Domoic acid (DA), a potent neurotoxin that has the potential to cause amnesic shellfish poisoning (ASP), is produced by members of the marine diatom genus Pseudo-nitzschia. Outbreaks of ASP in humans and of DA poisoning in birds and marine mammals have been reported across the United States and Canada since the late 1980's. Pseudo-nitzschia species can be extremely abundant in Florida waters, with densities often exceeding 106 cells/L, and sometimes exceeding 107 cells/L. Based on preliminary data, it is evident that at least nine species of Pseudo-nitzschia are found in Florida coastal waters. At least six of these species are known to produce DA in other parts of the world, and some are morphologically identical to some of the major toxin-producing species in Californian and Canadian waters. Despite the strong presence of Pseudo-nitzschia, there has never been a report of ASP or a DA-related animal mortality event from Florida. Data collected from 2004 to 2011 show maximum Pseudo-nitzschia abundances exceeded 4 x 107 cells/L. Six species of Pseudo-nitzschia were identified from central west and southwest Florida waters via light and electron microscopy. This is the first report of P. micropora from the Gulf of Mexico. Additionally P. calliantha, P. cuspidata, and P. pungens were identified as producers of DA in Florida coastal waters; although cell quotas of DA were low. Low levels of DA were detected in about one third of the water samples analyzed and DA concentrations measured in the majority of shellfish from the study area were at least an order of magnitude below the regulatory limit of 20 µg/g, suggesting that Pseudo-nitzschia currently poses little threat to human health in Florida. However, DA production in Pseudo-nitzschia species has been shown to be variable and dependent on nutrient conditions, indicating that the potential for DA-related events to occur in Florida warrants further investigation.

The objectives of this study were to measure injuries and impairments directly observed from gags Mycteroperca microlepis caught and released within a large-scale recreational fishery, develop methods that may be used to rapidly assess the condition of reef fish discards, and estimate the total portion of discards in the fishery that suffer latent mortality. Fishery observers were placed on for-hire charter and headboat vessels operating in the Gulf of Mexico from June 2009 through December 2012 to directly observe reef fishes as they were caught by recreational anglers fishing with hook-and-line gear. Fish that were not retained by anglers were inspected and marked with conventional tags prior to release. Fish were released in multiple regions over a large geographic area throughout the year and over multiple years. The majority of recaptured fish were reported by recreational and commercial fishers, and fishing effort fluctuated both spatially and temporally over the course of this study in response to changes in recreational harvest restrictions and the Deepwater Horizon oil spill. Therefore, it could not be assumed that encounter probabilities were equal for all individual tagged fish in the population. Fish size and capture depth when fish were initially caught-and-released also varied among individuals in the study and potentially influenced recapture reporting probabilities. The Cox proportional hazards regression model was used to control for potential covariates on both the occurrence and timing of recapture reporting events so that relative survival among fish released in various conditions could be compared. A total of 3,954 gags were observed in this study, and the majority (77.26%) were released in good condition (condition category 1), defined as fish that immediately submerged without assistance from venting and had not suffered internal injuries from embedded hooks or visible damage to the gills. However, compared to gags caught in shallower depths, a greater proportion of gags caught and released from depths deeper than 30 meters were in fair or poor condition. Relative survival was significantly reduced (alpha (underline)<(/underline)0.05) for gags released in fair and poor condition after controlling for variable mark-recapture reporting rates for different sized discards among regions and across months and years when individual fish were initially captured, tagged and released. Gags released within the recreational fishery in fair and poor condition were 66.4% (95% C.I. 46.9 to 94.0%) and 50.6% (26.2 to 97.8%) as likely to be recaptured, respectively, as gags released in good condition. Overall discard mortality was calculated for gags released in all condition categories at ten meter depth intervals. There was a significant linear increase in estimated mortality from less than 15% (range of uncertainty, 0.1-25.2%) in shallow depths up to 30 meters, to 35.6% (5.6-55.7%) at depths greater than 70 meters (p < 0.001, R2 = 0.917). This analysis demonstrated the utility of the proportional hazards regression model for controlling for potential covariates on both the occurrence and timing of recapture events in a large-scale mark-recapture study and for detecting significant differences in the relative survival of fish released in various conditions measured under highly variable conditions within a large-scale fishery.

Geologic sequestration has been suggested as a viable method for greenhouse gas emission reduction. Regional studies of CO₂ storage capacity are used to estimate available storage, yet little work has been done to tie site specific results to regional estimates. In this study, a 9,258,880 acre (37469.4 km²) area of the coastal and offshore Texas Miocene interval is evaluated for CO₂ storage capacity using a static volumetric approach, which is essentially a discounted pore volume calculation. Capacity is calculated for the Miocene interval above overpressure depth and below depths where CO₂ is not supercritical. The goal of this study is to determine the effectiveness of such a regional capacity assessment, by performing refinement techniques that include simple analytical and complex reservoir injection simulations. Initial refinement of regional estimates is performed through net sand picking which is used instead of the gross thickness assumed in the standard regional calculation. The efficiency factor is recalculated to exclude net-to-gross considerations, and a net storage capacity estimate is calculated. Initial reservoir-scale refinement is performed by simulating injection into a seismically mapped saline reservoir, near San Luis Pass. The refinement uses a simplified analytical solution that solves for pressure and fluid front evolution through time (Jain and Bryant, 2011). Porosity, permeability, and irreducible water saturation are varied to generate model runs for 6,206 samples populated using data from the Atlas of Northern Gulf of Mexico Gas and Oil Reservoirs (Seni, 2006). As a final refinement step, a 3D dynamic model mesh is generated. Nine model cases are generated for homogeneous, statistically heterogeneous, and seismic-based heterogeneous meshes to observe the effect of various geologic parameters on injection capacity. We observe downward revisions (decreases) in total capacity estimation with increasingly refined geologic data and scale. Results show that estimates of storage capacity can decrease significantly (by as much as 88%) for the single geologic setting investigated. Though this decrease depends on the criteria used for capacity comparison and varies within a given region, it serves to illustrate the potential overestimation of regional capacity assessments compared to estimates that include additional geologic complexity at the reservoir scale. / text

Populations of black mangroves (Avicennia sp.) are hypothesized to expand their latitudinal range with global climate change in the 21st century, induced by a reduction in the frequency and severity of coastal freezes, which are known to limit mangrove colony extent and individual tree size, as well as an overall warmer climate. The Gulf of Mexico is located at the northward limit of black mangrove habitat and is therefore a prime candidate for population expansion with global warming. This expansion may come at the expense of existing Gulf coastal saline wetlands that are dominantly Spartina spp. marsh grasses. The present study was conducted to focus, not on the extent to date of this replacement, but to examine the potential implications of a marsh to mangrove transition in Gulf wetlands, specifically 1) resistance to accelerating eustatic sea level rise (ESLR) rates, 2) wetland resistance to wave attack in large storms (increased cyclonic storm frequency/intensity is predicted with future climate warming), and 3) organic carbon sequestration and wetland soil geochemistry. Field sites of adjacent and intergrown Avicennia mangrove and Spartina marsh populations in similar geomorphological setting were selected in back-barrier areas near Port Aransas and Galveston, TX (two sites each) as part of a larger-scale planned study of the full latitudinal transition of the western Gulf funded by the National Institute for Climate Change Research (U.S. Department of Energy). The reconnaissance conducted for site surveys show that black mangrove populations in this part of Texas are clustered near inlet areas, suggesting seed transport vectors are a major control on colony establishment, and likely, on the potential rapidity of wetland habitat replacement. Resistance to ESLR was tested by 1) creating high-accuracy (±1 cm) elevation maps over ~5,000 m² areas of adjacent mangrove and marsh areas, and 2) measuring mineral and organic matter accumulation rates (Pb/Cs radiotracer geochronology, loss on ignition) from auger cores. Elevation surveys in Port Aransas indicate mangrove vegetated areas are 4 cm higher in elevation than surrounding marsh on an average regional scale, and 1 to 2 cm higher at the individual mangrove scale: at the Galveston sites, any trend is complicated by the area's pre-existing geomorphology and the relative youth of the mangrove colonies. ¹³⁷Cs accumulation rates and loss on ignition data indicate that mineral trapping is 4.1 times higher and sediment organics are 1.7 times lower in mangroves at Port Aransas; no such definable trends exist at the Galveston sites or in calculated ²¹⁰Pb sediment accumulation rates. This additional mineral particle trapping in mangroves does not differ in grain size character from marsh mineral accumulation. Elevation change may also be effected by root volume displacement: live root weight measurements in the rooted horizon (~0 to 20 cm depth) are consistently higher in mangrove cores from Port Aransas and the site at the west end of Galveston Island. Port Aransas porosities are lower in mangrove rooted horizons, with a corresponding increase in sediment strength (measured by shear vane in the cores), suggesting mangrove intervals may be more resistant to wave-induced erosion during storm events. Port Aransas mangroves exhibit higher pore water redox potentials and salinities over entire core depths and depressed pH over rooted intervals, suggesting a distinct diagenetic environment exists relative to marsh sites. Increased salinities and higher redox potentials may be a function of the rooting network, which introduces oxygen into the sediment and focuses evapo-transpiration and salt exclusion within this zone: this may prove advantageous when competing with marsh grasses by elevating salinities to levels that are toxic for Spartina. Trends observed in the more mature systems of Port Aransas are generally absent at the Galveston sites, suggesting the youth and physically shorter stature of these systems means they have not yet established a unique sediment signature. / text

Mixtures of bacterial and thermogenic methane are found both at vents at the seafloor and in reservoirs in the deep subsurface of the Gulf of Mexico continental slope. The C1-C5 gas that most recently charged reservoirs of Jolliet (GC 184), Genesis (GC 160/161) and Petronius (VK 786) fields is estimated to include 17%-28%, 31%-51%, 31%-49% bacterial methane, respectively. Geochemical assessment of the reservoir gas in the fields show that the gas may be the product of thermal cracking of Upper Jurassic crude oil before final migration to the reservoirs. The gas from three different fields is of similar thermal maturity levels. In contrast to oil in reservoirs in the fields, which shows biodegradation effects, the C1-C5 reservoir gas is unaltered by biodegradation. Late gas migration may have occurred at or near present burial depth and flushed the reservoir system of previously biodegraded hydrocarbon gas to include any previous bacterial methane. Molecular and isotopic properties of reservoir gas and oil suggest that bacterial methane mixed with thermogenic hydrocarbon gas before entering the reservoirs. Thus the source of the bacterial methane is logically deeper than the present depth (>~4 km) and temperatures of the reservoirs. High sedimentation rate and low geothermal gradient may offer conditions favorable for generation and preservation of bacterial methane in deep subsurface petroleum system of the Gulf slope. Bacterial methane dispersed across the large drainage areas of the deep subsurface petroleum system may have been swept by migrating fluids at >4 km, and then charged both vents (GC 185, GC 233 and GC 286) at the seafloor and reservoirs in the deep subsurface. The volume of bacterial methane from geologically significant depth in rapidly subsiding basins may be underestimated.

Using cryogenic SEM, we investigated the physical states of gas-hydrate-bearing samples recovered by drill core from several localities including the SE India margin (NGHP Expedition 01), Cascadia margin (IODP Leg 311), Gulf of Mexico (RV Marion Dufresne 2002), and Mackenzie River Delta (Mallik site, well 5L-38). Core material with a significant fraction of preserved hydrate has only been obtained for cryogenic SEM investigation from relatively few sites worldwide to date, yet certain consistent textural characteristics, as well as some clear differences between sites have been observed. Gas hydrate in cores recovered from Cascadia, Gulf of Mexico, and Mallik often occurs as a dense substrate with typical grain size of 30 to as large as 200 μm. The hydrate often contains a significant fraction of isolated macropores that are typically 5–100 μm in diameter and occupy 10-30 vol. % of the domain. In fine-grained sediment sections of marine samples, gas hydrate commonly forms small pods or lenses with clay platelets oriented sub-parallel around them, or as thin veins 50 to several hundred microns in thickness. In some sections, hydrate grains are delineated by a NaCl-bearing selvage that forms thin rinds along hydrate grain exteriors, presumably produced by salt exclusion during original hydrate formation. Preliminary assessment of India NGHP-01 samples shows some regions consistent with the observations described above, as well as other regions dominated by highly faceted crystals that line the walls or interior of cavities where the hydrate grows unimpeded. Here, we focus on gas hydrate grain morphology and microstructures, pore characteristics and distribution, and the nature of the hydrate/sediment grain contacts of the recovered samples, comparing them to each other and to laboratory-produced gas hydrates grown under known conditions.

I investigated how land use and human activities affect the sources and cycling of carbon (C) in subtropical rivers. Annually rivers receive a large amount of terrestrial C, process a portion of this C and return it to the atmosphere as CO2. The rest is transported to the ocean. Land use and human activities can affect the sources and fate of terrestrial C in rivers. However, studies on these effects are limited, especially in the humid subtropics. I combined measurements of the partial pressure of dissolved CO2 (pCO2), C isotopes (13C and 14C) and solid-state 13C nuclear magnetic resonance (NMR) to study C cycling in three subtropical rivers in Texas, two small rivers (Buffalo Bayou and Spring Creek) and a midsized river (the Brazos). My pCO2 data show that small humid subtropical rivers are likely a large source of atmospheric CO2 in the global C cycle. My measurements on pCO2, C isotopic and chemical composition of dissolved inorganic C (DIC) and particulate organic C (POC) revealed four types of effects of land use and human activities on river C cycling. First, oyster shells and crushed carbonate minerals used in road construction are being dissolved and slowly drained into Buffalo Bayou and the lower Brazos and may be a source of river CO2 released to the atmosphere. Second, river damming and nutrient input from urban treated wastewater stimulate algal growth and reduce CO2 evasion of the middle Brazos. Third, urban treated wastewater discharge is adding old POC to the middle Brazos and decomposition of the old POC adds to the old riverine DIC pool. Fourth, agricultural activities coupled with high precipitation enhance loss of old organic C (OC) from deep soils to the lower Brazos, and decomposition of the old soil OC contributes to the old CO2 evaded. I document for the first time the river C cycling effects of the use of carbonate minerals in construction and the riverine discharge of urban wastewater. Results presented here indicate the need to study disturbed river systems to better constrain the global C budget.

Water quality and wetlands represent two vital elements of a healthy coastal ecosystem. Both experienced substantial declines in the U.S. during the 20th century. Overall coastal wetland cover decreased over 50% in the 20th century due to coastal development and water pollution. Management and legislative efforts have successfully addressed some of the problems and threats, but recent research indicates that the diffuse impacts of climate change and non-point source pollution may be the primary drivers of current and future water-quality and wetland stress. In order to respond to these pervasive threats, traditional management approaches need to adopt modern technological tools for more synoptic, frequent and fine-scale monitoring and assessment. In this dissertation, I explored some of the applications possible with new, commercial satellite imagery to better assess the status of coastal ecosystems. Large-scale land-cover change influences the quality of adjacent coastal water. Satellite imagery has been used to derive land-cover maps since the 1960’s. It provides multiple data points with which to evaluate the effects of land-cover change on water quality. The objective of the first chapter of this research was to determine how 40 years of land-cover change in the Tampa Bay watershed (6,500 km2) may have affected turbidity and chlorophyll concentration – two proxies for coastal water quality. Land cover classes were evaluated along with precipitation and wind stress as explanatory variables. Results varied between analyses for the entire estuary and those of segments within the bay. Changes in developed land percent cover best explained the turbidity and chlorophyll-concentration time series for the entire bay (R2 > 0.75, p < 0.02). The paucity of official land-cover maps (i.e. five maps) restricted the temporal resolution of the assessments. Furthermore, most estuaries along the Gulf of Mexico do not have forty years of water-quality time series with which to perform evaluations against land-cover change. Ocean-color satellite imagery was used to derive proxies for coastal water with near-daily satellite observations since 2000. The goal of chapter two was to identify drivers of turbidity variability for 11 National Estuary Program water bodies along the Gulf of Mexico. Land cover assessments could not be used as an explanatory variable because of the low temporal resolution (i.e. approximately one map per five-year period). Ocean color metrics were evaluated against atmospheric, meteorological, and oceanographic variables including precipitation, wind speed, U and V wind vectors, river discharge, and water level over weekly, monthly, seasonal and annual time steps. Climate indices like the North Atlantic Oscillation and El Niño Southern Oscillation index were also examined as possible drivers of long-term changes. Extreme turbidity events were defined by the 90th and 95th percentile observations over each time step. Wind speed, river discharge and El Niño best explained variability in turbidity time-series and extreme events (R2 > 0.2, p < 0.05), but this varied substantially between time steps and estuaries. The background land cover analyses conducted for coastal water quality studies showed that there are substantial discrepancies between the wetland extent estimates mapped by local, state and federal agencies. The third chapter of my research sought to examine these differences and evaluate the accuracy and precision of wetland maps using high spatial-resolution (i.e. two-meter) WorldView-2 satellite imagery. Ground validation data showed that wetlands mapped at two study sites in Tampa Bay were more accurately identified by WorldView-2 than by Landsat imagery (30-meter resolution). When compared to maps produced separately by the National Oceanic and Atmospheric Administration, Southwest Florida Water Management District, and National Wetland Inventory, we found that these historical land cover products overestimated by 2-10 times the actual extent of wetlands as identified in the WorldView-2 maps. We could find no study that had utilized more than six of these commercial images for a given project. Part of the problem is cost of the images, but there is also the cost of processing the images, which is typically done one at a time and with substantial human interaction. Chapter four explains an approach to automate the preprocessing and classification of imagery to detect wetlands within the Tampa Bay watershed (6,500 km2). Software scripts in Python, Matlab and Linux were used to ingest 130 WorldView-2 images and to generate maps that included wetlands, uplands, water, and bare and developed land. These maps proved to be more accurate at identifying forested wetland (78%) than those by NOAA, SWFWMD, and NWI (45-65%) based on ground validation data. Typical processing methods would have required 4-5 months to complete this work, but this protocol completed the 130 images in under 24 hours. Chapter five of the dissertation reviews coastal management case studies that have used satellite technologies. The objective was to illustrate the utility of this technology. The management sectors reviewed included coral reefs, wetlands, water quality, public health, and fisheries and aquaculture.

Coastal zones receive massive terrestrial inputs of nutrients and organic matter, and play an important role in biogeochemical cycles. The interactions of river inputs, ocean currents, atmospheric exchanges, anthropogenic influences, and biologically active ecosystems make CO2 system studies in coastal waters highly challenging. This work focuses on improving our understanding of the CO2 system in coastal waters through (1) development of a new methodology for measurements of CO2 system parameters in the field; (2) observations of large spatial and temporal CO2 system variations in coastal waters; and (3) characterization of the influence of organics on CO2 system behavior in coastal waters. A novel portable light-emitting-diode (LED) photometer was developed to provide low-cost seawater pH measurements in the field. With meta cresol purple (mCP) as the indicator, the photometer produces pHT measurements within ± 0.01 units of state-of-the-art spectrophotometric measurements (7.6 ≤ pH ≤ 8.2, 30 ≤ S ≤ 36.2, and 15 oC ≤ t ≤ 30 oC). With a simple “do-it-yourself” (DIY) construction design, a hundredfold reduction in cost relative to benchtop spectrophotometric systems, and routine calibration-free operation in the field, the DIY photometer is an ideal replacement for pH test strips or consumer-level potentiometric probes. Applications of special interest include education, citizen science, coastal zone monitoring, and aquaculture and aquarium management. Subannual variability of total alkalinity (TA) distributions in the northeastern Gulf of Mexico (GOM) was examined through the use of TA data from ship-based water sampling, historical records of riverine TA, and contemporaneous model output of surface currents and salinity. Variability of TA observed in the upper 150 m of the GOM water column was primarily controlled by subannual variations in the extent of mixing between seawater and river water. A transition in TA distribution patterns between the river-dominated northern margin (near the Mississippi–Atchafalaya River System) and the ocean current-dominated eastern margin (West Florida Shelf) was observed. A riverine alkalinity input index was developed to highlight riverine TA contributions. Contributions of organic alkalinity (Org-Alk) to TA were investigated in coastal waters from three different environments (estuary, urban, mangrove) and offshore sites in the Gulf of Mexico. The difference in alkalinity (∆TA) between TA measured by direct titration (TAmeas) and calculated (TAcal) from observations of DIC and pH was used as an estimate of Org-Alk. Average values of ∆TA were 0.1 ± 5.0 µmol kg-1 at coastal sample sites outside the Mississippi-Atchafalaya River Estuary (n = 17), 1.9 ± 5.2 µmol kg-1 in offshore waters (n = 14) in the northern Gulf of Mexico, 33.6 ± 18.0 µmol kg-1 in the Suwannee River Estuary (n = 17), and 16.0 ± 25.4 µmol kg-1 in sites that included Tampa Bay, the Caloosahatchee River, and the Ten Thousand Islands area (n = 55). In addition to Org-Alk assessments based on measurements of ∆TA, a novel two-step spectophotometric titration method was developed for the characterization of Org-Alk. Direct titrations showed substantial Org-Alk in coastal samples (n = 5), and the Org-Alk values obtained from the two-step titrations showed good agreement with results from ∆TA calculations. The spectrophotometric titration data were used in model fits to evaluate the dissociation constants (pKi) of the natural organic acids. The pKi of the organic acids were within the previously reported range for riverine fulvic acids.

The objective of this thesis was to determine if there were any correlations in the distribution of cetaceans, especially sperm whales (Physeter macrocephalus), pantropical dolphins (Stenella attenuata), bottlenose dolphins (Tursiops truncatus), and Risso’s dolphins (Grampus griseus) in the northern Gulf of Mexico because of the influence of oil and gas production and exploration. This research is important because of the lack of knowledge about the impact of anthropogenic sounds from oil and gas exploration and production (E&P) on cetacean distribution in the Gulf of Mexico. I analyzed cetacean visual line-transect survey results from the Gulf of Mexico for period of 1992 – 2001. I divided this time span into an early period (1992 – 1997) and a late period (1998 – 2001). I overlayed the locations of cetacean sightings and the locations of oil and gas E&P platforms to demonstrate their close association in space, and tested a hypothesis that distribution would shift south correlated with changes in distribution of E&P. I compared the distributions of cetacean sightings in the entire Gulf of Mexico, and separated the Gulf of Mexico into east and west, between the early period and the late period. The east Gulf of Mexico represents an area without oil and gas E&P platforms and the west Gulf of Mexico is the area where oil and gas E&P platforms are located. The null hypothesis for these tests was that there was no difference in cetacean distribution between the early period and the late period. I also compared the distribution of sperm whales, pantropical dolphins, bottlenose dolphins, and Risso’s dolphins in the entire Gulf of Mexico, both east and west, between the early and late periods. I expect if distribution changes were correlated with changes in E&P distribution, then there will be a shift south in the western Gulf. Changes in distribution in the eastern Gulf would not be correlated with E&P. I found that the sightings per unit effort (SPUE) of all cetacean sightings in the entire Gulf of Mexico shifted to the south in the late period, as compared to the early period .The distribution of all cetacean sightings for the late period (1998-2001) was significantly different compared to the distributions of all cetacean sightings in the early period (1992-1997). The SPUE of sperm whale and bottlenose dolphin distributions were shifted to the north in the late period (1998-2001) compared to the early period (1992-1997). While pantropical dolphin distributions were significantly shifted to the south between the two time periods. I observed that the SPUE of all cetaceans sightings in the east Gulf of Mexico for the early period (1992-1997) were shifted to the south compared to the west, which were not different. The SPUE for sperm whales in the east for the early period were marginally shifted to the north in comparison to the west, which were also shifted further north. The SPUE for Risso’s dolphins in the east were shifted further north while in the west SPUE were shifted to the south. The SPUE for pantropical dolphin sightings were shifted to the north in both the east and west regions. While the SPUE for bottlenose dolphin sightings were shifted to the north in both the east and west Gulf of Mexico. My SPUE results suggest that pantropical dolphins, like the total cetaceans examined here, have shifted their distributions in the entire northern Gulf of Mexico to the south. However, in areas of high oil and gas E&P platforms the distributions of sperm whales and bottlenose dolphins did not shift their distributions from the early period to the late period to the south even though these E&P activities have shifted to the south over the past two decades as they expanded into the deeper waters of the northern Gulf of Mexico. Therefore, there is little evidence that large scale changes in the latitudinal distribution of marine mammals in the Northern Gulf have occurred as a result of greater offshore E&P activity.