Articles | Volume 23, issue 4
Research article
02 Mar 2023
Research article |  | 02 Mar 2023

Why do inverse models disagree? A case study with two European CO2 inversions

Saqr Munassar, Guillaume Monteil, Marko Scholze, Ute Karstens, Christian Rödenbeck, Frank-Thomas Koch, Kai U. Totsche, and Christoph Gerbig

We present an analysis of atmospheric transport impact on estimating CO2 fluxes using two atmospheric inversion systems (CarboScope-Regional (CSR) and Lund University Modular Inversion Algorithm (LUMIA)) over Europe in 2018. The main focus of this study is to quantify the dominant drivers of spread amid CO2 estimates derived from atmospheric tracer inversions. The Lagrangian transport models STILT (Stochastic Time-Inverted Lagrangian Transport) and FLEXPART (FLEXible PARTicle) were used to assess the impact of mesoscale transport. The impact of lateral boundary conditions for CO2 was assessed by using two different estimates from the global inversion systems CarboScope (TM3) and TM5-4DVAR. CO2 estimates calculated with an ensemble of eight inversions differing in the regional and global transport models, as well as the inversion systems, show a relatively large spread for the annual fluxes, ranging between 0.72 and 0.20 PgC yr−1, which is larger than the a priori uncertainty of 0.47 PgC yr−1. The discrepancies in annual budget are primarily caused by differences in the mesoscale transport model (0.51 PgC yr−1), in comparison with 0.23 and 0.10 PgC yr−1 that resulted from the far-field contributions and the inversion systems, respectively. Additionally, varying the mesoscale transport caused large discrepancies in spatial and temporal patterns, while changing the lateral boundary conditions led to more homogeneous spatial and temporal impact. We further investigated the origin of the discrepancies between transport models. The meteorological forcing parameters (forecasts versus reanalysis obtained from ECMWF data products) used to drive the transport models are responsible for a small part of the differences in CO2 estimates, but the largest impact seems to come from the transport model schemes. Although a good convergence in the differences between the inversion systems was achieved by applying a strict protocol of using identical prior fluxes and atmospheric datasets, there was a non-negligible impact arising from applying a different inversion system. Specifically, the choice of prior error structure accounted for a large part of system-to-system differences.

1 Introduction

Inverse modelling has been increasingly used to infer surface–atmosphere fluxes of carbon dioxide (CO2) from observations of dry mole fractions made at spatio-temporal points across an observational network (Enting and Newsam, 1990; Bousquet et al., 1999). Reducing uncertainty in the flux estimates is, therefore, essential to reliably quantify the carbon budget (Friedlingstein et al., 2022; Le Quéré et al., 2018) as well as to improve our understanding about the variability and trends of the carbon cycle over times at finer regional scales, in particular in response to the climate perturbation caused by the increase in anthropogenic emissions (Shi et al., 2021). The estimates obtained from atmospheric tracer inversions still demonstrate large deviations due to manifold sources of uncertainty such as using different data, inversion schemes, and atmospheric transport models (Baker et al., 2006; Gurney et al., 2016), either at global scales or, to a larger extent, at regional scales. Although the global inversions can provide convergent estimations of the global carbon budgets, they are limited by the coarse resolution of atmospheric transport that may not allow for a realistic representation of the observations at complex mesoscale terrains. In turn, performing regional inversions with mesoscale transport models has offered a better opportunity to represent and make use of the dense measurements available at all the sites across regional domains (Broquet et al., 2013; Kountouris et al., 2018a; Lauvaux et al., 2016), specifically after the expanding coverage of data over large areas in recent years as has been established, for example, over Europe by the Integrated Carbon Observation System (ICOS). Although CO2 fluxes constrained by atmospheric data in the Bayesian inversion framework inherit a dominant spatial and temporal pattern from the atmospheric signal, the a posteriori fluxes still suffer from a large spread when using different global and mesoscale transport models (Rivier et al., 2010).

As a first intercomparison between six regional inversions covering a wide range of system characteristics (e.g. prior fluxes, inversion approaches, and transport models), the EUROCOM experiment (Monteil et al., 2020) suggested large spreads in posterior estimates over Europe, particularly over regions that are poorly constrained by atmospheric data. This, on the one hand, partly indicates the sensitivity of the a posteriori estimates to the observations and to the a priori models as explained in Munassar et al. (2022). On the other hand, inaccuracies in atmospheric transport (Schuh et al., 2019), far-field contributions, and the configurations of inversions are responsible for part of that spread. A further study suggests that uncertainties in both transport and CO2 fluxes contribute equally to the uncertainties in CO2 dry mole fraction simulations, displaying similar temporal and spatial patterns (Chen et al., 2019).

The atmospheric transport relates the measured tracer concentration to its possible sources and sinks, which are adjusted in order to fit the modelled concentrations to observed data. However, inaccuracies in representing the real atmospheric dynamics by transport models lead to uncertainties in CO2 flux estimates. This kind of error can emerge from both simplified parameterizations of real physics and model parameters themselves (Engelen et al., 2002). The atmospheric transport models rely on a mesoscale representation of air mass movements, which cannot completely reproduce the observed fine-scale variability of tracer concentration, leading to the so-called representation error. As a result, inversions cannot solve for fluxes at lower spatial and temporal resolutions than that of their transport model, resulting in aggregation errors (Kaminski et al., 2001). Additionally, atmospheric transport models are typically driven by meteorological data available from operational weather forecast models or reanalysis data optimized against observations and dynamical model forecasts. However, such meteorological fields have uncertainties owing to errors and gaps in the observations and errors in the weather forecast models (Deng et al., 2017; Liu et al., 2011; Tolk et al., 2008).

As the lateral boundaries are provided from a global model run at lower resolution than the regional model (Davies, 2014), this leads to biases in CO2 lateral concentrations and thus affects the inversion estimates (Chen et al., 2019). The information of providing boundary conditions to regional inversions is necessary to isolate the influence of far-field contributions before performing the regional inversion. In Bayesian inversion setups, a proper information on prior error structures is also essential to determine the spatial pattern of the flux corrections based on the assumed error, especially at high spatial resolution inversions (Chevallier et al., 2012; Kountouris et al., 2015; Lauvaux et al., 2016). Therefore, the spatial pattern of flux corrections is dependent on the way the error covariance matrices are constructed, which can lead to large spatial discrepancies between the estimates from different inversion systems.

This study is dedicated to quantify the relative contributions of the differences in optimized fluxes resulting from varying as follows: (1) atmospheric transport models, (2) lateral boundary conditions, and (3) inversion configurations on flux estimates, as the error contributions from each component to the inversion's spread remain unclear in regional inversions, specifically at finer spatial scales over a continental domain such as Europe (Monteil et al., 2020; Petrescu et al., 2021; Thompson et al., 2020). We analysed results of a posteriori net ecosystem exchange (NEE) estimated from the two inversion systems CarboScope-Regional (CSR; Kountouris et al., 2018b; Munassar et al., 2022) and LUMIA (Monteil and Scholze, 2021). Both inversions employ pre-computed sensitivities of atmospheric mole fractions to surface fluxes, so-called source-weight functions or “footprints”, via two Lagrangian transport models at regional scales, and they make use of the two-step inversion approach established by Rödenbeck et al. (2009) to provide the lateral boundary conditions. The regional atmospheric transport models were used at a horizontal resolution of 0.25. The impacts of both global and regional models were compared by analysing the differences in space and time.

Section 2 presents detailed descriptions of the inversion setups, the transport models, and the a priori fluxes used. The observational stations that provide CO2 dry mole fraction data are described within the Methods section as well. We introduce the results obtained from eight inversions in Sect. 3. The results are discussed and interpreted through a spatial and temporal analysis of the differences between the elements of inversions in Sect. 4. Finally, Sect. 5 highlights a few concluding remarks on the impacts of regional transport, boundary conditions, and inversion setups on CO2 estimates in the inverse modelling.

2 Methods

An atmospheric tracer inversion framework is mainly made up of transport model, data source for boundary conditions (in case of regional inversions), datasets of atmospheric mole fractions, and surface flux fields. In this study, several inversion runs differing in atmospheric transport models are conducted using two tracer inversion systems, CSR and LUMIA (see Table 2). The default CSR inversion system utilizes pre-calculated footprints from the Stochastic Time-Inverted Lagrangian Transport (STILT) model (Lin et al., 2003) at the regional domain and the TM3 model at the global scale, applying the two-step scheme inversion approach (Rödenbeck et al., 2009), to provide the far-field contributions to the regional domain. In the default setup of the inversion system LUMIA, the footprints are pre-calculated using the Lagrangian particle dispersion model FLEXPART (Pisso et al., 2019), and the far-field contributions are calculated using the global transport model TM5 in a separate global inversion run, applying the two-step scheme inversion as well. These default configurations in both systems constitute the base cases. We strive to restrict the differences in the inversion runs to the targeted components, i.e. regional transport, boundary conditions, and the inversion systems, so as to outline the impact of each suite. That is, input data such as measurements of CO2 dry mole fraction and the a priori fluxes, used as constraints based on Bayesian inference, are identical for all runs. We exchangeably make use of the four combinations of transport model components, the regional and global models, in the two inversion systems. The impacts were evaluated using forward model runs to quantify the differences in CO2 concentrations (simulated with prior fluxes) and inversion runs to quantify the magnitude of differences in the flux space. The inversion setups and implementation are explained in the comparison protocol (Sect. 2.6).

2.1 Inversion framework

In the following description, we remind the reader about the basic principles of the inversion schemes. For detailed information about the mathematical schemes, the reader is referred to Rödenbeck (2005) for CSR and to Monteil and Scholze (2021) for LUMIA. Both systems rely on the Bayesian inference that accounts for observations and a priori knowledge to regularize the solution of the ill-posed inverse problem where a unique solution does not exist due to the spatial scarcity of observations. Therefore, the optimal state vector (x) is searched for in the Bayesian formalism by minimizing the cost function J(x) that is typically composed of the observational constraint term Jc(x) and the a priori flux constraint term Jb(x):

(1) J x = J c x + J b x ,



The a priori flux uncertainty defined in the covariance matrix B limits the departure of the control vector (x) to the a priori flux vector (xb). Similarly, the observational constraint is weighted by the observational covariance matrix Q that contains the so-called model–data mismatch error, including uncertainty of measurement, representativeness, and transport. This uncertainty is assigned to the diagonal of the matrix Q for the respective sites based on the ability of the transport model to represent the atmospheric circulation at such locations. H(x) represents the atmospheric transport operator (i.e. calculated by STILT and FLEXPART in our inversions) that determines the relation between fluxes and the modelled tracer concentration, which corresponds spatially and temporally to a given vector of measurements y. Following the gradient descent method, a variational algorithm is applied iteratively to reach the best convergence (global minimum) of the cost function that satisfies the optimal solution of the control vector. The default configurations for constructing the covariance matrices of a priori uncertainty are slightly different in CSR and LUMIA. A priori flux uncertainty is assumed to be around 0.47 PgC yr−1 over the full domain of Europe derived from the global uncertainty (2.80 PgC) assumed in the CarboScope global inversion for the annual biogenic fluxes (Rödenbeck et al., 2003). In CSR, this uncertainty is uniformly distributed spatially and temporally in a way that the annual uncertainty aggregated over the entire domain should arrive at the same value. The uncertainty structure is fit to a hyperbolic decay function in space (Eq. 4) and to an exponential function (Eq. 5) for the temporal decay as explained in Kountouris et al. (2015).


The correlation length scales ds and dt applied to flux uncertainties are chosen to be 66.4 km spatially and 30 d temporally, respectively, following Kountouris et al. (2018a) and Munassar et al. (2022). The spatial length in the zonal direction is set to be longer than that in the meridional direction by a factor of 2 (anisotropic), owing to larger spatial climate variability in the meridional as compared to zonal direction.

The spatio-temporal shape of the a priori uncertainty in LUMIA is computed in a way that each control vector comprises weekly uncertainty calculated as the standard deviation of NEE based on weekly flux variance; however, LUMIA agrees on the overall annually aggregated flux uncertainty over the entire domain with CSR. A Gaussian function of the spatial correlation decay (Eq. 6) is applied to the a priori uncertainty structure with a spatial length scale of 500 km,

(6) r s = e - s d s 2 ,

whereas the effective temporal decay was set to 30 d (same as in CSR). Given the difference in the spatial correlation decay of the a priori uncertainty, LUMIA is set to draw larger flux corrections in a broader radial area where stations exist following the Gaussian decay with a longer length scale compared to the hyperbolic decay in CSR. In turn, the hyperbolic function has a larger impact in the further radial distances than the Gaussian function does, regardless of the longer spatial scale assumed with the Gaussian decay in a factor of around 7.5 in comparison with the hyperbolic decaying function.

2.2 Atmospheric transport models

Surface sensitivities are calculated using the STILT (Lin et al., 2003) and FLEXPART (Pisso et al., 2019) models at a horizontal resolution of 0.25 and hourly temporal resolution. Both models simulate the transport of air masses via releasing an ensemble of virtual particles at the locations of stations. The virtual particles are transported backward in time and driven by meteorological fields obtained from the European Centre for Medium-Range Weather Forecasts (ECMWF). STILT particles are transported 10 d backward in time and forced by forecasting data obtained from the high-resolution implementation of the Integrated Forecasting System (IFS HRES). For the FLEXPART model in standard operation, particles are followed for 15 d backward in time driven by ERA-5 reanalysis data. To keep the consistency with STILT footprints, the backward time of FLEXPART footprints was limited to 10 d in the inversions. After this backward time integration, the particles are assumed to leave the domain, even though a large number of particles are expected to escape after a few days. To better represent air sampling in the mixed layer, day-time observations are considered, except for mountain stations where night-time observations are used instead (Geels et al., 2007). To ensure best mixing conditions, temporal windows were considered for simulating CO2 dry mole fractions over stations as explained in Sect. 2.4 (Table 1). In addition, release heights of particles are taken as the highest sampling level above ground at each measurement site. For high-altitude receptors, such as mountains, a correction height is used in STILT in a way that the actual elevation of the station can be represented in the corresponding vertical model level (Munassar et al., 2022). In FLEXPART, the elevation above sea level is taken as the model sampling height.

Table 1Atmospheric sites used in the inversions.

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Table 2List of the inversion setups.

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2.3 A priori and prescribed fluxes

Three components of prior and prescribed surface-to-atmosphere fluxes of CO2 are obtained from (1) biogenic terrestrial fluxes, (2) ocean fluxes, and (3) anthropogenic emissions and kept identical in both systems. Prior net terrestrial CO2 exchange fluxes, net ecosystem exchange (NEE), are calculated using the diagnostic biogenic model Vegetation Photosynthesis and Respiration Model (VPRM) (Mahadevan et al., 2008). VPRM calculates NEE at hourly temporal and 0.25 spatial resolutions, and it provides a partitioning of the net flux into gross ecosystem exchange (GEE) and ecosystem respiration. Data obtained from remote sensing provided through the MODIS instrument and meteorological parameters from ECMWF drive both quantities of the light-dependent GEE and the light-independent ecosystem respiration. The model parameters were also optimized against eddy covariance data selected within the global FLUXNET site network across Europe in 2007 (Kountouris et al., 2015). For more details on the VPRM model, the reader is referred to Mahadevan et al. (2008).

Ocean fluxes are taken from Fletcher et al. (2007), who provide climatological fluxes at a spatial resolution of 5×4, remapped to 0.25 to be compatible with the biosphere model fluxes. In addition, anthropogenic emissions are taken from the EDGAR_v4.3 inventory and are updated to recent years according to British Petroleum (BP) statistics of fossil fuel consumption, and they are distributed spatially and temporally based on fuel type, category, and country-specific emissions, using the COFFEE approach (Steinbach et al., 2011). The emissions are remapped to a 0.25 spatial grid and to an hourly temporal resolution.

Biogenic terrestrial fluxes are optimized in the inversions, while the ocean fluxes and anthropogenic emissions are prescribed, given the better knowledge about their spatial and temporal distribution in comparison with the heterogeneity, variability, and uncertainty of the biogenic fluxes. Moreover, in the absence of observational constraints that help discriminate the contributions from the three categories, we chose to prescribe the ocean fluxes and anthropogenic CO2 emissions. This is also justified by the fact that the observation sites are located in areas where the biospheric flux influence is expected to dominate the variability of CO2 concentration, but it means that errors in the fossil fuel or ocean fluxes might be compensated by the inversions, resulting in changes in the posterior NEE.

2.4 Observations

Measurements of CO2 dry mole fractions are collected through ICOS, NOAA, and pre-ICOS stations across the domain of Europe provided by Drought 2018 Team and ICOS Atmosphere Thematic Centre (2020). In total, datasets from 44 stations are used covering the domain of Europe in 2018, in which a maximum number of stations is present compared to the other years. Regarding model–data mismatch errors, in LUMIA a weekly value of 1.5 ppm is assumed for all sites, except for the Heidelberg site where 4 ppm was assumed due to the anthropogenic influence from the neighbourhood. Table 1 denotes the weekly values of uncertainty used in CSR for the corresponding sites. The uncertainty for the surface sites is inflated to 2.5 ppm as a slight difference to LUMIA. The inflation of uncertainty from weekly to hourly values is basically calculated by multiplying weekly errors by 7×n (where n refers to the number of hours in the daily measurements used in the inversion). The observations are mostly assimilated as hourly continuous measurements and are taken from the highest level, avoiding large vertical gradients near the surface that are hard to represent in the transport models. Model error in representing observations in the planetary boundary layer (PBL) is expected to be largest when the PBL is shallow. Therefore, for most sites, we considered data only when the PBL was expected to be well developed, i.e. during the afternoon, local time (LT). The exception is at high-altitude sites, which tend to sample the free troposphere during night (Kountouris et al., 2018b). The assimilated windows are reported in Table 1.

2.5 Boundary conditions

Far-field contributions of CO2 concentrations (originating from sources outside of the regional domain) are taken from global inversions. As default setups of the global runs, the Eulerian transport model TM3 is used in the CarboScope global inversion at 5 (long) × 4 (lat), while TM5-4DVAR (Transport Model 5 – Four Dimensional Variational model) is used to provide boundary conditions to LUMIA using the global transport model TM5 at 6 (long) × 4 (lat) (Babenhauserheide et al., 2015; Monteil and Scholze, 2021). Both inversion systems apply the two-step scheme inversion, explained in Rödenbeck et al. (2009), in which a global inversion is first used to estimate CO2 fluxes globally (based on observations inside and outside Europe). In a second step, the global transport model is used to estimate the influence of European CO2 fluxes on European CO2 observations. That regional influence is then subtracted from the total concentration to obtain a time series of the far-field influence directly at the locations of the observation sites. This prevents introducing biases by passing concentration fields from one model to another. For detailed information about the approach methodology, the reader is referred to Rödenbeck et al. (2009).

2.6 Comparison protocol

The results of the study are based on eight variants of inversions differing in global and regional transport models, as well as in inversion systems, as explained in Table 2. This implies that the two inversion systems (CSR and LUMIA) make use of two regional transport models (STILT and FLEXPART) and two global transport models (TM3 and TM5), which represent the boundary conditions (background) calculated from two global inversions. Hereafter, the identifier codes (see corresponding column in Table 2) will be used to refer to the individual runs within the inversion ensemble. For instance, to highlight the impact of regional transport models, we compare the inversions that only differ in regional transport models, regardless of the inversion system or boundary conditions used, such as CS3 and CF3 or LS5 and LF5. Similarly, we use the same specifications of transport models (indicated through the identifier codes) for the forward runs to outline the differences in CO2 concentrations simulated using prior fluxes with different transport models. In this case, using a different system should not result in discrepancies as long as prior fluxes remain identical. In terms of system-to-system comparison, the impact of flux uncertainty should be taken into account as the prior error structure is specific for each inversion system. With that said, this has been investigated by conducting additional tests in CSR and LUMIA using identical uncertainties with flat shape and Gaussian correlation decay.

3 Results

Estimates of the regional biosphere–atmosphere fluxes over the domain of Europe are calculated using CSR and LUMIA for 2018 from an ensemble of eight inversions as listed in Table 2. Generally, all the inversions showed that the estimates of NEE are constrained by the atmospheric data as can be seen from the positive flux corrections made by the inversions in comparison with the a priori fluxes calculated from the biosphere flux model VPRM, which obviously overestimates CO2 uptake, specifically during the growing season (Fig. 1a). This is also obvious in the ensemble-averaged annual estimates of posterior fluxes 0.29 PgC versus 1.49 PgC in the a priori fluxes (Fig. 1b). However, the spread among posterior estimates is still relatively large, ranging between 0.72 and 0.20 PgC yr−1 for the annual estimates, which is larger than the a priori uncertainty of 0.47 PgC yr−1. Likewise, the mean standard deviations of the monthly estimates over the ensemble of inversions is 0.72 PgC yr−1. The largest deviations occur between inversions that differ by the regional transport models (e.g. CS3 versus CF3 or LS5 versus LF5). In addition, the seasonal amplitude was found to be different between the STILT and FLEXPART inversions. The STILT-based inversions led to a larger amplitude of posterior NEE than the FLEXPART-based inversions.

Figure 1Panel (a) refers to a posteriori monthly NEE estimated using eight inversions, including a priori NEE shown in black, with CSR (solid lines) and LUMIA (dashed lines), and panels (b) denotes the corresponding annually aggregated fluxes. Orange and red colours correspond to TM3, and dark or light blue correspond to TM5. Orange and light blue colours refer to STILT, and red and dark blue refer to FLEXPART.


In terms of spatial distributions, the base cases of CSR and LUMIA inversions, i.e. CS3 and LF5 (default configurations of both systems), exhibit good agreement in predicting smaller uptake of CO2 compared to the a priori fluxes (Fig. 2a–c). The magnitude of flux corrections suggests additional sources inferred from the atmospheric signal, as shown in the innovations of fluxes (Fig. 2d, e). Major corrections are obtained over western and southern Europe where the inversions point to an overestimation of the CO2 uptake by the prior biogenic fluxes. The weak annual uptake of CO2 in 2018 was exceptional and caused by the drought episode in Europe (Bastos et al., 2020; Rödenbeck et al., 2020; Thompson et al., 2020), which even turned some areas in central, northern, and western Europe into a net source of CO2. The discrepancies between CS3 and LF3 noticed in the innovations, e.g. in northern France, the Netherlands, and south-eastern UK, are attributable to the combination of differences in regional transport models, lateral boundaries, and system configurations.

Figure 2Panels (a)(c) show the spatial distributions of annual NEE estimated with the base inversions CS3 and LF5, as well as their prior. Panels (d) and (e) depict the innovations of fluxes calculated for the inversions CS3 and LF5. Green circles denote the locations of observational sites.

In the following, we will focus on separating and quantifying the contributions of such differences caused by each driver.

3.1 Impact of mesoscale transport

Inversions that differ in the regional transport models (STILT and FLEXPART) demonstrate the largest differences in posterior fluxes, resulting in a relative contribution of about 61 % of the total differences compared to the boundary conditions and inversion systems. The differences in monthly estimates of NEE calculated with CS3 and CF3 inversion setups that vary in regional transport models are shown in Fig. 3a (“transport”). Additionally, the discrepancies caused by transport have an obvious seasonal pattern. The differences between CS3 and CF3 peak in November and June, reaching 2.11 and 1.82 PgC yr−1, respectively. The best agreement between both inversions is obtained during the transitional months (August and April) with differences of 0.10 and 0.18 PgC yr−1, respectively. This might be attributed to the decline of the net flux magnitude during these months.

Figure 3Differences in optimized fluxes (a) and prior concentrations (b) calculated with the regional transport models STILT and FLEXPART (CS3-CF3) and background provided through TM3 and TM5 (CS3-CS5). “system” refers to the differences between CSR and LUMIA inversion for optimized fluxes (CS5-LS5).


Furthermore, we assessed the impact of atmospheric transport in the simulations of CO2 concentrations, because this directly translates into differences in the optimized fluxes. These simulations were calculated using the total components of prior fluxes (biosphere, ocean, and fossil fuel emissions) with STILT and FLEXPART in forward model runs to sample the atmospheric concentrations at hourly time steps at the station locations across the site network. Note that since all runs use identical prior fluxes, it does not matter for the differences whether the prior fluxes were precise enough to reproduce the true concentration or not. Figure 3b (“transport”) illustrates the monthly differences in the forward simulations between STILT and FLEXPART averaged over all observational stations. Similarly to the discrepancies in the optimized fluxes, the differences in the forward simulations demonstrate a dominant impact of the regional transport model, preserving the same temporal pattern as seen in the flux differences but with opposite signs. The absolute difference ranges from 0.39 to 4.37 ppm when computed for the monthly means throughout all the sites. Geels et al. (2007) even found a larger spread up to 10 ppm when calculated with five transport models over 10 stations distributed across Europe. The notably large difference reported in that study is likely attributed to the large discrepancies in the model configurations, especially regarding the horizontal resolution and vertical levels used. The harmonized configurations used in STILT and FLEXPART lead to a reasonably consistent representation of the atmospheric variability at synoptic and diurnal timescales. The largest differences are observed during November and May with 4.37 and 3.60 ppm, respectively. On the other hand, the smallest differences were found to be 0.39, 0.42, and 0.56 ppm during September, April, and August, respectively. These results suggest a maximum impact of the mesoscale transport during the growing season and winter, while the impact converges to the minimum during transitional months such as May and September. Overall, the differences in posterior fluxes are consistent in the timing with the differences in the simulated concentrations computed using the prior fluxes.

Further diagnostics of model–data mismatches are provided in the Supplement, indicating the performances of STILT and FLEXPART with respect to the observations using prior and posterior fluxes across the site network at hourly, weekly, and yearly time steps (see Fig. 1S and Table 1S).

In terms of the spatial discrepancies in annual flux estimates, using STILT generally leads to predicting a larger sources of CO2 in the regional inversions, in particular over central Europe and the UK compared to using FLEXPART (Fig. 4, “diff: transport”). In turn, inversions using FLEXPART suggest less uptake over northern Italy, Switzerland, and south-eastern France. However, this impact refers to a spatial pattern of transport differences that might be caused either by meteorological data or by problematic sites that are hard to represent by transport models. Some areas such as north-western Italy exhibit a persistent impact over time as shown in Fig. 4 (“SD: transport”), which shows the standard deviation of monthly differences calculated for the CS3 and CF3 inversions. In terms of temporal variations, the inversions performed with different regional transport models indicate larger monthly flux variations in comparison with those differing in global models and inversion systems (see Fig. 4, “SD: background” and “SD: system”).

Figure 4Panels (a)(c) indicate differences in annual posterior NEE estimated with STILT and FLEXPART models, referred to as “transport” (CS3-CF3); TM3 and TM5 are referred to as “background” (CS3-CS5); and CSR and LUMIA are referred to as “system” (CF3-LF3). Panels (d)(f) demonstrate the standard deviations of the corresponding monthly differences.

Figure 5 shows the spatial flux differences together with differences in prior concentrations simulated using STILT and FLEXPART during June and December. Note that the differences in NEE, to a large extent, agree in their spatial patterns with the differences in prior concentrations calculated over the station network. In addition, there are notably particular areas that exhibit opposite signs of the spatial impact in the differences in posterior fluxes and prior concentrations such as western Europe during June and northern Europe during December. One important difference between STILT and FLEXPART is that the STILT model has higher sensitivities during summer than FLEXPART, while the opposite holds true during winter. However, there are exceptions at individual sites such as Weybourne (WAO) in the UK and Ispra (IPR) in Italy, indicating either difficult terrains that cannot be well represented by the models or real synoptic features that are resolved by one model but not by the other. The differences in forward simulations are inversely manifested in the posterior flux differences as large surface sensitivities result in smaller posterior flux corrections and vice versa. In this case, STILT computes higher surface sensitivities than FLEXPART in June; therefore, the CS3 inversion needs to adjust the prior fluxes less to fit the observations. On the contrary, a weaker uptake is suggested by the STILT inversion during December over Europe, except for the abovementioned areas around northern Italy and south-eastern France. The differences appeared to be larger during the months of growing season and winter, following the seasonal amplitude of CO2.

Figure 5Spatial differences of posterior NEE estimated from the inversions CS3 and CF3 with STILT and FLEXPART transport models during June and December; filled circles indicate the differences in prior concentrations at the locations of sites (horizontal legend explains the magnitude of differences).

3.2 Impact of lateral boundary conditions

The differences in lateral boundary conditions were found to account for about 27 % of the total differences resulting from the regional transport, lateral boundaries, and systems. This is a non-negligible contribution, albeit smaller than the regional transport contribution. The impact of using different far-field contributions was analysed by assessing the differences in the posterior NEE estimated with CS3 and CS5 inversions, which use boundary conditions from the global inversions CarboScope and TM5-4DVAR, respectively. Figure 3 (“background”) shows consistent differences over time between these inversion estimates aggregated over the entire domain of Europe. Larger flux corrections are suggested by CS5 than by CS3. This is because the global TM3-based inversion predicts higher influence at the lateral boundaries than the global TM5-based inversion does. Discrepancies in the monthly posterior fluxes between CS3 and CS5 inversions amount to a range of 0.11 to 0.64 PgC yr−1 and absolute differences with a mean of 0.40 PgC yr−1. Monthly-mean differences in CO2 concentrations throughout all sites simulated using TM3 and TM5 boundary conditions were found to range from 0.17 to 0.93 ppm with a mean of 0.55 ppm.

The distributions of spatial differences of posterior fluxes indicate a homogeneous impact across the full domain of Europe (Fig. 4, “diff: background”). Likewise, the standard deviations of the monthly posterior fluxes obtained from CS3-CS5 (”SD: background”) denote flat temporal variations throughout all the grid cells. These findings confirm the results obtained in Fig. 3 (“background”). This impact is consistent in space and time, with coherent deviation over all months, and is therefore expected to not affect the seasonal and interannual variability.

3.3 Impact of inversion systems

CS3 and LF5 differ by more than their regional transport and boundary conditions. In particular, the uncertainties are, by default, set up differently in CSR and LUMIA. The two systems optimize a different set of variables (weekly NEE offsets in LUMIA and 3-hourly NEE in CSR). Here we compare CS5 and LS5, which differ by their inversion systems but not by their transport model and boundary conditions. The differences in flux estimates between CS5 and LS5 inversions amount to 12 % relative to the total differences, including that caused by the mesoscale transport and lateral boundaries. This impact is, however, dependent upon system configurations, in particular the way the prior flux uncertainty is prescribed. The absolute monthly differences between CS5 and LS5 range between 0.06 and 0.56 PgC yr−1 with a mean of 0.15 PgC yr−1 (Fig. 3, “system”). This demonstrates the smallest differences amid inversions in comparison with the transport and lateral boundary differences, which yielded absolute monthly means of 1.27 and 0.40 PgC yr−1, respectively. The differences peaked during May, June, and November, while the differences remained rather small during the rest of the year. LS5 infers 6.42 and 2.39 PgC yr−1 during June and December, respectively, which is higher than CS5 estimates by 0.33 and 0.07 PgC yr−1. Generally, LS5 predicts slightly larger CO2 releases compared to CS5, which is partially due to differences in how uncertainties are assumed in both systems.

The impact of uncertainty definition is quantitatively assessed by using identical uncertainties for model–data mismatch as well as for prior fluxes in both CSR and LUMIA. The spatial flux corrections (innovation of fluxes) shown in Fig. 8 denote quite good agreement between CSR and LUMIA estimates. In this experiment, the differences in June and December decreased to 0.23 and 0.04 PgC yr−1, respectively, in comparison with the corresponding differences obtained from the default configurations of both systems. That is to say, the impact of uncertainty definition alone amounts to 0.09 and 0.03 PgC yr−1 in June and December, respectively, leading to approximately 30 % and 50 % of the overall system-to-system differences. The rest of the differences may be attributed to differences in the convergence of the cost function to reach the minimum values.

The spatial differences shown in Fig. 4 “diff: system” alternate between positive and negative differences over the domain (but these tend to compensate when aggregating the flux estimates over the full domain). It should be noted that the inversion systems mainly differ in the definition of the shape and structure of the prior uncertainty. Therefore, applying different structure and magnitude of prior flux uncertainty in the inversions may inflate the error in CO2 flux estimates over the underlying regions in the domain, in particular if the spatial differences do not cancel out. In addition, the corresponding standard deviations of monthly estimates (“SD: system”) show large temporal variations, specifically over areas that have large spatial differences. The spatial results indicate that the impact of inversion systems should not be neglected, especially at national and subnational scales.

4 Discussion

The regional inversions computed over Europe showed that posterior NEE is largely derived from the atmospheric signal. The seasonality of posterior NEE, inferred from the atmospheric signal, is strongly impacted by differences in the representation of atmospheric transport. Given the identical priors and observational datasets used in the inversions, using different mesoscale transport models leads to 61 % of the differences in posterior fluxes in comparison with 27 % and 12 % of the differences caused by the use of different boundary conditions and different inversion systems, respectively. In agreement with these results, Schuh et al. (2019) also found a large impact of mesoscale transport on estimating CO2 fluxes. Hence, any error in the atmospheric transport is translated into posterior fluxes as flux corrections. For instance, CS3 and LS3 suggest annual CO2 flux budgets of 0.20 and 0.72 PgC, respectively, indicating a difference of 0.51 PgC in the annual flux budget. This difference is even larger than the prior flux uncertainty (0.47 PgC). The transport also showed a large impact on flux seasonality, leading to a difference of 49 % relative to the mean seasonal cycle. However, Schuh et al. (2019) found smaller differences, amounting to about 10 %–15 % of the mean seasonal cycle. Unlike the regional transport model error, the impact of boundary conditions does not show any striking seasonality and thus can be thought of as a bias in dry mole fractions. The consistency of the lateral boundary impact over time and space is in agreement with results of lateral boundary uncertainties assessed by Chen et al. (2019) using four different global transport models, albeit over a different domain. Therefore, such an impact may be dealt with as a constant correction in mixing ratios before performing the regional inversions, which are potentially site-specific corrections. But there should be a reference for these corrections, e.g. taking the most robust model that has been validated against observations or simply a factor of the relative mean of the relevant models/approaches. Although the inversion systems showed the smallest differences in CO2 flux estimates, the specification of the control vector (regarding the construction of covariance matrices) that devises the flux correction can result in larger differences, specifically in the spatial flux patterns.

The large number of stations within central and western Europe leads to a strong observational constraint that is reflected in the spatially optimized fluxes over that area. Therefore, large spatial differences between the inversions are pronounced around areas where stations exist, precisely for grid cells that have non-zero footprints. The large temporal variations indicate a systematic error that possibly arises from the transport models themselves as well as from meteorological forcing data. Additionally, systematic differences between transport models occur due to discrepancies in representing vertical mixing and horizontal and vertical resolution of the models (Peylin et al., 2002). Gerbig et al. (2008) found large discrepancies in derived mixing heights between meteorological analysis from ECMWF and radiosonde data, which reached about 40 % for the day-time and about 100 % for the nocturnal boundary layer. The vertical mixing in tracer dispersion models was found to result in a significant variability in methane emission estimations (up to a factor of 3) given the same meteorology as investigated by Karion et al. (2019).

Drivers of STILT–FLEXPART differences

Although STILT and FLEXPART are run at the same spatio-temporal resolution, employing similar schemes to parametrize the atmospheric motion unresolved by meteorological forcing data such as turbulence, and similar diagnostics to determine mixing heights, they still exhibit large spatial and temporal differences. A first assumption was that the differences between STILT and FLEXPART could be caused by differences in the calculation of mixing height. However, we did not find a correlation between the differences in mixing heights, calculated with the two models, and the differences in prior concentrations (Fig. 6). This finding concludes that the discrepancies in representing mixed layer heights do not explain the major differences in simulated CO2 concentrations nor the differences in footprints.

Figure 6Scatter plot of differences of prior concentrations and mixing heights calculated with STILT and FLEXPART models (i.e. STILT-FLEXPART on the x and y axes). Red lines indicate the slopes.


The second assumption was that differences in the forcing data of meteorological products might lead to the discrepancies in both models, given that STILT uses meteorological parameters from IFS HRES, while FLEXPART uses the ERA-5 reanalysis. Results in Fig. 7, “meteo”, indicate that using different meteorological data results in pronounced differences when the FLEXPART model was forced by operational forecast data instead of the ERA-5 reanalysis. These differences notably occur during the time of net CO2 release, corresponding to quite small differences during the time of growing season. This, however, only explains a small part of the overall differences (shown in Fig. 7, “base”) that dominate all the months except August and September. In a previous study, Liu et al. (2011) concluded that uncertainties in meteorological fields lead to a significant contribution to the total transport error, as well as to an underestimation of the vertical turbulent mixing even when the same circulation model and mixing parameterizations were used to reconstruct vertical mixing from a single meteorological analysis. Tolk et al. (2008) also found meteorology to be a key driver of representation error, which varies spatially and temporally. They indicated that a large contribution to representation error is caused by unresolved model topography at coarse spatial resolution during night, while convective structures, mesoscale circulations, and the variability of CO2 fluxes dominate during day-time. Deng et al. (2017) found that assimilating meteorological observations such as wind speed and wind direction in transport models significantly improved the model performances, achieving an uncertainty reduction of about 50 % in wind speed and direction, especially when measurements in the mixed layer were assimilated. Nonetheless, they concluded that the differences in CO2 emissions reached up to 15 % at local-scale corrections after inversion and were limited to 5 % for the total emissions integrated across the regional domain of interest. These results refer to the limited impact of meteorological data. Note however that the main aim of this experiment was to test whether differences in driving meteorological data could explain the differences between STILT and FLEXPART, but we are not assessing the overall impact of meteorological uncertainties. Doing so would in particular require testing non-ECMWF meteorological products.

Figure 7Differences in prior concentration simulated at LIN with STILT and FLEXPART using different configurations. “s_layer”, yellow line, refers to the difference calculated with STILT using two assumptions of defining the surface layer height, once with the default as 0.5 of the mixed layer and once with 100 m as used in FLEXPART; “meteo”, red line, indicates the differences calculated with FLEXPART using two different types of meteorological data, IFS (the STILT default) and ERA-5; “model”, blue line, denotes the differences calculated with STILT and FLEXPART, given identical meteorological data (IFS) and surface layer height (100 m); “base”, black line, refers to the base configurations of STILT and FLEXPART encompassing all possible differences between models – i.e. (1) STILT with IFS forecasting data and a surface layer height as 0.5 times that of the mixed layer height and (2) FLEXPART with ERA-5 reanalysis and the surface layer height of 100 m.


Furthermore, we tested the possible impact of surface layer heights (the height up to which particles are sensitive to the fluxes) that may affect the particle dispersion, provided that STILT relies on the assumption of defining the surface layer as a half of the mixed layer height, while in FLEXPART it is defined as a fixed height of 100 m (these are default configurations of the models). In this experiment, STILT was run with a surface layer height of 100 m, so the impact of the surface layer on CO2 simulations is outlined by the comparison with another run using the default configurations of STILT. The differences in simulated CO2 concentrations due to differences in the surface layer were found to be quite small (Fig. 7, “s_layer”) and, therefore, can be negligible in both magnitude and temporal pattern compared to the overall differences. However, varying the models STILT and FLEXPART with identical meteorological data and identical surface layer leads to the largest differences, in particular during the growing season months and winter months (Fig. 7, “model”). As a result, model-to-model differences largely affect the simulations of CO2 concentrations and are likely originating from the transport model schemes. It is clearly noticeable that the overall differences combine the underlying differences of “model”, “meteo”, and “s_layer” and are yielded as the arithmetic summation of this partitioning.

Figure 8Innovation of fluxes calculated from CSR and LUMIA using identical uncertainties of prior flux and measurements. The uncertainty flux shape was flat and the decaying spatial correlation was fit to a Gaussian function with 500 km scale. FLEXPART and TM5 models were used in this experiment.

How do our results explain the range of uncertainties reported in scientific literature?

To shed more light on the drivers of differences in optimized CO2 fluxes, we analyse the spread in our inversions in line with the spreads in other inversion estimates that were reported in two previous studies over the same domain of Europe. Figure 9 shows the spreads amid the three studies: (1) eight inversions conducted in our results denoted as “Ensemble”, (2) six inversions of the EUROCOM experiment (denoted as “EUROCOM”) done by Monteil et al. (2020), and (3) five inversions of the drought study by Thompson et al. (2020), focusing on analysing the 2018 drought impact on NEE, denoted as “Drought”. Note that in “EUROCOM” and “Drought”, the tracer inversions differed in the atmospheric regional transport models, the definition of boundary conditions, the definition of control vector, the selection of atmospheric datasets, and the a priori fluxes. These differences are expected to span a large range of uncertainty sources in the posterior NEE. The climatological monthly estimates of NEE were averaged over “EUROCOM” inversion members for the respective years 2006–2015, except for one inversion (NAME), which was limited to 2011–2015. “Ensemble” and “Drought” were confined to the analysis year of 2018. The monthly NEE estimates were calculated for all ensembles as the average over their respective inversion members. The annual mean of NEE estimated with “EUROCOM”, “Ensemble”, and “Drought” amounts to 0.19, 0.29, and 0.05 PgC with standard deviations of 0.34, 0.29, and 0.46 PgC, respectively.

Figure 9Comparison of monthly NEE estimates calculated as the mean of six inversions taken from Monteil et al. (2020), denoted as “EUROCOM”; eight inversion members conducted in our study (setups listed in Table 2), denoted as “Ensemble”; and five inversions used in Thompson et al. (2020) for the 2018 drought study, denoted as “Drought”. The error bars refer to the spreads (min/max) over the respective members amid each ensemble of inversions.


The spreads amid each ensemble of inversions are illustrated by the min and max values bounded around the mean on the error bars (Fig. 9). The monthly mean of NEE estimates shows a good consistency in all the ensembles. The spreads are also relatively comparable, albeit variable over months. For instance, “EUROCOM” and “Drought” exhibit larger spreads during the growing season (April–August), while “Ensemble” has a larger spread in the rest of the months – i.e. during winter. Note that all ensembles experience large spreads during June and May. Although the participating inversions to “EUROCOM” and “Drought” had different configurations, the spreads were not largely different from our inversion spreads. This implies that the use of different atmospheric transport models could account for a large fraction of differences in posterior fluxes, although differences in the definition of uncertainty covariance matrices and lateral boundary conditions likely contribute as well. Moreover, the discrepancies in “EUROCOM” and “Drought” estimates are expected to be partially caused by using different atmospheric datasets in the inversion systems. Munassar et al. (2022) found that posterior fluxes can be more sensitive to changing the number of stations than changing the prior flux models.

5 Conclusions

Estimating atmospheric tracer fluxes through inverse modelling systems has been widely used, in particular for targeting the major greenhouse gases (GHGs) to improve the quantification of natural (both terrestrial and oceanic) sources and sinks. Here, an analysis of differences in posterior fluxes of CO2 was carried out using inversion systems deploying different regional transport models. The difference between minimum and maximum spreads for annually integrated fluxes was found to be 0.92 PgC yr−1 for the ensemble range of 0.20 and 0.72 PgC yr−1, with a mean estimate of 0.29 PgC yr−1 calculated over the full domain of Europe in 2018. We tested the regional transport, the boundary conditions, and the inversion systems. The regional transport accounts for the largest part of the discrepancies in the optimized fluxes as well as in the estimation of CO2 concentration. Temporal and spatial differences in posterior fluxes are consistent with the differences in simulated CO2 concentration sampled with STILT and FLEXPART over the station network. They demonstrate a spatial pattern over certain areas during June and December, suggesting rather systematic differences between STILT and FLEXPART. The differences in the regional transport are mainly caused by the transport schemes, while meteorological forcing data partially contribute to these differences, especially during the months in which net release of CO2 occurs. However, the differences in CO2 simulations did not show large sensitivities to other parameters such as the way the surface layer height (maximum altitude considered sensitive to the fluxes in Lagrangian models) and the mixing height are defined. In addition, the global transport models used in the global inversions that provide the far-field contributions to the regional domain are responsible for small but non-negligible differences in the inversion estimates. These differences appeared to be homogeneous spatially and temporally, which can be considered as bias-like. The differences arising from using different inversion systems integrated over the entire domain of Europe were on the contrary rather small, once differences such as the transport model and the uncertainties are controlled for. However, such an impact is partially a result of applying different structure and shape in the prior flux uncertainty, while the rest may be attributed to differences in the cost function convergence to reach the minimum. This reflects the importance of the way the uncertainty is prescribed in the tracer inversion systems.

The divergence in CO2 flux estimates resulting from swapping the regional transport model emphasizes the need for further evaluation of atmospheric transport models in order to improve the performance of the models. At the same time, it is important to realistically account for the transport errors in the tracer inversions. Errors in meteorology parameters assimilated in transport models as forcing data should also be accounted for explicitly, potentially through making use of an ensemble of meteorology data to estimate such errors. Despite the non-negligible difference between inversion systems, this study indicates the importance of following a common inversion protocol when reporting flux estimates from different inversion frameworks.

Code and data availability

The simulations of the ensemble of inversions (a posteriori NEE calculated using CSR and LUMIA) and their respective prior fluxes can be accessed from (Munassar and Monteil, 2023). The codes used to create the figures can be made available upon request to the corresponding author. The atmospheric datasets of CO2 dry mole fractions are available at the ICOS Carbon Portal and can be accessed from (Drought 2018 Team and ICOS Atmosphere Thematic Centre, 2020).


The supplement related to this article is available online at:

Author contributions

SM and GM designed the study. CG, MS, UK, and KUT gave valuable suggestions in frequent discussions that helped improve the design and the structure of the study. SM wrote the paper and performed the simulations of CSR. GM performed the simulations of LUMIA. CG prepared and provided the fluxes of VPRM, and FTK processed the anthropogenic emission datasets. CR designed and develops the code of CSR. All authors revised the paper and edited the text.

Competing interests

At least one of the (co-)authors is a member of the editorial board of Atmospheric Chemistry and Physics. The peer-review process was guided by an independent editor, and the authors also have no other competing interests to declare.


Publisher’s note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


The authors thank Mathias Göckede for his valuable comments on the manuscript in the internal review. Saqr Munassar, Christoph Gerbig, Christian Rödenbeck, and Frank-Thomas Koch acknowledge the computational support of Deutsches Klimarechenzentrum (DKRZ) where the CSR inversion system is implemented. The computations of LUMIA were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at NSC (National Supercomputer Centre), partially funded by the Swedish Research Council through grant agreement no. 2018-05973. Marko Scholze and Guillaume Monteil acknowledge support from the three Swedish strategic research areas ModElling the Regional and Global Earth system (MERGE), the e-science collaboration (eSSENCE), and Biodiversity and Ecosystems in a Changing Climate (BECC).

The authors acknowledge the provision of the atmospheric dataset of CO2 dry mole fractions compiled by ICOS ATC (Atmospheric Thematic Centre).

Financial support

This research has been supported by the H2020 projects VERIFY (grant no. 776810) and CoCO2 (grant no. 958927), as well as by BMBF through the ITMS-M project under contract 01LK2102A.

The article processing charges for this open-access publication were covered by the Max Planck Society.

Review statement

This paper was edited by Susannah Burrows and reviewed by Jia Jung and one anonymous referee.


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Short summary
Using different transport models results in large errors in optimized fluxes in the atmospheric inversions. Boundary conditions and inversion system configurations lead to a smaller but non-negligible impact. The findings highlight the importance to validate transport models for further developments but also to properly account for such errors in inverse modelling. This will help narrow the convergence of gas estimates reported in the scientific literature from different inversion frameworks.
Final-revised paper