In-situ measurements of turbulent flow over intertidal natural and degraded oyster reefs in an estuarine lagoon

Abstract Oysters are ecosystem engineers that form reefs with rough surfaces. The complex surface of a reference-condition reef contains clusters of live oysters that protrude into and interact with flows. A degraded oyster reef contains fewer live oyster clusters and subsequently has different bed roughness. Such morphological differences may translate to varied hydrodynamic function, with influence to local and larger-scale flow fields and sediment transport, as well as larval recruitment and long-term reef sustainability. The objective of this study is to compare a degraded and a reference-condition intertidal oyster reef, and assess how differences in structure (reef morphology and roughness) influence near-bed hydrodynamic function within the roughness sublayer defined by oysters. Sediment entrainment and bed deformation were observed only on the reference oyster reef, despite that mean velocities were lower than those at the degraded reef. This was attributed to slightly finer bed material and higher turbulent kinetic energy, k, at the reference reef (k = 29.2 ± 4.5 cm2/s2 with mean velocity 11.5 ± 0.6 cm/s at 1 cm above the bed) compared to the degraded reef (k = 22.6 ± 4.2 cm2/s2 with mean velocity 16.1 ± 1.7 cm/s at 1 cm above the bed). At 1 cm above the bed, shear turbulence production at the degraded reef was significantly larger than turbulence dissipation rate, while at the reference reef this pattern was observed only for time periods with low turbulent kinetic energy. For measurements 5 cm above the bed at the reference reef, shear turbulence production and turbulence dissipation rates exhibited a relatively balanced pattern, with dissipation exceeding shear production for the time period with elevated turbulence. Four bed shear stress calculation methodologies converged over the degraded oyster reef but deviated considerably at the reference oyster reef. The drag coefficient associated with bed shear stress at the reference reef was almost two times greater than that at the degraded reef and almost an order of magnitude greater than those observed at sand and mud beds.