Abstract
<p>This protocol describes the practical steps involved in the analysis of photosynthetic parameters of natural biofilm communities colonizing artificial substrates immersed in aquatic environments. However, it is also applicable to biofilms collected in situ from pebbles and rocks or macrophytes, as well as to microalgal cultures grown in the lab. The aim is to detail the procedure used to assess photosynthetic performances of phototrophic microorganisms, including measurements of chlorophyll fluorescence, proportions of photosynthetic groups, optimal and effective PSII quantum yield, light-use efficiency, light saturating point. The analysis is performed using a multi-wavelength Pulse-Amplitude Modulated fluorometer, the Phyto-PAM (Heinz Walz GmbH, Germany) device, which allows rapid, non-invasive and non-destructive fluorescence-based measurements of photosynthetic microorganisms under multiple illumination conditions. Sample illumination or not prior measurements is key to get reliable results.</p>