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Robust inference of ecosystem soil water stress from eddy covariance data

Eddy covariance data are invaluable for determining ecosystem water use strategies under soil water stress. However, existing stress inference methods require numerous subjective data processing and model specification assumptions whose effect on the inferred soil water stress signal is rarely quantified. These uncertainties may confound the stress inference and the generalization of ecosystem water use strategies across multiple sites and studies. In this research, we quantify the sensitivity of soil water stress signals inferred from eddy covariance data to the prevailing data and modeling assumptions (i.e., their robustness) to compile a comprehensive list of sites with robust soil water stress signals and assess the performance of current stress inference methods. To accomplish this, we identify the most prevalent assumptions from the literature and perform a digital factorial experiment to extract probability distributions of plausible soil water stress signals and model performance at 151 FLUXNET2015 and AmeriFlux-FLUXNET sites. Here, we develop a new framework that summarizes these probability distributions to classify and rank the robustness of each site’s soil water stress signal, which we display with a user-friendly heat map. We estimate that only 5%–36% of sites exhibit a robust soil water stress signal due to deficient model performance and poorly constrained ecosystem water use parameters. We also find that the lack of robustness is site-specific, which undermines grouping stress signals by broad ecosystem categories or comparing results across studies with differing assumptions. Lastly, existing stress inference methods appear better suited for eddy covariance sites with grass/annual vegetation. Our findings call for more careful and consistent inference of ecosystem water stress from eddy covariance data.

54 ENVIRONMENTAL SCIENCES↗

Better practices for inferring ecosystem water use strategy from eddy covariance data

Eddy covariance data are critical for inferring ecosystem water use strategies. Yet, such inferences are sensitive to a range of assumptions applied across studies, hindering our understanding of water use strategies within and across eddy covariance sites. A recent analysis across 151 FLUXNET2015 and AmeriFlux-FLUXNET datasets found that poor model performance was the key driver of non-robust inferences of ecosystem water use strategies. Here, we leverage this previous analysis to (i) identify the specific assumptions that improve inference model performance across most sites, (ii) explain the mechanisms behind the performance improvements, and (iii) check whether better performance improves water use inference. We find that the common practice of fitting a model to canopy conductance (G c ) derived from the evapotranspiration (ET) observations, rather than to observed ET itself, artificially amplifies data errors and degrades the model performance. Next, accounting for vegetation dynamics by applying a growing season filter or incorporating satellite LAI data improves performance, but the former practice may remove soil water stress periods. Lastly, using the leaf-to-air vapor pressure deficit (VPD l ) derived from ET observations as a model input may artificially inflate performance. Based on these results, we recommend selecting observed ET (rather than derived G c ) as the response variable, carefully accounting for vegetation dynamics, and avoiding derived VPD l as a model input; these best practices improve model performance by c. 20% and robustness by c. 80% across all eddy covariance sites. Nevertheless, the performance improvements do not always correspond to more robust inference of water use strategies, as model parameter selection and surface energy budget closure corrections still strongly influence the ecosystem water use parameter estimation in a site-specific manner.

AmeriFlux↗

Strong Correspondence in Evapotranspiration and Carbon Dioxide Fluxes Between Different Eddy Covariance Systems Enables Quantification of Landscape Heterogeneity in Dryland Fluxes

Abstract The eddy covariance method is widely used to investigate fluxes of energy, water, and carbon dioxide at landscape scales, providing important information on how ecological systems function. Flux measurements quantify ecosystem responses to environmental perturbations and management strategies, including nature‐based climate‐change mitigation measures. However, due to the high cost of conventional instrumentation, most eddy covariance studies employ a single system, limiting spatial representation to the flux footprint. Insufficient replication may be limiting our understanding of ecosystem behavior. To address this limitation, we deployed eight lower‐cost eddy covariance systems in two clusters around two conventional eddy covariance systems in the Chihuahuan Desert of North America for a period of 2 years. These dryland settings characterized by large temperature variations and relatively low carbon dioxide fluxes represented a challenging setting for eddy covariance. We found very good closure of energy and water balance across all systems (within ±9% of unity). We found very good correspondence between the lower‐cost and conventional systems' fluxes of sensible heat (with concordance correlation coefficient (CCC) of ≥0.87), latent energy (evapotranspiration; CCC ≥ 0.89), and useful correspondence in the net ecosystem exchange ((NEE); with CCC ≥ 0.4) at the daily temporal resolution. Relative to the conventional systems, the low‐frequency systems were characterized by a higher level of random error, particularly in the NEE fluxes. Lower‐cost systems can enable wider deployment affording better replication and sampling of spatiotemporal variability at the expense of greater measurement noise that might be limiting for certain applications. Replicated eddy covariance observations may be useful when addressing gaps in the existing monitoring of critical and underrepresented ecosystems and for measuring areas larger than a single flux footprint.

54 ENVIRONMENTAL SCIENCES↗

Eddy Covariance Theory: A Review

Eddy covariance (EC), the gold standard for measuring ecosystem scale gas and heat exchanges, has transformed our understanding of the breathing of the biosphere, and thus global change biology. Despite numerous methodological improvements and insights gained from the technique, the community faces persistent challenges that have been present since the first EC measurements. Here, we review the theoretical developments underpinning EC. We present theoretical developments in four important areas that have relevance to EC measurements of the net ecosystem exchanges (NEE) of gases and heat from a single tower: (i) measuring the total vertical flux density, (ii) flux attenuation, (iii) coordinate rotations, and (iv) energy balance closure. Persistent problems with EC measurements, such as the inability to close the energy budget, led us to identify two priorities for revisiting the theory underlying: (i) sensible heat flux calculations, and (ii) constraining the mean vertical wind velocity. We present a framework for improved calculation of sensible heat flux derived from first principles of fluid mechanics and thermodynamics that considers coupled heat and mass transfer so that conservation of both is obeyed. These refinements are motivated by the need for unbiased measurements of energy and mass transfer between the land surface and atmosphere for ecosystem research and to validate satellite observations and land surface models.

ecosystem fluxes↗

Upscaling Wetland Methane Emissions From the FLUXNET–CH4 Eddy Covariance Network (UpCH4 v1.0): Model Development, Network Assessment, and Budget Comparison

Wetlands are responsible for 20%–31% of global methane (CH 4 ) emissions and account for a large source of uncertainty in the global CH 4 budget. Data-driven upscaling of CH 4 fluxes from eddy covariance measurements can provide new and independent bottom-up estimates of wetland CH 4 emissions. Here, we develop a six-predictor random forest upscaling model (UpCH4), trained on 119 site-years of eddy covariance CH 4 flux data from 43 freshwater wetland sites in the FLUXNET-CH4 Community Product. Network patterns in site-level annual means and mean seasonal cycles of CH 4 fluxes were reproduced accurately in tundra, boreal, and temperate regions (Nash-Sutcliffe Efficiency ~0.52–0.63 and 0.53). UpCH4 estimated annual global wetland CH 4 emissions of 146 ± 43 TgCH 4 y –1 for 2001–2018 which agrees closely with current bottom-up land surface models (102–181 TgCH 4 y –1 ) and overlaps with top-down atmospheric inversion models (155–200 TgCH 4 y –1 ). However, UpCH4 diverged from both types of models in the spatial pattern and seasonal dynamics of tropical wetland emissions. We conclude that upscaling of eddy covariance CH 4 fluxes has the potential to produce realistic extra-tropical wetland CH 4 emissions estimates which will improve with more flux data. To reduce uncertainty in upscaled estimates, researchers could prioritize new wetland flux sites along humid-to-arid tropical climate gradients, from major rainforest basins (Congo, Amazon, and SE Asia), into monsoon (Bangladesh and India) and savannah regions (African Sahel) and be paired with improved knowledge of wetland extent seasonal dynamics in these regions.

54 ENVIRONMENTAL SCIENCES↗

Source Decomposition of Eddy-Covariance CO 2 Flux Measurements for Evaluating a High-Resolution Urban CO 2 Emissions Inventory

We present the comparison of source-partitioned CO2 flux measurements with a high-resolution urban CO 2 emissions inventory (Hestia). Tower-based measurements of CO and 14 C are used to partition net CO 2 flux measurements into fossil and biogenic components. A flux footprint model is used to quantify spatial variation in flux measurements. We compare the daily cycle and spatial structure of Hestia and eddy-covariance derived fossil fuel CO 2 emissions on a seasonal basis. Hestia inventory emissions exceed the eddy-covariance measured emissions by 0.36 µ mol m −2 s −1 (3.2%) in the cold season and 0.62 µ mol m −2 s −1 (9.1%) in the warm season. The daily cycle of fluxes in both products matches closely, with correlations in the hourly mean fluxes of 0.86 (cold season) and 0.93 (warm season). The spatially averaged fluxes also agree in each season and a persistent spatial pattern in the differences during both seasons that may suggest a bias related to residential heating emissions. In addition, in the cold season, the magnitudes of average daytime biological uptake and nighttime respiration at this flux site are approximately 15% and 27% of the mean fossil fuel CO 2 emissions over the same time period, contradicting common assumptions of no significant biological CO 2 exchange in northern cities during winter. This work demonstrates the effectiveness of using trace gas ratios to adapt eddy-covariance flux measurements in urban environments for disaggregating anthropogenic CO 2 emissions and urban ecosystem fluxes at high spatial and temporal resolution.

eddy-covariance flux measurements↗

Spatial Heterogeneity in CO2, CH4, and Energy Fluxes: Insights from Airborne Eddy Covariance Measurements Over the Mid-Atlantic Region

The exchange of carbon between the Earth’s atmosphere and biosphere influences the atmospheric abundances of carbon dioxide (CO2) and methane (CH4). Airborne eddy covariance can quantify surface-atmosphere exchange from landscape-to-regional scales, offering a unique perspective on carbon cycle dynamics. We use extensive airborne measurements to quantify fluxes of sensible heat, latent heat, CO2, and CH4across multiple ecosystems in the Mid-Atlantic region during September 2016 and May 2017. In conjunction with footprint analysis and land cover information, we use the airborne dataset to explore the effects of landscape heterogeneity on measured fluxes. Our results demonstrate large variability in CO2 uptake over mixed agricultural and forested sites, with fluxes ranging from -3.4 ± 0.7 to -11.5 ± 1.6μmol m-2s-1 for croplands and -9.1 ± 1.5 to -22.7 ± 3.2μmol m-2s-1for forests. We also report substantial CH4emissions of 32.3 ± 17.0to 76.1 ± 29.4nmol m-2s-1 from a brackish herbaceous wetland and 58.4± 12.0 to 181.2 ± 36.8nmol m-2s-1 from a freshwater forested wetland. Comparison of ecosystem-specific aircraft observations with measurements from eddy covariance flux towers along the flight path demonstrate that towers capture ~30–75% of the regional variability in ecosystem fluxes. Diel patterns measured at the tower sites suggest that peak, midday flux measurements from aircraft accurately predicts net daily CO2exchange. We discuss next steps in applying airborne observations to evaluate bottom-up flux models and improve understanding of the biophysical processes that drive carbon exchange from landscape-to-regional scales.

airborne measurements to quantify fluxes of sensib↗

Modeling Wind in Agrivoltaics and its Impact on Eddy Covariance Flux Measurements

Silicon Ranch is conducting a research study at their 138MW Bancroft Station agrivoltaics site, the largest agrivoltaics research array in the US, in which they are using an eddy covariance flux tower to measure the carbon budget. They are interested in finding out if the presence of the panels changes the effectiveness of these measurements. To investigate this topic, NLR performed numerical simulations of wind through the agrivoltaic array to identify under what environmental conditions (wind speed, wind direction, temperatures) and panel tilt angles the mean wind speeds at the measurement heights are significantly altered by the presence of the solar panels. NLR adapted and used the PVade simulation tool [1] to model wind in Silicon Ranch's agrivoltaic array and found that at the height of the flux tower (6m), the wind speed measured is not significantly altered by the presence of solar panels. The percent difference is less than 4% and is generally greatest during daytime conditions at higher wind speeds and perpendicular wind direction. Closer to the ground, the flow is significantly altered (wind speeds are reduced) by the presence of solar panels and the percent difference increases in strong winds. The work confirmed that eddy covariance flux towers can be used within the context of a solar array field.

14 SOLAR ENERGY↗

The effect of relative humidity on eddy covariance latent heat flux measurements and its implication for partitioning into transpiration and evaporation

While the eddy covariance (EC) technique is a well-established method for measuring water fluxes (i.e., evaporation or 'evapotranspiration’, ET), the measurement is susceptible to many uncertainties. One such issue is the potential underestimation of ET when relative humidity (RH) is high (> 70%), due to low-pass filtering with some EC systems. Yet, this underestimation for different types of EC systems (e.g. open-path or closed-path sensors) has not been characterized for synthesis datasets such as the widely used FLUXNET2015 dataset. Here, we assess the RH-associated underestimation of latent heat fluxes (LE, or ET) from different EC systems for 163 sites in the FLUXNET2015 dataset. We found that the LE underestimation is most apparent during hours when RH is higher than 70%, predominantly observed at sites using closed-path EC systems, but the extent of the LE underestimation is highly site-specific. We then propose a machine learning based method to correct for this underestimation, and compare it to two energy balance closure based LE correction approaches (Bowen ratio correction, BRC, and attributing all errors to LE). Our correction increases LE by 189% for closed-path sites at high RH (> 90%), while BRC increases LE by around 30% for all RH conditions. Additionally, we assess the influence of these corrections on ET-based transpiration (T) estimates using two different ET partitioning methods. Results show opposite responses (increasing vs. slightly decreasing T-to-ET ratios, T/ET) between the two methods when comparing T based on corrected and uncorrected LE. Overall, our results demonstrate the existence of a high RH bias in water fluxes in the FLUXNET2015 dataset and suggest that this bias is a pronounced source of uncertainty in ET measurements to be considered when estimating ecosystem T/ET and WUE.

54 ENVIRONMENTAL SCIENCES↗

Methodological challenges and new perspectives of shifting vegetation phenology in eddy covariance data

While numerous studies report shifts in vegetation phenology, in this regard eddy covariance (EC) data, despite its continuous high-frequency observations, still requires further exploration. Furthermore, there is no general consensus on optimal methodologies for data smoothing and extracting phenological transition dates (PTDs). Here, we revisit existing methodologies and present new prospects to investigate phenological changes in gross primary productivity (GPP) from EC measurements. First, we present a smoothing technique of GPP time series through the derivative of its smoothed annual cumulative sum. Second, we calculate PTDs and their trends from a commonly used threshold method that identifies days with a fixed percentage of the annual maximum GPP. A systematic analysis is performed for various thresholds ranging from 0.1 to 0.7. Lastly, we examine the relation of PTDs trends to trends in GPP across the years on a weekly basis. Results from 47 EC sites with long time series (> 10 years) show that advancing trends in start of season (SOS) are strongest at lower thresholds but for the end of season (EOS) at higher thresholds. Moreover, the trends are variable at different thresholds for individual vegetation types and individual sites, outlining reasonable concerns on using a single threshold value. Relationship of trends in PTDs and weekly GPP reveal association of advanced SOS and delayed EOS to increase in immediate primary productivity, but not to the trends in overall seasonal productivity. Drawing on these analyses, we emphasise on abstaining from subjective choices and investigating relationship of PTDs trend to finer temporal trends of GPP. Our study examines existing methodological challenges and presents approaches that optimize the use of EC data in identifying vegetation phenological changes and their relation to carbon uptake.

54 ENVIRONMENTAL SCIENCES↗

Contrasting Carbon–Water–Energy Dynamics in Perennial and Annual Bioenergy Agroecosystems Using Eddy Covariance and Interpretable Machine Learning

Understanding how agroecosystems respond to environmental variability is fundamental to predicting productivity and sustainability under a changing climate. We analyzed 55 site-years of high-frequency eddy covariance observations from five agroecosystems—two perennial grasses (miscanthus and switchgrass), two annual rotation systems (maize–soybean and sorghum–soybean), and a restored native prairie—to examine ecosystem-scale carbon, water, and energy fluxes. Using an interpretable machine-learning framework with regression tree ensembles, Shapley Additive Explanations, and Accumulated Local Effects, we quantified how environmental and temporal factors regulate gross primary productivity (GPP), evapotranspiration (ET), water-use efficiency, and the Bowen ratio. Perennials exhibited stronger physiological buffering and maintained fluxes across a broader range of temperature and moisture conditions, reflecting deeper rooting and persistent canopy cover. Annuals, in contrast, showed greater short-term variability and stronger coupling to atmospheric demand, with GPP and ET declining rapidly under low humidity or soil moisture. Differences in temperature sensitivity of Bowen ratio further revealed that perennials sustained proportionally greater sensible heat flux under cool conditions, whereas annuals exhibited constrained energy exchange when evaporative demand was low. Together, these results demonstrate that crop life cycle and canopy structure are fundamental determinants of ecosystem-scale carbon–water–energy coupling. By integrating long-term flux observations with interpretable machine learning, this study identifies the environmental drivers that shape agroecosystem function and highlights how conversion from annual to perennial feedstocks can enhance climatic resilience and alter land–atmosphere energy feedbacks. These findings provide a data-driven basis for improving crop and Earth-system models and for guiding bioenergy landscape design under future climate scenarios.

Accumulated Local Effects↗

A New Post‐Hoc Method to Reduce the Energy Imbalance in Eddy Covariance Measurements

Abstract Latent and sensible heat flux observations are essential for understanding land–atmosphere interactions. Measurements from the eddy covariance technique are widely used but suffer from systematic energy imbalance problems, partly due to missing large eddies from sub‐mesoscale transport. Because available energy drives the development of large eddies, we propose an available energy based correction method for turbulent flux measurements. We apply our method to 172 flux tower sites and show that we can reduce the energy imbalance from −14.99 to −0.65 W m −2 on average, together with improved consistency between turbulent fluxes and available energy and associated increases inr 2 at individual sites and across networks. Our results suggest that our method is conceptually and empirically preferable over the method implemented in the ONEFlux processing. This can contribute to the efforts in understanding and addressing the energy imbalance issue, which is crucial for the evaluation and calibration of land surface models.

Geology↗

New Data-Driven Estimation of Terrestrial CO2 Fluxes in Asia Using a Standardized Database of Eddy Covariance Measurements, Remote Sensing Data, and Support Vector Regression

The lack of a standardized database of eddy covariance observations has been an obstacle for data-driven estimation of terrestrial carbon dioxide fluxes in Asia. In this study, we developed such a standardized database using 54 sites from various databases by applying consistent postprocessing for data-driven estimation of gross primary productivity (GPP) and net ecosystem carbon dioxide exchange (NEE). Data-driven estimation was conducted by using a machine learning algorithm: support vector regression (SVR), with remote sensing data for 2000 to 2015 period. Site-level evaluation of the estimated carbon dioxide fluxes shows that although performance varies in different vegetation and climate classifications, GPP and NEE at 8 days are reproduced (e.g., r (exp 2) =0.73 and 0.42 for 8 day GPP and NEE). Evaluation of spatially estimated GPP with Global Ozone Monitoring Experiment 2 sensor-based Sun-induced chlorophyll fluorescence shows that monthly GPP variations at subcontinental scale were reproduced by SVR (r (exp 2)=1.00, 0.94, 0.91, and 0.89 for Siberia, East Asia, South Asia, and Southeast Asia, respectively). Evaluation of spatially estimated NEE with net atmosphere-land carbon dioxide fluxes of Greenhouse Gases Observing Satellite (GOSAT) Level 4A product shows that monthly variations of these data were consistent in Siberia and East Asia; meanwhile, inconsistency was found in South Asia and Southeast Asia. Furthermore, differences in the land carbon dioxide fluxes from SVR-NEE and GOSAT Level 4A were partially explained by accounting for the differences in the definition of land carbon dioxide fluxes. These data-driven estimates can provide a new opportunity to assess carbon dioxide fluxes in Asia and evaluate and constrain terrestrial ecosystem models.

chlorophyll fluorescence↗

Technical note: Uncertainties in eddy covariance CO 2 fluxes in a semiarid sagebrush ecosystem caused by gap-filling approaches

Abstract. Gap-filling eddy covariance CO2 fluxes is challenging at dryland sites due to small CO2 fluxes. Here, four machine learning (ML) algorithms including artificial neural network (ANN), k-nearest neighbors (KNNs), random forest (RF), and support vector machine (SVM) are employed and evaluated for gap-filling CO2 fluxes over a semiarid sagebrush ecosystem with different lengths of artificial gaps. The ANN and RF algorithms outperform the KNN and SVM in filling gaps ranging from hours to days, with the RF being more time efficient than the ANN. Performances of the ANN and RF are largely degraded for extremely long gaps of 2 months. In addition, our results suggest that there is no need to fill the daytime and nighttime net ecosystem exchange (NEE) gaps separately when using the ANN and RF. With the ANN and RF, the gap-filling-induced uncertainties in the annual NEE at this site are estimated to be within 16 g C m−2, whereas the uncertainties by the KNN and SVM can be as large as 27 g C m−2. To better fill extremely long gaps of a few months, we test a two-layer gap-filling framework based on the RF. With this framework, the model performance is improved significantly, especially for the nighttime data. Therefore, this approach provides an alternative in filling extremely long gaps to characterize annual carbon budgets and interannual variability in dryland ecosystems.

Yao, Jingyu↗

Assessing Spatial Representativeness of Global Flux Tower Eddy-Covariance Measurements Using Data from FLUXNET2015

Large datasets of carbon dioxide, energy, and water fluxes were measured with the eddy-covariance (EC) technique, such as FLUXNET2015. These datasets are widely used to validate remote-sensing products and benchmark models. One of the major challenges in utilizing EC-flux data is determining the spatial extent to which measurements taken at individual EC towers reflect model-grid or remote sensing pixels. To minimize the potential biases caused by the footprint-to-target area mismatch, it is important to use flux datasets with awareness of the footprint. This study analyze the spatial representativeness of global EC measurements based on the open-source FLUXNET2015 data, using the published flux footprint model (SAFE-f). The calculated annual cumulative footprint climatology (ACFC) was overlaid on land cover and vegetation index maps to create a spatial representativeness dataset of global flux towers. The dataset includes the following components: (1) the ACFC contour (ACFCC) data and areas representing 50%, 60%, 70%, and 80% ACFCC of each site, (2) the proportion of each land cover type weighted by the 80% ACFC (ACFCW), (3) the semivariogram calculated using Normalized Difference Vegetation Index (NDVI) considering the 80% ACFCW, and (4) the sensor location bias (SLB) between the 80% ACFCW and designated areas (e.g. 80% ACFCC and window sizes) proxied by NDVI. Finally, we conducted a comprehensive evaluation of the representativeness of each site from three aspects: (1) the underlying surface cover, (2) the semivariogram, and (3) the SLB between 80% ACFCW and 80% ACFCC, and categorized them into 3 levels. The goal of creating this dataset is to provide data quality guidance for international researchers to effectively utilize the FLUXNET2015 dataset in the future.

54 ENVIRONMENTAL SCIENCES↗

A new open‐path eddy covariance method for nitrous oxide and other trace gases that minimizes temperature corrections

Abstract Low‐power, open‐path gas sensors enable eddy covariance (EC) flux measurements in remote areas without line power. However, open‐path flux measurements are sensitive to fluctuations in air temperature, pressure, and humidity. Laser‐based, open‐path sensors with the needed sensitivity for trace gases like methane (CH 4 ) and nitrous oxide (N 2 O) are impacted by additional spectroscopic effects. Corrections for these effects, especially those related to temperature fluctuations, often exceed the flux of gases, leading to large uncertainties in the associated fluxes. For example, the density and spectroscopic corrections arising from temperature fluctuations can be one or two orders of magnitude greater than background N 2 O fluxes. Consequently, measuring background fluxes with laser‐based, open‐path sensors is extremely challenging, particularly for N 2 O and gases with similar high‐precision requirements. We demonstrate a new laser‐based, open‐path N 2 O sensor and a general approach applicable to other gases that minimizes temperature‐related corrections for EC flux measurements. The method identifies absorption lines with spectroscopic effects in the opposite direction of density effects from temperature and, thus, density and spectroscopic effects nearly cancel one another. The new open‐path N 2 O sensor was tested at a corn ( Zea mays L.) field in Southwestern Michigan, United States. The sensor had an optimal precision of 0.1 ppbv at 10 Hz and power consumption of 50 W. Field trials showed that temperature‐related corrections were 6% of density corrections, reducing EC random errors by 20‐fold compared to previously examined lines. Measured open‐path N 2 O EC fluxes showed excellent agreement with those made with static chambers ( m = 1.0 ± 0.3; r 2 = .96). More generally, we identified absorption lines for CO 2 and CH 4 flux measurements that can reduce the temperature‐related corrections by 10–100 times compared to existing open‐path sensors. The proposed method provides a new direction for future open‐path sensors, facilitating the expansion of accurate EC flux measurements.

47 OTHER INSTRUMENTATION↗