Modern observations of planktic foraminifera from sediment trap studies help to constrain the regional ecology of paleoceanographically valuable species. Results from a weekly-resolved sediment trap time series (2008–2014) in the northern Gulf of Mexico demonstrate that 92% of Globorotalia truncatulinoides flux occurs in winter (January, February, and March), and that encrusted and non-encrusted individuals represent calcification in distinct depth habitats. We use individual foraminiferal analysis (IFA) of G. truncatulinoides tests to investigate differences in the elemental (Mg/Ca) and isotopic composition (18O and 13C) of the encrusted and non-encrusted ontogenetic forms of G. truncatulinoides, and to estimate their calcification depth in the northern Gulf of Mexico. We estimate that non-encrusted and encrusted G. truncatulinoides have mean calcification depths of 66 ± 9 meters and 379 ± 76 meters, respectively. We validate the Mg/Ca-calcification temperature relationship for G. truncatulinoides and demonstrate that the 18O and Mg/Ca of the non-encrusted form is a suitable proxy for winter surface mixed layer conditions in the Gulf of Mexico. Care should be taken not to combine encrusted and non-encrusted individuals of G. truncatulinoides for down core paleoceanographic studies.

The Deepwater Horizon blowout occurred on April 20th, 2010, releasing 4.9 million barrels of Louisiana crude oil into the Gulf of Mexico (GoM). Subsequent to the Deepwater Horizon blowout, sediment cores revealed oil on the northern GoM seafloor and abnormal skin lesions were seen in GoM fishes. Exposure to polycyclic aromatic hydrocarbons (PAHs), a component of crude oil, in fish has been associated with many sublethal effects, including cancer and population-level effects. Using a biomarker of exposure to PAHs, this thesis evaluates inter-species, temporal and spatial differences in exposure to hydrocarbon contamination between three species of fish with varying levels of association with the sediment, that were potentially exposed to Deepwater Horizon crude oil: golden tilefish (Lopholatilus chamaeleonticeps), king snake eel (Ophichthus rex) and red snapper (Lutjanus campechanus), and examines patterns in these data using life history, behavior and environmental data. In 2011, 2012 and 2013, bile samples and biometric data were collected from fish via demersal longlining and bile was analyzed for three PAHs, naphthalene, phenanthrene and benzo[a]pyrene and their metabolites, using high performance liquid chromatography with fluorescence detection (HPLC-F). Bile of golden tilefish had significantly higher concentrations of naphthalene and phenanthrene metabolites, compared to red snapper and king snake eel. For biliary naphthalene metabolites, golden tilefish had an average concentration of 240 ug g-1, compared to 61 ug g-1 for red snapper and 38 ug g-1 for king snake eel, for the year 2012. Biliary naphthalene metabolite concentration has decreased 8% in golden tilefish samples, between 2012 and 2013, indicating continuous exposure to petrogenic pollution, while naphthalene metabolites decreased 49% over time for red snapper and 37% for king snake eel, indicating episodic exposure to elevated petrogenic pollution prior to 2011. The concentration of naphthalene metabolites measured in golden tilefish in this study are some of the highest concentrations measured in the GoM and internationally, while naphthalene metabolite concentrations for red snapper and king snake eel are similar to 1990's GoM data. In contrast, concentrations of benzo[a]pyrene metabolites were statistically similar for all three species, suggesting a difference in the disposition of or exposure to benzo[a]pyrene contamination. Concentrations of benzo[a]pyrene metabolites are relatively low when compared to other GoM and international data, for all three species. This study has identified a species of GoM fish, golden tilefish, that is exposed to a present-day source of petrogenic PAH pollution and certain fish species that were episodically exposed, in the years following the Deepwater Horizon blowout. With residual Deepwater Horizon oil still found in GoM sediments, coastal marshes and beaches, there is a need to identify these chronic exposures to persistent PAH pollution, monitor PAH concentrations in over time and evaluate the resulting sublethal effects to better understand the impacts of the Deepwater Horizon blowout on marine resources such as GoM fisheries.

Reef fish species tend to reside over high relief habitat which makes them difficult to sample with traditional gears such as nets and trawls. Therefore, implementing and understanding the strengths and weaknesses of new approaches which incorporate acoustic and optical methods has become a priority for reef fish stock assessment. Beginning in June of 2013, a towed camera system known as the Camera-Based Assessment Survey System (C-BASS) has been used to visualize over 500 kilometers of transect and record more than 80 hours of video over several habitats in the Gulf of Mexico. Surveys have been completed on the West Florida Shelf in the Florida Middle Grounds (FMG), Madison-Swanson (MS) and Steamboat Lumps (SL) closed areas. High resolution multibeam bathymetry is available for these areas and was important for the deployment of C-BASS which is towed just above the seafloor (2-3 meters above the bottom). This system can facilitate regular surveys of fishes which inhabit untrawlable bottom types (e.g. reefs, pinnacles, boulders) and within habitats where lethal, extractive techniques are prohibited such as in protected areas. To address potential biases resulting from fish reactions towards C-BASS, observed reactive behavior was analyzed in addition to far-field reactive behavior towards C-BASS using stationary camera pods. Most fish observed on C-BASS imagery exhibited weak negative or neutral behavior at proportions of 49% and 38%, respectively. Of those fish which did negatively react to C-BASS, almost all movement was in the 180° and 0° directions (right and left) relative to the tow body's movement. Preliminary results from the direct observation (far-field) experiments also demonstrated a general lack of reactive behavior as C-BASS was towed nearby with no significant decreases in mean abundance of fishes between the periods before, during and after C-BASS was towed over an area (95% confidence level). Although behavioral reactions are species-specific, results indicate that the system may not greatly deter the species of interest (i.e. snappers, groupers, porgies, lionfish, and amberjacks) in this study. Density estimates and subsequent first-order total abundance estimates were also developed for stratified habitat types in the FMG and MS. Overall abundance estimates were greater in 2014 than in 2013 which likely were a result of increased illumination, improvements to video quality, and lower chlorophyll and turbidity levels in 2014. With minor improvements and further behavior analysis, it is expected C-BASS can provide accurate, precise abundance estimates of target reef fish species for management purposes.

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico (GoM) released an estimated 4.9 million barrels of oil between April 20, 2010 and July 15, 2010. An estimated 36% of the oil formed a neutrally buoyant intrusion, containing both dissolved compounds and oil microdroplets, between 1000 and 1300 m depth. This study used geographic information systems software, and data from water samples that were collected as part of the National Resource Damage Assessment (NRDA), to determine that an area of at least 1,600 km2 was exposed to DWH oil. Toxic BTEX (benzene, toluene, ethylbenzene, and xylenes) compounds and polycyclic aromatic hydrocarbons (PAHs) reached concentrations 950 and 50 times higher than maximum background concentrations, respectively. BTEX and n-alkane concentrations above pre-2010 values were present through late August, more than a month after the wellhead was capped. This study is the first to examine the DWH intrusion over such a large temporal and spatial extent. We further estimated that an area between 500 and 1000 km2 may have been exposed to harmful PAH concentrations, based on studies of PAH toxicity and U.S. Environmental Protection Agency (EPA) guidelines. We also found evidence of aggregation and deposition of oil near the DWH wellhead, as well as an area of 400 km2 where the intrusion may have impinged on the seafloor. While relative rates of dilution, degradation, and deposition in the intrusion are unknown, we have shown evidence that supports two previously proposed processes that may have deposited DWH oil from this deep intrusion onto sediments, where toxic compounds could be resuspended and continue to be bioavailable to benthic organisms.

Graduation date: 1984

River plumes often develop in complex environments, where variable coastal and bottom topography, ambient currents, winds and tides may play important roles in shaping the plume evolution. When all these factors are present, the plume dynamics may become intricate and unclear. The objective of this study is to understand the processes controlling the dynamics of a large river plume that is affected by strong boundary currents, variable winds and complex topography. The Mississippi River (MR) plume is the study case of this dissertation work, and focus is given to the interactions between the plume and the offshore circulation of the Gulf of Mexico (GoM). A series of numerical experiments was designed to investigate the impact of different factors on the development of a large scale river plume in scenarios with variable degrees of complexity. First, a box-like model with an idealized estuary was designed to address the general development of a mid-latitude river plume and assess the variability of the plume with changes in the outflow conditions at the river mouth. The structure and development of the plume in the flat-bottom, receiving basin was highly dependent on the degree of freshwater mixing at the source. Larger freshwater mixing enhanced the estuarine gravitational circulation and modified the dynamical balance at the estuary mouth. Those changes effectively modified the shape of the bulge and length/transport scales of the coastal current. Sloping-bottom conditions further modified the development of the plume. Secondly, a Northern GoM model was designed and numerical experiments were conducted to investigate the specific dynamics of the MR plume, in the presence of both shelf and basin-wide circulation. In particular, buoyancy-driven (due to the MR and all other major Northern GoM rivers) and wind-driven currents were studied on the shelf, while the extension of the Loop Current and associated frontal eddies were considered as major factors in the shelf to offshore interactions; wind-driven, shelfbreak eddies were also considered. Process-oriented experiments demonstrate that westerly and southerly winds promoted the development of a surface Ekman layer that enhances the offshore advection of plume waters. The steep topography in the vicinity of the MR Delta was a favorable condition for that process. When the MR plume was subject to a full-blown scenario (realistically-forced experiment nested within a large-scale model), complex interactions between wind-driven and eddy-driven dynamics determined the fate of the plume waters. Offshore removal is a frequent plume pathway, and the offshore transport can be as large as the wind-driven shelf transport. The offshore pathways depend on the position of the eddies near the shelf edge, their life span and the formation of eddy pairs that generate coherent cross-shelf flows. Strong eddy-plume interactions were observed when the Loop Current (LC) system impinged against the shelfbreak, causing the formation of coherent, narrow low-salinity bands that extended toward the Gulf interior. The offshore transport of MR water is a year-round process, but the interactions between the MR plume and the LC system have large inter-annual variability. Plume to LC interactions are determined by episodic northward intrusions of the LC system in the NGoM. The interactions are dictated by the proximity of the LC system to the MR Delta and by wind effects. On average, plume to LC interactions correspond to ~ 12 % of the year-round, total freshwater transport near the MR Delta, but this percentage can go up to 30 % in individual years. At the time of the plume to LC interactions, an average value of LC freshwater entrainment was estimated to be ~ 4,150 m3 s-1. The findings presented here are a major contribution toward the understanding of the cross-marginal and basin-wide transport of MR waters by a large-scale current system, and the connectivity to remote regions, such as the South Florida region and the Florida Keys.

Natural hydrocarbon seeps harbor distinctive geological, chemical, and biological features in the marine environment. This thesis verified remote sensing signatures of seeps using in-situ observation and repeated collections of satellite imagery. Bubble streams in the Gulf of Mexico water column from four natural seep sites on the upper continental slope were imaged by a side-scan sonar, which was operated from a submarine near the seafloor, and by acoustic profilers, which were operated from surface ships. These data were correlated with sea surface slicks imaged by Synthetic Aperture Radar (SAR) on the RADARSAT satellite. Comparing non-oily bubble streams from rapidly venting mud volcanoes with oily bubble streams from shallow deposits of gas hydrate showed that they produced notably different signatures. Non-oily bubbles produced high backscatter on the side-scan sonar records, but were difficult to detect with the acoustic profilers. Oily bubbles from hydrate deposits produced acoustic shadows on the side-scan sonar records. The oily bubbles generated clear signatures extending from the seafloor to the near surface on the acoustic profile records. RADARSAT SAR images verified the presence of surface oil slicks over the hydrate deposits, but not over the mud volcanoes. This indicates that SAR imagery will not be able to capture every oil and gas seep in a region because non-oily bubble streams do not create surface oil slicks. A total of 113 natural oily seep sources were identified based on surface slicks in eleven SAR images collected over the northern continental slope. A persistence analysis verified that SAR is a dependable tool for capturing oil slicks because 93.5% of the slick sources identified in the 2001 images were corroborated with slicks in the 2002 images. The sources ranged in depth from 100 to 2000 m and 79% of the sources were in 900 meters or greater of water. Seventy-six percent of the seep sources were associated with salt less than 1500 m below the seafloor and none of the sources were located in the bottom of salt withdrawal basins. Geographical Information Systems (GIS) proved to be a useful tool in these analyses.

A molecular phylogenetic approach was used to characterize the composition of microbial communities from two gas hydrate sedimentary systems in the Gulf of Mexico. Nucleic acids were extracted from three distinct locales on surface breaching gas hydrate mounds, i.e., sediment overlaying gas hydrate, sediment/hydrate interface and sediment-free hydrate, and from three sediment depths, i.e., 0-2, 6-8 and 10-12 cm, in Beggiatoa sp. mat-associated sediments located several meters from exposed gas hydrate. Samples were collected from a research submersible (water depth 550-575 m) during two research cruises aboard the R/V Seward Johnson I and II funded by the NSF Life in Extreme Environments program. The 16S rRNA gene and 16S rRNA were amplified using PCR and reverse transcription-PCR, respectively, from DNA and RNA extracted from the total microbial community. The primers targeted microorganisms at the domain-specific, i.e., Bacteria and Archaea, and group-specific, i.e., sulfate-reducing bacteria (SRB) and putative anaerobic methane-oxidizing (ANME) archaea, level. Sequence analysis of the Bacteria clones revealed that the microbial communities were primarily dominated by Deltaproteobacteria. Other Proteobacteria classes, including Epsilon- and Gammaproteobacteria, represented a large fraction of the total microbial community isolated from the sediment overlying hydrate sample and the metabolically active fraction of the 0-2 cm sediment depth sampled from the Beggiatoa sp. mat-associated sediments. Sequence analysis indicated the majority of the archaeal clones were most closely related to Methanosarcinales, Methanomicrobiales and distinct lineages within the ANME groups. Several novel lineages were identified including a fourth ANME-2 clade, i.e., ANME-2D, and three clades with no closely related previously sequenced 16S rRNA gene clones or isolates, i.e., Unclassified Bacteria groups 1 and 2 and Unclassified Euryarchaeota. These studies represent the first 16S rRNA gene and 16S rRNA phylogenetic-based description of microbial communities extant in sediment-free gas hydrate and in methane-rich hydrate-associated and Beggiatoa sp.-associated sediments from a hydrocarbon seep region in the Gulf of Mexico.

The spatial structure and temporal evolution of sea breeze and the latitudinal distribution of propagation and mixing of sea breeze driven near-inertial ocean response in the Gulf of Mexico are investigated using comprehensive data sets and a non-linear numerical model. Near 30�N, inertial oceanic response is significantly enhanced by a near-resonant condition between inertial and diurnal forcing frequencies. Observational results indicate that sea breeze variability peaks in summer and extends at least 300 km offshore with continuous seaward phase propagation. The maximum near-inertial oceanic response occurs in June when there is a shallow mixed layer, strong stratification, and an approximately 10-day period of continuous sea breeze forcing. Near-inertial current variance decreases in July and August due to the deepening of the mixed layer and a more variable phase relationship between the wind and current. River discharge varies interannually and can significantly alter the oceanic response during summer. During 1993, the ?great flood? of the Mississippi River deepens the summer mixed layer and reduces the sea breeze response. The near-inertial currents can provide considerable vertical mixing on the shelf in summer, as seen by the suppression of bulk Richardson number during strong near-inertial events. Three-dimensional idealized simulations show that the coastal oceanic response to sea breeze is trapped poleward of 30� latitude, however, it can propagate offshore as Poincare waves equatorward of 30� latitude. Near 30� latitude, the maximum oceanic response to sea breeze moves offshore slowly because of the near-zero group speed of Poincare waves at this latitude. The lateral energy flux convergence plus the energy input from the wind is maximum near the critical latitude, leading to increased vertical mixing. This local dissipation is greatly reduced at other latitudes. Simulations with realistic bathymetry of the Gulf of Mexico confirm that a basin-wide ocean response to coastal sea breeze forcing is established in the form of Poincare waves. This enhanced vertical mixing is consistent with observations on the Texas-Louisiana Shelf. Comparison of the three-dimensional and one-dimensional models shows some significant limitations of one-dimensional simplified models for sea breeze simulations near the critical latitude.

Sailfish, Istiophorus platypterus, are commonly taken by the recreational and commercial fisheries in the Gulf of Mexico (Gulf) and larvae are frequently reported in the region, indicating the Gulf's potential role as spawning and/or nursery ground of sailfish. Five ichthyoplankton surveys were conducted in shelf and slope waters of the northern Gulf during the summers of 2005 (May, July, September) and 2006 (June, August). Surveys were conducted off the Texas and Louisiana coasts from 27 - 28N and 88 - 94W. During the two year study, 2,426 sailfish larvae were collected, ranging in size from 2.0 - 24.3 mm standard length (SL). Sailfish larvae were collected in 45.0% of collections with a peak density ranging of 51.5 larvae per 1000 m-2 of water sampled, and the highest larval abundances were observed within frontal features of the Loop Current. Sagittal otoliths were extracted from 1,236 larvae, and otolith microstructure analysis indicated sailfish ranged in age from 5 - 25 days post-hatch. Hatch-date distributions indicated fish were from early May to mid September spawning and/or hatching events. Instantaneous growth coefficients (g) ranged from 0.113 to 0.127 with intra- and inter-annual variations in growth observed. Growth coefficients correspond to a 10.7 - 11.9% increase in length per day. Instantaneous daily mortality rates (Z) were estimated from regressions of the decline in loge-transformed abundance on age and ranged from 20.4% to 29.2% per day suggesting large losses during the early life interval. Instantaneous weight-specific growth coefficients (G) ranged from 41.5% to 45.9% per day and were indexed to daily mortality to assess intra- and inter-annual variation in recruitment potential. Recruitment indices > 1.0 were observed during all surveys, suggesting cohort biomass was increasing and that conditions were favorable for growth, survival and recruitment. The results of this study indicate that the northern Gulf represents viable spawning and nursery habitat of sailfish and the sustainability of Atlantic sailfish populations may be linked to spawning in the Gulf.