Biology Theses and Dissertations
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Item PREDICTING THE SALINITY HISTORY OF OYSTERS IN DELAWARE BAY USING OBSERVING SYSTEMS DATA AND NONLINEAR REGRESSION(2022) HOWLADER, ARCHI; NORTH, ELIZABETH; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Salinity is a major environmental factor that influences the population dynamics of fish and shellfish along coasts and estuaries, yet methods for predicting the salinity history at specific sampling stations are not widely available. The specific aim of this research was to predict the history of salinity experienced by juvenile and adult oysters (Crassostrea virginica) collected at sampling stations in Delaware Bay as part of the Selection along Estuarine Gradients in Oysters (SEGO) project. To do so, empirical relationships were created to predict salinity at five oyster bed stations using observing systems data and then applied to construct indices of salinity exposure over an oyster’s lifetime. The desired accuracy was +/- 2 psu. Three independent sources of salinity data were used in conjunction with observing systems data to construct and validate the predictive relationships. Observing systems data from the USGS station at Reedy Island Jetty and continuous near-bottom measurements taken by the U.S. Army Corps of Engineers (ACOE) from 2012-2015 and 2018 were employed to fit nonlinear empirical models at each station. Haskin Shellfish Research Laboratory (Haskin) data were used to evaluate model fit, then ACOE data from 2018 (withheld from model fitting in the validation analysis) and SEGO data from 2021 were used to validate models. The best-fitting models for predicting salinity at the oyster bed stations given the salinity at Reedy Island Jetty were logarithmic in form. The root mean square error (RMSE) of the models ranged from 1.3 to 1.6 psu when model predictions were compared with Haskin data, 0.5 to 1.5 when compared with ACOE data, and 0.6 to 0.8 when compared with SEGO data. All of these models were within the desired accuracy range. Results demonstrate that observing systems data can be used for predicting salinity within +/- 2 psu at oyster bed stations within 39 km in upper Delaware Bay. When these models were applied to estimate low salinity exposure of 2-year-old oysters via the metric of consecutive days below 5 psu, the indices suggested that there could be as much as a 42-day difference in low salinity exposure for oysters at stations 31 km apart. This study helps further our understanding of the salt distribution in Delaware Bay as well as the effect of low-salinity stress on the life cycle and genetic differentiation of oysters. In addition, the approach of using observing systems data to predict salinity could be applied to advance understanding of salt distribution and the effect of low salinity exposure on living resources in other estuaries.Item A numerical investigation of variability in particulate organic matter transport and fate, phytoplankton and primary production, and denitrification in a partially mixed estuary(2020) Wang, Hao; Hood, Raleigh; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In Chesapeake Bay substantial quantities of organic matter are produced during the spring bloom, which contributes to severe chronic bottom oxygen depletion during the summertime. However, the details of this transport in the estuarine system under realistic forcing is still unclear. In this Research, a three-dimensional model was used to investigate the production, transport, and fate of organic matter in Chesapeake Bay. Analysis of a control volume in the deep channel revealed that the sinking flux of fast-sinking particulate organic nitrogen (PON) into the deep channel is comparable to the horizontal advective transport. The model analysis also revealed a pronounced east to west transport of PON during the springtime and a tendency to export mass from the eastern shore to the deep channel and from the deep channel to the western shore of the Chesapeake Bay, and also a convergence of mass transport on the western shore. This transport is consistent with the lateral estuarine circulation in Chesapeake Bay that arises due to the asymmetry of the flood-neap tidal cycle. In addition, the model revealed that seasonal variations in wind alter the magnitude and distribution of organic matter flux in the along channel and cross channel direction, with northerly winds during the springtime favoring more northward organic matter transport and more organic matter accumulation in the deep channel, however, the lateral net flux direction remains the same. In Chesapeake Bay, phytoplankton biomass typically peaks in spring whereas primary production peaks in summer. For this to happen, phytoplankton growth rates must be low in spring and high in summer and very likely there must be low grazing losses in spring and high grazing losses in summer as well. In this research, a three dimensional coupled physical-biological model is used to explore how these seasonal patterns in phytoplankton and primary production arise during the year from 2000 to 2005. It is shown that with the seasonal variation of maximum carbon to chlorophyll ratio, temperature control on phytoplankton growth, and temperature-dependent zooplankton grazing effects, my model can capture the spring peak in phytoplankton biomass and the summer peak in the primary production, agreeing well with the observations. The model simulates high phytoplankton growth rates in the summer, with the maximum growth rates occurring in late summer. The model also reveals that nutrient supply shifts from river-derived nitrate in the springtime to organic matter- derived ammonium during summer. The simulation results also reveal that a substantial fraction of the ammonium that supports the high summer production is derived from allochthonous transport rather than autochthonous ammonium production. The transport process provides as large as 50% ammonium needed for uptake during summertime in the mesohaline Chesapeake Bay. My research also confirms the importance of nutrient recycling in supporting high summer production in Chesapeake Bay. Denitrification is an essential process in the marine nitrogen cycle because it removes bioavailable nitrogen from the aquatic system. Current understanding of denitrification variability in Chesapeake Bay is severely constrained by the sparse observations that provide insufficient coverage in both space and time. In this research, denitrification variability is examined in the Chesapeake Bay using a three dimensional coupled physical-biogeochemical model based on the Regional Ocean Modelling System (ROMS). Model simulations indicate that denitrification occurs not only in the sediment but also in the water column at significant, though somewhat lower rates. Model results indicated that the water column accounts for around 7.5% of the total denitrification amount that occurred in the system during the 2001 and 2002 period of this study. This conflicts with the historical assumption that water column denitrification in Chesapeake Bay is negligible. The model also reveals the spatial patterns in denitrification with more denitrification occurring in the upper to middle bay due to higher availability of organic matter in these areas compared to the lower bay. In terms of temporal variability, denitrification peaks in the sediment in spring while in the water column it peaks in the summer. The reason for this difference in the timing is related to the availability of oxygen: In the spring oxygen levels in the water column are too high to allow denitrification so it happens only in the sediment where low oxygen levels persist all year around. In summer low oxygen and depletion of nitrate below the pycnocline completely shuts down denitrification in the sediment in the mesohaline and polyhaline region of the by. However, water column denitrification continues at the interface between oxygenated waters near the surface and oxygen-depleted waters below where coupled nitrification-denitrification happens. The model also reveals that denitrification removes significant quantities of biologically available nitrogen, meaning that without this process, more summertime primary production would occur in the form of more surface chlorophyll, increasing as much as 10ug/L in the middle bay region, which would, in turn, lead to more oxygen depletion.Item MODELING IMPACTS OF SUBMERSED AQUATIC VEGETATION ON SEDIMENT DYNAMICS UNDER STORM CONDITIONS IN UPPER CHESAPEAKE BAY(2019) Biddle, Mathew Michael; Sanford, Lawrence P; Palinkas, Cindy; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Submersed aquatic vegetation is an important modulator of sediment delivery from the Susquehanna River through the Susquehanna Flats into the Chesapeake Bay. However, the impact of vegetation coupled with the physical drivers of sediment transport through the region are not well understood. This study used a new vegetation component in a coupled flow-wave-sediment transport modeling system (COAWST) to simulate summer through fall 2011, when the region experienced a sequence of events including Hurricane Irene and Tropical Storm Lee. Fine sediment was exported under normal flows and high wind forcing but accumulated under high flows. The relative effect of vegetation under normal and high wind forcing depended on previous sediment dynamics. Vegetation doubled the accumulation of fine sediments under high flows. While further refinement of the bed model may be needed to capture some nuances, the COAWST modeling system provides new insights into detailed sediment dynamics in complex vegetated deltaic systems.Item Physical-Biological Interactions Driving the Distribution of the Pelagic Macroalgae Sargassum(2019) Brooks, Maureen Therese; Coles, Victoria J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The holopelagic macroalgae of the genus Sargassum are the ecosystem engineers of a unique open-ocean rafting ecosystem in the subtropical North Atlantic and tropical Atlantic. Over the last decade, increases in biomass in the tropics and Caribbean Sea have been observed. The underlying causes of this regime shift have been difficult to discern without a baseline understanding of the drivers of Sargassum distribution. The objective of this dissertation is to fill this knowledge gap using remote and in situ observations, and coupled ocean circulation, biogeochemical, Lagrangian particle, and Sargassum physiology models. A satellite-derived Sargassum abundance climatology shows the center-of-mass of Sargassum shifting between the tropics, Caribbean, Gulf of Mexico, and Sargasso Sea throughout the year. Model experiments demonstrate that advection alone can explain up to 60% of the observed distribution at time scales shorter than two months. At longer time scales, the growth and reproductive strategy of the macroalgae interact with physical processes to drive the overall observed pattern. Sargassum populations in the Western Tropical Atlantic and Gulf of Mexico appear to exert disproportionate influence over the basin-wide distribution. One key physical process influencing both transport and growth is inertia. A novel inverse method, developed from remote sensing to determine the effective radius of Sargassum rafts, facilitates modeling inertial effects. The effective radius is on the order of 0.95 m, much closer to the size of an individual plant than that of aggregations which can span kilometers. The inclusion of inertia alters modeled distributions of Sargassum by increasing retention in the Gulf of Mexico and the Caribbean, while increasing export from the Sargasso Sea by up to 20%. Inertia acting on buoyant Sargassum rafts also leads to their increased entrainment in cyclonic eddies. These eddies propagate toward the north-west in the northern hemisphere providing transport for Sargassum from the tropics through the Caribbean to the Gulf of Mexico and leading to increased biomass due to transport into regions with better growing conditions. Sargassum biology and its interaction with ocean circulation and mesoscale features is central to improving understanding of the changes in its distribution and for prediction of costly beaching events.Item Response of the coastal ocean and estuaries to tropical cyclones(2018) Zhang, Fan; Li, Ming; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Landfalling tropical cyclones (TC) pose great threats to public safety. The recent decades have witnessed major advances of knowledge in TC dynamics and improvement in TC forecast models, however, occasionally inaccurate TC intensity and storm surge predictions remain a vital concern. Different representations of subgrid-scale physics by various atmospheric model parameterization schemes lead to uncertainty in predictions of TC’s intensity and associated surges. In a case study for Hurricane Arthur (2014), local closure scheme for planetary boundary layer turbulence produces lower equivalent potential temperature than non-local closure schemes, leading to under-predicted TC intensity and surge heights. On the other hand, higher-class cloud microphysics schemes over-predict TC intensity and surge heights. Without cumulus parameterization for coarse-resolution grids, both TC intensity and surge heights are grossly under-predicted due to large precipitation decreases in the storm center. To avoid widespread predictions, the ensemble mean approach is shown to be effective. Another source of TC forecast error is inaccurate sea surface temperature (SST) prediction, and accurate SST prediction necessitates a better understanding of mixing processes in the coastal ocean. Previously, the importance of TC-induced near-inertial currents (NICs) to mixing in the coastal ocean was overlooked. With high-frequency radar and autonomous glider, long-lasting NICs with amplitudes of ~0.4 m s-1 were observed on the shelf during Arthur. With an atmosphere-ocean model, we find the NICs were dominated by mode-1 vertical structure and were a major contributor to the shear spectrum. Therefore, NICs may be important in producing turbulent mixing and surface cooling during Arthur’s passage. In the future, with warmer SST, sea level rise, and possible hard shorelines in estuaries, increased storm surge hazard is expected. Using Isabel (2003) as a case study, we find storm intensification under 2100 SST raises surge heights in Chesapeake Bay by 0.1-0.4 m given increased energy input. While sea level rise in 2100 reduces surge heights by 0-0.15 m through non-linear processes, it increases total water level by 0.4-1 m. Moreover, hard shoreline further increases surge heights by up to 0.5 m in the middle and upper Chesapeake Bay by prohibiting energy flux towards wetlands.Item LONGITUDINAL DYE DISPERSION AND SALT FLUX IN ESTUARIES(2017) Liu, Wei; Li, Ming; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Estuarine dispersion plays an important role in determining the fate of waterborne materials. It is a long-standing question in estuarine dynamics that is still not well understood. This dissertation revisits this problem by utilizing two tracers: dye and salt. Dye-release experiments and numerical modeling are conducted to investigate horizontal dispersion in a partially mixed estuary. Longitudinal dispersion of a dye patch shows strong flood-ebb asymmetry at early times after a dye release, with most of the dispersion occurring during ebb tides. Tidal straining enhances vertical current shear on ebb tides and promotes longitudinal dispersion. There are also large differences in the dispersion rate between spring and neap tides. Due to strong spring mixing, a dye patch quickly extends from the bottom to the surface, exposing to the full vertical shear in the water column and leading to strong longitudinal dispersion. In contrast most of the dye patch is limited to bottom few meters during neap tides. Although weak vertical mixing facilitates longitudinal dispersion, the vertical shear across the thin dye patch is much weaker, leading to weak longitudinal dispersion during neap tides. In first four tidal cycles, the second moment of the dye patch in the along-channel direction increases with time at a power of between 2 and 3. The longitudinal dispersion rate varies as the four-third power of the dye patch size, indicating scale-dependent diffusion. Salt dispersion and transport are examined in a comparative numerical modeling study between the partially-mixed Chesapeake Bay and the well-mixed Delaware Bay. To investigate how different physical mechanisms drive the salt transport into the estuaries, the longitudinal salt fluxes are decomposed using the Eulerian and quasi-Lagrangian methods. Under the Eulerian framework, the salt flux is decomposed into three parts: an advective term associated with the barotropic forcing, a steady shear dispersion term associated with the estuarine exchange flow, and a tidal oscillatory salt flux. In both estuaries, the advective term is dominant over steady shear dispersion and tidal oscillatory salt flux in the temporal variation of total salt flux. In Chesapeake Bay, the steady shear dispersion is the dominant mechanism and the tidal oscillatory salt fluxis small. In Delaware Bay, the steady shear dispersion and tidal dispersion are comparable. The along-channel variation of tidal oscillatory salt flux is mainly due to changes of the phase difference between the tidal current and salinity. Isohaline analysis using the quasi-Lagrangian methodology yields a new interpretation of the estuarine exchange flows and describes the evolution path of salinity classes.Item THE EFFECTS OF SURFACE GRAVITY WAVES ON AIR-SEA MOMENTUM TRANSFER AND VERTICAL MIXING IN A FETCH-LIMITED, ESTUARINE ENVIRONMENT(2017) Fisher, Alexander William; Sanford, Lawrence P.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Surface gravity waves are the principal pathway through which momentum and energy are transferred from the atmosphere to the ocean. Recent studies have contributed to a growing recognition that wind events can be of leading-order importance for mixing and circulation in estuaries, yet the specific nature of air-sea momentum transfer in coastal environments remains relatively understudied. As part of a collaborative investigation of wind-driven estuarine physics, this dissertation addresses the role that surface gravity waves play in the transfer of momentum from the air to the oceanic surface boundary layer in a fetch-limited, estuarine environment. Using a combination of direct field observations and numerical simulations, the role of surface gravity waves in structuring momentum transfer and vertical mixing were examined for a range of wind, wave, and stratification conditions. Results indicate that inclusion of surface gravity waves in bulk parameterizations of wind stress reduced bias to below 5% for nearly all observed wind speeds and that up to 20% of wind stress variability within Chesapeake Bay was directly attributable to surface wave variability. Furthermore, the 10-meter neutral drag coefficient was shown to vary spatially by more than a factor of two over the extent of Chesapeake Bay as a result of combined wind and wave variability. Anisotropic fetch-limitation resulted in dominant wind-waves that were commonly and persistently misaligned with local wind forcing. Direct observations of stress above and below the water surface demonstrated that, within the oceanic surface layer, stress was more aligned with wave forcing than wind forcing. Accounting for the surface wave field was needed to close the local momentum budget between the atmosphere and the mean flow. Directly observed turbulent profiles showed that breaking waves dominated the transfer of momentum and energy and resulted in a three-layer turbulent response consisting of a wave transport layer, surface log layer, and stratified bottom boundary layer. Comparisons to commonly employed second-moment turbulence closures suggest that the presence of breaking waves homogenized the surface layer to a greater extent than predicted by present parameterizations of turbulent kinetic energy transport away from a source at the surface.Item Influences of wave climate and sea level on shoreline erosion rates in the Maryland Chesapeake Bay(2015) Gao, Jia; Sanford, Lawrence Paul; Boicourt, William C.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)SWAN and a parametric wave model implemented by the Chesapeake Bay Program (CBP) were used to simulate wave climate from 1985 to 2005 in Chesapeake Bay (CB). Calibrated sea level simulations from the CBP hydrodynamic model were acquired. Spatial patterns of sea levels during high wave events were dominated by local north-south winds in the upper Bay and by remote coastal forcing in the lower Bay. A dataset comprising shoreline erosion rates and related characteristics was combined with the wave and sea-level climates to explore the most influential factors affecting erosion. The results show that wave power is the most significant factor for erosion in the Maryland CB. Marsh shorelines present a nearly linear relationship between wave power and erosion rates, whereas bank shorelines are less clear. The results of this study are applicable at large scales. A more comprehensive data set is needed for building detailed local predictive relationships.Item INVESTIGATIONS OF THE EFFECTS OF OYSTER ALLOMETRY AND REEF MORPHOLOGY ON FILTRATION RATE AND PARTICLE CAPTURE USING NUMERICAL MODELS(2014) Forsyth, Melinda; Harris, Lora A; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Crassostrea virginica, the eastern oyster, is a filter-feeding, particle clearing bivalve currently at low numbers in Chesapeake Bay. Accurately describing the filtration rate of these bivalves is essential to estuarine management and associated efforts to understand the impact of oyster populations on water quality. Here, the filtration rate equations for three existing models (Cerco and Noel (2005), Fulford et al. (2007), and Powell et al. (1992)) are assessed. I examine how each of the models define the maximum filtration rate and explore the various limitation factors that modify these maximum rates via environmental conditions that include salinity, temperature, total suspended solids, and dissolved oxygen. Based on the individual model strengths found in the model comparison and a literature review, I determine a maximum filtration rate of 0.17 m3 g-1 DW day-1 for a 1 g DW oyster to be a better filtration rate, which is then modified by a combination of limitation factors taken from a variety of sources. These include those described by Fulford et al. (2007) for total suspended solids and salinity, and a newly developed function to describe temperature dependence. Differences in size are incorporated by using a basic allometric formulation where a weight exponent alters filtration rate based on individual oyster size.Item IMPACTS OF WINDS AND RIVER FLOW ON ESTUARINE DYNAMICS AND HYPOXIA IN CHESAPEAKE BAY(2012) Li, Yun; Li, Ming; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In the stratified rotating estuary of Chesapeake Bay, the driving mechanisms of wind-induced lateral circulation are examined using a three-dimensional hydrodynamic model (ROMS). A new approach based on the streamwise vorticity dynamics is developed, and the analysis reveals a balance among three terms: the conversion of the planetary vorticity by along-channel current shear, baroclinicity due to cross-channel density gradient, and turbulent diffusion. It is found that the lateral flow in the Bay is mainly driven by the Ekman forcing, but the lateral baroclinicity creates asymmetry in the streamwise vorticity between down- and up-estuary winds. The traditional view of wind-driven circulation in estuaries ignores the lateral circulation, but wind-induced lateral flows can affect subtidal estuarine circulation and stratification. Coriolis acceleration associated with the lateral flows is of first-order importance in the along-channel momentum balance, with the sign opposite to the stress divergence in the surface layer and the pressure gradient in the bottom layer, thereby reducing the shear in the along-channel current. Moreover, the lateral straining of the density field by lateral circulation offsets the along-channel straining to control the overall stratification. Regime diagrams are constructed using the dimensionless Wedderburn (W) and Kelvin (Ke) numbers to clarify the net wind effects. A coupled hydrodynamic-biogeochemical model is developed to simulate the seasonal cycle of dissolved oxygen in Chesapeake Bay and investigate key processes which regulate summer hypoxia in the estuary. Diagnostic analysis of the oxygen budget for the bottom water reveals a balance between physical transport and biological consumption. In addition to the vertical diffusive flux, the along-channel and cross-channel advective fluxes are found to be important contributors in supplying oxygen to the bottom water. While the vertical diffusive oxygen flux varies over the spring-neap tidal cycle and is enhanced during wind events, the advective oxygen fluxes show long-term averages due to the gravitational estuarine circulation but display strong oscillations due to wind-driven circulations. It is found that water column respiration comprises about 74% of the total consumption and sediment oxygen demand contributes 26%. Sensitivity-analysis model runs are conducted to further quantify the effects of river flow, winds, water column respiration and sediment oxygen demand on the hypoxic volume in the estuary.