Freshwater lakes are essential hotspots for the removal of excessive anthropogenic nitrogen (N) loads transported from the land to coastal oceans. The biogeochemical processes responsible for N removal, the corresponding transformation rates and overall removal efficiencies differ between lakes, however, it is unclear what the main controlling factors are. Here, we investigated the factors that moderate the rates of N removal under contrasting trophic states in two lakes located in central Switzerland. In the eutrophic Lake Baldegg and the oligotrophic Lake Sarnen, we specifically examined seasonal sediment porewater chemistry, organic matter sedimentation rates, as well as 33-year of historic water column data. We find that the eutrophic Lake Baldegg, which contributed to the removal of 20 ± 6.6 gN m−2 year−1, effectively removed two-thirds of the total areal N load. In stark contrast, the more oligotrophic Lake Sarnen contributed to 3.2 ± 4.2 gN m−2 year−1, and had removed only one-third of the areal N load. The historic dataset of the eutrophic lake revealed a close linkage between annual loads of dissolved N (DN) and removal rates (NRR = 0.63 × DN load) and a significant correlation of the concentration of bottom water nitrate and removal rates. We further show that the seasonal increase in N removal rates of the eutrophic lake correlated significantly with seasonal oxygen fluxes measured across the water–sediment interface (R2 = 0.75). We suggest that increasing oxygen enhances sediment mineralization and stimulates nitrification, indirectly enhancing denitrification activity.

Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N 2 through microbial denitrification or anammox.

The nitrogen (N) cycle is of global importance as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbial transformation processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates in the sediments from porewater concentration gradients. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in the sediments were reflected in distinct microbial community compositions and significant differences in the abundance of various N transformation genes. Within each lake, we observed a more pronounced spatial than seasonal variability. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N2O reductase) abundance and higher nirS:nirK (nitrite reductase) ratio, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for DNRA and nitrification, and specifically a high abundance of Nitrospirae, including some capable of comammox. In general, the oligotrophic lake ecosystems had a higher microbial diversity, thus acting as an important habitat for oligotrophic microbes. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding the limitations of the N cycle response to environmental drivers.