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Given the global loss of biodiversity, trait-based studies are needed to assess the associated consequences for ecosystem functions and services. Many studies focus on the assessment of functional diversity of natural communities as a mechanistic link between biodiversity and ecosystem functioning. In freshwater ecosystems, diversity of primary producers is crucial for resource use efficiency and trophic transfer of energy. Furthermore, one indicator of the ecological status of surface waters is the composition of natural phytoplankton communities. The number of available techniques for the quantification and discrimination of different phytoplankton groups have increased in recent years. For example, phytoplankton community composition can indirectly be assessed via CHEMTAX, a matrix factorization program, which calculates the contribution of different phytoplankton taxa to the total chlorophyll-a using concentrations of pigments analysed via liquid chromatography. A more direct, in vivo assessment can be achieved with instruments based on spectral fluorometry, such as the Algae Lab Analyser, which allows for a differentiation of four phytoplankton groups depending on spectral fluorescence signatures. In this study, we compared both methods by analyses of phytoplankton biomass and functional diversity from phytoplankton communities of three lakes of different trophic states, while a subset of biomass and diversity estimates derived from microscopic counts served as a reference. We found marked differences in biomass estimates of all assessed phytoplankton groups, with cyanobacteria being significantly underestimated by the Algae Lab Analyser. Furthermore, we show that the level of agreement between the methods somewhat depends on the trophic state of the lake. We conclude that both methods are suitable to estimate phytoplankton functional diversity with specific advantages and disadvantages. Here we provide users with a flow chart to help them find the most suitable method for their respective purposes.

Essential polyunsaturated fatty acids (PUFAs) have been recognized as a crucial factor that determines the trophic transfer efficiency in plankton communities. As many animals cannot synthesize the classes of ω3‐ and ω6‐PUFAs, the dietary availability of these PUFAs can constrain the fitness of freshwater zooplankton such as Daphniaspp. In particular, eicosapentaenoic acid (EPA, 20:5ω3) is considered to be a crucial determinant of the transfer of biomass at the freshwater plant‐herbivore interface. In contrast to ω3‐PUFAs, the group of ω6‐PUFAs has previously been considered to be of less ecological relevance, although the potential role of the ω6‐PUFA arachidonic acid (ARA, 20:4ω6) remains controversial. To investigate its potential role, we conducted dose‐response growth experiments with two Daphniaspecies, D. pulexand D. magna, supplemented with EPA or ARA, which allowed us to calculate EPA and ARA saturation thresholds for growth and reproduction of both Daphniaspecies. Our results provide evidence that not only the availability of ω3‐PUFAs, but also the availability of a ω6‐PUFA, namely ARA, can limit both the growth and reproduction of Daphniaspp. to an equal extent. The saturation thresholds for growth and reproduction were consistently, but not significantly, higher for EPA than for ARA in both Daphniaspecies. As shifts in phytoplankton community composition might result in environmental fluctuations in the dietary availability of ω3‐ and ω6‐PUFAs, our findings present a significant step in understanding the consequences of the ongoing global biodiversity loss for trophic transfer efficiency at the phytoplankton‐zooplankton interface.