Sixteen years of MOPITT satellite data strongly constrain Amazon CO fire emissions

Despite consensus on the overall downward trend in Amazon forest loss in the previous decade, estimates of yearly carbon emissions from deforestation still vary widely. Estimated carbon emissions are currently often based on data from local logging activity reports, changes in remotely sensed biomass as well as remote detection of fire hotspots, and burned area. Here, we use sixteen years of satellite-derived carbon monoxide (CO) columns to constrain fire CO emissions from the Amazon basin between 2003 and 2018. Through data assimilation, we produce 3-daily maps of fire CO emissions over the Amazon that we verified to be consistent with a long-term monitoring program of aircraft CO profiles over five sites in the Amazon. Our new product independently confirms a long-term decrease of 54 % in deforestation-related CO emissions over the study period. Interannual variability is large, with known anomalously dry years showing a more than fourfold increase in basin-wide fire emissions. At the level of individual Brazilian states, we find that both soil moisture anomalies and human ignitions determine fire activity, suggesting that future carbon release from fires depends on drought intensity as much as on continued forest protection. Our study shows that the atmospheric composition perspective on deforestation is a valuable additional monitoring instrument that complements existing bottom-up and remote sensing methods for land-use change. Extension of such a perspective to an operational framework is timely considering the observed increased fire intensity in the Amazon basin in 2019&ndash;2021.</p

Sixteen years of MOPITT satellite data strongly constrain Amazon CO fire emissions

Despite the consensus on the overall downward trend in Amazon forest loss in the previous decade, estimates of yearly carbon emissions from deforestation still vary widely. Estimated carbon emissions are currently often based on data from local logging activity reports, changes in remotely sensed biomass, and remote detection of fire hotspots and burned area. Here, we use 16 years of satellite-derived carbon monoxide (CO) columns to constrain fire CO emissions from the Amazon Basin between 2003 and 2018. Through data assimilation, we produce 3 d average maps of fire CO emissions over the Amazon, which we verified to be consistent with a long-term monitoring programme of aircraft CO profiles over five sites in the Amazon. Our new product independently confirms a long-term decrease of 54 % in deforestation-related CO emissions over the study period. Interannual variability is large, with known anomalously dry years showing a more than 4-fold increase in basin-wide fire emissions relative to wet years. At the level of individual Brazilian states, we find that both soil moisture anomalies and human ignitions determine fire activity, suggesting that future carbon release from fires depends on drought intensity as much as on continued forest protection. Our study shows that the atmospheric composition perspective on deforestation is a valuable additional monitoring instrument that complements existing bottom-up and remote sensing methods for land-use change. Extension of such a perspective to an operational framework is timely considering the observed increased fire intensity in the Amazon Basin between 2019 and 2021

Glycomic analysis of life stages of the human parasite Schistosoma mansoni reveals developmental expression profiles of functional and antigenic glycan motifs

Contains fulltext : 155377.pdf (publisher's version ) (Open Access)Glycans present on glycoproteins and glycolipids of the major human parasite Schistosoma mansoni induce innate as well as adaptive immune responses in the host. To be able to study the molecular characteristics of schistosome infections it is therefore required to determine the expression profiles of glycans and antigenic glycan-motifs during a range of critical stages of the complex schistosome lifecycle. We performed a longitudinal profiling study covering schistosome glycosylation throughout worm- and egg-development using a mass spectrometry-based glycomics approach. Our study revealed that during worm development N-glycans with Galbeta1-4(Fucalpha1-3)GlcNAc (LeX) and core-xylose motifs were rapidly lost after cercariae to schistosomula transformation, whereas GalNAcbeta1-4GlcNAc (LDN)-motifs gradually became abundant and predominated in adult worms. LeX-motifs were present on glycolipids up to 2 weeks of schistosomula development, whereas glycolipids with mono- and multifucosylated LDN-motifs remained present up to the adult worm stage. In contrast, expression of complex O-glycans diminished to undetectable levels within days after transformation. During egg development, a rich diversity of N-glycans with fucosylated motifs was expressed, but with alpha3-core fucose and a high degree of multifucosylated antennae only in mature eggs and miracidia. N-glycan antennae were exclusively LDN-based in miracidia. O-glycans in the mature eggs were also diverse and contained LeX- and multifucosylated LDN, but none of these were associated with miracidia in which we detected only the Galbeta1-3(Galbeta1-6)GalNAc core glycan. Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. Lipid glycans with multifucosylated GlcNAc repeats were present throughout egg development, but with the longer highly fucosylated stretches enriched in mature eggs and miracidia. This global analysis of the developing schistosome's glycome provides new insights into how stage-specifically expressed glycans may contribute to different aspects of schistosome-host interactions

Improving estimates of the atmospheric oxidative capacity and Amazon fire emissions

The composition of the air outside, the atmosphere, is the end-result of complex chemistry, dynamical transport and emissions of gases. Anthropogenic activity contributes to a rapidly changing composition of the atmosphere, often with adverse effects: air quality issues, global warming and depletion of stratospheric ozone are some of the most complex and impactful problems that society must face. Many gases are removed from the atmosphere through the process of oxidation and the atmosphere’s primary oxidant is the hydroxyl radical (OH). Gases removed by OH include the potent greenhouse gas methane (CH4) and urban pollutants such as CO and NOX. Therefore, the oxidation capacity of the atmosphere, as determined by the "cleansing-agent” OH, is an important quantity that is central to this thesis.Since OH is very reactive, it has an atmospheric lifetime of seconds and a low atmospheric abundance. This makes it difficult to measure OH concentrations directly and impossible to extrapolate those measurements to larger scales. Consequently, despite the importance and omnipresence of OH, there are still open questions concerning its distribution around the globe and how this distribution has varied over past decades. For example, we know that OH concentrations are highest in the tropics, but the degree of hemispheric symmetry is uncertain. Such uncertainties limit our ability to interpret atmospheric budgets of a variety of pollutants, such as that of CH4.In Chapters 2 and 3, we investigate indirect observational constraints on the atmospheric oxidative capacity using the trace gas methyl chloroform (MCF). MCF is an anthropogenically produced gas, that was used mainly as a solvent in paints and degreasers. The production of MCF was phased out in the Montreal protocol and subsequent amendments (1987-1999), because its emissions harm the stratospheric ozone layer. Fortuitously, MCF is removed from the atmosphere mainly through oxidation by OH, resulting in an atmospheric lifetime of 5 to 6 years. Therefore, the production phase-out resulted in a rapid atmospheric decline in MCF abundance, and variations in this rate of decline provide a proxy for large-scale OH variations.The atmospheric decline of MCF has been monitored mainly from remote surface sites that represent the background atmosphere. Comprehensive interpretation of such observations requires the use of atmospheric models. Forward models simulate emissions of gases into the atmosphere, and their subsequent transport and chemistry. Such models can vary in complexity from a global one-box model to a complex 3D transport mode. In addition to forward models, we develop and use inverse models, which use observations of a gas such as MCF to estimate, for example, those MCF emissions and OH variations.In Chapter 2, we use a two-box model inversion of the troposphere to explore the constraints that MCF surface observations place on global-scale OH variations over the 1994-2014 period. The two-box model set-up incorporates important aspects of the real atmosphere, because the atmosphere is mixed significantly faster within hemispheres than between them and because most anthropogenic emissions enter the atmosphere in the Northern Hemisphere. Therefore, a similar set-up was applied to the MCF-OH problem in two previous studies. However, we find that the two-box model approach is susceptible to biases that we quantify with a 3D transport model.Firstly, we find, that the interhemispheric exchange rate that is used in two-box models is not only reflective of physical transport changes, but is also highly dependent on a tracer's distribution within hemispheres. The distribution of MCF has changed strongly over the 1994-2014 period that we investigate, due to the rapid drop in its emissions. We find that this change resulted in large, multi-annual variations in the interhemispheric exchange of MCF, that are very different from the variations derived for CH4. The same redistribution of MCF drove a rapid decrease in loss of tropospheric MCF to the stratosphere by up to 70%, as well as a shift in the effective interhemispheric OH ratio that MCF is exposed to.To test the impact of the identified biases on the OH variations and CH4 emissions derived in a tropospheric two-box model inversion, we perform two sets of inversions: one in which we correct for the biases, and one in which we do not. Notably, we find that the inversion that includes bias corrections produces OH variations that show a positive trend, while the standard inversion does not. However, we also find that the uncertainties driven by other two-box parameters that cannot be constrained from a 3D model simulation, for example related to MCF emissions, remain large. The implication for the CH4 budget is that it remains difficult to attribute variations in the atmospheric CH4 abundance to either emission or OH changes.In Chapter 3, we investigate how MCF constraints on OH change if we move the inversion to the 3D transport model TM5. In a TM5-4DVAR inversion, we can include observed MCF gradients within hemispheres and the tropical maximum in OH: examples of advantages over the two-box model approach. We co-optimize MCF emissions and the latitudinal distribution of OH over the 1998--2018 period, and we find that small interannual variations in OH (<3%) without a longterm trend already result in a good match with NOAA surface observations at most sites. The timing and sign of interannual OH variations are found to be robust with respect to the choice of prior OH and MCF emission distribution, while the amplitude of the variations depends on the degree of convergence and, relatedly, on assumed uncertainties in observations.However, we also find that, to reproduce observed intrahemispheric gradients of MCF, large adjustments in the latitudinal OH distribution are required, the amplitude of which we consider to be physically unrealistic. From a series of sensitivity tests we conclude that the most likely explanation for these MCF gradients includes a changed ocean flux. Specifically, while the ocean is principally a sink of MCF, earlier work has hypothesized that, in response to the emission drop, oceans at high latitudes have become a source of MCF, which fits the sign and approximate magnitude of the intrahemispheric bias we find for MCF. Positively, our study presents the first evidence from MCF surface observations for an ocean source. Negatively, the existence of an uncertain ocean source further complicates the derivation of OH variations from MCF observations. However, we consider that the most likely driver of interannual variations in MCF is still its OH oxidation sink. Therefore, we conclude that the reference twenty-year timeseries of OH that we have derived is worth including in future work, for example in global CH4 inversions.In Chapter 4, we move away from a global perspective to zoom in on one of Earth's most precious ecosystems: the Amazon basin. The Amazon is home to the world's largest rainforests and to a rich biodiversity, but large-scale deforestation and agricultural expansion threaten the ability of this ecosystem to survive in a rapidly changing climate. Every year, during the local dry season, fires burn through the Amazon forests and savanna. It is crucial to understand and monitor these fires, because they are driven by direct, local anthropogenic activity, but their extent is also sensitive to drought intensity and frequency that might increase due to climate change. Fires emit vast amounts of pollutants into the atmosphere, and we use satellite observations of one such trace gas, CO, to constrain fire emissions over South America. Specifically, we use the TM5-4DVAR inverse system, together with satellite-observed CO columns of the Measurements of Pollution in the Troposphere (MOPITT) instrument, to optimize reported fire emissions of CO (from the Global Fire Assimilation System; GFAS) over the 2003--2018 period.MOPITT CO columns over South America display strong seasonality and interannual variations that are matched in the optimized CO emissions. Additionally, a simulation with optimized fire emissions better reproduces independent aircraft profiles, which were sampled over five sites in the Brazilian Amazon, compared to a simulation with GFAS emissions. This confirms the skill of the inverse system to estimate emissions at sub-Amazon scales. Similarly, we find that we can firmly constrain emissions also at the level of individual Brazilian states, and interannual variations in emissions at state-level correlate well with local soil moisture anomalies. Superimposed on the interannual variations, we find that emissions have decreased between 2003 and 2012, and stabilized afterward. The decrease is especially strong over forest-covered areas (55%), and the timing and magnitude of this decrease is confirmed in deforestation rates reported by INPE. Optimized emissions are additionally found to be robust with respect to the input fields: for example, inversions based on a climatological fire prior retrieve largely the same interannual variations, even at state-level, as the standard inversions.These results demonstrate that our inverse system provides strong constraints on Amazon fire emissions that are a product of local anthropogenic activity and natural variability. In principle, our approach can straightforwardly be adapted into an operational system that would be a valuable addition to the existing palette of fire monitoring systems. Due to the integrated signal that CO observations provide, such a system will be less hampered by cloud occurrence or missed understory fires than existing systems that are based on land remote sensing. Moreover, constraints from CO can help better quantify the carbon release during fires

The isotopic composition of CO in vehicle exhaust

We investigated the isotopic composition of CO in the exhaust of individual vehicles. Additionally, the CO2 isotopes, and the CO:CO2, CH4:CO2 and H2:CO gas ratios were measured. This was done under idling and revving conditions, and for three vehicles in a full driving cycle on a testbench. The spread in the results, even for a single vehicle, was large: for δ13C in CO ∼ −60 to 0‰, for δ18O in CO ∼ +10 to +35‰, and for all gas ratios several orders of magnitude. The results show an increase in the spread of isotopic values for CO compared to previous studies, suggesting that increasing complexity of emission control in vehicles might be reflected in the isotopic composition. When including all samples, we find a weighted mean for the δ13C and δ18O in CO of −28.7 ± 0.5‰ and +24.8 ± 0.3‰ respectively. This result is dominated by cold petrol vehicles. Diesel vehicles behaved as a distinct group, with CO enriched in 13C and depleted in 18O, compared to petrol vehicles. For the H2:CO ratio of all vehicles, we found a value of 0.71 ± 0.31 ppb:ppb. The CO:CO2 ratio, with a mean of 19.4 ± 6.8 ppb:ppm, and the CH4:CO2 ratio, with a mean of 0.26 ± 0.05 ppb:ppm, are both higher than recent literature indicates. This is likely because our sampling distribution was biased towards cold vehicles, and therefore towards higher emission situations. The CH4:CO2 ratio was found to behave similarly to the CO:CO2 ratio, suggesting that the processes affecting CO and CH4 are similar. The δ13C values in CO2 were close to the expected δ13C in fuel, with no significant difference between petrol and diesel vehicles. The δ18O values in CO2 for petrol vehicles covered a range of 20–35‰, similar to the δ18O of CO. The δ18O values in CO2 for diesel vehicles were close to the δ18O in atmospheric oxygen. A set of polluted atmospheric samples, taken near a highway and inside parking garages, showed an isotopic signature of CO and a H2:CO ratio that were similar the high emitters in the individual vehicle measurements, with no significant differences between parking garage and highway samples. This suggests that in both environments, which are dominated by different driving conditions, the CO emissions from high emitters (either a few high emission vehicles, or many vehicles with brief bursts of high emissions) dominate the total traffic emissions

A three-dimensional-model inversion of methyl chloroform to constrain the atmospheric oxidative capacity

Variations in the atmospheric oxidative capacity, largely determined by variations in the hydroxyl radical (OH), form a key uncertainty in many greenhouse and other pollutant budgets, such as that of methane (CH4). Methyl chloroform (MCF) is an often-adopted tracer to indirectly put observational constraints on large-scale variations in OH.We investigated the budget of MCF in a 4DVAR inversion using the atmospheric transport model TM5, for the period 1998-2018, with the objective to derive information on large-scale, interannual variations in atmospheric OH concentrations. While our main inversion did not fully converge, we did derive interannual variations in the global oxidation of MCF that bring simulated mole fractions of MCF within 1 %-2% of the assimilated observations from the NOAA-GMD surface network at most sites. Additionally, the posterior simulations better reproduce aircraft observations used for independent validation compared to the prior simulations. The derived OH variations showed robustness with respect to the prior MCF emissions and the prior OH distribution over the 1998 to 2008 period. Although we find a rapid 8% increase in global mean OH concentrations between 2010 and 2012 that quickly declines afterwards, the derived interannual variations were typically small (<3 %/yr), with no significant long-term trend in global mean OH concentrations. The inverse system found strong adjustments to the latitudinal distribution of OH, relative to widely used prior distributions, with systematic increases in tropical and decreases in extra-tropical OH concentrations (both up to 30 %). These spatial adjustments were driven by intrahemispheric biases in simulated MCF mole fractions, which have not been identified in previous studies. Given the large amplitude of these adjustments, which exceeds spread between literature estimates, and a residual bias in the MCF intrahemispheric gradients, we suggest a reversal in the extratropical ocean sink of MCF in response to declining atmospheric MCF abundance (as hypothesized inWennberg et al., 2004). This ocean source provides a more realistic explanation for the biases, possibly complementary to adjustments in the OH distribution. We identified significant added value in the use of a 3D transport model, since it implicitly accounts for variable transport and optimizes the observed spatial gradients of MCF, which is not possible in simpler models. However, we also found a trade-off in computational expense and convergence problems. Despite these convergence problems, the derived OH variations do result in an improved match with MCF observations relative to an interannually repeating prior for OH. Therefore, we consider that variations in OH derived from MCF inversions with 3D models can add value to budget studies of long-lived gases like CH4. </p

Constraints and biases in a tropospheric two-box model of OH

The hydroxyl radical (OH) is the main atmospheric oxidant and the primary sink of the greenhouse gas CH4. In an attempt to constrain atmospheric levels of OH, two recent studies combined a tropospheric two-box model with hemispheric-mean observations of methyl chloroform (MCF) and CH4. These studies reached different conclusions concerning the most likely explanation of the renewed CH4 growth rate, which reflects the uncertain and underdetermined nature of the problem. Here, we investigated how the use of a tropospheric two-box model can affect the derived constraints on OH due to simplifying assumptions inherent to a two-box model. To this end, we derived species- A nd timedependent quantities from a full 3-D transport model to drive two-box model simulations. Furthermore, we quantified differences between the 3-D simulated tropospheric burden and the burden seen by the surface measurement network of the National Oceanic and Atmospheric Administration (NOAA). Compared to commonly used parameters in two-box models, we found significant deviations in the magnitude and timedependence of the interhemispheric exchange rate, exposure to OH, and stratospheric loss rate. For MCF these deviations can be large due to changes in the balance of its sources and sinks over time. We also found that changes in the yearly averaged tropospheric burden of CH4 and MCF can be obtained within 0.96 ppb yr-1 and 0.14%yr-1 by the NOAA surface network, but that substantial systematic biases exist in the interhemispheric mixing ratio gradients that are input to two-box model inversions. To investigate the impact of the identified biases on constraints on OH, we accounted for these biases in a two-box model inversion of MCF and CH4. We found that the sensitivity of interannual OH anomalies to the biases is modest (1 %-2 %), relative to the uncertainties on derived OH (3 %-4 %). However, in an inversion where we implemented all four bias corrections simultaneously, we found a shift to a positive trend in OH concentrations over the 1994-2015 period, compared to the standard inversion. Moreover, the absolute magnitude of derived global mean OH, and by extent, that of global CH4 emissions, was affected much more strongly by the bias corrections than their anomalies (∼ 10 %). Through our analysis, we identified and quantified limitations in the two-box model approach as well as an opportunity for full 3-D simulations to address these limitations. However, we also found that this derivation is an extensive and species-dependent exercise and that the biases were not always entirely resolvable. In future attempts to improve constraints on the atmospheric oxidative capacity through the use of simple models, a crucial first step is to consider and account for biases similar to those we have identified for the two-box model.</p