Estuaries are often seen as natural filters of riverine nitrate, but knowledge of this nitrogen sink in oligotrophic systems is limited. We measured spring and summer dinitrogen production (denitrification, anammox) in muddy and non-permeable sandy sediments of an oligotrophic estuary in the northern Baltic Sea, to estimate its function in mitigating the riverine nitrate load. Both sediment types had similar denitrification rates, and no anammox was detected. In spring at high nitrate loading, denitrification was limited by likely low availability of labile organic carbon. In summer, the average denitrification rate was ~138 μmol N m. The corresponding estuarine nitrogen removal for August was ~1.2 t, of which ~93% was removed by coupled nitrification−denitrification. Particulate matter in the estuary was mainly phytoplankton derived (> 70% in surface waters) and likely based on the riverine nitrate which was not removed by direct denitrification due to water column stratification. Subsequently settling particles served as a link between the otherwise uncoupled nitrate in surface waters and benthic nitrogen removal. We suggest that the riverine nitrate brought into the oligotrophic estuary during the spring flood is gradually, and with a time delay, removed by benthic denitrification after being temporarily 'trapped' in phytoplankton particulate matter. The oligotrophic system is not likely to face eutrophication from increasing nitrogen loading due to phosphorus limitation. In response, coupled nitrification−denitrification rates are likely to stay constant, which might increase the future export of nitrate to the open sea and decrease the estuary's function as a nitrogen sink relative to the load.

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Nitrification is important in nitrogen (N) cycling of aquatic environments, but knowledge about its regulation and importance is sparse. Here we examined nitrification and ammonia oxidizers in the Baltic Sea. We investigated two sites with different catchment characteristics (agricultural and forest), the Bay of Gdánsk (south) and the Öre Estuary (north), and measured pelagic nitrification rates and abundance, composition and expression of ammonia monooxygenase (amoA) genes. Highest nitrification rates were found in the nutrient rich Bay of Gdańsk. Interestingly, abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were orders of magnitude lower than reported from other sites. Although AOA were most abundant at both sites, the highest expression levels were from AOB. Interestingly, few AOA and AOB taxa dominated amoA gene expression, with a Nitrosomarinus related phylotype showing widespread expression. AOA and AOB communities differed between sites and depths, respectively, with the composition in rivers being distinct. A storm event, causing an even depth distribution of nitrification and particles in the Bay of Gdańsk, indicated that the presence of particles stimulate nitrification. The study highlights coastal regions as dynamic sites of extensive pelagic nitrification, which may affect local food web dynamics and loss of N mediated by denitrification.

Abstract. Estuaries worldwide act as “filters” of land-derived nitrogen (N) loads, yet differences in coastal environmental settings can affect the N filter function. We investigated microbial N retention (nitrification, ammonium assimilation) and N removal (denitrification, anammox) processes in the aphotic benthic system (bottom boundary layer (BBL) and sediment) of two Baltic Sea estuaries differing in riverine N loads, trophic state, geomorphology, and sediment type. In the BBL, rates of nitrification (5–227 nmol N L−1 d−1) and ammonium assimilation (9–704 nmol N L−1 d−1) were not enhanced in the eutrophied Vistula Estuary compared to the oligotrophic Öre Estuary. No anammox was detected in the sediment of either estuary, while denitrification rates were twice as high in the eutrophied (352±123 µmol N m−2 d−1) as in the oligotrophic estuary. Particulate organic matter (POM) was mainly of phytoplankton origin in the benthic systems of both estuaries. It seemed to control heterotrophic denitrification and ammonium assimilation as well as autotrophic nitrification by functioning as a substrate source of N and organic carbon. Our data suggest that in stratified estuaries, POM is an essential link between riverine N loads and benthic N turnover and may furthermore function as a temporary N reservoir. During long particle residence times or alongshore transport pathways, increased time is available for the recycling of N until its eventual removal, allowing effective coastal filtering even at low process rates. Understanding the key controls and microbial N processes in the coastal N filter therefore requires to also consider the effects of geomorphological and hydrological features.

Coastal waters have strong gradients in dissolved organic matter (DOM) quantity and characteristics, originating from terrestrial inputs and autochthonous production. Enclosed seas with high freshwater input therefore experience high DOM concentrations and gradients from freshwater sources to more saline waters. The brackish Baltic Sea experiences such salinity gradients from east to west and from river mouths to the open sea. Furthermore, the catchment areas of the Baltic Sea are very diverse and vary from sparsely populated northern areas to densely populated southern zones. Coastal systems vary from enclosed or open bays, estuaries, fjords, archipelagos and lagoons where the residence time of DOM at these sites varies and may control the extent to which organic matter is biologically, chemically or physically modified or simply diluted with transport off-shore. Data of DOM with simultaneous measurements of dissolved organic (DO) nitrogen (N), carbon (C) and phosphorus (P) across a range of contrasting coastal systems are scarce. Here we present data from the Roskilde Fjord, Vistula and Öre estuaries and Curonian Lagoon; four coastal systems with large differences in salinity, nutrient concentrations, freshwater inflow and catchment characteristics. The C:N:P ratios of DOM of our data, despite high variability, show site specific significant differences resulting largely from differences residence time. Microbial processes seemed to have minor effects, and only in spring did uptake of DON in the Vistula and Öre estuaries take place and not at the other sites or seasons. Resuspension from sediments impacts bottom waters and the entire shallow water column in the Curonian Lagoon. Finally, our data combined with published data show that land use in the catchments seems to impact the DOC:DON and DOC:DOP ratios of the tributaries most.

Respiration is a key metabolic process in the marine environment and contemporary phytoplankton production (PhP) is commonly assumed the main driver. However, respiration in the absence of contemporary PhP, termed baseline respiration, can influence the energetics of an ecosystem and its sensitivity to hypoxia. Direct studies of baseline respiration are currently lacking. This study aims to obtain a first estimate of baseline respiration in a sub-arctic estuary and determine its contribution to plankton community respiration. Three approaches used to define baseline respiration determined the average rate to be 4.1 ± 0.1 (SE) mmol O 2 m −3 d −1. A hypsographic model at the basin scale accounting for seasonal variation estimated an annual contribution of 30% baseline respiration to planktonic respiration. There was no correlation between plankton respiration and PhP, but a significant linear dependence was found with the total carbon supply from phytoplankton and riverine input. The sum of dissolved organic carbon transported by rivers, provided by both benthic and pelagic algae, could sustain 69% of the annual plankton respiration, of which as much as 25% occurred during winter. However, only 32% of the winter season respiration was explained, indicating that unknown carbon sources exist during the winter. Nitrification had a negligible (≤2.4%) effect on baseline respiration in the system. The results show that baseline respiration accounted for a significant percentage of coastal plankton respiration when allochthonous sources dominated the carbon supply, weakening the respiration-to-PhP relationship.

The impact of synoptic scale and mesoscale variability on the Lagrangian residence time (LRT) of the surface water in the Bay of Gdańsk was investigated using the results from an eddy-resolving model. The computed LRT of 53-60 days was up to four times longer than the estimated flushing time reported by Witek et al. (2003). The highest residence times were those of Puck Bay and near the coast, shallower than 50 m water depth, especially during the winter. These sites also had the highest annual mean in LRT. During the summer, when the level of biological activity is high, the LRT distribution was very heterogeneous and patchy, possibly due to the dynamics of varying eddy field and to variable wind forcing. Long-term run tracking of the inflowing water from the Vistula River (VR) showed a broad spectrum of tracer distribution. The potential impact of a much higher LRT on the near-coastal nitrogen cycle, coastal filter function and genetic differentiation is discussed, and the consequences for coastal zone management are considered. Since residence time is the most important factor regulating nutrient cycling, the incorporation of residence time into the Marine Strategy Framework Directive descriptors would result in an improved, unbiased evaluation of good environmental status.

<p><strong>Abstract.</strong> Estuaries worldwide are known to act as <q>filters</q> of land-derived N loads, yet their variable environmental settings can affect microbial nitrogen (N) retention and removal and thus the coastal filter function. We investigated microbial N-retention (nitrification, ammonium assimilation) and N-removal (denitrification, anammox) in the aphotic benthic systems (here defined as: bottom boundary layer [BBL] and sediment) of two Baltic Sea estuaries that differ in riverine N loads, trophic state, bottom topography, and sediment type. Contrary to our expectations, nitrification rates (5–227 nmol L<sup>−1</sup> d<sup>−1</sup>) in the BBL neither differed between the eutrophied Vistula estuary and the oligotrophic Öre estuary, nor between seasons. Ammonium assimilation rates were slightly higher in the oligotrophic Öre estuary in spring but did not differ between estuaries in summer (9–704 nmol L<sup>−1</sup> d<sup>−1</sup>). In the sediment, no anammox was found in either estuary and denitrification rates were higher in the eutrophied (349 ± 117 µmol N m<sup>−2</sup> d<sup>−1</sup>) than in the oligotrophic estuary (138 ± 47 µmol N m<sup>−2</sup> d<sup>−1</sup>). Irrespective of their differences, in both estuaries the quality of the mainly phytoplankton-derived particulate organic matter (POM) – evaluated by means of C : N and POC : Chl.<i>a</i> ratios – seemed to control N-cycling processes through the availability of particulate organic N and C as substrate sources. Our data suggest, that in stratified estuaries, phytoplankton-derived POM is an essential link between riverine N loads and benthic N cycling and may function as a temporary N reservoir via long particle residence time or coastal parallel transport. Even at low process rates, effective coastal filtering would thus be achieved by the increased time available for the recycling of N via microbial retention processes until its permanent removal via denitrification.</p>