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  • 1
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    Sears Foundation for Marine Research
    Publication Date: 2022-05-25
    Description: Author Posting. © Sears Foundation for Marine Research, 2006. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 64 (2006): 147-171, doi:10.1357/002224006776412359.
    Description: In intertidal regions with subtidal channels, effects of bathymetry on overlying flow vary greatly with tidal stage. Around low water when mudflats and marsh are exposed, flow is constrained to channels, but when water depths are greater, tidal forcing may not necessarily be aligned with meandering channel axes. Flow across the channel can generate strong shear and turbulence at the elevation of the channel banks and can significantly increase turbulent energy in the middle of the water column. Field observations in a mudflat channel of San Francisco Bay indicate that cross-channel shear regularly occurs there early in ebb tides. With increased freshwater flow, baroclinic forcing can enhance shear by decoupling flow between dense water flooding in the channel and fresher water ebbing above the channel banks. A water column numerical model with κ-ε turbulence closure is modified to represent the cross-channel shear production. Numerical results with uniform density indicate that turbulence production increases with the angle between the barotropic tidal forcing and the channel axis. When a longitudinal salinity gradient is imposed, cross-channel shear production contributes to breakdown of periodic stratification. Turbulence produced at the channel banks locally exceeds dissipation, and the excess energy is either lost to buoyancy or diffuses vertically to lower energy regions near the surface and near the bed. The balance among shear production, buoyancy production, and diffusion of turbulence depends on the flow angle and the strength of the longitudinal salinity gradient.
    Description: This research was funded by National Institutes of Health grant no. P42ES0475 from the National Institute of Environmental Health Sciences.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography 60 (2015): 2059–2078, doi:10.1002/lno.10155.
    Description: Transitions between life cycle stages by the harmful dinoflagellate Alexandrium fundyense are critical for the initiation and termination of its blooms. To quantify these transitions in a single population, an Imaging FlowCytobot (IFCB), was deployed in Salt Pond (Eastham, Massachusetts), a small, tidally flushed kettle pond that hosts near annual, localized A. fundyense blooms. Machine-based image classifiers differentiating A. fundyense life cycle stages were developed and results were compared to manually corrected IFCB samples, manual microscopy-based estimates of A. fundyense abundance, previously published data describing prevalence of the parasite Amoebophrya, and a continuous culture of A. fundyense infected with Amoebophrya. In Salt Pond, a development phase of sustained vegetative division lasted approximately 3 weeks and was followed by a rapid and near complete conversion to small, gamete cells. The gametic period (∼3 d) coincided with a spike in the frequency of fusing gametes (up to 5% of A. fundyense images) and was followed by a zygotic phase (∼4 d) during which cell sizes returned to their normal range but cell division and diel vertical migration ceased. Cell division during bloom development was strongly phased, enabling estimation of daily rates of division, which were more than twice those predicted from batch cultures grown at similar temperatures in replete medium. Data from the Salt Pond deployment provide the first continuous record of an A. fundyense population through its complete bloom cycle and demonstrate growth and sexual induction rates much higher than are typically observed in culture.
    Description: National Science Foundation Grant Number: OCE-0430724, OCE-0911031, and OCE-1314642; National Institutes of Health Grant Number: NIEHS-1P50-ES021923-01; National Park Service (NPS) Cooperative Agreement Grant Number: H238015504; Gordon and Betty Moore Foundation Grant Number: #2649 to HMS; IOF Grant Number: MOHAB PIOF-GA-252260
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-25
    Description: © 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.
    Description: 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.
    Description: This work was sponsored by a grant from the Dalio Foundation, Inc, through the Woods Hole Oceanographic Institution.
    Keywords: Swarms ; Ecological hotspot ; Patchiness ; Panama ; Eastern Pacific ; Seamount ; Pleuroncodes planipes ; Hypoxic environment ; Anomuran crabs
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2009. 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 114 (2009): C12006, doi:10.1029/2008JC005014.
    Description: A 3D hydrodynamic model (ROMS) is used to investigate lateral circulation in a partially mixed estuary driven by axial wind events and to explore the associated transport of sediments. The channel is straight with a triangular cross section. The model results suggest that driving mechanisms for lateral circulation during axial wind events are different between stratified and unstratified conditions. When the water column is largely unstratified, rotational effects do not drive significant lateral circulation. Instead, differential advection of the axial salinity gradient by wind-driven axial flow is responsible for regulating the lateral salinity gradients that in turn drive bottom-divergent/convergent lateral circulation during down/up-estuary winds. From the subtidal lateral salt balance, it is found that the development of lateral salinity gradient by wind-induced differential advection is largely counterbalanced by the advection of salt by lateral circulation itself. When the water column is stratified, the lateral flow and salinity structures below the halocline closely resemble those driven by boundary mixing, and rotational effects are important. Lateral sediment flux and the event-integrated sediment transport are from channel to shoals during down-estuary winds but reversed for up-estuary winds. Potential impacts of wind-generated waves on lateral sediment transport are evaluated with two cases representing event conditions typical of upper Chesapeake Bay. Accounting for wind wave effects results in an order of magnitude increase in lateral sediment fluxes because of greater bottom stresses and sediment resuspension.
    Description: Financial support from ONR through the Community Sediment Transport Modeling (CSTM) project.
    Keywords: Wind-driven lateral circulation ; Differential advection ; Sediment transport
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2009. 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 39 (2009): 915-933, doi:10.1175/2008JPO3933.1.
    Description: The temporal response of the length of a partially mixed estuary to changes in freshwater discharge Qf and tidal amplitude UT is studied using a 108-day time series collected along the length of the Hudson River estuary in the spring and summer of 2004 and a long-term (13.4 yr) record of Qf, UT, and near-surface salinity. When Qf was moderately high, the tidally averaged length of the estuary L5, here defined as the distance from the mouth to the up-estuary location where the vertically averaged salinity is 5 psu, fluctuated by more than 47 km over the spring–neap cycle, ranging from 28 to 〉75 km. During low flow periods, L5 varied very little over the spring–neap cycle and approached a steady length. The response is quantified and compared to predictions of a linearized model derived from the global estuarine salt balance. The model is forced by fluctuations in Qf and UT relative to average discharge Qo and tidal amplitude UTo and predicts the linear response time scale τ and the steady-state length Lo for average forcing. Two vertical mixing schemes are considered, in which 1) mixing is proportional to UT and 2) dependence of mixing on stratification is also parameterized. Based on least squares fits between L5 and estuary length predicted by the model, estimated τ varied by an order of magnitude from a period of high average discharge (Qo = 750 m3 s−1, τ = 4.2 days) to a period of low discharge (Qo = 170 m3 s−1, τ = 40.4 days). Over the range of observed discharge, Lo Qo−0.30±0.03, consistent with the theoretical scaling for an estuary whose landward salt flux is driven by vertical estuarine exchange circulation. Estimated τ was proportional to the discharge advection time scale (LoA/Qo, where A is the cross-sectional area of the estuary). However, τ was 3–4 times larger than the theoretical prediction. The model with stratification-dependent mixing predicted variations in L5 with higher skill than the model with mixing proportional to UT. This model provides insight into the time-dependent response of a partially stratified estuary to changes in forcing and explains the strong dependence of the amplitude of the spring–neap response on freshwater discharge. However, the utility of the linear model is limited because it assumes a uniform channel, and because the underlying dynamics are nonlinear, and the forcing Qf and UT can undergo large amplitude variations. River discharge, in particular, can vary by over an order of magnitude over time scales comparable to or shorter than the response time scale of the estuary.
    Description: This study was generously funded by Hudson River Foundation Grant 005/03A and NSF Grant OCE-0452054. Lerczak also received partial support from the Woods Hole Center for Oceans and Human Health, NSF Grant OCE-0430724 and NIEHS Grant 1-P50-ES012742-01.
    Keywords: Estuaries ; Rivers ; Tides ; Stability ; Vertical motion
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    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
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2012. 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 Continental Shelf Research 60, Suppl. (2013): S40–S57, doi:10.1016/j.csr.2012.02.004.
    Description: Tidal flats at a river mouth feature estuarine and fluvial processes that distinguish them from tidal flats without river discharge. We combine field observations and a numerical model to investigate hydrodynamics and sediment transport on deltaic tidal flats at the mouth of the Skagit River, in Puget Sound, WA during the spring freshet. River discharge over tidal flats supplies a mean volume flux, freshwater buoyancy, and suspended sediment. Despite the shallow water depths, strong horizontal density fronts and stratification develop, resulting in a baroclinic pressure gradient and tidal variability in stratification that favor flood-directed bottom stresses. In addition to these estuarine processes, the river discharge during periods of low tide drains through a network of distributary channels on the exposed tidal flats, with strongly ebb-directed stresses. The net sediment transport depends on the balance between estuarine and fluvial processes, and is modulated on a spring-neap time scale by the tides of Puget Sound. We find that the baroclinic pressure gradient and periodic stratification enhance trapping of sediment delivered by the river on the tidal flats, particularly during neap tides, and that sediment trapping also depends on settling and scour lags, particularly for finer particles. The primary means of moving sediment off of the tidal flats are the high velocities and stresses in the distributary channels during late stages of ebbs and around low tides, with sediment export predominantly occurring during spring low tides that expose a greater portion of the flats. The 3-d finite volume numerical model was evaluated against observations and had good skill overall, particularly for velocity and salinity. The model performed poorly at simulating the shallow flows around low tides as the flats drained and river discharge was confined to distributary channels, due in part to limitations in grid resolution, seabed sediment and bathymetric data, and the wetting-and-drying scheme. Consequently, the model predicted greater sediment retention on the flats than was observed.
    Description: This work was supported by the Office of Naval Research.
    Keywords: Tidal flats ; Sediment transport ; Sediment trapping ; Distributary channels ; Stratification ; Salinity fronts ; Tidal asymmetry ; Velocity skewness ; Numerical model
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2013. 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 Continental Shelf Research 65 (2013): 1-13, doi:10.1016/j.csr.2013.05.017.
    Description: An unstructured grid, phase-averaged wave model forced with winds from a high resolution atmospheric model is used to evaluate wind wave conditions in the Red Sea over an approximately 2-year period. The Red Sea lies in a narrow rift valley, and the steep topography surrounding the basin steers the dominant wind patterns and consequently the wave climate. At large scales, the model results indicated that the primary seasonal variability in waves was due to the monsoonal wind reversal. During the winter, monsoon winds from the southeast generated waves with mean significant wave heights in excess of 2 m and mean periods of 8 s in the southern Red Sea, while in the northern part of the basin waves were smaller, shorter period, and from northwest. The zone of convergence of winds and waves typically occurred around 19-20˚N, but the location varied between 15 to 21.5˚N. During the summer, waves were generally smaller and from the northwest over most of the basin. While the seasonal winds oriented along the axis of the Red Sea drove much of the variability in the waves, the maximum wave heights in the simulations were not due to the monsoonal winds but instead were generated by localized mountain wind jets oriented across the basin (roughly east-west). During the summer, a mountain wind jet from the Tokar Gap enhanced the waves in the region of 18 and 20˚N, with monthly mean wave heights exceeding 2 m and maximum wave heights of 14 m during a period when the rest of the Red Sea was relatively calm. Smaller mountain gap wind jets along the northeast coast created large waves during the fall and winter, with a series of jets providing a dominant source of wave energy during these periods. Evaluation of the wave model results against observations from a buoy and satellites found that the spatial resolution of the wind model significantly affected the quality of the wave model results. Wind forcing from a 10-km grid produced higher skills for waves than winds from a 30-km grid, largely due to under-prediction of the mean wind speed and wave height with the coarser grid. The 30-km grid did not resolve the mountain gap wind jets, and thus predicted lower wave heights in the central Red Sea during the summer and along the northeast coast in the winter.
    Description: This research is based on work supported by Award No. USA00001, USA00002, KSA00011, made by the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia.
    Repository Name: Woods Hole Open Access Server
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  • 9
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    American Meteorological Society
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2015. 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 45 (2015): 546–561, doi:10.1175/JPO-D-14-0082.1.
    Description: Model studies and observations in the Hudson River estuary indicate that frontogenesis occurs as a result of topographic forcing. Bottom fronts form just downstream of lateral constrictions, where the width of the estuary increases in the down-estuary (i.e., seaward) direction. The front forms during the last several hours of the ebb, when the combination of adverse pressure gradient in the expansion and baroclinicity cause a stagnation of near-bottom velocity. Frontogenesis is observed in two dynamical regimes: one in which the front develops at a transition from subcritical to supercritical flow and the other in which the flow is everywhere supercritical. The supercritical front formation appears to be associated with lateral flow separation. Both types of fronts are three-dimensional, with strong lateral gradients along the flanks of the channel. During spring tide conditions, the fronts dissipate during the flood, whereas during neap tides the fronts are advected landward during the flood. The zone of enhanced density gradient initiates frontogenesis at multiple constrictions along the estuary as it propagates landward more than 60 km during several days of neap tides. Frontogenesis and frontal propagation may thus be essential elements of the spring-to-neap transition to stratified conditions in partially mixed estuaries.
    Description: Support for this research was provided by NSF Grant OCE 0926427.
    Description: 2015-08-01
    Keywords: Circulation/ Dynamics ; Baroclinic flows ; Coastal flows ; Frontogenesis/frontolysis ; Fronts
    Repository Name: Woods Hole Open Access Server
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  • 10
    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
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