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

Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 4743–4760, doi:10.1002/2016JC012455.Estuarine mixing is often intensified in regions where topographic forcing leads to hydraulic transitions. Observations in the salt-wedge estuary of the Connecticut River indicate that intense mixing occurs during the ebb tide in regions of supercritical flow that is accelerated by lateral expansion of the channel. The zones of mixing are readily identifiable based on echo-sounding images of large-amplitude shear instabilities. The gradient Richardson number (Ri) averaged across the mixing layer decreases to a value very close to 0.25 during most of the active mixing phase. The along-estuary variation in internal Froude number and interface elevation are roughly consistent with a steady, inviscid, two-layer hydraulic representation, and the fit is improved when a parameterization for interfacial stress is included. The analysis indicates that the mixing results from lateral straining of the shear layer, and that the rapid development of instabilities maintains the overall flow near the mixing threshold value of Ri = 0.25, even with continuous, active mixing. The entrainment coefficient can be estimated from salt conservation within the interfacial layer, based on the finding that the mixing maintains Ri = 0.25. This approach leads to a scaling estimate for the interfacial mixing coefficient based on the lateral spreading rate and the aspect ratio of the flow, yielding estimates of turbulent dissipation within the pycnocline that are consistent with estimates based on turbulence-resolving measurements.NSF Grant Number: OCE 0926427; Devonshire Scholars program2017-12-1

Stratified turbulence and mixing efficiency in a salt wedge estuary

Author Posting. © American Meteorological Society, 2016. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 46 (2016): 1769-1783, doi:10.1175/JPO-D-15-0193.1.High-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 between Rif and Rig was consistent with a turbulent Prandtl number of 1. Acoustic backscatter imagery revealed coherent braids in the mixing layer during the early ebb and a transition to more homogeneous turbulence in the midebb. A temporal trend in efficiency was also visible, with higher efficiency in the early ebb and lower efficiency in the late ebb when the bottom boundary layer had greater influence on the flow. These findings show that mixing efficiency of turbulence in a continuously forced, energetic, free shear layer can be significantly greater than the broadly cited upper bound from Osborn of 0.15–0.17.Holleman was supported by the Devonshire Scholars program. The field study and the coauthors’ contributions were supported by NSF Grant OCE 0926427.2016-11-2

Longitudinal Versus Lateral Estuarine Dynamics and Their Role in Tidal Stratification Patterns in Lower South San Francisco Bay

The dynamics of shoal‐channel estuaries require consideration of lateral gradients and transport, which can create significant intratidal variability in stratification and circulation. When the shoal‐channel system is strongly coupled by tidal exchange with mudflats, marshes, or other habitats, the gradients driving intratidal stratification variations are expected to intensify. To examine this dynamic, hydrodynamic data were collected from 27 January 2017 to 10 February 2017 in Lower South San Francisco Bay, a small subembayment fringed by extensive shallow vegetated habitats. During this deployment, salinity variations were captured through instrumentation of six stations (arrayed longitudinally and laterally) allowing for mechanisms of stratification creation and destruction to be calculated directly and compared with observed time variability of stratification at the central station. We present observation‐based calculations of longitudinal straining, longitudinal advection, lateral straining, and lateral advection. The time dependence of stratification was observed directly and calculated by summing measured longitudinal and lateral mechanisms. We found that the stratification dynamics switch between being longitudinally dominated during the middle of ebb and flood tides to being laterally dominated during the tidal transitions. This variability is driven by the interplay between tidally variable lateral density gradients and turbulent mixing. Relatively constant along‐estuary density gradients are differentially advected during flood and ebb tides, resulting in maximal lateral density gradients around tidal transitions. Simultaneous decrease in turbulent mixing at slack tides allows lateral density‐driven exchange to stratify the estuary channel at the slack after flood. At the end of ebb, barotropic forcing drives negatively buoyant shoal waters toward the channel.Plain Language SummarySan Francisco Bay sits within a highly urbanized area. The dense population creates large wastewater effluent resulting in high nutrient levels. Scientists wonder why there have not been annual phytoplankton blooms like those observed in other estuaries with lower nutrient levels. Some have hypothesized it is due to high turbidity levels and tidal breakdown of stratification creating nonideal environments for phytoplankton growth. However, decadal trends show that the estuary is becoming less turbid, and with changes in climate patterns, there is potential for persistent stratification. We observed development of stratification over the ebb tide and destratification in two distinct events as the tide reverses over the flood tide. At the reversal of the tides, water in the shoals exchange with the water in the channel creating a pulse of salty water to the channel at the ebb to flood transition and a pulse of fresh water at the flood to the ebb transition. Destratification occurs in the early flood tide due to a pulse of saline water received from the shoals then due to the advection of less stratified water being pulled to the center channel of the estuary. Finally, stratification is destroyed completely due to longitudinal straining and turbulent mixing.Key PointsVertical stratification in shoal‐channel estuary is characterized by strong intratidal variabilityLateral circulation is a key driver of intratidal stratification dynamics at tide transitionsTiming and magnitude of longitudinal straining, advection, lateral straining, and advection set intratidal vertical stratification dynamicsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151865/1/jgrc23594_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151865/2/jgrc23594.pd

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

Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 692–712, doi:10.1002/2016JC011738.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 = 0.25, numerical mixing contributed about 1/2 the total mixing, while with Rist = 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.NSF Grant Number: OCE 0926427; ONR Grant Number: N00014-08-1-11152017-07-2

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

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 4 (2016): e1770, doi:10.7717/peerj.1770.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.This work was sponsored by a grant from the Dalio Foundation, Inc, through the Woods Hole Oceanographic Institution

Swimming behavior of emigrating Chinook Salmon smolts

Swimming behavior of Chinook Salmon (Oncorhynchus tshawytscha) smolts affects transit time, route selection and survival in complex aquatic ecosystems. Behavior quantified at the river reach and junction scale is of particular importance for route selection and predator avoidance, though few studies have developed field-based approaches for quantifying swimming behavior of juvenile migratory fishes at this fine spatial scale. Two-dimensional acoustic fish telemetry at a river junction was combined with a three-dimensional hydrodynamic model to estimate in situ emigration swimming behavior of federally-threatened juvenile Chinook salmon smolts. Fish velocity over ground was estimated from telemetry, while the hydrodynamic model supplied simultaneous, colocated water velocities, with swimming velocity defined by the vector difference of the two velocities. Resulting swimming speeds were centered around 2 body lengths/second, and included distinct behaviors of positive rheotaxis, negative rheotaxis, lateral swimming, and passive transport. Lateral movement increased during the day, and positive rheotaxis increased in response to local hydrodynamic velocities. Swim velocity estimates were sensitive to the combination of vertical shear in water velocities and vertical distribution of fish