Marine Biology Commons^™

Mathematical Modeling Of Emiliania Huxleyi And A Host-Specific Virus, Julia Middleton

Honors Theses

The world’s oceans provide the basis for life on the planet. One microscopic algae, the coccolithophores, and Emiliania huxleyi in particular, is a major source of carbon drawdown in the context of the global carbon cycle and account for a significant amount of the primary production in oceanic ecosystems. We know that the oceans are packed with marine viruses and they have an important role in the rise and fall of plankton populations but current mathematical models do not accurately account for virus-host interactions when predicting plankton blooms. Therefore I am using model optimization and comparison techniques to evaluate current …

Iron Supply And Demand In Antarctic Shelf Ecosystem, D. J. Mcgillicuddy Jr., Peter N. Sedwick, Michael S. Dinniman, K. R. Arrigo, T. S. Bibby, B. J. W. Greenan, Eileen E. Hofmann, John M. Klinck, W. O. Smith Jr., S. L. Mack, C. M. Marsay, B. M. Sohst, G. L. Van Dijken

OES Faculty Publications

The Ross Sea sustains a rich ecosystem and is the most productive sector of the Southern Ocean. Most of this production occurs within a polynya during the November-February period, when the availability of dissolved iron (dFe) is thought to exert the major control on phytoplankton growth. Here we combine new data on the distribution of dFe, high-resolution model simulations of ice melt and regional circulation, and satellite-based estimates of primary production to quantify iron supply and demand over the Ross Sea continental shelf. Our analysis suggests that the largest sources of dFe to the euphotic zone are wintertime mixing and …

Predicting Carbon Isotope Discrimination In Eelgrass (Zostera Marina L.) From The Environmental Parameters- Light, Flow, And [Dic], Meredith L. Mcpherson, Richard C. Zimmerman, Victoria J. Hill

OES Faculty Publications

Isotopic discrimination against ¹³C during photosynthesis is determined by a combination of environmental conditions and physiological mechanisms that control delivery of CO₂ to RUBISCO. This study investigated the effects of light, flow, dissolved inorganic carbon (DIC) concentration, and its speciation, on photosynthetic carbon assimilation of Zostera marinaL. (eelgrass) using a combination of laboratory experiments and theoretical calculations leading to a mechanistic understanding of environmental conditions that influence leaf carbon uptake and determine leaf stable carbon isotope signatures δ¹³C. Photosynthesis was saturated with respect to flow at low velocity ~ 3 cm s^-1, but …

Understanding Ocean Acidification Impacts On Organismal To Ecological Scales, Andreas J. Andersson, David I. Kline, Peter J. Edmunds, Stephen D. Archer, Nina Bednarsek, Robert C. Carpenter, Meg Chadsey, Philip Goldstein, Andrea G. Grottoli, Thomas P. Hurst, Andrew L. King, Janet E. Kübler, Ilsa B. Kuffner, Katherine R.M. Mackey, Bruce A. Menge, Adina Paytan, Ulf Riebesell, Astrid Schnetzer, Mark E. Warner, Richard C. Zimmerman

OES Faculty Publications

Ocean acidification (OA) research seeks to understand how marine ecosystems and global elemental cycles will respond to changes in seawater carbonate chemistry in combination with other environmental perturbations such as warming, eutrophication, and deoxygenation. Here, we discuss the effectiveness and limitations of current research approaches used to address this goal. A diverse combination of approaches is essential to decipher the consequences of OA to marine organisms, communities, and ecosystems. Consequently, the benefits and limitations of each approach must be considered carefully. Major research challenges involve experimentally addressing the effects of OA in the context of large natural variability in seawater …

New Tracer To Estimate Community Predation Rates Of Phagotrophic Protists, Alexander B. Bochdansky, Melissa A. Clouse

OES Faculty Publications

Predation of eukaryotic microbes on prokaryotes is one of the most important trophic interactions on Earth, representing a major mortality term and shaping morphology and composition of prokaryotic communities. Here we introduce and validate a new tracer to determine predation rates on prokaryotes. Minicells of Escherichia coli marked with a bright green fluorescent protein (GFP) vector have many operational advantages over previously used prey analogs such as fluorescently labeled bacteria. GFP-minicells are similar in size to naturally occurring bacteria from a variety of environments including the oligotrophic open ocean and the deep sea. They are relatively stable against microbial and …

Iron Deficiency Increases Growth And Nitrogen-Fixation Rates Of Phosphorus-Deficient Marine Cyanobacteria, Nathan S. Garcia, Feixue Fu, Peter N. Sedwick, David A. Hutchins

OES Faculty Publications

Marine dinitrogen (N²)-fixing cyanobacteria have large impacts on global biogeochemistry as they fix carbon dioxide (CO₂) and fertilize oligotrophic ocean waters with new nitrogen. Iron (Fe) and phosphorus (P) are the two most important limiting nutrients for marine biological N₂ fixation, and their availabilities vary between major ocean basins and regions. A long-standing question concerns the ability of two globally dominant N₂-fixing cyanobacteria, unicellular Crocosphaera and filamentous Trichodesmium, to maintain relatively high N₂-fixation rates in these regimes where both Fe and P are typically scarce. We show that under P-deficient …

Feasibility Of Using Biofuel By-Products As A Sustainable Nutritional Resource For Aquaculture Production Of Litopenaeus Vannamei, Erik David Demicco

HCNSO Student Theses and Dissertations

Many different algal species can provide an acceptable protein ingredient, with good digestibility, for shrimp feeds. Compared to fish meal, similar protein, carbohydrate, and lipid levels can be found in select algal species. Traditional shrimp diets in aquaculture rely on fish meal and fish oil from pelagic fish fisheries. A reduction or elimination of these ingredients would reduce the dependency of shrimp aquaculture on offshore fisheries and increase economic competiveness. Biofuel production produces algal by-products of potential use to aquaculturists that might reduce or eliminate the need for fisheries products in shrimp feed. Established uses for by-products from biofuel production …

The Role Of Citizens In Detecting And Responding To A Rapid Marine Invasion, Steven B. Scyphers, Sean P. Powers, J. Lad Akins, J. Marcus Drymon, Charles W. Martin, Zeb H. Schobernd, Pamela J. Schofield, Robert L. Shipp, Theodore S. Switzer

University Faculty and Staff Publications

Documenting and responding to species invasions requires innovative strategies that account for ecological and societal complexities. We used the recent expansion of Indo-Pacific lionfish (Pterois volitans/miles) throughout northern Gulf of Mexico coastal waters to evaluate the role of stakeholders in documenting and responding to a rapid marine invasion. We coupled an online survey of spearfishers and citizen science monitoring programs with traditional fishery-independent data sources and found that citizen observations documented lionfish 1–2 years earlier and more frequently than traditional reef fish monitoring programs. Citizen observations first documented lionfish in 2010 followed by rapid expansion and proliferation in …

Ecological Drivers And Habitat Associations Of Estuarine Bivalves, C. Seabird Mckeon, Björn G. Tunberg, Cora A. Johnston, Daniel J. Barshis

Biological Sciences Faculty Publications

Community composition of the infaunal bivalve fauna of the St. Lucie Estuary and southern Indian River Lagoon, eastern Florida was sampled quarterly for 10 years as part of a long-term benthic monitoring program. A total of 38,514 bivalves of 137 taxa were collected and identified. We utilized this data, along with sediment samples and environmental measurements gathered concurrently, to assess the community composition, distribution, and ecological drivers of the infaunal bivalves of this estuary system. Salinity had the strongest influence on bivalve assemblage across the 15 sites, superseding the influences of sediment type, water turbidity, temperature and other environmental parameters. …

Acclimation, Adaptation, Traits And Trade-Offs In Plankton Functional Type Models: Reconciling Terminology For Biology And Modelling, Kevin J. Flynn, Michael St. John, John A. Raven, David O. F. Skibinski, J. Icarus Allen, Aditee Mitra, Eileen E. Hofmann

CCPO Publications

We propose definitions in terminology to enhance ongoing collaborations between biologists and modellers on plankton ecology. Organism "functional type" should refer to commonality in ecology not biogeochemistry; the latter is largely an emergent property of the former, while alignment with ecology is also consistent with usage in terrestrial science. Adaptation should be confined, as in genetics, to consideration of species inter-generational change; most so-called "adaptive" plankton models are thus acclimative, modifying vital rates in response to stimuli. Trait trade-off approaches should ideally only be considered for describing intra-generational interactions; in applications between generations, and certainly between unrelated species, such concepts …

The Effect Of Parental Size On Spermatophore Production, Egg Quality, Fertilization Success, And Larval Characteristics In The Caribbean Spiny Lobster, Panulirus Argus, Mark J. Butler Iv, Alison Macdiarmid, Gaya Gnanalingam

Biological Sciences Faculty Publications

The average size of spiny lobsters (Decapoda; Palinuridae) has decreased worldwide over the past few decades. Market forces coupled with minimum size limits compel fishers to target the largest individuals. Males are targeted disproportionately as a consequence of sexual dimorphism in spiny lobster size (i.e. males grow larger than females) and because of protections for ovigerous females. Therefore, overexploitation of males has led to sperm limitation in several decapod populations with serious repercussions for reproductive success. In the Caribbean spiny lobster, Panulirus argus, little is known about the effect of reduced male size on fertilization success or the role …

River Report. State Of The Lower St. Johns River Basin, Florida: Water Quality, Fisheries, Aquatic Life, Contaminants, 2015, Environmental Protection Board, City Of Jacksonville, University Of North Florida, Jacksonville University, Lucy Sonnenberg, Gerry Pinto, Nisse Goldberg, Anthony Ouellette, Gretchen Bielmyer-Fraser, Stuart J. Chalk, Peter Bacopoulos, Brian P. Zoellner

State of the River Report

No abstract provided.

Empirical Modelling Of Solid-Blocking Effect In A Blazka Respirometer For Gag, A Large Demersal Reef Fish, Richard J. Kline, Daryl C. Parkyn, Debra J. Murie

School of Earth, Environmental, & Marine Sciences Faculty Publications

The effect of solid-body blocking in a large (257 l) Blazka-style respirometer was examined in gag Mycteroperca microlepis. Gag ranging from 376-690 mm total length were tested at velocities from 10 to 91 cm s-1 . The solid blocking effect (SBE) due to fish size, swimming speed, and water temperature was investigated by direct measurement of flow velocity at the area of the fish’s maximum girth as compared to measurements at the rear (center) of the swimming chamber. Three models were compared as corrections for the SBE: the standard Bell and Terhune (BT), a novel modification of the Bell and …

Octocoral Mitochondrial Genomes Provide Insights Into The Phylogenetic History Of Gene Order Rearrangements, Order Reversals, And Cnidarian Phylogenetics, Diego F. Figueroa, Amy R. Baco

School of Earth, Environmental, & Marine Sciences Faculty Publications

We use full mitochondrial genomes to test the robustness of the phylogeny of the Octocorallia, to determine the evolutionary pathway for the five known mitochondrial gene rearrangements in octocorals, and to test the suitability of using mitochondrial genomes for higher taxonomic-level phylogenetic reconstructions. Our phylogeny supports three major divisions within the Octocorallia and show that Paragorgiidae is paraphyletic, with Sibogagorgia forming a sister branch to the Coralliidae. Furthermore, Sibogagorgia cauliflora has what is presumed to be the ancestral gene order in octocorals, but the presence of a pair of inverted repeat sequences suggest that this gene order was not conserved …

An Examination Of El Niño's And Agricultural Runoff's Effect On Harmful Algal Blooms And California Sea Lion (Zalophus Californianus) Health In Monterey Bay, Nadine Lafeber

Scripps Senior Theses

An increase in marine mammal stranding and die-off events has been observed along the California coast. The exact cause to explain for these recent events is unknown, but El Niño and harmful algal blooms are established sources for temporary decreases in marine mammal health. To determine whether El Niño could be causing and amplifying harmful algal blooms, particularly in Monterey Bay where they occur frequently, data was analyzed from the Marine Mammal Center in Sausalito, California. Data analysis focused on California sea lions (Zalophus californianus), because they have the largest data set and are directly affected by harmful …

The Effects Of Chanellization And Channel Restoration On Aquatic Habitat And Biota Of The Pecos River, New Mexico, Darrel J. Mecham

Electronic Theses and Dissertations

River channelization has been shown to negatively impact riverine ecosystems by degrading aquatic habitat conditions, decreasing diversity of both fish and aquatic invertebrate assemblages and impairing fish recruitment. As knowledge of the negative impacts of channelization has increased, so have channel restoration efforts. We evaluated a recent channel restoration project on the Pecos River, New Mexico by comparing abiotic and biotic conditions among five reaches of river, including the restored reach, an unchannelized reach and a channelized reach all prone to streamflow intermittence and an unchannelized reach and channelized reach more perennial in nature. Our first objective was to assess …

Quantifying Florida Bay Habitat Suitability For Fishes And Invertebrates Under Climate Change Scenarios, Kelly A. Kearney, Mark J. Butler Iv, Robert Glazer, Christopner R. Kelble, Joseph E. Serafy, Erik Stabenau

Biological Sciences Faculty Publications

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due toclimate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, …

A Popular And Potentially Sustainable Fishery Resource Under Pressure-Extinction Risk And Conservation Of Brazilian Sciaenidae (Teleostei: Perciformes), Ning L. Chao, Flávia L. Frédou, Manuel Haimovici, Monica B. Peres, Beth Polidoro, Marcelo Raseira, Rosana Subira, Kent E. Carpenter

Biological Sciences Faculty Publications

Croakers (Sciaenidae) are major fishery resource in Brazil; constituting 22% of marine and 9% of freshwater fishery landings. Croakers are subject to heavy fishing pressure throughout Brazil, but habitat alteration is also an important threat to regional populations. In this regional Sciaenidae assessment, each species was analyzed for relative risk of extinction, including the identification and quantification of the impact of major threats and existing conservation measures, based on application of the Categories and Criteria of the IUCN Red List of Threatened Species. Of the 52 species of Sciaenid fishes (34 marine and 18 freshwater) present in Brazilian waters, the …

Casitas: A Location-Dependent Ecological Trap For Juvenile Caribbean Spiny Lobsters, Panulirus Argus, Benjamin C. Gutzler, Mark J. Butler Iv, Donald C. Behringer

Biological Sciences Faculty Publications

Casitas are artificial shelters used by fishers to aggregate Caribbean spiny lobsters (Panulirus argus) for ease of capture. However, casitas may function as an ecological trap for juvenile lobsters if they are attracted to casitas and their growth or mortality is poorer compared with natural shelters. We hypothesized that juvenile lobsters may be at particular risk if attracted to casitas because they are less able than larger individuals to defend themselves, and do not forage far from shelter. We compared the nutritional condition, relative mortality, and activity of lobsters of various sizes in casitas and natural shelters in adult and …

Population Dynamics Of The Little Gulper Shark (Centrophorus Uyato) And Community Analyses Of Elasmobranch Species In The Northern Gulf Of Mexico, Jacquelin Joye Hipes

USF Tampa Graduate Theses and Dissertations

In chapter 1 I describe the population dynamics of an understudied species of gulper shark, Centrophorus uyato (common name, the Little Gulper), found in the Northern Gulf of Mexico. Sharks in the family Centrophoridae are mid-sized, demersal fish, with seven species identified in North American waters. These deepwater species can be difficult to study due to the extreme depths at which they occur. During four longlining cruises from 2012-2014, 593 sharks were landed, predominantly in the Mississippi Canyon off the Louisiana coast. Mean depth of capture was 290 m. Supplementing these data are catch records for C. uyato from a …

Comparative Population Genetics And Evolutionary History Of Two Commonly Misidentified Billfishes Of Management And Conservation Concern, Andrea M. Bernard, Mahmood S. Shivji, Eric Prince, Fabio H.V. Hazin, Freddy Arocha, Andres Domingo, Kevin A. Feldheim

Marine & Environmental Sciences Faculty Articles

Background:  Misidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species. We provide the first population genetic evaluation of the …

Reproductive Parameters Of Two Coastal Pelagic Fishes Off Southeast Florida: Blackfin Tuna Thunnus Atlanticus And Little Tunny Euthynnus Alletteratus, Sonia Ahrabi-Nejad

HCNSO Student Theses and Dissertations

The ability to manage a fish stock relies on an understanding of life history characteristics and basic biology of the species. Numerous age-growth studies are facilitated by the relative ease of ageing fishes through hard-part analyses. Determining reproductive parameters for fish populations is equally important for stock assessments and management, and histological examination of gonads provides the most accurate determination of fecundity and spawning periods. Coastal pelagic fishes are often targeted commercially and recreationally due to their easy access by private vessels. However, there are few studies researching the biology and reproduction of recreational fishes in the waters of Southeastern …

Changes In Coral Community Composition At Devil's Crown, Galapagos Islands, Ecuador: A 7,700 Year Perspective, Katharine Jane Hendrickson

HCNSO Student Theses and Dissertations

Coral mortality caused by El Niño–Southern Oscillation (ENSO) activity and its related disturbances has been researched throughout the Eastern Pacific. In the past three decades, disturbances related to the El Niño–Southern Oscillation (ENSO) have been shown to influence coral growth in the Eastern Pacific. In the Galápagos Islands, Ecuador, more than 97% of corals experienced mortality after the severe 1982-1983 ENSO episode. However, two of the most dominant coral species found in a coral community adjacent to Devil’s Crown; Psammocora stellata and Diaseris distorta survived this severe ENSO event. By reconstructing sediment cores of the coral community, this study assessed …

Distribution, Growth, And Impact Of The Coral-Excavating Sponge, Cliona Delitrix, On The Stony Coral Communities Offshore Southeast Florida, Ari Halperin

HCNSO Student Theses and Dissertations

Bioerosion is a major process that affects the carbonate balance on coral reefs, and excavating sponges from the genus Cliona are some of the most important bioeroders on Caribbean reefs. The orange boring sponge, Cliona delitrix, is an abundant excavating sponge offshore southeast Florida that frequently colonizes dead portions of live stony corals, killing live coral tissue as it grows. With the recent decline in coral cover attributed to combined environmental and anthropogenic stressors, the increasing abundance of excavating sponges poses yet another threat to the persistence of Caribbean coral reefs.

In the first part of this study, I …

Assessment Of Macroinvertebrate Communities And Heavy Metal Contamination Along The Intracoastal Waterway In Fort Lauderdale, Florida, Robert Bernhard

HCNSO Student Theses and Dissertations

Sediments from four areas adjacent to marinas and a background site in the Intracoastal Waterway were assessed for macroinvertebrate composition and heavy metal contamination. Sediment core samples were collected in 2004 and 2005 for analyses of macroinvertebrate composition and sediment grain size. Additional sediment samples were collected in 2005 for chemical analyses of metals (Al, As, Cd, Cr, Cu, Fe, Pb, Hg, Ni and Zn). MANOVA and dendograms using Bray-Curtis similarity matrices grouped the sites into two clusters: the 3 sites closest to the New River formed one group, and the two end sites formed the other. The sites nearest …

Book Review - Wild Connection: What Animal Courtship And Mating Tell Us About Human Relationships, J. Matthew Hoch

Marine & Environmental Sciences Faculty Articles

No abstract provided.

Comment On “Chemically Mediated Behavior Of Recruiting Corals And Fishes: A Tipping Point That May Limit Reef Recovery”, Andrew H. Baird, Vivian R. Cumbo, Joana Figueiredo, Saki Harii, Tom Hata, Joshua S. Madin

Marine & Environmental Sciences Faculty Articles

Dixson et al. (2014) report that coral larvae navigate towards chemical cues associated with healthy reefs and avoid cues from degraded reefs. However, the swimming capabilities of coral larvae and well-established patterns of recruitment and reef hydrodynamics indicate that coral larvae will not be able to use these cues to recruit to healthy reefs. Perfuming degraded reefs, as suggested by Dixson et al (2014), will not enhance recovery rather it will distract from the difficult task of reducing fishing effort and improving water quality.

Effects Of Ocean Acidification On The Dissolution Rates Of Reef-Coral Skeletons, Robert Van Woesik, Kelly Van Woesik, Liana Van Woesik, Sandra Van Woesik

Ocean Engineering and Marine Sciences Faculty Publications

Ocean acidification threatens the foundation of tropical coral reefs. This study investigated three aspects of ocean acidification: (i) the rates at which perforate and imperforate coral-colony skeletons passively dissolve when pH is 7.8, which is predicted to occur globally by 2100, (ii) the rates of passive dissolution of corals with respect to coral-colony surface areas, and (iii) the comparative rates of a vertical reef-growth model, incorporating passive dissolution rates, and predicted sea-level rise. By 2100, when the ocean pH is expected to be 7.8, perforate Montipora coral skeletons will lose on average 15 kg CaCO3 m􀀀2 y􀀀1, which is approximately …

Marginal Coral Populations: The Densest Known Aggregation Of Pocillopora In The Galápagos Archipelago Is Of Asexual Origin, Iliana B. Baums, Meghann Devlin-Durante, Beatrice A. A. Laing, Joshua S. Feingold, Tyler B. Smith, Andrew Bruckner, Joao Monteiro

Marine & Environmental Sciences Faculty Articles

Coral populations at distributional margins frequently experience suboptimal and variable conditions. Recurrent El Niño-Southern Oscillation (ENSO) warming events have caused extensive mortality of reef-building corals in the Eastern Pacific, and particularly impacted branching pocilloporid corals in the Galápagos Islands. Pocillopora spp. were previously more common and formed incipient reefs at several locations in the archipelago but now occur as scattered colonies. Here, we report an unusually concentrated aggregation of colonies and evaluate their current genetic diversity. In particular we focus on a large population of 1614 live Pocillopora colonies found in a volcanic lagoon along the southern shore of Isabela …

Growth Rates In Gulf Of Mexico Red Snapper, Lutjanus Campechanus, Before And After The Deepwater Horizon Blowout, Elizabeth Shea Herdter

USF Tampa Graduate Theses and Dissertations

The Deepwater Horizon blowout occurred on April 20^th, 2010 and released nearly 5 million barrels of crude oil into the northern Gulf of Mexico causing pollution of the water and sediment inhabited by many fishes for at least 87 days while the wellhead went uncapped. Populations of the Gulf of Mexico Red snapper, Lutjanus campechanus, an important fish to the ecology and economy in the region, exhibit affinity to shallow water oil infrastructure such as the Deepwater Horizon making them especially vulnerable to crude oil contamination. The objective of this study is to determine growth of Red …