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Abstract Biophysical cohesion, introduced predominantly by Extracellular Polymeric Substances (EPS) during mineral flocculation in subaqueous environments, plays important role in morphodynamics, biogeochemical cycles and ecosystem processes. However, the mechanism of how EPS functioning with cohesive particles and affects settling behaviors remain poorly understood. We measure initial flocculation rate, floc size and settling velocity of mineral and artificial EPS (Xanthan gum) mixtures. Combining results from these and previous studies demonstrate coherent intensification of EPS-related flocculation compare with those of pure mineral and oil-mineral mixtures. Importantly, the presence of EPS fundamentally changes floc structure and reduces variability of settling velocity. Measured data shows that ratios of microfloc and macrofloc settling velocity for pure mineral flocs is 3.9 but greatly reduced to a lowest value of 1.6 due to biological EPS addition. The low variability of settling velocity due to EPS participation explains the seemingly inconsistent results previously observed between field and laboratory studies. 

Abstract We conducted field work in South San Francisco Bay to examine cohesive sediment flocculation dynamics in a shallow, wave‐ and current‐driven estuarine environment. Drawing on data collected using a suite of acoustic and optical instrumentation over three distinct seasons, we found that the factors driving floc size variability differed substantially when comparing locally sourced sediment (i.e., through wave‐driven resuspension) to suspended sediment advected from upstream. Statistical analysis of our extensive field data revealed additional seasonal variability in these trends, with wave stress promoting floc breakup during the summer and winter months, and biological processes encouraging floc growth during the spring productive period. Combining these data with fractal dimension estimates, we found that seasonally varying floc composition can lead to differences in floc settling velocity by a factor of approximately two to five for a given floc size. Finally, by analyzing co‐located turbulence and sediment flux measurements from the bottom boundary layer, we present evidence that the relationship between floc size and the inverse turbulent Schmidt number varies with floc structure. These results can be used to inform sediment transport modeling parameterizations in estuarine environments. 

Abstract Over the course of a year, we conducted three field deployments in South San Francisco Bay to examine seasonal variability in bottom drag. Our data consisted of turbulence measurements both within and outside the bottom boundary layer and benthic characterization surveys adjacent to our study site. Our results suggest that canopies of benthic worm and amphipod feeding tubes, which were denser during summer, can increase the drag coefficient by up to a factor of three relative to the smoother beds found in winter and spring. The extent of the drag increase varied depending on the measurement device, with the greatest increase inferred by measurements taken further from the bed. The small scale and temporally varying population densities of these living roughness elements pose significant challenges for hydrodynamic models, and future work is needed to begin incorporating benthic biology statistics into drag coefficient parameterizations. 

Abstract We took field observations on the shallow shoals of South San Francisco Bay to examine how sediment‐induced stratification affects the mean flow and mixing of momentum and sediment throughout the water column. A Vectrino Profiler measured near‐bed velocity and suspended sediment concentration profiles, which we used to calculate profiles of turbulent sediment and momentum fluxes. Additional turbulence statistics were calculated using data from acoustic Doppler velocimeters placed throughout the water column. Results showed that sediment‐induced stratification, which was set up by strong near‐bed wave shear, can reduce the frictional bottom drag felt by the mean flow. Measured turbulence statistics suggest that this drag reduction is caused by stratification suppressing near‐bed turbulent fluxes and reducing turbulent kinetic energy dissipation. Turbulent sediment fluxes, however, were not shown to be limited by sediment‐induced stratification. Finally, we compared our results to a common model parameterization which characterizes stratification through a stability parameter modification to the turbulent eddy viscosity and suggest a new nondimensional parameter that may be better suited to represent stratification when modeling oscillatory boundary layer flows. 

We present direct numerical simulation results of a wave-current boundary layer in a current-dominated flow regime (wave driven to steady current ratio of 0.34) over bumpy walls for hydraulically smooth flow conditions (wave orbital excursion to roughness ratio of 10). The turbulent, wave-current channel flow has a friction Reynolds number of $350$ and a wave Reynolds number of $351$ . At the lower boundary, a bumpy wall is introduced with a direct forcing immersed boundary method, while the top wall has a free-slip boundary condition. Despite the hydraulically smooth nature of the wave-driven flow, the phase variations of the turbulent statistics for the bumpy wall case were found to vary substantially when compared with the flat wall case. Results show that the addition of weak waves to a steady current over flat walls has a negligible effect on the turbulence or bottom drag. However, the addition of weak waves to a steady current over bumpy walls has a significant effect through enhancement of the Reynolds stress (RS) accompanied by a drag coefficient increase of $$11\,\%$$ relative to the steady current case. This enhancement occurs just below the top of the roughness elements during the acceleration portion of the wave cycle: Turbulent kinetic energy (TKE) is subsequently transported above the roughness elements to a maximum height of roughly twice the turbulent Stokes length. We analyse the TKE and RS budgets to understand the mechanisms behind the alterations in the turbulence properties due to the bumpy wall. The results provide a mechanistic picture of the differences between bumpy and flat walls in wave-current turbulent boundary layers and illustrate the importance of bumpy features even in weakly energetic wave conditions. 

Abstract Natural sediment flocs are fragile, highly irregular, loosely bound aggregates comprising minerogenic and organic material. They contribute a major component of suspended sediment load and are critical for the fate and flux of sediment, carbon and pollutants in aquatic environments. Understanding their behaviour is essential to the sustainable management of waterways, fisheries and marine industries. For several decades, modelling approaches have utilised fractal mathematics and observations of two dimensional (2D) floc size distributions to infer levels of aggregation and predict their behaviour. Whilst this is a computationally simple solution, it is highly unlikely to reflect the complexity of natural sediment flocs and current models predicting fine sediment hydrodynamics are not efficient. Here, we show how new observations of fragile floc structures in three dimensions (3D) demonstrate unequivocally that natural flocs are non-fractal. We propose that floc hierarchy is based on observations of 3D structure and function rather than 2D size distribution. In contrast to fractal theory, our data indicate that flocs possess characteristics of emergent systems including non-linearity and scale-dependent feedbacks. These concepts and new data to quantify floc structures offer the opportunity to explore new emergence-based floc frameworks which better represent natural floc behaviour and could advance our predictive capacity.