For most evaluations of biophysical and biogeochemical cycles, we ran ED-2.2 for two sites in the Amazon where both eddy flux towers and forest inventories were available for a long period: the Guyaflux tower (5∘17′ N, 52∘55′ W) at Paracou, French Guiana GYF;, and the Tapajós National Forest site (2∘51′ S, 54∘58′ W), located in the central Amazon TNF;. Both data sets underwent multiple-stage quality control. We used the meteorological variables measured at the eddy covariance tower sites to drive these ED-2.2 simulations. These variables included temperature, specific humidity, pressure, wind speed, incoming solar radiation, incoming longwave radiation, and precipitation. All meteorological variables used as inputs for ED-2.2 were gap-filled following . Net ecosystem exchange (NEE) was processed using the approach by , which corrects flux bias due to lack of turbulence and turbulent-independent divergence of CO2.

To ensure that model and observations at or near eddy covariance flux towers could be directly compared, and that the observed signal was strongly related to actual environment conditions, we saved model outputs every hour and only used the model output for the hours when each variable of interest was measured. Gross primary productivity (GPP) and ecosystem respiration (R˙Eco) are not measured but statistically modeled from NEE; therefore, we compared all times in which NEE could be estimated from tower observations. We also required that the 24 h period preceding any given time had less than 24 gap-filled values among all seven driver variables. Finally, in ED-2.2, we solve fluxes for each local plant community (patch) within the area of interest (polygon). Since eddy covariance towers provide flux measurements and estimates that are representative of the entire plant community, to assess ED-2.2 results against the eddy covariance fluxes, we compared the tower estimates with the ED-2.2 polygon averages (i.e., area-weighted average of fluxes for all simulated patches).

To evaluate the in-canopy radiation profile, we compared model results against measured profiles of photosynthetically active radiation at two sites in the Brazilian Amazon: Jaru Biological Reserve (RJA: 10∘05′ S, 61∘56′ W) near Ji-Paraná, and Adolpho Ducke Forest Reserve (MDK: 2∘57′ S, 59∘55′ W), near Manaus . At RJA, data were collected during two measurements campaigns as part of the Anglo-Brazilian Climate Observation Study ABRACOS; in August–September 1992 and April–June 1993, and measurements were taken at 2.3, 6.1, 11.6, 15.7, 21.3, and 35.0 m aboveground; at MDK, the measurement campaign occurred in July–August 1991, and sensors were installed at 5.0, 10.0, 15.0, 20.0, 25.0, and 35.0 m aboveground. In both cases, two to three sensors were installed in each level either east or west of the tower, and both sites used the same quantum radiation sensors of model SKP 215 (Skye Instruments Ltd, Powys, UK) . To reduce the impact of the towers on the measurements, we only used data from sensors east of the towers in the morning and west of the towers in the afternoon . The model was run for the same days of the year as the data. However, we simulated different years – 1999–2006 for MDK and 1999–2002 for RJA – using the Large-Scale Biosphere-Atmosphere Experiment in Amazonia Data Model Intercomparison Project (LBA-MIP) data , because we did not have data from all meteorological variables needed by ED-2.2 during the period when the radiation profile data were collected. Also, the diurnal cycle of any point measurement within the canopy depends on local heterogeneities and can be dramatically affected by the Sun's azimuth and zenith angles (e.g., Sun flecks when the sensor is aligned with an opening in the canopy). For this reason, we only used the average daily radiation relative to the top of canopy to compare with the model results. Although simulated days (from LBA-MIP) include the entire range of daily averages of temperature, humidity, and net radiation observed during the ABRACOS campaign, the simulated period had significantly (t test at 95% confidence) warmer average temperatures at MDK (0.67 ∘C) and higher net radiation at both RJA (13.7Wm-2) and MDK (18.5Wm-2) (Fig. S1 in the Supplement). Therefore, we also compared the predicted light extinction profile with observations for overcast hours, when the direct radiation (based on the model) would be zero. Under overcast conditions, the model predictions of relative light extinction do not depend on the total incoming radiation . To evaluate the model's ability to represent changes in light environment throughout the canopy, we compare the light profiles of model and observations as a function of the cumulative tree area index (TAI). TAI is defined as the sum of leaf area index (LAI) and the branch wood area index (WAI). TAI profiles were estimated from published data at RJA and near MDK .

To evaluate the model's ability to represent the long-term dynamics, we carried out multiple simulations intended to test the model's ability to describe regional variability as well as the structural and functional diversity of ecosystems in tropical South America.

First, to assess the model's ability to represent the distribution of biomass and leaf area index across tropical South America (18∘ S–13∘ N, 83–33∘ W), we carried out a 1∘ resolution 500-year regional simulation, starting from near-bare conditions (1400–1900) to produce the simulated potential vegetation. In these simulations, we assumed a constant tree-fall disturbance rate of 1.4%year-1 and allowed the occurrence of fire, using the original ED-1 implementation of the fire disturbance model . We then resumed the simulation in 1900, applying anthropogenic disturbance and ran the model until 2002, using a combination of land use transition matrices from , nudged to match the initial conditions from in the Amazon. We specified the soil texture for each grid cell using data from for the Amazon, RADAMBRASIL for non-Amazonian areas of Brazil, and the International Geosphere-Biosphere Programme (IGBP) for non-Amazonian areas elsewhere. Soil texture characteristics (sand, silt, and clay content) are used to determine the pedotransfer function, hydraulic and thermal conductivities, and heat capacity of soils . For the meteorological forcing, we used the Princeton University Global Meteorological Forcing data set PGMF; for 1969 to 2008, which was recycled multiple times to simulate a period equivalent to 1400 through 2002.

We examined the relationship between regional aboveground biomass (AGB) and light and water availability by comparing the model's AGB predictions against regional observations of these two quantities. Specifically for light availability, we compared the model predictions against two estimates of average annual shortwave radiation: one calculated from the PGMF shortwave measurements that were used to drive the model simulations, and the other being the annual average downwelling shortwave irradiance from the Clouds and the Earth's Radiant Energy System's Energy Balanced And Filled product CERES-EBAF; between 2001 and 2017. Similarly, for rainfall, we compared the model's AGB prediction to annual rainfall estimates calculated from both the PGMF meteorological data set and the average of annual precipitation calculated from the Tropical Rainfall Measurement Mission's (TRMM) Multi-Satellite Precipitation Analysis Product TMPA-3B43 V7; between 1998 and 2017. For maximum cumulative water deficit (MCWD, mm), we assumed a constant monthly evapotranspiration (ET0=100mm) and monthly precipitation (P, mm) from TMPA-3B43, following previous studies for the Amazon region . For any month t, we defined the cumulative water deficit (CWD, mm) to be 1CWDt=min⁡1200,max⁡0,CWDt-Δt+ET0-Pt, where Δt=1month. This integration is continuously carried over the entire time series. For each calendar year, we defined MCWD as the maximum monthly value of CWD. Note that this estimate of MCWD assumes evapotranspiration values that are typical of tropical rainforests (i.e., ET0=100mm) and therefore should be regarded as a forest-equivalent MCWD, not an actual measurement. High values of MCWD indicate regions where water losses would be too high to maintain forests. This baseline evapotranspiration (ET0) is high for arid regions, and consequently we imposed a cap of 1200mm on CWD to avoid extremely high deficits at the most arid regions, where precipitation is insufficient to bring the water deficit back to zero.

We re-projected the estimates of shortwave irradiance, precipitation, and MCWD to the same grid as ED-2.2 using spatial averaging. For each environmental variable, we divided the grid cells into 20 quantile-based groups (0–0.05; 0.05–0.10; ...; 0.95–1) and obtained the average and the 90% quantile range within each bin for the ED-2.2 model and three remote-sensing estimates of aboveground biomass: , , and . We also compared the model's predictions of LAI with estimates from the Moderate Resolution Imaging Spectroradiometer (MODIS, product MCD15A2H, Collection 6) . We used all cloud-free, high-quality data from MODIS-MCD15A2H that were available between August 2002 and July 2004. We selected this period to reduce temporal – and land-use-related – differences between the model simulation and MODIS-MCD15A2H, and we aggregated the average LAI to 1∘ resolution to be consistent with the ED-2.2 simulations. Finally, to evaluate the model's predictions of fire regime across tropical South America, we compared the average fire disturbance rate over predicted by ED-2.2 over one full cycle of the meteorological drivers (last 40 years of the simulation) with the Global Fire Emissions Database version 4.1 GFED4.1;. Similarly to aboveground biomass and LAI, we aggregated GFED4.1 relative burned area to 1∘; because GFED4.1 data have a short overlapping period with the PGMF drivers, we used all available years (1997–2015) to compute the average fire disturbance rate.

To evaluate the model's ability to predict emergent properties, we used published values of biomass and mortality obtained from the RAINFOR field inventory network in the Amazon and the results from long-term simulations near the field inventory sites . Specifically, we investigated the relationship between aboveground biomass and long-term average mortality rates, and community-averaged wood density across these sites. In ED-2.2, typical wood density and background mortality rates are prescribed for each cohort based on their plant functional type (PFT). However, the model allows for coexistence of PFTs that can be modulated by abiotic and biotic factors such as soil texture, climate, and direct competition for limiting resources (e.g., light and water) between PFTs . Consequently, mortality rates and community-level wood density are not prescribed parameters; instead, these properties emerge from the population structure comprised by different PFTs.

Finally, we tested both the forest structure predictions and the model's ability to represent variability of demographic rates at the two study sites (GYF and TNF) for which we had long-term forest inventory data. We ran the model from near-bare-ground conditions for 500 years for each location, driven by the site-specific meteorological conditions, to obtain the near-steady state of each forest and to evaluate the forest structure predicted by the model at steady state. Several factors that are not well constrained for these sites may affect the simulations. For example, at both sites, the meteorological drivers were not available for the period before the first inventory (in the case of TNF, meteorological data became available only 2 years after the first inventory). In addition, soil texture is known to be heterogeneous at local scale e.g.,. Likewise, leaf phenology strategies within the local community can be diverse and heterogeneous , and not known for the species included in the forest inventories. ED-2.2 model simulations are known to be modulated by such factors e.g.,; therefore, to evaluate the sensitivity of mortality and the growth rates to these factors, we carried out an ensemble of simulations using all 48 combinations of (1) different initial times, between 5 and 60 years before the first inventory (intervals of 5 years); (2) soil texture, using clayey loam and sandy clay loam for GYF, and clayey sand and clay for TNF following the typical soils found at each site ; (3) assuming that trees were all evergreen or all drought deciduous. Only cohorts with DBH≥10cm were considered for the comparison of structure and demographic rates, because this was the minimum size of trees measured at both locations .

Both GYF and TNF had measurements of outgoing shortwave radiation (Q˙SW↑) and outgoing photosynthetically active radiation (Q˙PAR↑). Here, we compared the outgoing radiation instead of net radiation because net radiation includes incoming radiation, which is input variables for the model. The seasonal variation of both Q˙SW↑ and Q˙PAR↑ is close to observations at both sites (Fig. a–d). This result is expected because the seasonality of outgoing radiation is strongly modulated by incoming radiation. Nevertheless, the differences between simulated and observed Q˙SW↑ and Q˙PAR↑ are also small: the bias in the annual average of Q˙SW↑ was 3.0Wm-2 (GYF) and 0.6Wm-2 (TNF), and the annual average bias of Q˙PAR↑ was -0.9µmolm-2s-1 (GYF) and -1.6µmolm-2s-1 (TNF) (Fig. a–d). Likewise, the vertical profiles of daily averages of relative incoming PAR are close to the simulations, especially considering the large uncertainties on the observed tree area index (TAI) profile and that the simulated years are not the same as the observations (Fig. a, b). When we only consider overcast hours (less sensitive to local horizontal heterogeneities), the model shows even better agreement with model predictions, particularly at RJA, where the average profile was measured at the same site as the original observations, albeit at different years. While limited by the observation constrains, this comparison suggests that the model is able to reasonably reproduce typical light profiles.

Compared to tower observations, the model predicted higher mean sensible heat flux at both sites. At GYF, ED-2.2 captures the seasonal cycle very similarly to the observations; however, the fluxes are on average 19.5Wm-2 higher in ED-2.2 than measured by the tower (Fig. a). On the other hand, the model predicts significantly higher values at TNF (average bias of 35.9Wm-2), in particular during the dry season (average dry-season bias of 44.5Wm-2). The predicted seasonal cycle at TNF is very similar to the model prediction for GYF, whereas the tower measurements at TNF suggest much less variation between wet and dry seasons (Fig. b). From the distribution of fluxes by time of the day, we found that ED-2.2 predicted higher than observed sensible fluxes during the afternoon at both sites (Fig. c, d). In addition, ED-2.2 was unable to capture events of strong nighttime negative flux as measured at both towers. The predicted canopy air space temperature at GYF is typically 0.5 ∘C lower than tower estimates (Fig. S2a). At TNF, the predicted canopy air space temperate shows close agreement with tower estimates during the wet season, and ED-2.2 predicts temperatures about 0.5 ∘C higher than tower estimates (Fig. S2b). Comparison with outgoing thermal infrared radiation, which is correlated with the vegetated surface temperature, shows that the model typically predicts higher-than-observed values at daily scale (Fig. S3a, b), as a result of the model predicting higher fluxes during the afternoon (Fig. S3c, d). Therefore, the results suggest that the excessive sensible heat flux may be attributable to the model's overestimation of canopy temperature.

Water flux above canopy was well represented at both study sites (Fig. ). The bias on annual average was -0.23kgWm-2d-1 for GYF and +0.28kgWm-2d-1 for TNF. The agreement was even better during the dry season (bias of -0.12kgWm-2d-1 for GYF and +0.12kgWm-2d-1 for TNF). ED-2.2 correctly represents increased water flux during the dry season in TNF (Fig. b), and that water flux does not increase during the dry season in GYF (Fig. a), although the model underestimates the fluxes during the first wet season (December–February) in GYF. Likewise, the diurnal cycle of water flux is well characterized at both sites, with median values predicted by the model similar to observations both during the day and during the night (Fig. c, d). The mean canopy air space humidity at GYF shows excellent agreement during the wet season and slight underestimation during the dry season (Fig. S2d). In contrast, the model predictions at TNF show slightly lower values during the wet season, consistent with higher water fluxes, and agree well during the dry season (Fig. S2d).

When we compared gross primary productivity (GPP) with estimates from eddy covariance towers, the model captured the weak seasonality with slightly higher values during the dry season at GYF although the magnitude was consistently lower (Fig. a), whereas it captured the magnitude of GPP at TNF but it could not represent the decreased GPP early in the dry season (Fig. b).

Ecosystem respiration from ED-2.2 is more seasonal than the tower estimates, and the model predicts the highest respiration rates during the wet season at both sites, whereas tower-based estimates do not show a consistent seasonal pattern. Based on tower estimates, respiration reaches the maximum early in the dry season in GYF (Fig. a), whereas the maximum occurs during the wet season in TNF (Fig. b). At both sites, the model response is largely driven by fluctuations in soil moisture affecting heterotrophic respiration (Fig. c, d).

Ecosystem respiration is not directly measured from eddy covariance towers. The magnitude of ecosystem respiration from towers often depends on the choice of the u⋆ filter and can be biased because the extrapolation of respiration from nighttime to daytime does not account the light inhibition of daytime leaf respiration, known as the Kok effect . Therefore, we also compared the model predictions against results from other studies that focused on measuring or estimating each component of the total respiration. For TNF, we used the respiration components estimated by a bottom-up assessment of the carbon cycle . For GYF, we estimated the respiration terms using previously published results and aggregated the components following (Sect. S1). The mean ecosystem respiration predicted by ED-2.2 overlaps with the 95% confidence interval at both sites (Table ). In GYF, differences in heterotrophic respiration are the largest and explain most of the difference in the total respiration, whereas in TNF the positive bias in total respiration is due to autotrophic respiration. Within the autotrophic respiration, ED-2.2 predicts stem respiration that is 89 %–134 % higher than the bottom-up assessment. In GYF, the excessive stem respiration is compensated by leaf and root respiration that is 36% and 19% lower than field estimates, respectively. As a result, the total autotrophic respiration at GYF is within 1 standard error from the expected rate based on the bottom-up analysis. In TNF, the reference leaf and root respiration is nearly half the magnitude for GYF; consequently, ED-2.2 autotrophic respiration is 57% higher than the estimates by .

The model correctly predicts the extension of the Amazon forest (Fig. a), and it also represents the regional distribution of aboveground biomass within the Amazon biome compared to regional biomass maps from , , and , the latter being based on the other two maps. For example, ED-2.2 predicts higher aboveground biomass in the Guiana Shield, similar to estimates from and (Fig. b, d); the higher biomass near the border between Brazil, Peru, and Colombia, similar to and (Fig. c, d); and the low-biomass, open-savanna area near the Brazil–Guyana–Venezuela border. The model generally predicts higher biomass than the three remote-sensing maps for most of the Amazon south of the Guiana Shield, particularly in the western part of the Amazon (Fig. S4b–d), resulting in a peak in the distribution of biomass at 16.5kgCm-2, whereas the high-biomass peaks ranged between 11.5 and 14.0kgCm-2 for the remotely sensed estimates of aboveground biomass (Fig. ). The ED-2.2 model and the remote-sensing estimates consistently predict a relatively lower density function for intermediate values of biomass and a pronounced peak of low biomass, even though the low-biomass peak predicted by ED-2.2 (0.65kgCm-2) is lower than the remote-sensing estimates (1.0–3.4kgCm-2; Fig. ). The shift in the low-biomass peak is mostly driven by ED-2.2 predictions of biomass in the savannas and xeric shrublands of eastern Brazil, which were consistently lower than the remote-sensing estimates (Fig. S4). We also found that ED-2.2 predicted a similar extent of LAI over the Amazon region when compared to MODIS estimates (Fig. S5). However, ED-2.2 predicted lower LAI than MODIS for most of the Amazon, in particular along the arc of deforestation, and higher LAI in northwestern Colombia and central Brazil (Fig. S5c).

The predicted transitions between the Amazon biome and the Cerrado (savanna biome in central Brazil) and Los Llanos (grassland area in Venezuela) are driven by increased fire activity, consistent with the Global Fire Emission Database GFED4.1 regional distribution of burned area (α; Fig. ). In addition, ED-2.2 correctly predicted higher burned area in the savanna region at the Brazil–Guyana–Venezuela border and low fire activity over most of the Amazon biome and in the Caatinga (low-biomass, semi-arid region in northeastern Brazil) (Fig. ). In contrast, ED-2.2 underestimated fire activity in El Beni (Bolivian savannas, Δα=αED-2.2-αGFED4.1=-6.8%year-1) in the Colombian Los Llanos (Δα=-9.2%year-1), while it overestimated fire disturbance in forest areas near the border of Brazil and Bolivia (Δα=1.9%year-1), the coastal areas of Brazilian states of Maranhão and Piauí, immediately east of the Amazon biome (Δα=5.0%year-1), and areas in eastern Brazil south of 15∘ S (Δα=3.7%year-1) (Figs. , S6). Because the original fire model in ED-2.2 does not predict fire ignitions based on human activities , ED-2.2 does not predict the burned areas along the arc of deforestation in the southern and eastern edges of the Amazon biome (Fig. a).

The predicted spatial variability of total carbon stocks in the region also emerged from variation in the environmental conditions such as variability in available light and water (Figs. , S7). Both ED-2.2 and the three remote-sensing estimates of biomass consistently showed the highest average biomass (11.7–15.1kgCm-2) at 195Wm-2, and the sharpest decline as a function of increased irradiance (0.53–0.77kgCW-1) near 225Wm-2 (Figs. a, S7a). Similarly, the relationship between annual precipitation and aboveground biomass was consistent between the model and remote-sensing estimates, with the highest changes in average biomass by increase in annual rainfall occurring between 1500 and 2200mmyear-1, and relatively stable values of aboveground biomass above 2500mm (Fig. b). Some of the variability of simulated biomass at low (<1000mm) annual rainfall can be attributed to discrepancies between TMPA-3B43 and PGMF, which was used to drive the simulations, as the simulated biomass is consistently low where PGMF estimates of annual rainfall are less than 1000mm (Fig. S7b). The increasing dry-season severity, summarized by MCWD, has a strong association with decreasing average aboveground biomass in both the model and the remote-sensing estimates when the annual MCWD is less than 500mm. The strongest declines in average biomass occurred at mean annual MCWD between 300 and 350mm in both ED-2.2 and the remote-sensing estimates (Figs. c, S7c). It must be noted, however, that the transition between high biomass and low biomass when MCWD is 300–350mm is substantially more pronounced in ED-2.2 (-0.075kgCm-2mm-1) than in the remote-sensing estimates (between -0.041 and -0.050kgCm-2mm-1) (Fig. c).

In addition to the total carbon stocks, the regional variability in forest function and composition at steady state is generally well characterized by ED-2.2. The range and variability of biomass across the network are similar to the range and variability observed across most of the network (Fig. a). However, the model does not accurately predict the AGB of individual plots at the wettest sites (black dots in Fig. a). The model predicts lower-than-observed biomass at the drier sites located in Bolivia (red dots in Fig. a) because of frequent fires occurring in the model simulation. Also, both the model and the field measurements show similar negative correlation between biomass and mortality rates (Fig. b), and a similar positive correlation between biomass and the mean wood density (Fig. c), albeit significant differences exist in biomass for any given value of mortality or wood density (Fig. b, c). Both wood density and mortality rates are related to the abundance of pioneers or late successional individuals both in the model and in observations e.g.,, suggesting that the model characterizes the variability in forest composition within the Amazon region. Fewer sites had estimates of both mortality rates and net primary productivity (NPP). At the available sites, the average predicted values at steady state (1.29kgCm-2year-1) were slightly lower than values reported in the literature (1.35kgCm-2year-1) (Fig. d). Consistent with previous observations in the Amazon e.g.,, the ED-2.2 predictions indicate a positive correlation between NPP and mortality. However, this correlation is highly uncertain because of the limited number of plots (n=7) and the large variability in both NPP and mortality across sites (Fig. d).

The model captured the general distribution slope of stem demographic density (abundance) at GYF (Fig. a), and both the total basal area and the typical distribution of basal area for individuals with DBH between 20 and 50cm (Fig. b). In contrast, the model predicted a lower contribution from trees with DBH<20cm to both abundance and basal area, and a higher contribution of individuals with DBH>50cm to basal area (Fig. a, b). Model comparison with TNF data also showed that the model reproduced the main characteristics of the forest structure, although the slope of abundance as a function of size was steeper in the model compared to observations (Fig. c). Basal area structure, on the other hand, showed good agreement with field inventory data, and total basal area was within 5% of the observed basal area.

Total mortality rates were generally higher in ED-2.2 simulations than based on the observed rates at both GYF and TNF (Fig. a, b), and the model showed little variability in mortality between different census intervals. Most of the modeled mortality was due to background mortality, which is a combination of density-independent factors such as aging and tree-fall mortality, both assumed time-invariant in the model . While the mortality due to environmental constrains (density-dependent) showed interannual variability, its magnitude was small, never exceeding 0.5%AGByear-1. The high mortality rates in the model are mostly attributable to early successional trees, for which the modeled mortality rates was near 7.5%AGByear-1, or 5-fold higher than late successional, whereas observations were typically 3.0%AGByear-1, or 3 times higher than late successional. Likewise, growth rates were also higher than in observations, particularly at GYF (Fig. c), whereas the values were closer to observations for most of the simulated period at TNF (Fig. d). Growth rates of both sites are significantly different, which could be related to the particularly nutrient-poor soils at GYF e.g., and that these ED-2.2 simulations did not account for nutrient limitation. Alternatively, higher growth rates may be due to tree allometry and low allocation to living tissues and contributing to high accumulation rates on structural tissues.

The comparisons with eddy covariance towers demonstrated the ability of ED-2.2 to simulate the magnitude and seasonality of both the evapotranspiration fluxes and the water storage in the canopy air space (Figs. , S2). The good agreement of evapotranspiration in the tropical sites using ED-2.2 contrasts with previous assessments using ED-2.1 for temperate sites, which found significant negative biases in simulated evapotranspiration and attributed the bias to the model overestimating the impacts of water stress on stomatal conductance . The average ratio between canopy evaporation and total rainfall ranged from 7 % to 11 % at the two forest sites tested here (Guyaflux, GYF; and Tapajós, TNF), which is at the low end but in the same range of values founds in previous studies 9 %–20 %;and references therein. The hydrological cycle, on the other hand, showed some important deviations in absolute value, particularly near the surface, despite being consistent with observations in relative terms (Fig. S9). Large biases in absolute soil moisture were caused by the mismatches in the soil hydraulic properties that ultimately define the residual moisture and wilting point, field capacity, and porosity, thence the range of possible values of soil moisture. Soil hydraulic properties were derived from texture characteristics previously published for all sites. In ED-2.2, these properties were simplified to a single fraction assumed constant at every patch and throughout the profile, whereas in reality soil properties are known to vary significantly within the same area and with depth e.g.,. Moreover, soils in ED-2.2 are assumed to be mineral, whereas in reality macropores and soil organic content can substantially affect such properties .

The model also realistically represented both the net absorption of visible irradiance and the vertical distribution throughout the canopy. The model showed similar magnitude and seasonality of the outgoing shortwave radiation, including photosynthetically active radiation, at the two long-term sites (Fig. ), and the average light level profiles within the canopy (Fig. ). Agreement was even higher during cloudy conditions (Fig. c, d), when the spatial distribution of individual trees has less of an impact on local variability in the light profile . Differences were more significant for photosynthetically active radiation than for total shortwave radiation, particularly during the dry season (Fig. c, d). These differences may result from two factors. First, leaf optical properties in ED-2.2 are assumed constant for any given PFT, whereas observations indicate that leaf reflectivity depends on leaf age . Second, ED-2.2 represents canopy structure in only one dimension for each patch; the effect of neighboring trees (or their absence) is not represented. A full three-dimensional approach similar to may not be feasible within the ED-2.2 because of the intensive computational burden and that the model does not represent the actual position of individual trees. Alternatively, the perfect plasticity approach , in which finite-crown individual trees are arranged to maximize light access, has been recently adapted to another cohort-based model, the Functionally-Assembled Terrestrial Ecosystem Simulator FATES;. The perfect plasticity approach has the advantage of allowing trees of similar size to experience the same light levels (as opposed to the sequential light interception in ED-2.2), which could contribute to improve the light extinction profile in closed canopy forests. Importantly, while the current representation of vertical light distribution in ED-2.2 may affect light availability of individual cohorts, it does not imply that the simulated understory in ED-2.2 is excessively dark. In fact, when we compared the modeled and observed vertical structure of diffuse light (which is less sensitive to the observed position of trees than direct light), we found that the model slightly overestimates understory light levels (Fig. ).

The model predictions of canopy air space temperature at TNF generally match observations well, except for a slight overestimation during the dry season at TNF (Fig. S2). However, the sensible heat flux also tends to be higher than tower estimates, particularly at the drier TNF site (Fig. ). The better agreement of simulated water fluxes with observations relative to sensible heat flux is very common among land surface models . One possible cause of this disagreement is that observations from eddy flux towers typically contain significant sources and sinks from lateral advection and air drainage that may result in departures from energy closure by as much as 30% . Energy conservation is an important requirement for terrestrial biosphere models, particularly in the context of coupled biosphere–atmosphere modeling studies where they need to ensure conservation of energy at the lower boundary of the atmosphere. In ED-2.2, conservation of energy is checked every model time step . Since ED-2.2 does not incorporate lateral advection of air within the plant canopy, in situations where significant lateral advective transport of energy occurs within the canopy, the model may compensate for the absence of lateral transport through an increased or decreased rate of vertical eddy fluxes. suggested that parameterization problems, rather than energy conservation, are the most likely cause for biases in land surface models. One potential issue in this regard in ED-2.2 is that the heat capacity of branches and leaves could be biased, allowing greater variability of temperature and higher sensible heat fluxes at the expense of reduced storage. To our knowledge, no long-term measurements of leaf or branch temperature exist for the Amazon sites, but differences in outgoing thermal-infrared irradiance (Fig. S3) suggest that the observed vegetation temperature during the afternoon may be lower and less variable than the model predictions. Additional measurements of leaf and wood heat capacity for tropical forests could improve the accuracy of leaf and branch temperatures in the model.

Comparisons of GPP between the ED-2.2 model and tower-based estimates show that the model captures both the magnitude of GPP and the typical GPP response to light (Fig. ). In ED-2.2, the seasonality at tropical forest sites is mostly driven by light; thus, the maximum productivity often occurs during the dry season (Fig. a, b). Estimates of GPP based on eddy covariance towers, however, suggest a more complex pattern, with the minimum occurring either during the wet season (GYF) or the transition from wet to dry season (TNF), and modestly increasing productivity during the dry season Fig. a, b; see also. GPP depends on multiple processes, and thus differences between ED-2.2 and tower estimates may be due to several factors including biases in the seasonality of leaf area and photosynthetic properties of leaves. In particular, empirical studies have shown that the seasonality of GPP in Amazon forests is linked to seasonal variation of photosynthetic capacity and leaf phenology , whereas in the current implementation of ED-2.2 both the leaf turnover rate and the maximum photosynthetic capacity are assumed, for simplicity, to be constant. Work from several modeling studies and a leaf-level carbon optimization model has shown that incorporating such seasonality into the dynamics of leaf longevity and photosynthetic capacity significantly improves predictions of the seasonality of carbon fluxes in tropical forests. However, data from multiple sites may be needed to develop a generalizable phenology model for evergreen forests.

The model estimates of ecosystem respiration were generally higher and more seasonal than the expected values either from eddy covariance tower estimates or from a bottom-up assessment, especially at GYF (Fig. ; Table ). In the model, the seasonality of ecosystem respiration was nearly exclusively driven by the seasonality in heterotrophic respiration, with a significant decline in the dry season due to lower soil moisture (Fig. c, d), whereas eddy covariance tower estimates suggest a dry-season reduction in respiration only at TNF Fig. a, b; . The ED-2.2 assumption that heterotrophic respiration at lower soil moisture is consistent with observations for total respiration at GYF e.g., Fig. 3 of ; however, the magnitude of the heterotrophic response to moisture is likely overestimated in the ED-2.2 model.

Total autotrophic respiration estimates from ED-2.2 were within range with independent bottom-up estimates for both sites, albeit only marginally within the 95% confidence level (2 standard errors) of the bottom-up estimates at TNF (Table ). At both sites, the simulated autotrophic respiration was driven by leaf and stem respiration, which contributed with roughly the same proportion to autotrophic respiration. In contrast, the bottom-up estimates at both sites suggest leaf respiration was 2- to 3-fold higher than stem respiration (Table ). One possibility is that the allocation of carbon gains to tissue growth was overestimated in ED-2, which is consistent with the overestimated growth rates compared to forest inventory plots (Fig. ). It must be noted, however, that several terms estimated from observations also carry large uncertainties and assumptions. For example, stem respiration is typically measured near the surface e.g.,, which may introduce biases given that branches may have significantly higher respiration rates . Furthermore, observed differences of expected values between sites are generally much larger than the differences obtained by the model, and such differences may reflect true differences of plant community functioning between sites or differences in sampling and techniques . Improved measurements of the different terms of ecosystem respiration would allow for better constraints on the individual processes driving the total respiration.

In addition to tropical sites, the model's ability to represent productivity and respiration has been previously assessed for temperate ecosystems. The model showed excellent agreement in magnitude and seasonality of both net ecosystem productivity (NEP) and GPP at three flux tower sites installed at Harvard Forest, in particular when the model was initialized with ground-based or remote-sensing-based data . In contrast, the model showed significant biases in net primary productive under ambient CO2 at two Free-air CO2 Enrichment (FACE) sites in the southeastern United States, overestimating NPP at Duke (evergreen forest) and underestimating at Oak Ridge (deciduous forest) . Also, a previous model-intercomparison study for 11 North American tower sites revealed significant negative biases in ED-2.1, although the model interannual variability of GPP and ecosystem respiration were within the observed range for both deciduous and evergreen sites . In addition, a wavelet analysis of the normalized error across nine tower sites across North America suggested that the errors in net ecosystem exchange (NEE) are dominated by subannual (but longer than daily) timescales . Together, these results indicate the need of quantifying which processes and parameters contribute the most to model uncertainties in order to improve the model predictions using ED-2.2, which is currently being pursued .

Finally, because ED-2.2 solves the carbon dioxide cycles at subhourly scale, it also accounts for changes in storage in the canopy air space. As described in the companion paper , in ED-2.2, canopy air space storage is accounted for energy, water, and carbon dioxide. While changes in storage are generally small on the seasonal or multi-annual scale (Fig. S8a, b), they are not negligible on the subdaily scale. The relevance of the storage of CO2 in the canopy air space has been long recognized by the eddy covariance community e.g., but only rarely included in biosphere or land surface models. For example, the strong release of carbon dioxide in the early morning hours, resulting from the nighttime accumulation of respired CO2, is well characterized by the model at both test sites (Fig. S8c, d). Accounting for this time lag between biologically driven emission or uptake and the emissions to the free atmosphere is particularly important for benchmarking the model with the column-integrated measurements of the recently launched CO2 Orbiting Carbon Observatory-3 (OCO-3), which will provide samples at multiple times of the day .

A key feature of the ED-2.2 model is the emergence of long-term, large-scale ecosystem composition, structure, and function from spatially localized, height-structured competition between individuals within the plant canopy. As seen in Fig. , the model's large-scale predictions are consistent with remote-sensing estimates of how AGB variability along key climatological gradients of incoming solar irradiance, rainfall, and dry-season severity. In addition, the regional pattern of AGB predicted by ED-2.2 reproduces several notable features present in the remotely sensed based estimates of AGB (Fig. ). In particular, the model captures the spatial extent of the Amazon forest, and reproduces two characteristic patterns of spatial variability in forest biomass, namely (i) the high-biomass forests found in the Guiana Shield (near GYF) and in the area south of the TNF flux tower, and (ii) the area of lower biomass forest that runs east to west spanning the TNF and MDK sites.

The model's predictions of regional AGB also reveal important discrepancies. First, the model estimates are generally lower than the remote-sensing estimates of AGB in the drier savannas and xeric shrublands of central and northeastern Brazil (Figs. –). The low-biomass estimates in drier regions is likely related to the simplified fire model used in the regional simulations . Following , fire occurrence within each climatological grid cell is controlled by a simple fixed soil moisture threshold, the area burned per year increases linearly as a function of the mean AGB within each grid cell, and no plants survive burn events. Although this simplified approach captures many patterns of fire regime in tropical South America (Fig. ), it has important shortcomings in representing fire ignition mechanisms and the ecosystem's response to fire disturbance. For example, as previous work has shown , fire frequency, burn area, and fire severity are also strongly influenced by environmental factors in addition to soil moisture, such as proximity to roads and deforested areas. Moreover, the model does not account for size-related differences in fire survivorship and plant-functional diversity-related differences in fire survivorship arising from variation in plant traits such as bark thickness and re-sprouting ability . Furthermore, the model simulations do not include plant functional types with adaptations for the semi-arid conditions typically observed in northeastern Brazil. Such adaptations include smaller leaf size; internal water storage; modular, independent, and redundant vascular systems; germination synchronized with rainfall; and Crassulacean acid metabolism (CAM) photosynthetic pathway . Incorporating these mechanisms that drive the ecosystem dynamics in drier areas could improve the model predictions outside tropical forests.

In the western Amazon, the model's predictions of AGB are generally higher than all three remote-sensing estimates, implying that the model is overpredicting AGB in this region (Fig. ). ED-2.2 also tends to overestimate the high-biomass peak of the regional distribution of biomass (Fig. ). One potential reason for the AGB overestimation in the western Amazon is the model's predicted dominance of late-successional plants over most of the Amazon region, whereas field observations indicate that forests in the western Amazon have higher stem turnover rates and lower wood densities than the eastern Amazon . This has been linked to the fact that soils in the western Amazon have higher nutrient availability , which was not accounted for in these ED-2.2 simulations. Moreover, the model assessment suggests that ED-2.2 overestimates growth rates (Fig. ) and AGB (Fig. ), despite evidence that ED-2.2 may be underestimating net primary productivity (NPP; Figs. , d; Table ). This result likely indicates that allocation to growth, maintenance, and reproduction may be biased. Trait and allometric databases have considerably expanded over the past decade e.g.,, with many of them have adopted open-access platforms. Incorporating these databases to develop and constrain allocation and maintenance costs of the functional groups in ED-2.2 could significantly reduce uncertainties in carbon stocks, productivity, and demographic rates. Finally, the regional simulation did not account for all types of anthropogenic disturbances from tropical forest degradation, which could also explain part of the overestimation by ED-2.2 compared to the remote-sensing estimates. Tropical forest degradation through selective logging, mining, and low-intensity understory fires in the Amazon is pervasive along the arc of deforestation Fig. b; and is known to significantly deplete aboveground biomass .

The regional model simulation also qualitatively captures two disturbance-mediated relationships between canopy AGB and other tropical forest attributes observed in plot measurements (Fig. ): the negative correlation between AGB and average stem mortality rates and the positive correlation between AGB and average wood density found by . The fact that the model qualitatively captures the directional trend of both these two relationships is encouraging and suggests that the model's predictions of regional biomass trends are arising from mechanisms similar to those observed in nature. However, the magnitudes of the predicted relationships differ from the observations: for a given value of AGB, the model predicts a higher mean stem mortality rate and a higher mean wood density value than is observed in the plot measurements. The reasons for the differences in the magnitude of these relationships are, at present, unclear. However, in the case of the mean mortality–AGB relationship, the mismatch is likely related to the overprediction of mortality rates seen in ED-2.2 (Figs. ; ). In addition, the predicted mortality rates at the two tropical forest sites showed nearly constant mortality rates during the period in which observed rates were available (Fig. ). In ED-2.2, density-independent rates are modulated only by changes in functional composition (i.e., relative increase in abundance of pioneer plants), which did not occur in these simulations. Density-dependent mortality is associated with environmental conditions such as droughts and can drive the interannual variability of simulated mortality rates, yet these rates also nearly constant during this period. We interpret this result to be consistent, as the droughts of 2005 and 2010 were significant in the southwestern part of the Amazon but not at our study sites. The low sensitivity to 2005 and 2010 droughts is also supported by the observations, which did not show significant increases in mortality after 2005 and 2010 (Fig. ); the increase in mortality at GYF between 2006 and 2008 is attributable to a substantial tree-fall event that affected one of the measurement plots in 2007. Nonetheless, the model does show sensitivity to historic droughts such as the 1992 and 1998 events in TNF and the model response is consistent with anomalously high coarse woody debris found at the site when field inventory measurements began in 1999 e.g.,.

In this paper, we focused on assessing the model's ability to represent the dynamics of tropical forests, but previous studies have also shown that the model reasonably describes the dynamics of temperate ecosystems. For example, demonstrated that the model captures regional variation in both growth and mortality rates across forests of northeastern North America, especially when using the optimized parameters from . Also, applied ED-2.1 at Duke's FACE experiment site (conifer-dominated) and found that the model accurately predicts biomass changes over time for both ambient and elevated CO2, and realistically characterizes the changes in gross and net primary productivity (NPP) as functions of stand age. This result is consistent with a previous model-intercomparison study, which found good agreement on observed and ED-2.1 modeled CO2 fertilization effect at Duke, whereas the model-predicted response to elevated CO2 at Oak Ridge (broadleaf-dominated) was overestimated . In contrast, in a millennium-long model intercomparison study for the northeastern United States, the model overestimated both the magnitude of NPP and its variability as a function of rainfall and CO2 when compared to tree-ring estimates , which indicates the need of constraining the model response for environmental conditions outside the current range. While these studies used versions of the model that contained many of the implementations of ED-2.2 described in the companion paper , future work using the ED-2.2 model in temperate ecosystems should critically evaluate processes that could not be assessed in our analysis, such as leaf phenology and processes related to snow dynamics. Such benchmarking efforts should be regarded as priorities in future studies.