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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.

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.

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.