Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), February 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The marine fecal indicator Enterococcus is measured at beaches to detect fecal contamination events, and beaches are closed to bathers when Enterococcus is found to exceed the federally mandated limit. This dissertation presents evidence that beach sands are an environmental reservoir of enterococci, tests the relationship between beach sand enterococci and water quality measurements, examines how real-time environmental conditions measured at beaches can be used to better understand and predict water quality violations, and uses molecular methods to provide an alternative characterization of water and sand fecal contamination. Initially, a qPCR method was developed and applied to monitor enterococci DNA in sands. Subsequently this qPCR method was used in tandem with traditional detection of culturable enterococci in sand and water at recreational beaches that have closures every summer. One field season was spent in Maine at beaches in the Wells National Estuarine Research Reserve, where high frequency water and weather measurements are routinely collected in situ. Two field seasons were spent at the beach in Provincetown Harbor, Massachusetts, where a weather station and ADCP were deployed to characterize the environmental conditions associated with observations of elevated enterococci. All studies revealed that environmental variables were related to the distribution of enterococci in sands and water, with water temperature and tides having the strongest relationship to enterococci in water. In dry weather, elevated enterococci in sands were strongly related to the increased moisture content of sands during spring tides. These environmental variables were used in multiple linear regressions to explain a significant amount of the variation observed in environmental enterococci abundance, which notably had no relationship to molecular markers of human fecal pollution. Results suggest that under certain conditions sands can contribute bacteria to the water and that tidal cycles, which are not taken into account in monitoring schemes, can bias routine sampling. / by Elizabeth Halliday. / Ph.D.

Thesis: Ph. D., Joint Program in 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. / While aerobic respiration is typically invoked as the dominant mass-balance sink for organic matter in the upper ocean, many other biological and abiotic processes can degrade particulate and dissolved substrates on globally significant scales. The relative strengths of these other remineralization processes - including mechanical mechanisms such as dissolution and disaggregation of sinking particles, and abiotic processes such as photooxidation - remain poorly constrained. In this thesis, I examine the biogeochemical significance of various alternative pathways of organic matter remineralization using a combination of field experiments, modeling approaches, geochemical analyses, and a new, high-throughput lipidomics method for identification of lipid biomarkers. I first assess the relative importance of particle-attached microbial respiration compared to other processes that can degrade sinking marine particles. A hybrid methodological approach - comparison of substrate-specific respiration rates from across the North Atlantic basin with Monte Carlo-style sensitivity analyses of a simple mechanistic model - suggested sinking particle material was transferred to the water column by various biological and mechanical processes nearly 3.5 times as fast as it was directly respired, questioning the conventional assumption that direct respiration dominates remineralization. I next present and demonstrate a new lipidomics method and open-source software package for discovery and identification of molecular biomarkers for organic matter degradation in large, high-mass-accuracy HPLC-ESI-MS datasets. I use the software to unambiguously identify more than 1,100 unique lipids, oxidized lipids, and oxylipins in data from cultures of the marine diatom Phaeodactylum tricornutum that were subjected to oxidative stress. Finally, I present the results of photooxidation experiments conducted with liposomes - nonliving aggregations of lipids - in natural waters of the Southern Ocean. A broadband polychromatic apparent quantum yield (AQY) is applied to estimate rates of lipid photooxidation in surface waters of the West Antarctic Peninsula, which receive seasonally elevated doses of ultraviolet radiation as a consequence of anthropogenic ozone depletion in the stratosphere. The mean daily rate of lipid photooxidation (50 ± 11 pmol IP-DAG L⁻¹ d⁻¹, equivalent to 31 ± 7 [mu]g C m⁻³ d⁻¹) represented between 2 and 8 % of the total bacterial production observed in surface waters immediately following the retreat of the sea ice. / by James R. Collins. / Ph. D.

Thesis: Ph. D., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 155-179). / Marine phytoplankton are central players in the global carbon cycle, responsible for nearly half of global primary production. The identification of the factors controlling phytoplankton ecology, physiology, and, ultimately, bloom dynamics has been a central problem in the field of biological oceanography for the past century. Molecular approaches enable the direct examination of species-specific metabolic profiles in mixed, natural communities, a task which was previously intractable. In this thesis, I developed and applied novel analytical tools and bioinformatic pipelines to characterize the physiological response of phytoplankton to their environment at various levels of taxonomic grouping. An in silico Bayesian statistical approach was designed to identify stable reference genes from high-throughput sequence data for use in RT-qPCR assays or metatranscriptome studies. Using a metatranscriptomic approach, the role of resource partitioning in the coexistence of two closely related diatom species in an estuarine system was examined. This study demonstrated that co-occurring diatoms in a dynamic coastal system have apparent differences in their capacity to use nitrogen and phosphorus, and that these differences may facilitate the diversity of the phytoplankton. The second field study focused on the diatom, haptophyte, and dinoflagellate functional groups, using simulated blooms to characterize the traits that govern the magnitude and timing of phytoplankton blooms in the oligotrophic ocean. The results indicated that blooms form when phytoplankton are released from limitation by resources and that the mechanistic basis for the success of one functional group over another may be driven by how efficiently the transcriptome is modulated following a nutrient pulse. The final study looked at the sub-species level, examining the balance of phenotypic plasticity and strain diversity in the success of the coccolithophore Emiliania huxleyi. Results indicated strong control of nitrogen on the species complex and showed that nutrient resupply shifted the strain composition as well as transcript abundance of key biogeochemical genes involved in nutrient acquisition and the life stage of the population. Together, these studies demonstrate the breadth of information that can be garnered through the integration of molecular approaches with traditional biological oceanographic surveys, with each illuminating fundamental questions around phytoplankton ecology and bloom formation. / by Harriet Alexander. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (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 137-149). / Significant changes occurred during the last deglaciation (roughly 10-20 thousand years (ka) before present) throughout the climate system. The ocean is a large reservoir of carbon and heat, however, its role during the deglaciation is still not well understood. In this thesis, I rely on radiocarbon measurements on fossil biogenic carbonates sampled from the seafloor to constrain deglacial ocean ventilation rates, using new data, an extensive data compilation, and inverse modeling. First, based on a sediment core that is absolutely dated from wooden remains, I argue that the deglacial ¹⁴C reservoir age of the upper East Equatorial Pacific was not very different from today. Combined with stable carbon isotope data, the results suggest that the deglacial atmospheric CO₂ rise was probably due to CO₂ released directly from the ocean (e.g., in the Southern Ocean) to the atmosphere rather than first mixed through the upper ocean. Then using a high-deposition-rate sediment core located close to deep water formation regions in the western North Atlantic, I show that compared to today, the mid-depth water production in the North Atlantic was probably stronger during the Younger Dryas cold episode, and weaker during other intervals of the late deglaciation. However, the change was not as large as suggested by previous studies. Finally, I compile published and unpublished deep ocean ¹⁴C data, and find that the ¹⁴C activity of the deep ocean mirrors that of the atmosphere during the past 25 ka. A box model of modern ocean circulation is fit to the compiled data using an inverse method. I find that the residuals of the fit can generally be explained by the data uncertainties, implying that the compiled data jointly do not provide strong evidence for basin-scale ventilation changes. Overall, this thesis suggests that, although deep ocean ventilation may have varied at some locations during the last deglaciation, the occurrence of basin-scale ventilation changes are much more difficult to be put on a firm footing. An imbalance between cosmogenic production and radioactive decay appears as the most natural explanation for the deglacial ¹⁴C activity decline observed in both the atmosphere and the deep ocean. / by Ning Zhao. / Ph. D.

Thesis (Ph.D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering/Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references (leaves 202-211). / The thesis develops and demonstrates methods of classifying ocean processes using an underwater moving platform such as an Autonomous Underwater Vehicle (AUV). The "mingled spectrum principle" is established which concisely relates observations from a moving platform to the frequency-wavenumber spectrum of the ocean process. It clearly reveals the role of the AUV speed in mingling temporal and spatial information. For classifying different processes, an AUV is not only able to jointly utilize the time-space information, but also at a tunable proportion by adjusting its cruise speed. In this respect, AUVs are advantageous compared with traditional oceanographic platforms. Based on the mingled spectrum principle, a parametric tool for designing an AUVbased spectral classifier is developed. An AUV's controllable speed tunes the separability between the mingled spectra of different processes. This property is the key to optimizing the classifier's performance. As a case study, AUV-based classification is applied to distinguish ocean convection from internal waves. The mingled spectrum templates are derived from the MIT Ocean Convection Model and the Garrett-Munk internal wave spectrum model. To allow for mismatch between modeled templates and real measurements, the AUVbased classifier is designed to be robust to parameter uncertainties. By simulation tests on the classifier, it is demonstrated that at a higher AUV speed, convection's distinct spatial feature is highlighted to the advantage of classification. Experimental data are used to test the AUV-based classifier. An AUV-borne flow measurement system is designed and built, using an Acoustic Doppler Velocimeter (ADV). The system is calibrated in a high-precision tow tank. In February 1998, the AUV acquired field data of flow velocity in the Labrador Sea Convection Experiment. The Earth-referenced vertical flow velocity is extracted from the raw measurements. The classification test result detects convection's occurrence, a finding supported by more traditional oceanographic analyses and observations. The thesis work provides an important foundation for future work in autonomous detection and sampling of oceanographic processes. / by Yanwu Zhang. / 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), 2003. / Includes bibliographical references (p. 343-369). / This thesis examines the evolution of a mud-dominated coastal sedimentary system on multiple time scales. Fine-grained systems exhibit different properties and behavior from sandy coasts, and have received relatively little research attention to date. Evidence is presented for shoreline accretion under energetic conditions associated with storms and winter cold fronts. The identification of energetic events as agents of coastal accretion stands in contrast to the traditional assumption that low-energy conditions are required for deposition of fine-grained sediment. Mudflat accretion is proposed to depend upon the presence of an unconsolidated mud sea floor immediately offshore, proximity to a fluvial sediment source, onshore winds, which generate waves that resuspend sediment and advect it shoreward, and a low tidal range. This study constrains the present influence of the Atchafalaya River on stratigraphic evolution of the inner continental shelf in western Louisiana. Sedimentary and acoustic data are used to identify the western limit of the distal Atchafalaya prodelta and to estimate the proportion of Atchafalaya River sediment that accumulates on the inner shelf seaward of Louisiana's chenier plain coast. The results demonstrate a link between sedimentary facies distribution on the inner shelf and patterns of accretion and shoreline retreat on the chenier plain coast. / by Amy Elizabeth Draut. / 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), 2009. / Includes bibliographical references. / The radionuclides ²³¹Pa and ²³⁰Th, produced in the water column and removed from the ocean by particle scavenging and burial in sediments, offer a means for paleoceanographers to examine past dynamics of both water column and sedimentary processes. I show for the first time that a state of balance exists between ²³⁰Th production and burial in the Central Arctic basins, based on measured sedimentary ²³⁰Th, inventories in box cores, establishing this nuclide's utility as a paleoceanographic indicator of sedimentary processes and as a normalization tool. I present the first ²³⁰Th-normalized particle fluxes calculated for the central Arctic: vertical particle fluxes were extremely low during the late glacial, rose during the deglaciation due to particle inputs from shelf inundation, increased productivity and ice-rafted debris, and fell again following the establishment of interglacial conditions. A major event of lateral sediment redistribution, inferred from surplus ²³⁰Th, inventories, occurred in the Makarov Basin during the deglaciation and may have been due to destabilization of slope and shelf sediments as sea level rose. I present the first high-resolution, radiocarbon-dated downcore records of sedimentary ²³¹Pa/²³⁰Th from the Arctic Ocean. Low ratios indicate that ²³¹Pa was exported from all sites during the late glacial period, with export decreasing during the deglaciation and Holocene. 231Pa/²³⁰Th measurements in cores from three continental slope sites show no evidence for a ²³¹Pa sink related to boundary scavenging on the continental slopes. Holocene ²³¹Pa/²³⁰Th ratios show a very significant variation by depth, with strong export of ²³¹Pa at deep sites but little or no export at shallow sites, a result which echoes findings for the South Atlantic and the Pacific. / (cont.) The Arctic thus appears fundamentally similar to other ocean basins in its ²³¹Pa and ²³⁰Th dynamics, despite its peculiar qualities of sea ice cover, low particle flux, and relatively isolated deep waters. / by Sharon Susanna Hoffmann. / 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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Trace metal cycling is one of many processes that influence ocean ecosystem dynamics. Cobalt, iron, and manganese are redox active trace metal micro-nutrients with oceanic distributions that are influenced by both biological and abiotic sources and sinks. Their open ocean concentrations range from picomolar to nanomolar, and their bioavailabilities can impact primary production. Understanding the biogeochemical cycling of these hybrid-type metals with an emphasis on cobalt was the focus of this thesis. This was accomplished by determining the dissolved distributions of these metals in oceanic regions that were characterized by different dominant biogeochemistries. A large subsurface plume of dissolved cobalt, iron, and manganese was found in the Eastern South Atlantic. The cause of this plume is a combination of reductive dissolution in coastal sediments, wind-driven upwelling, advection, biological uptake, and remineralization. Additional processes that are discussed as sources of metals to the regions studied during this thesis include isopycnal uplift within cold-core eddies (Hawaii), ice melt (McMurdo Sound, Antarctica), riverine input (Arctic Ocean), and winter mixing (McMurdo Sound). The biological influence on surface ocean distributions of cobalt was apparent by the observation of linear relationships between cobalt and phosphate in mid to low latitudes. The cobalt:phosphate ratios derived from these correlations changed over orders of magnitude, revealing dynamic variability in the utilization, demand, and sources of this micronutrient. Speciation studies suggest that there may be two classes of cobalt binding ligands, and that organic complexation plays an important role in preventing scavenging of cobalt in the ocean. These datasets provided a basis for comparing the biogeochemical cycles of cobalt, iron, and manganese in three oceanic regimes (Hawaii, South Atlantic, McMurdo Sound). The relative rates of scavenging for these metals show environmental variability: in the South Atlantic, cobalt, iron, and manganese were scavenged at very different rates, but in the Ross Sea, mixing and circulation over the shallow sea was fast, scavenging played a minor role, and the cycles of all three metals were coupled. Studying the distributions of these metals in biogeochemically distinct regions is a step toward a better understanding of their oceanic cycles. / by Abigail Emery Noble. / Ph.D.

Thesis (Ph.D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, and the Woods Hole Oceanographic Institution), 2001. / Includes bibliographical references. / by Paulo Salles. / Ph.D.

Thesis: S.M., Joint Program in Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 139-148). / Observations suggest that during the last deglaciation (roughly 20,000-10,000 years ago) the Earth warmed substantially, global sea level rose approximately 100 meters in response to melting ice sheets and glaciers, and atmospheric concentrations of carbon dioxide increased. This interval may provide an analog for the evolution of future climate. The ocean plays a key role in the modern climate system by storing and transporting heat, salt, and nutrients, but its role during the last deglaciation remains uncertain. Prominent signals of the last deglaciation in the ocean are a gradual warming and a decrease of the seawater oxygen isotope ratio 5180 (a signature of melting land ice sheets). These changes do not occur uniformly in the ocean, but propagate like plumes of dye over hundreds and thousands of years, the aggregate results of turbulent advective and diffusive processes. Information about changing temperatures and oxygen isotopes is stored in the shells of benthic organisms recovered in ocean sediment cores. This thesis develops and applies an inverse framework for understanding deglacial oxygen isotope records derived from sediment cores in terms of the Green functions of ocean tracer transport and ocean mixed layer boundary conditions. Singular value decomposition is used to find a solution for global mixed layer tracer concentration histories that is constrained by eight last-deglacial sediment core records and a model of the modern ocean tracer transport. The solution reflects the resolving power of the data, which is highest at model surface locations associated with large rates of volume flux into the deep ocean. The limited data resolution is quantified and rationalized through analyses of simple models. The destruction of information contained in tracers is a generic feature of advective-diffusive systems. Quantifying limitations of tracer records is important for making and understanding inferences about the long-term evolution of the ocean. / by Daniel Edward Amrhein. / S.M.