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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.

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.

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.