Observations of waves, setup, and wave-driven mean flows were made on a steep coral forereef and its associated lagoonal system on the north shore of Moorea, French Polynesia. Despite the steep and complex geometry of the forereef, and wave amplitudes that are nearly equal to the mean water depth, linear wave theory showed very good agreement with data. Measurements across the reef illustrate the importance of including both wave transport (owing to Stokes drift), as well as the Eulerian mean transport when computing the fluxes over the reef. Finally, the observed setup closely follows the theoretical relationship derived from classic radiation stress theory, although the two parameters that appear in the model-one reflecting wave breaking, the other the effective depth over the reef crest-must be chosen to match theory to data.

Phytoplankton form the basis of the marine food web and are responsible for approximately half of global carbon dioxide (CO2) fixation (∼ 50 Pg of carbon per year). Thus, these microscopic, photosynthetic organisms are vital in controlling the atmospheric CO2 concentration and Earth's climate. Phytoplankton are dependent on sunlight and their CO2-fixation activity is therefore restricted to the upper, sunlit surface ocean (that is, the euphotic zone). CO2 usually does not limit phytoplankton growth due to its high concentration in seawater. However, the vast majority of oceanic surface waters are depleted in inorganic nitrogen, phosphorus, iron and/or silica; nutrients that limit primary production in the ocean (Figure 1). Phytoplankton growth is mainly supported by either the recycling of nutrients or by reintroduction of nutrients from deeper waters by mixing. A small percentage of primary production, though, is fueled by 'external' or 'new' nutrients and it is these nutrients that determine the amount of carbon that can be sequestered long term in the deep ocean. For most nutrients such as phosphorus, iron, and silica, the external supply is limited to atmospheric deposition and/or coastal and riverine inputs, whereas their main sink is the sedimentation of particulate matter. Nitrogen, however, has an additional, biological source, the fixation of N2 gas, as well as biological sinks via the processes of denitrification and anammox. Despite the comparatively small contributions to the overall turnover of nutrients in the ocean, it is these biological processes that determine the ocean's capacity to sequester CO2 from the atmosphere on time scales of ocean circulation (∼ 1000 years). This primer will highlight shifts in the traditional paradigms of nutrient limitation in the ocean, with a focus on the uniqueness of the nitrogen cycling and its biological sources and sinks.

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 15 N-labeled substrates under near in situ conditions. In incubations with added 15 NH 3 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 N-labeling experiments show that these subtidal permeable sediments are, in sharp contrast to common belief, a substantial source of N 2 O. 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.

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 Damk€ ohler 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 22 d 21 were estimated.

Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions. We examined the response of benthic denitrification to fluctuating oxygen concentrations, finding that denitrification not only occurred at high O concentrations but was stimulated by frequent switches between oxic and anoxic conditions. Throughout a tidal cycle, in situtranscription of genes for aerobic respiration and denitrification were positively correlated within diverse bacterial classes, regardless of O concentrations, indicating that denitrification gene transcription is not strongly regulated by O in sandy sediments. This allows microbes to respond rapidly to changing environmental conditions, but also means that denitrification is utilized as an auxiliary respiration under aerobic conditions when imbalances occur in electron donor and acceptor supply. Aerobic denitrification therefore contributes significantly to N-loss in permeable sediments making the process an important sink for anthropogenic N-inputs.