Other Oceanography and Atmospheric Sciences and Meteorology Commons^™

Species Abundance, Spatial And Vertical Distributionsof Large Heteropods (Pterotracheidae And Carinariidae)In The Northern Gulf Of Mexico, Kristine A. Clark

USF Tampa Graduate Theses and Dissertations

A description of species abundance, richness and distribution, and eye size of heteropod molluscs from the families Pterotracheidae and Carinariidae in the oligotrophic ecosystem of the northern Gulf of Mexico (GOM) is described based on discrete-depth sampling protocols. The collections were comprised from two midwater sampling programs conducted sequentially after the 2010 Deepwater Horizon oil spill (DWHOS): the Offshore Nekton Sampling and Analysis Program (ONSAP, 2011) and the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND, 2015-2018). Study materials from DEEPEND were collected during the initial five cruises of 2015-2017. These programs collected over 3,495 heteropods in two …

Zooplankton Community Structure In The Ne Gulf Of Mexico: Impacts Of Environmental Variability And The Deepwater Horizon Oil Spill, Kate M. Dubickas

USF Tampa Graduate Theses and Dissertations

In the northeastern Gulf of Mexico, relating changes in zooplankton communities to environmental factors is crucial to understanding the marine ecosystem and impacts of perturbations such as oil spills on marine ecosystems. Zooplankton samples were collected each year between 2005–2014 in spring and summer in the vicinity of the oil spill (Deepwater Horizon) that occurred in spring 2010. Zooplankton assemblages and environmental conditions significantly differed seasonally, driven by strong variations in zooplankton at continental shelf stations, and by environmental factors including Mississippi River discharge, wind direction, temperature, and chlorophyll concentrations. Total zooplankton abundances were greatest at shelf stations, intermediate at …

Dna Barcoding Of Fish Eggs In The Gulf Of Mexico, Makenzie Burrows

USF Tampa Graduate Theses and Dissertations

DNA barcoding of fish eggs is a relatively new technique that enables more accurate identification of early life stages of ecologically and economically important fish species. Using DNA barcoding of individual planktonic percomorph eggs, this thesis determines putative spawning locations of neritic and oceanic fish species in the Gulf of Mexico (GoM). Surveys at 40 stations in the Gulf of Mexico showed a clear delineation of spawning sites, with neritic fish eggs generally found on continental shelves, and oceanic fish eggs found at the surface of deeper waters. However, samples collected between Florida and Cuba revealed exceptions to this trend …

Regeneration Of Trace Metals During Phytoplankton Decay: An Experimental Study, Adrienne P. Hollister

USF Tampa Graduate Theses and Dissertations

Trace metals act as important nutrients, and sometimes toxins, to phytoplankton and other marine microorganisms. When phytoplankton decay, the elements in their cells are released back into the water column through regeneration (also referred to as remineralization), one of the processes responsible for governing concentrations of dissolved trace metals and macronutrients in depth profiles. In order to experimentally study regeneration, controlled experimental incubations of mixed phytoplankton assemblages from the Gulf of Mexico (GoM) and monocultures of the diatom Pseudo-nitzschia dolorosa and the dinoflagellate Karenia brevis were placed in the dark and monitored as they decayed with naturally present bacteria. Over …

Dormancy In The Amphistegina Gibbosa Holobiont: Ecological And Evolutionary Implications For The Foraminifera, Benjamin J. Ross

USF Tampa Graduate Theses and Dissertations

Dormancy, a state of severely decreased or suspended metabolism, is a widespread survival strategy in nature. In the Foraminifera, one of the most studied groups of marine organisms, its presence had been suggested by circumstantial evidence, but rarely studied directly until recently. Despite the lack of research, stressor-induced dormancy can significantly alter the way in which foraminiferal ecology is understood, especially in marginal environments. In this dissertation, I reviewed the evidence for dormancy in the foraminiferal literature, concluding that evidence for dormancy is widespread across the Phylum. I then explored the role of dormancy in the survival of the diatom-bearing …

Quantifying The Probability Of Lethal Injury To Florida Manatees Given Characteristics Of Collision Events., B. Lynn Combs

USF Tampa Graduate Theses and Dissertations

Wherever wildlife share space with boaters, collisions are a potential source of mortality. Establishing protection and speed zones are the primary actions taken to mitigate collision risk. However, creation of protection zones may be a point of contention with stakeholders as new zones can have significant socioeconomic impacts. The Florida Manatee is a prime example of a species whose abundance and viability are constrained by this balance between the needs of humans and wildlife on a shared landscape. The goal of this work is to help further understand the risk to manatees by quantifying the probability of lethal collisions. I …

Integrating Towed Underwater Video With Multibeam Acoustics For Mapping Benthic Habitat And Assessing Reef Fish Communities On The West Florida Shelf, Alexander Ross Ilich

USF Tampa Graduate Theses and Dissertations

Using a towed underwater video camera system, benthic habitats were classified along transects in a popular offshore fishing area on the West Florida Shelf (WFS) known as “The Elbow.” Additionally, high resolution multibeam bathymetry and co-registered backscatter data were collected for the entire study area. Using these data, full coverage geologic and biotic habitat maps were developed using both unsupervised and supervised statistical classification methodologies. The unsupervised methodology used was k-means clustering, and the supervised methodology used a random forest algorithm. The two methods produced broadly similar results; however, the supervised methodology outperformed the unsupervised methodology. The results of the …

Using Ecosystem-Based Modeling To Describe An Oil Spill And Assess The Long-Term Effects, Lindsey N. Dornberger

USF Tampa Graduate Theses and Dissertations

The goal of the research conducted in this dissertation was to define and test methods to incorporate oil spill effects into an ecosystem-based assessment model. It was instigated by the Deepwater Horizon oil spill, an unprecedented oil spill in the United States for both depth and volume, with unknown implications for the health of the region. Using an ecosystem-based assessment model like Atlantis, with integrated oil spill dynamics, was the ideal candidate to predict long-term impacts such as decreased abundance or population recovery time. However no previous methodology existed for doing so in any ecosystem-based assessment model. Therefore, first I …

Evaluation Of Trace-Metal And Isotopic Records As Techniques For Tracking Lifetime Movement Patterns In Fishes, Jennifer E. Granneman

USF Tampa Graduate Theses and Dissertations

The focus of this work was on the use of otolith microchemistry and fish eye lens chemical profiles to measure fish movement and provided indirect support for the use of otolith microchemistry to examine exposure to crude oil. Chapter 1 provides an introduction to the applications of otolith microchemistry and eye lens isotopic profiles. In the second chapter, which examined associations between metal exposure and lesion formation in fishes collected after the Deepwater Horizon (DWH) oil spill, I did not observe any change in oil-associated metal concentrations in otoliths coinciding with the timing of the DWH oil spill. This suggests …

Spatial And Temporal Distributions Of Pelagic Sargassum In The Intra-Americas Sea And Atlantic Ocean, Mengqiu Wang

USF Tampa Graduate Theses and Dissertations

Pelagic Sargassum is one type of marine macroalgae that is known to be abundant in the Gulf of Mexico and Sargasso Sea. It is also known to serve as a critical habitat for many marine animals. In the past few years, large amounts of Sargassum have been reported in the Tropical Atlantic and Caribbean Sea (CS), causing significant environmental and economic problems. The goal of this study is to improve the understanding of Sargassum distributions, quantity, transport pathways, and bloom mechanisms in the CS and Tropic Atlantic through combining a variety of techniques including satellite remote sensing, field and laboratory …

An Interdisciplinary Approach To Understanding Predator-Prey Relationships In A Changing Ocean: From System Design To Education, Ileana M. Freytes-Ortiz

USF Tampa Graduate Theses and Dissertations

Climate change is ecologically and socially complex, deemed the most important issue of our generation. Through this dissertation I have approached climate change research through an interdisciplinary perspective, investigating how this phenomenon will affect marine ecological systems, how we can better develop experimental systems to answer ecological questions, and how we can effectively educate about this issue.

In Chapter 2, I provided accessible alternatives for researching the effects of climate change (elevated temperatures and pCO2) on marine ecosystems. I designed, built, and troubleshooted two accurate and inexpensive climate-controlled experimental systems capable of maintaining target conditions: a temperature-controlled system and an …

Diversity Of Ssdna Phages Related To The Family Microviridae Within The Ciona Robusta Gut, Alexandria Creasy

USF Tampa Graduate Theses and Dissertations

The gut microbiome is a complex ecosystem of bacteria, viruses, and fungi that strongly influences animal health. The bacterial component, for example, contributes orders of magnitude more gene products to host physiology than the host genome; thus, changes to the composition of these bacterial communities can have profound influences on the health of the animal. By infecting and lysing their hosts, viruses (particularly viruses infecting bacteria or phages) can affect critical functions in these environments, yet the consequences of these infections remain to be fully described. Most studies investigating gut viromes to date have focused on double-stranded DNA (dsDNA) phages …

Ecophysiology Of Oxygen Supply In Cephalopods, Matthew A. Birk

USF Tampa Graduate Theses and Dissertations

Cephalopods are an important component of many marine ecosystems and support large fisheries. Their active lifestyles and complex behaviors are thought to be driven in large part by competition with fishes. Although cephalopods appear to compete successfully with fishes, a number of their important physiological traits are arguably inferior, such as an inefficient mode of locomotion via jet propulsion and a phylogenetically limited means of blood-borne gas transport. In active shallow-water cephalopods, these traits result in an interesting combination of very high oxygen demand and limited oxygen supply. The ability to maintain active lifestyles despite these metabolic constraints makes cephalopods …

Evaluating Beach Water Quality And Dengue Fever Risk Factors By Satellite Remote Sensing And Artificial Neural Networks, Abdiel Elias Laureano-Rosario

USF Tampa Graduate Theses and Dissertations

Climatic variations, together with large-scale environmental forces and human development affect the quality of coastal recreational waters, creating potential risks to human health. These environmental forces, including increased temperature and precipitation, often promote specific vector-borne diseases in the Caribbean and Gulf of Mexico. Human activities affect water quality through discharges from urban areas, including nutrient and other pollutants derived from wastewater systems. Both water quality of recreational beaches and vector-borne diseases can be better managed by understanding their relationship with local environmental forces.

I evaluated how changes in vector-borne diseases and poor recreational water quality were related to specific environmental …

Spatial Dynamics And Productivity Of A Gulf Of Mexico Commercial Reef Fish Fishery Following Large Scale Disturbance And Management Change, Marcy Lynn Cockrell

USF Tampa Graduate Theses and Dissertations

The Gulf of Mexico commercial reef fish fishery has experienced significant management changes and disturbance in recent years, including transitioning two major fisheries from a traditional open access system into a limited entry individual fishing quota (IFQ) system in 2007 and 2010. Also in 2010, the Deepwater Horizon oil spill (DWH) released an estimated 4.9 million barrels of oil into the Gulf (~206 million U.S. gallons), and is still the largest U.S. environmental disaster to date. Emergency fishing closures initiated shortly after the oil spill began were successful in keeping tainted seafood from reaching markets. However, effects of DWH closures …

Investigating Marine Resources In The Gulf Of Mexico At Multiple Spatial And Temporal Scales Of Inquiry, Joshua Paul Kilborn

USF Tampa Graduate Theses and Dissertations

The work in this dissertation represents an attempt to investigate multiple temporal and spatial scales of inquiry relating to the variability of marine resources throughout the Gulf of Mexico large marine ecosystem (Gulf LME). This effort was undertaken over two spatial extents within the greater Gulf LME using two different time-series of fisheries monitoring data. Case studies demonstrating simple frameworks and best practices are presented with the aim of aiding researchers seeking to reduce errors and biases in scientific decision making. Two of the studies focused on three years of groundfish survey data collected across the West Florida Shelf (WFS), …

Reef Fish Biodiversity In The Florida Keys National Marine Sanctuary, Megan E. Hepner

USF Tampa Graduate Theses and Dissertations

The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower …

Packaging Of Genetic Material By Gene Transfer Agents (Gtas) Produced By Marine Roseobacter Species And Their Effect On Stimulating Bacterial Growth, Shahd Bader Aljandal

USF Tampa Graduate Theses and Dissertations

Horizontal gene transfer is one of the most important mechanisms for prokaryotic genome innovation and evolution. Gene Transfer Agents (GTAs) are phage-like particles that package small fragments of the genome of a GTA-producing bacterial cell. GTA chromosomal gene clusters usually contain 15-conserved open reading frames (ORFs) and are present in most of the sequenced marine alpha-proteobacteria genomes. Some marine strains have been shown to produce GTA particles that were biologically active in marine environment.

GTA particles range in size, morphology and the amount of host DNA they package. To date, the characteristics of GTAs are largely based on observations of …

Calibration-Free Spectrophotometric Measurements Of Carbonate Saturation States In Seawater, Erin E. Cuyler

USF Tampa Graduate Theses and Dissertations

This work describes efforts to improve methodologies and instrumentation for investigation of the marine CO₂ system. In the first section of my thesis, a method was developed that provides simple, calibration-free measurements of seawater carbonate saturation states (Ω_spec) based solely on the use of a laboratory spectrophotometer. Measurements of pH are made in paired optical cells, one with and one without added nitric acid. The amount of added nitric acid is determined through the direct proportionality between nitrate concentration and UV absorbance. After an initial calibration, the method is calibration-free and requires no volumetric or gravimetric analyses …

Genetic Identification And Population Characteristics Of Deep-Sea Cephalopod Species In The Gulf Of Mexico And Northwestern Atlantic Ocean, Amanda Sosnowski

USF Tampa Graduate Theses and Dissertations

Nearly all deep-sea cephalopod life history studies have been completed by examination of specimens collected in the wild. Much of this work is like piecing together a puzzle; knowledge of the life history of many species remains fragmented and hence, taxonomically and phylogenetically confused. Molecular approaches and sequencing technologies are powerful tools for deciphering wild-type cephalopod life history and population dynamics. Use of molecular markers offers additional certainty for identifying specimens damaged during deep-sea collections and can elucidate often cryptic, intra- and interspecific diversity. The research presented in this study assessed broad genetic patterns of biodiversity in deep-sea cephalopods from …

Stable Isotopes In The Eye Lenses Of Doryteuthis Plei: Exploring Natal Origins And Migratory Patterns In The Eastern Gulf Of Mexico, Brenna A. Meath

USF Tampa Graduate Theses and Dissertations

Stable isotope analysis is an emerging tool to examine trophic pathways and migratory patterns of marine organisms. Squid are widely distributed in coastal and deep water regions of the Gulf of Mexico. Stable isotope ratios of carbon and nitrogen found within cephalopod tissues can provide information on both trophic level and habitat of their food sources. More recently, ontogenetic changes in stable isotope ratios within squid eye lenses have been documented. Concentric layers of crystallin proteins are added to the lens as the squid ages; the center of the lens contains the oldest layer and the youngest layers are on …

Role Of Viruses Within Metaorganisms: Ciona Intestinalis As A Model System, Brittany A. Leigh

USF Tampa Graduate Theses and Dissertations

Marine animals live and thrive in a literal sea of microorganisms, yet are often able to maintain specific associations that are largely dictated by the environment, host immunity and microbial interactions. Animal-associated microbiomes include bacteria and viruses that vastly outnumber host cells, especially in the gut environment, and are considered to be integral parts of healthy, functioning animals that act as a metaorganism. However, the processes underlying the initial establishment of these microbial communities are not very well understood. This dissertation focuses on the establishment of a well-known developmental animal model, Ciona intestinalis (sea squirt), to study the establishment and …

Viruses In Marine Animals: Discovery, Detection, And Characterizarion, Elizabeth Fahsbender

USF Tampa Graduate Theses and Dissertations

Diseases in marine animals are emerging at an increasing rate. Disease forecasting enabled by virus surveillance presents a proactive solution for managing emerging diseases. Broad viral surveys aid in disease forecasting by providing baseline data on viral diversity associated with various hosts, including many that are not associated with disease. However, these viruses can become pathogens due to expansion in host or geographic range, as well as when changing conditions shift the balance between commensal viruses and the host immune system. Therefore, it is extremely valuable to identify and characterize viruses present in many different hosts in a variety of …

Characterizing Gross Lesions In Corals On Fringing Reefs Of Taiwan And Hainan Island, China, Adrienne George

USF Tampa Graduate Theses and Dissertations

Visible lesions on coral colonies are potential indicators that environmental stressors are influencing a reef. To test this hypothesis, pairs of near-shore reefs on Taiwan were surveyed along an anthropogenically influenced gradient that included locations near the cities of Taipei and Taitung, and more remote reefs off Green Island. Two fringing reefs at Sanya, Hainan Island, a popular Chinese resort area, were also assessed. Field surveys were undertaken to detect, quantify and visually describe the occurrence of lesions at each site. Coral mucus samples were collected from both normal-appearing polyps and lesion-afflicted areas of colonies to assess carbon requirements of …

A Habitat Analysis Of Estuarine Fishes And Invertebrates, With Observations On The Effects Of Habitat-Factor Resolution, Brianna Michaud

USF Tampa Graduate Theses and Dissertations

Between 1988 and 2014, otter trawls, seine nets, and plankton nets were deployed along the salinity gradients of 18 estuaries by the University of South Florida and the Florida Fish and Wildlife Research Institute (FWRI, a research branch of the Florida Fish and Wildlife Conservation Commission). The purpose of these surveys was to document the responses of aquatic estuarine biota to variation in the quantity and quality of freshwater inflows that were being managed by the Southwest Florida Water Management District (SWFWMD).

In the present analyses, four community types collected by these gears were compared with a diversity of habitat …

Seasonal Temperature Variations Controlling Cave Ventilation Processes In Cueva Larga, Puerto Rico, Rolf Vieten, Amos Winter, Sophie Friederike Warken, Andrea Schrӧder-Ritzrau, Thomas E. Miller, Denis Scholz

International Journal of Speleology

Two years of cave monitoring investigate ventilation processes in Cueva Larga, a tropical cave in Puerto Rico. The cave is 1,440 m long with a large main passage (about 120,000 m³). Cave air pCO₂ in the main passage varies seasonally, between 600 ppm in winter and 1,800 ppm in summer. The seasonal variability in cave pCO₂ permits the estimation of a cave air exchange time of 36 ± 5 days and a winter ventilation rate of 3,300 ± 1,000 m³/day for the main cave passage. Calculations of virtual temperature and differences between cave and …

Abundance Of Archaias Angulatus On The West Florida Coast Indicates The Influence Of Carbonate Alkalinity Over Salinity, Sean Thomas Beckwith

USF Tampa Graduate Theses and Dissertations

Archaias angulatus, a large symbiont-bearing foraminifer (Order Miliolida) that produces a Mg-calcite shell, is common throughout the Caribbean and warm western Atlantic region. This species lives abundantly in seagrass beds along the Springs Coast of northwest Florida (up to 4 adults per gram of sediment) where spring-fed rivers emerge from a limestone aquifer, and in Florida Bay to the southeast (25 adults/g) where the sediment is primarily biogenic carbonate. In contrast, live specimens are seldom found in the seagrass beds along the central-west coast of Florida, where barrier islands are dominated by quartz sand. My working hypothesis is that substratum …

Photic Stress In Symbiont-Bearing Reef Organisms: Analyses Of Photosynthetic Performance, Natasha Mendez-Ferrer

USF Tampa Graduate Theses and Dissertations

Photo-oxidative stress is one of the key factors that can induce bleaching in reef organisms. With the decline of coral reefs and recurrent bleaching events, many studies have focused on understanding the mechanism behind this phenomenon. Two of the hypotheses that explain how the photosynthetic performance of the symbiont is affected and influences bleaching are: (1) disruption of the photosynthetic pathway by direct damage to the photosystem II (PSII), and (2) by inhibition of the Calvin-Benson cycle. In this dissertation I examine different aspects of photosynthetic performance in symbiont-bearing reef organisms and how this is influenced by symbiont loss and …

Novel Techniques In Chemical Ecology To Examine Life Histories In Fishes, Orian Tzadik

USF Tampa Graduate Theses and Dissertations

Diet and movements in fishes are often logistically challenging to study. Trace element and stable isotope analyses have advanced these fields considerably, but are still constrained by methodological impediments, such as the tendency towards lethal sampling. Studying endangered fishes is particularly challenging as representative samples are difficult to obtain. However, the information gained from such studies is often critical to the recovery of endangered fishes as knowledge of life history attributes has the potential to greatly influence the success of management strategies.

I tested the viability of using fin rays in fishes as a non-lethal approach to study diet and …

Acropora Habitat Evaluation And Restoration Site Selection Using A Species Distribution Modeling Approach, Katherine Wirt Ames

USF Tampa Graduate Theses and Dissertations

While populations of nearly all stony coral species along the Florida reef tract have exhibited decline, the most notable decline has occurred in the once-dominant acroporid species (Acropora cervicornis, A. palmata). Both species were listed in 2006 as threatened under the Endangered Species Act. This listing, combined with their continued decline, has resulted in large-scale restoration efforts throughout Florida and the Western Caribbean. Currently, there is little to no information regarding spatial prioritization of sites for these restoration efforts. The primary objective of this dissertation was to utilize species distribution modeling, informed by existing data from the …