Regional atmospheric CO2 inversion reveals seasonal and geographic differences in Amazon net biome exchange

The CO2 record at the Amazon Tall Tower Observatory: A new opportunity to study processes on seasonal and inter-annual scales

High-quality atmospheric CO₂  measurements are sparse in Amazonia, but can provide critical insights into the spatial and temporal variability of sources and sinks of CO₂ . In this study, we present the first 6 years (2014-2019) of continuous, high-precision measurements of atmospheric CO₂ at the Amazon Tall Tower Observatory (ATTO, 2.1°S, 58.9°W). After subtracting the simulated background concentrations from our observational record, we define a CO₂ regional signal ( ΔCO2obs ) that has a marked seasonal cycle with an amplitude of about 4 ppm. At both seasonal and inter-annual scales, we find differences in phase between ΔCO2obs and the local eddy covariance net ecosystem exchange (EC-NEE), which is interpreted as an indicator of a decoupling between local and non-local drivers of ΔCO2obs . In addition, we present how the 2015-2016 El Niño-induced drought was captured by our atmospheric record as a positive 2σ anomaly in both the wet and dry season of 2016. Furthermore, we analyzed the observed seasonal cycle and inter-annual variability of ΔCO2obs together with net ecosystem exchange (NEE) using a suite of modeled flux products representing biospheric and aquatic CO₂ exchange. We use both non-optimized and optimized (i.e., resulting from atmospheric inverse modeling) NEE fluxes as input in an atmospheric transport model (STILT). The observed shape and amplitude of the seasonal cycle was captured neither by the simulations using the optimized fluxes nor by those using the diagnostic Vegetation and Photosynthesis Respiration Model (VPRM). We show that including the contribution of CO₂ from river evasion improves the simulated shape (not the magnitude) of the seasonal cycle when using a data-driven non-optimized NEE product (FLUXCOM). The simulated contribution from river evasion was found to be 25% of the seasonal cycle amplitude. Our study demonstrates the importance of the ATTO record to better understand the Amazon carbon cycle at various spatial and temporal scales.

Accurate Simulation of Both Sensitivity and Variability for Amazonian Photosynthesis: Is It Too Much to Ask?

Estimates of Amazon rainforest gross primary productivity (GPP) differ by a factor of 2 across a suite of three statistical and 18 process models. This wide spread contributes uncertainty to predictions of future climate. We compare the mean and variance of GPP from these models to that of GPP at six eddy covariance (EC) towers. Only one model's mean GPP across all sites falls within a 99% confidence interval for EC GPP, and only one model matches EC variance. The strength of model response to climate drivers is related to model ability to match the seasonal pattern of the EC GPP. Models with stronger seasonal swings in GPP have stronger responses to rain, light, and temperature than does EC GPP. The model to data comparison illustrates a trade-off inherent to deterministic models between accurate simulation of a mean (average) and accurate responsiveness to drivers. The trade-off exists because all deterministic models simplify processes and lack at least some consequential driver or interaction. If a model's sensitivities to included drivers and their interactions are accurate, then deterministically predicted outcomes have less variability than is realistic. If a GPP model has stronger responses to climate drivers than found in data, model predictions may match the observed variance and seasonal pattern but are likely to overpredict GPP response to climate change. High or realistic variability of model estimates relative to reference data indicate that the model is hypersensitive to one or more drivers.

Accounting for Transport Error in Inversions: An Urban Synthetic Data Experiment

We present and discuss the use of a high-dimensional computational method for atmospheric inversions that incorporates the space-time structure of transport and dispersion errors. In urban environments, transport and dispersion errors are largely the result of our inability to capture the true underlying transport of greenhouse gas (GHG) emissions to observational sites. Motivated by the impact of transport model error on estimates of fluxes of GHGs using in situ tower-based mole-fraction observations, we specifically address the need to characterize transport error structures in high-resolution large-scale inversion models. We do this using parametric covariance functions combined with shrinkage-based regularization methods within an Ensemble Transform Kalman Filter inversion setup. We devise a synthetic data experiment to compare the impact of transport and dispersion error component of the model-data mismatch covariance choices on flux retrievals and study the robustness of the method with respect to fewer observational constraints. We demonstrate the analysis in the context of inferring CO2 fluxes starting with a hypothesized prior in the Washington D.C. /Baltimore area constrained by a synthetic set of tower-based CO2 measurements within an observing system simulation experiment framework. This study demonstrates the ability of these simple covariance structures to substantially improve the estimation of fluxes over standard covariance models in flux estimation from urban regions.

Determination of Region of Influence Obtained by Aircraft Vertical Profiles Using the Density of Trajectories from the HYSPLIT Model

Aircraft atmospheric profiling is a valuable technique for determining greenhouse gas fluxes at regional scales (104–106 km2). Here, we describe a new, simple method for estimating the surface influence of air samples that uses backward trajectories based on the Lagrangian model Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT). We determined “regions of influence” on a quarterly basis between 2010 and 2018 for four aircraft vertical profile sites: SAN and ALF in the eastern Amazon, and RBA and TAB or TEF in the western Amazon. We evaluated regions of influence in terms of their relative sensitivity to areas inside and outside the Amazon and their total area inside the Amazon. Regions of influence varied by quarter and less so by year. In the first and fourth quarters, the contribution of the region of influence inside the Amazon was 83–93% for all sites, while in the second and third quarters, it was 57–75%. The interquarter differences are more evident in the eastern than in the western Amazon. Our analysis indicates that atmospheric profiles from the western sites are sensitive to 42–52.2% of the Amazon. In contrast, eastern Amazon sites are sensitive to only 10.9–25.3%. These results may help to spatially resolve the response of greenhouse gas emissions to climate variability over Amazon.

Systematic Orbital Geometry-Dependent Variations in Satellite Solar-Induced Fluorescence (SIF) Retrievals

While solar-induced fluorescence (SIF) shows promise as a remotely-sensed measurement directly related to photosynthesis, interpretation and validation of satellite-based SIF retrievals remains a challenge. SIF is influenced by the fraction of absorbed photosynthetically-active radiation at the canopy level that depends upon illumination geometry as well as the escape of SIF through the canopy that depends upon the viewing geometry. Several approaches to estimate the effects of sun-sensor geometry on satellite-based SIF have been proposed, and some have been implemented, most relying upon satellite reflectance measurements and/or other ancillary data sets. These approaches, designed to ultimately estimate intrinsic or physiological components of SIF related to photosynthesis, have not generally been applied globally to satellite measurements. Here, we examine in detail how SIF and related reflectance-based indices from wide swath polar orbiting satellites in low Earth orbit vary systematically due to the host satellite orbital characteristics. We compare SIF and reflectance-based parameters from the Global Ozone Mapping Experiment 2 (GOME-2) on the MetOp-B platform and from the TROPOspheric Monitoring Instrument (TROPOMI) on the Sentinel 5 Precursor satellite with a focus on high northern latitudes in summer where observations at similar geometries and local times occur. We show that GOME-2 and TROPOMI SIF observations agree nearly to within estimated uncertainties when they are compared at similar observing geometries. We show that the cross-track dependence of SIF normalized by PAR and related reflectance-based indices are highly correlated for dense canopies, but diverge substantially as the vegetation within a field-of-view becomes more sparse. This has implications for approaches that utilize reflectance measurements to help account for SIF geometrical dependences in satellite measurements. To further help interpret the GOME-2 and TROPOMI SIF observations, we simulated cross-track dependences of PAR normalized SIF and reflectance-based indices with the one dimensional Soil-Canopy Observation Photosynthesis and Energy fluxes (SCOPE) canopy radiative transfer model at sun–satellite geometries that occur across the wide swaths of these instruments and examine the geometrical dependencies of the various components (e.g., fraction of absorbed PAR, SIF yield, and escape of SIF from the canopy) of the observed SIF signal. The simulations show that most of the cross-track variations in SIF result from the escape of SIF through the scattering canopy and not the illumination.

A New Background Method for Greenhouse Gases Flux Calculation Based in Back-Trajectories Over the Amazon

The large amount of carbon stored in trees and soils of the Amazon rain forest is under pressure from land use as well as climate change. Therefore, various efforts to monitor greenhouse gas exchange between the Amazon forest and the atmosphere are now ongoing, including regular vertical profile (surface to 4.5 km) greenhouse gas measurements across the Amazon. These profile measurements can be used to calculate fluxes to and from the rain forest to the atmosphere at large spatial scales by considering the enhancement or depletion relative to the mole fraction of air entering the Amazon basin from the Atlantic, providing an important diagnostic of the state, changes and sensitivities of the forests. Previous studies have estimated greenhouse gas mole fractions of incoming air (‘background’) as a weighted mean of mole fractions measured at two background sites, Barbados (Northern Hemisphere) and Ascension (Southern hemisphere) in the Tropical Atlantic, where the weights were based on sulphur hexafluoride (SF6) measured locally (in the Amazon vertical profiles) and at the two background sites. However, this method requires the accuracy and precision of SF6 measurements to be significantly better than 0.1 parts per trillion (picomole mole−1), which is near the limit for the best SF6 measurements and assumes that there are no SF6 sources in the Amazon basin. We therefore present here an alternative method. Instead of using SF6, we use the geographical position of each air-mass back-trajectory when it intersects the limit connecting these two sites to estimate contributions from Barbados versus Ascension. We furthermore extend the approach to include an observation site further south, Cape Point, South Africa. We evaluate our method using CO2 vertical profile measurements at a coastal site in Brazil comparing with values obtained using this method where we find a high correlation (r2 = 0.77). Similarly, we obtain good agreement for CO2 background when comparing our results with those based on SF6, for the period 2010–2011 when the SF6 measurements had excellent precision and accuracy. We also found high correspondence between the methods for background values of CO, N2O and CH4. Finally, flux estimates based on our new method agree well with the CO2 flux estimates for 2010 and 2011 estimated using the SF6-based method. Together, our findings suggest that our trajectory-based method is a robust new way to derive background air concentrations for the purpose of greenhouse gas flux estimation using vertical profile data.

Stomatal optimization based on xylem hydraulics (SOX) improves land surface model simulation of vegetation responses to climate

Land surface models (LSMs) typically use empirical functions to represent vegetation responses to soil drought. These functions largely neglect recent advances in plant ecophysiology that link xylem hydraulic functioning with stomatal responses to climate. We developed an analytical stomatal optimization model based on xylem hydraulics (SOX) to predict plant responses to drought. Coupling SOX to the Joint UK Land Environment Simulator (JULES) LSM, we conducted a global evaluation of SOX against leaf- and ecosystem-level observations. SOX simulates leaf stomatal conductance responses to climate for woody plants more accurately and parsimoniously than the existing JULES stomatal conductance model. An ecosystem-level evaluation at 70 eddy flux sites shows that SOX decreases the sensitivity of gross primary productivity (GPP) to soil moisture, which improves the model agreement with observations and increases the predicted annual GPP by 30% in relation to JULES. SOX decreases JULES root-mean-square error in GPP by up to 45% in evergreen tropical forests, and can simulate realistic patterns of canopy water potential and soil water dynamics at the studied sites. SOX provides a parsimonious way to incorporate recent advances in plant hydraulics and optimality theory into LSMs, and an alternative to empirical stress factors.

Remote sensing of solar-induced chlorophyll fluorescence (SIF) in vegetation: 50 years of progress

Remote sensing of solar-induced chlorophyll fluorescence (SIF) is a rapidly advancing front in terrestrial vegetation science, with emerging capability in space-based methodologies and diverse application prospects. Although remote sensing of SIF - especially from space - is seen as a contemporary new specialty for terrestrial plants, it is founded upon a multi-decadal history of research, applications, and sensor developments in active and passive sensing of chlorophyll fluorescence. Current technical capabilities allow SIF to be measured across a range of biological, spatial, and temporal scales. As an optical signal, SIF may be assessed remotely using highly-resolved spectral sensors and state-of-the-art algorithms to distinguish the emission from reflected and/or scattered ambient light. Because the red to far-red SIF emission is detectable non-invasively, it may be sampled repeatedly to acquire spatio-temporally explicit information about photosynthetic light responses and steady-state behaviour in vegetation. Progress in this field is accelerating with innovative sensor developments, retrieval methods, and modelling advances. This review distills the historical and current developments spanning the last several decades. It highlights SIF heritage and complementarity within the broader field of fluorescence science, the maturation of physiological and radiative transfer modelling, SIF signal retrieval strategies, techniques for field and airborne sensing, advances in satellite-based systems, and applications of these capabilities in evaluation of photosynthesis and stress effects. Progress, challenges, and future directions are considered for this unique avenue of remote sensing.

Enhanced North American carbon uptake associated with El Niño

Long-term atmospheric CO₂ mole fraction and δ¹³CO₂ observations over North America document persistent responses to the El Niño-Southern Oscillation. We estimate these responses corresponded to 0.61 (0.45 to 0.79) PgC year^-1 more North American carbon uptake during El Niño than during La Niña between 2007 and 2015, partially offsetting increases of net tropical biosphere-to-atmosphere carbon flux around El Niño. Anomalies in derived North American net ecosystem exchange (NEE) display strong but opposite correlations with surface air temperature between seasons, while their correlation with water availability was more constant throughout the year, such that water availability is the dominant control on annual NEE variability over North America. These results suggest that increased water availability and favorable temperature conditions (warmer spring and cooler summer) caused enhanced carbon uptake over North America near and during El Niño.

Widespread reduction in sun-induced fluorescence from the Amazon during the 2015/2016 El Niño

The tropical carbon balance dominates year-to-year variations in the CO₂ exchange with the atmosphere through photosynthesis, respiration and fires. Because of its high correlation with gross primary productivity (GPP), observations of sun-induced fluorescence (SIF) are of great interest. We developed a new remotely sensed SIF product with improved signal-to-noise in the tropics, and use it here to quantify the impact of the 2015/2016 El Niño Amazon drought. We find that SIF was strongly suppressed over areas with anomalously high temperatures and decreased levels of water in the soil. SIF went below its climatological range starting from the end of the 2015 dry season (October) and returned to normal levels by February 2016 when atmospheric conditions returned to normal, but well before the end of anomalously low precipitation that persisted through June 2016. Impacts were not uniform across the Amazon basin, with the eastern part experiencing much larger (10-15%) SIF reductions than the western part of the basin (2-5%). We estimate the integrated loss of GPP relative to eight previous years to be 0.34-0.48 PgC in the three-month period October-November-December 2015.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Changes in surface hydrology, soil moisture and gross primary production in the Amazon during the 2015/2016 El Niño

The 2015/2016 El Niño event caused severe changes in precipitation across the tropics. This impacted surface hydrology, such as river run-off and soil moisture availability, thereby triggering reductions in gross primary production (GPP). Many biosphere models lack the detailed hydrological component required to accurately quantify anomalies in surface hydrology and GPP during droughts in tropical regions. Here, we take the novel approach of coupling the biosphere model SiBCASA with the advanced hydrological model PCR-GLOBWB to attempt such a quantification across the Amazon basin during the drought in 2015/2016. We calculate 30–40% reduced river discharge in the Amazon starting in October 2015, lagging behind the precipitation anomaly by approximately one month and in good agreement with river gauge observations. Soil moisture shows distinctly asymmetrical spatial anomalies with large reductions across the north-eastern part of the basin, which persisted into the following dry season. This added to drought stress in vegetation, already present owing to vapour pressure deficits at the leaf, resulting in a loss of GPP of 0.95 (0.69 to 1.20) PgC between October 2015 and March 2016 compared with the 2007–2014 average. Only 11% (10–12%) of the reduction in GPP was found in the (wetter) north-western part of the basin, whereas the north-eastern and southern regions were affected more strongly, with 56% (54–56%) and 33% (31–33%) of the total, respectively. Uncertainty on this anomaly mostly reflects the unknown rooting depths of vegetation.

This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.

Carbon dioxide and methane measurements from the Los Angeles Megacity Carbon Project - Part 1: calibration, urban enhancements, and uncertainty estimates

We report continuous surface observations of carbon dioxide (CO₂) and methane (CH₄) from the Los Angeles (LA) Megacity Carbon Project during 2015. We devised a calibration strategy, methods for selection of background air masses, calculation of urban enhancements, and a detailed algorithm for estimating uncertainties in urban-scale CO₂ and CH₄ measurements. These methods are essential for understanding carbon fluxes from the LA megacity and other complex urban environments globally. We estimate background mole fractions entering LA using observations from four "extra-urban" sites including two "marine" sites located south of LA in La Jolla (LJO) and offshore on San Clemente Island (SCI), one "continental" site located in Victorville (VIC), in the high desert northeast of LA, and one "continental/mid-troposphere" site located on Mount Wilson (MWO) in the San Gabriel Mountains. We find that a local marine background can be established to within ~1 ppm CO₂ and ~10 ppb CH₄ using these local measurement sites. Overall, atmospheric carbon dioxide and methane levels are highly variable across Los Angeles. "Urban" and "suburban" sites show moderate to large CO₂ and CH₄ enhancements relative to a marine background estimate. The USC (University of Southern California) site near downtown LA exhibits median hourly enhancements of ~20 ppm CO₂ and ~150 ppb CH₄ during 2015 as well as ~15 ppm CO₂ and ~80 ppb CH₄ during mid-afternoon hours (12:00-16:00 LT, local time), which is the typical period of focus for flux inversions. The estimated measurement uncertainty is typically better than 0.1 ppm CO₂ and 1 ppb CH₄ based on the repeated standard gas measurements from the LA sites during the last 2 years, similar to Andrews et al. (2014). The largest component of the measurement uncertainty is due to the single-point calibration method; however, the uncertainty in the background mole fraction is much larger than the measurement uncertainty. The background uncertainty for the marine background estimate is ~10 and ~15 % of the median mid-afternoon enhancement near downtown LA for CO₂ and CH₄, respectively. Overall, analytical and background uncertainties are small relative to the local CO₂ and CH₄ enhancements; however, our results suggest that reducing the uncertainty to less than 5 % of the median mid-afternoon enhancement will require detailed assessment of the impact of meteorology on background conditions.

Carbon dioxide and methane measurements from the Los Angeles Megacity Carbon Project - Part 1: calibration, urban enhancements, and uncertainty estimates

We report continuous surface observations of carbon dioxide (CO2) and methane (CH4) from the Los Angeles (LA) Megacity Carbon Project during 2015. We devised a calibration strategy, methods for selection of background air masses, calculation of urban enhancements, and a detailed algorithm for estimating uncertainties in urban-scale CO2 and CH4 measurements. These methods are essential for understanding carbon fluxes from the LA megacity and other complex urban environments globally. We estimate background mole fractions entering LA using observations from four "extra-urban" sites including two "marine" sites located south of LA in La Jolla (LJO) and offshore on San Clemente Island (SCI), one "continental" site located in Victorville (VIC), in the high desert northeast of LA, and one "continental/mid-troposphere" site located on Mount Wilson (MWO) in the San Gabriel Mountains. We find that a local marine background can be established to within ~1 ppm CO2 and ~10 ppb CH4 using these local measurement sites. Overall, atmospheric carbon dioxide and methane levels are highly variable across Los Angeles. "Urban" and "suburban" sites show moderate to large CO2 and CH4 enhancements relative to a marine background estimate. The USC (University of Southern California) site near downtown LA exhibits median hourly enhancements of ~20 ppm CO2 and ~150 ppb CH4 during 2015 as well as ~15 ppm CO2 and ~80 ppb CH4 during mid-afternoon hours (12:00-16:00 LT, local time), which is the typical period of focus for flux inversions. The estimated measurement uncertainty is typically better than 0.1 ppm CO2 and 1 ppb CH4 based on the repeated standard gas measurements from the LA sites during the last 2 years, similar to Andrews et al. (2014). The largest component of the measurement uncertainty is due to the single-point calibration method; however, the uncertainty in the background mole fraction is much larger than the measurement uncertainty. The background uncertainty for the marine background estimate is ~10 and ~15 % of the median mid-afternoon enhancement near downtown LA for CO2 and CH4, respectively. Overall, analytical and background uncertainties are small relative to the local CO2 and CH4 enhancements; however, our results suggest that reducing the uncertainty to less than 5 % of the median mid-afternoon enhancement will require detailed assessment of the impact of meteorology on background conditions.