Metabolic hormones and their axes, including the target tissues and receptors, regulate the tissue specific utilization of nutrients with in the body. The purpose of this research was to understand the hormonal control of complex nutrient partitioning mechanisms involved in young, growing animals. Specifically, this involved the investigation of metabolic hormones and the regulation of growth in two common species of phocids (true seals): harbor seal (Phoca vitulina) and Northern elephant seal (Mirounga angustirostris) pups. This longitudinal study examines young phocids from nutritional nadir through realimentation (realimentation) to investigate how metabolic hormones involved in both food intake and nutrient partitioning change with respect to nutritional state. To investigate the role of metabolic hormones during realimentation in a small phocid seal, chapter 2 focuses on the changes in the somatotropic axis and ghrelin during a 10-week period of realimentation following nutritional nadir. Chapter 3 focuses on the application of the results of previous research and the second chapter of this thesis to a specific experimental feeding project. Chapter 4 focuses on the response to changes in nutritional status in the fasting adapted NES. Given the changes in metabolism and priority of nutrient utilization associated with transitioning from a nursing neonate to a fasting adapted juvenile, NES provide a unique opportunity to assess the effect of age on the response to realimentation. Overall, this research will further expand the understanding of tissue specific demands and the effect on endocrine response to realimentation. By incorporating assessments of metabolic changes based on nutrition as well as age, this study will expound on how metabolic hormones are involved in regulating the trade-off between adipose and lean tissue development in this unique taxon.

Gill nets and longlines were compared as shark nursery sampling methodologies in inshore waters of Georgia to (1) assess differences in gear selectivity, bias, and stress of capture and (2) determine potential relationships between habitat features and shark distribution and abundance. Gear selectivity varied between gears as a function of both species and life stage resulting in significantly different estimates of species and life stage compositions. Juvenile bonnetheads (Sphyrna tiburo) and young of the year blacktip sharks (Carcharhinus limbatus) experienced significantly higher stress from gill net capture than longline. Major sources of bias are thought to result from dietary preferences and individual size. Juvenile sandbar shark (C. plumbeus) distribution revealed a potential preference for creeks rather than sounds, between 0.32-0.8km wide and 4.02-8.05km from the ocean. Adult Atlantic sharpnose sharks (Rhizoprionodon terraenovae) appear to prefer larger, open sound waters closer to the ocean. A potential preference for locations in close proximity to jetties over those near oyster reefs was also observed for adult Atlantic sharpnose sharks, and while statistical significance was observed, a stronger pattern may exist, as sample sizes in this study were relatively small yet still able to detect a difference. Future investigations that quantify proportions of habitat availability and shark abundance in a given area may be more useful for identifying preferences for the structures observed in this study. This study also provides strong evidence of finetooth shark (C. isodon) primary and potentially secondary nursery habitat in areas that had not yet been documented. Findings from these investigations can be useful for managers seeking to maintain healthy coastal shark populations.

Bottlenose dolphins exhibit fission-fusion social systems in which group size and composition change fluidly throughout the day. Societies are typically sexually segregated, and the quality and patterning of individual relationships in this social species shape the social structure of a population. Female dolphins usually have a large network of associates with whom they form recurring moderate bonds, while male associations are highly variable due to their mating strategies. Males employ one of two strategies; males may be solitary, and encounter and herd females individually, while others may form strong bonds with one to two other males and cooperatively herd individual females in the shape of a first-order alliance. Second-order alliances are more uncommon and have only been observed in Shark Bay, Australia, and more recently within the St. Johns River (SJR), Jacksonville, Florida. Given the inter-population variation in male mating strategies, greater documentation of social structure in neighboring populations along the Atlantic coast is needed. Therefore, chapter one documents the social structure of the Indian River Lagoon (IRL) estuarine system where dolphins have experienced recurrent cetacean morbillivirus (CeMV) epizootics. Although environmental disturbances can affect both social and mating systems, IRL dolphin sociality does not seem to be affected by the 2008 CeMV mass mortality event. Additionally, males only form first-order alliances within this population. Because multi-level alliances are unique to the SJR in this region, chapter two analyzes the stability and function of SJR alliances. Both first- and second-order alliances exhibited variation in stability, while alliance association appears dependent on female presence. Thus, SJR alliances likely function within a reproductive context. Together, this work provides insight into the social and mating systems of bottlenose dolphins, as well as the function of multi-level alliances at a relatively new study site.

Human activities have substantially increased the atmospheric concentrations of greenhouse gases, resulting in warmer ocean temperatures that are having a negative impact on reef corals, which are highly susceptible to changes in temperature. Understanding the degree to which species vary in their tolerance to elevated temperatures and whether this variation is heritable is important in determining their ability to adapt to climate change. In order to address this, Acropora cervicornis fragments from 20 genetically distinct colonies were kept at either ambient or elevated temperatures, and mortality was monitored for 26 days. Heritability of thermal tolerance was estimated using a clonal method comparing the difference in lifespan within and among clones in a one-way ANOVA, as well as a marker based method using the program MARK (Ritland 1996) to estimate relatedness between colonies. To understand the physiological basis of thermal tolerance, tissue samples from both treatments were taken after 12 hours to investigate gene expression associated with sub-lethal temperature stress at both the mRNA and the protein level. The results revealed that this population of A. cervicornis has a relatively high amount of total genetic variation in thermal tolerance (H2 = 0.528), but low additive genetic variation for this trait (h2 = 0.032). In addition, both gene expression and protein expression among colonies were highly variable and did not show consistent patterns related to differences in thermal tolerance among colonies. These results reveal that this population of A. cervicornis may have a limited capacity to respond to projected increases in ocean temperatures. In addition, the results suggest that the molecular basis of thermal tolerance in this species is complex and that there are potentially many genotypic combinations that can result in a heat-tolerant phenotype.

Ttc39c has been identified as a novel gene in skeletal muscle that is upregulated in response to neurogenic atrophy in mice. Quantitative PCR and Western blot analysis confirmed that Ttc39c is expressed in both proliferating and differentiated muscle cells. Furthermore, comparison of Ttc39c expression in undifferentiated and differentiated C2C12 cells demonstrated that Ttc39c levels peak in early differentiation, but decreases as cells become fully differentiated myotubes. The transcriptional regulation of Ttc39c was examined by cloning promoter fragments of the gene and fusing it with the SEAP reporter gene. The Ttc39c reporter gene constructs were transfected into muscle cells and confirmed to have significant transcriptional activity in cultured muscle cells and were also found to be transcriptionally repressed in response to ectopic expression of myogenic regulatory factors (MRF). Furthermore, conserved E-box elements in the proximal promoter region were identified, mutated, and analyzed for their role in the transcriptional regulation of Ttc39c expression. Mutation of the conserved E-box sequences reduced the activity of the Ttc39c reporter gene, suggesting that these elements are potentially necessary for full Ttc39c expression. To determine the sub-cellular location of Ttc39c in muscle cells, the Ttc39c cDNA was fused with the green fluorescent protein (GFP), expressed in muscle cells, and visualized by confocal microscopy revealing that Tct39c is localized to the cytoplasm of proliferating myoblasts and differentiating myotubes. Furthermore, Ttc39c appears to localize to the microtubule network and differentiating muscle cells developed elongated primary cilia in response to Ttc39c ectopic expression. Additionally, Ttc39c overexpression resulted in impaired muscle cell differentiation, attenuated Hedgehog and MAP Kinase signaling, and increased expression of IFT144, a component of the intraflagellar transport complex A involved in retrograde movement in primary cilia. Interestingly, Ttc39c knockdown also resulted in abrogated muscle cell differentiation and impaired Hedgehog and MAP Kinase signaling, but did not affect IFT144 expression levels. These results suggest that muscle cell differentiation is sensitive to aberrant Ttc39c expression, that Ttc39c is necessary for proper muscle cell differentiation, and that Ttc39c may participate in retrograde transport of the primary cilia of developing muscle cells.

Cyanobacteria are a group of photo-oxygenic bacteria found in nearly every ecosystem, but much cyanobacterial diversity, in various habitats, has yet to be explored. Cyanobacteria are often conspicuous components of photosynthetic flora, providing significant carbon and nitrogen inputs to surrounding systems. As possible primary colonizers of stone substrates not native to this region, cyanobacteria isolated from headstones may provide biogeographically informative data. An exploratory study of lichen-dominated microbial consortia, growing on headstones, was conducted to isolate and identify novel microaerophytic cyanobacteria, and resulted in the establishment of four novel cyanobacterial taxa. Phylogenetic analyses of photobionts in one tripartite lichen revealed two novel taxa: Brasilonema lichenoidesand Chroococcidiopsis lichenoides. Using a total evidence approach, analyzing ecology, morphology, ITS structure, and molecular data two additional taxa were described: Brasilonema geniculosusand Calothrix dumas. Analysis of secondary structures of the Internal Transcribed Spacer (ITS) regions of the 16S-23S operon in cyanobacteria are commonly used in cyanobacterial taxonomy studies and were applied to the identification of the new taxa in this study. However, the relationship between ITS structures, hairpin loops (helices) in a region of non-coding DNA, has not been thoroughly evaluated. The 16S-23S operon is one of many in prokaryotes with multiple copies and there is evidence that operons may vary due to differential selective pressures or drift. A study was undertaken analyzing ITS operons from 224 previously published cyanobacterial taxa for domain inclusion and exclusion, intragenomic heterogeneity of ITS operons, and the possible relevance of variable selective pressures affecting individual domains. Analysis revealed highly variable ITS domain inclusion even in complete sequences, as well as high variation between domains containing two or no tRNA sequences. Recommendations were made to standardize ITS analysis in the future to account for this possible variation. Further study is required to statistically demonstrate to what extent ITS secondary structures correlate with taxonomy.

Coral cover is in decline on a global scale, with increased mortality events being attributed to a number of global and regional stressors. While the impacts of global stressors (e.g. sea surface temperature rise, ocean acidification) are well documented, there is growing interest in identifying and understanding the impacts of regional stressors. The reason for this change in focus is that regional stressors can often work in combination, sometimes synergistically, with global stressors and that stressors on a regional scale tend to be more easily mitigated by management practices. One regional stressor that impacts a myriad of marine organisms in the southeastern United States is the annual red tide blooms produced by the dinoflagellate, Karenia brevis. Their impacts, along with the lipid soluble polyether neurotoxins they produce, termed brevetoxins, are well studied in economically important organisms, such as bivalves. However, little is known of their impacts on organisms that possess ecological importance, such as species of scleractinian coral. To address this gap in knowledge, a multifaceted study is discussed herein, which evaluated the effects of ecologically relevant concentrations of K. brevis and associated brevetoxins on different coral life history stages and coral species. The second chapter addresses the impacts of red tide on larval behavior, settlement and survival of the coral species Porites astreoides, as well as impacts of photochemical efficiency and oxidative stress within different coral species (P. astreoides larvae, P. astreoides adults, Acropora cervicornis, Cladocora arbuscula, and Phyllangia americana). The third chapter confers the use of broad-scale proteomic analysis to identify the cellular response of the non-model coral species, P. astreoides, following exposure to red tide. Coral larvae actively avoided both medium and high bloom conditions of K. brevis and brevetoxins, while percent larval settlement and survival were impacted following exposure to high bloom concentrations of K. brevis. Photochemical efficiency of in hospite Symbiodinium was reduced following exposure to both K. brevis and brevetoxin in P. astreoides larvae, as well as exposure to K. brevis in P. astreoides adults, while being unimpacted in A. cervicornis. Compared to controls, high bloom conditions resulted in an increase in biomarkers of lipid peroxidation in C. arbuscula. This was also seen in P. astreoides larvae at 24 hours; however, this difference was indistinguishable following 48 hours. Surprisingly, no other biomarker of oxidative stress analyzed were impacted. Broad-scale proteomic analysis of P. astreoides following exposure to red tide conditions revealed variable changes in proteome expression depending on if the corals were exposed to K. brevis or brevetoxins. Exposure to brevetoxins resulted in differential expression of proteins related to DNA organization, chromatin formation and transcription expression; while exposure to K. brevis resulted in differential expression of proteins related to redox homeostasis, protein folding, energy metabolism, and production of reactive oxygen species. The results of this study demonstrate the potential for annual red tide blooms to act as a regional stressor on coral species. They highlight the ability of red tide conditions to negatively impact coral at multiple life history stages and that the extent of these effects may be species specific. They also provide further incite of coral’s response to red tide exposure at the cellular level.

A growing body of evidence supports the observation that marine disease outbreaks, especially those caused by opportunistic pathogens, are increasing in frequency and severity. One genus of such pathogens, Labyrinthula, has been identified as the causative agent of seagrass wasting disease, an epidemic that has historically plagued seagrass beds around the world. It is suspected that pathogenicity is intimately linked to the ability of the host to initiate defense responses, but a lack of compelling evidence prevents any meaningful application of preliminary observations. This body of work investigated the roles of host genotype, host immune status, and environmental stressors in dictating the susceptibility of Thalassia testudinum (turtlegrass) to seagrass wasting disease, through two investigational studies. The first, a lab-based study, addressed the deficit in empirical methods through the development of techniques that measured: 1) Labyrinthula loading in host tissue through a novel qPCR-based assay and 2) immune status in the seagrass host via four immune biomarker assays, measuring peroxidase (POX), exochitinase (EXOC), polyphenol oxidase (PPO), and lysozyme (LYS) activity. These methods were used to analyze turtlegrass individuals exposed to 1) abiotic stressors alone or 2) abiotic stressors followed by pathogen-challenge, in a controlled laboratory setting. The qPCR assay successfully quantified pathogen loading in seagrass tissue with high specificity. All four biomarkers were constitutively active in host tissue, but expression was largely unaffected by the chosen abiotic stressors. There were significant positive relationships between pathogen loading and two of the four biomarkers (POX and EXOC), regardless of abiotic stress treatment. Finally, despite the widely variable response among individuals, regardless of treatment, we identify a potential trade-off mediated immune response in T. testudinum, when faced with pathogen invasion. The second investigation was a field study conducted in Florida Bay, a shallow, subtropical estuary characterized by many spatiotemporally unique basins, where T. testudinum dominates. Samples collected from 15 representative sites were analyzed using the methods developed in the first study as well as historical monitoring databases, in an effort to identify ecologically significant trends that existed in patterns between: 1) pathogen loading and immune status; 2) pathogen loading and geographic site; 3) pathogen loading and morphometric characteristics; 4) pathogen loading and water quality data; 5) immune status and geographic site; 6) immune status and morphometric characteristics; and 7) immune status and water quality data. The results revealed that both pathogen loading and immune status varied as a function of location in Florida Bay. Furthermore, based on the trends observed among and between sites with regards to pathogen loading, immune status, leaf morphology and water quality, a mechanism in which all four of these parameter sets interact is proposed as a potential explanation for the differences observed in Labyrinthula prevalence and severity within the bay. The results of both investigations address whether wasting disease susceptibility is driven primarily by variability in the environment or in the host species, and provide valuable insight regarding the extent to which seagrasses possess the capacity for resilience against marine pathogens.

Nearshore marine environments are known to be highly productive systems with relatively high faunal diversity and abundances, but these systems are particularly vulnerable to negative impacts from anthropogenic disturbances that can result in habitat degradation. Despite these challenges, many shark species of various life stages utilize coastal shelf habitats, inshore estuaries, and bays. The inshore habitats of Cumberland and Nassau Sounds in northeast Florida have been proposed as potential nursery grounds by earlier work, but this suggestion did not satisfy all of the standard criteria of shark nursery designation. It has recently been stated that the combination of surveys inside and outside suspected nursery habitats, especially those incorporating mark-recapture studies, would provide a very comprehensive test of the nursery criteria. A primary objective of the present study was to initially describe the composition and abundance of shark populations utilizing the nearshore habitats of northeast Florida, while also comparing them to inshore communities, with emphasis on spatial and temporal variations in assemblages. Fishery-independent longline sampling was conducted across the region and while considerable overlap of species were observed, significant differences in community structure between inshore and nearshore locations were detected. Specifically, the inshore waters of the First Coast support nursery habitat designation for Atlantic sharpnose, blacktip, and sandbar sharks after satisfying the accepted criteria. Given the high amounts of spatial and temporal overlap observed along the First Coast, relative trophic niche dynamics were also investigated via stable isotope analysis of two tissue types. These results revealed varying trophic niche sizes in the long term, but suggest some degree of shared resource use when animals are present on the First Coast. The identification of factors that influence coastal shark habitat utilization, such as competition and resource use, can contribute to understanding and predicting how they may respond to future environmental changes.

Many elasmobranchs are considered top predators with worldwide distribution, and in general these fish play an important role in the transfer of energy from the lower to the upper trophic levels within the marine ecosystem. Despite this, little research has been done regarding the rates of prey ingestion, digestion, and the processes of energy and nutrient absorption. Specifically understudied is enzymatic digestion within the intestinal brush border, which functions to break down macromolecules into smaller subunits for luminal absorption across the gastrointestinal epithelium. Given their carnivorous diet, the present study sought to expand knowledge on nutrient intake in elasmobranchs by focusing on the uptake of products of protein metabolism. To accomplish this, sequence encoding Peptide Transporter 1 (PepT1), a protein found within the brush border membrane (BBM) of higher vertebrates that is responsible for the translocation and absorption of small peptides released during digestion by luminal and membrane-bound proteases, was molecularly identified in the bonnethead shark (Sphyrna tiburo) using degenerate primers based on conserved portions of known PEPT1 sequences from other vertebrates. Sequence encoding Peptide Transporter 2 (PepT2) was also isolated from the S. tiburo scroll valve intestine using the same methodology. PepT1 was then localized using immunocytochemistry with rabbit polyclonal anti-rat PEPT1 in the esophagus, stomach, duodenum, scroll valve intestine, rectum, and pancreas. Vesicle studies were used to identify the apparent affinity of the transporter, and to quantify the rate of uptake by its H+-dependent cotransporter properties, using 3H-glycylsarcosine as a model dipeptide. The results of this study provide insight into the rate and properties of food passage within S. tiburo, and can lead to future work on topics such as physiological regulation of protein metabolism and absorption and how it may vary in elasmobranchs that exhibit different feeding strategies.