Marine Biology Commons^™

Infrared Detectability Of Whale Species And Behaviors To Enhance Automatic Detection For Real-Time Vessel Strike Avoidance, Laura J. Howes

Graduate Masters Theses

Real-time detection of large whales at sea is critical for mitigating serious injury and mortality from ship strikes and other human activities such as seismic surveys, especially for endangered species such as the critically endangered North Atlantic Right Whale (Eubalaena glacialis). Traditional marine mammal observers are limited by environmental conditions and human factors, necessitating a robust, 24-hour solution. This study investigates the efficacy of a novel onboard detection tool infrared (IR) technology to detect whale blows and body parts. While IR is a promising advancement, its performance under varying sea conditions (e.g., fog, humidity) and its ability to …

Changes In Water Quality And Microbiota Over Two Years In Florida Hard Clam (Mercenaria Mercenaria) Hatcheries, Bonnie Getter

Electronic Theses and Dissertations

This thesis characterized the water quality and bacterial communities in nine hard clam hatcheries over two production years through weekly or biweekly water quality and chemistry monitoring, monthly bacterial plating in the second year of production, and select 16S microbiome sampling at select hatcheries to address production bottlenecks and support the reliable production of high-quality seed for Florida’s growing hard clam aquaculture industry. Logistic regression models showed that water source was distinguished by pH, salinity, alkalinity, and nitrite, whereas geographic location was distinguished by temperature, salinity, nitrate, and calcium; temperature, dissolved oxygen, salinity, and alkalinity distinguished seasons. Vibrio bacteria differed …

Blue Crab Reproductive Output And Phenology In A Changing Climate, Blaise Rohan

Master's Theses

Globally, ecosystems are experiencing rising temperatures due to climate change, with potential consequences for reproductive investment and timing in many species. Blue crabs, Callinectes sapidus, support valuable commercial fisheries throughout the U.S. Atlantic and Gulf coasts, and understanding variation in reproductive output has important management and conservation implications. This study examined two components of blue crab reproduction: (1) reproductive investment across populations spanning multiple latitudes (New York, New Jersey, North Carolina, Mississippi, and Texas), using a space-for-time substitution to assess the effects of varying thermal regimes on fecundity and egg quality, and (2) spawning phenology in North Carolina from …

A Comparison Of Survival, Growth, And Stress Resilience In Three Different Lineages Of The Pacific Oyster (Crassostrea Gigas) Farmed On The California Central Coast, Victoria F. Hanshaw

Master's Theses

Aquaculture of Pacific oysters on the US West Coast is routinely impacted by seasonal unexplained mortality events. To better understand these large-scale mortality events in oyster aquaculture, shellfish growers and scientists in California have partnered together to conduct comparative, multi-estuary farm trials of discrete Pacific oyster (Crassostrea gigas) lineages. In this thesis we investigate how the more recently imported Midori lineage performs compared to the historically used Miyagi lineage, as well as a Hybrid (Midori x Miyagi) lineage. As part of a 7-month long field study from April-November of 2024 in Morro Bay and Tomales Bay, California, we evaluated …

Exploring Immune Priming In The Species Exaiptasia Diaphana, Torrence Campos

Biology Theses

Vibrio coralliilyticus is a pathogen that infects various coral species across several reef ecosystems and causes mortality within a span of a few days. With increasing temperatures, the pathogen becomes more virulent towards coral. Probiotics such as MCH1-7 have previously been used to treat infected corals before and after exposure to V. coralliilyticus. In this study, we will be using a species of sea anemone Exaiptasia diaphana in place of coral to evaluate the effects of two V. coralliilyticus strains ATCC BAA-450 and OFT6-21. It was determined that BAA-450 was more virulent. It led to immediate stress and higher mortality. …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

Evaluating The Commercial Aquaculture Potential Of The Native Pacific Littleneck Clam (Leukoma Staminea) As A Climate Resilient Alternative To The Non-Native Manila Littleneck Clam (Ruditapes Philippinarum)., Skylar M. Wuelfing

Master's Theses

The California shellfish industry’s near-exclusive reliance on the non-native Manila littleneck clam (Ruditapes philippinarum) creates an economic vulnerability to climate-driven disturbances, which can cause mortality events that eradicate up to 80% of stocks. This singular reliance on an introduced species highlights a need for the evaluation of native alternatives like the Pacific littleneck clam (Leukoma staminea). Our goal was to assess the feasibility of using the native Pacific littleneck in commercial aquaculture by comparing their performance to the non-native Manila littlenecks across the following conditions: 1) a five-month field outplant trial at high and low intertidal …

Kev's Dinghy Boat Workshops, Ruiyang Xiao

Masters Theses

In a culture where convenience replaces process, this project argues that making — even when inefficient, imperfect, or unnecessary — enables forms of engagement that buying cannot.

Technologies and Services nowadays are able to fulfill human’s desire to travel and explore at ease. However, this convenience proposes a mode of engagement based only in deeper knowledge of context and thus our experience with the world around us is hence diminished. Our engagement with the world becomes heavily mediated, regulated and controlled.

This project investigates how hands-on engagement with water can reintroduce + restore our sense of joy, curiosity, consequence, and …

Environmental Dna (Edna) Assessment Of Fish And Decapod Diversity And Their Association With Cetacean Distribution In Matang Coastal Waters, Perak, Lim Chuan Hui

Student Works (2020-2029)

The estuarine and coastal regions of Matang, Perak, Peninsular Malaysia, are vital fishing grounds and recognised biodiversity hotspots, but are increasingly exposed to human activities. Understanding the biodiversity of marine fish and decapods is crucial for effective conservation efforts. Conventional biodiversity monitoring methods face several challenges, including invasiveness, inconsistencies in sampling techniques, reduced taxonomic accuracy, time-consuming processes, high costs, and often only providing approximate estimates. In this study, we evaluated the use of environmental DNA (eDNA) metabarcoding to assess marine fish and decapod diversity in Matang waters and to explore possible associations between fish assemblages and local cetacean occurrence. Water …

A Sturdy Future: Mangrove Restoration Against Climate Extremes, Gabriella Marie Siasoco

Student Theses 2015-Present

This paper addresses the impacts of climate change on natural disasters and examines how rehabilitation of mangrove forests in Mesoamerica and the Caribbean can mitigate those effects. Rising ocean and atmospheric temperatures contribute to higher sea levels and more severe hurricanes and tropical storms, characterized by increased frequency, duration, and intensity in peak winds, storm surges, and rainfall. Mangrove ecosystems act as vital buffers against coastal disturbances such as tsunamis and extreme storms, while contributing to climate change mitigation through carbon sequestration. Additionally, they improve water quality by filtering nutrients, preventing eutrophication. Despite their ecological and economic value, mangroves in …

Photo Identification On Interactions Between Tursiops Trucatus And Humans To Promote The Importance Of Sustainability, Julia Bronneberg

Undergraduate University Honors Capstones

The Mediterranean Sea is one of the most biodiverse regions, and especially around the Maltese islands, a popular tourist destination where people come to enjoy the beautiful weather and blue waters. Because bottlenose dolphins (Tursiops truncatus) are the most common species people see in coastal areas, they are the primary focus of this research. We care about these bottlenose dolphins because they cannot protect themselves if we are the ones accidentally causing them harm. This study starts from the belief that if we cannot protect the ocean and marine life, then we cannot protect ourselves. We use many resources that …

Brachial Macroparasite Loads In Estuarine Young-Of-Year Striped Mullet (Mugil Cephalus), Triston Rice

Honors Theses

Climate change is a growing threat to marine habitats globally. One ecological impact that warming water temperatures poses is the increased metabolic rate of many parasite species. Their promoted reproductive and feeding rates could pose a threat to the stability of many host populations. Parasites of the gills, or brachial parasites, are especially concerning to fish populations globally. As parasitism is not limited to a specific taxon and comprises a large diversity of ecomorphs and behaviors, geographically distinct areas may be differentially affected by the changing prevalence of parasites. This study aimed to survey current brachial parasite abundance and prevalence …

Exploring Microbiome Communities Of Two Belize Coral Species Five Years After Reciprocal Transplant, Lily E. Kratz

Biology Honors Papers

Coral holobionts, which include the coral animal host, dinoflagellate algae, bacteria, etc., support coral reef biodiversity by providing habitat to many marine species. In the face of global change, identifying and understanding the microbial diversity of corals is extremely important because their survival indicates overall ocean health. Coral-associated bacterial and algal communities contribute to the health and survival of a coral species through creating resistance to stressors and supplying essential nutrients. As coral reef environments continue to change, microbial communities must respond to ensure the survival of reef-building corals. To investigate if coral microbiomes possess the ability to acclimatize to …

Transcriptomic Responses Of Teleost Fishes To Thermal And Environmental Stress: A Synthesis Of Rna-Seq Studies, Aleen Ammar

Theses, Dissertations and Culminating Projects

Climate change is driving rapid shifts in aquatic ecosystems, increasing the frequency and intensity of environmental stressors that affect survival, species distributions, and productivity. Alongside increases in temperature, stressors, such as hypoxia and acidification, are also intensifying with climate change. Teleost fishes exhibit substantial variation in tolerance to such environmental stressors. These range from specialists with narrow limits to generalists capable of persisting across fluctuating conditions, complicating predictions of vulnerability under ongoing environmental change. Transcriptomic approaches, particularly RNA sequencing (RNA-seq), provide a powerful approach for linking environmental stressors to physiological responses by quantifying genome-wide changes in gene expression. To assess …

Phenological Shifts In Reproductive Timing Of Bay Scallops (Argopecten Irradians) In New Jersey Following Subspecies Replacement, Ross John Choate Jr.

Theses, Dissertations and Culminating Projects

Bay scallops (Argopecten irradians) are commercially, ecologically, and recreationally important bivalves that have undergone major shifts in New Jersey over the past 25 years, including the extirpation of the southern subspecies from New Jersey in 2001 and its replacement by the northern subspecies from Long Island by 2004. This transition altered reproductive timing, reflected in changes to the Gonadal–Somatic Index (GSI) as well as the timing of visual gonadal conditions exhibited during specific months. Early post-reestablishment data showed peak GSI in June and July, consistent with Long Island populations, but recent observations indicate a shift toward August and September peaks, …

Assessing Decadal Changes In Eelgrass Communities From Barnegat Bay, Nj, Janelle Marie Delcastillo

Theses, Dissertations and Culminating Projects

Zostera marina (eelgrass) is a widely distributed marine angiosperm across northern hemisphere coastlines, yet many regions have experienced substantial declines due to disease, coastal development, and other anthropogenic stressors. Barnegat Bay is the only estuary in New Jersey that still supports extensive eelgrass beds, although it has undergone notable losses over the past five decades. To evaluate decadal-scale ecological change, we collected sediment cores in 2025 from a site with historical data spanning 2001–2010. Overall faunal densities remained relatively consistent, but several taxa exhibited clear shifts in abundance. Amphipods in the Phoxocephalidae and the isopod Erichsonella increased, whereas the cold-affinity …

Historic Patterns Of Growth And Destruction In Nj Seagrass Meadows, Masen Eck

Theses, Dissertations and Culminating Projects

Seagrass meadows are one of the many habitats worldwide under threat from human disturbance and worsening climate conditions. This habitat provides many critical ecosystem services to coastal environments, which is why conserving and restoring seagrass meadows is critical. This study investigates the long-term success and failures from several eelgrass restoration sites in Barnegat Bay, New Jersey. Aerial imagery from multiple years were digitized in ArcGIS to assess restoration trajectories over time. Three of the sites were assessed over a period of twelve years (2012-2023), and one site was assessed twice (2021 and 2023). Results from these time series analyses showed …

The Effects Of Impervious Land Cover And Red Tide (Karenia Brevis) On The Florida Manatee (Trichechus Manatus Latirostris) In The Gulf Coast Of Florida, Anna Compton

Honors College Theses

Red tide, caused by the dinoflagellate Karenia brevis, is an algal bloom event that occurs annually in the West Florida Continental Shelf. The algae releases brevetoxin, a toxin that can be fatal to wildlife in high concentrations. These algal bloom events are thought to be exacerbated by warming ocean temperatures and increased nutrient runoff from urbanization. Red tide is responsible for the mass mortality of various marine organisms like the Florida manatee (Trichechus manatus latirostris). This study analyzes the changes in nutrient runoff and sea surface temperatures, and how these factors affected red tide cell concentrations and Florida manatee mortalities …

Evaluating Fungal Endophytes Inoculation As A Mechanism For Salt Tolerance In Juncus Roemarianus, Rani Badve

Honors Theses

Salinity stress is increasing in coastal and estuarine ecosystems due to increasing temperatures and the reduction of freshwater inputs via precipitation pattern changes. Elevated salinity can negatively affect plant survival, threatening the stability of coastal wetlands and the ecosystem services they provide. Juncus roemerianus is a common and dominant marsh plant in the Northern Gulf Coast that lives in varying salinities. Growing evidence suggests that root-associated fungal endophytes may contribute to enhanced stress tolerance; however, the response of fungal communities to salinity remains poorly understood.

This study evaluated how salinity influences the abundance and diversity of culturable root-associated fungal communities …

Acute Effects Of The Psychoactive Pollutant Fluoxetine On The Antipredator Behavior Of The Gulf Killifish (Fundulus Grandis), Semyra Reus

Honors Theses

Pharmaceutical contaminants are increasingly prevalent in aquatic environments, yet their sublethal effects on ecologically relevant behaviors remain poorly understood, particularly in estuarine systems. Selective serotonin reuptake inhibitors (SSRIs), such as fluoxetine, are of particular concern due to the conserved role of serotonin in regulating behavior across vertebrates. Here, we investigated how acute exposure to environmentally relevant concentrations of fluoxetine influences anti-predator behavior in Gulf killifish (Fundulus grandis), a key estuarine fish commonly found in saltmarsh habitats. Killifish were exposed to control (0 ng/L), low (17.8 ng/L), and high (596 ng/L) fluoxetine concentrations and subsequently tested in the presence …

Recruitment Of Chrysaora Chesapeakei On Floating Docks Versus Bulkhead Surfaces: Which Axis Is Foulset?, Alyssa Lamberto

Theses, Dissertations and Culminating Projects

Blooms of Chrysaora chesapeakei (bay nettles) have increased sharply in Barnegat Bay, New Jersey, reducing both ecological integrity and economic value. Because population expansion is driven primarily by the benthic polyp stage, where individuals attach to hard substrates and reproduce asexually, effective management must target the surfaces where polyps settle and clone themselves. The rapid growth of artificial infrastructure, particularly vinyl docks and bulkheads, has expanded available habitat for polyp recruitment. Scrubbing these structures has been shown to reduce ephyrae production, but it remains unclear whether both docks and bulkheads warrant equal management attention. This study compared recruitment on horizontal …

Differential Salinity Tolerance And Compositional Shift In Zooplankton Communities From Coastal And Inland Wetlands, Marisa Contreras

Theses, Dissertations and Culminating Projects

Anthropogenic salinization from road salt application has degraded freshwater ecosystems across the United States, yet the tolerance of freshwater communities to elevated salinity may depend on their historical exposure. Coastal systems experience natural salt intrusion through tides and storm events, potentially fostering greater salinity tolerance amongst resident organisms, while inland systems lack this exposure history. To investigate, I studied the abiotic and biotic responses of zooplankton communities from four wetlands across a salinity gradient to assess tolerance to experimental salt exposure. Two inland freshwater wetlands are subject to anthropogenic salinization from road salt runoff, while two coastal wetlands experience natural …

Ecological Responses To Living Shoreline Restoration, Aaron S. Bland

Graduate Theses and Dissertations (2019 - present)

Coastal built communities and natural coastal ecosystems face similar and interrelated hazards: shoreline sediment erosion, shoreline retreat, and worsening storms, each of which is exacerbated by relative sea level rise. Living shorelines are coastal defense projects that incorporate natural habitats to provide more sustainable shoreline defense and improve the coastal ecosystem. Living shorelines have been widely adopted, but their performance has been highly variable, and the mechanisms of project success and failure are unclear. The overarching goal of this dissertation was to better understand the ecosystem responses to coastal restoration, focusing on the primary habitats of coastal salt marsh and …

Feeding Ecology In Coastal Systems, Randi L. Cannon

Graduate Theses and Dissertations (2019 - present)

Oysters (Crassostrea virginica) are critical foundation species in estuaries, providing numerous ecological and economic benefits. However, oyster populations have diminished worldwide. Effective oyster restoration and aquaculture require a mechanistic understanding of the physiological and environmental factors that govern oyster feeding, growth, and resilience under changing coastal conditions. We investigated how oyster ploidy and environmental conditions influenced oyster feeding and investigated how changes in abiotic conditions affected behavioral performance of oyster drills (Stramonita spp.), a key oyster predator. To better understand feeding responses and behaviors of both predator and prey we 1) used in-situ filter feeding assays to determine if feeding …

Assessment Of Morphological Differences And Genetic Variation In Head Shape Of Florida Pompano Trachinotus Carolinus, Neriah Nicholas

Electronic Theses and Dissertations

Genomics research can inform selective breeding programs to improve broodstock and seedstock quality for the U.S. warmwater marine finfish aquaculture industry. Florida pompano Trachinotus carolinus serves as a model species for the industry due to its commercial value and ability to spawn in captivity. This study examined a growth abnormality observed in commercially produced juveniles in partnership with Aquaco Farms LLC. Twenty fish were collected, culled, and euthanized by Aquaco staff, then classified into two head types: “normal” and “concaved”. Eleven morphological measurements were recorded before and after freezing to assess head variation and storage effects. DNA from pectoral fin …

Histological Analysis Of Six Atlantic Scleractinian Coral Species Exposed To Three Hydrocarbons, 1-Methylnapthalene, Phenanthrene, And Toluene, Jalyn R. Lee

All HCAS Student Capstones, Theses, and Dissertations

Coral reefs are biologically diverse marine ecosystems that provide numerous goods and ecosystem services. These sessile organisms are vulnerable to anthropogenic impacts, habitat degradation, climate change, and pollution, particularly Petroleum hydrocarbon contamination. Previous research has characterized coral species' sensitivity to hydrocarbons, using a continuous passive dosing system, but the specific histological impacts of petroleum hydrocarbons remain underexplored. This study investigates the histological effects of three petroleum hydrocarbons, 1-methylnaphthalene, phenanthrene, and toluene, on six Atlantic scleractinian coral species: Acropora cervicornis, Porites astreoides, Porites divaricata, Solenastrea bournoni, Stephanocoenia intersepta, and Siderastrea siderea. Coral fragments were exposed to species-specific hydrocarbon concentrations, and …

Elasmobranchii Oral Microbiome Diversity Within Southeast Florida: Implications Of Shark Zoonotic And Antibiotic Resistant Pathogens Associated With Human Interactions, Amanda Finnefrock

All HCAS Student Capstones, Theses, and Dissertations

Sharks are incredibly common in the Atlantic and Gulf waters surrounding Florida. Despite the prevalent nature of these animals, little research exists on the composition of their microbial communities (or “microbiomes”). Here we aim to determine the microbial makeup of the oral environment of sharks so that we can determine if there are any bacteria of clinical significance to humans, such as being antibiotic-resistant or having elevated capability for pathogenicity. A total of 41 samples were collected from the mouths and teeth of bull, Caribbean reef, great hammerhead, lemon, nurse, and sandbar sharks caught in Southeast Florida using sterile swabs …

Evaluating The Geographic Patterns In Isotopic Composition For Nesting Hawksbill Sea Turtles In The Wider Caribbean By Coupling Satellite Telemetry And Stable Isotopes, Anna Kreiger

Electronic Theses and Dissertations

Combining satellite telemetry and stable isotope analysis offers a framework for inferring sea turtle foraging habitats when spatial isotopic gradients exist. We evaluated this combined approach using carbon (δ13C) and nitrogen (δ1⁵N) isotope values from critically endangered hawksbill turtles (Eretmochelys imbricata) nesting at Buck Island Reef National Monument, U.S. Virgin Islands (N=31), and Long Island (Jumby Bay), Antigua (N = 31). Nesting females were satellite-tracked to identify foraging areas and sampled for skin tissue, and Empirical Bayesian Kriging was used to generate basin-scale δ13C and δ1⁵N isoscapes. Tracked turtles foraged widely across the Caribbean Basin, including the Greater …

The Effects Of Climate Change On Competition And Recovery From Disturbance In An Iconic Marine Community, Lauren Tibbits

Senior Theses

This paper explores how the recovery of populations of Semibalanus balanoides is affected by climate variation. In intertidal marine ecosystems, larval recruitment is important in shaping all ecological processes. S. balanoides is a cold-water barnacle species that is competitively dominant over Chthamalus montagui and C. stellatus, two warm-water species. This competitive interaction is well studied, though it is not understood how that competition influences the recovery of S. balanoides after a disturbance nor how this process varies over a temperature gradient. 19 sites were studied across the United Kingdom, spanning from northern Scotland to southwestern England. At each site, a …

Abundance Of Microplastics In The Water And Stream Fish Of Big Walnut Creek, David J. Hartman

Undergraduate Honors Thesis Projects

Microplastics are a major threat to both ecosystem and human health. In this study, I investigated the abundance of microplastics at five sites along Big Walnut Creek, Ohio including sites upstream, downstream, and within urban development. Samples were taken from the stream surface water and fish at each site. Microplastics were detected in the surface water and fish at all five sites with a total of 383 microplastic particles found in the 157 fish collected for this study. The mean concentration for all sites was 80.8 particles/m3 in the surface water and 2.4 particles per fish. Microplastics were almost entirely …