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Isoprene is a chemical compound emitted naturally by soil, microorganisms, plants, and animals into the atmosphere. But plants are the largest emission source, and the amount of emission depends on plant species, weather conditions, and environmental conditions, including exposure to environmental stresses such as heat and drought. Isoprene is very reactive in the atmosphere and is involved in atmospheric physicochemical processes that can impact atmospheric chemistry, air quality, and regional climate. Quantification and understanding of the atmospheric processes influenced by isoprene result from a combination of observational experiments and estimates obtained from computational models. However, only a few long-term observational experiments have been conducted in the largest source of isoprene to the global atmosphere – the Amazon rainforest, and there are still uncertainties in the model estimates. Recent experiments have also shown that the models have greater uncertainty when estimating intra- and inter-annual variations in isoprene. This study aimed to improve our understanding of isoprene emission from a central Amazonian site by considering biological and environmental factors influencing emission on intra- and interannual time scales. By combining observational datasets, we adapted a widely used computational model of isoprene emission to observed conditions in the field. Our observations indicated that isoprene emission was not as high as the model estimated when the forest experienced environmental stress, such as heat and drought, in the 2015 El-niño year. In addition, observations revealed that the model performed well when diurnal variations were analyzed but not when long-term variations occurred. The performance for estimating intra- and inter-annual isoprene emission improved when the model was modified on two biological factors – (i) the amount of different leaf ages throughout the year and (ii) the emission rates of these different leaf ages. This shows that isoprene emission estimates can be improved when biological processes are mechanistically incorporated into the model.

Isoprene emissions are a key component in biosphere–atmosphere interactions, and the most significant global source is the Amazon rainforest. However, intra- and interannual variations in biological and environmental factors that regulate isoprene emission from Amazonia are not well understood and, thereby, are poorly represented in models. Here, with datasets covering several years of measurements at the Amazon Tall Tower Observatory (ATTO) in central Amazonia, Brazil, we (1) quantified canopy profiles of isoprene mixing ratios across seasons of normal and anomalous years and related them to the main drivers of isoprene emission – solar radiation, temperature, and leaf phenology; (2) evaluated the effect of leaf age on the magnitude of the isoprene emission factor (Es) from different tree species and scaled up to canopy with intra- and interannual leaf age distribution derived by a phenocam; and (3) adapted the leaf age algorithm from the Model of Emissions of Gases and Aerosols from Nature (MEGAN) with observed changes in Es across leaf ages. Our results showed that the variability in isoprene mixing ratios was higher between seasons (max during the dry-to-wet transition seasons) than between years, with values from the extreme 2015 El Niño year not significantly higher than in normal years. In addition, model runs considering in situ observations of canopy Es and the modification on the leaf age algorithm with leaf-level observations of Es presented considerable improvements in the simulated isoprene flux. This shows that MEGAN estimates of isoprene emission can be improved when biological processes are mechanistically incorporated into the model.

The campaign Chemistry of the Atmosphere Field Experiment (CAFE) Brazil was conducted in the Amazon rainforest in December 2022 and January 2023 to study new particle formation in the outflow of convective systems over the Amazon rainforest. In the framework of this campaign, photochemical and aerosol processes in the tropical troposphere were investigated at different altitudes from the boundary layer up to 14 km using the High Altitude and Long Range Research Aircraft (HALO).The HydrOxyl Radical measurement Unit based on fluorescence Spectroscopy (HORUS) measures the OH and HO2 abundances as a highly relevant tracer for photochemical and aerosol processes in the tropical troposphere and new particle formation. The Hydroxyl radical (OH) oxidizes trace gases transported by convective systems from the boundary layer into the upper troposphere, leading to the formation of condensable matter. Contrasting conditions were measured, from pristine rainforest to polluted biomass burning and pollution conditions, and the occurrence of HOx during the day and nighttime in the outflow of electrified and non-electrified convective systems.The first results of these measurements will be presented, providing unique insights into the air chemistry and lifecycle of aerosols and clouds in the Amazon rainforest.

Hydroxyl radicals are the most predominant daytime initiator for atmospheric oxidation processes. Due to the COVID -19 pandemic, there was a considerable reduction in emissions from industry and all means of transportation during spring 2020. The main objective of the BLUESKY campaign is to understand the effect of these reduced emissions on atmospheric composition such as trace gases, aerosols, and cloud properties. OH and HO2 were measured with HORUS (HydrOxyl Radical measurement Unit based on fluorescence Spectroscopy), during eight research flights from the boundary layer up to 14 km. Here we present the impact of reduced aircraft emissions and the meteorological situation on the HOx Chemistry in the upper troposphere over Europe during the COVID-19 lockdown. We contrast the findings during BLUESKY with results from previous campaigns and analyze the occurrence of HOx during daytime in the outflow of electrified and non-electrified convective systems.

The atmospheric oxidation of biogenic volatile organic compounds (BVOC) by OH radicals over tropical rainforests impacts local particle production and the lifetime of globally distributed harmful and radiatively active gases. For the pristine Amazon rainforest during the dry season, we empirically determined the diurnal OH radical variability at the forest-atmosphere interface region between 80 and 325m from 07:00 to 15:00 LT using BVOC measurements. A dynamic time warping approach was applied showing that median averaged transport times between 80 m to 325 m decrease from 105 to 15 minutes over this time period. The inferred OH concentrations show evidence for an early morning OH peak (07:00–08:00 LT) and an OH maximum (13:00–14:00LT) reaching 1x106 ± 1.1x106 molecules cm− 3 controlled by the coupling between BVOC emission fluxes, convective turbulence, air chemistry and photolysis rates. The results were evaluated against a turbulence resolving transport (DALES), a regional scale (WRF-Chem) and a global (EMAC) atmospheric chemistry model.

Observations of the vertical structure of the turbulent flow in different stability regimes above and within the Amazon Forest at the Amazon Tall Tower Observatory (ATTO) site are presented. The shear length scale at the canopy top together with the coherent turbulent structures time and separation length scale were evaluated to determine influence of stability on the inception and development of the roughness sublayer. Five stability regimes were identified. The definition of an intense table regime allowed the identification of a peculiar condition characterized by low-wind and weak coherent structures confined close to the canopy top and producing negligible transport. Submeso motions dominate the flow dynamics in this regime both above and inside the roughness sublayer.The shear length scale increases with decreasing stability, presenting two asymptotes for large unstable and stable stratification and a linear behaviour close to neutral stratification. The coherent structure time and length scales are detected using an original method based on the autocorrelation functions of 5-min subsets of turbulent quantities. The vertical time scale is larger in neutral conditions and decreases for both increasing and decreasing stability, while the separation length scale at the canopy top presents a linear dependence on the shear length scale, whose slope is maximum in neutral conditions and decreases departing from neutrality. A new parameterization describing the dependence of the coherent eddies’ separation length scale on the h/L stability parameter is presented.

A central constituent of the ATTO project is the deployment of an array of sonic anemometers to measure vertical profiles of means and second-order moments of the wind velocity vector. The two instruments used are the Campbell Scientific Instruments CSAT-3B and the Thies Ultrasonic Anemometer 3D. The accuracy of the vertical profiles of turbulent quantities critically depensds on an absence of bias between the measurement levels; however, dedicated intercomparisons of the sonic anemometers used in ATTO have not been previously performed. The main objective of the experiment was to check how close the sonic anemometers designated to be installed respond to the same atmospheric conditions, and to develop confidence in interpreting the measured data.

Observational data from two field campaigns in the Amazon forest were used to study the vertical structure of turbulence above the forest. The analysis was performed using the reduced turbulent kinetic energy (TKE) budget and its associated two-dimensional phase space. Results revealed the existence of two regions within the roughness sublayer in which the TKE budget cannot be explained by the canonical flat-terrain TKE budgets in the canopy roughness sublayer or in the lower portion of the convective ABL. Data analysis also suggested that deviations from horizontal homogeneity have a large contribution to the TKE budget. Results from LES of a model canopy over idealized topography presented similar features, leading to the conclusion that flow distortions caused by topography are responsible for the observed features in the TKE budget. These results support the conclusion that the boundary layer above the Amazon forest is strongly impacted by the gentle topography underneath.

Observations of the vertical structure of the turbulent flow in different stability regimes above and within the Amazon Forest at the Amazon Tall Tower Observatory (ATTO) site have been presented in Part I. Here, the influence of stability on the inception and development of coherent structures is investigated. According to the mixing-layer analogy the coherent vortices that dominate the turbulent flows at the canopy-atmosphere interface are generated by hydrodynamical instabilities triggered by an inflection in the vertical profile of the mean wind speed at or near the canopy top. The coherent motions time, Tpeak and separation length scale, ?, depend on the shear length scale, Ls, close to the canopy top. The present analysis studies the characteristics of Ls, Tpeak and ? in the five stability regimes defined in Part I. The behaviour of Ls with stability is evaluated and parameterized. Ls increases with decreasing stability, presenting two asymptotes for large unstable and stable stratification and a linear behaviour close to neutral stratification. Coherent structures and their timescale are detected with an original method based on the autocorrelation functions of 5-min subsets of turbulent quantities. The vertical time scale is larger in neutral conditions and decreases for both increasing and decreasing stability. At the canopy top the separation length scale presents a linear dependence on Ls, whose slope is maximum in neutral conditions and decreases departing from neutrality. An original parameterization of the dependence of this slope on h/L, where h is the canopy height and L is the Obukhov length, is shown. Combining the parameterizations, the dependence of the separation length scale is finally presented. ? has a maximum for slightly unstable conditions, linearly decreases towards neutral and weakly stable stratifications and then it tends to zero for very intense unstable and stable stratifications.

Cryptogamic organisms such as bryophytes and lichens cover most surfaces within tropical forests, yet their impact on the emission of biogenic volatile organic compounds is unknown. These compounds can strongly influence atmospheric oxidant levels as well as secondary organic aerosol concentrations, and forest canopy leaves have been considered the dominant source of these emissions. Here we present cuvette flux measurements, made in the Amazon rainforest between 2016–2018, and show that common bryophytes emit large quantities of highly reactive sesquiterpenoids and that widespread lichens strongly uptake atmospheric oxidation products. A spatial upscaling approach revealed that cryptogamic organisms emit sesquiterpenoids in quantities comparable to current canopy attributed estimates, and take up atmospheric oxidation products at rates comparable to hydroxyl radical chemistry. We conclude that cryptogamic organisms play an important and hitherto overlooked role in atmospheric chemistry above and within tropical rainforests.

Nocturnal turbulent kinetic energy (TKE) and fluxes of energy, CO2 and O3 between the Amazon forest and the atmosphere are evaluated for a 20-day campaign at the Amazon Tall Tower Observatory (ATTO) site. The distinction of these quantities between fully turbulent (weakly stable) and intermittent (very stable) nights is discussed. Spectral analysis indicates that low-frequency, nonturbulent fluctuations are responsible for a large portion of the variability observed on intermittent nights. In these conditions, the low-frequency exchange may dominate over the turbulent transfer. In particular, we show that within the canopy most of the exchange of CO2 and H2O happens on temporal scales longer than 100 s. At 80 m, on the other hand, the turbulent fluxes are almost absent in such very stable conditions, suggesting a boundary layer shallower than 80 m. The relationship between TKE and mean winds shows that the stable boundary layer switches from the very stable to the weakly stable regime during intermittent bursts of turbulence. In general, fluxes estimated with long temporal windows that account for low-frequency effects are more dependent on the stability over a deeper layer above the forest than they are on the stability between the top of the canopy and its interior, suggesting that low-frequency processes are controlled over a deeper layer above the forest. Made available in DSpace on 2018-05-19T00:37:32Z (GMT). No. of bitstreams: 1 OliveiraACP2018.pdf: 2710275 bytes, checksum: 065c833d026306778501730602111723 (MD5) Previous issue date: 2018-05-18

Understanding the processes that govern the mixing and transport of scalars within and above the Amazon Forest is of great importance for many environmental applications. The impact of atmospheric stability on the roughness sublayer (RSL) as well as the influence on it by the processes in the overlying atmosphere are investigated using measurements collected at the Atmospheric Tall Tower Observatory. Five different stabilities are defined according to the turbulent fluxes' behaviour. Ejections dominate the transport in the RSL. In near neutral and unstable conditions coherent structures propagate up to 2-3 times the canopy height (h) and intermittently penetrate in the lowest part of the forest where sweeps drive the transport processes. In the unstable regime a weakening of the wind inflection at the canopy top and a transition to a convective regime above z = 2 h are observed. In stable conditions three regimes were defined characterised by a progressive lowering of the RSL and the weakening of the mixing-layer type coherent structures. In the 'weakly stable' regime the intense momentum and scalar fluxes appear driven by the coherent structures being able to penetrate inside the canopy intermittently coupling the flow above and within the forest. The 'very stable' regime is characterized by weak winds, a weakening of coherent structures and a decrease of the turbulent fluxes inhibited by buoyancy. The definition of a 'super stable' regime allowed the identification of a peculiar condition characterized by low-wind and weak coherent structures confined close to the canopy top and producing negligible transport. Submeso motions dominate the flow dynamics in this regime both above and inside the RSL. Multiresolution analysis highlights the ability of submeso motions to propagate inside the canopy and to modulate the exchange, particularly of scalars, fully driving the large positive CO2 flux observed inside the forest in the super stable regime.

The pristine Amazon rainforest is a unique place to study ozone (O3) deposition rates and tropospheric transport, due to the absence of nearby sources of anthropogenic pollution. Parts of the low background O3 are considered to be transported from the stratosphere into the troposphere. This occurs due to general entrainment of stratospheric air at the tropopause. Within the troposphere, downdrafts provide effective vertical mixing and are known to increase surface O3 values. Low-level jets can also enhance O3 concentrations due to long range transport and locally induced mixing in the nocturnal boundary layer. Therefore, we study these phenomena based on long term datasets from 2012 to present from tall measurements towers (80 m and 325 m).Ozone mixing ratios were measured at the ATTO site (Amazon Tall Tower Observatory) in the Central Amazon (02°08’38.8’’S, 58°59’59.5’’W) since 2012 at 8 different heights between 5 cm and 80 meters and additional measurements from 80 m up to 325 meters are running since 2017. From 2015 to 2017, 3-dimensional wind measurements have been performed in 150 meters height in 10 Hz sampling rate, showing evidences for the formation of a nocturnal low-level jet (LLJ), which leads to higher turbulent mixing inside the residual layer/ stable nocturnal layer. We were comparing the nocturnal LLJ with downdrafts of air due to strong thunderstorms which led to increases of O3 as well. We are analyzing these events regarding their in-canopy air exchange, their frequency and seasonality and comparing them with the effects of the nocturnal LLJ. As the data series comprises more than eight years of data we are also analyzing the interannual variability.

This study provides a detailed analysis of the influence of atmospheric stratification on the flow dynamics above and within a dense forest for a 19-days campaign at the Amazon Tall Tower Observatory (ATTO) site. Observations taken at seven levels within and above the forest along an 81-meter and a 325-meter towers allow a unique investigation of the vertical evolution of the turbulent field in the roughness sublayer and in the surface layer above it.Five different stability classes were defined on the basis of the behavior of turbulent heat, momentum and CO2 fluxes and variance ratio as a function of h/L stability parameter (where h is the canopy height and L is the Obukhov length). The novelty is the identification of a ‘super-stable’ (SS) regime (h/L>3) characterized by extremely low wind speeds, the almost completely suppression of turbulence and a clear dominance of submeso motions both above and within the forest.The obtained data classification was used to study the influence of atmospheric stratification on the vertical profiles of turbulent statistics. The spectral characteristics of coherent structures and of submeso motions (that may influence the energy and mass exchange above the Amazon forest) have been analyzed by wavelet analyses. The role of the main structures in momentum, heat and CO2 transport at the different levels inside and above the forest and in different diabatic conditions was thoroughly investigated through multiresolution and quadrant analyses.In unstable and neutral stability, the flow above the canopy appears modulated by ejections, whereas downward and intermittent sweeps dominate the transport inside the canopy. In the roughness sublayer (z £ 2h) the coherent structures dominating the transport within and above the canopy have a characteristic temporal scale of about 100 sec, whereas above this layer the transport is mainly driven by larger scale convection (temporal scale of about 15 min).In stable conditions the height of roughness sublayer progressively decreases with increasing stability reaching the minimum value (z2. In the weakly stable regime (0.152 transport.

Cryptogamic organisms such as bryophytes and lichens cover most surfaces within tropical forests, yet their impact on the emission of biogenic volatile organic compounds is unknown. These compounds can strongly influence atmospheric oxidant levels as well as secondary organic aerosol concentrations, and forest canopy leaves have been considered the dominant source of these emissions. Here we present cuvette flux measurements, made in the Amazon rainforest between 2016–2018, and show that common bryophytes emit large quantities of highly reactive sesquiterpenoids and that widespread lichens strongly uptake atmospheric oxidation products. A spatial upscaling approach revealed that cryptogamic organisms emit sesquiterpenoids in quantities comparable to current canopy attributed estimates, and take up atmospheric oxidation products at rates comparable to hydroxyl radical chemistry. We conclude that cryptogamic organisms play an important and hitherto overlooked role in atmospheric chemistry above and within tropical rainforests. Version of record

We investigated the role of turbulent coherent structures (CS), gravity waves (GW) and low-level jet (LLJ) propagation in the flow dynamics of the Nocturnal Boundary Layer (NBL) within and above a forest canopy at the Amazon Tall Tower Observatory (ATTO), in Central Amazon. Seven levels of wind velocity and temperature measurements allowed the study of the flow structure below and above the surface layer. We analyzed one dynamically rich night in 2015, which includes three distinct periods. In the first one, the NBL is characterized by CS generated at the canopy top. In the second period, the change in wind direction triggers the onset of a orographic GW above the roughness sublayer. The wave, suppressing the propagation of CS, strongly influences the boundary layer structure, both above and below the canopy. In the third period, low turbulence intensity at the canopy top enables the development of a LLJ. As the jet shear layer propagates upward, it disrupts the wave oscillations, while LLJ dominates the flow dynamics. The wavelet analyses identified i) turbulent and non-turbulent structures with different length and time-scales; ii) coupling of the flow at different levels and the vertical propagation of turbulent and wave motions; and iii) the ability of turbulent and low frequency processes associated with the orographic GW to penetrate within the canopy. Further, scalar measurements of methane, carbon monoxide and carbon dioxide identified the LLJ nose as upward limit for how far scalars can be transported.

Sesquiterpenes (C15H24) are highly reactive biogenic volatile organic compounds playing an important role in atmospheric chemistry. Once emitted from the Earth’s surface, primarily by vegetation, they are rapidly oxidized to semivolatile oxygenated organic species that can lead to secondary organic aerosols (SOA) that influence climate. In the pristine Amazon rainforest environment oxidation of sesquiterpenes is initiated by OH and ozone.We measured sesquiterpenes in March 2018 (wet season) and November 2018 (dry season) from central Amazonia, at the remote field site ATTO (Amazonian Tall Tower Observatory), Brazil. Samples were collected on adsorbent filled tubes equipped with ozone scrubbers at different heights above the forest canopy ; every three hours for two weeks at 80m and 150m (wet season) and every hour for three days at 80m, 150m and 320m (dry season). Samples were then analysed in the laboratory with a TD-GC-TOF-MS (Thermodesorption-Gas Chromatographer-Time Of Flight-Mass Spectrometer, Markes International). Simultaneous measurements of ozone and meteorological parameters were made at the nearby INSTANT tower. Identification of the chromatographic peaks was achieved by injection of standard molecules and by matching literature mass spectra. Quantification of the chemical compounds was achieved by injection of a standard mixture containing terpenes.The most abundant sesquiterpene measured at ATTO is (-)-α-copaene. Its diel profile varies with photosynthetically active radiation (PAR) and temperature, suggesting the canopy to be the main emission source. Interestingly, other identified sesquiterpenes show a consistent mirrored cycle, with their concentration being higher by night than by day. These varied mostly with RH suggesting the soil to be the main source of the emissions. Air samples taken at the ground are qualitatively and quantitatively different to those collected at different altitudes from the tower. Sesquiterpenes show a common maximum at sunrise (5 :00-7 :00 local time, UTC-4h) coincident with a strong decrease in ozone concentration (>50% decrease on average during the dry season). The strongest effect is registered during the dry season, when sesquiterpenes and ozone concentrations are highest and ozone loss is largest. The atmospheric impact of the measured sesquiterpenes will be discussed including ozone reactivity contributions and OH generation.

Isoprene regulates large-scale biogeochemical cycles by influencing atmospheric chemical and physical processes, and its dominant sources to the global atmosphere are the tropical forests. Although global and regional model estimates of isoprene emission have been optimized in the last decades, modeled emissions from tropical vegetation still carry high uncertainty due to a poor understanding of the biological and environmental controls on emissions. It is already known that isoprene emission quantities may vary significantly with plant traits, such as leaf phenology, and with the environment; however, current models still lack of good representation for tropical plant species due to the very few observations available. In order to create a predictive framework for the isoprene emission capacity of tropical forests, it is necessary an improved mechanistic understanding on how the magnitude of emissions varies with plant traits and the environment in such ecosystems. In this light, we aimed to quantify the isoprene emission capacity of different tree species across leaf ages, and combine these leaf measurements with long-term canopy measurements of isoprene and its biological and environmental drivers; then, use these results to better parameterize isoprene emissions estimated by MEGAN. We measured at the Amazon Tall Tower Observatory (ATTO) site, central Amazonia: (1) isoprene emission capacity at different leaf ages of 21 trees species; (2) isoprene canopy mixing ratios during six campaigns from 2013 to 2015; (3) isoprene tower flux during the dry season of 2015 (El-Niño year); (3) environmental factors – air temperature and photosynthetic active radiation (PAR) - from 2013 to 2018; and (4) biological factors – leaf demography and phenology (tower based measurements) from 2013 to 2018. We then parameterized the leaf age algorithm of MEGAN with the measurements of isoprene emission capacity at different leaf ages and the tower-based measurements of leaf demography and phenology. Modeling estimates were later compared with measurements (canopy level) and five years of satellite-derived isoprene emission (OMI) from the ATTO domain (2013-2017). Leaf level of isoprene emission capacity showed lower values for old leaves (> 6 months) and young leaves (< 2 months), compared to mature leaves (2-6 months); and our model results suggested that this affects seasonal ecosystem isoprene emission capacity, since the demography of the different leaf age classes varied a long of the year. We will present more results on how changes in leaf demography and phenology and in temperature and PAR affect seasonal ecosystem isoprene emission, and how modeling can be improved with the optimization of the leaf age algorithm. In addition, we will present a comparison of ecosystem isoprene emission of normal years (2013, 2014, 2017 years) and anomalous years (2015 - El-Niño; and 2016 - post El-Niño), and discuss how a strong El-Niño year can influence plant functional strategies that can be carried over to the consecutive year and potentially affect isoprene emission.