Our knowledge of phytoplankton primary productivity has far outstripped information on benthic productivity despite the significant contribution of microphytobenthos to the carbon budget of shallow or intertidal ecosystems. The highly stratified biofilms in the surficial layers of sediments are characterized by steep physico-chemical gradients which respond instantaneously to the microenvironment. Measurements of productivity must be made with as little disturbance as possible and on a scale appropriate to the spatial and temporal variability of the system.
These problems are being solved by the application of fluorescence measurements (PAM system). The use of fluorescence to assess the photo-physiology of biofilms is now gaining momentum and allows non-destructive measurement to be obtained. However, there are limits to the technique and experience is required to interpret the results. SERG has been applying this technique to intertidal and sub tidal systems including coral reefs and stromatolite assemblages.