The effects of advective pore water exchange driven by shallow water waves on the oxygen distribution in a permeable (k ϭ 3.3 ϫ 10 Ϫ12 to 4.9 ϫ 10 Ϫ11 m 2 ) natural sediment were studied with a planar oxygen optode in a wave tank. Our experiments demonstrate that pore water flow driven by the interaction of sediment topography and oscillating boundary flow changes the spatial and temporal oxygen distribution in the upper sediment layer. Oxygenated water intruding in the ripple troughs and deep anoxic pore water drawn to the surface under the ripple crests create an undulating oxic-anoxic boundary within the upper sediment layer, mirroring the topographical features of the sediment bed. Anoxic upwelling zones under ripple crests can separate the oxic sediment areas of neighboring ripple troughs with steep horizontal oxygen concentration gradients. The optode showed that migrating wave ripples are trailed by their pore water flow field, alternately exposing sediment volumes to oxic and anoxic pore water, which can be a mechanism for remobilizing particulate oxidized metal precipitates and for promoting coupled nitrification-denitrification. More rapid ripple migration (experimental threshold ϳ20 cm h Ϫ1) produces a continuous oxic surface layer that inhibits the release of reduced substances from the bed, which under slowly moving ripples is possible through the anoxic vertical upwelling zones. Swift, dramatic changes in oxygen concentration in the upper layers of permeable seabeds because of surface gravity waves require that sediment-dwelling organisms are tolerant to anoxia or highly mobile and enhance organic matter mineralization.The dominant boundary layer flows in shallow marine environments are those generated by surface gravity waves. This dominance is reflected by the presence of wave ripples structuring large areas of shallow sandy seabeds that are abundant in coastal, estuarine, and shelf environments. Most of these sandy sediments are permeable (k Ͼ 10 Ϫ12 m 2 ) and thus allow interstitial water motion. Pressure differences at the sediment-water interface might drive interfacial solute transport through the surface layers of these beds. This advective transport can exceed transport by molecular diffusion by several orders of magnitude (Huettel and Webster 2001). In contrast, the major transport mechanisms in fine-grained muddy sediments are molecular diffusion and locally bioturbation (Berner 1980;Aller 1982).Increased fluid exchange between sediment and overlying water affects the oxygen dynamics in permeable sediments and therefore also affects biogeochemical processes. Booij 1 Corresponding author (eprecht@mpi-bremen.de). 2 Present address: Florida State University, Department of Oceanography, Tallahassee, FL 32306-4320. AcknowledgmentsBo Barker Jørgensen is acknowledged for support and constant interest in this work. Hans Røy is thanked for initial discussions, helpful comments, and help during fieldwork. For assistance with the planar oxygen optodes, Gerhard Holst and Björn Grunwald are a...

The effects of surface gravity waves on pore-water release from permeable sediment (k ϭ 1.3-1.8 ϫ 10 Ϫ11 m 2 ) in shallow water were studied in a wave tank. Our tracer experiments demonstrated that shallow-water waves can increase fluid exchange between sandy sediment and overlying water 50-fold, relative to the exchange by molecular diffusion. The main driving force for this increased exchange are the pressure gradients generated by the interaction of oscillating boundary flows and sediment wave ripples. These gradients produce a pore-water flow field, with a regular pattern of intrusion and release zones, that migrates with ripple propagation. The ensuing topography-related filtering rates in the wave tank ranged from 60 to 590 L m Ϫ2 d Ϫ1 and exceeded the solute exchange rates caused by hydrostatic wave pumping (38 L m Ϫ2 d Ϫ1 ) and initial molecular diffusion (corresponding to 10-12 L m Ϫ2 d Ϫ1 ). Wave-induced filtration is ecologically relevant because permeable sandy sediments are very abundant on the continental margins and can be converted into effective filter systems, which suggests that these sediments are sites for rapid mineralization and recycling. We propose that the wave influenced continental shelf may be subdivided into two zones: a shallow zone (water depth Ͻ wavelength/2), where wave orbital motion at the sea floor creates ripples and causes topography related advective filtering; and a deeper zone (wavelength/2 Ͻ water depth Ͻ wavelength), where wave pumping enhances interfacial exchange by hydrostatic pressure oscillations.Physical and biological transport link the biogeochemical processes in the water column and sediment. Whereas molecular diffusion and, locally, also bioturbation are the major transport mechanisms in the cohesive, fine-grained deep-sea deposits (Berner 1980;Aller 1982Aller , 2001), solute transport caused by pore-water flows increases in importance in permeable sandy shelf sediments. Here, boundary layer flows, interacting with sea-bed topography, induce pressure differences at the sediment-water interface that lead to pore-water motion in permeable sediments. The ensuing advective transport can exceed transport by molecular diffusion by several orders of magnitude (Huettel and Webster 2001).In areas where water depth (D) is smaller than half the wavelength () of the surface gravity waves, oscillating flows are generated at the sediment-water interface by the wave orbital-water motion (e.g., Denny 1988). Webb andTheodor (1968, 1972) showed, by injecting dyed water into coarse sandy nearshore sediment and observing its reappearance at the sediment surface, that such oscillating boundary flows could drive sediment-water-interfacial fluxes. The trajectories of pore-water particles under a rippled bed over one wave period were calculated by Shum (1992). His results suggested that the zone of advection extends several ripple heights below the sediment surface over a wide range of wave conditions and sediment characteristics. Indications that surface gravity waves may b...

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We used a wave tank to study the influence of pore-water flow and diffusive transport on the degradation of labile particular organic matter (POM: Ulva lactuca pieces) embedded in permeable sediment. Pore-water advection, induced by the interaction of the wave-driven oscillatory boundary flow and stationary sediment ripples, reproducibly exposed POM buried in the top 2 cm of the sediment to oxic or anoxic conditions lasting between days and weeks. Planar oxygen optodes together with carbon and nitrogen analyses were used to visualize and quantify the degradation rates. Oxygen consumption rates (OCR) were up to 18-times higher at locations of the buried POM compared to the surrounding sediment. Elevated OCR were also detected downstream the POM locations. Despite high permeability of the sediment and exposure to oxygenated pore-water flows, suboxic and anoxic sites and suboxic pore-water ''plumes'' developed at and downstream of the locations of POM in otherwise oxygenated sediment regions. The carbon loss of the buried U. lactuca discs derived from the OCR measurements was only 4-15% of that measured by the carbon analysis of the recovered pieces, suggesting that the bacterial degradation of POM and the final degradation of dissolved organic matter (DOM) were spatially decoupled by the pore-water flow. Advection can thus enhance the rate of organic matter degradation by efficiently distributing DOM from the ''hotspots'' of organic matter mineralization to larger volumes of permeable sediments and associated microbial communities.Permeable sediments are abundant in the global continental shelf regions (Emery 1968). These nonaccumulating sands are generally poor in organic carbon and have been considered long time as relatively inactive habitats that do not contribute substantially to the cycling of organic matter (Boudreau et al. 2001). Recent studies, however, indicate that the low concentration of organics is more likely the result of rapid turnover and high exchange rates (Huettel et al. 1998; Rusch et al. 2003). When the interaction of the boundary-layer flow (e.g., unidirectional or oscillatory flow induced by currents and gravity surface waves, respectively) and sediment topography enables dynamic advective porewater flow, the solute exchange at the sediment-water interface can exceed transport by molecular diffusion by several

22Many coral reef communities thriving in inshore coastal waters characterised by chronically high 23 natural turbidity (>5 mg.l -1 ) have adapted to low light (<200 µmol photons m -2 s -1 ) and high 24 sedimentation rates (>10 mg.cm 2 .day -1 ). Yet, short (hours) acute sediment stress events driven by 25 wind waves, dredging operations involving suction or screening, or shipping activities with vessel 26 wake or propeller disturbance, can result in a rise in turbidity above the natural background level. 27Although these may not be lethal to corals given the time frame, there could be a considerable impact 28 on photo-trophic energy production. A novel sediment delivery system was used to quantify the 29 effects of three acute sediment resuspension stress events (turbidity = 100, 170, 240 mg. l ). Merulina was the least tolerant to acute sediment 36 resuspension with a photosynthesis and respiration ratio (P/R ratio) of <1.0 when turbidity levels 37 reached >170 mg.l -1

Flume tanks are becoming increasingly important research tools in aquatic ecology, to link biological to hydrodynamical processes.There is no such thing as a ''standard flume tank'', and no flume tank is suitable for every type of research question. A series of experiments has been carried out to characterise and compare the hydrodynamic characteristics of 12 different flume tanks that are designed specifically for biological research. These facilities are part of the EU network BioFlow. The flumes could be divided into four basic design types: straight, racetrack, annular and field flumes. In each facility, two vertical velocity profiles were 2006 measured: one at 0.05 m s -1 and one at 0.25 m s -1 . In those flumes equipped with Acoustic Doppler Velocimeters (ADV), time series were also recorded for each velocity at two heights above the bottom: 0.05 m and 20% of the water depth. From these measurements turbulence characteristics, such as TKE and Reynolds stress, were derived, and autocorrelation spectra of the horizontal along-stream velocity component were plotted. The flume measurements were compared to two sets of velocity profiles measured in the field.Despite the fact that some flumes were relatively small, turbulence was fully developed in all channels. Straight and racetrack flumes generally produced boundary layers with a clearly definable logarithmic layer, similar to measurements in the field taken under steady flow conditions. The two annular flumes produced relatively thin boundary layers, presumably due to secondary flows developing in the curved channels. The profiles in the field flumes also differed considerably from the expected log profile. This may either have been due the construction of the flume, or due to unsteady conditions during measurement. Constraints imposed by the different flume designs on the suitability for different types of boundary layer research, as well as scaling issues are discussed.

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