Studying how food web structure and function vary through time represents an opportunity to better comprehend and anticipate ecosystem changes. Yet, temporal studies of highly resolved food web structure are scarce. With few exceptions, most temporal food web studies are either too simplified, preventing a detailed assessment of structural properties or binary, missing the temporal dynamics of energy fluxes among species. Using long‐term, multi‐trophic biomass data coupled with highly resolved information on species feeding relationships, we analysed food web dynamics in the Gulf of Riga (Baltic Sea) over more than three decades (1981–2014). We combined unweighted (topology‐based) and weighted (biomass‐ and flux‐based) food web approaches, first, to unravel how distinct descriptors can highlight differences (or similarities) in food web dynamics through time, and second, to compare temporal dynamics of food web structure and function. We find that food web descriptors vary substantially and distinctively through time, likely reflecting different underlying ecosystem processes. While node‐ and link‐weighted metrics reflect changes related to alterations in species dominance and fluxes, unweighted metrics are more sensitive to changes in species and link richness. Comparing unweighted, topology‐based metrics and flux‐based functions further indicates that temporal changes in functions cannot be predicted using unweighted food web structure. Rather, information on species population dynamics and weighted, flux‐based networks should be included to better comprehend temporal food web dynamics. By integrating unweighted, node‐ and link‐weighted metrics, we here demonstrate how different approaches can be used to compare food web structure and function, and identify complementary patterns of change in temporal food web dynamics, which enables a more complete understanding of the ecological processes at play in ecosystems undergoing change.

Large‐scale alterations in marine ecosystems as a response to environmental and anthropogenic pressures have been documented worldwide. Yet, these are primarily investigated by assessing abundance fluctuations of a few dominant species, which inadequately reflect ecosystem‐wide changes. In addition, it is increasingly recognized that it is not species identity per se, but their traits that determine environmental responses, biological interactions and ecosystem functioning. In this study, we investigated long‐term, spatio‐temporal variability in trait composition across multiple organism groups to assess whether functional changes occur in a similar way across trophic levels and whether shifts in trait composition link to environmental change. We combined extensive trait datasets with long‐term surveys (30–40 yr) of four organism groups (phytoplankton, zooplankton, benthic invertebrates and fish) in three environmentally distinct areas of a large marine ecosystem. We found similar temporal trajectories in the community weighted mean trait time‐series of the different trophic groups, revealing ecosystem‐wide functional changes. The traits involved and their dynamics differed between areas, concurrent with climate‐driven changes in temperature and salinity, as well as more local dynamics in nutrients and oxygen. This finding highlights the importance of considering both global climate, as well as local external drivers when studying ecosystem changes. Using a multi‐trophic trait‐based approach, our study demonstrates the importance of integrating community functional dynamics across multiple trophic levels to capture ecosystem‐wide responses which could, ultimately, help moving towards a holistic understanding, assessment and management of marine ecosystems.

An ecosystem shift in the Baltic Proper at the end of the 1980s could be identified by a decreasing springtime diatom/dinoflagellate ratio. Therefore the suggested diatom/dinoflagellate index (Dia/Dino index) was developed as a descriptive indicator of ecosystem changes for applications pertaining to the Marine Strategy Framework Directive (MSFD). Changes in the dominance of these two phytoplankton classes impact the food web because both their quality as a food source for grazers and their periods of occurrence differ, which may lead to a mismatch in zooplankton growth. The rapid sinking of diatoms results in a high Dia/Dino index, indicative of low-level food availability for zooplankton but high-level food delivery to the zoobenthos. Consequently, the Dia/Dino index can be used to follow the food pathway (Descriptor 4 of MSFD: “food web”). Moreover, a low Dia/Dino index may indicate silicate limitation caused by eutrophication, whereas a high Dia/Dino index supports mitigated eutrophication, as the strong sedimentation of nutrients removes them from the water and deposits them in the sediment (Descriptor 5 of MSFD: “eutrophication”). Diatom dominance, and thus a high Dia/Dino index, is typical in historical data and is therefore assumed to reflect good environmental status (GES). The principles of the Dia/Dino index are explained herein using examples from two very different regimes, the Eastern Gotland Basin and Kiel Bay. In the assessment of the environmental status of these water bodies, GES boundaries of 0.5 and 0.75, respectively, are suggested. The conditions for calculating the Dia/Dino index are described and the limitations and advantages of this indicator are discussed.

A common and established view is that increased inputs of nutrients to the sea, for example via river flooding, will cause eutrophication and phytoplankton blooms in coastal areas. We here show that this concept may be questioned in certain scenarios. Climate change has been predicted to cause increased inflow of freshwater to coastal areas in northern Europe. River waters in these areas are often brown from the presence of high concentrations of allochthonous dissolved organic carbon (humic carbon), in addition to nitrogen and phosphorus. In this study we investigated whether increased inputs of humic carbon can change the structure and production of the pelagic food web in the recipient seawater. In a mesocosm experiment unfiltered seawater from the northern Baltic Sea was fertilized with inorganic nutrients and humic carbon (CNP), and only with inorganic nutrients (NP). The system responded differently to the humic carbon addition. In NP treatments bacterial, phytoplankton and zooplankton production increased and the systems turned net autotrophic, whereas the CNP-treatment only bacterial and zooplankton production increased driving the system to net heterotrophy. The size-structure of the food web showed large variations in the different treatments. In the enriched NP treatments the phytoplankton community was dominated by filamentous >20 µm algae, while in the CNP treatments the phytoplankton was dominated by picocyanobacteria <5 µm. Our results suggest that climate change scenarios, resulting in increased humic-rich river inflow, may counteract eutrophication in coastal waters, leading to a promotion of the microbial food web and other heterotrophic organisms, driving the recipient coastal waters to net-heterotrophy.