The successful application of variable chlorophyll fluorescence methodology to higher plants and other phototrophs inspired workers in the 1990s to apply the methods to microalgal communities inhabiting benthic soft sediments, the microphytobenthos (MPB) of estuarine and other coastal habitats. It was quickly identified that particular aspects of the physiology (cellular vertical migration within the sediment matrix), photophysiology (high capacity for down regulation, e.g. NPQ, and

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... ation in the dark) and the effects of the physical structure of the sediment/biofilm matrix (light attenuation by the matrix itself) confounded the interpretation of fluorescence information obtained. In this chapter, the authors attempt to explain these and other issues pertinent to MPB biofilms and to summarise how methods have been developed to alleviate the problems encountered. Although much work is still needed to fully understand fluorescence data for the MPB, studies to date have been highly illuminating with regard to rhythms of productivity, photoacclimatory mechanisms and the behavioural ecology and physiology of MPB at an integrated biofilm level and at a cellular level. This chapter therefore introduces benthic biofilms and relevant specific fluorescence methodological issues, expands on subsurface fluorescence signal and migration, discusses down regulatory nonphotochemical quenching (NPQ) resulting from xanthophylls cycle induction, compares measurement of electron transport rate proxies, examines light curve methodology, and concludes by comparing fluorescence productivity measurements with those of other methodologies such as oxygen evolution and carbon uptake.