<p>Sea turtles have experienced dramatic population declines during the last century as a consequence of direct harvest, by-catch in fisheries, and habitat loss. Despite almost 50 years of partial international protection, several populations of sea turtles are still at imminent risk of extinction. Our knowledge of their complex life histories is still far from complete; these knowledge gaps hinder our ability to provide scientific advice regarding their conservation and management. It is the very complexity of their life histories, which allows them to exploit widely separated habitats during development, often over the course of decades, which makes them inherently difficult to study. I used satellite telemetry (n=60) to investigate the movements and habitat use patterns of juvenile loggerhead (<italic>Caretta caretta</italic>), green (<italic>Chelonia mydas</italic>), and Kemp's ridley (<italic>Lepidochelys kempii</italic>) sea turtles on their summer feeding grounds in North Carolina estuaries. These turtles migrate into and out of the estuarine waters each spring and autumn, encountering a gauntlet of fishing gear on each journey. The by-catch of sea turtles is an important conservation issue in North Carolina, and throughout the world's oceans. I evaluated conservation measures established to reduce the by-catch of sea turtles in Pamlico Sound's autumnal large-mesh gill net fishery for southern flounder (<italic>Paralichthys lethostigma</italic>), using a spatially explicit predator/prey model. My findings indicated that species-specific habitat preferences contributed to a turtles' risk of encountering fishing gear and that areas of high by-catch are predictable from patterns of overlap between sea turtle habitat use and flounder fishing effort. I then examined how the behavior of green turtles affected their vulnerability to incidental capture in estuarine commercial fisheries. Individual green turtles interact with multiple gears per season as a result of strong site fidelity to habitats also preferred by fishers. Telemetry also allowed me to examine individual variation in movements, habitat use, and site fidelity patterns of juvenile loggerhead turtles, both within the estuary and as the turtles migrated out into the North Atlantic. I used these observations to test the hypothesis of a discrete ontogenetic shift in habitat and diet in juvenile loggerheads. Approximately one-third of large juvenile loggerheads tagged in North Carolina estuaries return to oceanic habitat, sometimes for several years, where they are vulnerable to by-catch in pelagic fisheries. This led me to conclude that the long held notion of a discrete ontogenetic habitat shift between the oceanic and neritic habitat was incorrect for juvenile loggerheads (and possibly also for green turtles). Finally, I explored variation in migratory destinations in these animals through multivariate analyses of carbon and nitrogen stable isotope ratios in blood plasma and red blood cells, and through analysis of sex, genetic, haplotype, body size, and remigration records, and described the trophic niche of these turtles with Bayesian isotope mixing models. Variation in migratory destination (oceanic or neritic habitat) was best described by stable isotope ratios of nitrogen and remigration tendency. Turtles that returned to the open ocean had significantly lower nitrogen ratios than those animals that remained in the neritic zone and their diets retained a substantial contribution of epipelagic prey items. The diet composition of neritic turtles, on the other hand, consisted primarily of estuarine benthic invertebrates during the summertime and autumn foraging season but shifted toward pelagic jellyfish, fish, and <italic>Sargassum</italic> during the overwintering period. Oceanic turtles likely came from open ocean regions prior to entering the summer foraging grounds while neritic turtles likely overwintered at the edge of the Gulf Stream. The agreement between the dietary compositions and migration patterns between the two groups of turtles suggest that these feeding and habitat use strategies were persistent characteristics in the turtles I sampled. My work has improved our understanding of sea turtle habitats in North Carolina estuaries and identified their migratory destinations and overwintering habitats. I hope that this work lays the groundwork for future studies that will explore how variation in habitat use and feeding strategies are manifested in life history traits that affect fitness directly, such as survivorship, growth rates, stage durations, and fecundity.</p> / Dissertation

<p>Whether through sea level rise, farmland abandonment, or wetland restoration, agricultural soils in coastal areas will be inundated at increasing rates, renewing connections to sensitive surface waters and raising critical questions related to environmental tradeoffs. Wetland restoration in particular is often implemented not only to promote wildlife habitat, but also to improve water quality through nutrient removal, especially in agricultural catchments. The microbial process of denitrification is the central mechanism of nitrogen removal in wetlands and flooded soils, and can be seen as a potential environmental benefit of flooding agricultural lands. While denitrification undoubtedly can remove nitrogen from soil and surface water, higher soil moisture or flooding in wetland soils can also increase the production of greenhouse gases, specifically nitrous oxide and methane, representing a potential environmental tradeoff. Understanding the likely benefits of denitrification and the likely greenhouse gas costs of wetland restoration could help inform environmental policies concerning wetland restoration. </p> <p>Determining whether restored wetlands are larger sources of greenhouse gases compared to contrasting land use types (agriculture and forested wetlands) was the first goal of this dissertation (Chapter 2). We measured gas fluxes from soil and water to the atmosphere, and related environmental variables, in four sites over two years to estimate fluxes of the three major greenhouse gases. We found that carbon dioxide was the major contributor to the radiative balance across all sites, but that in the agricultural site and one of the forested wetland reference sites, nitrous oxide was the second most important contributor. Many studies have shown that methane is more important that nitrous oxide in most freshwater wetlands, as we found in the other forested wetland reference site and in flooded parts of the restored wetland. Overall, we did not find higher greenhouse gas fluxes in the restored wetland compared to agricultural soils or forested wetlands.</p> <p>The controls over nitrous oxide are especially complex, because it can be produced by two complementary processes, nitrification and denitrification, which generally occur under different conditions in the environment. In Chapter 3, we determined the soil and environmental factors that best predicted nitrous oxide fluxes for a subset of our data encompassing gas fluxes measured in November 2007. We found that soil temperature and soil carbon dioxide flux, along with ammonium availability and denitrification potential, were good predictors of nitrous oxide (adj R<super>2</super>=0.81). Although the nitrous oxide model did not perform as well when applied to data from another sampling period, we expect to further develop our modeling efforts to include possible non-linear temperature effects and a larger range of environmental conditions. </p> <p>In Chapter 4, we present results of a stable isotope tracer experiment to determine the relative contribution of nitrification and denitrification to nitrous oxide fluxes in these different land use types, and to determine the response of these processes to changing soil moisture. We added two forms of nitrogen-15 to intact soil cores to distinguish nitrification from denitrification, and subjected the cores to drainage or to a simulated rain event. We found that across the range of soil moisture, the fraction of nitrous oxide produced by denitrification did not change, but within each soil type there was a response to the simulated rain. In mineral soils, the nitrous oxide fraction increased with increasing soil moisture, with the highest mole fraction [N₂O/(N₂+N₂O)] in the agricultural soils, while in the organic soils there was no change or even a decrease. The fraction of nitrous oxide derived from coupled nitrification-denitrification increased with increasing soil moisture, and was much higher than that from denitrification alone in the more organic soils. This suggests that, in these saturated acid-organic soils, nitrification plays an important and underappreciated role in contributing to nitrous oxide fluxes from freshwater wetlands. The results from the laboratory experiment were consistent with patterns we saw in the field and help explain the differential contribution of nitrification and denitrification to nitrous oxide fluxes in different land use types in coastal plain wetlands of North Carolina. </p> <p>Overall, we found that both nitrification and denitrification contribute to nitrous oxide fluxes in coastal plain wetlands in North Carolina, and that nitrification is an especially important source in acid-organic soils under both field-moist and saturated conditions. Although freshwater wetlands, with an average nitrous oxide mole fraction of 0.08, are generally seen as being insignificant sources of nitrous oxide, our study sites ranged from 0.10 to 0.30, placing them closer to agricultural fields (0.38; Schlesinger 2009). Although the ecosystems in our study produced more nitrous oxide than expected for freshwater wetlands, we found no significant tradeoff between the local water quality benefits conferred by denitrification and the global greenhouse gas costs in the restored wetland. These results suggest that, from a nitrogen perspective, wetland restoration in coastal agricultural lands has a net environmental benefit.</p> / Dissertation

Increased knowledge of stock mixing and migration patterns of Atlantic bluefin tuna (Thunnus thynnus) is required to appropriately manage and conserve declining populations. The nursery origin of giant bluefin tuna present in the Gulf of St. Lawrence was identified using stable carbon (δ13C) and oxygen (δ18O) isotopes in sagittal otoliths. Anthropogenic and natural processes are capable of impacting atmospheric and oceanic concentrations of δ13C and δ18O, affecting otolith concentrations. Therefore, inter-decadal variation of δ13C and δ18O in the otolith cores (corresponding to the first year of life) of bluefin tuna was examined prior to stock predictions and temporal variability was detected in both isotope ratios. Significant changes in both δ13C and δ18O were recorded in the otolith cores of individuals with birthdates between 1947 and 2003. Both δ13C and δ18O varied significantly as a function of year of birth, with δ13C decreasing and δ18O increasing over the time period investigated (-2.39×10-2 and 5.78×10-3 per year, respectively). The rate of change in otolith δ13C was nearly identical to the reported rates of atmospheric δ13C depletion, recently attributed to the burning of fossil fuels (referred to as the Suess effect). Observed shifts in otolith δ18O were less pronounced and likely linked to changing physicochemical conditions (i.e. salinity) in oceanic reservoirs over the time period investigated. The results show that otolith cores of bluefin tuna effectively track inter-decadal trends and record past oceanic δ13C and δ18O levels. After adjusting for inter-decadal trends, the isotopic composition of milled otolith cores of giants from three decades (1970s, 1980s, 2000s) and three regions were compared to otolith δ13C and δ18O values of yearling bluefin tuna collected from eastern and western nurseries. Maximum likelihood estimates indicated that 99% of bluefin tuna caught in the Gulf of St. Lawrence fishery originated from the western nursery, with no significant differences among the decades and regions examined. Results suggest that little to no mixing of eastern and western populations of adult bluefin tuna occurs in the Gulf of St. Lawrence, making it important for the management and conservation of the declining western population.

Veins are ubiquitous features in deformed rocks. Despite observations on syntectonic veins spanning two centuries, fundamental questions remain unanswered. Their origin as fractures is largely established but it is still not known why these fractures initiate where they do and how the vein evolves once started. We studied veins from the Lower Ordovician Mazarn Formation in the Arkansas’ Ouachitas combining textural observations, stable isotopes, fluid inclusions, SEM-based cathodoluminescence and electron back-scattered diffraction to understand the initial stage of vein formation, its later evolution, the role of fluids and their environment of formation. The veins are located at boudin necks and are synchronous with cleavage formation. Texturally, veins are characterized by veinlets (thin veins between 5 and 25 μm thick) that parallel the vein-host interface and fibers (columns of quartz or calcite) perpendicular to the vein-host interface between 30 and 350 μm wide. Veinlets are localized fractures filled with quartz. The crystallographic orientation of the precipitated material in veinlets is inherited from host grains at the micron scale and replicated as fibers’ lengths grow to centimeters. The vein-forming fluid was cyclically supersaturated yet never very far from saturation. δ18O values of vein quartz and host are within 2‰ of each other suggesting that the fluid was rock-buffered. Nevertheless, δ18O and δ13C define a ‘J’ shaped trend. Although it is not possible to date any portion of this curve, the simplest explanation is that the fluid evolved from rock-buffered in a closed system to fluid-dominated in an open system. The range of pressure-temperature conditions of vein formation is between 275 and 385 °C and 1100 and 3400 bars, from fluid inclusions and quartz-calcite oxygen isotopes thermometry. By examining a vein from tip to middle, we have established a sequence of events from inception to maturity in vein growth. Vein formation starts with folding followed by flattening of resistant sandstone layers which in turn gives rise to boudinage. Boudinage formation allowed for fracture localization along boudin-necks. The vein grew by the repeated addition of veinlets in the neck region. Recrystallization later modified the fibers by obliterating some evidence of the veinlets and moving fiber walls.

We test the fidelity of shallow-water gastropod skeletons as multi-proxy archives of seasonal paleo-environmental change by performing isotopic and trace-metal analyses on specimens of Conus ermineus from the Gulf of Mexico. Four adult specimens were collected from Stetson Bank in the Flower Garden Banks National Marine Sanctuary during the summer of 2002. Shell samples were milled along axes of growth to produce time-series profiles spanning up to eight years. We corrected the profiles for growth rate effects and compared the tuned results with in situ temperature and salinity records at the reef surface and temperature profiles from nearby surface buoys. Examination of sample densities in &#948;18O cycles shows that shell growth is faster during summers and slower during winters. Tuning the profiles versus time yields &#948;18O values that co-vary closely with seasonal temperatures to a high degree of coherency (R2 = 0.84). The &#948;13C profiles show cyclic variation modified by ontogenetic decreases in &#948;13C. These ontogenetic trends are attributable to decreasing metabolic efficiency, while seasonal cycles reflect hydrographic changes in the gastropods’ habitat. Salinity and &#948;13C of dissolved inorganic carbon show a strong correlation at Stetson Bank (R2 = 0.80), and early summer shell &#948;13C minima coincide with local salinity minima during times of peak river discharge. The terminations of these &#948;13C minima occur during annual upcoast reversals of shelf currents in this area. These effects are augmented by summer stratification and productivity minima that further decrease seawater &#948;13C. Sr/Ca ratios increase through ontogeny, most likely due to decreasing metabolic efficiency. However, seasonal variations in Sr/Ca profiles show strong similarity with &#948;18O profiles, confirming the temperature dependence of Sr/Ca and minimal influence of salinity on shell &#948;18O at Stetson Bank. The results of this study show that tuned &#948;18O and Sr/Ca profiles can be used to reconstruct seasonal paleotemperatures. Carbon isotope profiles and environmental data also demonstrate the utility of Conus &#948;13C as a proxy for freshwater flux and shelf circulation.

This study explored the effects of seasonal variability on the geochemistry of sinking pthesiss and on the nitrogen cycle of the Cariaco Basin. Pthesis fluxes were measured at the base of the euphotic zone (the depth of 1% of photosynthetically active radiation - PAR) with drifting sediment traps during months of upwelling and non-upwelling regimes from March 2007 to November 2009. Flux estimates were analyzed in the context of seasonal variations in sea surface temperature, primary productivity, and chlorophyll a concentrations using data generated by the CARIACO Time-series Program as well as satellite data. Additionally, nine years (1996-2000 and 2004-2007) of nutrients, phytoplankton taxonomy and δ15N of sinking pthesis data within the twilight zone (225 m) from the CARIACO Time-series Program were examined. Results showed that the flux of organic matter responded to changes in surface chlorophyll a but not to primary production. Sinking organic matter decreased by an order of magnitude from the base of the euphotic zone to the oxic-anoxic interface; most of the organic matter produced in surface waters was remineralized before leaving the upper 50-100 m. Lithogenic material often represented a large fraction of the flux. Isotopic analyses showed that 13C/12C ratios of sinking organic carbon were enriched (~-19‰) during the upwelling period and depleted during relaxation (~-23‰). This reflects seasonal changes in inorganic carbon utilization by phytoplankton and suggests that the δ13C of organic carbon in Cariaco sediments can be used as a proxy for carbon fixation by primary producers. The δ15N of the settling flux was influenced by the strength of the upwelling and the presence of the nitrogen fixer Trichodesmium thiebautii in the basin in different seasons; the 15N/14N ratio of sinking nitrogen reflects both imported and local nitrogen fixation signals. This result argues against previous interpretations of the δ15N from the basin's sedimentary record, which suggested that the nitrogen isotopic composition of flux is influenced by denitrification at the oxic-anoxic interface. Dissolved gas samples from the Cariaco eastern and western sub-basins from September 2008 (non-upwelling) and March 2009 (upwelling) were studied to assess the production of biogenic nitrogen gas through mass spectrometric N2/Ar ratiometry. Excess nitrogen gas indicated that upwelling affects the intensity of denitrification at the oxic-anoxic interface. In four of the six stations the concentration of biogenic nitrogen gas at the oxic-anoxic interface was 2.7-6.1 µM N higher during the upwelling period than during the relaxation season (p< 0.001), implying that denitrification in the basin was stimulated by the vertical flux of organic matter and/or the ventilation of the oxic-anoxic interface by oxygenated and nutrient-rich intermediate Caribbean waters.

Stable isotopes in ice cores drilled in the polar and high-mountain region have been used intensively to reconstruct past climatic changes and atmospheric dynamics. However, no similar studies have been conducted on perennial ice accumulations in caves due to a limited understanding of the links between the external and cave environments, and the way in which the climatic signal can be recorded by the cave ice. In this thesis, we successfully designed and build a research methodology for the reconstruction of past climatic changes based on perennial ice accumulation in caves, using as example the Scarisoara Ice Cave, Romania. The ice block in this cave preserves a large variety of candidate proxies for both past climate and environmental changes, the most significant ones being the stable isotopic composition of the ice (a proxy for air temperature) and pollen remains. The ice block has formed by the successive accumulation of layers formed by the freezing of water accumulated from late summer through mid-autumn precipitation. An original method has been developed for the reconstruction of the stable isotopic composition of water before freezing, and further, of the late summer air temperature. Pollen in the ice has been found to reflect changes in surface vegetation at both local and regional scale. A 22 m long ice core has been extracted from the ice block, and stable isotope analyses were performed at high resolution on its entire length. Twenty-sex radiocarbon ages have been used to derive a precise depth-age model for this core. The stable isotope data covers almost the entire Holocene, between 0.09 and 9.75 ka BP. The first order fluctuation broadly follows the orbitally induced Northern Hemisphere September insolation, with a minimum in the early Holocene, a slow climb towards a maximum at ~5.0 ka, followed by a very slow cooling towards the present, accentuated after ~0.5 ka. Superimposed on the long-term variations a series of rapid cooling events (RCE) are recorde, the most notable ones being at 9.5 ka, 8.2 ka, 7.9 ka, 6 ka, 4.2 ka, 3.2 ka and 0.9 ka. The timing of these RCEs agrees remarkably well with the Holocene rapid climatic changes and the ice rafted debris (IRD) events in the North Atlantic (NA). Our data suggests that the general trends of temperature changes in mainland Europe during the Holocene were governed by changes in solar output. RCEs were synchronous with NA IRD events, the NA climatic signal originating from sea surface temperature changes and being amplified by atmospheric dynamics. The stable isotope data spanning the past 2000 years clearly shows four climatic events over this interval, attributed to the Roman Warm period (RWP), the Dark Ages Cold Period (DACP), Medieval Warm Period (MWP) and the Little Ice Age (LIA). Our data suggests that air temperature was highly variable during the LIA and more stable during the warm MWP and RWP. As ice caves were described in many parts of the world otherwise poorly represented in ice-based paleoclimatology, the results of this study could open a new direction in paleoclimatic research, so that an array of significant paleoclimate data can be developed based on their study.

The global phenomenon of burgeoning coastal population growth has led to coastal watershed landscape transformation and ecosystem degradation, prompting policy-makers to set limits on freshwater withdrawals and labile nutrient loads. Important components of Florida’s economies lie in the state’s expansive coastal zone; the organisms driving the billion-dollar recreational fishing industry are rooted in coastal habitats, while the agriculture and real-estate industries sprawl throughout numerous coastal watersheds. This study aimed to identify the connections between anthropogenic land use and essential juvenile fish nursery habitats within the coastal zone, which is the first critical step for sustaining the ecology and related economies of the region. The need for this study arises from the fact that these economies are interconnected through nitrogen, and therefore nitrogen management can influence their prosperity or collapse. Juvenile fish nursery habitats are located in waters that receive nitrogen from adjacent landscapes. Runoff delivers nitrogen derived from human nitrogen use and processing within the watersheds to the juvenile fish nursery habitats. Ecosystem managers must understand that although copious amounts of nitrogen applied to land may ultimately support nursery habitat foodwebs, overwhelming nitrogen loads may also create algal blooms that decay and cause lethal hypoxic events leading to ecosystem degradation. This study aims to pinpoint the specific nitrogen sources that support primary production and ultimately fish production in watersheds dominated by agricultural landscapes and residential neighborhoods. Stable isotopes are versatile tools used to identify these connections. The nitrogen and carbon compounds that make up the moieties of an ecosystem inherently carry information on major nitrogen sources, trophic structure as well as the crucial information concerning dominant nitrogen removal and transformative processes that occur within sediments. Specifically in this study, the stable isotopes of carbon and nitrogen of dissolved inorganic nitrogen, primary producers, and fish were used to identify 1) the connections between urban and agricultural landscapes and the nutrients that percolate through the foodweb, 2) the primary producers that support fish biomass, 3) the origins of sedimentary organic matter that can provide new nitrogen via recycling, and 4) the heterogeneous function of fish nursery habitats in polluted systems. This study was conducted during the region’s wet and dry seasons and in over thirty watersheds that differ from each other in terms of size and anthropogenic influence. In agricultural watersheds, nitrogen derived from row crops and tree crops ultimately supported fish production during the wet season. Convective afternoon thunderstorms coupled with runoff delivered nitrogen from the landscape to receiving waters. These nutrients supported phytoplankton which deposited into the sediments and supported benthic foodwebs. During the dry season, nitrogen derived from row crops and nitrogen transformation in the sediments ultimately supported fish production. In this case, irrigation water used for agriculture delivered nitrogen from lands covered with row crops to the nursery habitats in receiving waters. The dry season was characterized by the nitrogen transformation process known as dissimilatory nitrogen reduction to ammonium (DNRA), where biologically available nitrate is converted to biologically available ammonium. Phytoplankton deposits, most likely delivered during the wet season, were recycled through the slow burning DNRA processes, which provided nitrogen for the benthic microalgae that dominated in the dry season. These organisms in turn supported benthic communities which ultimately supported dry season fish production.  In small urban watersheds, nitrogen derived from septic tanks, lawn irrigation, leaky sewage pipes, and atmospheric deposition ultimately supported fish production via phytoplankton, but unlike the nitrogen sources in agricultural watersheds, these sources (with the exception of atmospheric deposition) were seasonally consistent because a mechanisms to deliver nitrogen derived from septic tanks, lawn fertilizer, and leaky sewage pipes were, at least to some extent, available during both seasons. In polluted, tidal, fish-nursery habitats, the specific mechanism that allowed nursery habitats to decrease the ratio of mortality over growth rates of juvenile fish was not consistent among systems. These mechanisms were likely dependent on physical-chemical parameters and stream geomorphology. If the geomorphology or physical-chemical characteristics of nursery habitats are not adequate to set up an efficient nitrogen transfer process to fish, these habitats become more of a haven from predators rather than a source of food for fish.  This study has several implications for management. Managers must first recognize that microalgae are dominant supporters of tidal nursery foodwebs. Managers must define the relationship between nitrogen loads and fish abundance. If this relationship is unknown, the results of increasing nitrogen loads on fish production will remain uncertain; foodwebs in nursery habitats may collapse due to eutrophication, or fish abundance may increase due to increases in food supply. Connectivity factors derived from stable isotope mechanistic mass-balance models can be used as measurable targets for groups of watersheds. The use of wetlands as nitrogen remediation tools may not be effective at removing nitrogen; nitrogen transformation processes such as DNRA likely outweigh removal processes in wetland soils.

Sandy beach ecosystems have been studied worldwide; however, ecological data are sparse for the extensive barrier islands of Florida. Accordingly, I investigated the feeding patterns of the ghost crab (Ocypode quadrata), a dominant omnivore inhabiting beaches along the Floridian coast. Density data was collected for ghost crabs and swash macroinfaunal prey. In addition, I utilized stable isotopes in conjunction with the mixing models IsoSource and SIAR to characterize diets of ghost crabs across three barrier islands in spring and summer 2011. Results showed that ghost crabs at Cayo Costa feed primarily on swash macroinfauna, while those from Anclote Key shifted their diet to one comprised primarily of semi-terrestrial amphipods. However, at Honeymoon Island, ghost crab isotopic signatures were best explained by a mixed diet of both macroinfauna and wrack-associated prey. The unique consumption of wrack fauna at Anclote Key co-occurs with comparatively low infaunal densities and biomass, and modified ghost crab behavior due to trait-mediated effects. My results are novel because they suggest that wrack-associated fauna may be an important food source for ghost crabs in certain beach regimes.

Consumers in marine and estuarine environments have a strong reliance on planktonic and benthic primary production. These two basal resources form the foundation of aquatic food webs, yet the abundance of phytoplankton and benthic algae are frequently inversely related due to competition for light and nutrients. As a result, optimal habitats for benthic and planktonic consumers vary spatially and temporally. To investigate these trends, three studies were conducted focusing on light attenuation and basal resources in a bay, river, and on a continental shelf. δ13C and δ15N stable isotopes can be used as endogenous tracers to determine both the trophic level and basal resource use of consumers. δ13C values of primary producers are determined by the isotopic values of available CO2 and by the degree of photosynthetic fractionation (εp) that occurs during photosynthesis. εp by aquatic algae is greater in high CO2concentrations, high light, during slow growth rates, and for cells with a small surface area to volume ratio. Interaction among these parameters complicates prediction of algal εp in a natural setting, prompting the investigation as to which factors would impact εp and δ13C in a dynamic estuary. Community-level fractionation of an assemblage of filamentous algae, pennate diatoms, and centric diatoms grown on glass plates was found to be positively correlated with photosynthetically active radiation (PAR), resulting in higher δ13C values for organic matter in low-light conditions. These results support the concept that the low-light benthic environment may contribute to the widely observed phenomenon of ~5 / higher δ13C values in benthic algae compared to phytoplankton. Spatial and temporal variability in the isotopic baseline provides evidence of shifting biogeochemical controls on primary production. The West Florida Shelf in the eastern Gulf of Mexico transitions from a eutrophic ecosystem near the Mississippi River to an oligotrophic ecosystem in offshore continental shelf waters. Spatiotemporal variability in the δ13C and δ15N signatures of primary producers and fish populations were examined along this gradient. Muscle δ15N from three widely distributed fish species exhibited strong longitudinal isotopic gradients that coincided with the principal trophic gradient, whereas δ13C values of fish muscle and benthic algae were correlated with depth. The three fish species had relatively high site fidelity, as isotopic gradients were consistent between seasons and years. Isotopic mixing models showed all three fish species had a significant reliance on benthic algae as a basal resource. Dynamic models of the West Florida Shelf isotopic baseline were created using spatial data and satellite-derived water quality characteristics as predictors. Models were constructed using data from three fish species and tested on four other species to determine if the models could be extrapolated to new taxa. Both dynamic and static δ15N models had similar predictive capabilities, indicating a fairly stable δ15N baseline. The satellite-derived dynamic variables explained more variation in baseline δ13C than static spatial descriptors. Planktonic primary production can directly impact benthic food chains through phytoplankton deposition. A novel phytoplankton deposition detection method that combined water-column and benthic fluorometry with surficial sediment sampling was developed and assessed in a two-year study of the Caloosahatchee River estuary. Classifications based upon this detection method showed phytoplankton deposition dominated the upstream region and deposition was associated with reduced dissolved oxygen concentrations. Benthic algae dominated in downstream regions, particularly during low freshwater flow conditions when light absorption by colored dissolved organic matter was low. This same Caloosahatchee River estuary study was used to determine if zooplankton aggregate in regions with optimal basal resource availability. The isopod Edotia triloba was found to associate with chlorophyll peaks when freshwater velocity was constant. Chlorophyll peaks were offset downstream or upstream from isopod aggregations when freshwater flow was accelerating or decelerating, implying that phytoplankton and isopods have different response times to changes in flow. Temporal and spatial fluctuations in water quality and primary production introduce instability to aquatic consumers that primarily rely on one basal resource. The current global trends in eutrophication and increasing planktonic production are likely to be a liability for benthic consumers due to increased benthic hypoxia and light attenuation. The results of these studies indicate that both the location of consumers and their isotopic signatures can be impacted by factors, such as light attenuation, that control benthic and planktonic primary production.