Description: Food web research provides essential insights into ecosystem functioning, but practical applications in ecosystem-based management are hampered by a current lack of knowledge synthesis. To address this gap, we provide the first systematic review of ecological studies applying stable isotope analysis, a pivotal method in food web research, in the heavily anthropogenically impacted Baltic Sea macro-region. We identified a thriving research field, with 164 publications advancing a broad range of fundamental and applied research topics, but also found structural shortcomings limiting ecosystem-level understanding. We argue that enhanced collaboration and integration, including the systematic submission of Baltic Sea primary datasets to stable isotope databases, would help to overcome many of the current shortcomings, unify the scattered knowledge base, and promote future food web research and science-based resource management. The effort undertaken here demonstrates the value of macro-regional synthesis, in enhancing access to existing data and supporting strategic planning of research agendas.

Description: 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 sea‐sonal 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 car‐nivory feeding modes, FA trophic makers, and δ13C patterns in essential compounds emphasized that cyanobacterial FAs and AAs have been incorporated into meso‐zooplankton 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 meso‐zooplankton 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.