Marine turtles are distributed in temperate, sub-tropical and tropical waters and beaches worldwide, often in areas heavily impacted by humans. Although there are many threats to marine turtle populations, the growing threats of nutrient pollution and harmful algal blooms are relatively understudied despite their widespread impacts on coastal marine ecosystems that marine turtles depend on. By studying juvenile green turtles (Chelonia mydas) in the Indian River Lagoon, Florida, where nutrient pollution and HABs are a widespread and longstanding issue, I aimed to conduct a case study of how these threats may affect this federally Threatened species. In Chapter 2, I used four concurrent, 18-year data sets to characterize and assess the interrelatedness of long-term trends in seagrass cover, macroalgae occurrence, juvenile green turtle abundance, and juvenile green turtle growth rates. From 2000 to 2018, IRL seagrass cover declined precipitously, macroalgae rose slowly through 2011 then declined during two severe HABs, juvenile green turtle abundance declined slowly, and growth rates declined through 2011 then rose through 2018. In Chapter 3, I conducted a 9-year study of juvenile green turtle foraging ecology using a comparative stable isotope approach. I found that carbon and nitrogen stable isotopic variance declined during and after two severe HABs in the IRL. In Chapter 4, I used two complementary methods to assess the diet of juvenile green turtles after two severe algal blooms in order to assess changes compared to previous diet studies. Visual identification of forage items showed that juvenile green turtle diet remained dominated by nutrient-tolerant red macroalgae with smaller components of seagrass and green algae; metabarcoding techniques largely failed to resolve their diet. My results highlight the web of complex effects and responses that factor in to determining the effects of nutrient pollution and HABs on juvenile green turtles. Future studies of habitat selection, foraging ecology, and the effects of these on juvenile green turtle growth and survival are needed to fully assess the threat of nutrient pollution.

Through genome wide association of nonvolatile metabolites and leaf ecophysiological traits, historic breeding practices were found to have led to germplasm divergence within the cultivated sunflower Helianthus annuus. In genome-wide analyses of single nucleotide polymorphisms (SNPs) in relation to flower petal carotenoid content across the cultivated H. annuus germplasm, alternative methods of analysis proposed differing genetic architectures, which suggests that these methods can be used as complementary approach in prioritizing SNPs for function analysis. Leaf hyperspectral reflectance was leveraged in a machine learning framework to predict herbivore- and volatile induction across the genus with 95% accuracy, while characterizing changes in volatile metabolites. The body of work in this dissertation represents the first characterization of the standing genetic variation for nonvolatile specialized metabolite diversity in cultivated sunflower in the context of modern breeding practices, and the first assessment of hyperspectral reflectance and volatile metabolite diversity across the genus Helianthus.

Coastal habitats provide crucial nursery habitat for predatory fishes, but they are in decline worldwide, impacting economically important fisheries. Habitat restoration can simultaneously mitigate the effects of habitat loss and benefit predators (e.g., sportfish), although this relationship is understudied. Here, the response of juvenile sportfish to oyster reef and living shoreline restoration is compared to controls in the Indian River Lagoon, Florida prior to and following restoration for up to three years through examination of community (diversity, assemblage), population (abundance), biometric (size, body condition), ontogenetic, and trophic (gut contents, stable isotopes) dynamics. Stable isotopes were used to quantify dietary history, beyond the temporary record of gut content, using carbon (δ13C) and nitrogen (δ15N). This study found juvenile sportfish abundance and richness was higher at restored reefs compared to natural and degraded reefs and was comparable between stabilized and natural living shorelines. Biomass was higher at oyster reefs compared to living shorelines, which was likely driven by an ontogenetic shift of larger mangrove snapper Lutjanus griseus toward oyster habitat. Snappers and prey at live reefs were carbon (δ13C) enriched, with a smaller isotopic niche area compared to dead reefs, while restored reefs were intermediate and contracted over time. Therefore, sportfish at higher quality reefs likely exhibit greater site fidelity, particularly among less-mobile juveniles. Moreover, stabilized shorelines can achieve trophic equivalence to natural shorelines, as shown through their similar isotopic signatures and niche area. These responses were best predicted by benthic habitat (e.g., oyster density), prey abundances, and site location, demonstrating the connection between habitat quality and setting to provide prey that support sportfish populations. This study validates the benefits of habitat restoration to economically important fisheries, by augmenting various attributes of juvenile sportfish life history, which can improve their survival and recruitment into the adult population, and thus extend restoration outcomes.

Research provides biological and ecological information on Hydrilla Verticillata (L. f.) Royle in Gatun Lake, Panama for an ongoing management program of aquatic weeds in the Panama Canal. Morphological and genetic variation, standing crop and life cycle were determined.

Insect pests are the most widespread disturbance in Canadian forests, but resulting impacts of forest defoliation on stream ecosystem functions are poorly understood. This study investigated the effects of a spruce budworm outbreak on water quality and the structure and function of microbial communities in streams of 12 catchments across a gradient of cumulative defoliation severity in the Gaspésie Peninsula, Québec, Canada. Bi-weekly stream habitat sampling was conducted spring to fall 2019-2021, with stream flow rates measured and water samples collected and analyzed for water chemistry parameters, nutrients, and dissolved organic matter (DOM) structure and quality. Algal communities were assessed at the same time by measuring in-situ biomass. Bacteria and fungi communities on leaf packs were assessed by incubating six leaf packs for five weeks (mid-August- late September) in one stream reach per watershed. Microbial community composition of leaf packs was determined using metabarcoding of 16S and ITS rRNA genes, and functions were examined using extracellular enzyme assays, leaf litter decomposition rates, and taxonomic functional assignments. This study determined that cumulative defoliation increased stream temperatures, flow rates, and SUVA (DOM aromaticity), but not nutrients. It increased algal biomass and altered microbial community composition, with a stronger influence on bacteria than fungi. The observed increases in SUVA and algal biomass corresponded with changes to bacteria carbon cycling functions, which indicated that microbes were preferentially selecting carbohydrates produced by algae rather than the aromatic compounds from increased terrestrial inputs. There were no changes to other bacteria or fungi functions and no changes to taxonomic or functional diversity. Overall, results indicate that forest pest outbreaks alter carbon inputs to streams and the structure and function of stream microbial communities associated with carbon cycling. / Thesis / Master of Science (MSc) / Terrestrial and aquatic landscapes are tightly linked, and forest disturbances can influence stream ecosystems. Insect pests defoliate millions of hectares of forests each year, but the resulting impacts on stream ecosystems are poorly understood. This study investigated the effects of a spruce budworm outbreak on water quality and microbial communities in streams in Gaspésie, QC, Canada. Microbial communities are critical to the functioning of stream ecosystems as they convert energy (e.g., carbon) into useable forms for other organisms. Results indicate that defoliation altered stream flow rates, temperatures, and carbon composition, as well as the microbial communities involved in carbon cycling processes. Carbon is essential to aquatic food webs and this improved understanding of how carbon flow is altered by a widespread forest disturbance can inform pest management decisions for spruce budworm outbreaks.

Numerous causes have been implicated in contributing to amphibian population declines since the 1980's, with habitat modification, ultraviolet radiation (UV-B) and environmental contaminants (such as glyphosate-based herbicide) being among the most common. This study identifies the effects of a generic glyphosate-based herbicide (GLY- 4 Plus) on mortality, immune function, body condition, and morphological plasticity of larvae of the spotted salamander (Ambystoma maculatum) under conditions that reflect open and closed canopy light regimes. Larval salamander responses to glyphosate-based herbicide varied depending on UV-B conditions. In general, it appears that an open canopy (i.e. greater UV-B exposure) may confer fitness benefits. In the presence of herbicide, survival was higher in an open canopy UV-B regime and pooled open canopy survival was higher than that of closed canopy treatments. In the absence of herbicide, body condition and immune function were positively related with amount of UV-B. Finally, herbicide presence appeared to affect morphology under low UV-B conditions. UV-induced breakdown of surfactant or a complex interaction between temperature stratification and trophic relations is potentially responsible for the observed patterns in survival and body condition. However, the mechanistic underpinnings of improved immune function and morphological differences are less clear. As deforestation is likely to continue, amphibians may find themselves in ponds with increasingly open canopies. Combined with the knowledge that some amphibians can become locally adapted to UV exposure and develop pesticide tolerance, the probability of surviving exposure to this herbicide may be elevated in open canopy ponds. These results emphasize the complexity of natural systems and the importance of including multiple factors in experiments.

Two compartment (sediment and water) flow-through model ecosystems were constructed to investigate the compartmentalization of different organic chemicals. Lindane, naphthalene, and mirex were pumped into the systems and resultant compartmental chemical concentrations determined. Steady state concentrations were compared to those predicted by two environmental fate models - EXAMS (Exposure Analysis Modeling System) and SLSA (Simplified Lake and Stream Analysis) which were developed by EPA-Athens, Georgia and HydroQual, Inc., respectively.

<p>Elucidating the mechanisms structuring communities has been a challenge for community ecology since its beginnings. One theory argues that assembly rules structure communities by means of deterministic mechanisms arising from biological interactions. Another view maintains that patterns seen in community composition and species abundance result from stochastic processes such as migration and extinction. The dilemma has yet not been resolved unambiguously. The main issue is that communities shaped by deterministic mechanisms can produce stochastic patterns via priority effects. The main goal of this study was to determine whether assembly rules structure communities. My strategy was to minimize priority effects by controlling timing of colonization. To do this I used a null community by combining communities of 17 rock pools. This null community was later divided among experimental communities. I conducted three experiments: (1) Experimental communities were exposed to the same external conditions. (2) Communities were exposed to different environments, disturbance, dispersal and habitat heterogeneity. (3) Replicated null communities were connected to allow inter-replicate dispersal. After 4 months, communities (experiment 1) formed alternative states, suggesting the lack of assembly rules control in community structure. The second experiment showed that adding factors results in more alternative states. The increasing number of alternative states among replicate communities indicates that diversified environment and migration are needed to reproduce qualitative patterns observed in nature. The last experiment (3) showed that patterns observed among connected replicate communities resemble patterns that emerged in the presence of biological interactions in unconnected communities. Similarity of patterns between connected and unconnected groups of communities suggest that local biological interactions can be sufficient to structure communities to a considerable degree. Nevertheless, the regional processes appear necessary in their role of supplying species for local communities.</p> / Doctor of Philosophy (PhD)

<p>Aquatic vegetation in the pristine coastal marshes of eastern Georgian Bay (GB) provides critical spawning and foraging habitat for fish species, with complex habitat supporting the greatest diversity. These wetlands are threatened by a changing water level regime and forecasted lower water levels. To monitor and conserve these wetlands, we must understand how they function and respond to this stressor. The overall goals of this thesis are to determine the impact of declining water levels on both wetland fish habitat and the fish community as well as identify the spatial scale of habitat utilization by fishes.</p> <p>We first delineate all coastal wetlands in eastern GB, identifying 3771 wetlands that provide habitat for Great Lakes fishes. Using satellite imagery, we develop an object-based classification method to classify four types of wetland vegetation. Since submerged aquatic vegetation (SAV) is not visible from satellite imagery in GB, we develop a model to predict potential area of this important habitat. The model suggests that the response of SAV to declining water levels depends on wetland geomorphology, but generally, the area of SAV decreases. To assess the response of fish habitat coverage and structure to sustained low-water levels, we classify vegetation in images collected in 2002 and 2008. The result is increasingly homogeneous habitat, a net loss of fish habitat and a decrease in fish species richness. Finally, mark-recapture and radio-tracking are used to evaluate fish movement among closely situated wetlands. Results suggest that the current distance used to group and protect small wetlands provincially (750 m), likely protects most resident fish species, but does not cover movement patterns of a top predator. This research will advance our scientific understanding of freshwater coastal ecosystems and aid in the creation of conservation strategies to mitigate future threats from declining water levels.</p> / Doctor of Philosophy (PhD)

<p>Coastal wetlands are hydrologically connected to their watershed and the lake. Water levels in Georgian Bay have been at a sustained low for thirteen years and thus connectivity of wetlands to the lake is being threatened as water levels decline. Decreased connectivity has likely caused changes in ecological and chemical characteristics. Future climate change models predict further water declines and potentially increasing the number of wetlands that will be hydrologically disconnected. The over-arching goal of this thesis is to investigate the role of connectivity between the lake and coastal marshes in eastern Georgian Bay on the amount of potential fish habitat, water chemistry and larval amphibian habitat.</p> <p>Bathymetric information is needed in order to estimate fish habitat and two approaches were utilized in order to collect these data. A site-specific method completed in 2009 used an intensive field survey in seven wetlands to create a digital elevation model and calculated the amount of fish habitat at 10 cm increments. A second, regional method, selected 103 sites by using a stratified random sample in 18 quaternary watersheds. In both methods, changes in water levels between 173 and 176 m asl resulted in the most drastic loss of habitat. Approximately 24% of the current fish habitat has already been lost due to low water levels.</p> <p>Water chemistry in coastal marshes is influenced by hydrologic connection. In the summers of 2010 and 2011, 35 coastal marshes were sampled, 17 of which had been impounded and disconnected by a beaver dam. Beaver-impounded marshes resulted in significantly lower pH, conductivity, dissolved oxygen and sulphate concentrations, but had significantly higher soluble reactive phosphors concentrations. These conditions are indicative of the lack of connection and reduced mixing with lake water. This altered habitat was shown to support breeding area for 7 species of amphibians, the most common being green frogs and the least common being American Toads and chorus frogs.</p> / Master of Science (MSc)