The northern Gulf of Mexico (GOM) is one of the most productive oil and gas exploration areas in the world, currently containing approximately 3,800 offshore platforms. These platforms serve as artificial reefs in shallow water, which until their introduction was nearly devoid of shallow hard substrata. The question is raised whether this newly available substrate could help expand coral populations in the GOM. In this study, I examined adult scleractinian corals on oil and gas platforms in the northern GOM, in the vicinity of the Flower Garden Banks (FGB; approximately 180 km SE of Galveston, Texas) and attempted to determine the degree of genetic affinity among the natural and platform populations there. Adult coral tissue samples were collected from seven platforms surveyed in the region of the FGB at a depth range of 0-30 m. The three most abundant scleractinian, hermatypic species were sampled: Madracis decactis, Diploria strigosa, and Montastraea cavernosa. Genetic variation was revealed by Amplified Fragment Length Polymorphisms (AFLPs), a DNA-fingerprinting technique based on the polymerase chain reaction (PCR). This tool successfully distinguished between closely related colonies derived from populations on different platforms and on the two Flower Garden Banks. AMOVA analyses indicated that the East and West FGB were homogeneous for Madracis decactis and Diploria strigosa; however, the Montastraea cavernosa populations at the two banks were significantly different. Randomized data sets of two Madracis decactis populations were run with AFLPOP using a minimum log-likelihood difference of zero and one. These analyses determined that a log-likelihood difference of one is a more conservative and more reliable option, and all subsequent analyses were run using this setting. AFLPOP analyses showed that Montastraea cavernosa at the two banks was highly self-contained, indicating a possible high degree of self-seeding with regard to this species. It appears that Madracis decactis, a brooding species, is highly effective at dispersing to neighboring habitats over distances of kms to tens of kms. By comparison, Diploria strigosa and Montastraea cavernosa, both broadcasting species, are not. They may be more effective at larger scale dispersal, but this remains to be demonstrated.

The Mississippi Sound is a bar-built estuary that parallels the Mississippi Coast. It is bounded on the west by the St. Bernard lobe of the Mississippi River delta, Mobile Bay to the east, and the Gulf Coast barrier islands to the south. Few studies have investigated the late Holocene history of Mississippi Sound. In the present study, historical deposition in the Sound has been investigated using core data collected throughout the western, central, and eastern Mississippi Sound. The sediments within Mississippi Sound compose a complex depositional system that have responded to changes in sea level and hydrodynamics. Two factors that influence the wave dynamics within Mississippi Sound are changes in water depth and exposure to the open Gulf of Mexico. Decreases in water depths have an inverse relationship to the shear velocity produced by waves. Thus, by decreasing water depth from 3 m to 2.5 m, the shear velocity (U*), produced from a wave with H = 0.9 m and T = 4 s, would increase from ~0.006 m/s to 0.008 m/s. These changes may be recorded in the sedimentary fabric as changes in the sedimentary facies from a low-energy muddy facies to a higher-energy sandy facies. However, increased exposure to the open Gulf of Mexico allows for larger deep-water waves to impact the Sound. Therefore, by exposing Mississippi Sound to increased wave energy from the Gulf of Mexico, conditions become favorable for the deposition of the higher-energy sandy facies in the deeper water of Mississippi Sound. The sedimentary fabric and geochronology data of recent deposition suggest that physical processes actively rework the sediment in the top 5 cm of the sea-bed; however, biological processes continuously rework the sediment to a depth of 10-12 cm resulting in the destruction of most of the physical stratification. Tropical cyclones impact the sedimentary fabric such that they are recorded as sandy event beds within a muddy matrix. Approximately 8-26% of the sediment column was deposited by recordable storm events in the Western Mississippi Sound, whereas smaller storm events and typical estuarine processes deposited the other 74 92% of the sediment column.

The need for effective marsh restoration techniques in Louisiana is a pressing issue as the state continues to lose coastal wetlands. Returning spoil banks to canals, known as "backfilling", is an attractive restoration option because it restores marsh, prevents future wetland loss, and is cost effective. The direct conversion of marsh to canals and spoil banks accounted for over 22% of Louisiana's wetland loss from 1930 to 1990, and the indirect losses associated with canal dredging are even larger. The restoration success of 30 canals, backfilled twenty years ago, was examined in this study and compared to restoration success shortly after backfilling. Ultimately, the success of backfilling was controlled by the amount of spoil returned to the canal and the position of the canal in the marsh. Up to 95% of the spoil area was restored to marsh when the spoil banks were adequately removed, but only 5% of the spoil area was restored at sites where spoil removal was poor. Restoration of organic matter, bulk density, and water content of the former spoil areas was also constrained by the adequacy of spoil removal. Backfilling restored 80% of the organic matter and 94% of the bulk density and water content after twenty years at sites where spoil was properly removed. The plant species on the former spoil areas often did not match those of the surrounding marsh, and the differences were directly correlated with the amount of spoil removed. Canals backfilled in areas of more intact marsh showed greater restoration success than canals backfilled in highly degraded marshes. This study indicates that the benefits of backfilling continue to increase over time, although complete restoration will take longer than twenty years, particularly for soils. Improving the completeness of spoil removal, coupled with appropriate site selection, could speed up the restoration process and enhance the success of future backfilling projects.

The cownose ray, Rhinoptera bonasus, is an elasmobranch commonly observed throughout the Gulf of Mexico. Cownose rays appear to be sensitive to water temperature. I performed laboratory experiments and collected field data to obtain basic life history information, and used the information to configure an individual-based bioenergetics model. The bioenergetics model was coupled to a matrix projection model, and the coupled models were used to predict how warmer and cooler water temperatures, compared to current conditions, would affect the growth and population dynamics of the cownose rays. The life history study determined weight at age, maturity by weight, and fecundity for cownose rays. Verified vertebral age estimates ranged from 0+ to 18+ years. Likelihood ratio tests indicated that a combined sexes Gompertz model best described the growth of cownose rays. A relationship between maturity and weight was estimated; annual fecundity was determined to be one pup. The laboratory experiments resulted in the estimation of standard oxygen consumption rate as a function of weight and temperature, and a Q10 value of 2.33. The bioenergetics model predicted that rays would have a slower growth rate and reach smaller average weights at age (9.6-16.8% smaller) if they inhabited 2oC warmer water than baseline (current) conditions, while individuals would grow faster and attain heavier weights at age (13.4-17.2% heavier) under a 2oC cooler scenario. Changes in growth rates under the warmer and cooler conditions also lead to changes in age-specific survivorship, maturity, and pup production, which I used as inputs to a matrix projection model. Faster growth of individuals under the cooler scenarios translated into an increased population growth rate (4.4-4.7%/year versus 2.7%/year under baseline), shorter generation time, and higher net reproductive rates, while slower growth under the warmer scenarios translated into slower population growth rate (0.05-1.2%/year), longer generation times, and lower net reproductive rates. Elasticity analysis indicated that population growth rate was most sensitive to adult survival. Reproductive values by age were highest for intermediate ages. The combination of coordinated laboratory experiments, field data collection, and coupled individual-based bioenergetics and matrix projection models provides a powerful approach for relating physiology to demographic responses.

Bottom-water hypoxia (≤2 mg O₂ l^-1) usually occurs on an annual basis on the Louisiana/Texas continental shelf from mid-May through mid-September over a large area (up to 20,000 km² in mid-summer). The effects of hypoxia on the benthic infauna (potential prey) for demersal fish were examined, because changes in optimal diet can lead to negative impacts on growth and reproduction. Benthic samples were taken in three areas (inshore and offshore out of hypoxia and in the hypoxic area) during August 2003. Samples were also taken monthly from September 2003 to October 2004 at a fixed station (C6B) where summer hypoxia occurs consistently. The mean abundance of the benthic infauna in the three summer areas were not significantly different indicating similar prey abundances found in the study area. Diverse infaunal communities exist offshore of the hypoxic zone with similar species composition compared to the inshore but different compared to the hypoxic area. An abundance of benthos at the surface was not found at the summer 2003 hypoxic stations; therefore there was not an abundance of available prey at the surface. However, benthos migrated toward the surface at station C6B in June and July 2004 during hypoxia, providing an increase of prey at the surface compared to other months. During the spring months, the infaunal community was more diverse and abundant compared to the post hypoxic months (August, September, and October), which suggests fewer and less diverse potential prey in the fall for demersal predators. The most abundant prey items for demersal fish in the study area were polychaetes and secondarily molluscs. The benthic community abundances during the summer 2003 and 2004 were not expected and may be due to the storm events in summer 2003 and shorter duration of hypoxia in summer 2004.

Ecosystem response, stakeholder interactions, and the policy implications to a wetland assimilation project are reported here for the City of Mandeville, St. Tammany Parish, Louisiana. Between September 1998 and October 2004, input of secondarily treated wastewater effluent was found to have a net positive effect on the downstream wetland receiving basin. The major hydrologic inputs to the system are the effluent, precipitation, and back water flooding from Lake Pontchartrain. Nutrient levels were generally low except in the immediate vicinity of the outfall and removal efficiencies of N and P ranged from 44% to 87% and 25% to 93%, respectively. On average, TN and TP removal efficiencies were 59% and 69%, respectively, for the study period. Aboveground net primary production of the freshwater forest system was high downstream of the effluent discharge. Also downstream of the outfall, accretion rates were double the rate of relative sea level rise in the area. Re-direction of nutrient-enhanced effluents from open water bodies to wetland ecosystems may maintain plant productivity, sequester carbon, maintain coastal wetland elevations in response to sea-level rise in addition to improving overall surface water quality, reducing energy use, and increasing financial savings. Stakeholder interactions can often be as difficult to resolve as scientific questions. Further progress to improve water quality and regulate point source pollution often requires adjustment in policy strategies to enhance society's capacity to deal with more problematic issues of non-point source pollution. High cost and economic impacts on communities will propel the search for cost-effective water quality management. In addition, cooperation between the public and private sectors can build trust, consensus, and the ability to implement coastal resource projects. In this Mandeville, Louisiana, case, the use of science-driven solutions in natural resource management was successful in developing cost savings and coastal wetland preservation from the renewable ecological engineering technology of wetland wastewater assimilation. Integration of a national carbon and wetland policy may stimulate investments in energy efficiency and wetland enhancement. The next step must be the development of an annual revenue source to encourage state and private landowners to work together by providing incentive to promote wetland enhancement.

Studies in belowground dynamics are limited mainly due to the difficulty of studying roots despite wide recognition of its importance. This dissertation focused on methods for analyzing mangrove roots, root responses to phosphorus and flooding, and variation in root production between forest types. Techniques to separate live and dead roots such as colorimetric, fluorescence, buoyancy, and visual assessment were compared. The traditional method of visual assessment combined with root buoyancy was accurate, fast, and applicable to larger samples. Additionally, techniques such as rhizotrons, root ingrowth cores, and root image analysis were useful to study mangrove roots. Root and litter production, and hydro-edaphic conditions were determined seasonally for one year at eight sites (fringe, basin, and scrub forest types) in Southwest Florida. Root production was equal or greater than litter production showing spatial variation, especially in biomass allocation. Correlations with soil variables indicated that above and belowground processes respond differently to environmental conditions. The combined root+litter production was a good predictor of flooding and nutrient stress. Mangrove root production and morphology responded to nutrient enrichment (additions of nitrogen or phosphorus) depending upon forest type and stress factors interacting with resource acquisition. Root production increased with low nutrient availability and high flooding, and decreased with high salinity and nutrient availability. Nutrient enrichment increased the specific root length and surface area at the basin-monospecific site, and decreased the specific surface area at the scrub forest. Greenhouse experiments were conducted to study root dynamics of Rhizophora mangle and Avicennia germinans seedlings in response to phosphorus availability and flooding regimes. Mangrove species differed in their tolerance of flooding, and their plasticity to nutrients availability. The more flood tolerant species, R. mangle, was slower growing. The faster-growing species, A. germinans, exhibited limitations to flooding and changes in root morphology that altered the surface area for absorption of nutrients. These results indicate a trade-off between root strategies to tolerate flooding and to acquire nutrients. This study contributes to a better understanding of how mangrove ecosystems function. Additional work in other geographic areas and sedimentary settings is needed to provide a broader perspective on belowground processes in mangrove systems.

Floating marshes are wetlands of emergent vascular vegetation which have a significant mat of live and dead roots, decomposing and dead organic material, and mineral sediments. This mat moves vertically as ambient water levels rise and fall. These marshes have unique hydrology in that overland sheet flow is reduced or eliminated leaving no inorganic sediment input, but there is extensive belowground water exchange. The effect of significant sediment introduction into wetlands with floating marshes is unknown. The purpose of this study was to observe the marsh mat response to Mississippi River sediment addition and measure species composition change and growth response of vegetation. Study sites were Cypress Canal in Barataria Basin and Turtle Bayou in Terrebonne Basin, Louisiana, USA. Both are thin-mat floating marshes dominated by Eleocharis baldwinii. At each site, twenty plots were constructed around a boardwalk built on the marsh. Each 1 m² plot was randomly assigned one of five treatments: low, medium, and high sediment additions, and two controls. With increasing sediment addition, there were significant increases in bulk density and significant decreases in percent organic matter in the top 25 cm of the marsh mat. No significant differences in water level over the mat were found between treatments, indicating that buoyancy was not affected by sediment addition. Vegetation species composition after one growing season was not affected by the addition of sediment to the marsh mat. The number of species present was not affected. Aboveground biomass showed trends of increase with sediment addition, though these trends were not statistically significant. Belowground biomass was not significantly affected by the addition of sediment. Neither plant tissue nutrients nor soil nutrient levels showed much significant change with the addition of sediment to the marsh. Most of the sediment added remained in the top 25 cm of the marsh mat. Results presented suggest that some addition of sediment to the surface of a fresh water thin-mat floating marsh will not negatively affect the buoyancy of the mat. Increased bulk density facilitates increased vegetative growth, as is found in prior studies. Future data must be collected to determine more definite results.

This is the first study to compare nekton use and habitat value among Spartina alterniflora (Spartina), Avicennia germinans (black mangrove), and transition (S. alterniflora and A. germinans) sites within Louisiana's salt marsh-mangrove ecotone. Fishes and crustaceans were collected in Caminada Bay during fall 2003 and spring 2004 using 4 m2, bottomless lift nets. Although analyses were unable to demonstrate significant differences in fish (p=0.0753) and crustacean (p=0.1457) densities and species composition (p=0.8801) across sites, habitat-specific trends in nekton use were evident. Fishes, including gulf killifish and sheepshead minnows, showed affinities for the Spartina site, while crustaceans, especially white shrimp, were more associated with the mangrove site. Total fish biomass (p=0.0396) and gulf killifish biomass (p=0.0223) and densities (p=0.0543) were significantly greater at Spartina than mangrove sites. White shrimp biomass was significantly greater at mangrove than Spartina (p=0.0062) and transition sites (p=0.0143) and gulf stone crab densities were also higher at mangrove than transition sites (p=0.0061). Habitat type, areal stem cover (ASC), turbidity, and temperature explained 52% of the variability in nekton densities. Greater structural complexity (ASC, p<0.0001) at the mangrove site may increase refuge value for crustaceans given that (1) most were juveniles, including white shrimp, brown shrimp, blue crabs, and gulf stone crabs, and (2) white shrimp and brown shrimp were positively associated with ASC. Lower ASC and greater flooding depths (p=0.0318) and durations (p=0.0065) at Spartina than at the higher elevation mangrove site may benefit larger nekton by increasing access to the flooded marsh. The transition site had similar vegetation characteristics as the Spartina site, but flooding depths and durations resembled the mangrove site. Nekton densities were positively related to flooding duration at mangrove (fish, p=0.0031; crustacean, p=0.0040) and transition sites (fish, p=0.0018). Low fish use at mangrove and transition sites during spring 2004 suggests that (1) reduced hydroperiod negatively affects fishes, and (2) Spartina marshes may become especially important when meteorological events reduce access to mangrove and transition habitat types. More research is necessary to determine if these findings are representative of Louisiana's salt marsh-mangrove ecotone statewide, and to understand the fisheries implications of continued mangrove expansions.

There are currently over 4000 functioning oil and gas platforms in the northern Gulf of Mexico (Gulf). Platform operations, and their prior drilling operations, produce trace amounts of lead, barium, vanadium, and lanthanum residues that are leached into the surrounding waters and are deposited on the sea floor. These residues have isotopic ratios different from those typical of the Gulf seafloor and can be used as harmless fingerprints if they become incorporated into hard-parts or tissues in fishes associated with oil and gas platforms. From 2002 to 2004, 115 red snapper were collected from oil and gas platforms and artificial reefs off Louisiana and Alabama. Otoliths were removed and analyzed using Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). The objective of this study was to determine if a trace element isotope ratio fingerprint could be detected and described as unique to red snapper inhabiting the platforms. Stepwise and canonical discriminant function analyses were used to compare red snapper otolith fingerprints from on and off platforms, and from east and west of the Mississippi River. Classification accuracies based on the probability of an individual fish being correctly classified into the habitat from which it was sampled were over 90% for each of the two main comparisons. When comparing the elemental composition of red snapper otoliths from Louisiana oil and gas platforms and Louisiana artificial reefs, the classification accuracy was 93.75%. When comparing the elemental composition of red snapper otoliths from Louisiana artificial reefs and Alabama artificial reefs, the classification accuracy was 91.06%. Vanadium 51, Lead 206, Lead 207, and Lead 208 all appear to be linked with oil and gas platforms or their prior drilling operations, as the concentrations of these four elements or isotopes were significantly higher in otoliths sampled on platforms in Louisiana than in otoliths sampled from artificial reefs in either Louisiana or Alabama. Results from this study indicate that it may be possible in future studies to determine if oil and gas platforms contribute disproportionately to the survival of juvenile and adult red snapper, and as such can be considered viable management tools for stock rebuilding.