Benthic-pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling processes and their potential sensitivity to three anthropogenic pressures -climate change, nutrient loading, and fishing -using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic-pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic-pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world.

Studies focusing on the linkage between numerical and functional trait diversity frequently consider functional diversity indices but rarely evaluate them empirically or evaluate the use of other than continuous traits such as body size. Here, we present an extensive compilation on functional knowledge of benthic macrofauna using the categorical trait approach and scores of both common and rare species for 25 biological traits, including 102 modalities. We empirically quantify functional trait richness, within-trait species richness (redundancy), and trait variability on a large regional scale (> 1000 km), in three environmentally different areas (basins of a sea), over a long time-span (10 years). To develop further the usage of multiple categorical traits as an analysis tool, we examine the effect of sampling effort for the understanding of the functional properties of the benthic meta-assemblages. We also evaluate the relationship between species richness and trait richness in order to understand co-variation between trait modalities and how traits are packaged within species. Results show that the biological diversity in terms of traits could be distinguished between areas of higher and lower salinity, higher and lower anthropogenic stress, and higher and lower species richness. A considerably lower number of samples are needed to portray the functional structure of an area in relation to the taxonomic structure, thereby demonstrating the advantage of using traits when considering management and conservation issues. Using categorical traits empirically requires, as shown within this study, an understanding of the relationship between species richness and expression of traits, covariation of traits at different species richness and composition levels, acknowledgment of differences in trait expressions between common and rare species, and variability in abundance of species. Empirical trait-based analysis can reveal large-scale differences and insights into complexities between assemblage structure and function, and simultaneously be a valid tool for finding generalities.

Table S1. Species list and traits of demersal fish species present in the Baltic Sea International Trawl Survey (BITS) in Quarter 1 from 2003 to 2014. The 'diet' is taken from FishBase; 'Lmean' is the mean length of the species in the survey; 'A50' and 'Fecundity' are taken from Fishbase, ICES species sheet facts and stock assessment or from the literature as stated in Ref; 'caudal' and 'body' shape are derived from FishBase pictures. Species Diet Lmean A50 Fecundity Caudal Body Ref Area Agonus cataphractus benthivorous 135 2 3000 rounded elongated 1 Baltic Sea Amblyraja radiata generalist 390 5.5 50 continuous flat 2 North Sea Ammodytidae planktivorous 179 1.5 5000 forked elongated 3 North Sea Anguilla anguilla generalist 570 12 2000000 continuous eellike 4,5 Europe Arnoglossus laterna generalist 120 2 50000 rounded flat 6

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The rate at which biological diversity is altered on both land and in the sea, makes temporal community development a critical and fundamental part of understanding global change. With advancements in trait‐based approaches, the focus on the impact of temporal change has shifted towards its potential effects on the functioning of the ecosystems. Our mechanistic understanding of and ability to predict community change is still impeded by the lack of knowledge in long‐term functional dynamics that span several trophic levels. To address this, we assessed species richness and multiple dimensions of functional diversity and dynamics of two interacting key organism groups in the marine food web: fish and zoobenthos. We utilized unique time series‐data spanning four decades, from three environmentally distinct coastal areas in the Baltic Sea, and assembled trait information on six traits per organism group covering aspects of feeding, living habit, reproduction and life history. We identified gradual long‐term trends, rather than abrupt changes in functional diversity (trait richness, evenness, dispersion) trait turnover, and overall multi‐trait community composition. The linkage between fish and zoobenthic functional community change, in terms of correlation in long‐term trends, was weak, with timing of changes being area and trophic group specific. Developments of fish and zoobenthos traits, particularly size (increase in small size for both groups) and feeding habits (e.g. increase in generalist feeding for fish and scavenging or predation for zoobenthos), suggest changes in trophic pathways. We summarize our findings by highlighting three key aspects for understanding functional change across trophic groups: (a) decoupling of species from trait richness, (b) decoupling of richness from density and (c) determining of turnover and multi‐trait dynamics. We therefore argue for quantifying change in multiple functional measures to help assessments of biodiversity change move beyond taxonomy and single trophic groups.

Bottom trawling disturbance and hypoxia are affecting marine benthic habitats worldwide. We present an approach to predict their effects on benthic communities, and use the approach to estimate the state, the biomass relative to carrying capacity, of the Baltic Sea at the local, habitat, and regional scale. Responses to both pressures are expected to depend on the longevity of fauna, which is predicted from benthic data from 1558 locations. We find that communities in low-salinity regions mostly consist of short-lived species, which are, in our model, more resilient than those of the saline areas. The model predicts that in 14% of the Baltic Sea region benthic biomass is reduced by at least 50%, whereas an additional 8% of the region has reductions of 10–50%. The effects of hypoxia occur over larger spatial scales and lead to a low state of especially deep habitats. The approach is based on a simple characterization of the benthic community, which comes with high uncertainty, but allows for the identification of benthic habitats that are at greatest risk and prioritization of management actions at the regional scale. This information supports the development of sustainable approaches to manage impact of human activities on benthic ecosystems.