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Eutrophication, increased temperatures and stratification can lead to massive, filamentous, N2‐fixing cyanobacterial (FNC) blooms in coastal ecosystems with largely unresolved consequences for the mass and energy supply in food webs. Mesozooplankton adapt to not top‐down controlled FNC blooms by switching diets from phytoplankton to microzooplankton, resulting in a directly quantifiable increase in its trophic position (TP) from 2.0 to as high as 3.0. If this process in mesozooplankton, we call trophic lengthening, was transferred to higher trophic levels of a food web, a loss of energy could result in massive declines of fish biomass. We used compound‐specific nitrogen stable isotope data of amino acids (CSIA) to estimate and compare the nitrogen (N) sources and TPs of cod and flounder from FNC bloom influence areas (central Baltic Sea) and areas without it (western Baltic Sea). We tested if FNC‐triggered trophic lengthening in mesozooplankton is carried over to fish. The TP of cod from the western Baltic (4.1 ± 0.5), feeding mainly on decapods, was equal to reference values. Only cod from the central Baltic, mainly feeding on zooplanktivorous pelagics, had a significantly higher TP (4.6 ± 0.4), indicating a strong carry‐over effect trophic lengthening from mesozooplankton. In contrast, the TP of molluscivorous flounder, associated with the benthic food web, was unaffected by trophic lengthening and quite similar reference values of 3.2 ± 0.2 in both areas. This suggests that FNC blooms lead to a large loss of energy in zooplanktivorous but not in molluscivorous mesopredators. If FNC blooms continue to trigger the detour of energy at the base of the pelagic food web due to a massive heterotrophic microbial system, the TP of cod will not return to lower TP values and the fish stock not recover. Monitoring the TP of key species can identify fundamental changes in ecosystems and provide information for resource management. [ABSTRACT FROM AUTHOR]

Increasing sea surface temperatures (SST) and blooms of lipid‐poor, filamentous cyanobacteria can change mesozooplankton metabolism and foraging strategies in marine systems. Lipid shortage and imbalanced diet may challenge the build‐up of energy pools of lipids and proteins, and access to essential fatty acids (FAs) and amino acids (AAs) by copepods. The impact of cyanobacterial blooms on individual energy pools was assessed for key species temperate Temora longicornis and boreal Pseudo‐/Paracalanus spp. that dominated field mesozooplankton communities isolated by seasonal stratification in the central Baltic Sea during the hot and the cold summer. We looked at (a) total lipid and protein levels, (b) FA trophic markers and AA composition, and (c) compound‐specific stable carbon isotopes (δ13C) in bulk mesozooplankton and in a subset of parameters in particulate organic matter. Despite lipid‐poor cyanobacterial blooms, the key species were largely able to cover both energy pools, yet a tendency of lipid reduction was observed in surface animals. Omni‐ and carnivory feeding modes, FA trophic makers, and δ13C patterns in essential compounds emphasized that cyanobacterial FAs and AAs have been incorporated into mesozooplankton mainly via feeding on mixo‐ and heterotrophic (dino‐) flagellates and detrital complexes during summer. Foraging for essential highly unsaturated FAs from (dino‐) flagellates may have caused night migration of Pseudo‐/Paracalanus spp. from the deep subhalocline waters into the upper waters. Only in the hot summer (SST>19.0°C) was T. longicornis submerged in the colder subthermocline water (~4°C). Thus, the continuous warming trend and simultaneous feeding can eventually lead to competition on the preferred diet by key copepod species below the thermocline in stratified systems. A comparison of δ13C patterns of essential AAs in surface mesozooplankton across sub‐basins of low and high cyanobacterial biomasses revealed the potential of δ13C‐AA isoscapes for studies of commercial fish feeding trails across the Baltic Sea food webs. [ABSTRACT FROM AUTHOR]