In the eutrophic waters of the Indian River Lagoon (IRL), decreases in overall shellfish size have been reported, which may be related to coastal acidification. To understand the relationship between acidification and eutrophication, water samples from 20 sites spanning the IRL were collected and analyzed for dissolved nutrients and omega values in spring (dry season) and fall (wet season), 2016-2017. Additionally, three sites were sampled weekly to observe temporal variability of nutrients and omega values. For the IRL-Wide sampling, sites with higher dissolved nutrient concentrations showed lower omega values with significant negative relationships. Both sampling programs showed an overall positive linear relationship between salinity and omega values. This work suggests that salinity and dissolved nutrients have implications for acidification in the IRL and must be considered for future water quality, shellfish and coral reef restoration. / Includes bibliography. / Thesis (M.F.A.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

The Indian River Lagoon (IRL) FL, USA, is an Estuary of National Significance due to its economic and high biodiversity. Microbial populations are understudied in the IRL despite their numerous ecological services. A two-year, nineteen-site Lagoon-Wide Survey (LWS) was conducted to provide the first 16S rRNA amplicon sequencing data on the microbiome of the sediment in the IRL and determine how the microbiome changed in response to environmental and anthropogenic factors. The most influential variables that explained the variability between microbiomes were porewater salinity, total organic matter (TOM), and copper (Cu). These results correlated with some of the anthropogenic pressures the IRL faces such as freshwater discharges from St. Lucie Estuary (SLE), trace metal contamination, and the accumulation of fine-grained, highly organic sediment known as “IRL muck” (muck). Research then focused on determining the microbial differences between three sets of sample types: sediment from the IRL versus the SLE; sediment that had three muck characteristics versus those with zero; and high TOM sediment that had high Cu versus high TOM sediment that had low Cu. Differentially abundant prokaryotes between sample types were determined with novel indicator analysis techniques. One technique tested the effectiveness of an indicator list to separate samples based upon the product of the sensitivity and specificity of partitioning around medoids clustering in comparison to metadata classifications. The other technique allowed for the tracking of changes in the entire indicator microbiome. These new indicator analysis techniques were created using the original LWS data and tested to determine how sediment microbiomes responded during two opportunistic surveys: dredging of muck from an IRL tributary (Eau Gallie River) and Hurricane Irma. These studies have filled the knowledge gap regarding the unknown microbiome of the IRL and how sediment microbiomes respond to extreme events such as dredging and a hurricane. They also led to the development of new indicator analysis techniques that can be used by to track changes in the entire indicator microbiome. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

The Indian River Lagoon (IRL) spans approximately one-third of the east coast of Florida and faces numerous harmful algal blooms. The potentially toxic diatom, Pseudonitzschia, has been observed in many locations of the IRL. The goal of this study was to obtain a better understanding of the factors contributing to population dynamics of Pseudo-nitzschia in the southern IRL system. Bi-monthly surface water samples were collected for 18 months from five locations. Cell counts enumerated all microphytoplankton, and environmental data was collected at sampling sites throughout the study by the Indian River Lagoon Observatory Network. Six species of Pseudonitzschia were isolated and characterized through 18S Sanger sequencing and scanning electron microscopy, all showed toxicity. Surface water samples also showed domoic acid (DA) presence. We report the first known occurrence of Pseudo-nitzschia micropora in the IRL and the first known DA production from this taxon. / Includes bibliography. / Thesis (MS)--Florida Atlantic University, 2021. / FAU Electronic Theses and Dissertations Collection

Florida’s Indian River Lagoon (IRL) has experienced myriad anthropogenic impacts and knowledge on elasmobranchs (sharks and rays) in the southern IRL is lacking. A fishery independent survey (longline/gillnet) was implemented to 1) assess the effects of bait type [striped mullet (Mugil cephalus) versus Atlantic mackerel (Scomber scombrus)] and mesh size (15.2 cm versus 20.3 cm stretch mesh) on elasmobranch species composition, catch-per-unit effort, and size distributions and 2) characterize elasmobranch abundance and distribution. From 2016 - 2018, 630 individuals (16 species) were captured, more often in the gillnet than the longline. Catch-per-unit-effort was significantly higher with mullet than mackerel. Species composition differed among gears. Although dependent on gear, there was evidence of seasonal and spatial patterns in abundance and species composition. This study provides the first baseline abundance indices for many elasmobranchs in the IRL and develops the capacity to understand how elasmobranchs may respond to changes in this highly modified estuary. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

The objective of this research was to examine bottlenose dolphin (Tursiops truncatus) habitat use in the Indian River Lagoon (IRL) based on monthly relocation of photo-identified individuals, prey availability and environmental factors from 2003-2015. We focused on the variation of spatial and temporal abiotic and biotic factors and their influence on bottlenose dolphin habitat use patterns. Harbor Branch Oceanographic Institute (HBOI) conducted monthly photo-identification surveys along the length of the IRL and GPS locations of photographed dolphins were collected at the time of surveying. Stratified random samples of prey and environmental variables were collected monthly by the Florida Fish and Wildlife Conservation Commission (FWC) as part of the Fisheries-Independent Monitoring (FIM) program. Kernel density estimation was used to determine the magnitude-per-unit area of dolphins across a continuous raster surface of the IRL by wet and dry seasons each year, the values of which were used as a response variable in Classification and regression tree (CART) analyses with FIM fish community and environmental factors as predictors. Understanding how dolphins respond to environmental factors over time in the IRL could be used to predict future responses in estuaries and prioritize conservation and restoration actions. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

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

This study explored spatiotemporal patterns in movement, diet, and baseline phycotoxin concentrations in immature bull sharks (Carcharhinus leucas) of the Indian River Lagoon (IRL), an estuary of national significance that has been considerably impacted by multiple toxic harmful algal blooms (HABs). Long-term spatial use of the system was assessed for 29 acoustically tagged sharks over a 4 year period (2017–2020). Tissue samples for diet and toxin analysis were collected from a separate cohort of 50 individuals between 2018 and 2020. UPLC-MS/MS was used to screen tissues for 14 algal toxins. Young bull sharks were found to be mainly piscivorous and displayed high residency to the IRL as well as to specific regions of the IRL, with small activity spaces. Multiple phycotoxins were detected in screened tissues, indicating that young bull sharks in the IRL may be compromised by trophic transfer of HABs while they reside in this important nursery. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2021. / FAU Electronic Theses and Dissertations Collection

Contamination of recreational waters with fecal waste, indicated by the presence of enterococci, can have consequences for human and ecosystem health. The difficulty in determining the extent and origin of fecal pollution in dynamic estuarine systems is compounded by contributions from sources including septic tanks and agricultural runoff. This study investigated fecal pollution at five sites with variable hydrological conditions in the St. Lucie Estuary and Indian River Lagoon. The distribution and occurrence of enterococci was assessed using traditional cultivation. A human-associated microbial source tracking assay was validated and applied in these estuaries using qPCR. Results demonstrated a correlation between enterococci concentrations, rainfall, and salinity. The human-associated assay was sensitive and specific in the lab; however, human fecal pollution was not detected in the field even though samples contained high levels of enterococci. This study highlights the importance of expanding the range of water quality assessment. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

For over a decade, researchers at Harbor Branch Oceanographic Institute (HBOI) have conducted surveys of the bottlenose dolphin (Tursiops truncatus) population of Indian River Lagoon (IRL) in Florida. I have constructed a 4-stage population model using the statistical program R. The model is used to conduct a viability analysis by analyzing the relationship between birth, calf and adult survival rates. The power analysis compares survey frequency to expected confidence intervals in estimating abundance. The sensitivity analysis shows that the population is most sensitive to changes in adult survival, followed by birth rate and calf survival. The model shows a strong chance of viability over a 50 year time span. The population is vulnerable to long periods of decline if birth, calf or adult survival rates fall below certain thresholds. Overall, the model simulates the future impacts of demographic change, providing a tool for conservation efforts. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Seagrasses are important foundation species in coastal ecosystems. Genetic diversity of seagrasses can influence a number of ecological factors including, but not limited to, disturbance resistance and resilience. Seagrasses in the Indian River Lagoon (IRL), Florida are considered to be highly disturbed due to frequent events, like algal blooms, that impair water quality, reducing available light for seagrass growth. Halodule wrightii is a dominant seagrass throughout the IRL, but its genetic diversity has only been quantified in a few Gulf of Mexico and Florida Bay populations and little is known about its potential ecological consequences. I quantified the genetic variation of H. wrightii using microsatellite markers in the southern IRL to determine: (i) how disturbance history influenced genetic diversity, (ii) if morphology of clones was, in part, genetically controlled and related to disturbance history, and (iii) if genotypes showed phenotypic plasticity in response to disturbances. In the IRL, H. wrightii populations exhibited moderate genetic diversity that varied with disturbance history. The disturbance history of a population was classified by the variance in the percent occurrence of H. wrightii over a 16-year period. Genotypic richness and clonal diversity of H. wrightii increased with increasing disturbance histories. Other genetic diversity measures (e.g., allelic richness, observed heterozygosity) did not change with disturbance history. These findings suggest that impacts to seagrass coverage over time can change the genotypic composition of populations. When different genotypes of H. wrightii were grown in a common garden, differences in leaf characteristics among genotypes provided evidence that morphological trait variation is, in part, explained by genetic variance. The disturbance history of genotypes did not directly affect morphological traits. However, significant genotype x site (within disturbance history) interactions found greater variation in shoot density and below ground traits of H. wrightii genotypes from sites of intermediate disturbance history. Traits of H. wrightii were shown to be phenotypically plastic. Significant genotype x environment interactions for shoot density and height demonstrated that genotypes responded differently by increasing, decreasing, and not changing sizes in response to light reduction. Genetic diversity of H. wrightii has strong implications for ecological function in coastal communities. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection