Extraction and processing of uranium ore during the Cold-War era have left many sites around the world contaminated with uranium. Leaching of uranium into the groundwater is of major concern because oxidized uranium, U(VI), is toxic, soluble, and therefore mobile in subsurface environments where the majority of contamination resides. Uranium [U(VI)] can be immobilized from water by its reduction from UO22+ to insoluble U(IV) oxide, and biostimulation by the addition of carbon substrates has been shown to stimulate the microbial reduction of U(VI) in contaminated subsurface environments. However, in order to develop effective bioremediation strategies for contaminant metals, the microbial communities and mechanisms controlling metal reduction need to be better understood, especially in acidic subsurface environments. This dissertation research used an array of microbiological and geochemical techniques to examine metal reduction in materials from the U.S. Department of Energy (DOE) Natural and Accelerated Bioremediation Research (NABIR)'s Field Research Center (FRC), in Oak Ridge, Tennessee, where subsurface sediments are cocontaminated with high levels of U(VI) and nitrate. The combination of low pH and high concentrations of nitrate and radionuclides in an aerobic subsurface environment is representative of many sites within the U.S. nuclear weapons complex managed by the DOE. Thus, results are not only important for bioremediation research at the FRC but can also be applied to other sites. Iron(III)-reducing bacteria (FeRB) have been demonstrated to rapidly catalyze U(VI) reduction and Fe(III) is an abundant electron acceptor in uranium-contaminated subsurface sediments. Thus, FeRB communities were the focus of this dissertation. The abundance, diversity, and activity of indigenous metal-reducing microbial communities likely to contribute to uranium reduction was examined in the field and under more controlled conditions in the laboratory. In chapter one, a combination of cultivation-dependent and cultivation-independent microbiological techniques were utilized to characterize metal-reducing bacteria in FRC subsurface sediments. Iron(III)-reducing enrichment cultures were initiated from pristine and contaminated (high in uranium, nitrate; low pH) subsurface sediments at pH 7 and pH (4-5). In selected enrichments, nitrate contamination was removed from the sediment by washing. Using a most probable number (MPN) approach and a range of different carbon sources (glycerol, acetate, lactate, or glucose), sediments of lower pH typically yielded lower counts of FeRB except when glucose was utilized as an electron donor in acidic enrichments. Phylogenetic analysis of the 16S rRNA gene sequences extracted from the highest positive MPN dilutions revealed that the predominant members of Fe(III)-reducing consortia cultured from pristine background sediments were closely related to the family Geobacteraceae, whereas a recently characterized Fe(III)-reducer (Anaeromyxobacter) and organisms not previously shown to reduce Fe(III) (Paenibacillus, Brevibacillus) predominated the Fe(III)-reducing consortia of contaminated sediments. Analysis of enrichment cultures using terminal restriction fragment length polymorphism (T-RFLP) strongly supported the cloning and sequencing results. Enrichment cultures of Fe(III)-reducers from contaminated sites were also shown to rapidly reduce millimolar amounts of U(VI) in comparison to killed controls. Using DNA extracted directly from the subsurface sediments, quantitative analysis of 16S rRNA gene sequences with MPN-PCR indicated that Geobacteraceae sequences were one to two orders of magnitude less abundant in contaminated as compared to pristine environments. In contrast, Anaeromyxobacter sequences were more abundant in contaminated sediments. Thus, results from a combination of cultivation-based and cultivation-independent approaches indicate that the abundance/ community composition of Fe(III)-reducing consortia in subsurface sediments is dependent upon geochemical parameters (pH, nitrate concentration) and microorganisms capable of producing spores (gram positives) or spore-like bodies (Anaeromyxobacter) were representative of acidic subsurface environments. In chapter two, microbial communities were studied in sediment microcosms under near in situ conditions in order to establish rates of respiration and to assess which environmental parameters might be governing activity. Rates of nitrate reduction, metal reduction, and electron donor utilization were measured in acidic subsurface sediments across a range of environmental variables (pH, nitrate) relevant to bioremediation. Microbial activity was minimal at pH 5 or below and in the absence of added electron donor, indicating that acidity is a master variable controlling microbial metabolism in FRC sediments, while high nitrate concentrations were not found to be toxic to microorganisms. In microcosms of neutral pH sediment and neutralized acidic sediment, similar, rapid rates of terminal-electron-accepting pathways were observed. The pathways of nitrate reduction were dictated by sediment pH, as denitrification predominated in glucose-amended sediments originating from neutral pH zones, whereas in neutralized acidic microcosms, metabolism shifted to dissimilatory nitrate reduction (to ammonium). Electron donors were determined to stimulate microbial metabolism leading to metal reduction in the following order: glucose > ethanol > lactate > hydrogen. A mass balance of carbon equivalents was obtained in glucose- and ethanol-amended microcosms. In neutralized acidic sediments amended with glucose, 50 to 60 % of carbon equivalents were recovered as fermentation products (mainly as acetate) and glucose-amended microcosms showed the highest iron reduction activity, while the extended presence of ethanol seemed to hinder iron reduction. The presence of bicarbonate greatly increased both nitrate and iron reduction activity in glucose-amended microcosms, more so than raising the pH by washing. Washing did increase iron reduction in glucose-amended microcosms as compared to neutralized acidic sediments, indicating that soluble toxins may somehow decrease iron reduction potential. ethanol > lactate > hydrogen. A mass balance of carbon equivalents was obtained in glucose- and ethanol-amended microcosms. In neutralized acidic sediments amended with glucose, 50 to 60 % of carbon equivalents were recovered as fermentation products (mainly as acetate) and glucose-amended microcosms showed the highest iron reduction activity, while the extended presence of ethanol seemed to hinder iron reduction. The presence of bicarbonate greatly increased both nitrate and iron reduction activity in glucose-amended microcosms, more so than raising the pH by washing. Washing did increase iron reduction in glucose-amended microcosms as compared to neutralized acidic sediments, indicating that soluble toxins may somehow decrease iron reduction potential. lactate > hydrogen. A mass balance of carbon equivalents was obtained in glucose- and ethanol-amended microcosms. In neutralized acidic sediments amended with glucose, 50 to 60 % of carbon equivalents were recovered as fermentation products (mainly as acetate) and glucose-amended microcosms showed the highest iron reduction activity, while the extended presence of ethanol seemed to hinder iron reduction. The presence of bicarbonate greatly increased both nitrate and iron reduction activity in glucose-amended microcosms, more so than raising the pH by washing. Washing did increase iron reduction in glucose-amended microcosms as compared to neutralized acidic sediments, indicating that soluble toxins may somehow decrease iron reduction potential. hydrogen. A mass balance of carbon equivalents was obtained in glucose- and ethanol-amended microcosms. In neutralized acidic sediments amended with glucose, 50 to 60 % of carbon equivalents were recovered as fermentation products (mainly as acetate) and glucose-amended microcosms showed the highest iron reduction activity, while the extended presence of ethanol seemed to hinder iron reduction. The presence of bicarbonate greatly increased both nitrate and iron reduction activity in glucose-amended microcosms, more so than raising the pH by washing. Washing did increase iron reduction in glucose-amended microcosms as compared to neutralized acidic sediments, indicating that soluble toxins may somehow decrease iron reduction potential. For the first time, rates of metal reduction and electron donor utilization were measured in acidic subsurface sediments across a range of environmental variables (pH, nitrate) relevant to bioremediation. In concurrence with previous studies of neutrophilic uranium-contaminated subsurface environments, metal reduction in the acidic subsurface did not occur until after nitrate was depleted to low levels in response to pH neutralization and carbon substrate addition. Through quantification of the rates and pathways of terminal-electron-accepting pathways in acidic subsurface sediments, we provide important inputs for reaction-based biogeochemical models that will greatly aid in the development of in situ radionuclide remediation strategies. In chapter 3, a pure culture of Fe(III)-reducing bacteria isolated from the FRC subsurface was further examined for its ability to reduce U(VI). Uranium measurements were conducted using a Kinetic Phosphorescence Analyzer, which was cross-calibrated using alpha spectrometry. The uranium reduction ability of isolate FRC32, was compared to a known uranium-reducing organism, Geobacter metallireducens. FRC32 was tested under various cultivation conditions, including a range of uranium and cell concentrations and up to 90% of 0.1-5 mM uranium was reduced. However, reduction in killed-control cultures suggests either a strong potential for abiotic reduction or the ability to form spores. Thus, the potential for uranium reduction was observed, but further research is necessary to determine which environmental parameters are controlling uranium transformation by this organism. / 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, 2005. / Date of Defense: December 10, 2004. / Iron-reducing Microorganisms, Biostimulation, Bioremediation / Includes bibliographical references. / Joel E. Kostka, Professor Directing Dissertation; David Balkwill, Outside Committee Member; Lee R. Krumholz, Committee Member; Bill Burnett, Committee Member; Jeff Chanton, Committee Member.

State of the art fully three-dimensional ocean models are very computationally expensive and their adjoints are even more resource intensive. However, many features of interest are approximated by the first baroclinic mode over much of the ocean, especially in the lower and mid latitude regions. Based on this dynamical feature, a new type of data assimilation scheme to assimilate sea surface height (SSH) data, a reduced-space adjoint technique, is developed and implemented with a three-dimensional model using vertical normal mode decomposition. The technique is tested with the Navy Coastal Ocean Model (NCOM) configured to simulate the Gulf of Mexico. The assimilation procedure works by minimizing the cost function, which generalizes the misfit between the observations and their counterpart model variables. The "forward" model is integrated for the period during which the data are assimilated. Vertical normal mode decomposition retrieves the first baroclinic mode, and the data misfit between the model outputs and observations is calculated. Adjoint equations based on a one-active-layer reduced gravity model, which approximates the first baroclinic mode, are integrated backward in time to get the gradient of the cost function with respect to the control variables (velocity and SSH of the first baroclinic mode). The gradient is input to an optimization algorithm (the limited memory Broyden-Fletcher-Goldfarb-Shanno (BFGS) method is used for the cases presented here) to determine the new first baroclinic mode velocity and SSH fields, which are used to update the forward model variables at the initial time. Two main issues in the area of ocean data assimilation are addressed: 1. How can information provided only at the sea surface be transferred dynamically into deep layers? 2. How can information provided only locally, in limited oceanic regions, be horizontally transferred to ocean areas far away from the data-dense regions, but dynamically connected to it? The first problem is solved by the use of vertical normal mode decomposition, through which the vertical dependence of model variables is obtained. Analyses show that the first baroclinic mode SSH represents the full SSH field very closely in the model test domain, with a correlation of 93% in one of the experiments. One common way to solve the second issue is to lengthen the assimilation window in order to allow the dynamic model to propagate information to the data-sparse regions. However, this dramatically increases the computational cost, since many oceanic features move very slowly. An alternative solution to this is developed using a mapping method based on complex empirical orthogonal functions (EOF), which utilizes data from a much longer period than the assimilation cycle and deals with the information in space and time simultaneously. This method is applied to map satellite altimeter data from the ground track observation locations and times onto a regular spatial and temporal grid. Three different experiments are designed for testing the assimilation technique: two experiments assimilate SSH data produced from a model run to evaluate the method, and in the last experiment the technique is applied to TOPEX/Poseidon and Jason-1 altimeter data. The assimilation procedure converges in all experiments and reduces the error in the model fields. Since the adjoint, or "backward", model is two-dimensional, the method is much more computationally efficient than if it were to use a fully three-dimensional backward model. / 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, 2006. / Date of Defense: April 28, 2006. / Data Assimilation, Reduced Space, First Baroclinic Mode, Ocean Models, Vertical Normal Mode Decomposition, Variational / Includes bibliographical references. / James J. O'Brien, Professor Directing Dissertation; Xiaolei Zou, Outside Committee Member; William K. Dewar, Committee Member; Allan J. Clarke, Committee Member; Richard Iverson, Committee Member.

Gravity measurements from the Gravity Recovery and Climate Experiment (GRACE) satellite measuring system show that Greenland is losing mass as water is lost to the ocean. Past work has suggested that the freshwater flux from Greenland, particularly along the southeastern coast, may be affecting the Labrador Sea deep convection, a major driver of the world deep ocean circulation. The main objectives of this thesis are to examine (1) the relationship between Greenland freshwater flux and the near-surface Labrador Sea salinity; (2) the response of the Greenland shelf water flow to the freshwater flux from the coast; and (3) to predict when the Labrador Sea deep convection will shut down because of the near-surface Labrador Sea freshening. Using the GRACE results and analysis of Argo float hydrographic data showed that there is a strong correlation between the anomalous annual freshwater flux onto the southeastern Greenland shelf and the freshening of the Labrador Sea several months later. The corresponding regression coefficient is physically reasonable and the delay in freshening is what you would expect based on eddy propagation from the west Greenland coast to the site of Labrador Sea deep convection. Satellite altimeter data was used to estimate the interannual shelf water flow, but the flow trend was too small to be determined. Calculations of the heat flux during winter in the Labrador Sea region of deep convection showed that if the freshening continues at the present rate, in about 31 years the cooling heat flux in water will not be able to overcome the freshwater near-surface buoyancy and deep convection will cease. / A Dissertation submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2017. / June 2, 2017. / Along-shelf flow, Deep convection, Freshwater flux, Greenland, Labrador Sea / Includes bibliographical references. / Allan J. Clarke, Professor Directing Dissertation; Christopher Tam, University Representative; Angela Knapp, Committee Member; Mark Bourassa, Committee Member; William K. Dewar, Committee Member.

The ridge systems that frame the Lau Basin and Havre Trough, located east of Fiji and north of New Zealand, separating a large counterclockwise gyre at the surface into two smaller gyres at depth. A strong deep western boundary current (DWBC) has been observed flowing northward, following the Tonga and Kermadec Trench systems, transporting bottom water to the North Pacific. Though circulation has been described to some degree around the Lau Basin and the Havre Trough, these sub-basins have largely been ignored, presumed to act as a barrier to flow and separating the western South Pacific from the eastern South Pacific. An analysis of float data from several sources as well as traditional ship-board hydrographic data reveal a DWBC within the Lau Basin and Havre Trough that is fed by westward flowing jets from breaks within the ridge system. A simple analytical model predicts the large-scale dynamics observed in the basin, and indicates that the topographic structure of the ridge modulates the flow patterns. Sources of water into the Lau Basin and Havre Trough indicate intermediate water sources from the eastern South Pacific, while deep water sources originate to the west. This leads to a revised view of the role of the Lau Basin and Havre Trough with respect to circulation in the South Pacific. / A Dissertation submitted to the Geophysical Fluid Dynamics Institute in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester 2018. / March 30, 2018. / Includes bibliographical references. / Kevin Speer, Professor Directing Dissertation; Nick Cogan, University Representative; Bill Dewar, Committee Member; Philip Sura, Committee Member.

Energy is introduced into the oceans primarily at large scales by means of wind, tides and surface buoyancy forcing. This energy is transferred to the smaller mesoscale eld through the geostrophic instability processes. The mesoscale eld appears not to have accelerated appreciably over the last several decades, so we can assume that the mesoscale loses energy at roughly the same rate it receives energy. Interestingly, how the mesoscale loses energy is not quite clear. We have been exploring topographic interaction as a pathway by which the mesoscale may lose energy to unbalanced forward cascading flows. To demonstrate this phenomenon, an approximate model theory is developed which consists of solving a reduced set of the momentum equations in density coordinates for any topographic conguration. The equations are solved using a high order spectral element technique and the results are similar to already published MITgcm simulations. / A Thesis submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester 2017. / November 13, 2017. / Includes bibliographical references. / William Dewar, Professor Co-Directing Thesis; Eric Chassignet, Professor Co-Directing Thesis; Allan Clarke, Committee Member; David Kopriva, Committee Member.

We present an analysis of small scale processes associated with bathymetric sills in the Philippine Archipelago, with an emphasis on in situ observations made during the 2007-2009 Philippines Straits Dynamics Experiment (PhilEx). Due to their location at the margins of larger basins, the dynamics at these sills set the conditions under which water, heat, salt, and energy are transported internally and at the boundaries of the archipelago. The main connection between the internal Sulu Sea and the South China Sea to the north is through Mindoro Strait. Moored Acoustic Doppler Current Profiler (ADCP), Conductivity, Temperature, Depth (CTD), and lowered ADCP (LADCP) data are used to study the currents and stratification at Panay Sill, at the southern end of Mindoro Strait. We observe a strong bottom-intensified overflow; temporal mean velocity is greater than 0.75 m/s at 50 m above the sill. Both ADCP observations and a hydraulic control model based on hydrographic measurements estimate a transport of approximately 0.32 x 10^6 m^3/s. Analysis of Froude number variation across the sill shows the flow is hydraulically controlled. Turbulent dissipation and bulk diapycnal diffusivity measurements at the sill and downstream suggest mixing well above oceanic background levels. Downstream, Panay Sill overflow water is shown to ventilate a slab in the Sulu Sea between approximately 575 and 1250 dbar with a residence time of about 11 years. Below this, the salinity increases with depth. Deep Sulu Sea water is shown to most likely derive from the Sulawesi Sea to the south. We propose that Sulawesi Sea water between 245 to 527 m is mixed and transported by the energetic tidal environment at Sibutu Passage. Oxygen concentrations within the deep Sulu Sea suggest that the Sulawesi overflow is 0.15 x 10^6 m^3/s, with a residence time of Sulu Sea deep water of 60 years. The balance of ventilation from the northern and southern sources is likely to change on a range of time scales, associated with thermocline depth variability. Finally, we take advantage of our timing and location to investigate the energetics of large-amplitude non-linear internal waves generated at Sibutu Passage in the southern Sulu Sea. Water column displacement and velocity profile time series are used to track the passage of two solitary-like waves close to their generation site. These waves are repeatedly observed by hull-mounted ADCP as they travel north through the Sulu Sea. Wave amplitude is observed to be 43.5 m, and are reasonably fit by both a shallow water Korteweg-de Vries model and a finite depth Joseph model. Total potential energy per meter of wave crest in the modeled solitary waves are 1.6 x 10^8 J/m and 9.8 x 10^7 J/m for the K-dV and Joseph waves, respectively, while kinetic energy in the main wave crest contains 4.7 x 10^7 J/m, estimated from ADCP measurements. Attempting to compensate for the early development of the waves, a more broadly defined packet contains an estimated 1.5 x 10^8 J/m kinetic energy, comparable to the modeled potential energy.

The intraseasonal variability (ISV; 20-90 days) in Makassar Strait, the primary pathway for Pacific water flow into the Indian Ocean and a waveguide for transmitting subinertial energy from the tropical Indian Ocean to Indonesian seas, is investigated, using the 2004-2006 International Nusantara Stratification and Transport (INSTANT) observations. The INSTANT current and temperature timeseries in the Labani Channel, a narrow constriction in Makassar Strait, are used to identify the ISV. Additionally, insitu current measurements along with satellite-derived wind and sea level anomaly data in the region are employed to track the transmission of ISV from their likely origin. We find that the Makassar Strait ISV can be classified as locally or remotely forced features. Local winds and shear flow instability-generated eddies within Makassar Strait control the locally forced ISV component, while the remotely forced part is linked to equatorial Indian Ocean Kelvin waves and Sulawesi Sea eddies. The oceanic response to the local wind stress varying at periods of 45-90 days, with 60-day oscillation showing the strongest coherence, is constrained to along-strait flow primarily within the upper 50 m of the water column. At depths greater than 50 m, we observe that the 20-40 day variability reflects locally generated eddy signatures, while the 60-90 day variability agrees with remotely forced Kelvin wave characteristics. Moreover the Sulawesi Sea ISV, signifying eddy signatures, and along-strait flow across the Makassar Strait pycnocline of 50-450 m display significant coherence at periods of 45-90 days. The observed 60-90 day variability at depths of 100-450 m, coinciding with weaker Makassar Strait throughflow, exhibits Kelvin wave signatures including vertical energy propagation, energy equipartition, non-dispersive relationship and semi-geostrophic balance. Current meters at 750 m and 1500 m further provide evidence that the vertical structure of the Kelvin waves resembles that of a second baroclinic mode. We propose that the intraseasonal Kelvin waves emanate from the tropical Indian Ocean as wind-forced equatorial Kelvin waves and propagate along a waveguide which extends from the southwestern coasts of the Indonesian archipelago to Makassar Strait, via Lombok Strait. From Lombok Strait to Makassar Strait, the Kelvin waves navigate along the 100-m isobath. The intraseasonal Kelvin waves induce increased vertical shear of the along-strait flow across the pycnocline, which potentially leads to instability with a vertical mixing rate of 1-5x 10^-5 m^2s. Moreover the intraseasonal Kelvin waves also force the ITF transport anomalies in Makassar Strait. The 20-40 day variability is most evident in the across-strait flow, and in the across-strait gradient of the along-strait flow as well as in the vertical displacements of isotherms observed at depths of 100-300 m. The flow fields at 20-40 days are approximated by a vortex velocity structure, and the corresponding isotherm displacements signify potential vorticity conservation. We propose that southward-advected eddies, generated in the northern Makassar Strait at latitudes of 0.5-2S due to background flow instability, likely explain the 20-40 day variability observed in the Labani Channel.

Mesoscale eddies are ubiquitous in the World Ocean and dominate the energy content on subinertial time scales. However, due to a lack of in situ data from the deep ocean, most previous work has focused on signals near the sea-surface, that is, the signals of mesoscale eddies in the deep ocean and their influence on the deep ocean dynamics have not yet been intensively studied. In this thesis, the connections between mesoscale eddies and deep ocean dynamical processes, including low-frequency flows, internal waves and ocean mixing, are examined using observations from a collection of moored instruments located near the crest of the East Pacific Rise (EPR) between 9 and 10N. First, the relationship between mesoscale eddies and subinertial flows in the deep ocean over the EPR were examined. The subinertial velocities at depth are significantly correlated with geostrophic near-surface currents, which are dominated by westward-propagating mesoscale eddies. It is concluded that the subinertial velocity near the EPR crest is a super-position of velocities associated with eddies propagating westward across the ridge and "topographic flows". Second, the relationship between subinertial flows and internal waves were investigated. The observations reveal subinertial modulations of internal waves, particularly near-inertial oscillations and internal tides. These subinertial modulations are highly correlated with the subinertial flows in the deep ocean. Third, based on a finescale parameterization model, the deep ocean diapycnal diffusivity over the ridge crest was estimated. The estimated diapycnal diffusivity shows variation on the subinertial time scale. In particular, the measurements imply a significant increase in diapycnal diffusivity near the seafloor during episodes of increased subinertial flow. Fourth, combined with previous numerical and theoretical studies, the observations imply energy transfer near the crest of the EPR from low-frequency flows, including mesoscale eddies, to near-inertial oscillations, turbulence and mixing. Considering the ubiquitousness of mesoscale eddies in the ocean, it is expected that the circulation near other portions of the global mid-ocean ridge system is similarly dominated by mesoscale variability and topographic effects. This is particularly important for dispersal of larvae and geochemical tracers associated with hydrothermal sources that are found primarily along the crest of mid-ocean ridges. Also, the observed eddy-modulated mixing is expected to be useful for validating and improving numerical-model parameterizations of turbulence and mixing in the ocean. Furthermore, since the frequency and intensity of mesoscale eddies depend on the state of the climate, the observed eddy modulation of deep ocean mixing connects climate change and climate variability to physical and biogeochemical dynamics in the deep ocean and implies an unexplored feedback mechanism potentially affecting the global climate system.

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