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Models that have been developed to quantify the oxygen flux at the sediment‐water interface (SWI) generally do not explicitly consider the influence of bioroughness (mounds and burrows) and bioirrigation. We performed a numerical study of the influence of overlying water velocity, bioroughness, and bioirrigation on the oxygen flux across the SWI. We found that compared with a flat bed, bioroughness significantly increases O2 transport at the SWI as a result of enhanced turbulence and pressure differences across the roughness. Bioirrigation can also enhance O2 transport across the SWI by a factor of up to 10 when the roughness Reynolds number (Re*) is low, but the influence of bioirrigation decreases with increasing Re*. Burrows increase O2 penetration depth, and bioirrigation causes asymmetric distributions of O2 along burrows. Despite the complexity of O2 distribution in sediments, the net exchange across the SWI can be described by the relationship of O'Connor and Harvey (2008, https://doi.org/10.1029/2008WR007160) 0.25em()De/DmRe*Pe1.2=a=0.0005 when the shape is two‐dimensional or when the burrow density is low. When the burrow density is large, flow is three‐dimensional and flow interactions between burrows become important. Under these conditions the net exchange across the SWI increases by up to a factor of 4. A burrow number is introduced, Bu = [burrow density]1/2 [burrow height], to correct the coefficient in O'Connor and Harvey's relationship, that is, a = 0.005 for Bu < 0.05 and a = 0.02 for Bu ≫ 0.1.

Large eddy simulations (LESs) of turbulent flow in partially filled pipes at various filling degrees are conducted to investigate the response of the water surface to the turbulence and the secondary flow below it. LESs are validated first using experimental and direct numerical simulation data. At increasing water depth, the magnitude of water surface fluctuations increases with increasing strength of the main secondary flow. Visualizations of the instantaneous water surface and the turbulent flow underneath reveal that thin surface waves are generated by flow meandering in the shallower case, whereas surface waves in the deeper cases are influenced by the vertical velocity fluctuation. Pre-multiplied spectra of the water surface fluctuation, h′, provide further evidence of the origin of the surface waves. In the shallow flow, the peak frequency of the h′ spectra is consistent with the peak frequency of the u′ and v′ spectra, while for deeper flows, it agrees more with the w′ spectra. Furthermore, the transport patterns of the surface waves are investigated by the wavenumber-frequency spectra. Three types of surface waves are observed in the wavenumber-frequency spectra, i.e., (1) convective waves with phase velocity equaling the surface velocity, (2) irrotational dispersive gravity-capillary waves, and (3) stationary waves caused by secondary currents.

No abstract

A numerical model is developed to investigate metal release from estuarine sediments. The model includes three‐dimensional (3D) large‐eddy simulation of water above the sediment‐water interface, 3D advective and diffusive transport within sediments by both physical and biological processes (bioturbation and bioirrigation), and biogeochemical processes within the sediment including reduction of electron acceptors, acid‐base reactions, and metal sorption and precipitation. The model was applied to explore the influence of overlying water chemistry and sediment chemical, physical and biological processes on metal release from sediments. Overlying water conditions (pH, salinity, oxygen saturation) may vary diurnally due to tidal cycling and control the short‐term release of metals, while over longer times (months), metals are controlled by long‐term averages of sediment convective processes (groundwater upwelling, hyporheic exchange and bioirrigation). Metal release is significantly enhanced when there is bioroughness and bioirrigation due to local oxidation of surficial sediments.