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  • 1
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    Dynamics of Alexandrium fundyense blooms and shellfish toxicity in the Nauset Marsh System of Cape Cod (Massachusetts, USA) (2012)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Harmful Algae 12 (2011): 26–38, doi:10.1016/j.hal.2011.08.009.
    Description: Paralytic Shellfish Poisoning (PSP) toxins are annually recurrent along the Massachusetts coastline (USA), which includes many small embayments and salt ponds. Among these is the Nauset Marsh System (NMS), which has a long history of PSP toxicity. Little is known, however, about the bloom dynamics of the causative organism Alexandrium fundyense within that economically and socially important system. The overall goal of this work was to characterize the distribution and dynamics of A. fundyense blooms within the NMS and adjacent coastal waters by documenting the distribution and abundance of resting cysts and vegetative cells. Cysts were found predominantly in three drowned kettle holes or salt ponds at the distal ends of the NMS - Salt Pond, Mill Pond, and Town Cove. The central region of the NMS had a much lower concentration of cysts. Two types of A. fundyense blooms were observed. One originated entirely within the estuary, seeded by cysts in the three seedbeds. These blooms developed independently of each other and of the A. fundyense population observed in adjacent coastal waters outside the NMS. The temporal development of the blooms was different in the three salt ponds, with initiation differing by as much as 30 days. These differences do not appear to reflect the initial cyst abundances in these locations, and may simply result from higher cell retention and higher nutrient concentrations in Mill Pond, the first site to bloom. Germination of cysts accounted for a small percentage of the peak cell densities in the ponds, so population size was influenced more by the factors affecting growth than by cyst abundance. Subsurface cell aggregation (surface avoidance) limited advection of the vegetative A. fundyense cells out of the salt ponds through the shallow inlet channels. Thus, the upper reaches of the NMS are at the greatest risk for PSP since the highest cyst abundances and cell concentrations were found there. After these localized blooms in the salt ponds peaked and declined, a second, late season bloom occurred within the central portions of the NMS. The timing of this second bloom relative to those within the salt ponds and the coastal circulation patterns at that time strongly suggest that those cells originated from a regional A. fundyense bloom in the Gulf of Maine, delivered to the central marsh from coastal waters outside the NMS through Nauset Inlet. These results will guide policy decisions about water quality as well as shellfish monitoring and utilization within the NMS and highlight the potential for “surgical” closures of shellfish during PSP events, leaving some areas open for harvesting while others are closed.
    Description: This work was supported by NOAA Grant NA06OAR4170021, NPS Grant H238015504 and by the Woods Hole Center for Oceans and Human Health through NSF Grants OCE-0911031 and OCE-0430724 and NIEHS Grant 1P50-ES01274201. B.G.C. was supported by a Xunta de Galicia Ángeles Alvariño fellowship and the Stanley W. Watson Chair for Excellence in Oceanography under a Postdoctoral program at the Woods Hole Oceanographic Institution.
    Keywords: Paralytic shellfish poisoning ; Alexandrium fundyense ; Dinoflagellate cysts ; Bloom dynamics ; Retention mechanism ; Nauset Marsh System
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 2
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    Hydraulics and mixing in a laterally divergent channel of a highly stratified estuary (2017)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-25
    Description: 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.
    Description: 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.
    Description: NSF Grant Number: OCE 0926427; Devonshire Scholars program
    Description: 2017-12-12
    Keywords: Internal hydraulics ; Mixing ; Gradient Richardson number ; Estuary
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Turbulent mixing in a strongly forced salt wedge estuary (2011)
    American Geophysical Union
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    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2010. 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 115 (2010): C12024, doi:10.1029/2009JC006061.
    Description: Turbulent mixing of salt is examined in a shallow salt wedge estuary with strong fluvial and tidal forcing. A numerical model of the Merrimack River estuary is used to quantify turbulent stress, shear production, and buoyancy flux. Little mixing occurs during flood tides despite strong velocities because bottom boundary layer turbulence is dislocated from stratification elevated in the water column. During ebbs, bottom salinity fronts form at a series of bathymetric transitions. At the fronts, near-bottom velocity and shear stress are low, but shear, stress, and buoyancy flux are elevated at the pycnocline. Internal shear layers provide the dominant source of mixing during the early ebb. Later in the ebb, the pycnocline broadens and moves down such that boundary layer turbulence dominates mixing. Mixing occurs primarily during ebbs, with internal shear mixing accounting for about 50% of the total buoyancy flux. Both the relative contribution of internal shear mixing and the mixing efficiency increase with discharge, with bulk mixing efficiencies between 0.02 and 0.07. Buoyancy fluxes in the estuary increase with discharge up to about 400 m3 s−1 above which a majority of the mixing occurs offshore. Observed buoyancy fluxes were more consistent with the k-ɛ turbulence closure than the Mellor-Yamada closure, and more total mixing occurred in the estuary with k-ɛ. Calculated buoyancy fluxes were sensitive to horizontal grid resolution, as a lower resolution grid yielded less integrated buoyancy flux in the estuary and exported lower salinity water but likely had greater numerical mixing.
    Description: This research was funded by National Science Foundation Grant OCE‐0452054. Ralston also received support from The Penzance Endowed Fund in Support of Assistant Scientists and The John F. and Dorothy H. Magee Fund in Support of Scientific Staff at Woods Hole Oceanographic Institution.
    Keywords: Mixing ; Turbulence ; Salt wedge estuary
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Temperature and residence time controls on an estuarine harmful algal bloom : modeling hydrodynamics and Alexandrium fundyense in Nauset estuary (2015)
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Estuaries and Coasts 38 (2015): 2240-2258, doi:10.1007/s12237-015-9949-z.
    Description: A highly resolved, 3-d model of hydrodynamics and Alexandrium fundyense in an estuarine embayment has been developed to investigate the physical and biological controls on a recurrent harmful algal bloom. Nauset estuary on Cape Cod (MA, USA) consists of three salt ponds connected to the ocean through a shallow marsh and network of tidal channels. The model is evaluated using quantitative skill metrics against observations of physical and biological conditions during three spring blooms. The A. fundyense model is based on prior model applications for the nearby Gulf of Maine, but notable modifications were made to be consistent with the Nauset observations. The dominant factors controlling the A. fundyense bloom in Nauset were the water temperature, which regulates organism growth rates, and the efficient retention of cells due to bathymetric constraints, stratification, and cell behavior (diel vertical migration). Spring-neap variability in exchange altered residence times, but for cell retention to be substantially longer than the cell doubling time required both active vertical migration and stratification that inhibits mixing of cells into the surface layer by wind and tidal currents. Unlike in the Gulf of Maine, the model results were relatively insensitive to cyst distributions or germination rates. Instead, in Nauset, high apparent rates of vegetative cell division by retained populations dictated bloom development. Cyst germination occurred earlier in the year than in the Gulf of Maine, suggesting that Nauset cysts have different controls on germination timing. The model results were relatively insensitive to nutrient concentrations, due to eutrophic conditions in the highly impacted estuary or due to limitations in the spatial and temporal resolution of nutrient sampling. Cell loss rates were inferred to be extremely low during the growth phase of the bloom, but increased rapidly during the final phase due to processes that remain uncertain. The validated model allows a quantitative assessment of the factors that contribute to the development of a recurrent harmful algal bloom and provides a framework for assessing similarly impacted coastal systems.
    Description: This work was supported by the National Science Foundation (OCE-0430724, OCE-0911031, and OCE-1314642) and National Institutes of Health (NIEHS-1P50-ES021923-01) through the Woods Hole Center for Oceans and Human Health, and by National Park Service (NPS) Cooperative Agreement H238015504.
    Description: 2016-03-17
    Keywords: Harmful algal bloom ; Hydrodynamic-biological model ; Alexandrium fundyense ; Residence time ; Cyst germination ; Growing degree day
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 5
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    Stratified turbulence and mixing efficiency in a salt wedge estuary (2016)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: 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.
    Description: 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.
    Description: Holleman was supported by the Devonshire Scholars program. The field study and the coauthors’ contributions were supported by NSF Grant OCE 0926427.
    Description: 2016-11-24
    Keywords: Circulation/ Dynamics ; Mixing ; Shear structure/flows ; Turbulence ; Observational techniques and algorithms ; Ship observations
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
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    Using tracer variance decay to quantify variability of salinity mixing in the Hudson River Estuary (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-21
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Warner, J. C., Geyer, W. R., Ralston, D. K., & Kalra, T. Using tracer variance decay to quantify variability of salinity mixing in the Hudson River Estuary. Journal of Geophysical Research: Oceans, 125(12), (2020): e2020JC016096, https://doi.org/10.1029/2020JC016096.
    Description: The salinity structure in an estuary is controlled by time‐dependent mixing processes. However, the locations and temporal variability of where significant mixing occurs is not well‐understood. Here we utilize a tracer variance approach to demonstrate the spatial and temporal structure of salinity mixing in the Hudson River Estuary. We run a 4‐month hydrodynamic simulation of the tides, currents, and salinity that captures the spring‐neap tidal variability as well as wind‐driven and freshwater flow events. On a spring‐neap time scale, salinity variance dissipation (mixing) occurs predominantly during the transition from neap to spring tides. On a tidal time scale, 60% of the salinity variance dissipation occurs during ebb tides and 40% during flood tides. Spatially, mixing during ebbs occurs primarily where lateral bottom salinity fronts intersect the bed at the transition from the main channel to adjacent shoals. During ebbs, these lateral fronts form seaward of constrictions located at multiple locations along the estuary. During floods, mixing is generated by a shear layer elevated in the water column at the top of the mixed bottom boundary layer, where variations in the along channel density gradients locally enhance the baroclinic pressure gradient leading to stronger vertical shear and more mixing. For both ebb and flood, the mixing occurs at the location of overlap of strong vertical stratification and eddy diffusivity, not at the maximum of either of those quantities. This understanding lends a new insight to the spatial and time dependence of the estuarine salinity structure.
    Description: This study was funded through the Coastal Model Applications and Field Measurements Project and the Cross‐shore and Inlets Project, US Geological Survey Coastal Marine Hazards and Resources Program. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.
    Keywords: Hudson River Estuary ; Mixing ; Numerical modeling ; Tracer variance
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Frontogenesis, mixing, and stratification in estuarine channels with curvature (2022)
    American Meteorological Society
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    Publication Date: 2022-12-09
    Description: Author Posting. © American Meteorological Society, 2022. 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 52(7), (2022): 1333-1350, https://doi.org/10.1175/jpo-d-21-0298.1.
    Description: Idealized numerical simulations were conducted to investigate the influence of channel curvature on estuarine stratification and mixing. Stratification is decreased and tidal energy dissipation is increased in sinuous estuaries compared to straight channel estuaries. We applied a vertical salinity variance budget to quantify the influence of straining and mixing on stratification. Secondary circulation due to the channel curvature is found to affect stratification in sinuous channels through both lateral straining and enhanced vertical mixing. Alternating negative and positive lateral straining occur in meanders upstream and downstream of the bend apex, respectively, corresponding to the normal and reversed secondary circulation with curvature. The vertical mixing is locally enhanced in curved channels with the maximum mixing located upstream of the bend apex. Bend-scale bottom salinity fronts are generated near the inner bank upstream of the bend apex as a result of interaction between the secondary flow and stratification. Shear mixing at bottom fronts, instead of overturning mixing by the secondary circulation, provides the dominant mechanism for destruction of stratification. Channel curvature can also lead to increased drag, and using a Simpson number with this increased drag coefficient can relate the decrease in stratification with curvature to the broader estuarine parameter space.
    Description: The research leading to these results was funded by NSF Awards OCE-1634481 and OCE-2123002.
    Description: 2022-12-09
    Keywords: Estuaries ; Mixing ; Secondary circulation ; Fronts ; Tides ; Numerical analysis/modeling
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    Impacts of storm surge barriers on drag, mixing, and exchange flow in a partially mixed estuary (2022)
    American Geophysical Union
    Details
    Publication Date: 2022-10-20
    Description: Author Posting. © American Geophysical Union, 2022. 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 127(4), (2022): e2021JC018246, https://doi.org/10.1029/2021jc018246.
    Description: Storm surge barriers are increasingly being considered as risk mitigation measures for coastal population centers. During non-storm periods, permanent barrier infrastructure reduces the flow cross-sectional area and affects tidal exchange. Effects of barrier structures on estuarine tidal and salinity dynamics have not been extensively examined, particularly for partially mixed estuaries. A nested, high-resolution model is used to characterize impacts of a potential storm surge barrier near the mouth of the Hudson River estuary. Maximum tidal velocities through barrier openings are more than double those in the base case. Landward of the barrier, tidal amplitude decreases on average by about 6% due to increased drag. The drag coefficient with the barrier is about 5 times greater than the base case due primarily to form drag from flow separation at barrier structures rather than increased bottom friction. The form drag scales with barrier geometry similar to previous studies of flow around headlands. Tidal water levels are reduced particularly during spring tides, such that marsh inundation frequency is reduced up to 25%. Strong tidal velocities through barrier openings enhance salinity mixing locally, but overall mixing in the estuary decreases due to reduced tidal velocities. Correspondingly, stratification decreases near the barrier and increases landward in the estuary. The salinity intrusion length increases by 5%–15% depending on discharge due to the decreased mixing and increased exchange flow. Exchange flow increases near the barrier due reflux into the lower layer with the increased mixing, which has the potential to increase estuarine residence times.
    Description: Funding from Hudson Research Foundation (Award #003/19A).
    Description: 2022-10-11
    Keywords: Storm surge barrier ; Form drag ; Mixing ; Stratification ; Exchange flow ; Salinity intrusion
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Estuarine exchange flow variability in a seasonal, segmented estuary (2020)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. 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 50(3),(2020): 595-613, doi:10.1175/JPO-D-19-0108.1.
    Description: Small estuaries in Mediterranean climates display pronounced salinity variability at seasonal and event time scales. Here, we use a hydrodynamic model of the Coos Estuary, Oregon, to examine the seasonal variability of the salinity dynamics and estuarine exchange flow. The exchange flow is primarily driven by tidal processes, varying with the spring–neap cycle rather than discharge or the salinity gradient. The salinity distribution is rarely in equilibrium with discharge conditions because during the wet season the response time scale is longer than discharge events, while during low flow it is longer than the entire dry season. Consequently, the salt field is rarely fully adjusted to the forcing and common power-law relations between the salinity intrusion and discharge do not apply. Further complicating the salinity dynamics is the estuarine geometry that consists of multiple branching channel segments with distinct freshwater sources. These channel segments act as subestuaries that import both higher- and lower-salinity water and export intermediate salinities. Throughout the estuary, tidal dispersion scales with tidal velocity squared, and likely includes jet–sink flow at the mouth, lateral shear dispersion, and tidal trapping in branching channel segments inside the estuary. While the estuarine inflow is strongly correlated with tidal amplitude, the outflow, stratification, and total mixing in the estuary are dependent on the seasonal variation in river discharge, which is similar to estuaries that are dominated by subtidal exchange flow.
    Description: We thank two anonymous reviewers for constructive comments, the staff of the South Slough National Estuarine Research Reserve for providing time series data, and Parker MacCready for sharing LiveOcean boundary conditions. This work was partially sponsored by the National Estuarine Research Reserve System Science Collaborative, which supports collaborative research that addresses coastal management problems important to the reserves. The Science Collaborative is funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NAI4NOS4190145). Computations were performed on the University of Oregon high performance computer Talapas.
    Description: 2020-08-26
    Keywords: Estuaries ; North Pacific Ocean ; Baroclinic flows ; Channel flows ; Dispersion ; Mixing
    Repository Name: Woods Hole Open Access Server
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