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ABSTRACT The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone. 

Eddy covariance serves as one the most effective techniques for long-term monitoring of ecosystem fluxes, however long-term data integrations rely on complete timeseries, meaning that any gaps due to missing data must be reliably filled. To date, many gap-filling approaches have been proposed and extensively evaluated for mature and/or less actively managed ecosystems. Random forest regression (RFR) has been shown to be stable and perform better in these systems than alternative approaches, particularly when filling longer gaps. However, the performance of RFR gap filling remains less certain in more challenging ecosystems, e.g., actively managed agri-ecosystems and following recent land-use change due to management disturbances, ecosystems with relatively low fluxes due to low signal to noise ratios, or for trace gases other than carbon dioxide (e.g., methane). In an extension to earlier work on gap filling global carbon dioxide, water, and energy fluxes, we assess the RFR approach for gap filling methane fluxes globally. We then investigate a range of gap-filling methodologies for carbon dioxide, water, energy, and methane fluxes in challenging ecosystems, including European managed pastures, Southeast Asian converted peatlands, and North American drylands. Our findings indicate that RFR is a competent alternative to existing research standard gap-filling algorithms. The marginal distribution sampling (MDS) is still suggested for filling short (< 12 days) gaps in carbon dioxide fluxes, but RFR is better for filling longer (> 30 days) gaps in carbon dioxide fluxes and also for gap filling other fluxes (e.g. sensible heat, latent energy and methane). In addition, using RFR with globally available reanalysis environmental drivers is effective when measured drivers are unavailable. Crucially, RFR was able to reliably fill cumulative fluxes for gaps > 3 moths and, unlike other common approaches, key environment-flux responses were preserved in the gap-filled data.