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Atmospheric inversions provide estimates of carbon dioxide (CO2) fluxes between the surface and atmosphere based on atmospheric CO2 concentration observations. The number of CO2 observations is projected to increase severalfold in the next decades from expanding in situ networks and next‐generation CO2‐observing satellites, providing both an opportunity and a challenge for inversions. This study introduces the TRACE Regional Atmosphere–Carbon Ensemble (TRACE) system, which employ an ensemble‐based simultaneous state and parameter estimation (ESSPE) approach to enable the assimilation of large volumes of observations for constraining CO2 flux parameters. TRACE uses an online full‐physics mesoscale atmospheric model and assimilates observations serially in a coupled atmosphere–carbon ensemble Kalman filter. The data assimilation system was tested in a series of observing system simulation experiments using in situ observations for a regional domain over North America in summer. Under ideal conditions with known prior flux parameter error covariances, TRACE reduced the error in domain‐integrated monthly CO2 fluxes by about 97% relative to the prior flux errors. In a more realistic scenario with unknown prior flux error statistics, the corresponding relative error reductions ranged from 80.6% to 88.5% depending on the specification of prior flux parameter error correlations. For regionally integrated fluxes on a spatial scale of 106 km2, the sum of absolute errors was reduced by 34.5%–50.9% relative to the prior flux errors. Moreover, TRACE produced posterior uncertainty estimates that were consistent with the true errors. These initial experiments show that the ESSPE approach in TRACE provides a promising method for advancing CO2 inversion techniques. Plain Language Summary: To gain a better understanding of the main drivers behind atmospheric carbon dioxide (CO2) variations and trends, it is essential to accurately quantify CO2 exchanges—also known as fluxes—between the atmosphere and other components of the Earth system. It is generally not possible to directly measure surface CO2 fluxes at regional scales; however, fluxes can be inferred from a network of atmospheric CO2 concentration observations combined with atmospheric modeling and inversion methods, which seek to find the most likely fluxes given prior knowledge and observational evidence. This paper presents a new regional inversion framework called TRACE Regional Atmosphere–Carbon Ensemble (TRACE) for deriving CO2 fluxes at high resolution in space and time. One of the major innovations in TRACE is the ensemble‐based dual state and parameter estimation approach, which makes it computationally feasible to ingest large volumes of observations into the system. A series of experiments were carried out in a domain over North America to test the new framework in a controlled setting. In the experiments, we used synthetic tower observations of atmospheric CO2 concentrations to constrain parameters controlling terrestrial biogenic and oceanic CO2 fluxes. The results show that TRACE is capable of accurately estimating both the magnitude and spatial pattern of regional CO2 fluxes. Key Points: An ensemble‐based simultaneous state and parameter estimation approach is introduced for regional CO2 flux inversionsThe new dual‐state TRACE Regional Atmosphere–Carbon Ensemble (TRACE) framework provides a flexible platform for conducting coupled atmosphere–carbon data assimilationControlled experiments show that TRACE is effective at constraining regional CO2 fluxes using in situ CO2 concentration observations [ABSTRACT FROM AUTHOR]

Computational requirements often impose limitations on the spatial and temporal resolutions of atmospheric CO2 inversions, increasing aggregation and representation errors. This study enables higher spatial and temporal resolution inversions with spatial and temporal error structures similar to those used in other published inversions by representing the prior flux error covariances as a Kronecker product of spatial and temporal covariances and by using spectral methods for the spatial correlations. Compared to existing inversion systems that are forced to degrade the resolution of the problem in order to bring the dimensionality down to computationally tractable levels, this inversion framework is able to take advantage of mesoscale transport simulations and more of the complexity of spatial and temporal covariances in the surface CO2 fluxes. This approach was successfully implemented over one month with an identical‐twin observing system simulation experiment (OSSE) using a set of assumptions about the prior flux uncertainties compatible both with continental‐scale uncertainty estimates and with comparisons of vegetation models to flux towers. The demonstration illustrates the potential of the newly developed inversion system to use high‐temporal‐resolution information from the North American tower network, to extract high‐resolution information about CO2 fluxes that is inaccessible to coarser resolution inversion systems, and to simultaneously optimize an ensemble of prior estimates. This demonstration sets the stage for regional flux inversions that can take full advantage of the high‐resolution data available in tower CO2 records and mesoscale atmospheric transport reanalyses, include more realistic prior error structures, and explore specifying prior fluxes with ensembles. Plain Language Summary: This paper describes a new inverse framework for deriving surface carbon dioxide (CO2) fluxes at high spatial and temporal resolutions from atmospheric mole fraction measurements. We demonstrate the potential of the system over North America by inverting for subdaily biogenic CO2 fluxes while accounting for the complexity of spatio‐temporal structures in flux error covariances in a data‐based manner. Key Points: A new inversion system uses spectral methods for spatial correlations to do a 27 km subdaily inversion over North AmericaThe software package allows simultaneous optimization of multiple prior mean flux estimatesThe system is demonstrated over continental North America for a network of seven towers [ABSTRACT FROM AUTHOR]