PAM FLUORESCENCE: A BEGINNERS GUIDE FOR BENTHIC DIATOMISTS

Abstract

Chlorophyll a fluorescence techniques have increasingly been applied in and ex situ for the study of microphytobenthic ecology and photophysiology. Fluorescence measurements have gained popularity, as they can be made rapidly, non-intrusively and, because of the portable nature of many fluorimeters, in situ. However, there is a paucity of literature for those new to the technique and most scientific papers assume a degree of prior knowledge. This paper provides a basic introduction for fluorescence techniques, particularly for benthic diatomists, explaining complex photophysiological theory in a simplified manner to allow inexperienced workers to interpret their data and understand fluorescence-based scientific papers. The commercially available fluorimeters and their specific applications are discussed. Fluorescence parameters can be used to provide information on the biomass, “health” and primary productivity of microphytobenthic biofilms. However, benthic biofilms offer their own challenges for photophysiologists, with the sedimentary environment complicating measurements as well as the ability of microphytobenthic taxa, such as diatoms, to migrate as fluorescence measurements are being made. Therefore, the paper ends by discussing some of the inherent problems and limitations of using fluorescence, presenting a constructively critical overview of these techniques so that the reader can make informed decisions about the validity of their data and be aware of many potential pitfalls.