Nutrient distribution correlates with discharge of freshwater from Franklin Lock and Dam structure (S-79) by delivery into the Caloosahatchee Estuary (CE) and out of this area, including the surrounding San Carlos Bay (SCB) and adjacent West Florida Shelf. This study analyzed the temporal and spatial distribution of nutrients along the CE waterway and illustrates the effects high freshwater discharge from S-79 has on the coastal and offshore environments, providing a potential source of nutrient input. This study consisted of a 7-station transect monitored biweekly from April 2005 thru August 2006 for nutrients, dissolved oxygen, chlorophyll a, and salinity, along with the corresponding freshwater discharge from S-79. High flow rates correlated (r²=0.7488) with decreased salinity downstream from S-79. At high discharge, over 140 m³ s-¹, nutrients were noticeably transported downstream to SCB; during extreme high flow rates of 285 m³ s-¹, it takes a little less than 4 days for a particle of water to travel from S-79 to the mouth of the estuary. There is evidence from the SATlantic ISUS deployment that pulses of water from S-79 correlated with downstream increased concentrations of nitrate on a daily temporal scale. The assumption that upstream estuarine waters are potentially carrying nutrients downstream can only be conjectured for high flow rates. Low flow rates (less than approximately 28 m³ s-¹) corresponded to hypoxia during the summer months of 2006. The highest chlorophyll a concentrations were found either during decreased flow rates or summer months. Chl a (>3.0 µm) in SCB and the mouth of the CE was above 4 µg l-¹ in July through October 2005 and ranged from 1.24 to 9.62 µg l-¹ in June through August 2006. Karenia brevis blooms were also present during this time. Nutrient loading rates into SCB provided enough DIN and DON to support the maintenance of K. brevis. Therefore monitoring and studying the amount of nutrient loading into coastal and offshore water can elucidate their importance on the surrounding ecology.

Harmful algal blooms (HABs, or "red tides") of the brevetoxin-producing dinoflagellate Karenia brevis occur periodically along Florida's Gulf coast. Mass mortalities of marine birds have long been associated with these blooms, yet there are few data documenting the accumulation of brevetoxins (PbTx) in the tissues of birds. Post-mortem evaluations were performed on 185 birds representing 22 species collected from October 2001 through May 2006 during red tide and non-red tide events to quantify their body burdens of brevetoxins. A variety of tissues and organs were selected for brevetoxin analysis including blood, brain, heart, fat, stomach or gut contents, intestinal contents or digestive tract, muscle, lung, liver or viscera, kidney, gonads, gallbladder and spleen. Brevetoxin levels in avian tissues ranged from K. brevis which may amass in various tissues of the body. As a consequence, the birds may exhibit acute brevetoxicosis during red tide events or show chronic accumulation effects during non-red tide events.

As human populations increase along coastal watersheds, the understanding and monitoring of Harmful Algal Blooms (or red tides) is an increasingly important issue. A consistent method for accurately detecting red tides using satellite measurements would bring tremendous societal benefits to resource managers, the scientific community and to the public as well. In the West Florida Shelf, blooms of the toxic dinoflagelate Karenia brevis are responsible for massive red tides causing fish kills, massive die-offs of marine mammals, shellfish poisoning, and acute respiratory irritation in humans. In this work, for the first time a long-term dataset (2002~2006) the MODerate Resolution Imaging Spectroradiometer (MODIS) is compared (i.e., matched-up) to an extensive data set of in situ cell counts of K. brevis; provided by the Florida Fish and Wildlife Conservation Commission's Fish and Wildlife Research Institute. The pairing of remote sensing data with near-coincident field measurements of cell abundance was successfully used to derive the basis for the development of an alternative ocean color based algorithm for detecting the optical signatures associated with blooms of K. brevis in waters of the West coast of Florida. Conclusions are geographically limited to the Central West Florida Shelf during the boreal Summer-Fall (i.e., the K. brevis blooming season). The new simpler Empirical approach is compared with other two more complicated published techniques. Their potential is verified and uncertainties involved in the identification of blooms of K. brevis are presented. The results shown here indicate that the operational NOAA method for detecting red tides in the Gulf of Mexico (Stumpf et al., 2003; Tomlinson et al., 2004) performs less accurately than the other two algorithms at identifying K. brevis blooms. The sensitivity and specificity of the Bio-optical (Cannizzaro, 2004; Cannizzaro et al., 2008) and Empirical algorithms are simultaneously maximized with an optimization procedure. The combined use of these two optimized algorithms in sequence provides another new monitoring tool with improved accuracy at detecting K. brevis of blooms. The ability of this Hybrid scheme ranges about 80% for both sensitivity and specificity; and the capability at predicting a correct red tides is 70%, and ~85% for non-blooms conditions. The spatial and temporal knowledge of K. brevis blooms can improve the direction of field monitoring to areas that should receive special attention, allowing better understanding of the red tide phenomenon by the scientific community. The relevant agencies can also develop more appropriate mitigation action plans, and public health guidance can be improved with the enhancement of sustainable costal management strategies.

The southwestern Florida shelf marine environment has often been characterized as oligotrophic, yet these waters can support large, high biomass, persistent phytoplankton blooms, including blooms of the toxin producing dinoflagellate Karenia brevis. Little is known regarding which major nutrient potentially limits primary production in these waters as both inorganic nitrogen and phosphorus concentrations are often near the limits of analytical detection and it is difficult to estimate what percentage of the dissolved organic pool is available for phytoplankton uptake. To assess the nutrient status of phytoplankton populations on the southwest Florida shelf, this project examines the particulate nutrient stoichiometry of ambient phytoplankton assemblages from 1998-2000 as part of the ECOHAB: Florida Program. Particulate C, N, P concentrations and particulate ratios display a large range of values across the West Florida Shelf (WFS). The average particulate stoichiometry is well above the classic Redfield ratio with a geometric mean of 410C:56N:1P. Frequency percentages of particulate ratio values to total sample number binned according to potential nutrient limitation indicate that 39% (C:N) of the data have values suggesting N limitation and that from 88% (N:P) to 95% (C:P) of the data have values which suggest P-limitation. It is difficult to discern whether phytoplankton biomass is truly P-limited as related to the nutrient regime on the WFS or whether detrital contributions, which can potentially be large on this shallow shelf, are skewing the N:P and C:P ratios towards higher values. Errors which could potentially be related to the different methodologies of determining C, N and P concentrations must also be considered when interpreting the particulate nutrient ratios. The data were also analyzed as subsets to determine near-shore to offshore, latitudinal, seasonal, inter-annual and K. brevis bloom versus non-bloom trends. The near-shore to offshore transect indicates decreasing concentrations of particulate C, N, P concentrations and increasing C:N, N:P, C:P ratios with increasing distance offshore. Particulate nutrient concentrations and particulate ratio values are very similar between the Tampa Bay, Sarasota and Fort Meyers transects indicating that these latitudes are not spatially distinct with regards to these variables. There does not appear to be any relationship between the particulate C, N, P concentrations or C:N, N:P, C:P ratios and rainfall as indicated by Spearman Ranking Correlation coefficients. However, there does appear to be monthly trends across the shelf where peak particulate nutrient concentrations and particulate ratio values occur during the spring, summer and fall. The average particulate nutrient concentrations and ratios differ for each year as well as each K. brevis bloom which occurred during the study period. In summary, the particulate C, N, P concentrations and particulate nutrient ratios vary both spatially and temporally on the WFS and are potentially related to the flexibility of phytoplankton uptake kinetics in response to the varying nutrient regimes of the WFS.

A coupled, three-dimensional, time-dependent numerical model of water circulation, spectral light, plankton dynamics, nutrient/CDOM loadings, and zooplankton grazing provided an assessment of the factors affecting the growth and maintenance of red tides on the west Florida shelf (WFS). The coupled biophysical model consisted of state variable quantities for temperature, salinity, horizontal/vertical velocity components, turbulent diffusion, spectral light, colored dissolved organic matter (CDOM), dissolved organic and inorganic carbon, particulate silica, four dissolved inorganic nutrient pools (nitrate, ammonium, phosphate, and silicate), and four phytoplankton groups (diatoms, microflagellates, non-toxic dinoflagellates, and the red tide organism Karenia brevis). The model also included a complex grazing scheme that utilized thirteen different zooplankton groups to explore the effects of selective herbivory, feeding periodicity, diel vertical migration, fecal pellet egestion, and ammonium/phosphate excretion within a diverse zooplankton community. Over the shelf and slope of the eastern Gulf of Mexico, from the Mississippi River delta to the Florida Keys, four cases of the model were run during August -- November to explore the dynamics of red tide maintenance with respect to: (1) no refuge from grazing for K. brevis; (2) grazer avoidance of K. brevis during CDOM shading; (3) grazer avoidance of K. brevis in Case II waters; and (4) increased grazing stress on K. brevis competitors. NEGOM and ECOHAB data sets during July -- November 1999 were used to establish the initial/boundary conditions and provided validation data for the coupled model as well. Model results indicate that the red tide of 5.9 x 10 6 cells L-1 witnessed offshore Sarasota, Florida on 07 October 1999 was initiated by an inoculum of K. brevis observed in near-bottom waters above the 30 m isobath offshore Sarasota on 31 August 1999. Flowfields measured at moored ADCPs, observations from AVHRR satellite imagery, and west Florida shelf circulation models indicate that conditions of coastal upwelling existed during the period of bloom development, such that the K. brevis inoculum was delivered to the coast in the bottom Ekman layer. As a shade-adapted species capable of vertical migration, K. brevis cells aggregated near the bottom in order to escape photo-inhibitive light intensities in the overlying water column during the day and harvested the recycled nitrogen excreted by zooplankton grazers. This concomitant relaxation of light inhibition and nitrogen-limitation ultimately led to the growth and maintenance of the red tide, constrained in near-bottom waters during much of the day and preferentially advected inshore as a result of coastal upwelling. As K. brevis was advected inshore, self-shading, CDOM, and suspended inorganic particulates all contributed to the prevention of photo-inhibitive light intensities that, in combination with the excretion of recycled ammonium, ultimately led to the maintenance of a significant red tide at the coast.

Harmful algal blooms (HABs) of the brevetoxin-producing dinoflagellate Karenia brevis occur periodically along the central west coast of Florida. Mass mortalities of marine birds have long been associated with these blooms, yet there is little data documenting the accumulation of brevetoxins in the tissues of birds and their prey items. An intense HAB event impacted the region from Tampa Bay to Charlotte Harbor during most of 2005. More than one hundred marine birds, representing twenty three species, were collected during this bloom. All birds sampled were found dead or had died within 24 hours of admittance to local wildlife rehabilitation centers. In order to determine if fish were vectors for brevetoxin ingestion, the stomach contents of all birds were examined and any recovered fish were identified to the extent possible. The gastrointestinal tissues and contents from all avian samples were analyzed for brevetoxin levels, with results ranging from Shorebirds and gulls may also be exposed to brevetoxins via scavenging of red tide-killed fish deposited on beaches during blooms. Samples from scavenged fish were found to have brevetoxin levels ranging from 31 to 95,753 ng PbTx per gram tissue.

Algae are important to marine and fresh-water ecosystems. However, some species of algae are harmful or even toxic. They can consume oxygen or block sunlight that is essential for other organisms to live. Indeed, some algae blooms can produce toxins that damage the health of the environment, plants, animals, and humans. Harmful algal blooms (HABs) which are often more green, brown, or dark-colored than red have spread along the coastlines and in the surface waters of the United States. Therefore, scientists are making great efforts to study HABs in order to maintain human and ecosystem health. Karenia brevis, the major harmful algal bloom dinoflagellate of the Gulf of Mexico, plays a destructive role in the region. Karenia brevis, responsible for Florida red tide, is the principle HAB dinoflagellate in the Gulf of Mexico. K. brevis blooms can produce brevetoxin: ladder-shaped polyether (LSP) compounds, which can lead to adverse human health effects, like reduced respiratory function through inhalation exposure, or neurotoxic shellfish poisoning through consumption of contaminated shellfish. The poisoning has been attributed to their affinity for voltage-sensitive sodium ion channels causing channel opening and depolarization of excitable cell membranes. Conservative estimate suggests that the economic impact from all harmful algal bloom events in the United States is at least $82 million/year. The public health costs occupy $37 million alone. The study presented herein utilized fluorescent and photolabile brevetoxin probes to demonstrate that brevetoxin localizes in the chloroplast of K. brevis where it binds to light harvest complex II (LHC II) and thioredoxin (Trx). It had been discovered that the TrxR/Trx system was inhibited by brevetoxin-2 (PbTx-2) with an IC50 of 25 µM. The mechanism of the inhibition was discussed in this work. The research also revealed that the K. brevis high-toxic and low-toxic strains have a significant difference in their ability, not only to produce brevetoxin, but also to perform NPQ and in the production of ROS. I compared and contrasted various metabolic and biochemical parameters in two strains of K. brevis which had a ten-fold difference in toxin content. The work could shed light on the physiological role that brevetoxin fills for K. brevis and may contribute to understanding the effect of ladder-shaped polyether compounds on both marine animals and exposed humans and shall inform improved treatments for brevetoxicosis.

The objective of this research is to evaluate a coastal prediction system under various real world scenarios to test the efficacy of the system as a management tool in Tampa Bay. The prediction system, comprised of a three-dimensional numerical circulation model and a Lagrangian based particle tracking model, simulates oceanographic scenarios in the bay for past (hindcast), present (nowcast) and future (forecast) time frames. Instantaneous velocity output from the numerical circulation model drives the movement of particles, each representing a fraction of the total material, within the model grid cells. This work introduces a probability calculation that allows for rapid analysis of bay-wide particle transport. At every internal time step a ratio between the number of particles in each individual model grid cell to the total number of particles in the entire model domain is calculated. These ratios, herein called transport quotients, are used to construct probability maps showing locations in Tampa Bay most likely to be impacted by the contaminant. The coastal prediction system is first evaluated using dimensionless particles during an anhydrous ammonia spill. In subsequent studies biological and chemical characteristics are incorporated into the transport quotient calculations when constructing probability maps. A salinity tolerance is placed on particles representing Karenia brevis during hindcast simulations of a harmful algal bloom in the bay. Photobleaching rates are incorporated into probability maps constructed from hindcast simulations of seasonal colored dissolved organic matter (CDOM) transport. The coastal prediction system is made more robust with the inclusion of biological parameters overlaid on top of the circulation dynamics. The system successfully describes the basic physical mechanisms underlying the transport of contaminants in the bay under various real world scenarios. The calculation of transport quotients during the simulations in order to develop probability maps is a novel concept when simulating particle transport but one which can be used in real-time to support the management decisions of environmental agencies in the bay area.

Red tides pose a significant economic and environmental threat in the Gulf of Mexico. Detecting red tide is important for understanding this phenomenon. In this thesis, machine learning approaches based on Random Forests, Support Vector Machines and K-Nearest Neighbors have been evaluated for red tide detection from MODIS satellite images. Detection results using machine learning algorithms were compared to ship collected ground truth red tide data. This work has three major contributions. First, machine learning approaches outperformed two of the latest thresholding red tide detection algorithms based on bio-optical characterization by more than 10% in terms of F measure and more than 4% in terms of area under the ROC curve. Machine Learning approaches are effective in more locations on the West Florida Shelf. Second, the thresholds developed in recent thresholding methods were introduced as input attributes to the machine learning approaches and this strategy improved Random Forests and KNearest Neighbors approaches' F-measures. Third, voting the machine learning and thresholding methods could achieve the better performance compared with using machine learning alone, which implied a combination between machine learning models and biocharacterization thresholding methods can be used to obtain effective red tide detection results.

Harmful Algal Blooms (HABs) in the Gulf of Mexico (GOM) are natural phenomena that can have negative impacts on marine ecosystems on which human health and the economy of some Gulf States depends. Many of the HABs in the GOM are dominated by the toxic dinoflagellate Karenia brevis. Non-toxic phytoplankton taxa such as Scrippsiella sp. also form intense blooms off the Mexican coast that result in massive fish mortality and economic losses, particularly as they may lead to anoxia. The main objectives of this dissertation were to (1) evaluate and improve the techniques developed for detection of Karenia spp. blooms on the West Florida Shelf (WFS) using satellite remote sensing methods, (2) test the use of these methods for waters in the GOM, and (3) use the output of these techniques to better understand the dynamics and evolution of Karenia spp. blooms in the WFS and off Mexico. The first chapter of this dissertation examines the performance of several Karenia HABs detection techniques using Moderate Resolution Imaging Spectroradiometer (MODIS) satellite images and historical ground truth observations collected on the WFS from August 2002 to December 2011. A total of 2323 in situ samples collected by the Florida Fish and Wildlife Research Institute to test for Karenia spp. matched pixels with valid ocean color satellite observations over this period. This dataset was used to systematically optimize variables and coefficients used in five published HAB detection methods. Each technique was tested using a set of metrics that included the F-Measure (FM). Before optimization, the average FM for all techniques was 0.47. After optimization, the average FM increased to 0.59, and false positives decreased ~50%. The addition of a Fluorescence Line Height (FLH) criterion improved the performance of every method. A new practical method was developed using a combination of FLH and Remote Sensing Reflectance at 555 nm (Rrs555-FLH). The new method resulted in an FM of 0.62 and 3% false negatives, similar to those from more complex techniques. The first chapter concludes with a series of recommendations on how to improve the detection techniques and how to take these results a step further into a Gulf wide observing systems for HABs. In chapter two, ocean color techniques were used to examine the extension, evolution and displacement of four Karenia spp. events that occurred in the WFS between 2004 and 2011. Blooms were identified in the imagery using the new Rrs-FLH method and validated using in situ phytoplankton cell counts. The spatial extension of each event was followed in time by delineating the blooms. In 2004 and 2005, the WFS was affected by a series of hurricanes that led to high river discharge and intense sediment resuspension events. Both processes had an impact on HAB occurrence. For example, I tracked a Karenia spp. bloom found in late December 2004 approximately 40-80 km offshore Saint Petersburg, which then expanded reaching an extension of >8000 km2 in February 2005. The bloom weakened in spring 2005 and intensified again in summer reaching >42,000 km2 after the passage of hurricane Katrina in August 2005. This bloom covered the WFS from Charlotte Harbor to the Florida Panhandle. Two other cases were studied in the WFS. The results of the Hybrid Coordinate Ocean Model from the U.S. Navy aid understanding the dispersal of the blooms. During fall 2011, three field campaigns to study HABs in Mexico were conducted to do an analysis of optical properties and explore the possibility of using ocean color techniques to distinguish between the main phytoplankton blooms in that region. Three main bloom scenarios were observed in the Campeche Bank region: massive diatom blooms, blooms dominated by Scrippsiella spp., and Karenia spp. blooms. The normalized specific phytoplankton absorption spectra were found to be different for Karenia spp. and Scrippsiella sp. blooms. A new technique that combines phytoplankton absorption derived from MODIS data and the new technique developed in Chapter One showed potential for a detection technique that can distinguish between Karenia and Scrippsiella blooms. Additional work is needed to improve the new technique developed for Mexican waters, but results show potential for detection techniques that can be used Gulf-wide. This will help better understand the dynamic and possible connectivity of phytoplankton blooms in the GOM.