Long term management plans for restoration of natural flow conditions through the Everglades increase the importance of understanding potential nutrient impacts of increased freshwater delivery on coastal biogeochemistry. The present study sought to increase understanding of the coastal marine system of South Florida under modern conditions and through the anthropogenic changes in the last century, on scales ranging from individual nutrient cycle processes to seasonal patterns in organic material (OM) under varying hydrodynamic regime, to century scale analysis of sedimentary records. In all applications, carbon and nitrogen stable isotopic compositions of OM were examined as natural recorders of change and nutrient cycling in the coastal system. High spatial and temporal variability in stable isotopic compositions were observed on all time scales. During a transient phytoplankton bloom, ä15N values suggested nitrogen fixation as a nutrient source supporting enhanced productivity. Seasonally, particulate organic material (POM) from ten sites along the Florida Reef Tract and in Florida Bay demonstrated variable fluctuations dependent on hydrodynamic setting. Three separate intra-annual patterns were observed, yet statistical differences were observed between groupings of Florida Bay and Atlantic Ocean sites. The POM ä15N values ranged on a quarterly basis by 7‰, while ä13C varied by 22‰. From a sediment history perspective, four cores collected from Florida Bay further demonstrated the spatial and temporal variability of the system in isotopic composition of bulk OM over time. Source inputs of OM varied with location, with terrestrial inputs dominating proximal to Everglades freshwater discharge, seagrasses dominating in open estuary cores, and a marine mixture of phytoplankton and seagrass in a core from the boundary zone between Florida Bay and the Gulf of Mexico. Significant shifts in OM geochemistry were observed coincident with anthropogenic events of the 20th century, including railroad and road construction in the Florida Keys and Everglades, and also the extensive drainage changes in Everglades hydrology. The sediment record also preserved evidence of the major hurricanes of the last century, with excursions in geochemical composition coincident with Category 4-5 storms.

Efforts that are underway to rehabilitate the Florida Bay ecosystem to a more natural state are best guided by a comprehensive understanding of the natural versus human-induced variability that has existed within the ecosystem. Benthic foraminifera, which are well-known paleoenvironmental indicators, were identified in 203 sediment samples from six sediment cores taken from Florida Bay, and analyzed to understand the environmental variability through anthropogenically unaltered and altered periods. In this research, taxa serving as indicators of (1) seagrass abundance (which is correlated with water quality), (2) salinity, and (3) general habitat change, were studied in detail over the past 120 years, and more generally over the past ~4000 years. Historical seagrass abundance was reconstructed with the proportions of species that prefer living attached to seagrass blades over other substrates. Historical salinity trends were determined by analyzing brackish versus marine faunas, which were defined based on species’ salinity preferences. Statistical methods including cluster analysis, discriminant analysis, analysis of variance and Fisher’s α were used to analyze trends in the data. The changes in seagrass abundance and salinity over the last ~120 years are attributed to anthropogenic activities such as construction of the Flagler Railroad from the mainland to the Florida Keys, the Tamiami Trail that stretches from the east to west coast, and canals and levees in south Florida, as well as natural events such as droughts and increased rainfall from hurricanes. Longer term changes (over ~4000 years) in seagrass abundance and salinity are mostly related to sea level changes. Since seawater entered the Florida Bay area around ~4000 years ago, only one probable sea level drop occurring around ~3000 years was identified.

The nursery effect is a process where juvenile fish utilize coastal habitats to help them survive before moving to their adult habitat. This process establishes an important link between marine ecosystems. This study examines the nursery effect and nursery habitat utilization in the Indian River Lagoon and Florida Bay systems, and the coral reefs adjacent to them. Quantitative and spatial techniques were utilized to identify patterns of presence and abundance and the size structure of select fish species. Spatial analyses were also used to investigate distribution patterns. Findings from this study suggest that several species utilize to a high degree the Indian River Lagoon and Florida Bay as nurseries. Furthermore, the abundance of adults on coral reefs is strongly connected to the presence of nurseries. This study has implications in fisheries management such as locating where juveniles of species develop. With such knowledge, better management plans could be implemented to ensure healthy fish stocks. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Anthropogenic disturbances are ubiquitous in coastal marine ecosystems. As such, more intensive monitoring efforts are necessary to conserve these valuable habitats. Bioindicators, organisms that predictably respond to changes in environmental variables, may be utilized in monitoring efforts to assess ecosystem functioning. To incorporate organisms into monitoring programs as bioindicators managers need to first understand the difference between the natural phenology of the focal organisms and their responses to different forms of anthropogenic disturbance. To determine if gammaridean amphipods could be used as indicators of changes in environmental quality in sub-tropical seagrass ecosystems, I conducted spatial and temporal surveys of amphipod communities in south Florida. Amphipod community structure varied significantly across sites and seasons. Variation in community structure was largely driven by macrophyte biomass, food availability, seasonally variable factors (epiphyte abundance, dissolved oxygen, salinity, and temperature), water-column nitrogen concentration, and factors related to freshwater input, including low Thalassia testudinum and high Halodule wrightii densities, and salinity. Amphipods are also susceptible to mechanical damage in seagrass habitats and could be used as indicators of ecological functioning of a region. A major source of mechanical damage in seagrass ecosystems is caused by boat propellers. I simulated propeller scars in continuous seagrass beds to investigate the effects of scarring on seagrass ecosystem functioning. Seagrasses located adjacent to propeller scars experienced a shift in the limiting resource from light to phosphorus. Amphipod community structure, however, was not impacted by scarring, but amphipod density was reduced in fragmented patches. To determine if plant-herbivore interactions were impacted by propeller scarring, we removed amphipods from half of the experimental plots and measured epiphyte biomass and community composition. Top-down control on epiphyte biomass or community composition by amphipods was not affected by fragmentation, despite reduced amphipod densities. My dissertation research demonstrates that amphipods could be incorporated into existing management programs in sub-tropical seagrass ecosystems as environmental indicators. Reduced amphipod densities in fragmented seagrass beds suggests that amphipods could also be used as ecological indicators, but more research is needed to determine the extent of the impacts of fragmentation on higher trophic levels.

Bacterio-phytoplanktonic coupling and bacterial growth efficiency (BGE) measurements were used to analyze microbial trophic dynamics and the influence of environmental factors in Florida Bay, Florida. Phytoplankton gross primary productivity (GPP) was measured using 24-hour in situ oxygen incubations; bacterial productivity (BP) was measured using 3H- thymidine incorporation. Weak bacterio-phytoplanktonic coupling was observed over the sampling period. BP was more influenced by local total nitrogen concentrations while GPP was more evenly distributed. BGE rates were low but consistent with marine and estuarine ecosystems worldwide. Results suggest that bacterioplankton growth in Florida Bay is relatively uncoupled from phytoplankton production, which may be due in part to the low levels of phytoplankton biomass in the water column, the large amount of seagrass-derived DOM production in this shallow lagoon, the loading of nitrogen and organic matter associated with terrestrial runoff, and/or their combination.

Modeling is a powerful tool that can be used to identify important relationships between organisms and their habitat (Guisan & Zimmermann, 2000). Understanding the dynamics of how the two relate to one another is important for conserving and managing ecosystems, but the extreme complexity of those ecosystems makes it very difficult to fully diagram. Unlike many other modeling techniques, Multivariate Regression Trees (MRTs) are not limited by a prior assumptions, pre-determined relationships, transformations, or correlations. MRTs have the power to provide both explanation and prediction of ecological data by producing simple models that are easy to interpret. This study proposed to use MRTs to evaluate and model relationships between Lucania parva and the environment and habitat of Florida Bay. Counts were transformed to presence-absence and abundance groupings. Models were first run using a variety of combination of response variables and all explanatory variables. Results of these models were used to select the best combination of response and explanatory variables in an effort to create a best fit model. Models indicated that Lucania parva populations are found in the dense (cover ≥50%), shallow water (<1.8 m) grass beds that occur in the western portion of Florida Bay. A best fit model was able to explain 63.7% of the variance with predictive error of 0.43.

This study examined mercury and methylmercury concentrations in shark species in order to determine differences between shark species and between locations. Stable isotope ratios were determined to see if interaction existed between approximate trophic level and mercury concentrations. Sharks were sampled from Florida Bay where muscle tissue biopsies and blood samples were extracted upon capture. Stable isotope ratios for carbon-13 (δ13C) and nitrogen-15 (δ15N) from freezedried blood samples were compared with levels of organic and inorganic mercury species from tissue samples in seven different shark species, focusing on blacknose, blacktip, bull, and lemon sharks. Pre-caudal length (PCL) was strongly correlated to mercury concentration and δ13C but not with δ15N. Ratios of δ15N between shark species were in agreement with observed trophic-level behavior of blacktip sharks feeding on blacknose sharks, indicated by greater values for δ15N ratios in blacktip sharks. Calculated length-normalized stable isotope ratio values correlated strongly to values for mercury concentrations in blacktip sharks, indicating a potential method for forecasting inorganic or organic mercury concentrations without the use of more expensive mercury tests. This calculation also provided validity for a new metric involving the use of stable carbon isotope ratio divided by length (PCL) to be compared with other metrics. Correlations between δ15N values and mercury values indicate some level of interaction between trophic level and quantity of mercury contaminants in shark muscle tissue.

An ecological risk assessment was conducted on the risk to fish of chemical contaminants detected in the habitat of Albula vulpes in South Florida, to evaluate whether contaminants may be a driver of declines in the recreational bonefish fishery. All available contaminant detection data from Biscayne Bay, Florida Bay, and the Florida Keys were compared to federal and state guidelines for aquatic health to identify Contaminants of Potential Ecological Concern (COPECS). For these COPECs, species sensitivity distributions were constructed and compared with recent detections at the 90th centile of exposure. Copper in Biscayne Bay was identified as the highest risk of acute and chronic effects to fish, followed by a risk of chronic effects from both the recently phased-out pesticide endosulfan in Florida Bay, and the pharmaceutical hormone estrone in the Florida Keys.

Everglades National Park is a hydro-ecologically significant wetland experiencing salinity ingress over the years. This motivated our study to map water salinity using a spatially weighted optimization model (SWOM); and soil salinity using land cover classes and EC thresholds. SWOM was calibrated and validated at 3-km grids with actual salinity for 1998–2001, and yielded acceptable R2 (0.89-0.92) and RMSE (1.73-1.92 ppt). Afterwards, seasonal water salinity mapping for 1996–97, 2004–05, and 2016 was carried out. For soil salinity mapping, supervised land cover classification was firstly carried out for 1996, 2000, 2006, 2010 and 2015; with the first four providing average accuracies of 82%-94% against existing NLCD classifications. The land cover classes and EC thresholds helped mapping four soil salinity classes namely, the non saline (EC = 0~2 dS/m), low saline (EC = 2~4 dS/m), moderate saline (EC = 4~8 dS/m) and high saline (EC >8 dS/m) areas. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

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.