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.

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.

This Dissertation combines the investigation of the sedimentological impacts of the Deepwater Horizon (DwH) blowout event in the deep-sea benthos, with the refinement and advancement of methods and approaches for high-resolution investigations of events preserved in sedimentary records. An approach that combined, rapid collection of cores, a continued annual time series collection of cores, and high-resolution sampling and analyses, in particular short-lived Radioisotopes (SLRad), enabled the temporal resolution required to detect the sedimentary response to the short-duration DwH event, and evaluate post-event sedimentation patterns at a comparable time scale (months). The collection of 179 sediment cores from 80 sites between the fall of 2010 and 2016 included four sites that were utilized as an annual time-series collection to define the sedimentary response to the DwH blowout event and how the sedimentary system evolved/recovered post-event. High-resolution (2mm) sub-sampling was utilized to maximize the temporal resolution of analyses and age control using SLRad. The rapid collection of cores to define the immediate benthic impact(s), as well as the use of time-sensitive indicators of the event that may degrade over time, as well as indicators for very short time scale (months) sedimentation, such as 234Thxs. 234Thxs inventories and mass accumulation rates (MAR’s) were one of the most diagnostic characteristics of the sedimentary response. The DwH blowout event led to a Marine Oil Snow Sedimentation and Flocculent Accumulation (MOSSFA) event that caused a depositional pulse to the seafloor. This was defined by increased sedimentation rates and the shutdown of bioturbation as indicated by 234Thxs inventories and MAR’s. The annual collection of sediment cores as a time-series allowed for continued high-resolution analyses and use of 234Thxs to determine post-event sedimentation rates and baselines on monthly time scales for direct comparison to the depositional pulse. Within ~one year sedimentation rates decreased and within three years site specific return of bioturbation occurred and sedimentation rates on monthly scale (234Thxs) stabilized. Also, within ~three years the sedimentary signature of the depositional pulse became undetectable with respect to sediment texture and composition possibly due to dilution of this indicator by mixing/bioturbation and/or compaction of the event layer. Without the use of high-resolution sampling and geochronological tools such as 234Thxs the depositional pulse would not have been detected in the sedimentary system. The continued use of these high-resolution methods allowed for further defining the magnitude of the sedimentary response to the DwH event as well as provide baseline sedimentation patterns at a monthly time scale. The annual time series defines the post-event evolution of the sedimentary system as well as the assessment of the post-depositional alterations that influence the integration and preservation of such sedimentation events in the sedimentary record. This includes the potential for re-mobilization of event sediments, potential re-exposure of ecosystems to contaminated sediments and redistribution of event sediments. Alternatively, burial and alteration of the sedimentary signature over time influences the preservation potential of sedimentation events such as DwH, with decreasing ability to detect events due to bioturbation, degradation of signature and compaction. The refinement of methodology and approaches, in particular short-lived radioisotope (SLRad) geochronology, allowed for the high-resolution determination of the sedimentary impacts of the DwH blowout event. In turn, the opportunity to investigate the DwH event in real time provided the opportunity to advance high-resolution methodologies in an applied fashion. Continued refinement of high-resolution approaches and methods, in particular geochronologies, will allow for the detection of short-duration and subtle sedimentary events in real time as well as in the sedimentary record. Through the application of such approaches and methods to real events, these methods can be further refined and assessed for their utility and limitations.

archives@tulane.edu / Salt basins are complex structural systems, showing genetic relationships between salt structures, faults, and variable sediment depositional patterns. The dynamics of salt-fault interaction, the role of shale deformation, and the influence of salt evacuation on surface features have been poorly understood. A link between all these processes is the throw history of faults adjacent to and within a salt basin. In this dissertation, I interpret industry well logs and 3D seismic data from the Terrebonne Salt Withdrawal Basin (TSWB) of southeastern Louisiana, to understand these processes. The methodology includes the use of fault throw maps, throw variations along strike and with depth, and sediment expansion indices to understand fault kinematics adjacent to sediment loads and mobile material, i.e., salt or shale. I address the histories of three faults along the northern margin of the TSWB: the Lake Boudreaux, Montegut, and Isle de Jean Charles faults. Each shows Miocene and Quaternary active phases correlated with sediment loading, separated by relative inactivity during the Pliocene. The pattern of Quaternary activity and the surface projections of these faults are consistent with a fault-controlled pattern of wetland loss, suggesting that faults in southeastern Louisiana are active. Isle de Jean Charles fault and the Lake Boudreaux fault interact with the Bully Camp and Lake Barre Salt stocks, respectively. Each stock is interpreted to have grown by a different diapiric mechanism, consistent with different spatial patterns of throw variation on the two faults, despite similar temporal histories. Throw on the Isle de Jean Charles fault increases towards the Bully Camp stock, suggesting deformation inside and outside the stock. In contrast, a decrease in the throw on the Lake Boudreaux fault and an increase in diameter of the Lake Barre stock indicate that deformation exists only within the stock. Additionally, this dissertation considers throw patterns along the southern margin of the TSWB, showing that faults linking the Dog Lake and Caillou Island salt stocks are affected by shale deformation adjacent to salt. These results show that studies of fault-related subsidence and wetland loss in coastal Louisiana need to include observations from nearby salt structures. / 1 / Akinbobola Akintomide