The Calvin-Benson-Bassham (CBB) pathway is the primary pathway for the entry of inorganic carbon in the biosphere. Autotrophic organisms use this cycle to ultimately convert CO2 into carbohydrates using a key enzyme known as ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). The gene that encodes for the large subunit of RubisCO is rbcL and detection of its expression can be used to determine the autotrophic organisms present in the environment. Recently, microarrays have been used to study functional gene expression from environmental samples such as those obtained from sediments and soil. The purpose of this thesis is to combine microarray technology and rbcL expression analysis to investigate phytoplankton populations in the Mississippi River Plume (MRP). Initially, a macroarray was constructed to determine its capabilities of quantifying gene expression in MRP. PCR amplicons were spotted onto a nylon membrane and labeled transcript RNA was hybridized to each array. Due to the large amount of cross hybridization that was observed, a microarray was used. Microarray analysis revealed large amounts of Synechococcus, pelagophyte and prymnesiophyte expression in the surface waters. Furthermore, there was no chlorophte or Prochlorococcus expression observed in the surface waters. Subsurface microarray data showed high levels of pelagophytes and other Form ID organisms. A significant chlorophyte signal was also observed in the subsurface. This study provides a third level of specificity at which phylogenetic diversity has been sampled in the MRP. Although a limited number of samples were analyzed by microarrays, this technology shows promise and this study was viewed as a pilot for their application. The rbcL probes designed were based upon published sequences from 2003 and we now have a much greater understanding of the diversity of rbcL-containing phytoplanktonic phylotypes. Future studies should employ this knowledge for judicious probe selection.

Optically stimulated luminescence (OSL) dating beach ridge sediments is one method for resolving barrier island growth at intermediate scales (decades-centuries), information that is lacking for Louisiana. This research combines OSL, GPR, aerial imagery, and cores to document temporal and spatial evolution of a Louisiana barrier island. Grand Isle is composed of beach ridges organized in distinct, unconformable sets that began forming 0.75 ka until 0.575 ka when deposition ceased, the ridges were partially eroded, and deposition resumed in a more eastward direction. The central ridges formed between 370±30 and 170±10 years ago at a rate of one ridge every 11.6 years with sand from the eroding Caminada headland that, with flanking barriers, forms the Bayou Lafourche transgressive depositional system. Grand Isle’s lithosome (92,600,000 cubic meters) requires an annual longshore transport of 128,625 cubic meters. The lithosome thickness (10 meters) and steady sediment supply stabilize the island relative to other Louisiana barriers.

This thesis details the work completed in order to develop a hydrodynamic and nitrate transport and reaction model for Round Lake, a backwater on UMR Pool 8. This work begins with investigating the fundamentals of nitrogen removal in aquatic ecosystems and reviewing other combined hydrodynamic and nutrient modeling efforts. Field data were gathered to determine model boundary conditions and provide a basis for calibration and validation. Using this data, the flow regime in Round Lake was simulated. CFD applications to model particle residence times and species transport and reaction were used to analyze the effects local hydraulics have on nitrogen removal in the lake. Results demonstrated an ability for CFD to predict spatial variation of nitrate with this ecosystem.

The Upper Mississippi River System (UMRS) is a diverse and dynamic ecosystem that includes the main stem river channel, side channels, backwater floodplains and lakes, islands, wetlands, grasslands, and floodplain forests. The hydrology of this rich ecosystem is one of the key drivers for physical, chemical and biological processes. However, the hydrology and hydraulics of the UMRS has been drastically altered from its natural state as a result of the construction of the locks and dams in the 1930s. Beginning with the Water Resources Development Act of 1986, biologists, ecologists, and engineers have been working to restore the river to a more natural state within the current constraints imposed by the lock and dam system. In an effort to restore rivers to a more natural state, the determination of a hydraulic reference condition is essential to understanding the "why and how" of historical river system function. Understanding the fundamental processes of historical conditions will help prioritize resources and better quantify possible outcomes for riverine restoration. The main goal of this study was to construct a hydrodynamic reference condition for Pool 8 of the Upper Mississippi River System using hydrodynamic computational fluid dynamic (CFD) modeling. The CFD model will provide a better understanding of pre-impoundment flow conditions as compared to post-impoundment conditions today. The numerical model was constructed and developed primarily from a pre-impoundment 1890s topographic map with bathymetric cross-sections in the channels. The 1890s map and other sources from the U.S. Army Corps of Engineers provided historic elevation and hydraulic reference data for model calibration. The calibrated historic model was then compared with a current model of similar scale representing post-impoundment conditions, allowing for quantitative analysis of the differences between the two conditions. Model results indicated large changes in average depth and average velocity between historic and current conditions in certain parts of the pool, while others remained relatively unchanged. For example, velocities decreased in main channel aquatic areas in the lower part of Pool 8 from an average of 0.6 m/s (2.0 ft/s) under historic conditions to 0.1 m/s (0.3 ft/s) under current conditions. In the same part of the pool, however, velocities in contiguous backwater areas remained relatively constant, with most remaining less than 0.25 m/s (0.82 ft/s). Additionally, in the lower part of the pool, discharge distribution between the floodplain areas and the main channel was historically much more dynamic, with flow concentrated in the main and secondary channels at discharges less than 2265 m3/s and in the floodplains at greater than 2265 m3/s. Under current conditions, discharge distribution is much less dynamic, with approximately 2/3 of the total discharge conveyed on the floodplain for all discharges modeled (283 m3/s to 2832 m3/s or 10,000 ft3/s to 100,000 ft3/s).

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No description available.

River plumes often develop in complex environments, where variable coastal and bottom topography, ambient currents, winds and tides may play important roles in shaping the plume evolution. When all these factors are present, the plume dynamics may become intricate and unclear. The objective of this study is to understand the processes controlling the dynamics of a large river plume that is affected by strong boundary currents, variable winds and complex topography. The Mississippi River (MR) plume is the study case of this dissertation work, and focus is given to the interactions between the plume and the offshore circulation of the Gulf of Mexico (GoM). A series of numerical experiments was designed to investigate the impact of different factors on the development of a large scale river plume in scenarios with variable degrees of complexity. First, a box-like model with an idealized estuary was designed to address the general development of a mid-latitude river plume and assess the variability of the plume with changes in the outflow conditions at the river mouth. The structure and development of the plume in the flat-bottom, receiving basin was highly dependent on the degree of freshwater mixing at the source. Larger freshwater mixing enhanced the estuarine gravitational circulation and modified the dynamical balance at the estuary mouth. Those changes effectively modified the shape of the bulge and length/transport scales of the coastal current. Sloping-bottom conditions further modified the development of the plume. Secondly, a Northern GoM model was designed and numerical experiments were conducted to investigate the specific dynamics of the MR plume, in the presence of both shelf and basin-wide circulation. In particular, buoyancy-driven (due to the MR and all other major Northern GoM rivers) and wind-driven currents were studied on the shelf, while the extension of the Loop Current and associated frontal eddies were considered as major factors in the shelf to offshore interactions; wind-driven, shelfbreak eddies were also considered. Process-oriented experiments demonstrate that westerly and southerly winds promoted the development of a surface Ekman layer that enhances the offshore advection of plume waters. The steep topography in the vicinity of the MR Delta was a favorable condition for that process. When the MR plume was subject to a full-blown scenario (realistically-forced experiment nested within a large-scale model), complex interactions between wind-driven and eddy-driven dynamics determined the fate of the plume waters. Offshore removal is a frequent plume pathway, and the offshore transport can be as large as the wind-driven shelf transport. The offshore pathways depend on the position of the eddies near the shelf edge, their life span and the formation of eddy pairs that generate coherent cross-shelf flows. Strong eddy-plume interactions were observed when the Loop Current (LC) system impinged against the shelfbreak, causing the formation of coherent, narrow low-salinity bands that extended toward the Gulf interior. The offshore transport of MR water is a year-round process, but the interactions between the MR plume and the LC system have large inter-annual variability. Plume to LC interactions are determined by episodic northward intrusions of the LC system in the NGoM. The interactions are dictated by the proximity of the LC system to the MR Delta and by wind effects. On average, plume to LC interactions correspond to ~ 12 % of the year-round, total freshwater transport near the MR Delta, but this percentage can go up to 30 % in individual years. At the time of the plume to LC interactions, an average value of LC freshwater entrainment was estimated to be ~ 4,150 m3 s-1. The findings presented here are a major contribution toward the understanding of the cross-marginal and basin-wide transport of MR waters by a large-scale current system, and the connectivity to remote regions, such as the South Florida region and the Florida Keys.

Understanding specific pathways for sand transport in the lower reaches of large rivers, particularly the Mississippi, is the key to addressing multiple significant geologic problems and for environmental restoration efforts. Field studies were performed in the Mississippi River 75-100 km upstream of the Gulf of Mexico outlet in April 2010 (water discharge: 23,000 m³ s⁻¹), May 2010 (18,500-20,500 m³ s⁻¹), and March 2011 (27,000 m³ s⁻¹) to examine sediment transport phenomena in the river channel. Methods comprised multibeam sonar bathymetric surveys, acoustic Doppler current profiler measurements of current velocity and acoustic backscatter, point-integrated isokinetic suspended sediment sampling, and channel-bed grab sampling. Channel morphology surveys revealed a 30-60 m deep thalweg, alternating between banks every 2-3 km, opposite bedform-covered lateral sand bars. Dune sizes nearest the thalweg ranged from 7 m wavelength and 0.3 m height to over 100 m wavelength and 2.3 m height as a function of water discharge, with decreasing dune sizes towards shallow water. Material comprising the dunes was well-sorted, 125-500 [mu]m sand. Bedload transport rates increased exponentially with water discharge in April 2010 and March 2011 comparable to previous studies in this reach, though rates in May 2011 were well below predicted values for a site (Myrtle Grove) immediately downriver of a sand-mining project. Average water velocities ranged from 1.3 m s⁻¹ in May 2010 to 2 m s⁻¹ in March 2011. Skin-friction shear stress increased with water discharge, but varied over an order of magnitude at all measured discharges. Suspended sand concentration and grain size increased with proximity to the bed during all study periods, and was most pronounced in March 2011. Suspended sand concentrations were greatest over the center of lateral bars, and lowest in the thalweg, indicating that sand transport downstream occurs primarily over lateral sand bars where there is a combination of high shear stress and available bed material. Total bed-material discharge increased exponentially with water discharge. Bedform-induced turbulence may be responsible for the bed material suspension. These results are relevant to coastal restoration efforts by river diversion which seek to distribute sand from the upper water column to deltaic interdistributary wetlands. / text

This dissertation examines the dynamics of sediment transport and channel morphology in the lower Mississippi River. The area of research includes the portion of the river where reach-averaged downstream flow velocity responds to the boundary condition imposed by the relatively uniform water-surface elevation of the receiving basin. Observational studies provided data that are used to identify channel-bed sediment composition, and measure bed-material sediment flux and the properties of the fluid-flow field over a variety of water-discharge conditions. The analyses demonstrate that a significant portion of the channel bed of the final 165 kilometers of the Mississippi River consists of exposed and eroding underlying relict sedimentary strata that qualify as surrogate bedrock. The exposed bedrock is confined to the channel thalweg, particularly in river-bend segments, and actively mobile bed-material sediments are positioned on subaqueous bars fixed by river planform. The analyses for sediment flux provides insight to the nature of sediment transport: during low- and moderate-water discharge, bed-material movement occurs primarily as minimal bedform flux, and so bed materials are not transferred between alluvial bars. During high-water discharge, bed-material transport increases one-hundred fold, and sands move as a part of both suspended and bedform transport. Physical models are used to show that skin-friction shear stress increases by a factor of ten for the measured water-discharge range. This change is not possible given conditions of uniform water flow, and therefore non-uniform flow in response to the Mississippi River approaching its outlet has a significant impact on the timing and magnitude of sediment flux through the lower river. In order to estimate the dynamics of bed material movement from the uniform to non-uniform segment of the river (lower 800 km), data for channel morphology are used to construct a model that predicts spatial changes in water-flow velocity and bed-material flux over a range of water-discharge conditions. The model demonstrates that non-uniform flow tends to produce a region of net channel-bed aggradation between 200-700 kilometers above the outlet, and a region of channel-bed degradation for the final 200. The implication for these results for the spatial variability of channel morphology and kinematics is explored. / text

The evolution of landscapes and seascapes in time is the result of the constant interaction between flows and topography. Flows change topography, which in turn change the flow. This feedback causes evolution processes to be highly non-linear and complex. When full analytical derivations of the co-evolution of topography and flow are not possible without oversimplifications, as is the case in river bends, recent large topographical datasets and modern computers allow for correlations between horizontal (planview) and cross-sectional geometry of channels. Numerical analysis in the Mississippi and Trinity rivers indicate that the type of correlation between river radius of curvature and bankfull channel width depends on the migration behavior of the river. In other cases, channel topography may only have a second-order effect on its own evolution, as is the case for fully depositional turbidity currents, and the evolution of aeolian field topography may only be a function of this topography. I show that in these situations, changes in topography may be decoupled from details of the flow field and modeled very easily with a good accuracy. / text