Rusty C. Holleman

Coupling of Sea Level Rise, Tidal Amplification, and Inundation

AbstractWith the global sea level rising, it is imperative to quantify how the dynamics of tidal estuaries and embayments will respond to increased depth and newly inundated perimeter regions. With increased depth comes a decrease in frictional effects in the basin interior and altered tidal amplification. Inundation due to higher sea level also causes an increase in planform area, tidal prism, and frictional effects in the newly inundated areas. To investigate the coupling between ocean forcing, tidal dynamics, and inundation, the authors employ a high-resolution hydrodynamic model of San Francisco Bay, California, comprising two basins with distinct tidal characteristics. Multiple shoreline scenarios are simulated, ranging from a leveed scenario, in which tidal flows are limited to present-day shorelines, to a simulation in which all topography is allowed to flood. Simulating increased mean sea level, while preserving original shorelines, produces additional tidal amplification. However, flooding of adj...

Stratified Turbulence and Mixing Efficiency in a Salt Wedge Estuary

AbstractHigh-resolution observations of velocity, salinity, and turbulence quantities were collected in a salt wedge estuary to quantify the efficiency of stratified mixing in a high-energy environment. During the ebb tide, a midwater column layer of strong shear and stratification developed, exhibiting near-critical gradient Richardson numbers and turbulent kinetic energy (TKE) dissipation rates greater than 10−4 m2 s−3, based on inertial subrange spectra. Collocated estimates of scalar variance dissipation from microconductivity sensors were used to estimate buoyancy flux and the flux Richardson number Rif. The majority of the samples were outside the boundary layer, based on the ratio of Ozmidov and boundary length scales, and had a mean Rif = 0.23 ± 0.01 (dissipation flux coefficient Γ = 0.30 ± 0.02) and a median gradient Richardson number Rig = 0.25. The boundary-influenced subset of the data had decreased efficiency, with Rif = 0.17 ± 0.02 (Γ = 0.20 ± 0.03) and median Rig = 0.16. The relationship be...

Turbulent and numerical mixing in a salt wedge estuary : dependence on grid resolution, bottom roughness, and turbulence closure

The Connecticut River is a tidal salt wedge estuary, where advection of sharp salinity gradients through channel constrictions and over steeply sloping bathymetry leads to spatially heterogeneous stratification and mixing. A 3-D unstructured grid finite-volume hydrodynamic model (FVCOM) was evaluated against shipboard and moored observations, and mixing by both the turbulent closure and numerical diffusion were calculated. Excessive numerical mixing in regions with strong velocities, sharp salinity gradients, and steep bathymetry reduced model skill for salinity. Model calibration was improved by optimizing both the bottom roughness (z0), based on comparison with the barotropic tidal propagation, and the mixing threshold in the turbulence closure (steady state Richardson number, Rist), based on comparison with salinity. Whereas a large body of evidence supports a value of Rist 0.25, model skill for salinity improved with Rist 0.1. With Rist 5 0.25, numerical mixing contributed about 1/2 the total mixing, while with Rist 5 0.10 it accounted for 2/3, but salinity structure was more accurately reproduced. The combined contributions of numerical and turbulent mixing were quantitatively consistent with high-resolution measurements of turbulent mixing. A coarser grid had increased numerical mixing, requiring further reductions in turbulent mixing and greater bed friction to optimize skill. The optimal Rist for the fine grid case was closer to 0.25 than for the coarse grid, suggesting that additional grid refinement might correspond with Rist approaching the theoretical limit. Numerical mixing is rarely assessed in realistic models, but comparisons with high-resolution observations in this study suggest it is an important factor.

A crab swarm at an ecological hotspot: patchiness and population density from AUV observations at a coastal, tropical seamount

A research cruise to Hannibal Bank, a seamount and an ecological hotspot in the coastal eastern tropical Pacific Ocean off Panama, explored the zonation, biodiversity, and the ecological processes that contribute to the seamount’s elevated biomass. Here we describe the spatial structure of a benthic anomuran red crab population, using submarine video and autonomous underwater vehicle (AUV) photographs. High density aggregations and a swarm of red crabs were associated with a dense turbid layer 4–10 m above the bottom. The high density aggregations were constrained to 355–385 m water depth over the Northwest flank of the seamount, although the crabs also occurred at lower densities in shallower waters (∼280 m) and in another location of the seamount. The crab aggregations occurred in hypoxic water, with oxygen levels of 0.04 ml/l. Barcoding of Hannibal red crabs, and pelagic red crabs sampled in a mass stranding event in 2015 at a beach in San Diego, California, USA, revealed that the Panamanian and the Californian crabs are likely the same species, Pleuroncodes planipes, and these findings represent an extension of the southern endrange of this species. Measurements along a 1.6 km transect revealed three high density aggregations, with the highest density up to 78 crabs/m2, and that the crabs were patchily distributed. Crab density peaked in the middle of the patch, a density structure similar to that of swarming insects.

Three-dimensional wave-coupled hydrodynamics modeling in South San Francisco Bay

In this paper, we present a numerical model to simulate wind waves and hydrodynamics in the estuary. We employ the unstructured-grid SUNTANS model for hydrodynamics, and within this model we implement a spectral wave model which solves for transport of wave action density with the finite-volume formulation. Hydrodynamics is coupled to the wave field through the radiation stress. Based on the unstructured grid and finite-volume formulation of SUNTANS, the radiation stress is implemented in a way that directly calculates the divergence of transport of the wave-induced orbital velocity. A coupled hydrodynamics-wave simulation of San Francisco Bay is then performed. Through the input of wind forcing that is obtained from the reconstructed wind field, the model is capable of predicting wave heights that are in good agreement with the field measurements. We examine the importance of modeling sea bed dissipation in muddy shallow water environments by using a bottom friction model and a bed mud model with different mud layer thicknesses. Moreover, currents driven by wave shoaling and dissipation are investigated in the presence of abrupt bathymetric change. We find that spatially varying wave heights induced by spatially heterogeneous bottom mud dissipation produce wave-driven currents that are stronger than those induced by wave shoaling and can be of the same order as the tidal currents in shallow water. HighlightsAn unstructured-grid model is presented to simulate hydrodynamics under wind-wave and tidal forcing.Simulations are performed to study wave-coupled hydrodynamics in San Francisco Bay.Currents driven by waves are investigated in the presence of abrupt bathymetric change.

Exchange Between an Estuary and an Intertidal Marsh and Slough

The hydrodynamic characteristics of small, intertidal perimeter habitats make flushing and residence times in these environments difficult to quantify using conventional approaches. The flooding and draining of intertidal shallows surrounding small perimeter sloughs result in large volume changes relative to total system volume during each tidal cycle. In such environments, an Eulerian framework of flushing and residence time may not be the best approach for quantifying tidal exchange; thus, alternative approaches should be considered in analyzing hydrodynamic exchange in small perimeter habitats. In this study, the results of applying such an approach to a small intertidal perimeter slough in South San Francisco Bay are presented. Previous work has shown that hydrodynamic exchange in an estuarine system can be analyzed by making Eulerian measurements of hydrodynamic fluxes and binning them according to salinity and temperature classes, thus providing a quasi-Lagrangian method of analyzing exchange and transport in an estuarine system. We apply a method which uses this approach to estimate the volumetric exchange ratio M, which is used to estimate the tidal exchange within an estuary during each tidal cycle. We find that the estimation of volumetric exchange ratios and the calculation of hydrodynamic residence times in estuarine systems can be complicated by mixing conditions associated with very strong tidal forcing, particularly in small-volume systems such as small perimeter sloughs, where the tidal prism can be on the scale of or greater than the total system volume.

Hydraulics and mixing in a laterally divergent channel of a highly stratified estuary

Author Posting.

Three‐Dimensional Modeling of Fine Sediment Transport by Waves and Currents in a Shallow Estuary

A suspended sediment transport model is implemented in the unstructured-grid SUNTANS model and applied to study fine-grained sediment transport in South San Francisco Bay. The model enables calculation of suspension of bottom sediment based on combined forcing of tidal currents and wind waves. We show that accurate results can be obtained by employing two-size classes which are representative of microflocs and macroflocs in the Bay. A key finding of the paper is that the critical calibration parameter is the ratio of the erosion of the microflocs to macroflocs from the bed. Different values of this erosion ratio are needed on the shallow shoals and deeper channels because of the different nature of the sediment dynamics in these regions. Application of a spatially variable erosion ratio and critical shear stress for erosion is shown to accurately reproduce observed suspended sediment concentration at four-field sites located along a cross-channel transect. The results reveal a stark contrast between the behavior of the suspended sediment concentration on the shoals and in the deep channel. Waves are shown to resuspend sediments on the shoals, although tidal and wind-generated currents are needed to mix the thin wavedriven suspensions into the water column. The contribution to the suspended sediment concentration in the channel by transport from the shoals is similar in magnitude to that due to local resuspension. However, the local contribution is in phase with strong bottom currents which resuspend the sediments, while the contribution from the shoals peaks during low-water slack tide.