We measure the shoot respiration by the same measurement setup as photosynthesis.
Trunk respiration needs a special measurement chamber. Root respiration cannot, however, be measured directly. We derive the root respiration from the CO2 exchange at forest floor where the flux is a sum of the photosynthesis of ground vegetation, root respiration and the carbon dioxide emissions from the decomposition of soil organic matter by microbial activity. We measure the flux at forest floor using soil chambers.