MEES Theses and Dissertations
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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 Impact of salinity on morphology, growth, and pigment profiles of Scenedesmus obliquus HTB1 under ambient air and elevated CO2 (10%) conditions(2024) Jiao, Fanglue; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Certain microalgal species tolerate high CO2 concentrations and proliferate faster with elevated CO2 than with ambient air. This feature makes them attractive for carbon sequestration, a tool for mitigating climate change due to increasing atmospheric CO2. Scenedesmus species are among these microalgae. Scenedesmus obliquus strain HTB1 is a microalgal strain isolated from the Baltimore Inner Harbor (brackish water) and has shown a faster growth with 10% CO2 compared to air. However, how HTB1 grows under different salinity and if the salt response is affected by elevated CO2 remains elusive. Two experiments were set up to address these questions. The first experiment tested the impact of salinity gradient (0, 17.5, 20, 22.5, 25, 27.5, and 30 ppt) on HTB1 under ambient air. With increasing salinity, HTB1 cells became smaller, and the cultures changed color from green to brown, yellowish brown, and then to pale white. The pigment analysis showed that HTB1 reduced several pigments (i.e. zeaxanthin, lutein, chlorophyll b) in response to salt stress. However, HTB1 produced higher concentrations of canthaxanthin under the salt stress. The growth of HTB1 decreased with increasing salinity and was inhibited when the salinity was greater than 22.5 ppt. In the second experiment, we compared the impact of salinity (0, 10, and 20 ppt) on HTB1 under air and 10% CO2, respectively. HTB1 cultures showed little color change with increasing salinity under 10% CO2. In contrast, the change of culture color from dark green to brown was observed with increasing salinity when HTB1 was grown with air. Interestingly, the growth of HTB1 was less inhibited with salt under 10% CO2 than with air, suggesting that elevated CO2 mitigates the salt stress of HTB1. Lutein and canthaxanthin increased with increasing salinity when HTB1 was grown with 10% CO2. Our results indicate that increased salinity affects the growth of Scenedesmus obliquus HTB1 more with air than with 10% CO2. This study provides insight into the impact of salt stress on algal morphology, growth, and pigment composition.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 Investigating the Microbial Diversity and Ecophysiology of Filamentous Cyanobacteria on the Susquehanna Flats, Chesapeake Bay(2024) Keller, Shayna Aryn; O'Neil, Judith M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Susquehanna Flats is a biodiverse and resilient submerged aquatic vegetation (SAV) bed just below the mouth of the Susquehanna River in the Chesapeake Bay. The Susquehanna River, the largest tributary of the Chesapeake Bay, discharges more water than all other tributaries in the Bay combined. This makes the SAV bed at the Susquehanna Flats important for nutrient removal of the water discharged into the headwaters of the Bay. The Susquehanna Flats is also a unique part of the oligohaline portion of the Chesapeake Bay as it is one of the most prolific and diverse SAV beds that make up ~8% of SAV in the Chesapeake Bay. The SAV bed was devastated by Hurricane Agnes in 1972 and did not reappear until the early 2000s when an extended dry period and long-term reductions in nutrient loading facilitated its resurgence. Since then, it has recovered to be the most abundant and biodiverse SAV bed within the upper Chesapeake Bay. However, a nitrogen fixing filamentous Cyanobacteria, morphologically identified as Microseira (Lyngbya) wollei, has seasonally bloomed at the Susquehanna Flats since the early 2000s. Over the ensuing decade, anecdotal evidence suggested an overall increase of Cyanobacteria on the SAV beds on the Susquehanna Flats, which raised concerns about the impact of this growth on the resilience of the recovering SAV bed. Despite the consistent summer blooms, the filamentous Cyanobacterial mats and its microbiome at the Susquehanna Flats has not been molecularly identified and its characteristics have not been investigated to date. Additionally, new DNA sequencing technology has become more readily available, and the identification and taxonomy of the Cyanobacteria family Oscillatoriaceae, of which Microseira (Lyngbya) wollei is a part of, has become more refined and organized. Due to this, molecularly identifying the filamentous Cyanobacterial mats and investigating its microbiome has become much easier with current methods that can provide detailed taxonomic information that can help implement management strategies. Using PacBio long-read amplicon sequencing on the 16S rRNA genes and Illumina short-read amplicon sequencing on the nifH genes of the filamentous Cyanobacteria mats and a newly observed mucilaginous Cyanobacteria mat collected at the Susquehanna Flats, the host organisms and microbial compositions were revealed. The results indicate that the dominant filamentous Cyanobacterial mat host is Microseira (Lyngbya) wollei and these mats contain a complex microbial community. The host of a newly observed mucilaginous mats was revealed to be a novel strain of Phormidium sp. To understand the basic nutrient requirements and preferences of the Microseira (Lyngbya) wollei at the Susquehanna Flats, nutrient bioassay growth and nitrogen fixation experiments were initiated to assess its growth and nitrogen fixation qualities. Samples received nutrient treatments of nitrate, phosphate, nitrate + phosphate, and ammonium compared to the growth of control samples that did not receive nutrient treatments in the summers of 2022 and 2023. The results demonstrated that Microseira (Lyngbya) wollei has variable growth rates, with higher rates in the mid to late part of the summer season, with significant growth stimulations from added nitrogen and phosphorus. In terms of nitrogen fixation, rates were higher in the beginning of the season, with significant stimulation with phosphorus additions. It is likely that lower rates measured at the end of the season, were due to the increased availability of regenerated nitrogen within the system. More detailed investigation of the seasonal nutrient dynamics are warranted to fully understand the dynamics between these Cyanobacterial mats and the SAV beds.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 MESOSCALE EDDIES INFLUENCE ZOOPLANKTON DISTRIBUTION AND GRAZING IN THE GULF OF MEXICO(2024) Atkinson, William August; Coles, Victoria J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Carbon biomass and net primary productivity, for two size classes of phytoplankton in the Gulf of Mexico (GoM), are calculated from ocean color remote sensing data. Combining these estimates with mechanistic ecosystem model equations allows for analysis of how changes in phytoplankton biomass and community structure propagate through the food web to zooplankton. Biomass and grazing rates are calculated for three size classes of zooplankton (small, large, and predatory) by solving equations from the NEMURO model describing the growth of small and large phytoplankton and zooplankton using the remote sensing net primary productivity, biomass, temperature, and mixed layer depth. The ecosystem model and approach are validated for the GoM and used to assess error propagation. An eddy detection algorithm, tuned for the GoM, is used to calculate the phytoplankton and zooplankton biomass within eddy centers, around eddy edges, and in the immediate surroundings of the eddy to determine the impact of cyclonic and anticyclonic eddies and submesoscale edge effects on patterns of trophic transfer variability. Cyclonic eddy centers increase biomass and anticyclonic eddy centers decrease biomass in the oligotrophic GoM. Eddy edges contribute to variability in biomass but to a lesser extent than eddy centers. Zooplankton grazing varies in a similar pattern as biomass, and in this oligotrophic region, most grazing is on the largest size class of prey available. Nutrient injection stimulated by eddy dynamics more strongly projects onto biomass in zooplankton trophic levels and their associated grazing which suggests many eddies in the oligotrophic GoM experience top-down control. An understanding of mesoscale eddy impacts on zooplankton dynamics may explain variations in larval fish growth. Advances in remote sensing that allow the discrimination of phytoplankton functional types, such as the new PACE satellite, will be useful for providing a more complete base of the food web and thus enhance estimation of zooplankton biomass.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 The Role of Urban Agriculture in Baltimore Food Systems(2024) Mathews, Meghna Anjali; Zhang, Xin; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The United States is one of the most agriculturally productive countries; and yet, food insecurityremains a significant issue. Urban agriculture in Baltimore, Maryland should be studied further because of its potential to address food insecurity while overcoming systemic barriers created and embedded within food systems. While numerous previous studies have explored food insecurity, knowledge gaps still exist regarding how urban agriculture has influenced food accessibility, and how availability, cultural values of foods, etc. can be improved through increased production and distribution practices of fresher fruits and vegetables in Healthy Food Priority Areas. To address these knowledge gaps, we queried food insecure community members and urban farmers in Baltimore, Maryland to better understand the underlying factors that influence low fruit and vegetable consumption and how they can be mitigated through the establishment of urban agriculture. Urban farmers were interviewed in detail about their production and distribution patterns, and factors influencing the low consumption of fresh fruits and vegetables by community members in Baltimore. Food insecure individuals were asked about their food consumption habits and the accessibility of fruit and vegetables, their food purchasing behavior and related challenges, and community needs. Results indicate that while accessibility and availability are two main factors in fresh produce consumption, there are other important factors that might have received limited attention in existing literature. Our interviews revealed that income, cultural value, and a lack of knowledge in food preparation are key factors in low consumption and purchase of fresh fruits and vegetables. To address the underlying factors and improve the accessibility and availability of fresh produce to low-income communities, it is important to assess community needs and provide policy recommendations that can potentially enhance their nutrition. Ensuring access to individuals with limited resources is a critical component of advancing social justice.Item MICROBIAL COMMUNITIES IN COASTAL ECOSYSTEMS(2024) Kim, Carol; Malkin, Sairah Y; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Firstly, I examined microbial community succession along a chronosequence of constructed salt marshes using the Poplar Island restoration project site as a case study. By comparing 16S rRNA gene amplicon sequences across 6 constructed low marshes spanning a chronosequence of 1-16 years at Poplar Island (Chesapeake Bay) and a nearby natural reference marsh, I found strong evidence that the development of soil microbial communities is on a trajectory towards natural marsh conditions following marsh restoration with successional rates within timescales expected for soil development. Results from this study showed the value of microbial communities to serve as effective bioindicators for monitoring the recovery of microbially mediated biogeochemical processes in restored or newly constructed salt marshes, as well as potentially for assessing the marsh inundation period and by extension marsh health and resiliency. Secondly, I conducted a manipulation experiment to explore microbial communities associated with cable bacteria using RNA stable isotope probing (RNA-SIP). I traced the uptake of isotopically labeled bicarbonate and acetate in sediments with baseline and with stimulated cable bacteria activity, to test the hypothesis that cable bacteria activity can stimulate chemoautotrophic bacteria in anaerobic sediments. I used 16S rRNA sequencing to identify the active “incorporators” of bicarbonate (as a tracer of chemoautotrophy) and acetate (as a tracer of heterotrophy). I found that estuarine cable bacteria activity stimulated the chemoautotrophic activity of Gammaproteobacteria (Nitrosomonas, Thioalkalispira-Sulfurivermis) and Campylobacterota (Sulfurovum, Sulfurimonas) at anaerobic depths. This result is not explainable with conventional understanding of chemoautotrophic activity. Rather, this study contributes to the emerging concept that cable bacteria activity stimulates metabolic activities at suboxic sediment depths, potentially by serving as an electron sink for other microbes. Furthermore, I found that heterotrophic activity, measured as 13C-acetate assimilation into RNA, was stimulated amongst known chemoautotrophic sulfur oxidizers at depth, highlighting that metabolic flexibility, and specifically mixotrophy, may be widespread in complex natural sediment environments. Lastly, I characterized the composition and metabolic potential of microbial communities in estuarine sediment enriched with cable bacteria. By using metagenomic and 16S rRNA sequencing, I constructed 23 medium- to high-quality metagenome-assembled genomes (MAGs) that span across 9 phyla. I retrieved MAGs exhibiting mixotrophy and a range of capabilities for extracellular electron transport. This study revealed a diverse range of metabolically flexible communities of microbes that contribute to the biogeochemical cycling of carbon, nitrogen, and sulfur.Item Fish Bioacoustics: From Basic Science to Policy(2024) Colbert, Benjamin; Bailey, Helen R; Popper, Arthur N; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Sound is critically important to fishes. Sound is used to communicate with conspecifics, to detect predators and prey, or to otherwise understand the world around them. Within this dissertation, I used a variety of methods to investigate multiple aspects of fish bioacoustics, including hearing, hearing in noise, the effects of anthropogenic sound, and the morphology of peripheral auditory structures.In Chapter 2, I reviewed international policy on the regulation of underwater sound and the effects of underwater sound on marine and aquatic habitats. I found that while there are increasing efforts to regulate underwater noise, the policy efforts are hampered by a lack of quantifiable metrics associated with impacts of anthropogenic sound in aquatic habitats and species. In Chapter 3, I measured auditory sensitivity of cyprinids using physiological methods. Auditory evoked potentials, a physiological measure of auditory sensitivity, have been used in previous studies to measure hearing sensitivity. However, while physiological methods have their place, they are measuring the sensitivity of the ear rather than the entirety of the auditory pathway. Therefore, I further measured hearing sensitivity of goldfish using behavioral methods that encompass the full auditory pathway. I found that physiological methods tend to underestimate actual hearing sensitivity at frequencies less than 1000 Hz. In Chapter 4, I investigated cyprinid hearing in noise, using both physiological and behavioral measures. Critical ratios were measured for four species of carp and goldfish using auditory evoked potentials. Behavioral methods were also used to measure critical ratios for goldfish. These data represent the first measurements of critical ratios for carp and the first comparative analysis between critical ratios measured using both physiology and behavior. I found that critical ratios for carp increase by as much as 25 dB between 300 Hz and 1500 Hz. I also found that physiological methods likely overestimate actual critical ratios for fish. In Chapter 5, I used micro-computed tomography (micro-CT) and three dimensional geometric morphometrics to compare the peripheral auditory structures of three species of carp. Three dimensional models of the tripus ossicle, the posterior most Weberian ossicle, and the sagitta otolith were created and the shape of these structures for silver carp (Hypophthalmichthys molitrix), bighead carp (H. noblis), and grass carp (Ctenopharyngodon idella) quantified and contrasted. I found that the shape of the tripus differed between the Hypophthalmichthys genus (i.e., silver and bighead carp) and Ctenopharyngodon (grass carp), demonstrating a possible phylogenetic signal in the shape of the Weberian ossicles. In Chapter 6, I studied the response of wild oyster toadfish (Opsanus tau) to underwater radiated noise from boats. I used passive acoustic monitoring to record toadfish vocalizations and vessel passages in the Chesapeake Bay, U.S.A. The effect of acute vessel passage was determined by comparing the number of calls after a vessel had passed to a control period. The effect of both aggregate vessel passage over an hour and environmental variables were investigated using generalized additive mixed models. I found that there was no significant effect on toadfish call rates from acute vessel passage but when vessel generated sound was higher over an hour long period (i.e., aggregate effect), call rate declined.