Biology Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2749
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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 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 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 GEOSTATISTICAL ESTIMATION OF BLUE CRAB CALLINECTES SAPIDUS ABUNDANCE IN CHESAPEAKE BAY AT LOCAL SCALES(2022) Jones, Sarah Ann; Miller, Thomas J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Increases in the sizes of container ships due to the expansion of the Panama Canal has increased the need for dredging activities in the Chesapeake Bay. Placement of dredged material in the Bay is restricted to winter months owing to concerns for threatened and endangered species. Placement of dredged material in the lower Chesapeake Bay in Wolf Trap Alternate Open Water Placement Site (WTAPS) overlaps with overwintering locations for mature female blue crab. To estimate the potential magnitude of winter mortality in WTAPS and WTAPS Northern Extension (WTAPSNE) resulting from placement of dredged material, a range of geostatistical tools (e.g., inverse distance weighting and kriging) were used to map the distribution and estimate the abundance of blue crab in Chesapeake Bay, WTAPS, and WTAPSNE (i.e., small-scale estimation) from 1990–2020 using data from the winter dredge survey. These analyses indicated that a low proportion of the age-1+ female blue crab population occurs within WTAPS and WTAPSNE (<1.18% and <1.5% respectively). Variability of abundance estimates was high when female age-1+ abundance was less than 150 million in the Chesapeake Bay. Therefore, we suggest the Port limit placement of dredged materials in WTAPS and WTAPSNE when female age-1+ abundance is less than 150 million; we recommend the Port not undertake placement activities when the stock is declared overfished (i.e., when female age-1+ abundance is less than 72.5 million).Item Discerning the roles of ocean acidification, eutrophication, and river alkalization in driving long-term pH trends in the Chesapeake Bay(2022) Guo, Yijun; Li, Ming; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Rising anthropogenic CO2 in the atmosphere and oceanic uptake of CO2 have led to a gradual decrease in seawater pH and ocean acidification, but pH changes in estuaries and coastal systems are more complicated due to a multitude of global and regional environmental drivers. Increasing global fertilizer use due to agricultural production has led to a doubling of riverine nutrient loading since the 1950s, leading to widespread eutrophication in estuarine and coastal waters. Excessive nutrient loading stimulates primary production in the surface euphotic layer, which consumes CO2 and elevates pH, but unassimilated organic matter sinks and decomposes in bottom waters, producing CO2 and reducing pH. In the meantime, human-accelerated chemical weathering, such as acid rain and mining, has resulted in rising alkalinity in many rivers and basification in estuarine and coastal waters. To discern how these environmental drivers influence long-term pH trends in coastal waters, a coupled hydrodynamic-biogeochemical-carbonate chemistry model was used to conduct hindcast simulations of the Chesapeake Bay between 1951 and 2010. The model reproduced the observed chlorophyll increase and hypoxia expansion due to the increased nutrient loading. In contrast, low-pH bottom waters and acidic volume shrank from 1950 to 1980. GAM analysis of long-term pH trends in different regions of Chesapeake Bay revealed increasing pH in the upper Bay driven by the river alkalinization, a peak pH in the mid-Bay in the 1980s coincident with the peak nutrient loading and decreasing pH in the lower Bay driven by ocean acidification. Four scenario runs were performed to assess the individual effects of rising pCO2, river alkalinization, riverine nutrient loading, and climate change (warming and sea-level rise) on long-term pH changes in the Chesapeake Bay. The model results suggested that river alkalinization was more important than ocean acidification in driving the long-term pH changes in the estuary.Item MICROBIAL BIOFILMS ON MICROPLASTICS: A LOOK INTO THE ESTUARINE PLASTISPHERE OF THE CHESAPEAKE BAY(2021) Sosa , Ana Paula; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Microplastics are plastic particles that are smaller than 5 millimeters and are often found as pollution in our waterways. These polymer particles are globally distributed and are a direct result of human activity. Because of their rigidity and durability, microplastics are an ideal substrate for enhanced microbial growth and biofilm development. While microplastics have been studied in various contexts, only few studies have characterized the microbial communities on different types of plastic particles, but no study has been done in the estuarine water. In this study, we exposed three different types of plastics (polypropylene, polystyrene, and polylactic acid) to the water of Baltimore’s Inner Harbor, along with a non-plastic glass control. We used both in situ and in vitro incubations to understand the development of biofilm communities on microplastics. Microbial communities were analyzed based on the 16S rRNA gene sequences. We found that microbial composition on biofilm is distinct from that in the surrounding water, and different microplastic types have a minor impact on the composition of biofilm communities. The similarity between microbial communities on plastic and non-plastic particles suggests that surface supports rather than material types could be more critical for biofilm formation. Succession of microbial communities on the microplastics and interesting bacterial groups were described. Isolation and microscopic observations were also applied in this study. The presence of phototrophic organisms like filamentous cyanobacteria and Auxenochlorella on microplastic biofilms is interesting, and little is known about their contribution to carbon fixation in the ocean. Biofilms formed on microplastic surfaces could potentially affect the ecosystems via different mechanisms, including local nutrient cycling and the transportation of invasive or harmful species. As plastic production and mismanagement continues to be pervasive in our society, it is paramount that we include biofilm development into the framework of general ecology in order to truly understand the impact of plastic pollution and safeguard our ecosystems.Item NUTRIENT RETENTION BY RIPARIAN FORESTED BUFFERS IN WESTERN MARYLAND: DO THEY WORK AND ARE THEY WORTH IT?(2021) Siemek, Stephanie Melissa; Eshleman, Keith N; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Riparian buffers are a best management practice (BMP) implemented to improve water quality. In 1997, Maryland established the Conservation Reserve Enhancement Program (CREP) to give landowners incentives to install riparian buffers that would help restore the Chesapeake Bay. Although many studies support riparian buffers as a BMP, many have also reported a wide range of nutrient reductions. It is uncertain what factors control buffer function, yet they continue to be installed with high expectations. Water quality predictions become less accurate in hydrogeologically complex systems such as the Ridge and Valley (R&V) physiographic province. The purpose of this research was to assess the riparian buffer’s nutrient removal function of dissolved nitrogen and phosphorus in the R&V to understand the hydrologic controls further. Throughout western Maryland, we conducted two synoptic stream chemistry studies that contained forest buffers planted under CREP and a range of pre-existing natural forested riparian zones. We used a steady-state reach mass balance model to estimate lateral groundwater inputs and tested several nutrient models to describe the nutrients in groundwater discharge. We then aimed to understand if incentives given through CREP to landowners were adequate by performing a benefit-cost analysis (BCA) using three scenarios. We used the BCA results to estimate nutrient reduction costs using results from the Chesapeake Bay Watershed Model (CBWM) and our synoptic studies. Streams along CREP sites did not show strong evidence of nutrient retention. However, those containing a mix of natural forests with planted buffers showed significant nutrient declines in both synoptic studies. Several models tested (i.e., The Nature Conservancy model, Gburek and Folmar (1999), our base model) inadequately described nutrient discharge; however, our actual flow model performed best. Our BCA results found newly planted forest buffers under CREP provide the greatest financial gains to landowners, but grass buffers are the most cost-effective practice based on CBWM’s estimated nutrient reductions. Although our research did not assess grass buffers, our synoptic studies showed little indication that newly planted forest buffers significantly reduce nutrients in the R&V, suggesting stream water quality greatly depends on the watershed’s hydrogeomorphology that controls how major contributing sources filter through the landscape.Item Evaluating white perch (Morone americana) fecundity in select Chesapeake Bay tributaries in repsonse to pathology and fitness(2020) Shaner, Jacob; Harrell, Reginal M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Fecundity studies have emerged as a complement to generalized stock assessment methods in an effort to more accurately determine reproductive potential, as well as explain a lack of stock recovery in some cases. The Chesapeake Bay presents an interesting case study, in that widespread anthropogenic influence has created the potential to reduce reproductive fitness among resident species, including white perch (Morone americana). This study seeks to investigate white perch population fecundity in response to habitat quality, as well as disease and nutrition, through the use of stereological and automated counting methods to assess agreement between stock assessments and reproductive potential. Results indicate lack of impact on fecundity from degraded habitat, limited impact of individual nutrition, and no conclusive effect from disease. These findings, coupled with stable recruitment, indicate that white perch reproduction in the Chesapeake Bay is unaffected by increased population stress.Item THE POPULATION BIOLOGY AND ECOSYSTEM EFFECTS OF THE SEA NETTLE, CHRYSAORA CHESAPEAKEI(2020) Tay, Jacqueline; Hood, Raleigh R; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Some of the longest population records of jellyfish are collected from visual shore-based surveys. As surface counting is inexpensive and simple, it is of interest to determine what can be learned from such records as well as the usefulness of the method. A 4-year time series of Chrysaora chesapeakei (formerly quinquecirrha) medusa counts collected using three sampling methods was analyzed. Medusa abundance was modeled by change points and was highly correlated between the sampling methods. The remaining signal was random, and indices indicated that medusae were aggregated. This study suggests more monitoring from visual shore-based surveys is an effective, low-cost method to increase information on jellyfish. Data from another long-term visual survey show that C. chesapeakei in the Cheasapeake Bay have declined since the 1960s. It is hypothesized that their loss results in a trophic cascade and increases in phytoplankton. However, due to confounding factors, it is not clear that C. chesapeakei drives the changes observed. A new 0-dimensional mechanistic model was formulated to include jellyfish. A data assimilation method, Approximate Bayesian Computation, was used to objectively calibrate the model and guide its development. The model fit to observations was improved by the addition of refractory non-living organic materials. Additionally, comments and suggestions related to the model development process are provided. Using the model, perturbation experiments were conducted to study the effect of changing modeled C. chesapeakei (CHRY). Then, sensitivity experiments of the environmental and ecological parameters were conducted to understand the conditions that are important in driving the response. The change in CHRY had the potential to affect every state variable and throughflow but the response did not always conform to the trophic cascade concept and was highly dependent on the parameters. The parameters that were most important in varying the response were related to the energetics of the zooplankton and parameters related to alternative pathways of loss or gains of the state variables. The resulting complexity highlights the far-reaching ecosystem effects of C. chesapeakei as well as the need for new frameworks to understand the response of ecosystems to perturbations.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.