Over 25% of Mississippi delta (MRDP) wetlands were lost over the past century. There is currently a major effort to restore the MRDP focused on a 50-year time horizon, a period during which the energy system and climate will change dramatically. I modeled hydraulic dredging to sustain marsh from 2016-2066 and 2016-2100 under a range of scenarios for sea level rise, energy price, and management regimes. A marsh elevation model was calibrated to data from MRDP marshes. I developed a model to simulate dredging costs based on the price of crude oil and a project efficiency factor. Crude oil prices were projected using forecasts from global energy models. The costs to sustain marsh between 2016 and 2100 changed from $128,000 ha-1 in the no change scenario to ~$1,010,000 ha-1 in the worst-case scenario in sea level rise and energy price, an ~8-fold increase. Increasing suspended sediment load raised created marsh lifespan and decreased long term dredging costs. Created marsh lifespan changed nonlinearly with dredging fill elevation and suspended sediment level. Costs and benefits of marsh creation can be optimized by adjusting dredging fill elevations based on the local sediment regime. Regardless of management scenario, sustaining the MRDP with hydraulic dredging suffered declining returns on investment due to the convergence of energy and climate. Marsh creation will likely become unaffordable in the mid to late 21st century, especially if river sediment diversions are not constructed before 2030. Planners must take into consideration coupled energy and climate scenarios for long-term risk assessments and adjust restoration goals accordingly.

Coastal wetlands provide several valuable services, such as carbon (C) storage and nitrogen (N) removal. Although wetlands serve as net C sinks, wetland soils release greenhouse gases (GHGs) including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Wetlands can buffer the influx of nitrate (NO3-) by transforming it into gaseous N (N2O, N2) through denitrification microbial pathway. Salinity is a regulator of soil biogeochemistry and long- (e.g. saltwater intrusion) and short-term (e.g. storm surges, river diversions) exposures may affect soil GHG production and denitrification. In this study, soil GHG production and denitrification enzyme activity (DEA) rates were examined over the course of a growing season (May, July, October) in soils from a freshwater, intermediate, brackish, and saline marsh. The response of GHG production and DEA rates were determined both under ambient and altered salinities (0, 10, 20, 30 psu). Soil CO2 and CH4 production rates decreased by 83% and >99%, respectively from the freshwater to saline marsh at ambient salinity. Soil N2O production rates did not vary across marshes, whereas, DEA was highest in May in the intermediate and brackish marshes. Short-term salinity exposure increased soil CO2 production in May and October, however, in July, soils displayed lower quality organic matter (high soil C:N), constraining respiration rates. Short-term salinity exposure decreased CH4 production, but increased N2O production in all months. Soil DEA displayed minor decreases with short-term salinity exposure. Soil GHG production in low salinity marshes (e.g. freshwater) had stronger responses to short-term salinity exposure than high salinity marshes (e.g. saline). Collectively, these results indicate that GHG and DEA rates do not always show the same responses to long-term salinity exposure, which results in shifts of vegetation structures, microbial communities, and soil properties compared to short-term salinity exposure. Sustained shifts to fresher conditions along salinity gradients may increase soil CO2 and CH4 production and short-term salinity exposure may increase CH4 production, but decrease soil CO2 and N2O production. Restoration activities (i.e. river diversions) that consider the interactive effect of salinity on C and N cycling can help reduce GHG footprint and increase nutrient buffering capacities of coastal wetlands.

The Louisiana-Texas coast is one of the largest areas of seasonal, coastal hypoxia. The hypoxic zone has increased in size since the 1900s and has significantly increased in thickness since 1985. Hypoxia can negatively affect fish through direct mortality, reduced fecundity, and reduced preyavailability. Movement algorithms were used to model fish movement and avoidance of hypoxia in 2-D and 3-D with static and dynamic environmental fields. Output from a 3-D, coupled, hydrodynamic-water quality model was used for the environmental conditions of the model. A particle tracking module for the hydrodynamic model was used to track fish movement. Movement algorithms were added to the tracking module to allow for active movement. Three movement algorithms for use outside of hypoxic conditions were compared in static 2-D scenarios. There was not a large difference in hypoxia exposure for the three algorithms, but there was a difference in sinuosity (amount of wiggle in the fish track). Comparing static and dynamic environmental fields in 2-D resulted in higher exposures for dynamic conditions. There was also an unexpected effect from a narrow region of normoxic water surrounded by hypoxic water. The presence of this thin area resulted in more outliers in hypoxia exposure. Three algorithms for hypoxia avoidance were compared in dynamic conditions. Two of the algorithms were found to be similar, but a third that used both dissolved oxygen and temperature as inputs had much higher exposures. Balancing the two environmental cues resulted in poor hypoxia avoidance. Comparing 2-D and 3-D scenarios resulted in lower exposure for fish in 3-D scenarios. Two different methods of perception ranges were used and found to result in similar hypoxia exposures. The research highlighted the need to include 3-D movement in fish models for the Gulf of Mexico hypoxia region. Also, high-resolution field data need to be collected to calibrate and validate such models and facilitate selection of appropriate movement algorithms.

The impact (i.e., defoliation and mortality) associated with large-scale natural disturbance events is capable of significantly altering ecosystem structure (e.g., biomass) and function (e.g., productivity) in mangrove wetlands. These pulsing events provide an opportunity to assess ecosystem resilience (i.e., recovery to pre-disturbance conditions) by evaluating the immediate and long-term ecosystem response trajectory (i.e., disturbance magnitude, recovery time). I hypothesized that 1) there are specific properties of disturbance that can be characterized and fit to a general forest disturbance model, and that 2) a mangrove forest recovery trajectory (i.e. recovery duration and rate) is dependent on the disturbance magnitude and initial forest structure, such that species with optimal ecophysiological traits (i.e., resprouting capacity, shade tolerance) will recover at a faster rate. I used long-term (15 year) data sets obtained from three mangrove sites (SRS-4, SRS-5, SRS-6) along the Shark River estuary, southwestern Florida Everglades, USA. The disturbance events I evaluated included three hurricanes (category range: 1-Cat.4) that preceded two major events: Hurricane Wilma (category 3) in 2005 and a cold snap in 2010. Hurricane Wilma caused >90% defoliation and 6-15% tree mortality and the resulting disturbance magnitude was a decrease in annual Litterfall Net Primary Productivity (NPPL) by at least 65% in SRS-5 (5.53 Mg C ha-1 yr-1) and SRS-6 (7.84 Mg C ha-1 yr-1), yet, NPPL recovered within 4-5 years. Similarly, the SRS-6 had the greatest reduction from pre- (2001-2004) to post-Wilma (2009-2015) periods for the stem Net Primary Productivity (NPPS; 20%), basal area (28%), and stem density (40%) variables. The cold snap also caused significant defoliation (3-fold increase in NPPL), but productivity recovered within one month. Impact from the hurricanes preceding Wilma showed that lower intensity storms were also capable of significantly impacting NPPL via defoliation (up to 2-fold increase). My results showed that disturbance impact and magnitude are directly coupled and resulted in different response trajectories among the sites and forest properties. The findings and discussion of the mechanisms influencing response trajectory included in this thesis will help to further advance the development of such models and provide comparative information to advance our understanding of disturbance theory.

Water quality is examined in two contrasting estuaries, Barataria Bay and Apalachicola Bay, in the northern Gulf of Mexico (NGOM) using in situ and satellite observations. The two estuaries considered in this study are unique - Barataria Bay represents a sediment-starved degrading system while Apalachicola Bay, a naturally intact system, is threatened by a two decade long tri-state water distribution conflict. The present state of water quality parameters, their controlling processes, and distributions are largely limited due to scarcity of synoptic measurements in these estuaries. In this study, a Landsat-based band-ratio algorithm is presented first to examine spatial variability of CDOM abundance during major forcing events in Barataria Bay. The results show that the meteorological and hydrological forcings tend to disrupt general trends of CDOM in spring and winter when the bay experiences elevated Mississippi River discharge and the passages of cold fronts. The idea of using a band-ratio algorithm is extended further to study CDOM dynamics, for the first-time using VIIRS sensor, in Apalachicola Bay. With conservative CDOM-DOC relationships, NCOM-based surface currents, and empirically-derived CDOM maps, DOC export fluxes are estimated which represent ~7% and ~21% of the 110-year mean spring and fall exports for the Mississippi River. A 7-year time-series of turbidity and Landsat imagery are used to demonstrate a simple but robust technique to monitor turbidity in Apalachicola Bay. Seasonal turbidity maps indicate distinct patterns of moderate to high turbid waters in spring and winter, and low to moderately turbid waters in summer and fall. Water quality monitoring strategy presented in this study supports the US EPAs Clean Water Act to protect human-health and the environment. The empirical relationships presented in the previous studies of this dissertation are limited to area of studies; however, a VIIRS-based tuned quasi-analytical algorithm (QAA-V) is presented to monitor water inherent optical properties (IOPs) in different estuaries in the NGOM. As IOPs are directly associated to the abundance of water constituents, QAA-V can provide a useful tool for regional, state, and federal agencies to monitor water quality for making decisions concerning strategies and plans to mitigate environmental problems.

Deltas are globally important locations of diverse ecosystems, human settlement and economic activity that are threatened by reduced sediment delivery, accelerated sea level rise, and subsidence. In this dissertation I investigated a number of aspects of the ecosystem development over time within an actively prograding river dominated delta along the northern Gulf of Mexico coast. I outlined a conceptual model of deltaic floodplain wetland establishment and succession focused on the vegetated deltaic floodplain ecosystem, which includes subtidal, intertidal and supratidal zones. This was used to guide the experimental design and statistically driven hypothesis testing in order to ascertain the validity of the processes outlined therein. I attempted to determine how sediment surface elevation of delta floodplain wetlands changed in a prograding delta as a result of flooding, hurricanes, and cold front passage, and to compare the patterns of change between years. I also investigated the patterns in island edge cross-sectional morphology over time within a chronosequence framework which encompassed the entire period of subaerial expression of the Wax Lake Delta (WLD) in Louisiana, USA. The zonation and patterns of the herbaceous vegetation community were also investigated in response the elevation as well as hurricane storm surge passage. The forest structure of Salix nigra (black willow) on deltaic floodplain islands, was investigated in response to the estimated age of the stand, (i.e. time since establishment) and the major river floods, using both the chronosequence map and aerial imagery analysis of willow stands. Based on these finding I suggest refinements and expansion of the conceptual model to allow for inclusion of the temporal aspect of the ecosystem as a whole, which at any one time consists of numerous phases of ecological development. The findings of this dissertation and the proposed refinements of the conceptual model add to a better understanding of the deltaic floodplain ecosystem and provide a framework on which to investigate further questions of ecological development.

The Deepwater Horizon (DWH) oil spill in 2010 triggered extensive research on the impacts of crude oil contamination in the Gulf of Mexico. This research focuses on the impact of the longer-term presence of oil from the DWH spill on denitrification and soil reduction-oxidation (redox). Cores were collected from a salt marsh heavily oiled by the DWH spill, and a nearby, non-oiled site in Barataria Bay, LA to investigate the effects of the long-term presence. Denitrification is typically the dominant process of nitrate removal in coastal wetlands, converting bioavailable N in surface waters into gases released to the atmosphere through microbial respiration. Potential denitrification rates were lower in soils mixed well with compared to non-oiled samples, suggesting suppressed microbial activity due to the presence of oil. However, nitrate removal, a proxy measurement of denitrification, from the overlying water column in intact cores with a persistent layer of buried oil was significantly higher, compared to non-oiled cores over an 11-day period. Redox conditions in wetland soils provide an excellent indicator of oxygen levels which control biogeochemical functions. Treatments tested were a non-oiled control, weathered crude oil at the soil profile surface, fresh crude oil at the soil profile surface, and a layer of buried weathered crude oil, 5-cm beneath the soil surface. No significant differences in redox potentials were detected among treatments at any depth at the end of the 35-day flooded, anaerobic portion of the study. After draining the cores, mean redox values for each set of treatments (n=3) were calculated for each sample time to determine the time necessary for the rhizosphere to reach the aerobic threshold (+300 mV). Mean redox values for the control cores reached +300 mV after 193 h. Both fresh and weathered crude oil surface treatments reached +300 mV after 316 h. The buried crude oil treatment reached the aerobic threshold after 418 h. Future studies should investigate the fate and impact of buried crude oil released back into the environment driven by the erosion of coastal salt marshes.

Apalachicola Bay is a productive estuary located in the northern Gulf of Mexico. The high productivity is, in part, the result of the Apalachicola River delivering freshwater and nutrients to the Bay. Nutrient input supports high levels of phytoplankton productivity, which supports the Bay's secondary productivity. Diversion of water from headwaters of the Apalachicola River during summer has been proposed to satisfy upstream freshwater requirements for recreation and agriculture. Knowledge of the ecology of phytoplankton and zooplankton in the Bay is needed to help predict the effects of upstream water diversion on Apalachicola Bay. In this study, the temporal and spatial distribution of phytoplankton size composition, growth, biomass, productivity, microzooplankton bacterivory, herbivory, production, and Acartia tonsa herbivory, carnivory, egg production rate, and egg production efficiency were determined in Apalachicola Bay during 2003 and 2004. Phytoplankton growth, biomass, productivity, total ingestion rates and production rates of microzooplankton, and total ingestion rates and egg production rates of Acartia tonsa peaked during summer within lower salinity (psu) waters. Microzooplankton ingested, on average, ten times more phytoplankton productivity than A. tonsa. Compared to the 24 year average river discharge, river discharge into Apalachicola Bay was above average during 2003 and below average during 2004. On average, 100% and about 50% of the surface salinity of the Bay was 2004, respectively. Nutrient concentrations, at a specific salinity, were higher during 2003 than during 2004. Phytoplankton growth and productivity, as well as total ingestion rates and production rates of microzooplankton, at a specific salinity, were higher during summer 2003 than during summer 2004. It is expected that withdrawal of freshwater from the Apalachicola River during summer will lead to reduced higher trophic level production in Apalachicola Bay because of (1) reduced productivity of phyto- and microzooplankton at a specific salinity and (2) increased areal extent of higher salinity water (>20 psu) where phytoplankton growth, biomass, and productivity and zooplankton productivity is low. Implications of these results are also discussed with respect to our understanding of estuarine planktonic food web structure.20 psu) where phytoplankton growth, biomass, and productivity and zooplankton productivity is low. Implications of these results are also discussed with respect to our understanding of estuarine planktonic food web structure. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Fall Semester, 2005. / Date of Defense: October 28, 2005. / Food Web Structure, River Discharge, Fisheries, Ecology, Estuary / Includes bibliographical references. / Richard Iverson, Professor Directing Dissertation; Sherwood Wise, Outside Committee Member; Nancy Marcus, Committee Member; Joel Kostka, Committee Member; Behzad Mortazavi, Committee Member.

This study focused on the combined use of radon and radium isotopes as tracers of near-shore geophysical processes including submarine groundwater discharge (SGD), water exchange rates, and atmospheric evasion. Methods were developed for easier measurement of long-lived radium isotopes in natural waters and for continuous radon surveying over larger areas in the coastal zone. These tracer techniques were used to study the mentioned processes at study sites in Shelter Island Sound (New York), the Gulf of Thailand, and Apalachicola Bay, Florida. Groundwater fluxes calculated for Shelter Island using isotopic techniques produced results consistent with those measured directly via seepage meters. Groundwater discharge in the Chao Phraya Estuary (Thailand) was shown to be in the range of 2 to 20 m3/s, small compared to river discharge but much higher than seepage rates measured in nearby locations. An experimental assessment of Rn-222 evasion to the atmosphere was performed using radon and Ra-224 profiles in the Chao-Phraya Estuary in Thailand. The different trends in radium and radon isotopes measured in the estuary provided an estimate of atmospheric exchange that agreed with a theoretical approach. Short-lived radium isotopes were applied in a seasonal study of water residence time in Apalachicola Bay, Florida. The water transport within different sectors of the bay was evaluated as a result of advective (estuarine) and dispersive physical mixing. The distribution of the radium isotope ratios was used to determine apparent radium ages of the water within the bay. The results clearly showed how the water-residence time in the bay changes seasonally and that the winds and tides influence the water circulation in the bay. The radium tracer approach gave turnover times of 6 to 12 days in Apalachicola Bay during the studied periods. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Summer Semester, 2005. / Date of Defense: June 28, 2005. / Submarine Groundwater Discharge, Atmospheric Evasion, Estuarine Residence Time, Radon, Radium / Includes bibliographical references. / William C. Burnett, Professor Directing Dissertation; Joseph F. Donoghue, Outside Committee Member; Jeffrey P. Chanton, Committee Member; William M. Landing, Committee Member; Willard S. Moore, Committee Member; Joel E. Kostka, Committee Member.

Lagged correlation of dynamic height from the gappy California Cooperative Oceanic Fisheries Investigation (CalCOFI) with monthly San Diego sea level for the period 1949-2001 shows that the dynamic height propagates westward at 4.10 cm/s, about double the speed of the large-scale low frequency Rossby wave (2.2 cm/s). TOPEX/Poseidon/Jason1 along-track sea level height estimates since January 1993, filtered interannually, propagate westward at 4.3 cm/s, verifying that observed westward propagation is about double that expected. Including the effect of the mean California current on the Rossby wave propagation does not explain the discrepancy but rather slightly increases it. Because of the westward propagation, interannual variations in alongshore geostrophic surface current are proportional to the time derivative of sea level. This means that such large scale interannual current variability can be monitored with appropriate lag, by the time derivative of coastal sea level. The anomalous alongshore flow advects particles, the anomalous alongshore particle displacement being proportional to sea level. Since nutrient concentration is lower in the south, the anomalous alongshore displacement results in lower nutrient concentration when sea level is anomalously high and higher nutrient concentration when the sea level is anomalously low. Vertical displacement also results in a similar relationship between nutrients and sea level. The anomalous alongshore and vertical particle displacements associated with the Rossby waves also act on the mean temperature and salinity fields to produce temperature and salinity anomalies. Theory suggests that these anomalies should be proportional to the anomalous dynamic height. Consistent with this, observed salinity anomalies at depths of 100-200 m are well correlated with dynamic height anomalies. At depths greater than 200 m the observed anomalies are small and, consistent with a smaller signal to noise ratio, the correlation falls. At depths shallower than 100 m the correlation between salinity and dynamic height anomalies also falls rapidly. The flow anomalies can similarly be used to explain the temperature fluctuations except that the correlation between temperature and dynamic height fluctuations does not fall rapidly in the surface layer as in the salinity case. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Spring Semester, 2007. / Date of Defense: November 20, 2006. / Rossby Wave, Interannual Frequency, Zooplankton, E / Includes bibliographical references. / Allan J. Clarke, Professor Directing Dissertation; Christopher Tam, Outside Committee Member; Doron Nof, Committee Member; Georges Weatherly, Committee Member; Thorsten Dittmar, Committee Member.