MEES Theses and Dissertations

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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
SPATIOTEMPORAL DISTRIBUTION OF CHESAPEAKE BAY MYSIDS IN THE CHOPTANK AND PATUXENT RIVERS, MARYLAND
(2024) Quill, Danielle; Woodland, Ryan; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The importance of mysids as trophic links in key Chesapeake Bay food webs has been well documented. However, their abundance, distribution, and demographics haven’t been examined in Chesapeake Bay since 1930. The goal of this study was to examine patterns of mysid abundances and demographic dynamics between and within two key Chesapeake Bay tributaries (the Choptank and Patuxent rivers). I hypothesized that mysid abundances would be greater in the Choptank River due to its historically better water quality (particularly dissolved oxygen saturation) than the Patuxent River. Secondarily, I hypothesized that Neomysis americana (hereafter, Neomysis) would be the most abundant mysid species in both the Chopank and Patuxent rivers. Six stations in each river were sampled monthly from May to September of 2018. Numerical dominance of the mysid assemblage in both rivers shifted from Neomysis in the early summer to a mixed-species group belonging to the genus Americamysis (Americamysis spp.) between August and September. Total abundance across genera and abundance of Neomysis were significantly greater in the Choptank River in early summer, then did not differ from Americamysis spp. abundance thereafter. Neomysis abundance was greater than Americamysis spp. from May through June, did not differ from Americamysis spp. abundance in July, and was less abundant than Americamysis spp. from August through September in the Patuxent River. The Patuxent River displayed overall lower dissolved oxygen saturation in the summer, which correlated with lower mysid abundances, providing support for my hypothesis. Understanding the intricacies of mysid population dynamics within nursery areas for ecologically and economically important predators should strengthen ecosystem-based management strategies for those areas.
NITROGEN, MICROBES, PARTICLES AND OXYGEN DEFICIENT ZONES
(2024) Huanca Valenzuela, Paulina Alejandra; Fuchsman, Clara A.; Cram, Jacob A.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Single-celled microbes mediate most biogeochemical cycling in the ocean. Ammonium is generally the preferred reduced nitrogen form microbes use for assimilation and growth. However, ammonium is often removed to undetectable levels from offshore waters. Microorganisms can metabolize alternative organic reduced nitrogen forms in the absence of ammonium, if they possess genes encoding for the enzymes cyanase (cynS), and urease (ureC), which catalyze the decomposition of cyanate and urea respectively. It is unknown which microbes contain these genes in the environment.In my first chapter, I quantified the microbes that can use cyanate and/or urea in oxic and anoxic (ODZ) environments by using a phylogenetic read placement technique. First, I explored depth profiles of metagenomes from two Pacific Ocean regions: an oxic region represented by the nutrient limited Hawaii Ocean Time series, and two ODZ environments represented by the Eastern Tropical South and the North Pacific. A larger proportion of N2 producing anammox bacteria in ODZs have the ability to utilize cyanate than urea, while a larger proportion of nitrite oxidizing Nitrospina have the ability to utilize urea than cyanate. Ammonia-oxidizing Thaumarchaeota had the ability to use urea in deep oxic waters. Contrastingly, the majority of heterotrophic SAR11 bacteria had the ability to use urea in surface waters, but none did in deep waters. This structuring of who can utilize which reduced N form could reflect competition between microbes and N availability. For my second chapter, I examined microbial ability to use urea and cyanate across time and space using metagenomes from two oceanic Geotraces transects in the North Atlantic; GA02 a North-South spring transect, and GA03, a Fall West to East transect. The two transects differed in nutrient concentrations, affecting the composition of phytoplankton communities. Though eukaryotic phytoplankton were abundant on the spring GA02 transect, they did not have the ability to use urea or cyanate, probably because ammonia was present. However, the ability to use urea was still common in SAR11. Cyanobacteria Synechococcus was abundant on this transect and had the ability to use cyanate. In the nutrient limited fall GA03 transect, the results were similar to oxic waters in chapter 1 except that towards the east, cyanobacteria Prochlorococcus gained the ability to utilize cyanate. Both seasonal and spatial changes were observed in the distribution of ureC and cynS genes in microbial groups in the North Atlantic. My third chapter focuses on organisms living on suspended particles. Marine particles constitute a niche that provides ample nutrient and carbon sources. Large particles have been postulated to support anaerobic metabolism that cannot occur in the surrounding water. We examined how microbial diversity changes among a range of 7 different particle sizes in a depth profile at the East Pacific Rise, an area of the ocean with a distinct oxygen minimum. By combining a quantitative 16S rRNA amplicon sequencing dataset with size fractionated organic matter concentrations, we estimated numbers of each microbial taxa per gram of carbon. Results show differences in microbial composition at different particle sizes and depths.
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.
EFFECTS OF ENVIRONMENTAL VARIABLES AND CHANGES IN SEASONAL PATTERNS ON SPATIAL DISTRIBUTIONS OF JONAH CRABS (CANCER BOREALIS) AND ATLANTIC ROCK CRABS (CANCER IRRORATUS) IN GEORGES BANK AND THE MID-ATLANTIC BIGHT, USA
(2023) Wade, Kaitlynn Jean; Wilberg, Michael J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The economic and commercial importance of Jonah crabs (Cancer borealis) and Atlantic rock crabs (Cancer irroratus) has increased greatly in the USA. The objectives of my research were to determine spatial distributions, habitat preferences, and potential seasonal movements of both species. Data were obtained from the offshore Northeast Fishery Science Center bottom trawl surveys. Analyses included kernel density estimates, generalized additive models, empirical cumulative distribution functions, and ANOVAs. The spatial distributions of Jonah and Atlantic rock crabs changed over time during the 1970s – 2000s. Compared to Atlantic rock crabs, Jonah crabs preferred slightly warmer temperatures, deeper depths, and muddier sediments. Seasonally, Jonah crabs were found farther offshore in the winter and closer to shore in the fall and spring. Atlantic rock crabs were found closer inshore in the winter and spring and more offshore in the fall. Both species were found to have different seasonal patterns in the Mid-Atlantic Bight
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).
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.
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.
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.
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.
DETERMINING FEEDING RATES IN EASTERN OYSTERS (Crassostrea virginica) USING NATURAL SESTON FLOW- THROUGH SYSTEM
(2023) Wiltsee, Laura E.; Gray, Matthew W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Bivalves are prized for the ecosystem services they provide. The removal of particles from the water column through filter feeding and resulting water quality benefits, known as the biofiltration services, of bivalves have been studied for over a century. This has created a wealth of knowledge around the mechanistic drivers of bivalve feeding activity. Recently, Chesapeake Bay ecosystem-wide models have begun incorporating Eastern Oyster (Crassostrea virginica) biofiltration. Acute feeding variability is critically important when estimating oyster biofiltration services at ecosystem scale. Typically, natural seston clearance rate studies last a limited timeframe, with a focus on specific environmental events such as an increase in temperature, drop in salinity, or a tidal cycle.To capture the highly variable filter feeding rate of bivalves, such as the Eastern Oyster, studies have used highly controlled laboratory conditions, with single environmental variable modification. These studies often use indirect methods for estimating clearance rates that commonly lack high-resolution capability. Furthermore, these studies are labor intensive and time consuming, and as a result, few studies have monitored bivalve feeding activities over long periods to understand variation in activity or how these rates may change with seasonal shifts in conditions. These limitations have led to a shortage of knowledge around how clearance rates of oysters vary in response to ambient conditions over both short-term (hourly) and long-term (seasonal) time scales. This study leverages advances in semi-autonomous aquatic observing to track high- resolution, long-term feeding responses of bivalves to subtle variations in environmental conditions. Oyster ex situ clearance rates in the Choptank River (Maryland, USA) were estimated under flow-through conditions, and logged in real-time using fluorometers among replicate oysters over 5-day experiments for 9 months. The measured clearance rates from this system were compared to a mechanistic clearance rate model used by the Chesapeake Bay Program, which is used to estimate the role of oysters in controlling water quality in the Bay. Environmental data were evaluated to build a statistical and random forest model to predict how oyster clearance rates respond to prevailing environmental conditions. This monitoring system and resulting models enable a deeper understanding of feeding variability and how natural seston and environmental variability directly influence oyster physiology.

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