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  • 1
    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
    Type: Article
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fringer, O. B., Dawson, C. N., He, R., Ralston, D. K., & Zhang, Y. J. The future of coastal and estuarine modeling: findings from a workshop. Ocean Modelling, 143, (2019): 101458, doi:10.1016/j.ocemod.2019.101458.
    Description: This paper summarizes the findings of a workshop convened in the United States in 2018 to discuss methods in coastal and estuarine modeling and to propose key areas of research and development needed to improve their accuracy and reliability. The focus of this paper is on physical processes, and we provide an overview of the current state-of-the-art based on presentations and discussions at the meeting, which revolved around the four primary themes of parameterizations, numerical methods, in-situ and remote-sensing measurements, and high-performance computing. A primary outcome of the workshop was agreement on the need to reduce subjectivity and improve reproducibility in modeling of physical processes in the coastal ocean. Reduction of subjectivity can be accomplished through development of standards for benchmarks, grid generation, and validation, and reproducibility can be improved through development of standards for input/output, coupling and model nesting, and reporting. Subjectivity can also be reduced through more engagement with the applied mathematics and computer science communities to develop methods for robust parameter estimation and uncertainty quantification. Such engagement could be encouraged through more collaboration between the forward and inverse modeling communities and integration of more applied math and computer science into oceanography curricula. Another outcome of the workshop was agreement on the need to develop high-resolution models that scale on advanced HPC systems to resolve, rather than parameterize, processes with horizontal scales that range between the depth and the internal Rossby deformation scale. Unsurprisingly, more research is needed on parameterizations of processes at scales smaller than the depth, including parameterizations for drag (including bottom roughness, bedforms, vegetation and corals), wave breaking, and air–sea interactions under strong wind conditions. Other topics that require significantly more work to better parameterize include nearshore wave modeling, sediment transport modeling, and morphodynamics. Finally, it was agreed that coastal models should be considered as key infrastructure needed to support research, just like laboratory facilities, field instrumentation, and research vessels. This will require a shift in the way proposals related to coastal ocean modeling are reviewed and funded.
    Description: We thank Carmen Torres at Stanford University and Jennifer Warrillow at North Carolina State University for their assistance with workshop logistics. Helpful comments and suggestions were provided by two anonymous reviewers and Hans Burchard and John Warner. The workshop and preparation of this paper were funded by U.S. National Science Foundation Grant OCE-1749613.
    Keywords: Coastal ocean modeling ; Physical processes ; Model subjectivity ; Development of standards ; High-resolution modeling ; Parameter estimation
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    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
    Type: Article
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 39 (2016): 311-332, doi:10.1007/s12237-015-0011-y.
    Description: Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.
    Description: NKG, ALA, and RPS acknowledge support from the USGS Coastal and Marine Geology Program. DKR gratefully acknowledges support from NSF (OCE-1314642) and NIEHS (1P50-ES021923-01). MJB and JMPV gratefully acknowledge support from NOAA NOS NCCOS (NA05NOS4781201 and NA11NOS4780043). MJB and SJL gratefully acknowledge support from the Strategic Environmental Research and Development Program—Defense Coastal/Estuarine Research Program (RC-1413 and RC-2245).
    Keywords: Numerical modeling ; Hydrodynamics ; Ecological modeling ; Ecosystem modeling ; Skill assessment
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    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
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    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
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ralston, D. K., Yellen, B., & Woodruff, J. D. Watershed suspended sediment supply and potential impacts of dam removals for an estuary. Estuaries and Coasts, (2021), https://doi.org/10.1007/s12237-020-00873-3.
    Description: Observations and modeling are used to assess potential impacts of sediment releases due to dam removals on the Hudson River estuary. Watershed sediment loads are calculated based on sediment-discharge rating curves for gauges covering 80% of the watershed area. The annual average sediment load to the estuary is 1.2 Mt, of which about 0.6 Mt comes from side tributaries. Sediment yield varies inversely with watershed area, with regional trends that are consistent with substrate erodibility. Geophysical and sedimentological surveys in seven subwatersheds of the Lower Hudson were conducted to estimate the mass and composition of sediment trapped behind dams. Impoundments were classified as (1) active sediment traps, (2) run-of-river sites not actively trapping sediment, and (3) dammed natural lakes and spring-fed ponds. Based on this categorization and impoundment attributes from a dam inventory database, the total mass of impounded sediment in the Lower Hudson watershed is estimated as 4.9 ± 1.9 Mt. This represents about 4 years of annual watershed supply, which is small compared with some individual dam removals and is not practically available given current dam removal rates. More than half of dams impound drainage areas less than 1 km2, and play little role in downstream sediment supply. In modeling of a simulated dam removal, suspended sediment in the estuary increases modestly near the source during discharge events, but otherwise effects on suspended sediment are minimal. Fine-grained sediment deposits broadly along the estuary and coarser sediment deposits near the source, with transport distance inversely related to settling velocity.
    Description: This work was sponsored by the National Estuarine Research Reserve System Science Collaborative, which is funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NAI4NOS4190145). Additional support for participating graduate and undergraduates was provided by the Northeast Climate and Adaptation Center and the Hudson River Fund. Additional support for DKR was provided by the Hudson River Foundation (Grant No. 003/19A). Data from sediment cores that were collected in association with this manuscript are archived here: https://doi.org/10.7275/dh3v-0x33.
    Keywords: Dam removal ; Suspended sediment ; Watershed sediment yield ; Sediment supply ; Sediment trapping
    Repository Name: Woods Hole Open Access Server
    Type: Article
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