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Laboratory experiments on a rotating tank of fluid are used to study the fundamental aspects of geophysical fluid flows. The present set of experiments are an attempt to study the effect of a rectangular ridge on the flow of a rotating fluid confined by lateral boundaries and forced by a source. First dye and later Particle Image Velocimetry (PIV) are used to understand the circulation in the domain. A strong southern boundary flow near the western wall of the domain and a cyclonic circulation in the trench are observed in these experiments. Overflow from the eastern side to the west of the ridge is seen along the N-S length of the ridge, though the overflow is pronounced near the northern boundary of the domain. Simplified mathematical models are used to describe the observed circulation. Numerical simulations are conducted using the MIT general circulation model on a large scale idealized box domain with a topography similar to the one we used in the laboratory tank as well as a rectangular trench parallel to the eastern wall of the domain. A point mass source contributes to the upwelling at the free surface. This set up represents a homogeneous abyssal layer upwelling slowly due to a polar source. Results indicate a cyclonic sense of circulation and a poleward eastern boundary current over the ridge wall. This intensification can be attributed to the vortex stretching over the slopes of the ridge, as the vertical walls appear in the numerical model as having a steep slope. Friction on vertical walls of the ridge are also a cause of this intensification. Some features of the observed and modeled circulation are compared to the oceanic flow in the deep Pacific Ocean. / 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. / Spring Semester 2019. / March 5, 2019. / Deep eastern boundary current, Numerical model, Particle image velocimetry, Topographic ridge, Trench, vorticity / Includes bibliographical references. / Kevin Speer, Professor Directing Thesis; Christopher Tam, Committee Member; William Dewar, Committee Member.

Coastal ecosystems are among the most productive in the world, and they serve as an invaluable resource to society. Despite many decades of biogeochemical research in the coastal zone, carbon and nutrient budgets remain uncertain largely due to the inherent complexity and spatiotemporal variability observed in coastal ecosystems. This dissertation addresses the rates, pathways, and microorganisms responsible for organic-matter mineralization and nutrient release in the sediments of coastal marine ecosystems. In particular, the research herein focuses on the role of macrobenthos and spatial/ temporal variability in impacting organic matter and nutrient cycles in such ecosystems. The common theme throughout the dissertation research was to combine ecology with biogeochemistry to explore the impacts of benthic organisms in the macroscale on microbial processes that mediate organic matter mineralization and nutrient release over the microscale. Sulfate-reducing prokaryotes (SRP) play a key role in carbon and nutrient cycles of coastal marine, vegetated ecosystems, but interactions of SRP communities with aquatic plants remain little studied. In the subtidal zone of Santa Rosa Sound, Florida, SRP abundance, activity, and community composition were studied in relation to sediment geochemical gradients and plant growth state in a Thalassia testudinum seagrass bed and in adjacent unvegetated areas (Chapter 1). The community composition of SRP was determined using restriction fragment length polymorphism (RFLP) screening and amino acid sequence comparisons inferred from partial dissimilatory bisulfite reductase (dsrA and B) genes that were PCR-amplified and cloned from DNA extracted from sediment samples. Our results indicate that seagrass growth state affects the abundance and activity of SRP, while SRP community composition remains relatively stable across the environmental parameters tested. Sequence data from this study may be used to direct future cultivation efforts and to design new genetic probes for sulfate-reducers in seagrass sediments. The remaining dissertation research focused on a second coastal marine ecosystem, the saltmarsh, on Skidaway Island near Savannah, Georgia. The Georgia saltmarsh contrasts with seagrass beds from the west coast of Florida in that it exists in the intertidal zone, contains a large tidal range of 2-3 m, and the sediments are exposed to extensive burrowing and feeding activities by macrofauna. In addition, larger seasonal change may be observed in the Georgia marsh because it is intertidal and exposed to slightly larger annual temperature extremes. In chapter two, extensive biogeochemical field characterization was combined with state-of-the-art diagenetic modeling to elucidate feedbacks between macrobenthic organisms (macrophyte plants, bioturbating macrofauna) and the controls of organic matter mineralization in saltmarsh sediments. A multicomponent, inverse model was used to support the field work by quantifying properties and processes that in some cases could not be experimentally determined. Modeled rates of organic matter diagenesis were determined by attempting to find the best agreement with measured profiles of major redox species. Results indicated that sulfate reduction is the dominant degradation pathway for sites with less bioturbation, while iron reduction outcompeted sulfate reduction where intense bioturbation activity caused the rapid recycling of Fe(III)-oxyhydroxides. These results were fairly consistent across seasons, however, the magnitude of degradation rates decreased dramatically in the winter, and microbial sulfate reduction was more greatly affected by changes in temperature than microbial iron reduction. The objective of the third and final study was to scale up biogeochemical measurements over an entire ecosystem (saltmarsh basin) in order to address spatial variability that has confounded estimates of organic matter and nutrient mineralization at the whole ecosystem level. A 100,000 m2 area of Georgia marsh was mapped using a combination of aerial photography, Geographic Information Systems (GIS), and localized identification of plant types. Major habitats were delineated according to the predominant vegetation, including the short form of Spartina alterniflora (SS), the tall form of S. alterniflora (TS) and unvegetated creekbank (CB). Spatial variability was addressed across all major habitats with a statistically-sound experimental design to carry out determinations of porewater and solid-phase geochemistry, sulfate reduction rates (SRR), bacterial abundances, macrofaunal burrow size/density, plant stem height/density, and above/belowground plant biomass. Habitat type had a large influence on the rates and pathways of carbon oxidation. Consideration of spatial variability revealed that overall carbon oxidation rates in saltmarsh ecosystems may be higher than previously thought. Surprisingly, microbial Fe(III) reduction (and not sulfate reduction) was observed to be the predominant terminal-electron-accepting process coupled to carbon oxidation for the majority of the marsh basin studied. Together with the observation that most of the Georgia marsh studied was not sulfidic, results indicate that our perceptions of the redox poise, and the impacts of redox poise on biogeochemical cycles, need to be revised for marsh ecosystems taking into account spatial variability driven by macrobenthic activities. Typically, coastal sediments rapidly become anaerobic just below the sediment surface, and the flux of oxidants into sediments is limited. Under these conditions, anaerobic bacteria are responsible for the majority of organic matter remineralization. Increased solute and particle transport via macroorganismal activities (bioturbation, bioirrigation, and phytoirrigation) aids in mixing reactants throughout sediments, thereby encouraging microbial activities, and increasing organic matter remineralization rates. The following research employed an array of new and diverse multidisciplinary approaches from molecular biological techniques and GIS mapping to state-of-the-art diagenetic modeling in order to elucidate the impacts of macrobenthos on carbon and nutrient cycles mediated by anaerobic microorganisms in coastal marine ecosystems. In all three studies, geochemical parameters indicated that bacterial activities were stimulated in vegetated sediments, while saltmarsh studies revealed that macrofaunal burrows strongly influenced the pathways of terminal electron acceptor (TEA) usage. The uncertainty of current estimates of carbon and nitrogen cycling in saltmarsh habitats indicates the need for a more comprehensive approach to address the spatial variability that exists in these habitats. From the research reported in this dissertation, it is clear that macrobenthos have a profound impact on the rates and pathways of organic matter mineralization and that the resulting spatial variability in sediment biogeochemical cycles must be incorporated into future studies that attempt to determine elemental budgets in coastal marine ecosystems. / 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, 2004. / Date of Defense: November 19, 2004. / Thalassia testudinum, Saltmarsh, Seagrass bed, Fiddler crabs, Spartina alterniflora, Carbon cycling, Sulfate-reducing bacteria, Microbial iron reduction / Includes bibliographical references. / Joel E. Kostka, Professor Directing Dissertation; David Balkwill, Outside Committee Member; David Thistle, Committee Member; Nancy Marcus, Committee Member; Richard Devereux, Committee Member; Yoko Furukawa, Committee Member.

The Bering Strait's Grip On The World Climate: The Holocene interglacial period of the last 10,000 years and the penultimate interglacial ~125,000 years ago have been characterized by distinctly stable climates. During the intervening glacial period, climate records are marked by rapid large-amplitude oscillations, general known as Dansgaard-Oeschger events. These millennial-scale cycles are generally believed to be a result of freshwater anomalies in the North-Atlantic, followed by a reorganization of the thermohaline circulation. Here, we propose that such long lasting instabilities in the thermohaline circulation are only possible during glacial periods when the Bering Strait (BS) is closed. A semi-global analytical ocean model (which includes both wind and thermohaline processes) is used to show that, during interglacial periods (when the BS is open) perturbations in North Atlantic Deep Water (NADW) formation are rapidly damped out because of a novel BS freshwater feedback mechanism. This new feedback mechanism is due to the strong winds in the Southern Ocean (SO) which, with an open BS, quickly [O(10)years)] flush any low salinity anomalies out of the Atlantic and into the Pacific Ocean. During glacial periods, the stabilizing feedback is prevented by the closure of the BS which traps the anomalies within the Atlantic, causing long lasting perturbations. The sensitivity of the mean stable state to steady changes in the external forcing, namely the wind or the precipitation field, is also tested. A relevant example is a prolonged increase in precipitation due to anthropogenic warming, (predicted by global circulation models). We find that both stronger winds (especially the SO Winds) and a decrease in precipitation over the North Atlantic (NA) will lead to a new (stable) enhanced overturning. Conversely, weaker winds or increased precipitation will reduce the overturning to a slower stable state. The Island Wind-Bouyancy Paradox: In reent years, a variety of studies have suggested that the meridional overturning circulation is at least partially controlled by the Southern Ocean winds. The paraadoxical implication is that a link exists between the surface bouyancy flux to the ocean (which is needed for the density transfor4matio between surface and deep water) and the wind. These forcings have traditionally been viewed as independent drivers of the ocean circulation. Here, the paradox is formally stated in the framework of a gigantic island that lies between latitude bands free of continents (such as the land mass of the Americas). The choice of such an island on a sphere was made because it enables one to obtain analytical solutions and it circumvents the need to calculate the torque exerted on zonal sills adjacent to the island tips (e.g., the Bering Strait). The torque calculation is notoriously difficult and is avoided here by the clockwise integration which goes twice through the western boundary of the island (in opposite directions) eliminating any unknown pressure torques. The derived wind-driven overturning is shown to be consistent with Godfrey's Island Rule when the rule is extended to include the sinking or upwelling adjacent to the island. In addition, the consideration of vertical exchange in the Island Rule eliminates the need to make the level-of-no-motion assumption. The paradox is resolved quanlitatively, using salinity and temperature mixed dynamical-box models and a temperature slab model, and quantitatively, employing a numerical model. We show that in all cases the ocean stratification and thermocline depth adjust themselves to allow the overturning imposed by the wind. The salinity and temperature box model suggests that stronger southern winds will tend to weaken the virtical and horizontal salinity stratfication so that it is esier for the conversion of deep to surface water (and vice versa) to take place. A temperature slab model (i.e., y-dependent)offers a more detailed picture;stronger southern winds flatten the meridional temperature profile and shift it northwards (so that it lags the atmospheric temperature). The (process orientated) numericl model is adapted to include a thermodynamic parameterization for the surface heat and freshwater fluxes. In response to stronger southern winds, the thermocline thickens in the north, releases more heat to the atmosphere and, therefore, converts more surface to deep water. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the degree of Doctor of Philosophy. / Degree Awarded: Spring Semester, 2003. / Date of Defense: January 7, 2003. / Southern Ocean Winds', World Climate / Includes bibliographical references. / Doron Nof, Professor Directing Dissertation; Christopher Hunter, Committee Member; William Burnett, Committee Member; Alan J. Clarke, Committee Member; Kevin Speer, Committee Member; Georges L. Weatherly, Committee Member.