Biology Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2749
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Item AUGMENTING TIDAL WETLAND VEGETATION AND ELEVATION MONITORING USING UNOCCUPIED AERIAL SYSTEMS (UAS)(2024) Malmgren, Benjamin A; Palinkas, Cindy M; Staver, Lorie W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tidal wetlands provide numerous ecosystem services that promote coastal resilience. Live vegetation coverage and elevation are key metrics for assessing the health of these crucial systems. However, traditional monitoring methods can be resource- intensive, intrusive, and lack adequate spatial and temporal resolution. This thesis explores the immense potential of Unoccupied Aerial Systems (UAS, or “drones”) for expanding coastal monitoring capabilities. Chapter 1 compared two tree-based classifiers against in situ observations for estimating live vegetation percent cover. While agreement with field observations varied among both model types, random forest models proved to be more robust than simple thresholding decision stump models when applied to validation data. Chapter 2 evaluated the accuracy of Digital Surface Models (DSMs) generated from drone imagery with Structure-from-Motion, and the influence of vegetation presence on vertical error. While vegetation presence significantly increased vertical error rates, it did not explain all differences in elevation model accuracy across sites. Together, this work underscores the role drones can play in connecting researchers and management practitioners with meaningful data to drive decision- making.Item DEVELOPMENT AND EVALUATION OF SPATIALLY-EXPLICIT POPULATION MODELS FOR ESTIMATING THE ABUNDANCE OF CHESAPEAKE BAY FISHES(2024) Nehemiah, Samara; Wilberg, Michael J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although fish populations typically experience spatially varying abundance and fishing mortality, stock assessments that inform management decisions commonly model a population that is assumed to be well-mixed with homogenous mortality rates. When assumptions about population mixing are not met, these models can result in biased estimates. Spatial population estimates are particularly beneficial to the Chesapeake Bay because this region faces unique challenges as a result of climate change and fishing pressure. However, use of spatial population models for fisheries management relies on models that can provide more accurate estimates of biological parameters than non-spatial models. Objectives for this research were to 1) develop and implement a multi-stock, spatially-explicit population model for Striped Bass (Morone saxatilis) to estimate abundance and fishing mortality in the Chesapeake Bay and along the Atlantic coast; 2) assess the performance of spatially-explicit models compared to spatially-implicit models (i.e., fleets-as-areas) to estimate abundance, determine how improved data quality (e.g., stock composition) affects model performance, and determine the effect of aging error on model accuracy; and 3) determine how spatial model performance is affected by potential changes in population dynamics resulting from climate change (e.g., time-varying natural mortality). The population model was a two-stock model with two sub-annual time-steps and two regions with stock and age-specific occupancy probabilities representing movement into and out of the Chesapeake Bay. Fishing mortality was estimated to be higher in the Ocean than the Chesapeake Bay, and abundance increased during 1982-2004 for both stocks before declining slightly until 2017. Simulations were conducted to test the ability of models to estimate abundance and fishing mortality under alternative scenarios of data availability and quality. Spatially-explicit estimates were approximately unbiased when they closely matched the assumptions of the data generating model. Models that ignored potential aging bias in datasets resulted in highly biased estimates of abundance and fishing mortality. Although the performance of all models degraded under most climate change scenarios, spatially-explicit models produced the most accurate model estimates compared to fleets-as-areas models. This research highlights the potential benefits of implementing spatially-explicit population models for Striped Bass and ecologically valuable fish species in the Chesapeake Bay.Item The Impact of Marsh Sill Living Shorelines on Coastal Resilience and Stability: Insights from Maryland's Chesapeake Bay and Coastal Bays(2024) Sun, Limin; Nardin, William WN; Palinkas, Cindy CP; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Climate change and coastal urbanization are accelerating the demand for strategies to reduce shoreline erosion and enhance coastal resilience to storms and sea-level rise. Generally adverse ecological impacts of hardened infrastructure (e.g., seawalls, revetments, and dikes) have led to growing interest in alternative solutions. Living shorelines, increasingly recognized as sustainable Natural and Nature-Based Features (NNBFs; or Nature-Based Solutions (NBSs)) for their dual benefits of stabilizing shorelines while preserving or restoring coastal habitats, represent a promising approach to shoreline stabilization. Marsh sill living shorelines (created marshes with adjacent rock sills) have been extensively constructed in the Chesapeake Bay, notably in Maryland. Despite their popularity, significant uncertainties remain regarding their effectiveness and resiliency, especially during high-energy events. This dissertation investigates the dynamics of marsh sill living shorelines in Maryland’s Chesapeake Bay and Coastal Bays, aiming to fill knowledge gaps and inform effective shoreline stabilization strategies. First, the dissertation examines marsh boundary degradation into open water during high-energy conditions, contrasting mechanisms between living shorelines and natural marshes. Field surveys and numerical modeling reveal that while natural marshes experience erosion through undercutting and slumping at the scarp toe, living shorelines degrade primarily through open-water conversion at the marsh boundary behind rock sills. Differences in sediment characteristics and vegetation between the two ecosystems drive variations in marsh boundary stability between them. Next, the study assesses the impacts of rock sill placement on sediment dynamics and shoreline stability, highlighting the role of tidal gaps in enhancing sediment flux to the marsh and increasing vertical accretion during high-energy events. Numerical modeling demonstrates that while continuous sills mitigate erosion at the marsh edge of living shorelines, they diminish sediment deposition on the marsh platform compared to segmented sills with tidal gaps. Finally, the research identifies key factors driving marsh boundary degradation that are needed to assess the stability of marsh sill living shorelines. Analysis of eco-geomorphic features and hydrodynamics across 18 living shoreline sites reveals that metrics such as the Unvegetated/Vegetated Ratio (UVVR) and sediment deposition rate often used to assess the resilience of natural marshes also apply to the created marshes of living shorelines. Multivariate analyses further reveal that the Relative Exposure Index (REI) and Gap/Rock (G/R) ratio are crucial predictors of shoreline stability in marsh sill living shorelines, and thus should be particularly considered in shoreline design. By integrating remote sensing, field observations, and numerical modeling, this dissertation advances the understanding of sediment dynamics and stability in living shorelines and provides actionable insights for effective shoreline design and management to promote coastal resilience.Item EXPANDING THE HISTORIC NARRATIVE OF AFRICAN AMERICAN WATERMEN IN CHESAPEAKE BAY COMMERCIAL FISHERIES: PRESERVING CULTURAL HERITAGE AND ENSURING FUTURE AFRICAN AMERICAN MARITIME PARTICIPATION THROUGH A SOCIAL-ECOLOGICAL SYSTEMS PERSPECTIVE(2024) Black, Imani; Gray, Dr. Matthew; Shaffer, Dr. Jen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis investigates African Americans' historical and contemporary contributions to the Chesapeake Bay commercial fishing industry, employing a social-ecological system (SES) framework to explore their roles, challenges, and the decline in their participation. Utilizing methods such as oral histories, participant observations, and historical analysis, the research highlights the significant yet underrecognized contributions of African American communities to the maritime heritage of Chesapeake Bay. Through in-depth interviews with African American watermen, historians, and community members, the study examines their achievements, obstacles, and the impacts of ecological and social change on their participation trends. Additionally, it assesses the influence of prominent African American coastal communities on commercial fisheries and discusses strategies for future engagement and adaptation in a rapidly evolving industry. The findings challenge prevailing perceptions of marginal involvement by revealing substantial African American participation across various aspects of the fisheries, emphasizing the importance of acknowledging this legacy and promoting diversity and inclusion for industry sustainability. By showcasing the rich heritage and ongoing excellence of Black maritime traditions in Chesapeake Bay, this thesis underscores the critical need for greater recognition of African American contributions to the Bay’s preservation, restoration, and strong ties to the cultural heritage that have built the coastal communities along its shoreline.Item REFINING METAGENETIC ENVIRONMENTAL DNA TECHNIQUES FOR SENSITIVE BEE COMMUNITY MONITORING(2023) Avalos, Grace; Richardson, Rodney T; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular taxonomic detection is now widespread across the sciences, because of advances in direct PCR, improved marker selection, and increases in sequencing throughput. Facilitated by these advances in sequencing, methodological sensitivity of sample identification has improved substantially. Metagenetic techniques to infer what species are present in a sample by sequencing unknown samples and comparing them to known references has the potential to advance our understanding of biodiversity. Metagenetic analysis of environmental DNA (eDNA) represents a novel, non-lethal method for characterizing floral-associated arthropod communities. Diverse arthropod assemblages interact with flowers, and floral surfaces have been shown to harbor arthropod DNA. We performed metagenetic sequencing on eDNA isolated from flower samples and honey bee-collected pollen samples using multiple markers and compared the frequency and taxonomic breadth of eDNA detections across these genetic markers and substrate types. Understanding which markers and substrates are most effective for eDNA characterization of floral-associated arthropod communities will guide future research and enable low-risk detection of threatened or endangered arthropods.Item MEGAPOOLS: VEGETATION DIEBACK AND RESTORATION POTENTIAL OF A DITCHED COASTAL SALT MARSH(2023) Stahl, Katherine A.; Baldwin, Andrew H; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In many ditched coastal salt marshes, megapools, or large ponded areas of vegetation dieback,have formed. In combination with sea level rise, this interior marsh loss can decrease wildlife habitat suitability, resilience to storms, and other ecosystem services. However, mechanisms of megapool formation are poorly understood, hampering restoration efforts. Here, we explored differences in environmental characteristics between megapools in different stages of formation (Fully Formed, Partially Formed and Nonformed/Control) and between Elevations within megapools (High, Medium, Low). Using IRIS Films (Indicator of Reduction in Soil), we found that Fully Formed megapools had higher sulfide concentrations than Partially formed, which in turn were greater than Nonformed megapools. We additionally found that lower elevations correlated with higher sulfides, lower plant coverage, lower belowground biomass, lower Carbon Density, and predicted megapool type. We noted that in terms of elevation, vegetative cover, and biomass, Nonformed and Partially formed were more similar as were High and Medium elevations. Whereas in terms of soil characteristics, Fully Formed and Partially formed were more similar as were Medium and Low Elevations. To combat megapools and dieback, we will assess the effectiveness of two restoration techniques, the first of which is assessing the survival and growth of plantings at different spacings, elevations, and megapool formation levels. We found survival and growth was higher in Partially formed megapools than Fully formed, and no impact by spacing or elevation. Our second restoration technique is runnels, or 15” channels that reconnect megapools to ditches, which were installed in January of 2023. The data collected above will act as baseline data, repeated again. These baseline results support a close relationship between pool stages of formation, carbon storage, elevation, vegetation health, biomass production, and sulfide levels (Graphical Abstract).Item INTERACTIONS BETWEEN NITROGEN AND TEMPERATURE ON THE METABOLISM OF THE RED-TIDE MIXOTROPHIC DINOFLAGELLATE KARENIA SPP. IN SUPPORT OF PREDICTIVE MODELS: IMPLICATIONS FOR BLOOM DYNAMICS ON THE WEST FLORIDA SHELF(2023) Ahn, So Hyun; Glibert, Patricia; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The toxic mixotrophic dinoflagellate Karenia spp. forms blooms almost annually in the Gulf of Mexico, especially on the West Florida Shelf (WFS). Blooms typically initiate in early fall but can persist from months to years. Daily, Karenia vertically migrates to the surface water during the day, possibly experiencing changes in temperature, light, nitrogen (N), and prey type and availability. Therefore, this dissertation aimed to examine the interplay between Karenia’s photo-autotrophic and phago-mixotrophic metabolism and the short-term fluctuations in environmental conditions to understand how these factors may relate to the conditions under which Karenia spp. are found in the WFS.Title of Dissertation: INTERACTIONS BETWEEN NITROGEN AND TEMPERATURE ON THE METABOLISM OF THE RED-TIDE MIXOTROPHIC DINOFLAGELLATE KARENIA SPP. IN SUPPORT OF PREDICTIVE MODELS: IMPLICATIONS FOR BLOOM DYNAMICS ON THE WEST FLORIDA SHELF So Hyun (Sophia) Ahn, Doctor of Philosophy, 2023 Dissertation directed by: Professor Patricia M. Glibert, Marine Estuarine Environment Sciences A culture of K. mikimotoi balanced photon flux pressure (light availability) with consumption in overall metabolism when pulsed with 15N-NO3-, 15N-NH4+, or 15N-urea over the range of 15-25°C as shown by photosynthetic fluorescence. However, when shifted to 30°C, cells were significantly stressed, but urea-enriched cells showed a smaller decline in fluorescence, implying that urea might induce a photoprotective mechanism by increasing metabolic “pull.” Studies conducted with natural K. brevis winter and summer populations during 2021 showed that thermal history played a critical role. Unusually, summer blooms had higher biomass but were stressed photosynthetically and nutritionally. However, 15N-urea enriched summer cells had higher uptake rates as well as carbon (C) and N cell-1, especially in warmer waters, showing differential thermal responses based on N forms. Mixotrophy grazing measurements showed that K. brevis grazed both the picoplankter Synechococcus as well as the cryptophyte Rhodomonas. Grazing did not selectively target specific qualities of Synechococcus (based on differing N and P of the prey growth media), but ingestion rates were a function of prey-to-grazer ratios (R2=0.76) as well as prey amounts (R2=0.71). NanoSIMS confirmed 15N incorporation from Synechococcus in K. brevis. In natural communities of K. brevis, ingestion rates were also significantly related to prey-to-grazer ratios (p < 0.01) and by temperatures (p < 0.05) to a lesser degree (R2= 0.75) when incubated at ambient (24°C) and ambient temperature ± 5°C (19, 29°C). The grazer effects on the photosynthetic performance of grazer and prey were also examined. Grazing on Synechococcus indirectly reduce the photosynthetic performance of prey, especially at warmer temperatures but had little or no effect on the photosynthesis of K. brevis itself.Item Investigating the Utility of Environmental DNA Analysis for the Monitoring and Management of Mid-Atlantic Alosine Fishes(2023) Fowler, Chelsea; Plough, Louis V; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Environmental DNA (eDNA) tools can address gaps in fish assessment data while reducing the cost and the impact of sampling on threatened anadromous alosine fishes in Chesapeake Bay. Here, I tested the ability of high-frequency eDNA sampling of river herring to predict fish abundances from sonar-based fish counts on the Choptank River and developed and validated novel species-specific eDNA assays for American and hickory shads. River herring eDNA concentrations from daily eDNA sampling were highly correlated to sonar-based fish counts (Spearman’s Rho = 0.84). This relationship informed a model that could accurately predict fish count from eDNA and relevant covariates (R2 = 0.88). The two new shad assays are highly specific and quantitative, and field testing validated detections in Delaware, Maryland, and North Carolina. This work provides a set of eDNA monitoring tools for the Mid-Atlantic alosines and highlights the capacity for eDNA data to generate quantitative metrics of fish abundance.Item NONLINEAR INTERNAL WAVES AND SHORT-TERM VARIABILITY OF CARBON SYSTEM DRIVEN BY LATERAL CIRCULATION IN COASTAL PLAIN ESTUARY(2023) Li, Renjian; Li, Ming; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Recent observations in Chesapeake Bay showed that the interaction between lateral circulation and channel-shoal bathymetry generated internal lee waves which subsequently propagated onto shallow shoals and evolved into internal solitary waves, leading to overturning and enhanced turbulent mixing. However, it is unknown under what hydrodynamic conditions the lee waves could be generated and how the nonlinear internal waves evolved. Using an idealized straight channel representative of a coastal plain estuary, we conducted numerical simulations to investigate internal wave generation over a range of river flows and tidal amplitudes. The model results are summarized using the estuarine classification diagram based on the freshwater Froude number Frf and the mixing parameter M. Δh decreases with increasing Frf as stronger stratification suppresses waves, and no internal waves are generated under large Frf. Δh initially increases with increasing M as the lateral flows become stronger with stronger tidal currents, but decreases or saturates to a certain amplitude as M further increases. This regime diagram suggests that internal lee waves can be generated in a wide range of estuarine conditions. To examine the nonlinear evolution of internal waves, a three-dimensional nonhydrostatic model with nested model domains and increasing grid resolution was configured. The lee wave steepens into a shorter elevation wave due to shoaling and soon evolves into a depression with a train of undular waves at its tail as bottom boundary mixing elevates the halocline above the mid-depth. These nonlinear internal waves enhance the turbulent dissipation rate over the deep channel and shallow shoal, suggesting an important energy source for mixing in stratified coastal plain estuaries. In addition, a pH sensor deployed at the middle reach of Chesapeake Bay recorded high-frequency variability in bottom pH driven by along-channel winds. Though wind-driven lateral circulation can advect high pH water downward, the slow air-sea exchange of CO2 limits the lateral ventilation. With DIC and TA budget analysis and comparison with cross-sections at upper- and lower-Bay where strong lateral circulation was confined in the surface layer, we found vertical mixing and replenishment of oceanic water by longitudinal advection could be more important mechanisms to ventilate bottom pH.Item OYSTERS’ INTEGRATION ON SUBMERGED BREAKWATERS AS NATURE-BASED SOLUTION FOR COASTAL PROTECTION WITHIN ESTUARINE ENVIRONMENTS(2023) Vona, Iacopo; Nardin, William; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Rising sea levels and the increased frequency of extreme events put coastal communities at serious risk. Due to SLR, traditional solutions such as breakwaters (or gray/artificial structures) will become ineffective for wave attenuation and shoreline erosion control. Moreover, gray solutions do not consider the ecological aspects of the coast, and may negatively affect surrounding ecosystems. The “living shoreline” technique includes natural habitat features, such as oysters and/or vegetation into shoreline stabilization, to provide both protection and ecosystem services. Oysters create three-dimensional, complex reef structures that attenuate wave energy and increase sedimentation rates. If coupled with breakwaters, oysters may maintain breakwaters’ efficiency over time as they are expected to grow with SLR. However, guidance for the correct implementation of Natural and Nature Based Features (NNBF) for coastal protection is still unclear, and many authors within the literature have been repeatedly requested more insights. In this thesis, we have therefore studied the coupling between oysters and breakwaters via field, modeling and laboratory experiments, in order to highlight the benevolent aspects of NNBF regarding coastal defense. Field results showed gray breakwaters allowed for shoreline protection (by reducing incoming wave energy) and increased sedimentation rates. However, SLR modeling scenarios showed a gradual reduction of wave attenuation over time, as well as increased sediment export from the coast. When oysters were included in the modeling, on the other hand, wave dampening and sediment retention were preserved through the time. Laboratory experiments showed oyster-reef breakwaters in emergent or near-emergent conditions produced higher drag coefficient compared to gray structures, resulting in greater dissipative features. Higher water levels simulated in our experiments produced less reliable results that will require further investigation. This thesis supports oysters for coastal protection, and emphasizes the positive aspects of NNBF regarding wave attenuation and sediment retention in the face of climate changes and SLR. However, challenges encountered during field studies underlined the importance of environmental and biogeochemical conditions (such as water level, aerial exposure, temperature and seasonality) for oyster reefs’ establishment, growth and survivability. Future restoration plans involving oysters in coastal defense should definitely take these environmental and biogeochemical aspects into account, in order to properly protect the coast in the face of climate changes and SLR, while also providing many other useful ecosystem services for the environment. The coupling between oysters and breakwaters may represent a valuable and effective methodology to protect our coast over a changing climate and a rising sea, where optimal conditions for oysters’ survivability occur and are maintained over time.