The dynamics of individual phytoplankton species are often more variable than predicted for their functional groups. This observation is poorly understood in highly perturbed coastal systems. Trends in the abundance of 54 phytoplankton species spanning a volumetric size range from ~102 to ~105 µm3 in shelf waters of the NW Iberian upwelling system since the late 1980s were modelled as a function of environmental variables. Functional traits were assessed for their ability to explain the across-species changes in occurrence and abundance due to the environmental drivers. Species-specific responses to the environment were heterogeneous, precluding any generalisation by taxonomic groups, although these responses were partially related to cell size. Smaller species showed a high probability of occurrence and higher abundance under high nitrate concentration in the euphotic layer, pointing to a major role of the upwelling of Eastern North Atlantic Central Water but also to inputs of nutrients mineralised over the shelf. However, cell size explained only a small amount of the variability in the individual species’ responses to the environment. Growth rate and maximum rate of nitrogen uptake normalised to cell size provided additional explanation for the individual species’ responses to the environmental drivers. Fast-growing species, though less efficient in taking up upwelled nutrients, thrived in favourable upwelling conditions. These results support the dominance of species of intermediate size during blooms in this upwelling region, and suggest that variability in functional traits among species rather than cell size alone affects the response of phytoplankton to environmental changes in upwelling ecosystems.

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