runoff. Changes in ET (latent heat flux) revise the surface energy and water budgets, which further affects large-scale atmospheric dynamics and feeds back positively or negatively to long-term forest sustainability. In this study, we used observations from a recent synthesis of 29 pairs of adjacent intact and deforested FLUXNET sites to improve model parameterization of stomatal characteristics, photosynthesis, and soil water dynamics in version 1 of the Energy Exascale Earth System Model (E3SM) Land Model (ELMv1). We found that default ELMv1 predicts an increase in ET after deforestation, likely leading to incorrect estimates of the effects of deforestation on land-atmosphere coupling. The calibrated model accurately represented the FLUXNET observed deforestation effects on ET. Importantly, the search for global optimal parameters converged at values consistent with recent observational syntheses, confirming the reliability of the calibrated physical parameters. Applying this improved model parameterization to the globe scale reduced the bias of annual ET simulation by up to ~600 mm/year. Analysis on the roles of parameters suggested that future model development to improve ET simulation should focus on stomatal resistance and soil water-related parameterizations. Finally, our predicted differences in seasonal ET changes from deforestation are large enough to substantially affect land-atmosphere coupling and should be considered in such studies.

We evaluated global soil organic carbon (SOC) stocks and turnover time predictions from a global land model (ELMv1-ECA) integrated in an Earth System Model (E3SM) by comparing them with observed soil bulk and Δ14C values around the world. We analyzed observed and simulated SOC stocks and Δ14C values using machine learning methods at the Earth System Model grid cell scale (~200 km). In grid cells with sufficient observations, the model provided reasonable estimates of soil carbon stocks across soil depth and Δ14C values near the surface but underestimated Δ14C at depth. Among many explanatory variables, soil albedo index, soil order, plant function type, air temperature, and SOC content were major factors affecting predicted SOC Δ14C values. The influences of soil albedo index, soil order, and air temperature were primarily important in the shallow subsurface (≤30 cm). We also performed sensitivity studies using different vertical root distributions and decomposition turnover times and compared to observed SOC stock and Δ14C profiles. The analyses support the role of vegetation in affecting soil carbon turnover, particularly in deep soil, possibly through supplying fresh carbon and degrading physical-chemical protection of SOC via root activities. Allowing for grid cell-specific rooting and decomposition rates substantially reduced discrepancies between observed and predicted Δ14C values and SOC content. Our results highlight the need for more explicit representation of roots, microbes, and soil physical protection in land models.

Plant growth and distribution in high-latitude tundra ecosystems is strongly limited by nutrient availability and is critical for quantifying centennial-scale carbon-climate interactions. However, land model representations of plant-nutrient interactions are uncertain, leading to poor comparisons with high-latitude observations. Although it has been recognized for decades in the observational community that plants continue to acquire nutrients well past when aboveground activity has ceased, most large-scale land models ignore this process. Here we address the role tundra plant nutrient acquisition during the non-growing season (NGS) has on centennial-scale vegetation growth and dynamics, with a focus on shrub expansion. We apply a well-tested mechanistic model of coupled plant, microbial, hydrological, and thermal dynamics that explicitly represents nutrient acquisition based on plant and microbial traits, thereby allowing a prognostic assessment of NGS nutrient uptake. We first show that the model accurately represents observed seasonality of NGS plant nutrient uptake in a northern Alaskan tundra site. Applying the model across the North America tundra indicates that NGS nutrient uptake is consistent with observations and ranges between ∼5% and 50% of annual uptake, with large spatial variability and dependence on plant functional type. We show that NGS plant nutrient acquisition strongly enhances modeled 21st century tundra shrub growth and expansion rates. Our results suggest that without NGS nutrient uptake, total shrub aboveground dominance would be ∼50% lower, limited primarily by their inability to grow tall enough to maximize their inherent capacity for light competition. Evergreen shrubs would be more strongly affected because of their relatively lower capacity for nutrient remobilization and acquisition compared to deciduous shrubs. Our results highlight the importance of NGS plant and soil processes on high-latitude biogeochemistry and vegetation dynamics and motivate new observations and model structures to represent these dynamics.

Land surfaces dissipate energy through latent (LE) and sensible (H) heat fluxes that modulate atmospheric temperature and humidity, which in return affect land surface vegetation and soil processes. Within this two-way land-atmosphere coupling, surface energy partitioning (LE versus H) plays a central role in connecting the land and atmosphere states and fluxes. However, considerably large uncertainties still exist in earth system land models, i.e. the phase 6 of the Coupled Model Intercomparison Project (CMIP6). Further, the underlying controls from climate and biological factors on surface energy partitioning over different biome types are not well understood. In this study, we combined machine learning (ML) and causal inference models to investigate and reduce the uncertainties (i.e., parametric, structural, and forcing uncertainties) of CMIP6 simulated evaporative fraction (defined as LE / (LE + H)) across 64 FLUXNET sites that cover five major biomes. We found that CMIP6 model ensembles overestimated evaporative fraction with considerable spread at deciduous broadleaf forest, evergreen needleleaf forest, and savanna sites. Accounting for the biases from all related surface climate and biological driving variables, the CMIP6 model simulated EF could be largely improved (e.g., R between model and observed EF improved from 0.47 to 0.66), with leaf area index, vapor pressure deficit, and precipitation dominated the model improvement. Furthermore, ML-based parameterization generally showed a promising opportunity to further reduce model biases (e.g., R improved from 0.66 to 0.80) in spite of the limited improvement at evergreen broadleaf forest sites where model bias may be dominated by structural imperfection. This study provided an effective framework to understand and reduce model uncertainties in simulating land surface energy flux partitioning and, more importantly, highlighted the need of effective model structure improvement for the next generation earth system land model development.