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Anneville, O. ; Chang, C. ; Dur, G. ; Souissi, S. ; Rimet, F. ; Hsieh, C.Oikos, 2019, 128 (11) : 1666-1677. ArticleIncreases in phytoplankton biomass have been widely observed over the past decades, even in lakes experiencing nutrient reduction. However, the mechanisms giving rise to this trend remain unclear. Here, we unveil the potential mechanisms through quantifying the relative contribution of bottom-up versus top-down control in determining biomasses of phytoplankton assemblages in Lake Geneva. Specifically, we apply nonlinear time series analysis, convergent cross mapping (CCM), to decipher the degree of bottom-up versus top-down control among phytoplankton assemblages via quantifying 1) causal links between environmental factors and various phytoplankton assemblages and 2) the relative importance of bottom-up, top-down, and environmental effects. We show that the recent increase in total phytoplankton biomass, albeit with phosphorus reduction, was mainly caused by a particular phytoplankton assemblage which was better adapted to the re-oligotrophicated environment characterized by relatively low phosphorus concentrations and warm water temperature, and poorly controlled by zooplankton grazing. Our findings suggest that zooplankton act as a critical driver of phytoplankton biomass and strongly impact the dynamics of recovery from eutrophication. Therefore, our phytoplankton assemblage approach in combination with causal identification of top-down versus bottom-up controls provides insights into the reason why phytoplankton biomass may increase in lakes undergoing phosphorus reduction.