Many processes in the ocean are interrelated. The direction with which an eddy rotates will determine if nutrients are moved closer to the surface where they can be utilized by plankton to increase the base of the food chain, or it can restrict growth by causing the surface layer of nutrient poor water to deepen below the photic layer. The direction of current flow will also affect the temperature structure, which is a contributing factor in the density of water. A change in density can act as a barrier between the surface and deeper waters, effectively isolating the surface from deep waters. It is important to understand the physical properties in a study area in order to understand the dynamics controlling the distributions of nutrients, which influence the distribution of plankton, which influences the distribution of predator species like squid and whales. The Sperm Whale Seismic Study (SWSS) tracked the locations of sperm whales in the Gulf of Mexico. This study seeks to describe the physical environment in which they live. To that end, various physical properties observed during the SWSS cruises were processed and used in conjunction with sea surface height (SSH) fields from satellite altimetry data. The data from different years and from the same years are used to provide descriptions of the physical environment present during the SWSS cruises and how that environment changed between cruises. A time-series of currents, collected over a six month time period in 2006, is included to document how the currents are influenced by different processes found along the continental slope in the northern Gulf of Mexico. The findings indicate the observed currents are related to local SSH features. Temperature structure can be influenced throughout the upper 1000 m by these SSH features. The temperature structure is stable over time but depends on local SSH features. Properties nearer to the surface are more variable than at depth. Although the overlying wind field most likely influences the currents at 51 m no correlation between winds observed at the Brutus platform and currents observed at 51 m at the Ocean Star platform was found.

A 1-D tidal, salinity and water quality model that analyzes the impacts of freshwater diversions with median and high flow on the water level, salinity and nutrient concentration of the Barataria Basin over a 2 period is presented here. The model predicts that the salinity of Lower Barataria decreases with the introduction of freshwater diversions. The model also predicts that nutrient concentration increases in Barataria Basin and decreases in Northern Gulf of Mexico with the introduction of diversions. The model shows the impact of freshwater diversions on water level except in the neighborhood of the diversion sites are small.

Ocean nitrogen fixation and denitrification are crucial nitrogen source and sink mechanisms for the global ocean environment. While recent studies have reported that oceanic denitrification has increased over the last few decades, others have suggested that global ocean nitrogen fixation rates have been underestimated, and still others that anthropogenic perturbations have altered the global nitrogen cycle. This implies that the current estimates of the oceanic nitrogen inventory are incomplete and they need to be revised with more information. In addition, current denitrification estimates need to be reexamined due to their large associated uncertainties. Thus, I have conducted research estimating denitrification rates in three different locations: the northern Gulf of Mexico (GOM), the East/Japan Sea (EJS), and the South Pacific: from coastal to marginal to open ocean scale in different oceanographic conditions. Denitrification rates in the bottom layer (including bottom waters+sediments) at the shallow and often hypoxic northern GOM ranged from 103-544 [mu]mol N m⁻² d⁻¹ (=1.4 to 7.4 Gg N mon⁻¹ with area=3.24x10¹⁰m²), and were controlled not only by biogeochemical factors (i.e. organic matter supply and remineralization), but also by physical factors (i.e. stratification and relative contributions from different water masses). Despite high dissolved oxygen concentrations, the significant decrease in nitrate concentrations below the expected levels, low N/P ratio (<12.4), and deep nitrite peak in the bottom layer indicate a presence of denitrification in EJS, confined at the Tatar Strait and the Ulleung Basin areas. The estimated denitrification rates range from 0.3 to 33.2 [mu]mol N m⁻² d⁻¹, and was comparable to the directly measured denitrification rates from sediment samples. The high-quality repeat hydrographic datasets observed at 32°S of the South Pacific Ocean offer an opportunity to estimate water column denitrification rates on a basin-scale in the open ocean away from the Eastern Tropical Pacific oxygen minimum zones. The mean water column denitrification rates in the oxygen minimum layer of P06 line (32°S) were estimated to range between 7.1 and 18.5 [mu]mol N m⁻² d⁻¹. The results imply that, although very small at any particular site, once integrated over a basin-scale, the open ocean water column denitrification can be a significant component of the oceanic nitrogen budget. Denitrification is subject to seasonal, decadal and possibly climate scale variations. While it is commonly estimated at the oxygen minimum zones or sediments, denitrification is not merely confined to such regions only, and small amounts of denitrification occur in other oceanic parts. Once integrated, it may be quantitatively significant for the world's oceans. Denitrification is playing a significant role in local, regional, and global ocean scales. In the future, we need to consider variability of denitrification in coastal regions, and to investigate denitrification in unexpected and unexplored regions, in order to improve our knowledge on global oceanic mass balance. / text

Natural vents in the Gulf of Mexico are actively expelling water and hydrocarbons. They are ubiquitous along continental margins, and I characterize a single vent in the Ursa Basin at leaseblocks MC852/853. Seismic data reveal that the vent is elevated ~75 meters above the seafloor and is roughly circular with a ~1.2 km diameter. A transparent zone centered underneath the vent extends to ~1500 meters below seafloor; this zone is commonly interpreted to record the presence of gas. There is a strong negative polarity seismic reflection that rises rapidly at the vent’s boundaries and is horizontal within a few meters of the seafloor beneath the vent edifice. I interpret that this reflection records a negative impedance contrast, marking the boundary between hydrate and water above and free gas and water below: it is the bottom-simulating reflector. Salinities beneath the vent increase from seawater concentrations to >4x seawater salinity one meter below seafloor. Temperature gradients within the vent are ~15x the background geothermal gradient. I model the coexistence of high salinity fluids, elevated temperature gradients, and an uplifted bottom-simulating reflector with two approaches. First, I assume that high salinity fluids are generated by dissolution of salt bodies at depth and that these hot, saline fluids are expelled vertically. Second, I model the solidification of gas hydrate during upward flow of gas and water. In this model, free gas combines with water to form hydrate: salt is excluded and heat is released, resulting in the generation of a warm, saline brine. The two models result in predictable differences of salinity and temperature. A better understanding of the hydrogeological processes at vent zones is important for quantifying the fluxes of heat and mass from submarine vents and is important for understanding the conditions under which deep-sea biological vent communities exist. / text

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 Mississippi Alluvial Valley (MAV) was dominated by extensive lowland forests, but during the 20th century most of the MAV was converted to agricultural, aquaculture, and other human uses. These land-use changes created stopover migration and wintering habitats for waterfowl, shorebirds and other waterbird species. Before landscape modification of the MAV, shorebirds likely migrated past the MAV to wetlands along the northern Gulf of Mexico (NGoM). In 2010, the Deepwater Horizon oil spill impacted coastal marshes of the NGoM. The USDA Natural Resources Conservation Service implemented the Migratory Bird Habitat Initiative (MBHI) to provide waterbirds with wetlands inland of oil-impacted areas. My objectives were to 1) statistically model the waterbird community on wetlands in the MAV and NGoM, 2) estimate relative abundance of shorebird and other waterbirds in idled aquaculture ponds enrolled in MBHI and associated wetlands in the MAV and NGoM, and 3) collect shorebird feathers and blood for stable isotope analysis (13C/12C, 15N/14N) to assess foraging niches and potential migratory connectivity between MAV and NGoM habitats during 2012 – 2013. Consequently, autumns of these years were under a drought, extensively wet from Hurricane Isaac, and exhibited average precipitation in the post-hurricane recovery period which may have had an effect on waterbird assemblages differing by year, month, twice-monthly survey period, latitude, region, state, site, and water depth index. Latitude shifted north and water depth was narrowest when abundant wet habitat existed on the landscape in 2012. Bird abundances were greatest in 2011 and never recovered to these levels in 2012 or 2013, which may have reflected effects of drought concentrating birds on remaining wetlands in 2011 and subsequent to the hurricane. Stable isotope analysis of blood indicated spatial segregation of shorebird species. Neither blood nor feather carbon and nitrogen values revealed definitive linkage of sites between the MAV and NGoM. Shallow water habitat inland may be a limiting resource during migration for waterbirds, especially in drought years when other wetlands may have been limited. Thus, provision of wetlands (mudflat – 15 cm) by MBHI and other conservation strategies across the landscape may allow waterbirds access to needed resources during migration.

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.

Nearly half of the population of the United States lives in coastal regions, and millions of visitors from across the nation and world enjoy the coasts every year. Coastal and marine areas provide for recreation, economic activities essential for the financial health of the nation, and vital ecological services. As they provide so many benefits to the U.S., it is vital to protect and preserve the coastal and ocean areas from the increasing, competing demands they are facing. In order to protect and preserve these complex systems, a comprehensive approach incorporating science, engineering, humanities, and social sciences should be taken; this approach is commonly referred to as Ecosystem-Based Management. This dissertation focuses on developing a framework that can be used to identify appropriate sub-regions in Northern Gulf of Mexico coastal and marine environments for the purposes of Ecosystem-Based Management. Through this work, the roles of three management protocols used for managing coastal areas – coastal and marine spatial planning, ecosystem-based management, and integrated ecosystem assessment – were examined individually as well as their integrations with each other. Biological, ecological, physical, human, and economic indicators for partitioning an ecosystem were developed and weighted for each management protocol using the analytic hierarchy process and expert elicitation. Using the weighted indicators, a framework for identifying sub-regions and estuarine classification system was developed. The framework and classification system were applied to five estuaries within the Northern Gulf of Mexico: Barataria, Galveston, Mobile, and Perdido Bays and Mississippi Sound. Initial results from this work show that: 1. Sub-regions can be identified as associated to each other based upon indicator data values and not upon physical location. 2. Even though the weights calculated for the management protocols vary significantly, for systems that were not highly homogeneous in indicator data values, the different weights did not produce the vastly different cluster maps expected. 3. The scale work indicates that to identify appropriate sub-regions using the developed framework, a larger grid size produces more consistent results for larger systems whereas a smaller grid size produces more consistent results for smaller systems. Recommendations for further research are also presented.