Decoupling of air flow above and in plant canopies and gravity waves affect micrometeorological estimates of net scalar exchange

Turbulence within open canopies is shown to undergo a dramatic change in character during the transition from convective to stable conditions. In convective conditions the flow within the canopy is coupled through turbulent exchange to the flow aloft. As the transition proceeds, the within- and above-canopy flows decouple and vertically coherent waves form within the canopy. The intensity of above-canopy turbulence is not a good indicator of flow decoupling. Within-canopy waves can lead to large random error in the measurement of the change of storage and the advection terms in the mass balance equation. More importantly, errors associated with sampling over incomplete wave cycles will inevitably be combined with true advective flux divergences at non-ideal sites. Quantitative estimates of likely errors on storage of heat and CO2 within the canopy are presented.