This chapter discusses the factors known to influence the photosynthesis, primary production and biomass of these two groups of primary producers, and the application of new techniques. Phytoplankton and microphytobenthos are important components of estuarine ecosystems. Phytoplankton in estuaries experience rapid changes in the type of limitation (nutrients, light) and different physical environments (mixing, salinity), and these changes may influence species composition. Interannual variability in primary production can to a large extent be explained by changing weather conditions and changing land use, as the watershed and rainfall determine the nutrient and sediment input in estuaries. In order to understand ecosystem functioning better, it is required to be able to understand what determines phytoplankton species composition and succession during blooms, what happens when blooms decay, how contaminants influence bloom dynamics and what is the interplay between nutrient enrichment and harmful algal blooms. Microphytobenthic biofilms plays an important role (or barrier) in the exchange of nutrients between the sediments and the water phase, and in effecting bacterial processes. Perhaps one of the obvious gaps in microphytobenthic data sets is the general scarcity of long-term data sets.
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