Gas hydrate has been identified by drilling in Alaminos Canyon block 818, within the Perdido Fold Belt, outboard of the Sigsbee Escarpment, in approximately 2750 meters (9000 feet) of water. At the location of the AC818 #1 (“Tigershark”) well, the gas hydrate occurs within the top 20 m (65 feet) of an approximately 90 meter (300 feet) thick Oligocene Frio sand, a volcaniclastic sandstone rich in lithic fragments, feldspar, and volcanic ash. The Frio reservoir is folded into a 4-way closed anticline. At the crest of the anticline, the sand is partly eroded and is unconformably overlain by 450 m (1500 feet) of Pleistocene shale and sand. The unconformity surface is also in a 4-way closed geometry and defines the top of the hydrate reservoir at the well. The rock is poorly consolidated and has porosity as high as 42% from log data. LWD logs indicate that the hydrate zone has high resistivity and high P-velocity (2750 mps: 9000 fps). The underlying wet sand at the base of the gas hydrate stability zone (GHSZ) has low resistivity and P-velocity (Vp: 1500 mps: 5000 fps). The very low Vp indicates the presence of low-saturation free gas ("fizz gas"). The large velocity contrast creates a strong response in seismic data which was inverted into a 3D gas hydrates saturation (Sgh) volume. Elsewhere in the GHSZ, seismic character was used to predict predominant sediment facies. Relative high stand facies, which are more clay-rich, will generally be characterized by more continuous and parallel seismic reflectors. In contrast, relative low stand facies, which have more sand content, will be characterized by more hummocky, discontinuous seismic character and will often lie on erosional surfaces, particularly in uncompacted sediments. Understanding the stratigraphy throughout the section is important, since sand will often provide beneficial reservoir conditions, while clay will provide more impervious sealing qualities. The seismic interpretation also identifies migration pathways, such as faults and gas chimneys, and the presence of available gas, which are necessary to charge reservoirs within the HSZ.

In the northern Gulf of Mexico, hypoxia occurs annually during the summer on the Texas-Louisiana shelf. This study examines the distribution of particulate and dissolved components relative to hydrography, to better understand the processes controlling the development of hypoxia. Particulate matter on the Texas-Louisiana Shelf has three major sources – river plumes, primary production, and resuspended sediments. The sources and processes controlling distribution and transport of particles are investigated using optical proxies (backscattering, chlorophyll fluorescence, Colored Dissolved Organic Matter fluorescence (CDOM)), temperature, salinity, dissolved oxygen (DO), and in-situ sampling during June and August 2011 cruises of the Mechanisms Controlling Hypoxia program (hypoxia.tamu.edu). Discrete samples of particulate matter (PM) and particulate organic carbon (POC) concentration were obtained for analysis and calibration of optical instruments interfaced with a profiling CTD, a towed undulating CTD (Acrobat), and the ship’s flow-through system along the shelf from south of Galveston, Texas, to east of the Mississippi delta. The results of this study support a previously hypothesized concept of three primary areas of organic and inorganic particle composition and processes that dominate those areas – river-dominated water, highly productive surface waters, and clear, nutrient-poor low-productivity surface waters. The distribution and bulk composition of particulate matter in the northern Gulf of Mexico, plus the distribution of chlorophyll fluorescence and CDOM suggest that subpycnocline primary production plays a role in determining oxygen concentration in subpycnocline waters away from the river-dominated water.

The overall objective of the research presented here was to combine multiple geochemical parameters and molecular characterizations to provide a novel view of active microbial community ecology of sediments in a large-river deltaic estuary. In coastal and estuarine environments, a large portion of benthic respiration has been attributed to sulfate reduction and implicated as an important mechanism in hypoxia formation. The use of high-resolution sampling of individual sediment cores and high throughput nucleic acid extraction techniques combined with 454 FLX sequencing provided a robust understanding of the metabolically active benthic microbial community within coastal sediments. This was used to provide further understanding and show the importance of simultaneously analyzing the connectivity of sulfur and iron cycling to the structure and function of the microbial population. Although aqueous sulfide did not accumulate in the sediments of the northern Gulf of Mexico, active sulfate reduction was observed in all locations sampled. Microbial recycling and sequestration as iron sulfides prevented the release of sulfide from the sediment. Prominent differences were observed between the sample locations and with depth into the sediment column. This study emphasized the importance of combining novel molecular techniques with simultaneous traditional geochemical measurements to show the interdependence of microbiology and geochemistry. In addition, this study highlights the need to consider microbial community biogeography along with small-scale variations in geochemistry and biology that impact the overall cycling of redox elements when constructing biogeochemical models in marine sediments.

The long-term fate of hydrocarbons in the Gulf of Mexico (GOMx) following the 2010 Deepwater Horizon oil spill has yet to be fully characterized. Elemental (% C and % N), stable isotopes (δ13Corganic), and polycyclic aromatic hydrocarbon (PAH) molecular signatures were investigated in shelf and slope sediments collected in October 2010 and 2011 to gain insight into processes affecting the distribution and fate of spilled Macondo oil. Particulate organic carbon (POC) ranged between 1.55 and 2.22 wt. % in 2010 and 0.55 and 2.06 % in 2011 while the corresponding δ13Corganic ranges were from -23.37 to -20.77 ‰ (vs. PDB) in 2010, and -22.68 to -20.75 ‰ (vs. PDB) in 2011. Ranges of total polycyclic aromatic hydrocarbon (TPAH) concentrations were from 72.57 to 7,543.53 ng/g in 2010 and 25.55 to 16,582.77 ng/g in 2011. The range of measured values represented significant deviations from previous background measurements. This provided the basis for concluding that the Macondo spill altered the “background” organic carbon and hydrocarbon signature, that Macondo oil has weathered and/or biodegraded in the year following the spill, and that a significant spatial trend of hydrocarbons extended from the Macondo well across the northern GOMx in October 2010 and 2011.

This dissertation addresses large-scale trends in composition, density, taxonomic and functional diversity in deep-sea benthic polychaete communities in the Gulf of Mexico (GoM). The study includes samples from two major sampling programs: the Deep Gulf of Mexico Benthos (DGoMB) program (2000–2002) (51 stations, 200-3700 m) and the SIGSBEE program (Universidad Nacional Autónoma de México), 2008-2010 (27 stations on the Sigsbee Abyssal Plain). Polychaete density decreased exponentially with depth. Alpha diversity did not show a mid-depth maximum and reached its peak near the Mississippi trough. Feeding guild diversity was also highest in the Mississippi trough. The environmental parameters that determine diversity and density of polychaete assemblages and species distribution ranges were examined. Depth, export flux of particulate organic carbon (POC), percent sand and silt were the best predictors of heterogeneity of polychaetes in the GoM. We performed an ecological niche modeling analysis (ENM) based on ‘presence-only’ data of four cosmopolitan species belonging to the Cirratulidae and Spionidae in the GoM. The GoM, being a semi-enclosed ocean basin, offers complex topographic features and hydrographic processes. Comparisons of the overall polychaete diversity and richness patterns from this study for this region indicate a strong geographic variation with increasing depth and distance from the shore. Additionally, the environmental gradients observed play a major role in shaping the spatial distribution of polychaete communities in this region.

A combination of in situ sampling and real-time ocean observations was used to investigate the processes responsible for the formation and the areal extent of Texas coastal hypoxia from 2002 to 2011. In situ sampling, real-time mooring and buoy observations, and multivariate statistical modeling were used to investigate the physical processes driving hypoxia formation. Geostatistical interpolation (ordinary kriging) models were tested to compare the differences in annual hypoxia area on the Texas shelf. Results from these two sections were integrated into recommendations for improving federal hypoxia monitoring and mitigation strategies in the northwestern Gulf of Mexico. Winds, currents, temperature, salinity, and dissolved oxygen records revealed the annual, seasonal, and daily variability of hypoxia formation on the Texas coast from 2009 to 2011. Hypoxic events occurred from late May to late October lasting from hours to weeks. Hypoxia formation was either the result of salinity stratification, associated with the freshening of surface waters by the advection of Mississippi-Atchafalaya River freshwater westward or the wind- and current-driven upcoast or downcoast flow of Brazos River discharge. Records from 2010 and 2011 showed the variability and frequency of stratification development differs on the north and south Texas shelf. Multivariate linear model results showed contributing factors on the north Texas shelf vary annually and that primary factors for hypoxia development are near-surface current speeds and salinity-driven stratification. Interpolation models resulted in three size categories for hypoxia area: small (100 – 1,000 km^2), moderate (1,001 – 3,000 km^2), and large (3,001+ km^2). Moderate years include 2002, 2004, and 2007 and a large year was 2008. There was no increase in hypoxic area from years 2002 to 2011, but years 2007 and 2008 resulted in a hypoxic area over 5,000 km^2, which is the federally mandated hypoxia reduction target for the northwestern Gulf of Mexico. Geostatistical interpolators represent and predict the structure and spatial extent of the hypoxic area on the Texas shelf by accounting for the anisotropy of physical processes on the Texas shelf. Geostatistical interpolation models are preferred to deterministic models for developing and improving federal hypoxia monitoring and mitigation strategies on the northwestern Gulf of Mexico shelf.

Seasonal hypoxia in the northern Gulf of Mexico has been mapped extensively and is known to overlap the habitat of the brown shrimp Farfantepenaeus aztecus on the Louisiana continental shelf. Yet the impacts of Gulf hypoxia on the profitable brown shrimp fishery in Louisiana remain largely unknown. The problem is primarily attributable to nonpoint source pollution in the Mississippi River, but awareness of the problem has not resulted in an effective policy solution to stem this pollution to date. Using the combination of a quantitative data analysis to look for a correlation between Farfantepenaeus aztecus and hypoxic water, a survey mailed to shrimp fishers in Louisiana, and qualitative interviews with shrimp fishers and environmental activists and lawyers in Louisiana, I will examine the potential of a legal tool, the Public Trust doctrine, to slow nonpoint source pollution into the Mississippi River.

Pleuronectiformes (flatfishes) occur throughout the global oceans, and have high ecological and commercial importance in some areas. Though much is known regarding life history, abundance, and distribution for the benthic adult stage of flatfish species, much less is known about the pelagic larval phases of flatfishes in the open ocean. Taxonomic uncertainty and limited sampling in the oceanic Gulf of Mexico contribute to data gaps with respect to the distribution of early life history stage of flatfishes in this region. Knowledge of the faunal composition, abundance and distribution of larval flatfishes, such as members of Bothus, which have extended pelagic phases, is important for modeling their population dynamics as well as for understanding the importance of connectivity between neritic and oceanic ecosystems in their life histories. Pleuronectiform specimens utilized in this study were collected in the northern offshore Gulf of Mexico during several cruises conducted throughout 2010-2011 as part of the NOAA Natural Resource Damage Assessment (NRDA) after the Deepwater Horizon Oil Spill (DWHOS). The Offshore Nekton Sampling and Analysis program (ONSAP) was established to determine composition, abundance and distribution of deep-water invertebrates and fishes in Gulf of Mexico waters that were potentially affected by the DWHOS. Results of the first large-scale discrete-depth distributional analysis of fishes in this region revealed that flatfishes were an intrinsic component of the oceanic ichthyofauna of these waters. A total of 2365 flatfish specimens were collected in offshore waters, representing four families and 11 of the 18 genera that occur in the Gulf of Mexico. Species composition was dominated by members of the genus Bothus, which had a high frequency of occurrence in the epipelagic zone throughout the year. Citharichthys spilopterus and Trichopsetta ventralis were the second- and third-most abundant and frequently occurring taxa, respectively. Detailed spatial analyses of taxa in the epipelagic zone revealed that larvae of Citharichthys spilopterus were only collected in winter and occurred most frequently near the continental shelf break, while early life stages of Bothus spp. were more abundant at the northern convergence flow of a large anticyclonic Loop Current eddy during spring and summer.

Paracalanus quasimodo and Temora turbinata are two calanoid copepods prominent in the planktonic communities of the southeastern United States. Despite their prominence, the species and population level structure of these copepods is yet unexplored. The phylogeographic, temporal and phylogenetic structure of P. quasimodo and T. turbinata are examined in my study. Samples were collected from ten sites along the Gulf of Mexico and Florida peninsular coasts. Three sites were sampled quarterly for two years. Individuals were screened for unique ITS-1 sequences with denaturing gradient gel electrophoresis. Unique variants were sequenced at the nuclear ITS-1 and mitochondrial COI loci. Sampling sites were analyzed for pairwise community differences and for variances between geographic and temporal groupings. Genetic variants were analyzed for phylogenetic and coalescent topology. Paracalanus quasimodo is highly structured geographically with populations divided between the Gulf of Mexico, temperate Atlantic and subtropical Atlantic, in addition to isolation by distance. No significant differences were detected between the T. turbinata samples. Both P. quasimodo and T. turbinata are stable within sites over time and between sites within a sampling period, with two exceptions. The first was a pilot sample from Miami taken two years prior to the general sampling whose community showed significant differences from most of the other Miami samples. Paracalanus quasimodo had a positive correlation of Fst with time. The second was high temporal variability detected in the samples from Fort Pierce. Phylogenetically, both P. quasimodo and T. turbinata were in well supported, congeneric clades. Paracalanus quasimodo was not monophyletic, divided into two well-supported clades. Temora turbinata variants were in one clade with insignificant support for topology within the clade and very little intraspecific variation. Paracalanus quasimodo and T. turbinata populations show opposite trends. Paracalanus quasimodo occurs near shore and shows population structure mediated by hydrological features and distance, both geographic and temporal. The phylogeny shows two deeply divergent clades suggestive of cryptic speciation. In contrast, T. turbinata populations range further offshore and show little geographic or temporal structure. However, the low genetic variation detected in this region suggests a recent bottleneck event.

Low-pass Fourier filter, wavelet filter, as well as matched filter detection methods were used to detect baleen whale signals in northern Gulf of Mexico data collected by the Littoral Acoustic Demonstration Center (LADC) consortium. Some potential low frequency signals appeared on the matched filter output figure. The shape of the signals is in line with one of the typical signal shapes of fin whales--vertical down-sweeps with 18s-time interval. Another shape of the signals is in line with one of the call type shapes of Bryde's whales--down-sweeps with 7s-time interval. A high-pass Fourier filter was also used to find toothed whale high frequency sounds in the Gulf of Mexico data. The sounds featuring click trains and codas belonging to sperm whales have been clearly identified.