Patterns in community structure and functioning of motile epibenthic fauna were investigated in shallow (0–1 m) sediment habitats along the Skagerrak–Baltic estuarine gradient (salinity range from 4 to 34). The study area was divided into five regions, reflecting different sea-basins along the 1260 km coastline, and fauna was collected at six sites within each region. Ten replicate samples of motile epibenthic fauna were taken randomly at each site with a portable drop trap (bottom area 1 m 2) in June and September in 2004. All together, 110 taxa were found, of which 45 had a marine and 65 a limnic origin. The marine species decreased along the salinity gradient while the limnic showed the opposite pattern. Number of species and abundance of epibenthic fauna exhibited considerable local and regional variation, with a trend of increase with decreasing salinity. Fauna biomass, on the other hand was significantly higher (six times) in the Skagerrak–Kattegat area compared to the Baltic. There was a significant difference in fauna composition among regions and season, but with high similarity within the five regions, which implies that management of such coastal habitats should preferably be based on scales of a region (ca. 100 km) or smaller. Predators were the dominant functional group in all coastal regions, with a species shift from Crustacea to Insecta along the salinity gradient and with gobid fish occurring in all regions. Grazers were the second most important group in the Skagerrak–Kattegat area, but planktovores were more important in two of the Baltic regions. The importance of shallow sediment bottoms as feeding and nursery grounds for coastal fish assemblages is discussed and compared throughout the investigated area.
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