Other Oceanography and Atmospheric Sciences and Meteorology Commons^™

Mapping Seafloor Habitats And Characterizing Demersal Reef Fish Communities On The West Florida Shelf Across Multiple Spatial Scales Using Multibeam Sonar And Underwater Video, Alexander R. Ilich

USF Tampa Graduate Theses and Dissertations

In this dissertation, I examine the role of spatial scale in deriving seafloor terrain attributes, modeling benthic habitat, and analyzing ecological patterns of the demersal reef fish communities on the West Florida Shelf (WFS), with implications for improving predictive habitat mapping and understanding fish-environment relationships. Spatial scale plays a central role in benthic habitat mapping and ecological inference, influencing how terrain attributes are derived, how habitats are modeled, and how ecological responses are manifested. This work integrates multiscale terrain analysis, acoustic remote sensing, and community ecology to evaluate how spatial scale influences both physical habitat representation and ecological analysis.

Chapter …

Trophic Structure Of Reef-Fish Assemblages In The Eastern Gulf Of Mexico Varies By Depth And Reef Type, Jessica L. Van Vaerenbergh

USF Tampa Graduate Theses and Dissertations

Globally, marine ecosystems are increasingly threatened by anthropogenic stressors, leading to reef degradation, changes in reef-fish assemblages, and altered trophic structure. In this study, I investigated reef-fish underwater visual survey data collected over a decade (2013-2023) from paired natural and artificial reefs in the eastern Gulf of Mexico. I applied the novel Normalized Reef Status Index (NRSI) to evaluate how biomass was distributed across the three trophic categories (i.e., Lower Trophic Position (LTP; 2.0-2.9), Central Trophic Position (CTP; 3.0-3.9), and Upper Trophic Position (UTP; ≥4.0). This index is a metric to assess the ecological status of reef systems by investigating …

Speleoco: An Open, Low-Cost Arduino Co₂ Datalogger For Cave Microclimate Monitoring, Christos Pennos, Dimitrios Christaras

International Journal of Speleology

Carbon dioxide (CO₂) dynamics in caves are critical for karst processes, speleothem growth and dissolution, microclimate regulation, and caver safety. In cave atmospheres, CO₂ commonly derives from soil respiration, epikarst degassing, microbial activity, and, in tectonically active regions, deep-seated fault-related emissions. Fault-related CO₂ degassing may also track tectonic activity. However, continuous monitoring remains limited due to the cost and inflexibility of commercial instruments. Here we present an open-source, low-cost Arduino-based CO₂ datalogger designed for cave applications. The logger integrates a COZIR NDIR CO₂ sensor, a DS1337 real-time clock, microSD storage, and power-gating for extended deployment in humid environments. Firmware and …

Amplicon Sequencing Reveals Shifts In Microbial Community Composition In Response To Nutrient-Dense Piney Point Emergency Discharges, Christa A. Baranowski

USF Tampa Graduate Theses and Dissertations

Due to a leak in the lining of a phosphogypsum pond at the former Piney Point phosphate-processing facility in Tampa Bay (Florida, U.S.A.), experienced a large influx of nutrient-dense waters in the early summer of 2021. As an emergency response effort, water samples were collected by researchers at the University of South Florida, College of Marine Science (USF CMS), covering the lower and middle regions of Tampa Bay (TB), over the span of three months (April – June). Illumina amplicon sequencing was performed on DNA from water samples, targeting bacterial and eukaryotic ribosomal rRNA genes, and processed into Amplicon Sequence …

Spatio-Temporal Characterization Of Trace Metals Across The West Florida Shelf And During The Decline Of The North Atlantic Spring Bloom, Delfina Paola Navarro-Estrada

USF Tampa Graduate Theses and Dissertations

Phytoplankton in the marine environment require the trace metals manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), and cadmium (Cd) to catalyze cellular processes driving photosynthesis, including macronutrient (nitrogen, phosphorus, and carbon) acquisition, light harvesting, and protection from oxidative stress. The high biological demand for these elements, coupled with their low concentrations in the ocean, can limit primary production and shape community composition in marine ecosystems, highlighting the need to understand the drivers behind trace metal distributions and their interplay with phytoplankton growth across biogeochemical regimes. This dissertation characterizes the spatial and temporal distributions of dissolved …

Mapping Seagrass Extent Using Sentinel-2 Satellite Imagery: A Case Study In Salt River Bay, United States Virgin Islands, Chelsea O. Bryant

USF Tampa Graduate Theses and Dissertations

Seagrass beds provide important services in many coastal ecosystems. They provide habitat and food for a wide range of marine species, stabilize sediments, and prevent coastal erosion. These services support local fisheries and tourism-driven economies. Yet, seagrass ecosystems are threatened by changes in water quality, sedimentation, and other stressors. This study investigated the interannual variability in seagrass extent in Salt River Bay, United States Virgin Islands (USVI), from 2018 to 2024. The goals were to better understand temporal dynamics in seagrass extent and evaluate the influence of turbidity as a driver of seagrass health and distribution. The overarching research question …

What Controls Ice Shelf Isotopic Variability? Local And Global Processes Preserved Within Ice Cores Across The Larsen C Ice Shelf, Antarctica, Orion Laurene Schomber

USF Tampa Graduate Theses and Dissertations

The Antarctic Peninsula (AP) is one of the foremost indicators of anthropogenic global warming as it interacts with both atmospheric and oceanic processes. Although ice shelves across the AP have undergone increased rates of disintegration over the last 30 years, limited in-situ measurements have been investigated. Assessment of three short (~30 m) firn cores (J108, J208, and J409) across the Larsen C ice shelf (LCIS) provide insight into local, regional, and global processes. Average core densities and isotopic variability (δ¹⁸O and δ²H) fall within expected ranges for all cores, indicating signal preservation through firn. However, isotopic maxima in J108 and …

Identifying B-Vitamin Requirements And Phycosphere Interactions For The Hab-Forming Dinoflagellate, Pyrodinium Bahamense Var. Bahamense, Lydia A. Ruggles

USF Tampa Graduate Theses and Dissertations

Harmful Algal Blooms (HAB) negatively affect economies, ecosystems, and public health through mass proliferation and toxin production. The HAB species, Pyrodinium bahamense var. bahamense, is a saxitoxin-producing dinoflagellate found in tropical and subtropical estuarine waters globally. In two Florida estuaries, Old Tampa Bay and the Indian River Lagoon, P. bahamense is a recurrent HAB species, and the exact timing and intensity of bloom peaks in these estuaries vary interannually. Factors that are suspected to contribute to blooms include temperature, residence times, nutrients, and salinity. However, many HAB dinoflagellates require vitamin B12 for growth and bloom development. Thus, B12 may influence …

Concentration And Composition Of Organic Contaminants In Blackfin Tuna, Yellowfin Tuna, And The Common Clubhook Squid In The Western Gulf Of Mexico, Lisa Rose-Mann

USF Tampa Graduate Theses and Dissertations

Cephalopods are an important component of pelagic food webs. They play ecological roles not only as predators but also as prey. However, their role as prey in the trophic transfer of organic contaminants to apex predators such as tunas in the Gulf of Mexico (GoM) is not well known. To investigate the importance of cephalopods in tuna diets, stomach samples were collected in February 2020 from tunas caught by rod and reel aboard the F/V Gulf Eagle near two large offshore floating oil/gas platforms in the northwestern GoM. Cephalopod samples were obtained from gut content analysis of 41 tunas caught …

Isotopic Fingerprints Of The Coastal Margins: Tracing Dissolved Iron Sources From Land To Sea, Hannah R. Hunt

USF Tampa Graduate Theses and Dissertations

Dissolved iron (dFe) is an essential micronutrient for sustaining life in the surface ocean. Nearly four decades of research dedicated to understanding sources, cycling and biogeochemical modifications of Fe sources in the global oceans has generated a significant body of research supporting the idea that the concentration of Fe in the surface ocean exerts significant controls on primary production and carbon uptake in the surface ocean. Creation of the GEOTRACES program greatly increased the spatial and temporal resolution of high-quality trace element and trace element isotope data revealing new insights into the global Fe cycle, especially through the use of …

Characterizing West Florida Shelf Reef Fish Communities Using A Scientific Echosounder, Edmund A. Hughes

USF Tampa Graduate Theses and Dissertations

The advancement and application of non-invasive fisheries survey technologies, such as the scientific echosounder, have significantly enhanced our understanding of fish populations and their habitats, more recently in regions where traditional sampling methods are limited, such as complex reef habitats. This research, conducted as part of the Continental Shelf Characterization, Assessment, and Mapping Project (C-SCAMP) on the West Florida Shelf, leverages acoustic and visual technologies to investigate the distribution of fish densities, fish target strength and length relationships, and the relationship between seafloor topography and fish biomass distribution.

The first study compared reef fish densities estimated from near-concurrent acoustic (Simrad …

Artificial Reefs As Management Tools, Tiff Raetzel

USF Tampa Graduate Theses and Dissertations

Artificial reefs are attractive tools for fisheries management and reef conservation, as they can host large fish biomasses, including fisheries-important species, and they may supplement natural recruitment. Prior studies have established that artificial and natural reefs differ in habitat complexity and host both taxonomically and functionally distinct assemblages. These differences may impact how the reef types respond to environmental disturbance because ecosystem stability is dependent upon habitat structure, species composition, and trophic interactions. A question of management importance is whether artificial reefs host a less- or more-sensitive suite of species than natural reefs, and whether the assemblage is conducive to …

Seasonal And Interannual Abundance, Distribution, And Carbon Production Estimates In The Northeastern Gulf Of Mexico Using The Sipper Camera Imaging System, Carlyn Scott

USF Tampa Graduate Theses and Dissertations

Larvaceans are filter-feeding gelatinous zooplankton whose contributions to marine biogeochemical processes are poorly constrained. By frequently shedding their particle-rich houses and producing dense fecal pellets, larvaceans contribute large amounts of particulate organic matter to deeper waters and to the sea floor. Despite their importance, little is known about larvacean abundance, distribution, and carbon production in the highly productive northeastern Gulf of Mexico (NEGOM). To address this gap in knowledge, we collected images of larvaceans at discrete depths in the upper 300 m of the water column between August 2010 –2014 using the Shadowed Image Particle Profiling and Evaluation Recorder (SIPPER) …

Spatiotemporal Dynamics Of Coastal Nekton Metacommunities In The Western Atlantic, Jonathan A. Peake

USF Tampa Graduate Theses and Dissertations

The processes of diversification, selection, dispersal, and stochastic drift can combine in many ways to assemble ecological communities. A key focus in ecology is to describe and quantify the relative influences of these processes for different systems and explain the mechanisms by which these processes produce patterns of community structure. To accomplish this goal, ecologists have developed several frameworks that seek to integrate processes that occur locally andregionally. The metacommunity concept treats local communities as pieces of a broader landscape that are connected through dispersal of their constituent organisms. Empirical studies have generally lagged behind the development of metacommunity theory. …

Satellite-Based Mapping Of Seagrass Habitats And Coastal Wetlands In The Us Gulf Of Mexico And Florida: A Remote Sensing Approach For Environmental Conservation And Management, Luis Lizcano-Sandoval

USF Tampa Graduate Theses and Dissertations

Coastal wetlands and seagrass meadows provide multiple services to nature and human society, but their spatial and temporal changes are often not well characterized. They are habitats that are threatened by natural and human causes such as changes in water quality, urban development, pollution, and climate change, among others. Coastal ecosystems rely on water quality and sea level variability for survival, and changes in those variables and their potential effects are of concern to many coastal communities. Satellite remote sensing is a powerful tool that has been used for mapping ecosystem distribution on land and in the ocean. Satellite sensors …

Characterizing The Temporal And Nearshore To Offshore Spatial Scale Of Phytoplankton Assemblages Within The Florida Keys National Marine Sanctuary, Sebastian P. Di Geronimo

USF Tampa Graduate Theses and Dissertations

This study investigates the spatial and temporal dynamics of phytoplankton communities within the Florida Keys National Marine Sanctuary (FKNMS) from 2016 to 2021. Phytoplankton biomass and community composition were analyzed across four seasons and from both Nearshore (within 2 km of shore) and Offshore (8 to 10 km from shore) locations along the Florida Keys from Miami to the Western Sambo Ecological Reserve. High-performance liquid chromatography (HPLC) quantified chlorophyll-a (tchla) as a proxy for bulk biomass, and other pigments. CHEMTAX, a chemotaxonomic identification method, was employed to estimate phytoplankton community composition. Our results revealed significant seasonal variability in bulk biomass, …

Zooplankton Abundance, Composition, And Diversity And Associated Environmental Factors Across The Gulf Of Mexico And Along The Northwestern Coast Of Cuba, Shaniqua J. Gladney

USF Tampa Graduate Theses and Dissertations

My research focused on characterizing the zooplankton community of two regions in the Gulf of Mexico (GOM) along two transects, one across the middle of the GOM from Tuxpan, Mexico, to St. Petersburg, FL, and one along the northwestern coast of Cuba. Zooplankton bongo samples and associated environmental and physical processes were examined. These data were collected during two Center for Integrated Modeling and Analysis of Gulf Ecosystems (C-IMAGE) expeditions aboard the R/V Weatherbird II, during September 2015 (GOM) and May 2017 (Cuba). A Zooscan imaging system was used to identify and enumerate zooplankton taxa. Then zooplankton abundance, composition, and …

Quantification And Diversity Of A Ubiquitous Ssdna Phage Group (Gokushovirinae) In The Red Sea Through The Polony Technique, Natalie A. Sawaya

USF Tampa Graduate Theses and Dissertations

With average concentrations of 107 virus-like particles per milliliter of seawater, viruses comprise the second largest biomass in the ocean, where they are a driving force of microbial evolution and constitute important roles in Earth’s biogeochemical cycles. Bacteriophage (phage), viruses that infect bacteria, are of particular importance in the marine ecosystem as they impact the efficiency of the microbial loop, which recycles carbon in surface waters, counteracting vertical export through the biological pump. Although double-stranded DNA phage have been researched extensively, single-stranded DNA (ssDNA) phage remain understudied, mostly due to methodological limitations.

The incorporation of rolling circle amplification (RCA) into …

Subtropical Estuarine Ecosystems Display Both Long-Term Stability And Change, Garrett L. Miller

USF Tampa Graduate Theses and Dissertations

Subtropical estuaries often support abundant and diverse faunal assemblages, but it is unclear how these productive ecosystems are responding to climate change. In the eastern Gulf of Mexico, estuarine faunal assemblages have been sampled for decades as part of a fisheries-independent long-term monitoring program. I assessed trends in submerged aquatic vegetation, water temperature, and the abundance, richness, and structure of faunal assemblages over more than two decades in four estuarine systems using this dataset. I used both univariate and multivariate analyses to quantify and describe the dynamics of these habitat and faunal variables. Further, I separated my analyses for summer …

Predicting Ph At In-Situ Temperature For Aquatic Environments, Sarah E. Bartoloni

USF Tampa Graduate Theses and Dissertations

pH is typically measured at a constant temperature and, as needed, converted to in-situ temperature using a system of thermodynamic equations. Using this equilibrium approach, adjustment of pH to in situ conditions requires two measured CO2 system parameters (pH, total alkalinity, dissolved inorganic carbon, or CO2 fugacity). Currently, when pH is the only measured CO2 system parameter, linear models are used to adjust the pH to in-situ temperature. Although many studies have attempted to optimize CO2 equilibrium constants (K1 and K2) for the CO2 system over a range of conditions, very little prior work has experimentally examined which CO2 system …

Exploring The Dynamics Of September Fish Spawning On The West Florida Shelf Through The Dna Barcoding Of Fish Eggs, Keith G. Keel

USF Tampa Graduate Theses and Dissertations

Identifying spawning areas for economically and ecologically important fishes is critical for fisheries conservation and ecosystem-based management. Additionally, monitoring the spawning dynamics of fishes is increasingly important as temperatures and oceanic conditions change. I used genetic barcoding to identify fish eggs collected across the West Florida Shelf (WFS) during September of 2013, 2014, and 2019. Fish eggs were collected on National Oceanic and Atmospheric Administration (NOAA) Southeast Area Monitoring and Assessment Program (SEAMAP) ichthyoplankton cruises using a Continuous Underway Fish Egg Sampler (CUFES). Analysis of 4,400 fish eggs from the three years resulted in the identification of 83 unique species …

Abundance, Distribution, And Diversity Of The Paralarval Cephalopod Community In The Northern Gulf Of Mexico, Shannon Leah Riley

USF Tampa Graduate Theses and Dissertations

The abundance, distribution, and diversity of cephalopod paralarvae from the upper water column (0-130 meters) in the northern Gulf of Mexico (GOM) was studied using samples collected during six ichthyoplankton surveys between 2009 and 2012. A total of 2240 cephalopod paralarvae belonging to 21 families were examined. Octopodidae, Enoploteuthidae, and Ommastrephidae were the most abundant taxa collected in the time series. Five taxa had significantly different abundances between some sampling periods, while no significant differences in abundance occurred between any GOM regions (northwest GOM shelf, north-central GOM shelf, West Florida Shelf, GOM slope, and GOM basin). The majority of taxa …

Iron Isotope Transformations In Saanich Inlet, Claire Onak

USF Tampa Graduate Theses and Dissertations

Iron (Fe) is required for many biogeochemical processes, with Fe bioavailability and chemistry being controlled by redox reactions that transform Fe between oxidation states and dissolved and particulate phases. In oxic seawater, Fe is present in the Fe(III) oxidation state, mainly as Fe oxyhydroxides. Under anoxic marine conditions, such as margin sediments under oxygen minimum zones or restricted basins with anoxic bottom water, Fe(III) is reduced to Fe(II), which is highly soluble and can be present at high concentrations ([Fe]). Fe isotope ratios (δ56Fe relative to IRMM-14) can be used to characterize Fe redox transformations, constrain Fe sources of Fe …

Dissolved Nickel Speciation At The Bermuda Atlantic Time-Series Study (Bats) Site, Caitlyn E. Parente

USF Tampa Graduate Theses and Dissertations

Here I present the first depth profiles of dissolved nickel (DNi) speciation over an annual cycle at the Bermuda Atlantic Time-series Study (BATS) site in the North Atlantic. Seawater samples were collected in March, May, August, and November 2019 and analyzed for labile DNi using competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-AdCSV). Labile DNi was measured by CLE-AdCSV as the fraction of DNi that exchanges with an added competitive ligand in an overnight equilibration. Results revealed two distinct fractions of DNi present throughout the water column: a labile fraction, and a strongly organically complexed (i.e., non-labile) fraction. More than 50% …

Trace Metal Cycling During Phytoplankton Growth In The Southern Ocean, North Pacific, And Tampa Bay, Shannon Michelle Burns

USF Tampa Graduate Theses and Dissertations

The trace metals iron (Fe), manganese (Mn), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), and cadmium (Cd) are essential to primary production in the oceans. They act as micronutrients, used in intracellular enzymes for macronutrient acquisition, light harvesting, and mediation of reactive oxygen species. In some cases, they can also substitute for each other when a primary trace metal micronutrient is depleted. Characterizing the interplay amongst trace metals, macronutrients, and phytoplankton growth is vital for understanding the biogeochemical underpinnings of primary production, and for modelers who develop biological pump frameworks for global carbon cycling.

In Chapter two, I investigated …

Procedures For Assessment Of The Marine Carbon System And Evaluation Of Access And Ocean Acidification Literacy In The Deaf Community, Loraine Martell-Bonet

USF Tampa Graduate Theses and Dissertations

One major goal of this dissertation addresses the need for improved laboratory procedures to measure chemical changes in seawater caused by the uptake of atmospheric CO2, especially in coastal environments. Due to the proximity of anthropogenic stressors in the coastal zone, the biogeochemical complexity of the CO2 system is more dynamic than the open ocean. My principal research objectives were addressed by developing methods for (1) improving the accuracy of pH measurements over a wide range of salinities and (2) investigating the acid-base properties of natural organics in the coastal ocean.

The accuracy of pH electrode calibrations is affected when …

Labile Dissolved Nickel (Ni) Concentrations In The North Pacific, Calyn M. Crawford

USF Tampa Graduate Theses and Dissertations

Nickel (Ni) is an important micronutrient for phytoplankton and bacteria that serves as a required co-factor in several metalloenzymes. Despite these known biological uses, total dissolved Ni concentrations remain elevated in global surface waters, in contrast to the surface depletion commonly observed for macronutrients and other nutrient-type trace elements. A prevailing hypothesis for the muted depletion of dissolved Ni concentrations in surface waters is that dissolved Ni in seawater is not in a bioavailable form. The chemical lability of Ni in seawater provides insight into Ni speciation and bioavailability, but few measurements have been made in the open ocean to …

Time-Series Analysis Of Coral Reef And Reef-Fish Biodiversity In The Florida Keys National Marine Sanctuary, Cara L. Estes

USF Tampa Graduate Theses and Dissertations

The general decline in coral-reef ecosystem health throughout the Caribbean between the 1970’s and late 1990’s seems to have slowed down or stopped, with only slight decreases in coral reef cover observed in the 2000’s through 2019. The earlier decline can be attributed to many different local and regional stressors that have acted together, and include naturally occurring (hurricanes, diseases) and anthropogenic pressures (increased sedimentation, fishing). These ecosystems provide a range of services to people, including food and protection from storms, with an annual benefit of billions of dollars. This has driven a desire to better understand these ecosystems. The …

Stable Isotope Analysis On Yellowfin And Blackfin Tuna Eye Lenses Reveals Life History Patterns In The Gulf Of Mexico, Kylee M. Rullo

USF Tampa Graduate Theses and Dissertations

Spatial geography, ontogenetic movement, and trophic patterns of mobile species are key elements of effective marine resource management. A number of methods are currently available for tracking movements of pelagic migratory species, including the use of conventional and electronic tags. However, tagging campaigns can take years to provide useful data, can be expensive, and only capture a portion of a fish’s lifetime. For this project, I used stable-isotopic ratios of nitrogen (δ15N) and carbon (δ13C) in metabolically inert, chronologically-layered fish-eye lenses to explore lifetime movement and trophic patterns of yellowfin tuna (Thunnus albacares) and blackfin tuna (Thunnus atlanticus) in the …

Meta-Analysis Of United States Seabird Populations Based On Ocean Biodiversity Information System (Obis) Records (1965–2018), Savannah Hartman

USF Tampa Graduate Theses and Dissertations

Understanding the distribution of organisms is an important priority for society as we live through ecosystem transformations that threaten the well-being of all organisms. I have approached the dynamic and complex issue of studying biodiversity by using open-access seabird data collected along the Americas since the 1960s. I explained how these data have changed over time and space, how certain species populations could have shifted over time, and possible correlations between this potential geographic change and select environmental variables.

In Chapter 2 I evaluated the suitability of the open-access data archive Ocean Biodiversity Information System (OBIS) for supporting detailed inquiry …