Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1988. / Includes bibliographical references. / Inverse methods are applied to historical hydrographic data to address two aspects of the general circulation of the Atlantic Ocean. The method allows conservation statements for mass and other properties, along with a variety of other constraints, to be combined in a dynamically consistent way to estimate the absolute velocity field and associated property transports. The method is first used to examine the exchange of mass and heat between the South Atlantic and the neighboring ocean basins. The Antarctic Circumpolar Current (ACC) carries a surplus of intermediate water into the South Atlantic through Drake Passage which is compensated by a surplus of deep and bottom water leaving the basin south of Africa. As a result, the ACC loses .25+.18x10' 5 W of heat in crossing the Atlantic. At 32*S the meridional flux of heat is .25±.19x1015 W equatorward, consistent in sign but smaller in magnitude than other recent estimates. This heat flux is carried primarily by a meridional overturning cell in which the export of 17 Sv of North Atlantic Deep Water (NADW) is balanced by an equatorward return flow equally split between the surface layers, and the intermediate and bottom water. No "leak" of warm Indian Ocean thermocline water is necessary to account for the equatorward heat flux across 32*S; in fact, a large transfer of warm water from the Indian Ocean to the Atlantic is found to be inconsistent with the present data set. Together these results demonstrate that the Atlantic as a whole acts to convert intermediate water to deep and bottom water, and thus that the global thermohaline cell associated with the formation and export of NADW is closed primarily by a "cold water path," in which deep water leaving the Atlantic ultimately returns as intermediate water entering the basin through Drake Passage. The second problem addressed concerns the circulation and property fluxes across 24*and 36*N in the subtropical North Atlantic. Conservation statements are considered for the nutrients as well as mass, and the nutrients are found to contribute significant information independent of temperature and salinity. Silicate is particularly effective in reducing the indeterminacy of circulation estimates based on mass conservation alone. In turn, the results demonstrate that accurate estimates of the chemical fluxes depend on relatively detailed knowledge of the circulation. The zonal-integral of the circulation consists of an overturning cell at both latitudes, with a net export of 19 Sv of NADW. This cell results in a poleward heat flux of 1.3±.2z10'5 W and an equatorward oxygen flux of 2900±180 kmol s-' across each latitude. The net flux of silicate is also equatorward: 138±38 kmol s-1 and 152±56 kmol s-1 across 36 0and 24*N, respectively. However, in contrast to heat and oxygen, the overturning cell is not the only important mechanism responsible for the net silicate transport. A horizontal recirculation consisting of northward flow of silica-rich deep water in the eastern basin balanced by southward flow of low silica water in the western basin results in a significant silicate flux to the north. The net equatorward flux is thus smaller than indicated by the overturning cell alone. The net flux of nitrate across 36*N is 119±35 kmol s- to the north and is indistinguishable from zero at 24*N (-8±39 kmol s-1), leading to a net divergence of nitrate between these two latitudes. Forcing the system to conserve nitrate leads to an unreasonable circulation. The dominant contribution to the nitrate flux at 36*N results from the correlation of strong northward flow and relatively high nitrate concentrations in the sub-surface waters of the Gulf Stream. The observed nitrate divergence between 24*and 36 0N, and convergence north of 36*N, can be accounted for by a shallow cell in which the northward flow of inorganic nitrogen (nitrate) in the Gulf Stream is balanced by a southward flux of dissolved organic nitrogen in the recirculation gyre. Oxidation of the dissolved organic matter during its transit of the subtropical gyre supplies the required source of regenerated nitrate to the Gulf Stream and consumes oxygen, consistent with recent observations of oxygen utilization in the Sargasso Sea. / by Stephen Rich Rintoul. / Ph.D.

Thesis (Ph.D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2012. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student submitted PDF version of thesis. / Includes bibliographical references (p. 91-98). / This thesis presents a system for automatically building 3-D optical and bathymetric maps of underwater terrain using autonomous robots. The maps that are built improve the state of the art in resolution by an order of magnitude, while fusing bathymetric information from acoustic ranging sensors with visual texture captured by cameras. As part of the mapping process, several internal relationships between sensors are automatically calibrated, including the roll and pitch offsets of the velocity sensor, the attitude offset of the multibeam acoustic ranging sensor, and the full six-degree of freedom offset of the camera. The system uses pose graph optimization to simultaneously solve for the robot's trajectory, the map, and the camera location in the robot's frame, and takes into account the case where the terrain being mapped is drifting and rotating by estimating the orientation of the terrain at each time step in the robot's trajectory. Relative pose constraints are introduced into the pose graph based on multibeam submap matching using depth image correlation, while landmark-based constraints are used in the graph where visual features are available. The two types of constraints work in concert in a single optimization, fusing information from both types of mapping sensors and yielding a texture-mapped 3-D mesh for visualization. The optimization framework also allows for the straightforward introduction of constraints provided by the particular suite of sensors available, so that the navigation and mapping system presented works under a variety of deployment scenarios, including the potential incorporation of external localization systems such as long-baseline acoustic networks. Results of using the system to map the draft of rotating Antarctic ice floes are presented, as are results fusing optical and range data of a coral reef. / by Clayton Gregory Kunz. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 99-100). / Signal detection and synchronization in the time varying ocean environment is a difficult endeavor. The current common methods include using a linear frequency modulated chirped pulse or maximal length sequence as a detection pulse, then match filtering to that signal. In higher signal to noise ratio (SNR) environments (- 0 dB and higher) this has been a suitable solution. As the SNR drops lower however, this solution no longer provides an acceptable probability of detection for a given tolerable probability of false alarm. The issue derives from the inherent coherence issues in the ocean environment which limit the useful matched filter length. This thesis proposes an alternative method of detection based on a recursive least squares linearly adaptive equalizer which we term the Adaptive Linear Equalizer Detector (ALED). This detectors performance has demonstrated reliable probability of detection with minimal interfering false alarms with SNR as low as -20 dB. Additionally this thesis puts forth a computationally feasible method for implementing the detector. / by Ryan Thomas Gieleghem. / S.M.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Zooplankton, such as copepods, are highly abundant environmental reservoirs of many bacterial pathogens. Although copepods are known to support diverse and productive bacterial communities, little is understood about whether copepods are affected by bacterial attachment and whether they can regulate these associations through mechanisms such as the innate immune response. This thesis investigates the potential role that copepod physiology may play in regulating Vibrio association and the community structure of its microbiome. To this end, the intrinsic ability of oceanic copepod hosts to transcriptionally respond to mild stressors was first investigated. Specifically, the transcriptional regulation of several heat shock proteins (Hsps), a highly conserved superfamily of molecular chaperones, in the copepod Calanusfinmarchicus was examined and demonstrated that Hsps are a conserved element of the copepod's transcriptional response to stressful conditions and diapause regulation. To then investigate whether copepod hosts respond to and regulate their microbiota, the transcriptomic response of an estuarine copepod Eurytemora affinis to two distinct Vibric species, a free-living strain (V. ordalii 12B09) and a zooplankton specialist (V. sp. F10 9ZB36), was examined with RNA-Seq. Our findings provide evidence that the copepod E. affinis does distinctly recognize and respond to colonizing vibrios via transcriptional regulation of innate immune response elements and transcripts involved in maintaining cuticle integrity. Our work also suggests that association with E. affinis can significantly impact the physiology of Vibrio colonists. Finally, the inter-individual variability of the C.finmarchicus microbiome was examined to identify how specifically and predictably bacterial communities assemble on copepods and whether host physiology influences the bacterial community structure. Our findings suggest that copepods have a predictable "core microbiome" that persists throughout the host's entrance into diapause, a dormancy period characterized by dramatic physiological changes in the host. However, diapausing and active populations harbor distinct flexible microbiomes which may be driven by factors such including the copepod's feeding history, body size, and bacterial interactions. This thesis work highlights the role of copepods as dynamic reservoirs of diverse bacterial communities and implicates copepod host physiology as an important contributor to the activity, abundance, and community structure of its microbiome. / by Amalia Aruda Almada. / Ph. D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / The mechanisms of faunal dispersal across ocean basins are key unknowns toward understanding of the modern biogeography and biodiversity of deep-sea fauna. Seamounts are considered to play a defining role in faunal evolution, acting as regional centers of speciation, "stepping-stones" for dispersal, and/or refugia for deep-sea populations. The overarching goal of this dissertation was to examine the role of seamounts in structuring marine biodiversity and biogeography. This study focused on North Atlantic seamounts, specifically the New England seamount chain, the Corner Rise seamounts, and Muir seamount, areas damaged and threatened by deep-sea fisheries and currently a focus of conservation efforts. Videographic analyses of biological community structure revealed distinct faunal assemblages, dominated by the Porifera, Cnidaria, and Echinodermata and structured by geographic region, depth regions (with apparent taxonomic breaks at 1300 m, 2300 m, and 2600 m), and substrate type (including natural/anthropogenic and abiotic substrates and biotic substrates). Amongst these assemblages, seven highly specific coral host- invertebrate associate relationships were identified. To investigate whether or not these broad community patterns were discernible at a genetic level, the 16S mtDNA gene was utilized as a genetic "barcode" within the Class Ophiuroidea, through which 22 putative species were identified, including four target species (Asteroschema clavigera, Ophiocreas oedipus, Ophioplinthaca abyssalis, and Ophioplinthaca chelys) for subsequent population genetic studies. Analyses of mitochondrial 16S and COI gene sequences revealed evidence for recent population expansion and estimates of recent high gene flow across all four species throughout the North Atlantic seamount region. / (cont.) However, genetic differentiation within populations of A. clavigera and 0. chelys within seamount regions was significant, suggesting that historical diversification has been mediated by a long-distance dispersal mechanism that homogenizes this genetic signal on a regional scale. In addition, comparisons of all ophiuroid populations revealed no congruent pattern of historical migration amongst seamounts, which may also be attributed to the varying levels of host specificity and reproductive strategy of each ophiuroid species. These results will guide future studies and conservation efforts to protect seamount communities vulnerable to deep-sea fishery activities. / by Walter W. Cho. / Ph.D.

Thesis (Ph.D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences and the Woods Hole Oceanographic Institution), 2000. / Vita. / Includes bibliographical references. / by Robert P. Ackert, Jr. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / As the only low-latitude connection between ocean basins, the Indonesian Throughflow allows the direct transmission of heat and salinity between the Pacific and Indian Oceans. Despite its potential importance, the role of the Indonesian Throughflow in global ocean circulation and regional climate is still not clear due to sparse measurements and the relative difficulty of modeling the region. The Mg/Ca and [delta]¹⁸0 of calcite of the calcitic planktic foraminifera Globigerinoides ruber (G. ruber) were used to estimate the sea surface temperature and [delta]¹⁸0 of water, an indicator of hydrologic conditions, over the past 20,000 years. I also attempted to estimate thermocline structure using the foraminifera, Pulleniatina obliquiloculata, but the Mg/Ca and [delta]¹⁸0 of calcite data yield conflicting interpretations, indicating further work on this proxy is required. The G. ruber Mg/Ca results suggest that the sea surface temperature of the outflow passages was influenced by high latitude Southern Hemisphere temperature. This connection is likely via intermediate waters that upwell in the Banda Sea. At approximately 10,000 years before present, there was a warming in the Makassar Strait. This local warming was coincident with the flooding of the Sunda Shelf, which opened a connection between the South China Sea and the Indonesian Throughflow. Regional [delta]¹⁸0 of seawater reconstructions show that during the last glacial maximum the [delta]¹⁸0 of seawater pattern was very similar to modern, but there were relatively enriched values over the equatorial IndoPacific during high latitude Northern Hemisphere cold events (Heinrich Stadial 1 and the Younger Dryas). From these results we postulate that the mean position of the Intertropical Convergence Zone was approximately the same as modern at the last glacial maximum and was likely displaced to the south during the Younger Dryas and Heinrich Stadial 1, suggesting the Intertropical Convergence Zone primarily responds to changes in the interhemispheric temperature gradient. These results shed light on the primary controls of the temperature and hydrology of Indonesian Throughflow region. / by Fern Tolley Gibbons. / Ph.D.

Thesis: Ph. D., Joint Program in Marine Chemistry and Geochemistry (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Hydrophobic organic chemicals (HOCs) are a class of environmental contaminants responsible for numerous acute and chronic health effects in humans and wildlife. This thesis illustrates three applications of polyethylene (PE) passive sampling, which enhance our toolbox for estimating environmental hazards associated with HOCs. First, we present a methodology that can be used to estimate the bioaccumulation potential of numerous organic chemicals based on passive sampling and comprehensive two dimensional gas chromatography (GC x GC). Using GC x GC retention times, we show that lipid-water and samplerwater partition coefficients can be estimated within a factor of 2 and 3, respectively. The method was then applied to estimate body burdens of various HOCs in benthic organisms from GC x GC analysis of PE equilibrated with contaminated sediment. Empirical observations of accumulation in the Nereis virens polychaete were in good agreement with PE-based predictions for PCBs, but were lower by at least an order of magnitude for other classes of HOCs (such as PAHs) presumably due to metabolism. Second, we applied the same methodology to a set of contaminated sediments and estimated the cumulative baseline toxicity associated with environmental mixtures of HOCs. The predictions were compared against empirical measurements of baseline toxicity using the water flea Daphnia magna. The estimated total body burdens of HOCs were in good agreement with measured toxicity, with toxicity occurring at body burdens larger than 30 mg/gipid. In contrast, the toxicity estimated based on priority pollutants severely underestimated the observed toxicity, emphasizing the importance of cumulative effects. Lastly, to advance our understanding of the processes that affect passive sampling results in situ (when they are operating away from equilibrium), a mathematical model was developed for reactive chemicals transferring between PE and sediment beds. The reaction diffusion model was used to infer in situ degradation rates of dichlorodiphenyltrichloroethane (DDT), which in the sediments of a freshwater lake were found to be between 0.09 and 0.9 d-1. A second mathematical model describing the kinetics of exchange between passive samplers and water was also developed, which can be used in both field (infinite baths) and laboratory (finite baths) conditions. / by Alexandra Patricia Tcaciuc. / Ph. D.

Thesis: Ph. D., Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 169-190). / Terrestrial organic carbon (OC) erosion, remineralization, transport through river networks, and burial in marine sediments is a major pathway of the global carbon cycle. However, our ability to constrain these processes and fluxes is largely limited by (i) analytical capability and (ii) temporal sampling resolution. To address issue (i), here I discuss methodological advancements and data analysis techniques for the Ramped PyrOx serial oxidation isotope method developed at WHOI. Ramped-temperature pyrolysis/oxidation coupled with the stable carbon (¹²C, ¹³C) and radiocarbon (¹⁴C) analysis of evolved CO₂ is a promising tool for understanding and separating complex OC mixtures. To quantitatively investigate distributions of OC source, reservoir age, and chemical structure contained within a single sample, I developed a kinetic model linking RPO-derived activation energy, ¹³C composition, and radiocarbon content. This tool provides a novel method to fundamentally address the unknown relationship between OC remineralization rates and chemical structure in various environmental settings. To address issue (ii), I additionally present results from time-series sample sets collected on two end-member systems: the Congo River (Central Africa) and the LiWu River (Taiwan). For the Congo River, bulk and plant-wax-lipid ¹³C compositions indicate that a majority of particulate OC is consistently derived from downstream, C₃-dominated rainforest ecosystems. Furthermore, bulk radiocarbon content and microbial lipid molecular distributions are strongly correlated with discharge, suggesting that pre-aged, swamp-forest-derived soils are preferentially exported when northern hemisphere discharge is highest. Combined, these results provide insight into the relationship between hydrological processes and fluvial carbon export. Lastly, I examined the processes controlling carbon source and flux in a set of soils and time-series fluvial sediments from the LiWu River catchment located in Taiwan. A comparison between bedrock and soil OC content reveals that soils can contain significantly less carbon than the underlying bedrock, suggesting that this material is remineralized to CO₂ prior to soil formation. Both the presence of bacterial lipids and a shift toward lower activation energy of ¹⁴C-free OC contained in soil saprolite layers indicate that this process is microbially mediated and that microbial respiration of rock-derived OC likely represents a larger geochemical flux than previously thought. The results presented in this thesis therefore provide novel insight into the role of rivers in the global carbon cycle as well as their response to environmental perturbations. / by Jordon Dennis Hemingway / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 131-149). / This thesis evaluates the nature and magnitude of tropical climate variability from the Last Glacial Maximum to the present. The temporal variability of two specific tropical climate phenomena is examined. The first is the position of the Intertropical Convergence Zone (ITCZ) in the Atlantic basin, which affects sea surface temperature (SST) and precipitation patterns throughout the tropical Atlantic. The second is the strength of the Indian Monsoon, an important component of both tropical and global climate. Long-term variations in the position of the ITCZ in the Atlantic region are determined using both organic geochemical techniques and climate modeling. Upwelling in Cariaco Basin is reconstructed using chlorin steryl esters as proxies for phytoplankton community structure. We find that the diatom population was larger during the Younger Dryas cold event, indicating that upwelling was enhanced and the mean position of the ITCZ was farther south during the Younger Dryas than it is today. A climate simulation using an ocean-atmosphere general circulation model confirms these results by demonstrating that the ITCZ shifts southward in response to high-latitude cooling. The climate of the Arabian Sea region is dominated by the Indian Monsoon. / (cont.) Results from modern sediments from a suite of cores located throughout the Arabian Sea suggest that wind strength is well represented by the accumulation rate and carbon isotopic composition of terrestrially-derived plant waxes in sediments. Arabian Sea SST patterns, reconstructed from a suite of sediment cores representing four time slices utilizing the Mg/Ca SST proxy, suggest that both the summer and winter monsoons were enhanced 8,000 yr BP relative to today while the summer monsoon was weaker and the winter monsoon stronger at 15,000 and 20,000 yr. These results are confirmed by a time-series reconstruction of SST on the Oman Margin that reveals that SST at this site is sensitive to both regional and global climate processes. The results of this thesis demonstrate that tropical climate, as evaluated by a number of different proxies as well as climate models, has varied substantially over the past 20,000 years and is closely coupled to climate at high-latitudes. / by Kristina Ariel Dahl. / Ph.D.