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  • 1
    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
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  • 2
    Publication Date: 2022-05-25
    Description: © 2008 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Environmental Fluid Mechanics 8 (2008): 495-509, doi:10.1007/s10652-008-9107-2.
    Description: Estuarine turbulence is notable in that both the dissipation rate and the buoyancy frequency extend to much higher values than in other natural environments. The high dissipation rates lead to a distinct inertial subrange in the velocity and scalar spectra, which can be exploited for quantifying the turbulence quantities. However, high buoyancy frequencies lead to small Ozmidov scales, which require high sampling rates and small spatial aperture to resolve the turbulent fluxes. A set of observations in a highly stratified estuary demonstrate the effectiveness of a vessel-mounted turbulence array for resolving turbulent processes, and for relating the turbulence to the forcing by the Reynolds-averaged flow. The observations focus on the ebb, when most of the buoyancy flux occurs. Three stages of mixing are observed: (1) intermittent and localized but intense shear instability during the early ebb; (2) continuous and relatively homogeneous shear-induced mixing during the mid-ebb, and weakly stratified, boundary-layer mixing during the late ebb. The mixing efficiency as quantified by the flux Richardson number Rf was frequently observed to be higher than the canonical value of 0.15 from Osborn (J Phys Oceanogr 10:83–89, 1980). The high efficiency may be linked to the temporal–spatial evolution of shear instabilities.
    Description: The funding for this research was obtained from ONR Grant N00014-06-1-0292 and NSF Grant OCE-0729547.
    Keywords: Turbulence ; Estuaries ; Shear instability ; Buoyancy flux
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2008. 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 38 (2008): 753-770, doi:10.1175/2007JPO3808.1.
    Description: A tidally and cross-sectionally averaged model based on the temporal evolution of the quasi-steady Hansen and Rattray equations is applied to simulate the salinity distribution and vertical exchange flow along the Hudson River estuary. The model achieves high skill at hindcasting salinity and residual velocity variation during a 110-day period in 2004 covering a wide range of river discharges and tidal forcing. The approach is based on an existing model framework that has been modified to improve model skill relative to observations. The external forcing has been modified to capture meteorological time-scale variability in salinity, stratification, and residual velocity due to sea level fluctuations at the open boundary and along-estuary wind stress. To reflect changes in vertical mixing due to stratification, the vertical mixing coefficients have been modified to use the bottom boundary layer height rather than the water depth as an effective mixing length scale. The boundary layer parameterization depends on the tidal amplitude and the local baroclinic pressure gradient through the longitudinal Richardson number, and improves the model response to spring–neap variability in tidal amplitude during periods of high river discharge. Finally, steady-state model solutions are evaluated for both the Hudson River and northern San Francisco Bay over a range of forcing conditions. Agreement between the model and scaling of equilibrium salinity intrusions lends confidence that the approach is transferable to other estuaries, despite significant differences in bathymetry. Discrepancies between the model results and observations at high river discharge are indicative of limits at which the formulation begins to fail, and where an alternative approach that captures two-layer dynamics would be more appropriate.
    Description: This research was supported by the Hudson River Foundation Grant 005/03A, NSF Grant OCE-0452054, and by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the J. Seward Johnson Fund.
    Keywords: Estuaries ; Salinity ; Rivers ; Tides ; Wind stress
    Repository Name: Woods Hole Open Access Server
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  • 4
    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
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  • 5
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Clark, S., Hubbard, K. A., McGillicuddy Jr, D. J., Ralston, D. K., & Shankar, S. Investigating Pseudo-nitzschia australis introduction to the Gulf of Maine with observations and models. Continental Shelf Research, 228, (2021): 104493, https://doi.org/10.1016/j.csr.2021.104493.
    Description: In 2016, an unprecedented Pseudo-nitzschia australis bloom in the Gulf of Maine led to the first shellfishery closures due to domoic acid in the region's history. In this paper, potential introduction routes of P. australis are explored through observations, a hydrodynamic model, and a Lagrangian particle tracking model. Based on particle tracking experiments, the most likely source of P. australis to the Gulf of Maine was the Scotian Shelf. However, in 2016, connectivity between the Scotian Shelf and the bloom region was not significantly different from the other years between 2012 and 2019, nor were temperature conditions more favorable for P. australis growth. Observations indicated changes on the Scotian Shelf in 2016 preceded the introduction of P. australis: increased bottom salinity and decreased surface salinity. The increased bottom salinity on the shelf may be linked to anomalously saline water observed near the coast of Maine in 2016 via transport through Northeast Channel. The changes in upstream water mass properties may be related to the introduction of P. australis, and could be the result of either increased influence of the Labrador Current or increased outflow from the Gulf of St. Lawrence. The ultimate source of P. australis remains unknown, although the species has previously been observed in the eastern North Atlantic, and connectivity across the ocean is possible via a subpolar route. Continued and increased monitoring is warranted to track interannual Pseudo-nitzschia persistence in the Gulf of Maine, and sampling on the Scotian Shelf should be conducted to map upstream P. australis populations.
    Description: This research was funded by the National Science Foundation (Grant Number OCE-1840381), the National Institute of Environmental Health Sciences (Grant Number 1P01ES028938), the Woods Hole Center for Oceans and Human Health, and the Academic Programs Office of the Woods Hole Oceanographic Institution.
    Keywords: Gulf of Maine ; Pseudo-nitzschia australis ; Harmful algal blooms ; Lagrangian particle tracking ; ROMS
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-07-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Clark, S., Hubbard, K., Ralston, D., McGillicuddy, D., Stock, C., Alexander, M., & Curchitser, E. Projected effects of climate change on Pseudo-nitzschia bloom dynamics in the Gulf of Maine. Journal of Marine Systems, 230, (2022): 103737, https://doi.org/10.1016/j.jmarsys.2022.103737.
    Description: Worldwide, warming ocean temperatures have contributed to extreme harmful algal bloom events and shifts in phytoplankton species composition. In 2016 in the Gulf of Maine (GOM), an unprecedented Pseudo-nitzschia bloom led to the first domoic-acid induced shellfishery closures in the region. Potential links between climate change, warming temperatures, and the GOM Pseudo-nitzschia assemblage, however, remain unexplored. In this study, a global climate change projection previously downscaled to 7-km resolution for the Northwest Atlantic was further refined with a 1–3-km resolution simulation of the GOM to investigate the effects of climate change on HAB dynamics. A 25-year time slice of projected conditions at the end of the 21st century (2073–2097) was compared to a 25-year hindcast of contemporary ocean conditions (1994–2018) and analyzed for changes to GOM inflows, transport, and Pseudo-nitzschia australis growth potential. On average, climate change is predicted to lead to increased temperatures, decreased salinity, and increased stratification in the GOM, with the largest changes occurring in the late summer. Inflows from the Scotian Shelf are projected to increase, and alongshore transport in the Eastern Maine Coastal Current is projected to intensify. Increasing ocean temperatures will likely make P. australis growth conditions less favorable in the southern and western GOM but improve P. australis growth conditions in the eastern GOM, including a later growing season in the fall, and a longer growing season in the spring. Combined, these changes suggest that P. australis blooms in the eastern GOM could intensify in the 21st century, and that the overall Pseudo-nitzschia species assemblage might shift to warmer-adapted species such as P. plurisecta or other Pseudo-nitzschia species that may be introduced.
    Description: This research was funded by the National Science Foundation (Grant Number OCE-1840381), the National Institute of Environmental Health Sciences (Grant Number 1P01ES028938), the Woods Hole Center for Oceans and Human Health, and the Academic Programs Office of the Woods Hole Oceanographic Institution.
    Keywords: Gulf of Maine ; ROMS ; Pseudo-nitzschia ; Climate change ; Harmful algal blooms
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  • 7
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. 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 49(6), (2019):1619-1637, doi:10.1175/JPO-D-18-0175.1.
    Description: Although the hydrodynamics of river meanders are well studied, the influence of curvature on flow in estuaries, with alternating tidal flow and varying water levels and salinity gradients, is less well understood. This paper describes a field study on curvature effects in a narrow salt-marsh creek with sharp bends. The key observations, obtained during times of negligible stratification, are 1) distinct differences between secondary flow during ebb and flood, with helical circulation as in rivers during ebb and a reversed circulation during flood, and 2) maximum (ebb and flood) streamwise velocities near the inside of the bend, unlike typical river bend flow. The streamwise velocity structure is explained by the lack of a distinct point bar and the relatively deep cross section in the estuary, which means that curvature-induced inward momentum redistribution is not overcome by outward redistribution by frictional and topographic effects. Through differential advection of the along-estuary salinity gradient, the laterally sheared streamwise velocity generates lateral salinity differences, with the saltiest water near the inside during flood. The resulting lateral baroclinic pressure gradient force enhances the standard helical circulation during ebb but counteracts it during flood. This first leads to a reversed secondary circulation during flood in the outer part of the cross section, which triggers a positive feedback mechanism by bringing slower-moving water from the outside inward along the surface. This leads to a reversal of the vertical shear in the streamwise flow, and therefore in the centrifugal force, which further enhances the reversed secondary circulation.
    Description: This project was funded by NSF Grant OCE-1634490. During this work W.M. Kranenburg was supported as USGS Postdoctoral Scholar at Woods Hole Oceanographic Institution. A.M.P. Garcia was supported by the Michael J. Kowalski Fellowship in Ocean Science and Engineering (AMPG), and the Diversity Fellowship of the MIT Office of the Dean of Graduate Education (AMPG). The authors thank Jay Sisson for the technical support and Peter Traykovski for providing the bathymetric data. Also, the suggestions for improvement by Dr. K. Blanckaert and an anonymous reviewer are thankfully acknowledged.
    Keywords: Estuaries ; Advection ; Baroclinic flows ; Barotropic flows
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Clark, S., Hubbard, K. A., Anderson, D. M., McGillicuddy, D. J.,Jr, Ralston, D. K., & Townsend, D. W. Pseudo-nitzschia bloom dynamics in the Gulf of Maine: 2012-2016. Harmful Algae, 88, (2019): 101656, doi:10.1016/j.hal.2019.101656.
    Description: The toxic diatom genus Pseudo-nitzschia is a growing presence in the Gulf of Maine (GOM), where regionally unprecedented levels of domoic acid (DA) in 2016 led to the first Amnesic Shellfish Poisoning closures in the region. However, factors driving GOM Pseudo-nitzschia dynamics, DA concentrations, and the 2016 event are unclear. Water samples were collected at the surface and at depth in offshore transects in summer 2012, 2014, and 2015, and fall 2016, and a weekly time series of surface water samples was collected in 2013. Temperature and salinity data were obtained from NERACOOS buoys and measurements during sample collection. Samples were processed for particulate DA (pDA), dissolved nutrients (nitrate, ammonium, silicic acid, and phosphate), and cellular abundance. Species composition was estimated via Automated Ribosomal Intergenic Spacer Analysis (ARISA), a semi-quantitative DNA finger-printing tool. Pseudo-nitzschia biogeography was consistent in the years 2012, 2014, and 2015, with greater Pseudo-nitzschia cell abundance and P. plurisecta dominance in low-salinity inshore samples, and lower Pseudo-nitzschia cell abundance and P. delicatissima and P. seriata dominance in high-salinity offshore samples. During the 2016 event, pDA concentrations were an order of magnitude higher than in previous years, and inshore-offshore contrasts in biogeography were weak, with P. australis present in every sample. Patterns in temporal and spatial variability confirm that pDA increases with the abundance and the cellular DA of Pseudo-nitzschia species, but was not correlated with any one environmental factor. The greater pDA in 2016 was caused by P. australis – the observation of which is unprecedented in the region – and may have been exacerbated by low residual silicic acid. The novel presence of P. australis may be due to local growth conditions, the introduction of a population with an anomalous water mass, or both factors. A definitive cause of the 2016 bloom remains unknown, and continued DA monitoring in the GOM is warranted.
    Description: This research was funded by the National Science Foundation (Grant Numbers OCE-1314642 and OCE-1840381), the National Institute of Environmental Health Sciences (Grant Numbers P01 ES021923-01 and P01 ES028938-01), the Woods Hole Center for Oceans and Human Health, the Academic Programs Office of the Woods Hole Oceanographic Institution, the National Oceanic and Atmospheric Administration's Ecology and Oceanography of HABs (ECOHAB) project (contribution number ECO947), and the National Oceanic and Atmospheric Administration’s HAB Event Response Program (Grant numbers NA06NOS4780245 and NA09NOS4780193). We thank Maura Thomas at the University of Maine for support with nutrient collection and analysis. We also thank Kohl Kanwit at the Maine Department of Marine Resources, Anna Farrell, Jane Disney, and Hannah Mogenson at the Mt. Desert Island Biological Laboratory, Steve Archer at Bigelow Laboratory for Ocean sciences, and Bruce Keafer at the Woods Hole Oceanographic Institution for their work collecting samples and data used in the study. We also thank Maya Robert, Christina Chadwick, Laura Markley, Stephanie Keller Abbe, Karen Henschen, Emily Olesin, Steven Bruzek, Sheila O'Dea, April Granholm, Leanne Flewelling, and Elizabeth Racicot at the Florida Fish and Wildlife Conservation Commission-Fish and Wildlife Research Institute for processing samples for DA, DNA-based analyses, and cellular abundance.[CG]
    Keywords: Pseudo-nitzschia australis ; Pseudo-nitzschia plurisecta ; Domoic acid ; ARISA ; Gulf of Maine ; Silicic acid
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  • 9
    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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