Marine Biology Commons^™

Focus-Stacked Images Of Fish Jawbones For Stomach Content Analyses: A Case Study With Select Taxa From Tampa Bay, Florida, Gabriel E. Ramos-Tafur, Kevin A. Thompson, Julianne Knight-Gray, Brittany J. Hall-Scharf, David D. Chagaris, Ted S. Switzer, Richard E. Matheson, Robert H. Mcmichael Jr.

Gulf and Caribbean Research

Trophodynamics and ecosystem models have been increasingly used in evaluating fish stocks, requiring accurate diet data; however, complications with identifications arise when the soft tissues of fish prey break down during digestion, limiting the taxonomic resolution obtained during stomach content analyses. Although scales and otoliths are relatively resistant to digestion, their usefulness for distinguishing among fish prey species is limited. Jawbones are frequently observed in predator stomach contents, and while morphologies of some fishes have been described, available information is frequently inadequate for practical application in stomach content analyses. Line drawings have long been the traditional means to convey complex …

Coral Reefs In The Gulf Of Mexico Large Marine Ecosystem: Conservation Status, Challenges, And Opportunities, Diego L. Gil-Agudelo, Carlos E. Cintra-Buenrostro, Jorge Brenner, Patricia Gonzalez-Diaz, William Kiene, Caitlin Lustic, Horacio Perez-Espana

School of Earth, Environmental, & Marine Sciences Faculty Publications

The importance of coral reefs (CR) within marine ecosystems has become widely recognized. Although shallow CR are not as abundant in the Gulf of Mexico (GoM) as in other areas such as the Caribbean, their uniqueness, singularity, isolation, and conservation status make their conservation highly important. Corals and CR, both shallow and deep, are more widely distributed throughout the GoM than previously thought, providing new venues of research but also new challenges for their sustainable management. They are widely present in the three countries circumscribing the GoM (Cuba, Mexico, and the United States). Corals are also distributed throughout different depths, …

Hepatobiliary Analyses Suggest Chronic Pah Exposure In Hakes (Urophycis Spp.) Following The Deepwater Horizon Oil Spill, Rachel E. Struch, Erin Pulster, Andrea D. Schreier, Steven A. Murawski

C-IMAGE Publications

Prior to the Deepwater Horizon oil spill, we lacked a comprehensive baseline of oil contamination in the Gulf of Mexico's sediments, water column, and biota. Gaps in prespill knowledge limit our ability to determine the aftereffects of the Deepwater Horizon blowout or prepare to mitigate similar impacts during future oil spill disasters. We examined spatiotemporal differences in exposure to and metabolism of polycyclic aromatic hydrocarbons (PAHs) in 2 hake species (Urophycis spp.) to establish a current baseline for these ecologically important, abundant, and at-risk demersal fishes. Gulf hake (Urophycis cirrata) and southern hake (Urophycis floridana) were collected throughout the Gulf …

Development And Employment Of Environmental Dna Methods For The Detection Of Bull Sharks (Carcharhinus Leucas) In A Freshwater And Estuarine Interface In The Mobile-Tensaw Delta And Mobile Bay, Alabama, Katherine Schweiss

Master's Theses

Species conservation and management is influenced by the quality of monitoring methods employed, especially when targeting elusive, but ecologically significant species, like elasmobranchs. Bull Sharks (Carcharhinus leucas) are highly mobile predators that rely on estuaries and freshwater rivers for maturation, resources, and refuge; their ability to withstand changing environmental conditions may mean they are linking ecosystems through their habitat usage and movements. Rather than setting nets or attaching acoustic monitoring devices, which can be expensive, time-consuming, and invasive, the analysis of environmental DNA (eDNA) for tracing species presence was used to target C. leucasDNA. The present research …

The Complete Mitochondrial Genome Of Tanacetipathes Thamnea Warner, 1981 (Antipatharia: Myriopathidae), Diego F. Figueroa, David Hicks, Nicole J. Figueroa

School of Earth, Environmental, & Marine Sciences Faculty Publications

Specimens of the black coral Tanacetipathes thamnea were collected from the Northwestern Gulf of Mexico. The complete mitochondrial genome of one of these specimens was obtained from genomic DNA by next-generation sequencing technology on the Illumina HiSeq 2500. Only three species of black corals have a completely sequenced mitochondrial genome. These were used to reconstruct the phylogeny for the order Antipatharia. The mitochondrial genome of T. thamnea is 17,712 base pairs and contains 13 protein-coding genes, 2 ribosomal RNAs, and 2 transfer RNAs in the following order: 16s RNA, COX3, COX1 (with intron), ND4L, COX2, ND4, …

Improving The Integration Of Restoration And Conservation In Marine And Coastal Ecosystems: Lessons From The Deepwater Horizon Disaster, Richard L. Wallace, Gilbert Gilbert, John E. Reynolds Iii

C-IMAGE Publications

In the wake of the Deepwater Horizon disaster, much has been learned about the biological, ecological, physical, and chemical conditions of the Gulf of Mexico. In parallel, the research community has also gained insight about the social and organizational structures and processes necessary for oil spill response and subsequent marine and coastal restoration. However, even with these lessons from both the Deepwater Horizon and previous spills, including 1989’s Exxon Valdez and the Ixtoc 1 in 1979, our understanding of how to avoid future crises has not advanced at the same pace as offshore oil and gas development. We argue that …

Trust And Influence In The Gulf Of Mexico’S Fishery Public Management Network, Anthony Lima, Dongkyu Kim, Andrew M. Song, Gordon M. Hickey, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

Sustainable fishery management is a complex multi-sectoral challenge requiring substantial interagency coordination, collaboration, and knowledge sharing. While scholars of public management network theory and natural resource management have identified trust as one of the key ideational network properties that facilitates such interaction, relatively few studies have operationalized and measured the multiple dimensions of trust and their influence on collaboration. This article presents the results of an exploratory study examining the Gulf of Mexico fishery management network comprised of more than 30 stakeholder organizations. Using an empirically validated survey instrument, the distribution of four types of trust, three gradations of influence, …

Characterization Of The Microbiome And Bioluminescent Symbionts Across Life Stages Of Ceratioid Anglerfishes Of The Gulf Of Mexico, Lindsay L. Freed, Cole Easson, Lydia Baker, D. Fenolio, Tracey Sutton, Yasmin Khan, Patricia Blackwelder, Tory Hendry, Jose Lopez

Biology Faculty Articles

The interdependence of diverse organisms through symbiosis reaches even the deepest parts of the oceans. As part of the DEEPEND project (deependconsortium.org) research on deep Gulf of Mexico biodiversity, we profiled the bacterial communities (‘microbiomes’) and luminous symbionts of 36 specimens of adult and larval deep-sea anglerfishes of the suborder Ceratioidei using 16S rDNA. Transmission Electron Microscopy was used to characterize the location of symbionts in adult light organs (esca). Whole larval microbiomes, and adult skin and gut microbiomes, were dominated by bacteria in the genera Moritella and Pseudoalteromonas genera. 16S rDNA sequencing results from adult fishes corroborate …

Associations Between Chronic Exposure To Polycyclic Aromatic Hydrocarbons And Health Indices In Gulf Of Mexico Tilefish (Lopholatilus Chamaeleonticeps) Post Deepwater Horizon, Susan M. Syder, Erin Pulster, Steven Murawski

C-IMAGE Publications

A time series of polycyclic aromatic hydrocarbon (PAH) data was collected for Gulf of Mexico demersal fishes in the years following the Deepwater Horizon oil spill (2012–2017). Tilefish (Lopholatilus chamaeleonticeps ) were sampled via demersal longline at repeat stations in the northern Gulf of Mexico in 2012 to 2015 and 2017. Bile samples (n  = 256) were analyzed via high‐performance liquid chromatography with fluorescence detection for PAH metabolites as a biomarker of exposure to PAHs. Liver tissues (n  = 230) were analyzed for accumulation of PAHs and alkylated homologs via quick, easy, cheap, effective, rugged, and safe …

Shallow- Water Hardbottom Communities Support The Separation Of Biogeographic Provinces On The West- Central Florida Gulf Coast, Shelby Eagan

HCNSO Student Theses and Dissertations

Several studies have found separation of biogeographic provinces on the West Florida Shelf (WFS), but the location of this separation differs depending on different organisms with faunal boundaries proposed at Apalachicola, Cedar Key, Anclote Key. Tampa Bay, Charlotte Harbor, Cape Romano, or Cape Sable. Biogeographic boundaries can be gradual over a given space and are often species-specific. Analyses of marine benthic mapping and community characterization of Florida’s West-central coast shallow water (depth) hardbottom habitats indicate a major shift in the benthos across Tampa Bay. Quantitative benthic surveys of 29 sites yielded a total of 4,079 individuals of nine stony coral …

In Situ Observations Of Fish Larvae Encased Within A Pelagic Gelatinous Matrix, Adam T. Greer, Luciano M. Chiaverano, James G. Ditty, Frank J. Hernandez

Faculty Publications

The degree to which marine fish larvae aggregate (i.e. patchiness) is predominantly determined by the physical oceanographic environment. Biological traits, however, can also influence spatial distributions and have adaptive value for larvae (e.g. favorable transport or reducing predation mortality). Although several fish families are known to release eggs within a gelatinous matrix, hatched larvae have not been found inside this type of structure. We present observations of hatched, preflexion yolk-sac larvae encased within a pelagic gelatinous matrix (mass). Two different masses (40-60 mm in length) containing free swimming, elongate larvae were imaged in the northern Gulf of Mexico (nGOM) near …

Assessing Seasonality And Density From Passive Acoustic Monitoring Of Signals Presumed To Be From Pygmy And Dwarf Sperm Whales In The Gulf Of Mexico, John A. Hildebrand, Kaitlin E. Fraiser, Simone Baumann-Pickering, Sean M. Wiggins, Karlina P. Merkens, Lance P. Garrison, Melissa S. Soldevilla, Mark A. Mcdonald

C-IMAGE Publications

Pygmy sperm whales (Kogia breviceps) and dwarf sperm whales (Kogia sima) are deep diving cetaceans that commonly strand along the coast of the southeast US, but that are difficult to study visually at sea because of their elusive behavior. Conventional visual surveys are thought to significantly underestimate the presence of Kogia and they have proven difficult to approach for tracking and tagging. An approach is presented for density estimation of signals presumed to be from Kogia spp. based on passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period following …

Depth-Dependent Environmental Drivers Of Microbial Plankton Community Structure In The Northern Gulf Of Mexico, Cole Easson, Jose Lopez

Biology Faculty Articles

The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the …

Complete Mitochondrial Genome Of Callogorgia Cf. Gracilis (Octocorallia: Calcaxonia: Primnoidae), Erin E. Easton, David Hicks

School of Earth, Environmental, & Marine Sciences Faculty Publications

We report the first complete mitochondrial genome of Callogorgia. Callogorgia cf. gracilis isolate DFH32_518B was collected by a remotely operated vehicle at 98 m on McGrail Bank (27.9840725°N, 92.604242°W). The complete mitogenome is 18,937 bp (27.8% A, 18.3% C, 19.8% G, and 34.1% T) and has the ancestral octocoral gene order for its 14 protein-coding genes, two rRNA genes, and one tRNA gene. It is sister to and ∼96.6% similar (uncorrected) to Narella hawaiiensis, the only other complete mitogenome reported for Primnoidae. The cox1 + igr1 + mtMutS region differs by two base pairs (0.12%) from the only reported …

Spatial And Temporal Variability Of PCo2, Carbon Fluxes, And Saturation State On The West Florida Shelf, L. L. Robbins, Kendra L. Daly, L. Barbero, R. Wanninkhof, R. He, H. Zong, J. T. Lisle, W. J. Cai, C. G. Smith

C-IMAGE Publications

The West Florida Shelf (WFS) is a source of uncertainty for the Gulf of Mexico carbon budget. Data from the synthesis of approximately 135,000 p CO₂ values from 97 cruises from the WFS show that the shelf waters fluctuate between being a weak source to a weak sink of carbon. Overall, the shelf acts as a weak source of CO₂ at 0.32 ± 1.5 mol m⁻² yr⁻¹. Subregions, however, reveal slightly different trends, where surface waters associated with 40–200‐m isobath in the northern and southern WFS are generally weak sinks all year, except for summer …

Laboratory Growth Of Denitrifying Water Column Microbia Consortia From Deep-Sea Shipwrecks In The Northern Gulf Of Mexico, Dhanya Haridas, Justin C. Biffinger, Thomas J. Boyd, Preston A. Fulmer, Leila J. Hamdan, Lisa A. Fitzgerald

Faculty Publications

Background: Shipwrecks serve as a rich source for novel microbial populations that have largely remained undiscovered. Low temperatures, lack of sunlight, and the availability of substrates derived from the shipwreck’s hull and cargo may provide an environment in which microbes can develop unique metabolic adaptations.

Methods: To test our hypothesis that shipwrecks could influence the microbial population involved in denitrification when a consortium is grown in the laboratory, we collected samples proximate to two steel shipwrecks in the northern Gulf of Mexico. Then under laboratory conditions, we grew two independent denitrifying microbial consortia. Each consortium was grown by …

A Phylogeographic Analysis Of Black Coral (Antipatharia) On Artificial And Natural Reefs In The Northwestern Gulf Of Mexico, Heather Otte

Theses and Dissertations

NOAA's Islands in the Stream concept (IitS) of designating networks of marine protected areas as refugia in the Gulf of Mexico depends on genetic connectivity. Isolated habitats like those proposed by the IitS occur naturally off the Texas coast where hard-bottom structures protrude from mudflats, offering a small-scale study of the IitS feasibility. Two sequences, mitochondrial 16S ribosomal RNA and nuclear internal transcribed spacer, were used to build haplotype networks of Antipatharians (Anthozoa: Hexacorallia), corals with planktonic larvae that can act as a proxy for connectivity of other organisms. Two species showed no significant genetic differentiation or pattern of genetic …

Descriptive Density Models Of Scyphozoan Jellyfish In The Northern Gulf Of Mexico, Katrina T. Aleksa, Redwood W. Nero, Jerry D. Wiggert, William M. Graham

Faculty Publications

Jellyfish play an important role in the food web of many coastal environments but are generally considered a nuisance to scientific fieldwork and industrial and economic trades. A better understanding of how jellyfish densities and distributions are affected by environmental parameters could elucidate population trends and provide assistance in ecological research and undesirable human interactions. In this study, abundance data for scyphozoan medusae, Chrysaora sp. and Aurelia spp., were extracted from Southeast Area Monitoring and Assessment Program trawling surveys for the northern Gulf of Mexico (nGoM) during the summer and fall months. Both in situ and satellite oceanographic measurements were …

Preliminary Age Estimates For Female Southern Stingrays (Hypanus Americanus) From Southwestern Florida, Usa, Abigail H.P. Hayne, Gregg R. Poulakis, Jason C. Seitz, James A. Sulikowski

Gulf and Caribbean Research

No abstract provided.

Ecological And Oceanographic Influences On Leatherback Turtle Behavior And Scyphozoan Jellyfish Distributions In The Gulf Of Mexico, Katrina Aleksa

Dissertations

Leatherback turtles (Dermochelys coriacea) are a wide-ranging, oceanic species that feed exclusively on gelatinous zooplankton. Leatherback have been spotted in the Gulf of Mexico (GoM) for several decades and consistently had a high level of interactions with longline fisheries. However, no quantitative studies have been performed to address the spatiotemporal distribution of these turtles in the GoM. This research determines 1) leatherback movements and high-use areas in the GoM, 2) their association with oceanographic features, 3) the distribution and density of two abundant medusae in the northern GoM and any association with biophysical parameters, and 4) the body …

Utilizing Accelerometer Telemetry Tags To Compare Red Snapper (Lutjanus Campechanus) Behavior On Artificial And Natural Reefs, Ethan T. Getz

Theses and Dissertations

The Texas Parks and Wildlife Department Artificial Reef Program has deployed over 2,800 hectares of reefing area composed of petroleum platforms, steel vessels, and concrete. Artificial reefs have been shown to support many important reef fishes such as red snapper (Lutjanus campechanus), however, few studies have compared fish behavior on artificial reefs and natural habitats. We examined activity levels, behavioral patterns and habitat preferences of red snapper over natural reefs, oil platforms and submerged ships. Telemetry tags (Sonotronics model MTT) with tri-axial acceleration range, average depth, and average temperature were programmed to optimize data collection and tag life. …

Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose

Biology Faculty Research

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO₂, thus acting as effective biofilters. A relative decrease of these gases with a concomitant ¹³C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain …

Modeling The Population Effects Of Hypoxia On Atlantic Croaker (Micropogonias Undulatus) In The Northwestern Gulf Of Mexico: Part 1—Model Description And Idealized Hypoxia, Kenneth A. Rose, Sean Creekmore, Peter Thomas, J. Kevin Craig, Md. Saydur Rahman, Rachael Miller Neilan

School of Earth, Environmental, & Marine Sciences Faculty Publications

We developed a spatially explicit, individual-based model to analyze how hypoxia effects on reproduction, growth, and mortality of Atlantic croaker in the northwestern Gulf of Mexico lead to population-level responses. The model follows the hourly growth, mortality, reproduction, and movement of individuals on a 300 × 800 spatial grid of 1-km² cells for 140 years. Chlorophyll-a concentration, water temperature, and dissolved oxygen (DO) were specified daily for each grid cell and repeated for each year of the simulation. A bioenergetics model was used to represent growth, mortality was assumed stage- and age-dependent, and the movement behavior of juveniles and …

Modeling The Population Effects Of Hypoxia On Atlantic Croaker (Micropogonias Undulatus) In The Northwestern Gulf Of Mexico: Part 2—Realistic Hypoxia And Eutrophication, Kenneth A. Rose, Sean Creekmore, Dubravko Justić, Peter Thomas, J. Kevin Craig, Rachael Miller Neilan, Lixia Wang, Md Saydur Rahman, David Kidwell

School of Earth, Environmental, & Marine Sciences Faculty Publications

Quantifying the population-level effects of hypoxia on coastal fish species has been challenging. In the companion paper (part 1), we described an individual-based population model (IBM) for Atlantic croaker in the northwestern Gulf of Mexico (NWGOM) designed to quantify the long-term population responses to low dissolved oxygen (DO) concentrations during the summer. Here in part 2, we replace the idealized hypoxia conditions with realistic DO concentrations generated from a 3-dimensional water quality model. Three years were used and randomly arranged into a time series based on the historical occurrence of mild, intermediate, and severe hypoxia year types.We also used another …

Life History Of The Non-Native Invasive Red Lionfish (Pterois Volitans) In The Northern Gulf Of Mexico, Alexander Q. Fogg

Master's Theses

Invasive Red Lionfish (Pterois volitans) were first detected in the northern Gulf of Mexico (nGOM) in 2010 and since then their numbers have increased dramatically. From 2010 to 2015, more than 15,000 Red Lionfish were collected opportunistically from the nGOM for this study. Length and weight relationships differed significantly among ecoregions by sex and there was clear sexual dimorphism in size with males being larger and heavier. Red Lionfish age ranged from 0-4.5 years old and males achieved greater growth rate (K) and asymptotic maximum lengths (L_inf) compared to females and these parameters were also different …

Distribution And Condition Of Stony Corals In The Veracruz Reef System National Park: A Management Perspective, Mauricio López Padierna

HCNSO Student Theses and Dissertations

The Veracruz Reef System (VRS) is located in the southwestern Gulf of Mexico. It is comprised of 28 coral reefs in various stages of development and conservation. They are protected under the Parque Nacional Sistema Arrecifal Veracruzano National Park created in 1992. There are many threats to the reefs of the VRS, including the Port and city of Veracruz, which hosts half a million inhabitants and Mexico’s oldest active port. The inhabitants of Veracruz have used reef resources for thousands of years, as evidenced in archaeological sites on Sacrificios island, and constructions throughout the city, most notably in the San …

Fish Assemblage Structure Indicates Limited Restoration Progress Over A Lustrum Of A Severely Degraded Estuary In Southern Tamaulipas, Mexico, Alejandro Fierro-Cabo, Carlos E. Cintra-Buenrostro

School of Earth, Environmental, & Marine Sciences Faculty Publications

Today the biggest incentive to attempt the restoration and protection of estuarine systems is their widely recognized ecological and economic importance. In the reconstruction of an estuary where the original aquatic communities disappeared before the restoration interventions, the fish assemblage is an adequate source of indicators of initial recovery. Following substantial restoration efforts, this study reports on the biannual for a lustrum monitoring and assessment of a severely degraded estuary (Garrapatas) in terms of its fish assemblage using a reference estuary (Barberena) in Tamaulipas, Mexico. Twenty fishes were associated with the restoring and reference estuaries. Species composition (richness, abundance, dominance) …

Loop Current Spin-Off Eddies, Slope Currents And Dispersal Of Reef Fish Larvae From The Flower Gardens National Marine Sanctuary And The Florida Middle Grounds, Donald R. Johnson, Harriet Perry, Guillermo Sanchez-Rubio, Mark A. Grace

Gulf and Caribbean Research

Large energetic spin—off eddies from Loop Current intrusions into the Gulf of Mexico play a major role in water exchange between the continental shelf and the deep basin in the northern Gulf. Reef fish larvae, spawned on the outer shelf and planktonic during their early life history, are broadly dispersed by this mechanism, but may be lost to the cohort by transport away from suitable settlement habitat. In this study, satellite altimeter data—assimilative ocean model currents (HYCOM) from 2003—2015 are used to calculate kinetic energy of the mixed layer over the upper continental slope (200 m —1000 m) due to …

The Vertical And Horizontal Distribution Of Deep-Sea Crustaceans Of The Order Euphausiacea (Malacostraca: Eucarida) From The Northern Gulf Of Mexico With Notes On Reproductive Seasonality., Charles Douglas Fine

HCNSO Student Theses and Dissertations

The vertical and horizontal distributions of Euphausiacea in the northern Gulf of Mexico, including the location of the Deepwater Horizon oil spill, were analyzed from 340 trawl samples collected between April-June, 2011. This study is the first comprehensive survey of euphausiid distributions from depths deeper than 1000 m in the Gulf of Mexico and included stratified sampling from five discrete depth ranges (0-200 m, 200-600 m, 600-1000 m, 1000-1200 m, and 1200-1500 m). In addition, this study encompasses the region heavily impacted by the Deepwater Horizon oil spill. Data presented here could potentially be used in ecosystem models investigating trophic …

Condition Of Larval Spanish Mackerel Scomberomorus Maculatus In Relation To The Deepwater Horizon Oil Spill, John Timothy Ransom, J.E. Filbrun, Frank J. Hernandez Jr.

Faculty Publications

The Deepwater Horizon oil spill (DWHOS) coincided with the pelagic larval stages of many valued commercial and recreational fishes in the northern Gulf of Mexico. Larval fish survival and eventual recruitment into adult populations may have been impacted directly through toxicity or indirectly through changes in the planktonic food web caused by the release of oil and chemical dispersants during the DWHOS event. Using samples from a long-term ichthyoplankton survey off the coast of Alabama, USA, in a region impacted by the DWHOS, the abundance and condition of larval Spanish mackerel Scomberomorus maculatus were compared during summer months in years …