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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.

Local and regional modelling of NH3 surface exchange is required to quantify nitrogen deposition to, and emissions from, the biosphere. However, measurements and model parameterisations for many remote ecosystems – such as tropical rainforest – remain sparse. Using 1 month of hourly measurements of NH3 fluxes and meteorological parameters over a remote Amazon rainforest site (Amazon Tall Tower Observatory, ATTO), six model parameterisations based on a bidirectional, single-layer canopy compensation point resistance model were developed to simulate observations of NH3 surface exchange. Canopy resistance was linked to either relative humidity at the canopy level (RHz0′), vapour pressure deficit, or a parameter value based on leaf wetness measurements. The ratio of apoplastic NH4+ to H+ concentration, Γs, during this campaign was inferred to be 38.5 ± 15.8. The parameterisation that reproduced the observed net exchange of NH3 most accurately was the model that used a cuticular resistance (Rw) parameterisation based on leaf wetness measurements and a value of Γs=50 (Pearson correlation r=0.71). Conversely, the model that performed the worst at replicating measured NH3 fluxes used an Rw value modelled using RHz0′ and the inferred value of Γs=38.5 (r=0.45). The results indicate that a single-layer canopy compensation point model is appropriate for simulating NH3 fluxes from tropical rainforest during the Amazonian dry season and confirmed that a direct measurement of (a non-binary) leaf wetness parameter improves the ability to estimate Rw. Current inferential methods for determining Γs were noted as having difficulties in the humid conditions present at a rainforest site.

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 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.

The vegetation and soils of the Amazon contain large amounts of carbon that may be vulnerable to loss given ongoing climate and land use change in the Amazon basin. Previous studies predicted that the Amazon rainforest would start to act as a net carbon source to the atmosphere by 2030-2040, and that it has switched from being a sink to source over the last decade. Using data from eddy covariance and vertical carbon dioxide profile measurement systems installed at the 80 m walk-up tower in the Amazon Tall Tower Observatory (ATTO) site, located in well-preserved central Amazon upland rainforest, we assessed net ecosystem exchange (NEE), gross primary productivity (GPP), and ecosystem respiration (Reco) for the period 2014-2019. The NEE results indicate that the central Amazon upland rainforest was carbon neutral or a source during this 6-year period. Seasonal GPP variations were related to soil water availability and vapor pressure deficit. The strong 2015-2016 El Niño event decreased both GPP and Reco due to the unusually long dry period, but also contributed to carbon flux dynamics in post El Niño periods. In the 2017-dry season, we measured higher dry-season GPP compared with the other years, which we hypothesize was triggered by photosynthesis activation in sub-canopy and understory trees. This is supported by the minimum green crown fraction at upper canopy trees, indicating more light availability in lower canopy trees, and the higher fraction of absorbed photosynthetically active radiation, both recorded during the dry-season of 2017. Our results show that the ground-based measurement setup at ATTO is well suited to investigate the local carbon fluxes on seasonal to interannual time scales.

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.

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.

The vegetated canopy plays a key role in regulating the surface fluxes and, therefore, the global energy, water and carbon cycles. In particular, vulnerable ecosystems like the Amazonia basin can be very sensitive to changes in vegetation that exert subsequent shifts in the partition of the energy, water and carbon in and above the canopy. Despite this relevance, most 3D atmospheric models represent the vegetated canopy as a flat 2D layer with, at most, a rough imitation of its effect in the atmospheric boundary layer through a modified roughness length. Thus, the representations often describe quite crudely the surface fluxes. In this work, particular emphasis is placed in the biophysical processes that take place within the canopy and its impact above. Our approach is to represent the coupling of the flow between the canopy and the atmosphere including the following processes: radiative transfer, photosynthesis, soil evaporation and CO2 respiration, combined with the mostly explicit atmospheric turbulence within and above the canopy. To this end, we implemented in LES a detailed multi-layer canopy model that solves the leaf energy balance for sunlit and shaded leaves independently, regulating the exchange of heat, moisture and carbon between the leaves and the air around. This allows us to connect the mechanistically represented processes occurring at the leaf level and strongly regulated by the transfer of diffuse and direct radiation within the canopy to the turbulent mixing explicitly resolved at the meter scale.We test and validate this combined photosynthesis-turbulence-canopy model by simulating a representative clear day transitioning to shallow cumulus. We based our evaluation on observations by the GoAmazon2014/5 campaign in Brazil in 2014. More specifically, we systematically validate the in-canopy radiation profiles; sources, sinks and turbulent fluxes of moisture, heat and CO2, and main state variables within the canopy, and also study the effects of these in the air above. Preliminary results show an encouraging satisfactory match to the observed evolution of the profiles. As a first exploration and demonstration of the capabilities of the model, we test the effects of a coarser in-canopy resolution, a different radiation scheme and the use of a more simple 2D canopy representation.

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.

Local and regional modelling of NH3 surface exchange is required to quantify nitrogen deposition to, and emissions from, the biosphere. However, measurements and model parameterisations for many remote ecosystems – such as tropical rainforest – remain sparse. Using one month of hourly measurements of NH3 fluxes and meteorological parameters over a remote Amazon rainforest site (Amazon Tall Tower Observatory, ATTO), six model parameterisations based on a bi-directional, single-layer, canopy compensation point resistance model were developed to simulate observations of NH3 surface exchange. Canopy resistance was linked to either relative humidity at the canopy level (RHz′0), vapour pressure deficit, or a parameter value based on leaf wetness measurements. The ratio of apoplastic NH4+ to H+ concentration, Γs, during this campaign was inferred to be 38.5 ± 15.8. The parameterisation that reproduced the observed net exchange of NH3 most accurately was the model that used a cuticular resistance (Rw) parameterisation based on leaf wetness measurements and a value of Γs = 50 (Pearson correlation r = 0.71). Conversely, the model that performed the worst at replicating measured NH3 fluxes used an Rw value modelled using (RHz′0) and the inferred value of Γs = 38.5 (r = 0.45). The results indicate that a single layer, canopy compensation point model is appropriate for simulating NH3 fluxes from tropical rainforest during the Amazonian dry season, and confirmed that a direct measurement of (a non-binary) leaf wetness parameter improves the ability to estimate Rw. Current inferential methods for determining Γs were noted as having difficulties in the humid conditions present at a rainforest site.

The Wavelet and the Multiresolution analysis are applied to ten nocturnal hours of observations of 3-D wind velocity taken within and above a forest canopy in Central Amazonia. Data from the ATTO Project, consisting in 7 levels of turbulence observations along both 81 and 325-meter towers, are used. The presented night is dynamically rich presenting three distinct periods. In the first one the boundary layer is characterized by canopy waves and coherent structures generated at the canopy top. In the second period an intense orographic gravity wave generated at around 150 m strongly influences the boundary layer structure, both above and below the canopy. In the third period, a very stable stratification at the canopy top enables the development of a low-level jet that interferes and disrupts the vertical orographic wave. During the night the wavelet cospectra identified turbulent and non-turbulent structures with different length and time-scales that are generated at different levels above the canopy and propagated inside it. The contributions of the different temporal scales of the flow above and within the canopy were identified using Wavelet and Multiresolution two-point cospectra. The analysis showed how turbulent and wave-like structures propagates in different ways and, further, the ability of low-frequency processes to penetrate within the canopy and to influence the transport of energy and scalar in the roughness sublayer and within canopy.Keywords: Coherent structures, Canopy Waves, Gravity Waves, Stable Boundary Layer, Low-Level Jet, wave-turbulence interaction.

Amazon rainforests and soils contain large amounts of carbon, which is under pressure from ongoing climate and land use change in the Amazon basin. It is estimated that methane (CH4), an important greenhouse gas, is largely released from the flooded wetlands of the Amazon, but the trends and balances of CH4 in the Amazon rainforest are not yet well understood. In addition, the change in atmospheric CH4 concentration is strongly associated with a change in carbon monoxide (CO) concentration, often caused by the human-induced combustion of biomass that usually peaks during dry season. Understanding the long-term fluctuations in the fluxes of greenhouse gases in the Amazon rainforest is essential for improving our understanding of the carbon balance of the Amazon rainforest.Since March 2012, we have continuously measured atmospheric CO2/CH4/CO concentrations at five levels (79, 53, 38, 24, and 4 m a.g.l.) using two wavelength-scanned cavity ring-down spectroscopy analyzers (G1301 and G1302, Picarro Inc., USA), which are automatically calibrated on site every day. In addition, we measured the CO2 flux by the eddy covariance method at the same tower. We estimated the CO2/CH4/CO fluxes by combining the vertical profile of the CO2/CH4/CO concentrations with the flux gradient method. Our results generally show no major difference in CO2 flux between the wet and dry seasons except for year 2017, when an elevated CO2 uptake was documented during the dry season despite the lowest precipitation between 2014 and 2018. The CH4 flux showed the largest CH4 emission during the dry season in year 2016. Further results will be analyzed and discussed in the presentation.

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.

Direct eddy covariance flux measurements of O3 in tropical forests are sparse and deposition velocities of O3 for tropical forest have large uncertainties in models. Therefore, we measured O3 fluxes at different heights ( 4 m, 12 m, 46 m and 81 m), which is 2 levels within canopy (below crown layer) and two levels above. At the same levels heat and CO2 fluxes were measured by eddy covariance to differentiate upper canopy fluxes from understory and soil fluxes and to infer stomatal conductance based on the inverted Penman-Monteith equation. Further measurements include the profiles of O3, NOx, CO2 and H2O which are used to calculate storage fluxes and reactions of O3 with NOx within the air volume. Additionally, leaf surface temperature and leaf wetness were measured in the upper canopy (26 m) to infer their influence on the non-stomatal deposition. The measurements took place at the ATTO (Amazon Tall Tower Observatory) site that is located about 150 km northeast of the city of Manaus in the Amazon rainforest. (02°08’38.8’’S, 58°59’59.5’’W). The climate in this region is characterized by a rainy (350 mm around March) and a dry season (ca. 80 mm in September). During the wet months, the air quality is close to pristine, while strong pollution from biomass burning is evident in the dry season. Therefore, we will present results from two intensive campaigns (3- 4 flux levels) for the rainy season (March to May) and the dry season (September to December) 2018. The focus of the analysis is the partitioning between a) the crown layer and understory and b) stomatal and non-stomatal deposition with a further analysis of the non-stomatal pathways. Non-stomatal deposition is analyzed by quantifying gas-phase reactions of O3 with NOx and an estimate of O3 reactivity by VOCs. Furthermore, the remaining (surface) deposition is analyzed according to its relations with leaf surface temperature and leaf wetness.

Dry deposition of ozone is an important sink of ozone in near-surface air. When dry deposition occurs through plant stomata, ozone can injure the plant, altering water and carbon cycling and reducing crop yields. Quantifying both stomatal and nonstomatal uptake accurately is relevant for understanding ozone's impact on human health as an air pollutant and on climate as a potent short-lived greenhouse gas and primary control on the removal of several reactive greenhouse gases and air pollutants. Robust ozone dry deposition estimates require knowledge of the relative importance of individual deposition pathways, but spatiotemporal variability in nonstomatal deposition is poorly understood. Here we integrate understanding of ozone deposition processes by synthesizing research from fields such as atmospheric chemistry, ecology, and meteorology. We critically review methods for measurements and modeling, highlighting the empiricism that underpins modeling and thus the interpretation of observations. Our unprecedented synthesis of knowledge on deposition pathways, particularly soil and leaf cuticles, reveals process understanding not yet included in widely used models. If coordinated with short-term field intensives, laboratory studies, and mechanistic modeling, measurements from a few long-term sites would bridge the molecular to ecosystem scales necessary to establish the relative importance of individual deposition pathways and the extent to which they vary in space and time. Our recommended approaches seek to close knowledge gaps that currently limit quantifying the impact of ozone dry deposition on air quality, ecosystems, and climate.

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.

The 2015/16 El Niño event caused unprecedented drought and warming in the Amazon basin. How tropical forests react to such extreme events in terms of volatile organic compound (VOC) emissions is of interest as the frequency of these events is predicted to increase through climate change. The diverse VOCs emitted can be significant for plants' carbon budgets, influence ozone and particle production, and through their reactivity impact OH concentrations. Total OH reactivity is a directly measureable quantity that gives the reaction frequency of OH radicals with all reactive species in the atmosphere in s?1. Here we present a comparison of the OH reactivity diel cycle from November 2015, i.e., extreme drought and elevated temperatures associated with strong El Niño conditions, with November 2012, a ?normal? El Niño Southern Oscillation (ENSO)-neutral period. Interestingly, the diel maximum of OH reactivity during the El Niño event occurred at sunset instead of, under normal conditions, early afternoon. The absolute total diel OH reactivity, however, did not change significantly. Daytime OH reactivity averages were 24.3 ± 14.5 s?1 in 2012 and 24.6 ± 11.9 s?1 in 2015, respectively. Our findings suggest that a combination of stronger turbulent transport above the canopy with stress-related monoterpene and, possibly, other biogenic volatile organic compound (BVOC) emissions were responsible for the increased reactivity at sunset. Made available in DSpace on 2019-03-02T00:42:38Z (GMT). No. of bitstreams: 1 ffgc0100012.pdf: 4348193 bytes, checksum: 1104061953b5e93aea6d22f2494c9c22 (MD5) Previous issue date: 2019-02-28

The failure of the Monin–Obukhov Similarity Theory (MOST) in the roughness sublayer is a major problem for the estimation of fluxes over tall forests, whenever indirect methods that rely on MOST, such as flux-gradient or the variance method, are involved. While much research focuses on micrometeorological measurements over temperate-climate forests, very few studies deal with such measurements over tropical forests. In this paper, we show evidence that some similarity functions over the Amazon forest are somewhat different from temperate forests. Comparison of the nondimensional scalar gradients canonical values for the inertial sublayer with our measurements in the roughness sublayer showed smaller deviations than what is usually reported for temperate forests. Although the fluxes of water vapor and CO2 derived from mean profiles show considerable scatter when compared with the eddy covariance measurements, using calibrated dimensionless gradients it is possible to estimate their mean daily cycle during the period of measurement (36 days in May and June, transition between rainy and dry season). Moreover, since mean ozone profiles were available, although without the corresponding eddy covariance measurements, mean daily ozone fluxes were calculated with the flux-gradient method, yielding a nighttime value of −0.05 and a daily peak of −0.45 μg m−2 s−1 (−1.04 and −9.37 nmol m−2 s−1, respectively). These values are comparable to previously measured fluxes in the literature for the Amazon forest.

In this study, high-frequency, multi-level measurements performed from late October to mid-November of 2015 at a 80-m tall tower of the Amazon Tall Tower Observatory (ATTO) project in central Amazonas State, Brazil, were used to diagnose the evolution of thermodynamic and kinematic variables as well as scalar fluxes during the passage of outflows generated by deep moist convection (DMC). Outflow associated with DMC activity over or near the tall tower was identified through the analysis of storm echoes in base reflectivity data from S-band weather radar at Manaus, combined with the detection of gust fronts and cold pools utilizing tower data. Four outflow events were selected, three of which took place during the early evening transition or nighttime hours and one during the early afternoon. Results show that the magnitude of the drop in virtual potential temperature and changes in wind velocity during outflow passages vary according to the type, organization, and life cycle of the convective storm. Overall, the nocturnal events highlighted the passage of well-defined gust fronts with moderate decrease in virtual potential temperature and increase in wind speed. The early afternoon event lacked a sharp gust front and only a gradual drop in virtual potential temperature was observed, probably because of weak or undeveloped outflow. Sensible heat flux (H) experienced an increase at the time of gust front arrival, which was possibly due to sinking of colder air. This was followed by a prolonged period of negative H, associated with enhanced nocturnal negative H in the storms' wake. In turn, increased latent heat flux (LE) was observed following the gust front, owing to drier air coming from the outflow; however, malfunctioning of the moisture sensors during rain precluded a better assessment of this variable. Substantial enhancements of Turbulent Kinetic Energy (TKE) were observed during and after gust front passage, with values comparable to those measured in grass fire experiments, evidencing the highly turbulent character of convective outflows. The early afternoon event displayed slight decreases in the aforementioned quantities in the passage of the outflow. Finally, a conceptual model of the time evolution of H in nocturnal convective outflows observed at the tower site is presented.

Nitrous acid (HONO) is a precursor of the hydroxyl radical (OH), a key oxidant in the degradation of most air pollutants. Field measurements indicate a large unknown source of HONO during the day time. Release of nitrous acid (HONO) from soil has been suggested as a major source of atmospheric HONO. We hypothesize that nitrite produced by biological nitrate reduction in oxygen-limited microzones in wet soils is a source of such HONO. Indeed, we found that various contrasting soil samples emitted HONO at high water-holding capacity (75-140%), demonstrating this to be a widespread phenomenon. Supplemental nitrate stimulated HONO emissions, whereas ethanol (70% v/v) treatment to minimize microbial activities reduced HONO emissions by 80%, suggesting that nitrate-dependent biotic processes are the sources of HONO. High-throughput Illumina sequencing of 16S rRNA as well as functional gene transcripts associated with nitrate and nitrite reduction indicated that HONO emissions from soil samples were associated with nitrate reduction activities of diverse Proteobacteria. Incubation of pure cultures of bacterial nitrate reducers and gene-expression analyses, as well as the analyses of mutant strains deficient in nitrite reductases, showed positive correlations of HONO emissions with the capability of microbes to reduce nitrate to nitrite. Thus, we suggest biological nitrate reduction in oxygen-limited microzones as a hitherto unknown source of atmospheric HONO, affecting biogeochemical nitrogen cycling, atmospheric chemistry, and global modeling.

The increasing use of intensive agricultural practices can lead to damaging consequences for the atmosphere through enhanced emissions of air pollutants. However, there are few direct measurements of the surface–atmosphere exchange of trace gases and water-soluble aerosols over agricultural grassland, particularly of reactive nitrogen compounds. In this study, we present measurements of the concentrations, fluxes and deposition velocities of the trace gases HCl, HONO, HNO 3 , SO 2 and NH 3 , and their associated water-soluble aerosol counterparts Cl − , NO 2 − , NO 3 − , SO 4 2− , NH 4 + as determined hourly for one month in May–June 2016 over agricultural grassland pre- and post-fertilisation. Measurements were made using the Gradient of Aerosols and Gases Online Registration (GRAEGOR) wet–chemical two–point gradient instrument. Emissions of NH 3 peaked at 1460 ng m −2 s −1 three hours after fertilisation, with an emission of HONO peaking at 4.92 ng m −2 s −1 occurring five hours after fertilisation. Apparent emissions of NO 3 − aerosol were observed after fertilisation which, coupled with a divergence of HNO 3 deposition velocity ( V d ) from its theoretical maximum value, suggested the reaction of emitted NH 3 with atmospheric HNO 3 to form ammonium nitrate aerosol. The use of the conservative exchange fluxes of tot-NH 4 + and tot-NO 3 − indicated net emission of tot-NO 3 − , implying a ground source of HNO 3 after fertilisation. Daytime concentrations of HONO remained above the detection limit (30 ng m −3 ) throughout the campaign, suggesting a daytime source for HONO at the site. Whilst the mean V d of NH 4 + was with 0.93 mm/s in the range expected for the accumulation mode, the larger average V d for Cl − (3.65 mm/s), NO 3 − (1.97 mm/s), SO 4 2− (1.89 mm/s) reflected the contribution of a super-micron fraction and decreased with increasing PM 2.5 / PM 10 ratio (a proxy measurement for aerosol size), providing direct evidence of a size-dependence of aerosol deposition velocity for aerosol chemical compounds.

An important current problem in micrometeorology is the characterization of turbulence in the roughness sublayer (RSL), where most of the measurements above tall forests are made. There, scalar turbulent fluctuations display significant departures from the predictions of Monin?Obukhov similarity theory (MOST). In this work, we analyze turbulence data of virtual temperature, carbon dioxide, and water vapor in the RSL above an Amazonian forest (with a canopy height of 40 m), measured at 39.4 and 81.6 m above the ground under unstable conditions. We found that dimensionless statistics related to the rate of dissipation of turbulence kinetic energy (TKE) and the scalar variance display significant departures from MOST as expected, whereas the vertical velocity variance follows MOST much more closely. Much better agreement between the dimensionless statistics with the Obukhov similarity variable, however, was found for the subset of measurements made at a low zenith angle Z, in the range 0°

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, non-turbulent 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 the 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.

Exchange conditions at the forest floor are complex due to the heterogeneity of sources and sinks and the inhomogeneous radiation but are important for linking soil respiration to measurements in the trunk space or above canopy. Far more attention has therefore been paid to above and within canopy flows, but even studies that addressed forest floor exchange do not present measurements below 1 m or 2 m. We used a multilayer model that explicitly resolves the laminar layer, the buffer layer, and the turbulent layer to calculate fluxes from the measured profiles in the lowest meter above ground and to calculate effective surface concentrations from given fluxes. The calculated fluxes were compared to measured eddy covariance fluxes of sensible heat and O3 and to chamber derived soil fluxes of CO2 and 222Rn. Sensible heat fluxes agreed surprisingly well given the heterogeneity of radiative heating and the generally low fluxes (max. 25 W m−2). The chamber fluxes turned out to be not comparable as the chamber fluxes were too low, probably due to one of the well-known problems of enclosures such as pressure differences, disturbed gradients and exclusion of naturally occurring turbulence events and surface cooling. The O3 fluxes agreed well for high O3 values reaching down to the forest floor during full coupling of the canopy by coherent structures. During most of the time, the model overestimated the fluxes as chemical reactions were dominating within the profile. One new approach was to calculate the effective surface concentration from a given flux and compare this to measured surface concentrations. This allowed the identification of situations with a coupled and decoupled forest floor layer, which has important consequences for respiration measurements in the trunk space or above canopy and should be considered in upcoming studies.

Quantifying the atmosphere-surface exchange of reactive trace gases and aerosols is extremely important for a full understanding of biogeochemical cycles and their implications for air quality and climate. However, turbulent fluxes of reactive gases such as ozone and volatile organic compounds (VOC) as well as aerosol particles are still difficult to measure. Chemical reactions contribute to changes in trace gas or aerosol concentrations, and production or loss processes have to be carefully separated from turbulent transport. Also, for many trace gas measurements and for size-resolved and chemically speciated aerosol measurements, instruments are limited with respect to time resolution, sensitivity, and accuracy, which restricts their application in micrometeorological techniques. Here, we present flux measurements of reactive trace gases and aerosols above tall vegetation. We focus on ozone deposition and its implications for the NO/NO2/O3 triad, biogenic emissions of volatile organic compounds and their subsequent oxidation reactions, and finally, turbulent aerosol fluxes in a spruce forest ecosystem.

Gaseous nitrous acid (HONO), the protonated form of nitrite, contributes up to similar to 60% to the primary formation of hydroxyl radical (OH), which is a key oxidant in the degradation of most air pollutants. Field measurements and modeling studies indicate a large unknown source of HONO during daytime. Here, we developed a new tracer method based on gas-phase stripping-derivatization coupled to liquid chromatography-mass spectrometry (LC-MS) to measure the N-15 relative exceedance, psi(N-15), of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye, purified by solid phase extraction (SPE), and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). In the optimal working range of psi(N-15) = 0.2-0.5, the relative standard deviation of psi(N-15) is

International audience; Gaseous nitrogen dioxide (NO2) represents an oxidant that is present in relatively high concentrations in various indoor settings. Remarkably increased NO2 levels up to 1.5 ppm are associated with homes using gas stoves. The heterogeneous reactions of NO2 with adsorbed water on surfaces lead to the generation of nitrous acid (HONO). Here, we present a HONO source induced by heterogeneous reactions of NO2 with selected indoor paint surfaces in the presence of light (300 nm < lambda < 400 nm). We demonstrate that the formation of HONO is much more pronounced at elevated relative humidity. In the presence of light (5.5 W m(-2)), an increase of HONO production rate of up to 8.6 . 10(9) molecules cm(-2) s(-1) was observed at [NO2] = 60 ppb and 50 % relative humidity (RH). At higher light intensity of 10.6 (W m(-2)), the HONO production rate increased to 2.1 . 10(10) molecules cm(-2) s(-1). A high NO2 to HONO conversion yield of up to 84 % was observed. This result strongly suggests that a light-driven process of indoor HONO production is operational. This work highlights the potential of paint surfaces to generate HONO within indoor environments by light-induced NO2 heterogeneous reactions.

The Crenarchaeon Ignicoccus hospitalis lives in symbiosis with Nanoarchaeum equitans providing essential cell components and nutrients to its symbiont. Ignicoccus hospitalis shows an intriguing morphology that points toward an evolutionary role in driving compartmentalization. Therefore, the bioenergetics of this archaeal host-symbiont system remains a pressing question. To date, the only electron acceptor described for I. hospitalis is elemental sulfur, but the organism comprises genes that encode for enzymes involved in nitrogen metabolism, e.g., one nitrate reductase and two octaheme cytochrome c, Igni_0955 (IhOCC) and Igni_1359. Herein, we detail functional and structural studies of the highly abundant IhOCC, including an X-ray crystal structure at 1.7 Å resolution, the first three-dimensional structure of an archaeal OCC. The trimeric IhOCC is membrane associated and exhibits significant structural and functional differences to previously characterized homologs within the hydroxylamine oxidoreductases (HAOs) and octaheme cytochrome c nitrite reductases (ONRs). The positions and spatial arrangement of the eight hemes are highly conserved, but the axial ligands of the individual hemes 3, 6 and 7 and the protein environment of the active site show significant differences. Most notably, the active site heme 4 lacks porphyrin-tyrosine cross-links present in the HAO family. We show that IhOCC efficiently reduces nitrite and hydroxylamine, with possible relevance to detoxification or energy conservation.Structural data are available in the Protein Data Bank under the accession number 4QO5.

We study the interactions between atmospheric boundary layer (ABL) dynamics and atmospheric chemistry using a mixed-layer model coupled to chemical reaction schemes. Guided by both atmospheric and chemical measurements obtained during the DOMINO (Diel Oxidant Mechanisms in relation to Nitrogen Oxides) campaign (2008), numerical experiments are performed to study the role of ABL dynamics and the accuracy of chemical schemes with different complexity: the Model for Ozone and Related chemical Tracers, version 4 (MOZART-4) and a reduced mechanism of this chemical system. Both schemes produce satisfactory results, indicating that the reduced scheme is capable of reproducing the O3-NOx-VOC-HOx diurnal cycle during conditions characterized by a low NOx regime and small O3 tendencies (less than 1 ppb per hour). By focusing on the budget equations of chemical species in the mixed-layer model, we show that for species like O3, NO and NO2, the influence of entrainment and boundary layer growth is of the same order as chemical production/loss. This indicates that an accurate representation of ABL processes is crucial in understanding the diel cycle of chemical species. By comparing the time scales of chemical reactive species with the mixing time scale of turbulence, we propose a classification based on the Damköhler number to further determine the importance of dynamics on chemistry during field campaigns. Our findings advocate an integrated approach, simultaneously solving the ABL dynamics and chemical reactions, in order to obtain a better understanding of chemical pathways and processes and the interpretation of the results obtained during measurement campaigns.

During the DOMINO (Diel Oxidant Mechanism In relation to Nitrogen Oxides) campaign in southwest Spain we measured simultaneously all quantities necessary to calculate a photostationary state for HONO in the gas phase. These quantities comprise the concentrations of OH, NO, and HONO and the photolysis frequency of NO2, j(NO2) as a proxy for j(HONO). This allowed us to calculate values of the unknown HONO daytime source. This unknown HONO source, normalized by NO2 mixing ratios and expressed as a conversion frequency (% h−1), showed a clear dependence on j(NO2) with values up to 43% h−1 at noon. We compared our unknown HONO source with values calculated from the measured field data for two recently proposed processes, the light-induced NO2 conversion on soot surfaces and the reaction of electronically excited NO2* with water vapour, with the result that these two reactions normally contributed less than 10% (

We have combined chemical and micrometeorological measurements to investigate the formation and distribution of HONO throughout a forest canopy. HONO was measured simultaneously at two heights, close to the forest floor and just above canopy. The turbulent exchange between the forest and the atmosphere above was studied using vertical profiles of eddy covariance measurements of wind velocity, sonic temperature, water vapour and CO2. HONO mixing ratios at both heights showed typical diel cycles with low daytime values (~80 ppt) and high nighttime values (up to 500 ppt), but were influenced by various sources and sinks leading to mixing ratio differences (above canopy minus below) of up to +240 ppt at nighttime. In the late afternoon and early night mixing ratios increased at higher rates near the forest floor, indicating a possible ground source. Due to the simultaneous decoupling of the forest from the air layer above the canopy, mixing ratio differences reached about −170 ppt. From the late night until the early morning mixing ratios above the forest were typically higher than close to the forest floor. For some cases, this could be attributed to advection above the forest, which only partly penetrated the canopy. Measured photolysis frequencies above and below the forest canopy differed by a factor of 10–25 resulting in HONO lifetimes of about 10 min above and 100–250 min below the canopy at noontime. However, these differences of the main daytime HONO sink were not evident in the mixing ratio differences, which were close to zero during the morning hours. Effective turbulent exchange due to a complete coupling of the forest to the air layer above the canopy in the morning has offset the differences caused by the daytime photolytic sink and added to the interplay between different HONO production and loss processes.

Reactive nitrogen species have a strong influence on atmospheric chemistry and climate, tightly coupling the Earth's nitrogen cycle with microbial activity in the biosphere. Their sources, however, are not well constrained, especially in dryland regions accounting for a major fraction of the global land surface. Here, we show that biological soil crusts (biocrusts) are emitters of nitric oxide (NO) and nitrous acid (HONO). Largest fluxes are obtained by dark cyanobacteria-dominated biocrusts, being ∼20 times higher than those of neighboring uncrusted soils. Based on laboratory, field, and satellite measurement data, we obtain a best estimate of ∼1.7 Tg per year for the global emission of reactive nitrogen from biocrusts (1.1 Tg a(-1) of NO-N and 0.6 Tg a(-1) of HONO-N), corresponding to ∼20% of global nitrogen oxide emissions from soils under natural vegetation. On continental scales, emissions are highest in Africa and South America and lowest in Europe. Our results suggest that dryland emissions of reactive nitrogen are largely driven by biocrusts rather than the underlying soil. They help to explain enigmatic discrepancies between measurement and modeling approaches of global reactive nitrogen emissions. As the emissions of biocrusts strongly depend on precipitation events, climate change affecting the distribution and frequency of precipitation may have a strong impact on terrestrial emissions of reactive nitrogen and related climate feedback effects. Because biocrusts also account for a large fraction of global terrestrial biological nitrogen fixation, their impacts should be further quantified and included in regional and global models of air chemistry, biogeochemistry, and climate.