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

Since the soils nutrient composition along with the associated biotic and abiotic factors direct the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies have been focused on sediment types with unique features characteristic of extreme environments. Red Sea lagoon ecosystems are environments with such unique features as they are highly saline. However, not much is known about the potential of their microbiomes to produce bioactive compounds. Here, we explored sediment types such as mangrove mud, microbial mat, and barren soil collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL) as sources for antibiotic bioprospecting. Our antibiotic bioprospecting process started with a metagenomic study that provides a more precise view of the microbial community inhabiting these sites and serves as a preliminary screen for potential antibiotics. Taking the outcomes of the metagenomic screening into account, the next step we established a library of culturable strains from the analyzed samples. We screened each strain from that library for antibiotic activity against four target strains (Staphylococcus aureus ATCC 25923, Escherichia coli dh5 α, Pseudomonas syringae pv. tomato dc3000 and Salmonella typhimurium dt2) and for the presence of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes known to support synthesis of secondary metabolites that act like antimicrobial agents. The metagenomics study showed a shift in dominant phyla consistent with a historical exposure to hydrocarbon contamination and that AKL unexpectedly displayed more contamination than RHL. This may be due to dominant phyla in AKL being consistent with early hydrocarbon exposure (when contamination levels are still high) and the dominant phyla in RHL being consistent with late hydrocarbon exposure (when contamination levels are lower as a result of an extended period of hydrocarbon degradation). Additionally, RHL samples showed a higher percentage of enzymes associated with antibiotic synthesis, PKS and NRPS. When considering sediment type, mangrove mud samples showed a higher percentage of enzymes associated with antibiotic synthesis than microbial mat samples. Taken together, RHL was shown to be the better location with an increased probability of successful antibiotic bioprospecting, while the best sediment type in RHL for this purpose is microbial mat. Moreover, the phylum Actinobacteria tends to be the common target for research when it comes to antibiotic bioprospecting. However this culture-independent metagenomic study suggests the tremendous potential of Proteobacteria, Bacteroidetes, Cyanobacteria and Firmicutes for this purpose. Taking into account that the metagenomic screen suggests other phyla beyond Actinobacteria for antibiotic bioprospecting, the culture-dependent experiments were not designed to target actinobacteria alone. A total of 251 bacterial strains were isolated from the three collected sediments. Phylogenetic characterization of 251 bacterial isolates, based on 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity of ≤ 98 % to other strain sequences in the NCBI database. We demonstrate that 52 of the 251 isolates exhibit the potential to produce an antimicrobial effect. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 52 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards all target strains. In conclusion, this study demonstrated the significant microbial diversity associated with Red Sea harbor/lagoon systems and their potential to produce antimicrobial compounds and novel secondary metabolites. To the best of our knowledge, this is the first study that has analyzed the microbiomes in Red Sea lagoons for antibiotic bioprospecting.

Atlantic Tarpon Megalops atlanticus support a catch-and-release fisheries in the United States and other territories such as Puerto Rico. Survival of angled fish is imperative to catch-and-release fishing yet numerous factors have yet to be looked at over a timescale to determine if laboratory and wild Puerto Rico tarpon experience increased stress and risk of mortality. To evaluate stress in simulated catch-and-release angling, laboratory trials were conducted over a 24-hour time scale with 2 varying intensities of simulated angling and various physiological parameters were explored. Blood samples concluded that simulating angling only had an interaction effect in time and fishing intensity in the factor of osmolality. In field studies, tarpon studied physiologically gave inconclusive results due to lack of a time scale. Field studies tracking mortality were completed by acoustic telemetry of angled fish in the San Juan Lagoon network. Studies resulted in a mortality that ranges from 4.5-20.5%.

Coastal wetland plants serve as ecological engineers in a physiologically stressful environment and the loss of coastal wetlands can cause negative effects throughout the estuarine system. Due to increased degradation of coastal habitats worldwide, interest in restoration has increased around the world. An understanding of the biotic processes affecting species distribution and diversity is critical for future conservation, management, and restoration of coastal wetlands. The purpose of my study was to test the effects of biotic interactions on native coastal wetland plants and determine how these interactions may be incorporated into current and future restoration projects. I had three primary goals for my dissertation. First, I evaluated the effectiveness of natural regeneration of coastal wetland communities following hydrological restoration. Second, I examined effects of biotic interactions between mangroves and other wetland species by experimentally testing: 1) trapping capabilities of early successional plant species on Rhizophora mangle propagules, 2) effects of pre-dispersal propagule damage on native mangrove species, 3) facilitative and competitive interactions between the plants Rhizophora mangle, Batis maritima, Sarcocornia perennis, and the fiddler crab, Uca pugilator using mesocosms. Third, I evaluated the combined effects of biotic and abiotic interactions on survival and growth of R. mangle propagules during their first year of establishment using a manipulative field experiment. Results from my study increase our knowledge of the importance of biotic interactions in coastal wetland communities, their role in early successional stages, and have direct applications to coastal wetland restoration and management.

This study combined documentation of four boat propeller scar types in Halodule wrightii seagrass beds in Mosquito Lagoon, Florida with manipulative field experiments to document scar recovery times with and without restoration. Scar types ranged from the most severe scar type (Type 1) with trench formation which had no roots or shoots in the trench, to the least severe (Type 4) scars that had no depth, intact roots and shoots shorter than the surrounding canopy. For 110 measured existing scars, the frequency of each scar type was 56% for Type 1, 10% for Type 2, 7% for Type 3, and 27% for Type 4. In the first manipulative experiment, experimental scars were created to document the natural recovery time of H. wrightii for each scar severity within one year. Type 4 scars recovered to the control shoot density at 2 months, while Types 1, 2, and 3 scars did not fully recover in one year. Mean estimated recovery for H. wrightii is expected in 25 months for Type 1, and 19 months for Types 2 and 3. For the second manipulative experiment, three restoration methods were tested on the Type 1 scars over a 1 year period. Restoration methods included: (1) planting H. wrightii in the scar trench, (2) filling the trench with sand, and (3) filling with sand plus planting H. wrightii. There was complete mortality of all transplants at 2 months and only 25% of scars retained fill sand after 1 year. With dense adjacent seagrass beds, natural recovery was more successful than any of my restoration attempts. Thus, I suggest that managers should concentrate on preventing seagrass destruction rather than restoration.

Algal blooms have caused significant losses in seagrass and macroalgae in the Indian River Lagoon, FL. To gain an understanding of these effects, samples of Gracilaria sp., Halodule wrightii, pinfish, and white mullet were taken throughout October and November of 2013. Samples from 2001 of Gracilaria sp., Halodule wrightii, Syringodium filiforme, Thalassia testudinum, pinfish, spotted seatrout, and white mullet were also obtained. Stable isotope data were obtained from these samples and compared by year and species. Halodule wrightii and pinfish had a significantly larger 2013 [delta]C13 values. Halodule wrightii also displayed lower total %C and total %N averages for 2013 when compared to 2001 data. These results may indicate a link between Halodule wrightii and pinfish, with pinfish consuming organisms that use Halodule wrightii as their source of nutrients. The location of collections also seemed to play a role in stable isotope values, as indicated by samples of Halodule wrightii.

The arsenic maximum contaminant level (MCL) for drinking water is likely to be lowered sometime in 2001 or 2002. If the MCL is lowered, it is speculated that there will be stricter limits imposed on the disposal and handling of arsenic-containing residuals. The purpose of this study is to determine the properties of drinking water residuals, including the chemical characteristics, the amount of arsenic that leaches in common residual handling and dewatering processes, and the hazardous potential of the residuals. Residual samples were collected from seven utilities with high arsenic concentrations in their raw water. Included in the study were four plants that coagulate with ferric chloride, two with aluminum hydroxide, and one softening plant. The residuals from each facility were acid digested and chemically characterized using ICP-AES to determine the total arsenic, aluminum and iron present. TCLP and California WET were performed to verify if the residuals were hazardous. Simulated lagoons were set up and monitored over a six-month period to determine the amount of arsenic that was leached to the liquid portion over time. Toxicity testing was performed on the residuals at 20% and 100% after two months and six months of storage. Bench-scale sand drying beds were used to dewater residuals, and the leachates were analyzed to determine if arsenic leached from residuals. The residuals were found to contain high levels of arsenic during the chemical characterization. However, all of the facilities passed the current TCLP limit of 5 mg/L. For all residuals, the California WET values were much higher than the TCLP values. In the lagoon study, redox potentials decreased and the arsenic and iron concentrations in the liquid portions increased. In the sand drying beds, very little arsenic leached; arsenic concentrations in the leachate were less than 10 ppb. Lagoon storage may not be a safe alternative for residuals containing arsenic. However, sand drying does not appear to present any threats. There were differences between the toxicity tests performed at 100% solids and 20% solids in the lagoon study. Some of the values increased and others decreased. Additionally, toxicity testing conducted after lagoon aging differed from earlier toxicity testing, due to the changing soluble arsenic. These discrepancies suggest that the test results can be affected by the percent solids and age of the residuals, and specific instructions should be given for consistent residuals testing. / Master of Science

A coastal lagoon is a landform that is influenced by natural processes and human activities. All human activities at the upstream, particularly agriculture and cultivation bring soil, waste, and other materials to the downstream area through the river drains into the lagoon. Even though its position is inland of water bodies, the lagoon is still affected by waves and winds from the sea. Additionally, coastal lagoon will be the depository place for sedimentation from the upland area. Segara Anakan (SA), which is located in Indonesia, is an example of a coastal lagoon area, which has a unique biophysical characteristic. The region has a great natural ability to ensure the sustainability of the interrelationships between terrestrial, estuarine and marine ecosystems in harmony and balance as a habitat for flora and fauna. The region is an area of migration of various types of protected animals and it is a place of breeding for diverse species of the shrimp and fish, which have a highly economical value. Segara Anakan lagoon (SAL), currently experiencing acceleration narrowed on its area due to a very intensive sedimentation from the mainland. The research aims to answer the question of how ecological dynamic occurs in the SAL area due to sedimentation. Achieving the objectives of this study required examining the morphology and land use changes with multitemporal remote sensing approaches. While, to assess the role of community participation and planning management strategies is using qualitative descriptive methods and SWOT analyze. The using of multitemporal remote sensing Landsat images is possible to analyze the morphological and land use changes with different time and sensors. These Landsat has image accuracy about 92.66%. It can be used for image interpretations resulting 13 classes of land use. The morphodynamics of SAL indicated by the changes of area of lagoon and accreted land and also the distance of coastlines during the periods 1979-2013. In addition, the land use or land cover also changes during that time. The bigger portions of land use changes are in the tropical and mangrove\'s forests. There are distinctive forms of participation in conservation efforts. The upstream community involvement in conservation tends to be different participating in the way of ideas, money, materials, properties, skills and expertise or social activities. In addition, the community at downstream area has a sufficiently high level of participation in environmental conservation. There are also strong relationships between the level of education and level of income and basic knowledge in conservation with the participation of SA conservation. The ecological dynamics of the SAL area are described with a historical time line. It is divided into three time periods: the 1970s - 1980s, the 1990s and from 2000 onwards. Each of these has occurrences that can lead to changes in the environment. The implementation of appropriate conservation technique can reduce the sedimentation rate. Hence, the synergic coordination measures between upstream and downstream regions are necessary in the future. Increasing community awareness and participation in the conservation by improving educational sector, providing information, and applying sustainable development land use are the ways to match human activities with the temporal and spatial dynamics of the coastal resources.

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

As ecosystems degrade globally, ecosystem services that support life are increasingly threatened. Indications of degradation are occurring in the Northern Indian River Lagoon (IRL) estuary in east central Florida. Factors associated with ecosystem degradation are complex, including climate and land use change. Ecosystem research needs identified by the Millennium Ecosystem Assessment (MA) include the need to: consider the social with the physical; account for dynamism and change; account for complexity; address issues of scale; and focus on ecosystem structure and process. Ecosystems are complex, self-organizing, multi-equilibrial, non-linear, middle-number systems that exist in multiple stable states. Results found are relative to the observation and the frame of analysis, requiring multi-scaled analytical techniques. This study addresses the identified ecosystem research needs and the complexity of the associated factors given these additional constraints. Relativity is addressed through univariate analysis of dissolved oxygen as a measure of the general health of the Northern IRL. Multiple spatial levels are employed to associate social process scales with physical process scales as basin, sub-basins, and watersheds. Scan statistics return extreme value clusters in space-time. Wavelet transforms decompose time-scales of cyclical data using varying window sizes to locate change in process scales in space over time. Wavelet transform comparative methods cluster temporal process scales across space. Combined these methods describe the space-time structure of process scales in a complex ecosystem relative to the variable examined, where the highly localized results allow for connection to unexamined variables. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection