Sensitivity analysis of a coupled hydrodynamic-vegetation model using the effectively subsampled quadratures method (ESQM v5.2)

Abstract. Coastal hydrodynamics can be greatly affected by the presence of submerged aquatic vegetation. The effect of vegetation has been incorporated into the Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST) modeling system. The vegetation implementation includes the plant-induced three-dimensional drag, in-canopy wave-induced streaming, and the production of turbulent kinetic energy by the presence of vegetation. In this study, we evaluate the sensitivity of the flow and wave dynamics to vegetation parameters using Sobol' indices and a least squares polynomial approach referred to as the Effective Quadratures method. This method reduces the number of simulations needed for evaluating Sobol' indices and provides a robust, practical, and efficient approach for the parameter sensitivity analysis. The evaluation of Sobol' indices shows that kinetic energy, turbulent kinetic energy, and water level changes are affected by plant stem density, height, and, to a lesser degree, diameter. Wave dissipation is mostly dependent on the variation in plant stem density. Performing sensitivity analyses for the vegetation module in COAWST provides guidance to optimize efforts and reduce exploration of parameter space for future observational and modeling work. </jats:p

Seasonal circulation over the Catalan inner-shelf (northwest Mediterranean Sea)

This study characterizes the seasonal cycle of the Catalan inner-shelf circulation using observations and complementary numerical results. The relation between seasonal circulation and forcing mechanisms is explored through the depth-averaged momentum balance, for the period between May 2010 and April 2011, when velocity observations were partially available. The monthly-mean along-shelf flow is mainly controlled by the along-shelf pressure gradient and by surface and bottom stresses. During summer, fall, and winter, the along-shelf momentum balance is dominated by the barotropic pressure gradient and local winds. During spring, both wind stress and pressure gradient act in the same direction and are compensated by bottom stress. In the cross-shelf direction the dominant forces are in geostrophic balance, consistent with dynamic altimetry data. Key Points A hydrodynamic model is implemented for the first time in Catalan inner-shelf. Frictional and pressure gradient are revealed as the main forcing mechanisms A clear seasonal pattern is found in the current velocity.Peer ReviewedPostprint (published version

Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molino, G. D., Defne, Z., Aretxabaleta, A. L., Ganju, N. K., & Carr, J. A. Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States. Frontiers in Environmental Science, 9, (2021): 616319, https://doi.org/10.3389/fenvs.2021.616319.Coastal salt marshes, which provide valuable ecosystem services such as flood mitigation and carbon sequestration, are threatened by rising sea level. In response, these ecosystems migrate landward, converting available upland into salt marsh. In the coastal-plain surrounding Chesapeake Bay, United States, conversion of coastal forest to salt marsh is well-documented and may offset salt marsh loss due to sea level rise, sediment deficits, and wave erosion. Land slope at the marsh-forest boundary is an important factor determining migration likelihood, however, the standard method of using field measurements to assess slope across the marsh-forest boundary is impractical on the scale of an estuary. Therefore, we developed a general slope quantification method that uses high resolution elevation data and a repurposed shoreline analysis tool to determine slope along the marsh-forest boundary for the entire Chesapeake Bay coastal-plain and find that less than 3% of transects have a slope value less than 1%; these low slope environments offer more favorable conditions for forest to marsh conversion. Then, we combine the bay-wide slope and elevation data with inundation modeling from Hurricane Isabel to determine likelihood of coastal forest conversion to salt marsh. This method can be applied to local and estuary-scale research to support management decisions regarding which upland forested areas are more critical to preserve as available space for marsh migration.Funding for this study was provided by the United States Geological Survey’s Coastal/Marine Hazards and Resources Program and Ecosystems Mission Area

Monthly climatology of the continental shelf waters of the South Atlantic Bight

Monthly circulation of the South Atlantic Bight is diagnosed using a 3-D, shallow water, finite element model forced with monthly wind stress and hydrographic climatology. Temperature and salinity observations from the period 1950-1999 are objectively interpolated onto the model domain, and Comprehensive Ocean-Atmosphere Data Set (COADS) wind velocities from 1975-1999 are used to prescribe the model surface wind stress. The resulting monthly temperature and salinity fields compare favorably to existing shelf climatology. River discharge maxima are evident in the spring temperature and salinity fields, and the rapid heating and cooling of the shelf are captured. The diagnostic circulation is largely wind-driven in the inner and mid-shelf, and the Gulf Stream is apparent in the solutions on the outer shelf. We present the monthly fields, including the temporal and spatial distribution of available hydrographic data, the regional COADS data that provide surface wind stress forcing, the objective analysis, and the model response to these forcings. The hydrographic and velocity fields provide best-prior-estimates of the circulation for data assimilation studies in the region, as well as initial conditions for process-oriented prognostic model studies in the Georgia coastal region

Issues in the balancing of the SMOS ocean salinity trieval cost function

Peer Reviewe

Near-bottom circulation and dispersion of sediment containing Alexandrium fundyense cysts in the Gulf of Maine during 2010–2011

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 96–111, doi:10.1016/j.dsr2.2013.11.003.The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010–May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s−1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment were small compared to the inventory of cysts in the upper few centimeters of sediment but could potentially have more relevance immediately after deposition.Research support to all authors, except DJM and VAS, was provided by U.S. Geological Survey. DJM gratefully acknowledges financial support of the National Oceanic and Atmospheric Administration (Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program) and the Woods Hole Center for Oceans and Human Health through National Science Foundation Grant OCE-1314642 and National Institute of Environmental Health Sciences Grant 1P01ES021923-01. VAS was supported by the North East Consortium Grant NA05NMF4721057

Investigating the importance of sediment resuspension in Alexandrium fundyense cyst population dynamics in the Gulf of Maine

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 79–95, doi:10.1016/j.dsr2.2013.10.011.Cysts of Alexandrium fundyense, a dinoflagellate that causes toxic algal blooms in the Gulf of Maine, spend the winter as dormant cells in the upper layer of bottom sediment or the bottom nepheloid layer and germinate in spring to initiate new blooms. Erosion measurements were made on sediment cores collected at seven stations in the Gulf of Maine in the autumn of 2011 to explore if resuspension (by waves and currents) could change the distribution of over-wintering cysts from patterns observed in the previous autumn; or if resuspension could contribute cysts to the water column during spring when cysts are viable. The mass of sediment eroded from the core surface at 0.4 Pa ranged from 0.05 kg m−2 near Grand Manan Island, to 0.35 kg m−2 in northern Wilkinson Basin. The depth of sediment eroded ranged from about 0.05 mm at a station with sandy sediment at 70 m water depth on the western Maine shelf, to about 1.2 mm in clayey–silt sediment at 250 m water depth in northern Wilkinson Basin. The sediment erodibility measurements were used in a sediment-transport model forced with modeled waves and currents for the period October 1, 2010 to May 31, 2011 to predict resuspension and bed erosion. The simulated spatial distribution and variation of bottom shear stress was controlled by the strength of the semi-diurnal tidal currents, which decrease from east to west along the Maine coast, and oscillatory wave-induced currents, which are strongest in shallow water. Simulations showed occasional sediment resuspension along the central and western Maine coast associated with storms, steady resuspension on the eastern Maine shelf and in the Bay of Fundy associated with tidal currents, no resuspension in northern Wilkinson Basin, and very small resuspension in western Jordan Basin. The sediment response in the model depended primarily on the profile of sediment erodibility, strength and time history of bottom stress, consolidation time scale, and the current in the water column. Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m−3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.Research support to Donald M. Anderson and Bruce A. Keafer provided through the Woods Hole Center for Oceans and Human Health; National Science Foundation Grants OCE-0430724 and OCE-0911031; and National Institute of Environmental Health Sciences Grant 1-P50-ES012742-01; the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and A09NOS4780193; the MERHAB Grant program through NOAA Grant NA11NOS4780025; and the PCMHAB Grant program through NOAA Grant NA11NOS4780023. Research support to all other authors was provided by U.S. Geological Survey

Cold event in the South Atlantic Bight during summer of 2003: Model simulations and implications

A set of model simulations are used to determine the principal forcing mechanisms that resulted in anomalously cold water in the South Atlantic Bight (SAB) in the summer of 2003. Updated mass field and elevation boundary conditions from basin-scale Hybrid Coordinate Ocean Model (HYCOM) simulations are compared to climatological forcing to provide offshore and upstream influences in a one-way nesting sense. Model skill is evaluated by comparing model results with observations of velocity, water level, and surface and bottom temperature. Inclusion of realistic atmospheric forcing, river discharge, and improved model dynamics produced good skill on the inner shelf and midshelf. The intrusion of cold water onto the shelf occurred predominantly along the shelf-break associated with onshore flow in the southern part of the domain north of Cape Canaveral (29° to 31.5°). The atmospheric forcing (anomalously strong and persistent upwelling-favorable winds) was the principal mechanism driving the cold event. Elevated river discharge increased the level of stratification across the inner shelf and midshelf and contributed to additional input of cold water into the shelf. The resulting pool of anomalously cold water constituted more than 50% of the water on the shelf in late July and early August. The excess nutrient flux onto the shelf associated with the upwelling was approximated using published nitrate-temperature proxies, suggesting increased primary production during the summer over most of the SAB shelf

Temporal evolution of the momentum balance terms and frictional adjustment observed over the inner shelf during a storm

We investigate the rapidly changing equilibrium between the momentum sources and sinks during the passage of a single two-peak storm over the Catalan inner shelf (NW Mediterranean Sea). Velocity measurements at 24¿m water depth are taken as representative of the inner shelf, and the cross-shelf variability is explored with measurements at 50¿m water depth. During both wind pulses, the flow accelerated at 24¿m until shortly after the wind maxima, when the bottom stress was able to compensate for the wind stress. Concurrently, the sea level also responded, with the pressure-gradient force opposing the wind stress. Before, during and after the second wind pulse, there were velocity fluctuations with both super- and sub-inertial periods likely associated with transient coastal waves. Throughout the storm, the Coriolis force and wave radiation stresses were relatively unimportant in the along-shelf momentum balance. The frictional adjustment timescale was around 10¿h, consistent with the e-folding time obtained from bottom drag parameterizations. The momentum evolution at 50¿m showed a larger influence of the Coriolis force at the expense of a decreased frictional relevance, typical in the transition from the inner to the mid-shelf.Postprint (published version

Progress and challenges in coupled hydrodynamic-ecological estuarine modeling

© 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.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.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)