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The spatial and temporal distribution of modern diatom assemblages in surface sediments, on the most dominant macrophytes, and in the water column at 96 locations in Florida Bay, Biscayne Bay and adjacent regions were examined in order to develop paleoenvironmental prediction models for this region. Analyses of these distributions revealed distinct temporal and spatial differences in assemblages among the locations. The differences among diatom assemblages living on subaquatic vegetation and sediments, and in the water column were significant. Because concentrations of salts, total phosphorus (WTP), total nitrogen (WTN) and total organic carbon (WTOC) are partly controlled by water management in this region, diatom-based models were produced to assess these variables. Discriminant function analyses showed that diatoms can also be successfully used to reconstruct changes in the abundance of diatom assemblages typical for different habitats and life habits. To interpret paleoenvironmental changes, changes in salinity, WTN, WTP and WTOC were inferred from diatoms preserved in sediment cores collected along environmental gradients in Florida Bay (4 cores) and from nearshore and offshore locations in Biscayne Bay (3 cores). The reconstructions showed that water quality conditions in these estuaries have been fluctuating for thousands of years due to natural processes and sea-level changes, but almost synchronized shifts in diatom assemblages occurred in the mid-1960’s at all coring locations (except Ninemile Bank and Bob Allen Bank in Florida Bay). These alterations correspond to the major construction of numerous water management structures on the mainland. Additionally, all the coring sites (except Card Sound Bank, Biscayne Bay and Trout Cove, Florida Bay) showed decreasing salinity and fluctuations in nutrient levels in the last two decades that correspond to increased rainfall in the 1990’s and increased freshwater discharge to the bays, a result of increased freshwater deliveries to the Everglades by South Florida Water Management District in the 1980’s and 1990’s. Reconstructions of the abundance of diatom assemblages typical for different habitats and life habits revealed multiple sources of diatoms to the coring locations and that epiphytic assemblages in both bays increased in abundance since the early 1990’s.

As top-level piscivores, Bald Eagles are a compelling subject for the study of territory dynamics and are highly representative of the distinctive suite of avian species that occupy Florida Bay. Despite successful recovery of Bald Eagles (Haliaeetus leuocephalus) throughout the species range, the population breeding within Florida Bay has not mirrored this trend. Beginning in the late 1980s, Florida Bay has suffered in its capacity to support species diversity and abundance as a result of extreme changes in hydrology related to altered flows of incoming freshwater. In fact, Bald Eagle territory use in Florida Bay has declined by as much as 43% as year to year variation and sensitivity to transitions between territory states have increased. Florida Bay’s populations of other large, conspicuous fish-eating birds, including Ospreys, Great White Herons, Roseate Spoonbills, and Reddish Egrets each exhibit a similar pattern of decline. The effects of environmental degradation throughout Florida Bay are magnified at higher trophic levels. The negative trend in territory occupancy is most pronounced in southeast Florida Bay whereas effects on territory occupancy in the northwest are minimal. The presence of spatial patterns in territory occupancy, despite regionally available breeding birds, suggests that individuals are evaluating differences in habitat quality for which certain territories are no longer considered viable. Building on our current understanding of the health of this population of Bald Eagles, we have successfully implemented modeling approaches that identify key territory breeding decisions. Loss of early breeding season activity (occupied and active territories) despite maintaining high breeding success indicates that changes in territory dynamics are the result of a failure to breed and not a reproductive failure. As such, future conservation actions should promote early breeding season activity (decisions by breeding pairs to initiate nesting) in areas of Florida Bay that were historically occupied but are now abandoned. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

Aquatic plants and submerged aquatic vegetation (SAV) are some of the most wide-ranging species and create important habitat for fish and wildlife in many ecosystems, including highly variable coastal ecotones. Mechanistically understanding factors controlling current distributions of these species is critical to project future distribution and abundance under increasing variability and climate change. I used a population-based approach to quantify the effects of spatial and temporal variability on life history transitions of the SAV Ruppia maritima L. (widgeongrass) in the highly dynamic Everglades-Florida Bay ecotone as a model to (1) examine which life history stages were most constrained by these conditions and (2) determine how management can promote life history development to enhance its distribution, an Everglades restoration target. Ruppia maritima life history transitions were quantified in a series of laboratory and field experiments encompassing a ra nge of abiotic and biotic factors known to affect seagrass and SAV (salinity, salinity variability, temperature, light and nutrients and seed bank recruitment and competition). These studies revealed that R. maritima life history varied east to west across the Everglades ecotone, driven by multiple gradients in abiotic factors that constrained different life history transitions in distinct ways. Based on this examination, persistence of SAV populations from dynamic coastal environments is highly dependent on large reproductive events that produce high propagule densities for recruitment. Large productive meadows of SAV also depend on high rates of clonal reproduction where vegetation completely regenerates in a short amount of time. Therefore, in hydrologically variable systems, maintenance or increases in SAV reproduction is required for population persistence through recruitment. However, SAV communities that do not experience high rates of sexual reproduction are dependent on successful seed germination, seedling and adult survival and clonal reproduction for biomass production and maintenance. Seedling survival and to a lesser extent, adult survival, are bottlenecks that can limit life history transitions under highly variable hydrological conditions. To ensure long-term survival in these communities, management activities that increase survival and successful life history development through these critical stages will be beneficial. If not, SAV populations may become highly reduced and ephemeral, providing less productive habitat. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

Human activities in the past century have caused a variety of environmental problems in South Florida. In 2000, Congress authorized the Comprehensive Everglades Restoration Plan (CERP), a $10.5-billion mission to restore the South Florida ecosystem. Environmental projects in CERP require salinity monitoring in Florida Bay to provide measures of the effects of restoration on the Everglades ecosystem. However current salinity monitoring cannot cover large areas and is costly, time-consuming, and laborintensive. The purpose of this dissertation is to model salinity, detect salinity changes, and evaluate the impact of salinity in Florida Bay using remote sensing and geospatial information sciences (GIS) techniques. The specific objectives are to: 1) examine the capability of Landsat multispectral imagery for salinity modeling and monitoring; 2) detect salinity changes by building a series of salinity maps using archived Landsat images; and 3) assess the capability of spectroscopy techniques in characterizing plant stress / canopy water content (CWC) with varying salinity, sea level rise (SLR), and nutrient levels. Geographic weighted regression (GWR) models created using the first three imagery components with atmospheric and sun glint corrections proved to be more correlated (R^2 = 0.458) to salinity data versus ordinary least squares (OLS) regression models (R^2 = 0.158) and therefore GWR was the ideal regression model for continued Florida Bay salinity assessment. J. roemerianus was also examined to assess the coastal Everglades where salinity modeling is important to the water-land interface. Multivariate greenhouse studies determined the impact of nutrients to be inconsequential but increases in salinity and sea level rise both negatively affected J. roemerianus. Field spectroscopic data was then used to ascertain correlations between CWC and reflectance spectra using spectral indices and derivative analysis. It was determined that established spectral indices (max R^2 = 0.195) and continuum removal (max R^2= 0.331) were not significantly correlated to CWC but derivative analysis showed a higher correlation (R^2 = 0.515 using the first derivative at 948.5 nm). These models can be input into future imagery to predict the salinity of the South Florida water ecosystem. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

Understanding and resolving the water quality problems that Florida Bay has endured requires an understanding of its salinity drivers. Because salinity is the prime factor that drives estuarine ecosystem, Florida Bay’s ecosystem health depends on the correct salinity balance of the Bay. In this thesis, the Regional Oceanic Modeling System - a hydrodynamic prognostic model -was implemented on Florida Bay and it was tailored for shallow waters. Results show that the model captures most of the salinity spatial and temporal variability of Florida Bay. Furthermore, it establishes the role of the major drivers like evaporation, precipitation, and runoff on Florida Bay’s salinity. The model resolves region specific salinity drivers in all four areas of Florida Bay characterized by their own salinity regimes. The model was also able to reveal the impact of surface runoff on salinity in the later part of the year when evaporation increases. A new technique was developed to estimate the discharge and salinity of unmonitored small creeks north of Florida Bay. Those data were estimated from the relationship between net freshwater flux, runoff, and salinity. Model results revealed the importance of accounting for these small creeks to accurately simulate Florida Bay’s salinity. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Shallow water availability coupled with anthropogenic degradation of seagrass beds limits wading bird food resources in dynamic coastal ecosystems. Identifying prey species critical to wading bird reproductive success and the environmental drivers of key prey species abundance is important for understanding how environmental stressors influence prey and change the quality of foraging patches. Little Blue Herons (Egretta caerulea) are reportedly generalists eating insects, crustaceans, and fish; however, the proportions of prey items in the diet may shift spatially and temporally from freshwater to marine systems during breeding and non-breeding periods. I investigated prey selection by Little Blue Herons in Florida at the Great White Heron National Wildlife Refuge and the western Florida Bay, during 2016 and 2017 breeding seasons by investigating prey availability at low-tide locations along mudflats compared to stomach regurgitate samples collected from Little Blue Heron chicks 1 to 4 weeks old. Little Blue Herons selected Gulf toadfish (Opsanus beta) and prawns (Farfantepenaeus spp.) from the estuarine environment, but also consumed terrestrial prey (e.g. tree crabs) suggesting Little Blue Heron foraging habitat is not restricted to tidal flats. Additionally, these results support the characterization of Little Blue Herons as a generalist. After identifying important prey species, I modeled the associations of selected prey species with submerged aquatic vegetation density and abiotic variables to better understand habitat preferences and important habitat characteristics that drive prey density. Models support total seagrass density and algal density as having the greatest effect on prey selected by Little Blue Herons. Prawn density has a strong positive association with seagrass density. Gulf toadfish (Opsanus beta) and prawns (Farfantepenaeus spp.) had strong positive association with algae while pipefish (Syngnathidae) had a strong negative association with algae suggesting algae density in seagrass meadows should be considered when assessing the quality of seagrass meadows for Little Blue Heron prey and habitat suitability. My results varied from previous studies where prawns and gulf toadfish were associated with specific seagrass species. Therefore, some Little Blue Heron prey species in south Florida may not be affected by changes in submerged aquatic vegetation community composition if submerged aquatic vegetation densities remain constant. Studies are needed that clarify the complex interactions between prey and specific habitat metrics to validate the strength of landscape scale drivers of wading bird prey densities in dynamic coastal ecosystems and to determine how these communities will respond to anthropogenic environmental change. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

The heterogeneous landscape of Florida Bay provides habitats for a variety of predators and prey. This dissertation examined the bottom-up transfer of affects from environmental variability through prey composition up to competition and predation affects on top predator distribution and foraging ecology in Florida Bay. Line transect surveys for bottlenose dolphins and seabirds were conducted in Florida Bay during the summer months of 2002 - 2005. Photo-identification techniques were implemented to identify individual dolphins. Synoptic with this survey effort, habitat characteristics (temperature, salinity, dissolved oxygen, turbidity, chlorophyll a, depth and bottom type) and prey composition (bottom trawl or gillnet) were sampled. Comparison of envelope maps from generalized additive models determined that predictive capacity of dolphin habitat did not improve by incorporating fish distribution data. However, models of dolphin distribution based solely on environmental proxies of fish distribution resulted in high predictive capacity. During the 2005 summer, shark distribution was sampled using a longline. The abundance of sharks was only correlated to fish catch from trawls on a regional scale. Larger sharks, of species that may threaten dolphins, were only caught in the Gulf zone of the Bay. Analysis of dolphin distribution revealed high individual site and foraging tactic fidelity. Dolphins were spatially coincident with habitat characteristics that encouraged the use of each individual's preferred foraging tactic. Depth was identified as the primary variable determining dolphin foraging tactic choice. Depth plays a significant role in the benthic composition of Florida Bay, which subsequently impacts prey communities and affects dolphin distribution, foraging and social ecology. Ordinations determined that fish distribution was also principally affected by depth and bottom type. Shallow environments frequently corresponded with mudbank habitat (depth < 1m) where the sighting rates of seabirds (cormorants, osprey, pelicans, terns) and foraging dolphins peaked. In conclusion, subtle relief in South Florida's bedrock topography dramatically affect benthic composition within Florida Bay, providing patchy habitats for prey and predators. The Florida Bay ecosystem will change with expected sea level rise, including spatial shifts of mudbank habitats. Top predator populations in Florida Bay will be forced to modify their distribution and foraging ecology accordingly. / Dissertation

Florida Bay is a shallow, subtropical lagoon located south of the Florida mainland. Bordered by the Florida Keys to the east and south, and shallow mud banks to the west, the Bay is protected from wave action and is considered a low energy environment. Utilizing a 100 year bathymetric dataset the geomorphology of Florida Bay was examined to see if significant changes were occurring despite the lack of strong wave action and water circulation. Changes in bathymetry were investigated from using a high-resolution bathymetric dataset from 1890 and 1990. Analysis was concentrated on the three main ecological habitats of Florida Bay: seagrass beds, mud banks and basins. This study of changes in geomorphology revealed that percent coverage of seagrass beds was positively correlated to amount of shallowing, basins larger than 27 km2 have gotten deeper and the mud banks of Florida Bay have been migrating southward at approximately 1 m/y. The significant changes to bathymetry within Florida Bay reveal that the environment is quite dynamic despite being sheltered from open waters. Most importantly, the presence of the 1890 bathymetric dataset allows for remote sensing techniques to be used to follow geological processes.

Recent studies have characterized coastal estuarine systems as important components of the global carbon cycle. This study investigated carbon cycling through the microbial loop of Florida Bay by use of bacterial growth efficiency calculations. Bacterial production, bacterial respiration, and other environmental parameters were measured at three sites located along a historic phosphorus-limitation gradient in Florida Bay and compared to a relatively nutrient enriched site in Biscayne Bay. A new method for measuring bacterial respiration in oligotrophic waters involving tracing respiration of 13C-glucose was developed. The results of the study indicate that 13C tracer assays may provide a better means of measuring bacterial respiration in low nutrient environments than traditional dissolved oxygen consumption-based methods due to strong correlations between incubation length and δ13C values. Results also suggest that overall bacterial growth efficiency may be lower at the most nutrient limited sites.