Changes in sediment morphology on the West Florida Shelf is investigated over a 14-year time period using multibeam bathymetry and backscatter in water depths between 10 m and 20 m, off the coast of Indian Rocks Beach, Pinellas County, Florida. Bathymetric surveys collected in 2002 (Kongsberg EM 3000 at 300 kHz) and 2016 (Reson 7125 at 400 kHz) were processed using CARIS Hips and Sips to create bathymetric maps and backscatter images. These data were then interpreted and compared in order to test hypotheses and answer questions related to sediment migration and sediment volume change. The following questions prompted this study: A. How mobile is the sediment on the limestone? B. What sedimentary changes occurred following the 2002 and 2003 deployments of mines for an Office of Naval Research project? C. How much sediment was removed during dredging and how closely does it compare to the Army Corps of Engineers’ reported estimate during the beach renourishment of Sand Key in 2012? In order to answer these questions, hypotheses were proposed: Hypothesis A: The sediment ridges in the study site have not migrated significantly over the limestone hard bottom during the 14-year time period (Hafen, 2001; Edwards et al. 2003). Hypothesis B: There is no change in sediment volume where the mine-like object were placed and removed after the ONR mine burial experiment (Wolfson 2005 Wolfson et al. 2007). Hypothesis C: Changes in sediment volume between 2002 and 2016 will match the amount estimated by the Army Core of Engineers who dredged the area. Results show that the sediment ridges in the study area had some migration over the limestone hard bottom during the 14-year time period. The results also found that there was a sediment volume change where mine-like objects were placed and removed during the Office of Naval Research mine burial experiment because of a dredging operation in 2012 that dredged sediment from the experimental area. Specific areas investigated that surround the dredging area showed significant loss of sediment, with the change in hydrodynamics from dredging influencing this sediment loss. The volume of sediment removed from the aforementioned dredging cut was found to be within 16% of that estimated in the Army Corps of Engineers report prior to the dredging. Geologic interpretations of the backscatter images interpreted strong backscatter returns as limestone, mid strength returns as coarse shell hash and weak returns as fine to medium-grained sediments. The weak returns were found primarily on the sediment ridges. The dredging cut showed stronger returns than the surrounding ridge, indicating that underlying coarse sediments were most likely compacted and composed of shell hash. Using satellite remote sensing as a way to gather continual repeat coverage at high resolution (2 m) data to determine absolute depth in these water depths is investigated and preliminary results suggest that processed 250 m pixel MERIS data will give a similar depth range as multibeam bathymetry. The higher-resolution 0.5 m pixel raw WorldView 2 data shows NW-SE trending structure, suggesting the seafloor morphology will be more visible.

Characterization of Colored Dissolved Organic Matter (CDOM) in surface and ground waters in South Florida was conducted using fluorescence and absorption spectroscopy. Waters of the West Florida Shelf are heavily influenced by many river systems on Florida's Gulf Coast that, to the first order control CDOM distributions on the shelf. Seasonal surveys revealed that changes in the underwater light field as a result of major hurricanes and resuspension events are linked closely with a number of factors prior to a storm's passing such as the presence of persistant blooms, rainfall and discharge. Additionally, storm track and wind direction were found to play a significant role in CDOM signatures. A study of ten riversheds located between the Mississippi / Atchafalya River system and the Shark River in the Everglades revealed a wide range in CDOM seasonality. A regional dependence of CDOM was also found, where highest aromaticity and concentration of organic material was found for the southernmost watersheds. Basin characteristics, vegetation differences, land use and climatic patterns are implicated in the cause for regional differences. In addition to surface flow, organic material in groundwater was measured in deep and shallow aquifers surrounding the Tampa Bay Estuary. As a result of strong hydrologic links between shallow aquifers and the overlying surface waters, CDOM in both reservoirs were found to be quite similar. Deep aquifers (> 150 ft) however are less concentrated and have CDOM signatures more similar to marine waters. This suggests similar biogeochemical pathways of the material, including the influence of the aquatic microbial community. Furthermore, multi-spectral CDOM fluorescence measurements were shown to be a potential indicator of groundwater presence in Tampa Bay during times of low surficial discharge to the bay, and when some rivers are almost entirely spring-fed. Investigating CDOM distribution and signatures is vital to carbon budget and cycling questions. The amount and quality of organic material has significant implications for ecosystems, thereby affecting organisms that use CDOM as a food source, light availability for photosynthesis, UV shading provided to biota, satellite estimates of chlorophyll a, metal binding, materials transport and overall water quality.

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.

The objective of this study was to determine if fronts sustained up to three days will result in an aggregation of kingfish due to the anticipated accumulation of forage, increasing fishing success at these locations. Automated algorithms to detect frontal features in satellite-derived sea surface temperature, chlorophyll concentration, water clarity, and fluorescence images were successfully adapted for the coastal waters off west-central Florida. The surface ocean fronts were used to study the linkages between environmental conditions and recreational catch statistics of king mackerel (Scomberomorus cavalla) during 19 seasonal tournaments held in April to May and October to November of 2004 and 2005. The local winds estimated from a USF Coastal Ocean Monitoring and Prediction System observing station were analyzed with the frontal data to examine factors that influence oceanic frontal formation and stability. The front detection algorithms were also applied to high-r esolution bathymetry data which serves as a new technique for analyzing bottom topography. The spatial relationships between catch data collected through 415 angler interviews, frontal boundaries and stability, bathymetric gradients, bottom structure, and baitfish presence were identified using ESRI ArcGIS.Fishing success and fishing effort were highly variable regarding the distance of fishing activity to the nearest front. This was attributed to non-persistent winds. Intermediate water clarity (0.7 to 1.0 mW cm-2 microm-1 sr-1), the presence of baitfish, and the side of the front with relatively less chlorophyll showed the greatest influence on the king mackerel catch rates. Fishing success was found to be significantly higher at fishing locations where baitfish were reported present compared to where they were not reported. Concurrent with the 2005 harmful algal bloom event, a significant decrease in king mackerel catch occurred in the fall of 2005 (208 fish) compared to fall 20 04 (818) and spring 2005 (538). Additionally, fishing locations with baitfish present were observed about 15% less often during the fall of 2005 than the preceding seasons. From this, a model can be developed to diagnose the environmental conditions that can be used by resource managers to better understand variations in catch, which result from naturally occurring phenomena or man-induced overfishing.

Diel vertical migration (DVM) can offer motile phytoplankton a competitive advantage over other phytoplankton species. DVM has been well documented in the harmful dinoflagellate, Karenia brevis; however, the extent to which changes in nutrient regimes and density stratification modify migration patterns has not been thoroughly investigated. A 2 m experimental column was constructed with sensors and sampling ports at four depths to obtain fluorescence and temperature measurements and discrete water samples. The environmental parameters of the experimental column represented temperature and nutrient conditions found on the West Florida Shelf (WFS), where Karenia blooms frequently occur. Results demonstrated a clear DVM pattern for K. brevis where surface aggregations occurred during light periods, and bottom aggregations occurred in dark periods. However, the rate and intensity of migration varied between experimental conditions. Injections of nutrient replete water at the surface and bottom did not appear to modify migratory behavior, in that a portion of the population resided at depth regardless of light or dark periods. Weak density stratification caused a delay in downward migration in dark periods, whereas strong density stratification caused a complete cessation of downward migration. In a weakly stratified environment with a bottom injected replete water mass, DVM patterns most closely replicate the pattern under weakly stratified conditions alone. Modifications in the natural DVM pattern of K. brevis with respect to varying environmental and nutrient conditions that occur on the WFS can have major implications current forecast model predictions, and for monitoring and mitigation strategies.

Marine epibenthic communities are influenced by both pre- and post-recruitment processes. For instance, the larval supply and cues that influence settlement (pre-recruitment), as well as the growth and mortality of individuals (post-recruitment), may differ across reef type and depth. Determining the relative influence of these processes is important to understanding how epibenthic communities can develop in a region. Using both a recruitment experiment that controlled grazing by urchins and in situ photographic surveys of epibenthic communities, this study examined the recruitment and composition of epibenthos on natural limestone and artificial reefs in the eastern Gulf of Mexico (eGOM). In the experiment, tiles that were open to urchin grazing had lower percent cover of algae (-12%) and higher cover of crustose coralline algae (CCA) (13%) than those that excluded urchins. Patterns in tile cover were likely the result of CCA either resisting grazing mortality or recolonizing exposed areas after algae were removed. Prevalence of estuarine species on inshore tiles was indicative of variation in recruitment across depth. Urchin density was positively correlated with the structural complexity of the habitats, which was higher on artificial reefs than natural ones, a factor that potentially had important effects on several observed patterns. Results from photographic surveys indicated that natural reef communities had higher algal cover and lower cover of invertebrates (e.g., corals and hydroids) than artificial reefs. These findings were consistent with previous work conducted in both temperate and tropical ecosystems, and suggested that grazing from urchins plays an important role in shaping epibenthic community structure in the subtropical eGOM.

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.

Artificial reefs have been deployed throughout the world’s oceans to act as habitat and fishing enhancement tools. To expand current research on the role of artificial reefs in the marine community, ordination and multivariate regression methods were used here to analyze survey data of natural and artificial reefs. The reefs, located in the Northern Gulf of Mexico (NGOM) and on the West Florida Shelf (WFS), had been previously surveyed from 2004 to 2015 using remote operated vehicle and stationary video techniques. This study tested the hypothesis that similar functional roles are accounted for at both natural and artificial reef sites even if species composition varies. Secondly, it examines the role of environment and fisheries in determining the assemblages. Artificial reefs tended to host communities that were as biodiverse as natural reefs, although not necessarily composed of the same species. Results of an ordination confirmed that as the classification was broadened from the level of species, to family, to functional group, the assemblages on each reef type (natural vs. artificial and NGOM vs WFS) appeared more similar. Dominant groups were present at all levels of classification and included the families Lutjanidae and Carangidae, as well as functional groups Red Snapper and Small Reef Fish. Both natural and artificial reefs tended to be dominated by one of the following: Lutjanidae, Carangidae, or Small Reef Fish, although a continuous gradient was found across the extremes of natural versus artificial reefs. Generalized Additive Models were developed to examine the influence of reef type, location, environment and fishing intensity covariates. Results indicated that for both natural and artificial reefs, the abundance of families and functional groups can be influenced by environmental factors. In both cases, there is strong spatial autocorrelation suggesting connectivity with neighboring reefs.

Several studies have found separation of biogeographic provinces on the West Florida Shelf (WFS), but the location of this separation differs depending on different organisms with faunal boundaries proposed at Apalachicola, Cedar Key, Anclote Key. Tampa Bay, Charlotte Harbor, Cape Romano, or Cape Sable. Biogeographic boundaries can be gradual over a given space and are often species-specific. Analyses of marine benthic mapping and community characterization of Florida’s West-central coast shallow water (depth) hardbottom habitats indicate a major shift in the benthos across Tampa Bay. Quantitative benthic surveys of 29 sites yielded a total of 4,079 individuals of nine stony coral species and 1,918 soft coral colonies. Populations were dominated by four species of corals: Siderastrea radians, Oculina robusta, Solenastrea hyades, and Cladacora arbuscula. Most corals were less than 10 cm in diameter. Cluster analyses of coral density and major functional group percent cover showed distinct differences in hard and soft coral densities and species demographics from south to north with clear spatial patterns between regions. These benthic hardbottom coral communities change over a relatively small spatial scale (10’s of km), indicating a biogeographical province or ecosystem region boundary in marine benthic communities at, or very near, the mouth of Tampa Bay. Broader studies are needed to identify the shifts in benthic community biogeography along the West Florida Shelf.

Commonly referred to as “red tide”, harmful algal blooms (HABs) formed by Karenia brevis occur frequently in the Gulf of Mexico (GOM). A bloom is defined as cell abundances >105 cells L-1. This thesis will focus primarily on Karenia brevis, formerly known as Gymnodinium breve, in the Gulf of Mexico. K. brevis is harmful because it produces brevetoxin, a ladder-frame polyether that acts as a potent neurotoxin in vertebrates. K. brevis commonly causes fish kills, respiratory irritation in humans, and Neurotoxic Shellfish Poisoning (NSP) if ingested. Blooms of K. brevis occur almost annually along the West Florida Shelf (WFS) in the late summer and early fall, when the coastal current is favorable for bloom initiation. Along the Texas-Louisiana shelf (TLS) however, blooms of K. brevis are infrequent and sporadic. While much is known of the blooms along the WFS due to their frequent presence, little is known of the mechanisms driving the blooms along the TLS due to their inconsistent presence. To understand the stochastic nature of HABs along the TLS, historical data of bloom occurrences from 1996 to present were compared with NOAA station PTAT2 wind, sea-level pressure, air and water temperature data and NCEP NARR-A sea-level pressure data. The difference in the monthly-mean along-shore component of the wind was statistically significant between bloom and non-bloom years in September (p<<0.001) and April (p=0.0015), with bloom years having a strong downcoast current. Monthly mean water temperature values yielded similar results between bloom and non-bloom years. Both March and September monthly-mean water temperature values were lower during non-bloom years with p-values of 0.01 and 0.048, respectively. These results suggest the possibly of forecasting for HABs along the TLS with currently measured, publicly available data.