Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 µM O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.

Under current circumstances, coastal lagoons are net emitters of nitrous oxide (N₂O) to the atmosphere. We hypothesize that widespread nitrogen‐driven coastal eutrophication will enhance N₂O production and emissions from coastal lagoons. Here, we quantified spatial and temporal patterns of sediment‐water and water‐air N₂O fluxes in three large eutrophic lagoons in Europe. Annual sediment N₂O fluxes ranged between −0.3 ± 0.3 (summer) and 10.6 ± 2.0 μmol m⁻² d⁻¹ (spring). In spring, conspicuous sediment effluxes were mainly supported by high nitrate concentrations (89–202 μM) and incomplete denitrification. In summer, a small sediment influx was related to nitrate limitation (0–9 μM), potentially leading to N₂O demand for denitrification. The water‐air N₂O fluxes were comparable with benthic fluxes, indicating that sediment was the main source of N₂O to the atmosphere. The hypereutrophic Curonian Lagoon had the largest N₂O emission at 4.9 ± 2.1 μmol m⁻² d⁻¹, while the less eutrophic Oder and Vistula lagoons emitted 2.5 ± 1.0 and 2.0 ± 0.7 μmol m⁻² d⁻¹, respectively. Our observations, combined with earlier measurements in coastal lagoons worldwide, revealed a lagoon median (Q1–Q3) N₂O emission of 14.2 (2.7–29.8) Gg yr⁻¹, which is about 48% higher than previous estimates. Eutrophication driven by large nitrogen inputs is thus a significant driver of coastal N₂O emissions globally.

The combination of biogeochemical methods and molecular techniques has the potential to uncover the black-box of the nitrogen (N) cycle in bioturbated sediments. Advanced biogeochemical methods allow the quantification of the process rates of different microbial processes, whereas molecular tools allow the analysis of microbial diversity (16S rRNA metabarcoding) and activity (marker genes and transcripts) in biogeochemical hot-spots such as the burrow wall or macrofauna guts. By combining biogeochemical and molecular techniques, we analyzed the role of tube-dwelling Chironomus plumosus (Insecta, Diptera) larvae on nitrification and nitrate reduction processes in a laboratory experiment with reconstructed sediments. We hypothesized that chironomid larvae stimulate these processes and host bacteria actively involved in N-cycling. Our results suggest that chironomid larvae significantly enhance the recycling of ammonium (80.5 ± 48.7 µmol m⁻² h⁻¹) and the production of dinitrogen (420.2 ± 21.4 µmol m⁻² h⁻¹) via coupled nitrification–denitrification and the consumption of water column nitrates. Besides creating oxygen microniches in ammonium-rich subsurface sediments via burrow digging and ventilation, chironomid larvae serve as hot-spots of microbial communities involved in N-cycling. The quantification of functional genes showed a significantly higher potential for microbial denitrification and nitrate ammonification in larvae as compared to surrounding sediments. Future studies may further scrutinize N transformation rates associated with intimate macrofaunal–bacteria associations.

Coastal lagoons display a wide range of physico-chemical conditions that shape benthic macrofauna communities. In turn, benthic macrofauna affects a wide array of biogeochemical processes as a consequence of feeding, bioirrigation, ventilation, and excretion activities. In this work, we have measured benthic respiration and solute fluxes in intact sediment cores with natural macrofauna communities collected from four distinct areas within the Sacca di Goro Lagoon (NE Adriatic Sea). The macrofauna community was characterized at the end of the incubations. Redundancy analysis (RDA) was used to quantify and test the interactions between the dominant macrofauna species and solute fluxes. Moreover, the relevance of macrofauna as driver of benthic nitrogen (N) redundancy analysis revealed that up to 66% of the benthic fluxes and metabolism variance was explained by macrofauna microbial-mediated N processes. Nitrification was stimulated by the presence of shallow (corophiids) in combination with deep burrowers (spionids, oligochaetes) or ammonium-excreting clams. Deep burrowers and clams increase ammonium availability in burrows actively ventilated by corophiids, which creates optimal conditions to nitrifiers. However, the stimulatory effect of burrowing macrofauna on nitrification does not necessarily result in higher denitrification as processes are spatially separated.