From prototypical regimes to observed complex dynamics and CO ₂ transport in the Amazonian nocturnal boundary layer

We investigated the characteristics of the nocturnal boundary layer (NBL) above and within the Amazon rainforest canopy during the 2022 dry season. We analysed observed NBL dynamics and CO ₂ transport from the perspective of the prototypical NBL represented in weather and climate models. To this end, using the CloudRoots-Amazon22 dataset, we characterised the main NBL features and governing processes. We identified NBL height using five methods based on thermal stratification, wind, and turbulent criteria, finding a distinct stable layer above the canopy with an average height between 142–164 m. To examine the drivers of the dynamic NBL evolution, we classified the data into weakly and strongly stable regimes, determined by the interplay between stabilising longwave radiative cooling and destabilising mechanical wind shear. Budget equations for turbulent kinetic energy (TKE), heat, and CO ₂ allowed us to quantify the relative contributions of these drivers to transport across the canopy-atmosphere interface. In the weakly stable regime, increased TKE at the canopy top promoted mixing between the within- and above-canopy layers. Conversely, TKE was nearly absent in the strongly stable regime, decoupling the two layers. This decoupling favoured strong thermal stratification above the canopy and well-mixed conditions within the canopy. Our results show that only about 6 % of observed profiles conform to prototypical NBL regimes, emphasising the need to revisit parameterisations to explicitly account for canopy-induced effects and intermittent turbulence. Our observational analysis provides a critical benchmark for improving the representation of NBL dynamics and CO ₂ transport in models.