16S rRNA sequences of sediment incubations from a eutrophic marine lake

Coastal ecosystems are susceptible to eutrophication and deoxygenation, which alter the redox balance of the system. Therefore, we investigated the microbial nitrogen cycling potential in the sediment of seasonally euxinic marine Lake Grevelingen in winter and summer. Porewater profiles showed ammonium (NH4+) concentrations exceeding 10 mM and depletion of electron acceptors. Activity tests revealed NH4+ oxidation potential with rates up to 53 umol g-1 day-1, also in anoxic sediment layers. A nitrifying microbial community was present in all sediment sections at a relative abundance up to 1.4%. Nitrate (NO3-), nitrite (NO2-), and nitrous oxide (N2O) reduction potential was prominent across all sediment sections, with the highest rates (167 umol NO3- g-1 day-1) observed in the upper 0-2 cm sediment in summer. Denitrification (79.3-98.4%) and dissimilatory nitrate reduction to ammonium (DNRA; 1.6-20.7%), were the major pathways for NO3- removal, as supported by the detection of the narG/napA, nirK/nirS, norB, nosZ and nrfA/otr genes at all sediment sections. The contribution of DNRA increased with depth and with the addition of electron donor, such as monomethylamine. Anaerobic ammonium oxidation (anammox) was not detected in these eutrophic sediments. Combining incubation experiments, 16S rRNA amplicon and metagenome sequencing and geochemical profiling, we shed light on the microbial nitrogen cycle in eutrophic coastal ecosystems.