Abstract Filter‐feeding mussels couple benthic and pelagic environments and create biogeochemical hot spots. Mussels may exert either top‐down control (via filtration) or bottom‐up stimulation (via biodeposition and excretion) of primary producers. Mussel metabolism may be species‐specific and the disappearance of native species or their replacement by invasive species may affect ecosystem functioning, notably gas exchange, nutrient fluxes, and stoichiometry at the sediment–water interface. In this study, we tested experimentally how native (unionids) and invasive (dreissenids) mussels, singly and in association, affect benthic fluxes of dissolved gas and nutrients in the light and in the dark, and indirectly phytoplankton growth from a freshwater estuary, the Curonian Lagoon, where the two species of mussel coexist. We show that native and invasive mussels stimulated O2 consumption and the production of total dissolved inorganic carbon and N2 increasing sediment heterotrophy and nutrient regeneration, with species‐specific effects on nutrient stoichiometry and algal growth. Ammonium and SiO2 exchanges were similar for both species, while soluble reactive phosphorus fluxes and excretion rates were significantly higher in sediments with dreissenids. Phytoplankton growth was also significantly higher in the presence of dreissenids as compared to unionids. Dreissenid mussels decreased the dissolved inorganic N to P ratio of regenerated nutrients and may favour the growth of cyanobacteria. Hence, the replacement of native with invasive mussels may produce large changes in benthic nutrient cycling and in phytoplankton growth and community composition.
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