Description: Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N‐loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of N2O which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of N2O within the sediment supports a subset of Flavobacteriia which appear to be specialized on N2O reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine N2O emissions.

Description: Sandy sediments cover 50–60% of the continental shelves and are highly efficient bioreactors in which organic carbon is remineralized and inorganic nitrogen is reduced to N2. As such they seem to play an important role, buffering the open ocean from anthropogenic nitrogen inputs and likely remineralizing the vast amounts of organic matter formed in the highly productive surface waters. To date however, little is known about the interrelation between porewater transport, grain properties and microbial colonization and the consequences for remineralization rates in sandy sediments. To constrain the effect of theses factors on remineralization in silicate sands, we incubated North Sea sediments in flow-through reactors after separating into five different grain size fractions. Bulk sediment and sediment grain properties were measured along with microbial colonization and cell abundances, oxygen consumption and denitrification rates. Volumetric oxygen consumption ranged from 14 to 77 µmol O2 l−1 h−1 while nitrogen-loss via denitrification was between 3.7 and 8.4 µmol N l−1 h−1. Oxygen consumption and denitrification rates were linearly correlated to the microbial cell abundances, which ranged from 2.9 to 5.4·108 cells cm−3. We found, that cell abundance and consumption rates in sandy sediments are influenced (i) by the surface area available for microbial colonization and (ii) by the exposure of these surfaces to the solute-supplying porewater flow. While protective structures such as cracks and depressions promote microbial colonization, the oxygen demand is only met by good ventilation of these structures, which is supported by a high sphericity of the grains. Based on our results, spherical sand grains with small depressions, i.e. golf ball like structures, provide the optimal supporting mineral structure for microorganisms on continental shelves.

Description: Advective flows of seawater and fresh groundwater through coastal aquifers form a unique ecohydrological interface, the subterranean estuary (STE). Here, freshly produced marine organic matter and oxygen mix with groundwater, which is low in oxygen and contains aged organic carbon (OC) from terrestrial sources. Along the groundwater flow paths, dissolved organic matter (DOM) is degraded and inorganic electron acceptors are successively used up. Because of the different DOM sources and ages, exact degradation pathways are often difficult to disentangle, especially in high-energy environments with dynamic changes in beach morphology, source composition, and hydraulic gradients. From a case study site on a barrier island in the German North Sea, we present detailed biogeochemical data from freshwater lens groundwater, seawater, and beach porewater samples collected over different seasons. The samples were analyzed for physico-chemistry (e.g., salinity, temperature, dissolved silicate), (reduced) electron acceptors (e.g., oxygen, nitrate, and iron), and dissolved organic carbon (DOC). DOM was isolated and molecularly characterized via soft-ionization ultra-high-resolution mass spectrometry, and molecular formulae were identified in each sample. We found that the islands’ freshwater lens harbors a surprisingly high DOM molecular diversity and heterogeneity, possibly due to patchy distributions of buried peat lenses. Furthermore, a comparison of DOM composition of the endmembers indicated that the Spiekeroog high-energy beach STE conveys chemically modified, terrestrial DOM from the inland freshwater lens to the coastal ocean. In the beach intertidal zone, porewater DOC concentrations, lability of DOM and oxygen concentrations, decreased while dissolved (reduced) iron and dissolved silicate concentrations increased. This observation is consistent with the assumption of a continuous degradation of labile DOM along a cross-shore gradient, even in this dynamic environment. Accordingly, molecular properties of DOM indicated enhanced degradation, and “humic-like” fluorescent DOM fraction increased along the flow paths, likely through accumulation of compounds less susceptible to microbial consumption. Our data indicate that the high-energy beach STE is likely a net sink of OC from the terrestrial and marine realm, and that barrier islands such as Spiekeroog may act as efficient “digestors” of organic matter.

Description: Permeable sediments are found wide spread in river beds and on continental shelves. The transport of these sediments is forced by bottom water currents and leads to the formation of bedforms such as ripples and dunes. The bottom water flow across the bedforms results in pressure gradients that drive pore water flow within the permeable sediment and enhance the supply of reactive substrates for biogeochemical processes. This transport-reaction system has been extensively studied for the case of stationary bedforms, whereas bedform migration—the most ubiquitous form of sediment transport—has been often ignored. To study the impact of sediment transport on pore water flow, we incorporated an empirical model of bedform migration into a numerical transport-reaction model for porous media, using oxygen as reactive solute. The modeled oxygen flux changes significantly as soon as the sediment divides into an upper mobile layer (migrating bedform) and a stationary layer underneath. The bedform is increasingly flushed with oxic bottom water, whereas pressure gradients and pore water flow reverse at increasing rate underneath the bedform. This suppresses net pore water displacement and reduces the oxygen penetration depth up to 90%. In effect, the overall oxygen uptake decreases significantly with bedform migration although bottom water velocities increase. This counterintuitive effect is systematically described for a range of different sediment types, current velocities, and respiration rates and should be considered in future studies.

Description: We investigated microbial pathways of nitrogen transformation in highly permeable sediments from the German Bight (South-East North Sea) by incubating sediment cores percolated with 15N-labeled substrates under near in situ conditions. In incubations with added math formula, production of math formula occurred while the sediment was oxic, indicating ammonia oxidation. Similarly, math formula production during math formula incubations indicated nitrite oxidation. Taken together these findings provide direct evidence of high nitrification rates within German Bight sands. The production of 15N-N2 on addition of math formula revealed high denitrification rates within the sediment under oxic and anoxic conditions. Denitrification rates were strongly and positively correlated with oxygen consumption rates, suggesting that denitrification is controlled by organic matter availability. Nitrification and denitrification rates were of the same magnitude and the rapid production of 15N-N2 in incubations with added math formula confirmed close coupling of the two processes. Areal rates of N-transformation were estimated taking advective transport of substrates into account and integrating volumetric rates over modeled oxygen and nitrate penetration depths, these ranged between 22 μmol N m−2 h−1 and 94 μmol N m−2 h−1. Furthermore, results from the 15N-labeling experiments show that these subtidal permeable sediments are, in sharp contrast to common belief, a substantial source of N2O. Our combined results show that nitrification fuels denitrification by providing an additional source of nitrate, and as such masks true N-losses from these highly eutrophic sediments. Given the widespread occurrence of anthropogenically influenced permeable sediments, coupled benthic nitrification–denitrification might have an important but so far neglected role in N-loss from shelf sediments.

Description: A series of multibeam bathymetry surveys revealed the emergence of a large pockmark field in the southeastern North Sea. Covering an area of around 915 km2, up to 1,200 pockmarks per square kilometer have been identified. The time of emergence can be confined to 3 months in autumn 2015, suggesting a very dynamic genesis. The gas source and the trigger for the simultaneous outbreak remain speculative. Subseafloor structures and high methane concentrations of up to 30 mmol/l in sediment pore water samples suggest a source of shallow biogenic methane from the decomposition of post-glacial deposits in a paleo river valley. Storm waves are suggested as the final trigger for the eruption of the gas. Due to the shallow water depths and energetic conditions at the presumed time of eruption, a large fraction of the released gas must have been emitted to the atmosphere. Conservative estimates amount to 5 kt of methane, equivalent to 67% of the annual release from the entire North Sea. These observations most probably describe a reoccurring phenomenon in shallow shelf seas, which may have been overlooked before because of the transient nature of shallow water bedforms and technology limitations of high resolution bathymetric mapping.

Description: Most anoxic environments are populated by small (〈10 μm) heterotrophic eukaryotes that prey on different microbial community members. How predatory eukaryotes engage in beneficial interactions with other microbes has rarely been investigated so far. Here, we studied an example of such an interaction by cultivating the anerobic marine flagellate, Carpediemonas frisia sp. nov. (supergroup Excavata), with parts of its naturally associated microbiome. This microbiome consisted of so far uncultivated members of the Deltaproteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Nanoarchaeota. Using genome and transcriptome informed metabolic network modeling, we showed that Carpediemonas stimulated prokaryotic growth through the release of predigested biomolecules such as proteins, sugars, organic acids and hydrogen. Transcriptional gene activities suggested niche separation between biopolymer degrading Bacteroidetes, monomer utilizing Firmicutes and Nanoarchaeota and hydrogen oxidizing Deltaproteobacteria. An efficient metabolite exchange between the different community members appeared to be promoted by the formation of multispecies aggregates. Physiological experiments showed that Carpediemonas could also benefit from an association to these aggregates, as it facilitated the removal of inhibiting metabolites and increased the availability of prey bacteria. Taken together, our results provide a framework to understand how predatory microbial eukaryotes engage, across trophic levels, in beneficial interactions with specific prokaryotic populations.

Description: Permeable sediments are found wide spread in river beds and on continental shelves. The transport of these sediments is forced by bottom water currents and leads to the formation of bedforms such as ripples and dunes. The bottom water flow across the bedforms results in pressure gradients that drive pore water flow within the permeable sediment and enhance the supply of reactive substrates for biogeochemical processes. This transport-reaction system has been extensively studied for the case of stationary bedforms, whereas bedform migration—the most ubiquitous form of sediment transport—has been often ignored. To study the impact of sediment transport on pore water flow, we incorporated an empirical model of bedform migration into a numerical transport-reaction model for porous media, using oxygen as reactive solute. The modeled oxygen flux changes significantly as soon as the sediment divides into an upper mobile layer (migrating bedform) and a stationary layer underneath. The bedform is increasingly flushed with oxic bottom water, whereas pressure gradients and pore water flow reverse at increasing rate underneath the bedform. This suppresses net pore water displacement and reduces the oxygen penetration depth up to 90%. In effect, the overall oxygen uptake decreases significantly with bedform migration although bottom water velocities increase. This counterintuitive effect is systematically described for a range of different sediment types, current velocities, and respiration rates and should be considered in future studies.

Description: Large areas of the oceanic shelf are composed of sandy sediments through which reactive solutes are transported via porewater advection fueling active microbial communities. The advective oxygen transport in permeable sands of the North Sea was investigated under in situ conditions using a new benthic observatory to assess the dynamic interaction of hydrodynamics, sediment morphodynamics, and oxygen penetration depth. During 16 deployments, concurrent measurement of current velocity, sediment topography, and porewater oxygen concentration were carried out. In all cases the oxyclines were found at depths of 1–6 cm, correlating with the topography of stationary and migrating bedforms (ripples). Different conditions in terms of bottom water currents and bedform migration led to fluctuating oxygen penetration depths and, hence, highly variable redox conditions in up to 2.5 cm thick layers beneath the surface. Volumetric oxygen consumption rates of surface sediments were measured on board in flow-through reactors. Bedform migration was found to reduce consumption rates by up to 50%, presumably caused by the washout of organic carbon that is otherwise trapped in the pore space of the sediment. Based on the observations we found oxygen penetration depths to be largely controlled by oxygen consumption rates, grain size, and current velocity. These controlling variables are summarized by an adapted Damköhler number which allows for prediction of oxygen penetretion depths based on a simple scaling law. By integrating the oxygen consumption rates over the oxygen penetration depth, oxygen fluxes of 8–34 mmol m−2 d−1 were estimated