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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 165-172). / Glacial fjords form conduits between glaciers of the Greenland Ice Sheet and the North Atlantic. They are the gateways for importing oceanic heat to melt ice and for exporting meltwater into the ocean. Submarine melting in fjords has been implicated as a driver of recent glacier acceleration; however, there are no direct measurements of this melting, and little is known about the fjord processes that modulate melt rates. Combining observations, theory, and modeling, this thesis investigates the circulation, heat transport, and meltwater export in glacial fjords. While most recent studies focus on glacial buoyancy forcing, there are other drivers - e.g. tides, local wind, shelf variability - that can be important for fjord circulation. Using moored records from two major Greenlandic fjords, shelf forcing (from shelf density fluctuations) is found to dominate the fjord circulation, driving rapid exchange with the shelf and large heat content variability near the glacier. Contrary to the conventional paradigm, these flows mask any glacier-driven circulation in the non-summer months. During the summer, when shelf forcing is reduced and freshwater forcing peaks, a mean exchange flow transports warm Atlantic-origin water towards the glacier and exports glacial meltwater. Many recent studies have inferred submarine melt rates from oceanic heat transport, but the fjord budgets that underlie this method have been overlooked. Building on estuarine studies of salt fluxes, this thesis presents a new framework for assessing glacial fjord budgets and revised equations for inferring meltwater fluxes. Two different seasonal regimes are found in the heat/salt budgets for Sermilik Fjord, and the results provide the first time-series of submarine meltwater and subglacial discharge fluxes into a glacial fjord. Finally, building on the observations, ROMS numerical simulations and two analytical models are used to investigate the dynamics of shelf-driven flows and their importance relative to local wind forcing across the parameter space of Greenland's fjords. The fjord response is found to vary primarily with the width relative to the deformation radius and the fjord adjustment timescale relative to the forcing timescale. Understanding these modes of circulation is a step towards accurate modeling of ocean-glacier interactions. / by Rebecca H. Jackson. / 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 124-131). / Dinoflagellates are a diverse group of single-celled eukaryotic phytoplankton that are important for their unique genetics and molecular biology, the multitude of ecological roles they play, and the ability of multiple species to produce toxins that affect human and ecosystems health. Two dinoflagellate genera, Alexandrium and Gambierdiscus each contain species that can cause human poisoning syndromes, although the methods of toxin transfer, accumulation, and exposure are very different. Gambierdiscus is a benthic organism that produces lipophilic ciguatoxins that can bioaccumulate in coral reef fish and cause ciguatera fish poisoning (CFP) in human consumers. Alexandrium is a planktonic species that produces saxitoxins that can directly accumulate in shellfish and cause paralytic shellfish poisoning (PSP) in humans. Both genera contain multiple species that vary dramatically in toxicity and physiology. Through transcriptomic analysis, this thesis describes the genetic diversity present across dinoflagellates that produce saxitoxin, elaborating on differences in their complement of genes within the saxitoxin biosynthesis pathway. This study demonstrated retention and expression of some of these saxitoxin genes by non-toxic species within Alexandrium, as well as in Gambierdiscus, which does not produce saxitoxins. Furthermore it confirmed the presence of certain transcripts only in toxin-producing species. This thesis then developed novel fluorescence in situ hybridization (FISH) probes that can be used to identify and enumerate six Gambierdiscus species, thereby enabling the community composition of Gambierdiscus to be examined in a quantifiable manner. The probes were tested in the laboratory on cultures, and then successfully applied to field samples from Florida Keys and Hawai'i. Gambierdiscus species are diverse in both their toxicity and optimal temperature ranges for growth. Analysis of Gambierdiscus community composition in an area of variable temperature allowed the characterization of species shifts that were driven both by a seasonal increase in mean seawater temperatures and spatial variability of temperature experienced between tidal pools. Overall this thesis advances the knowledge of dinoflagellate genetics and ecology, aids in the characterization of species harmful to public health, and provides tools and approaches to help monitor and manage harmful effects from these species, including some that are projected to increase with climate change. / by Kathleen Johnson Pitz. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), June 2014. / Cataloged from PDF version of thesis. "June 2014." / Includes bibliographical references (pages 103-112). / Evolutionary pressures have led to some astonishing camouflage strategies in the animal kingdom. Cephalopods like cuttlefish and octopus mastered a rather unique skill: they can rapidly adapt the way their skin looks in color, texture and pattern, blending in with their backgrounds. Showing a general resemblance to a visual background is one of the many camouflage strategies used in nature. For animals like cuttlefish that can dynamically change the way they look, we would like to be able to determine which camouflage strategy a given pattern serves. For example, does an inexact match to a particular background mean the animal has physiological limitations to the patterns it can show, or is it employing a different camouflage strategy (e.g., disrupting its outline)? This thesis uses a computational and data-driven approach to quantify camouflage patterns of cuttlefish in terms of color and pattern. First, we assess the color match of cuttlefish to the features in its natural background in the eyes of its predators. Then, we study overall body patterns to discover relationships and limitations between chromatic components. To facilitate repeatability of our work by others, we also explore ways for unbiased data acquisition using consumer cameras and conventional spectrometers, which are optical imaging instruments most commonly used in studies of animal coloration and camouflage. This thesis makes the following contributions: (1) Proposes a methodology for scene-specific color calibration for the use of RGB cameras for accurate and consistent data acquisition. (2) Introduces an equation relating the numerical aperture and diameter of the optical fiber of a spectrometer to measurement distance and angle, quantifying the degree of spectral contamination. (3) Presents the first study assessing the color match of cuttlefish (S. officinalis) to its background using in situ spectrometry. (4) Develops a computational approach to pattern quantification using techniques from computer vision, image processing, statistics and pattern recognition; and introduces Cuttlefish 72x5, the first database of calibrated raw (linear) images of cuttlefish. / by Derya Akkaynak. / 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), 2011. / 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. 139-148). / This thesis discusses sensor management methods for multiple-vehicle fleets of autonomous underwater vehicles, which will allow for more efficient and capable infrastructure in marine science, industry, and naval applications. Navigation for fleets of vehicles in the ocean presents a large challenge, as GPS is not available underwater and dead-reckoning based on inertial or bottom-lock methods can require expensive sensors and suffers from drift. Due to zero drift, acoustic navigation methods are attractive as replacements or supplements to dead-reckoning, and centralized systems such as an Ultra-Short Baseline Sonar (USBL) allow for small and economical components onboard the individual vehicles. Motivated by subsea equipment delivery, we present model-scale proof-of-concept experimental pool tests of a prototype Vertical Glider Robot (VGR), a vehicle designed for such a system. Due to fundamental physical limitations of the underwater acoustic channel, a sensor such as the USBL is limited in its ability to track multiple targets-at best a small subset of the entire fleet may be observed at once, at a low update rate. Navigation updates are thus a limited resource and must be efficiently allocated amongst the fleet in a manner that balances the exploration versus exploitation tradeoff. The multiple vehicle tracking problem is formulated in the Restless Multi-Armed Bandit structure following the approach of Whittle in [108], and we investigate in detail the Restless Bandit Kalman Filters priority index algorithm given by Le Ny et al. in [71]. We compare round-robin and greedy heuristic approaches with the Restless Bandit approach in computational experiments. For the subsea equipment delivery example of homogeneous vehicles with depth-varying parameters, a suboptimal quasi-static approximation of the index algorithm balances low landing error with safety and robustness. For infinite-horizon tracking of systems with linear time-invariant parameters, the index algorithm is optimal and provides benefits of up to 40% over the greedy heuristic for heterogeneous vehicle fleets. The index algorithm can match the performance of the greedy heuristic for short horizons, and offers the greatest improvement for long missions, when the infinite-horizon assumption is reasonably met. / by Brooks Louis-Kiguchi Reed. / S.M.

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 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/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology, and the Woods Hole Oceanographic Institution), 2002. / Includes bibliographical references (p. 130-138). / Mark-recapture analysis of populations is becoming an important tool in population biology. Mark-recapture methods can be used to estimate transition probabilities among life-stages from capture histories of marked individuals for which stages can be determined at each sampling occasion. This method is called a multi-stage mark-recapture (MSMR) method. In this thesis, I describe advances I made in the MSMR method and present analyses that apply this method to actual data. The advances I made in the MSMR method are motivated by a need to provide a link between mark-recapture data and demographic models such as matrix population models and integrodifference models. I resolve some issues that are commonly encountered during sampling, such as the fact that the sex or life-stage of some individuals is unknown during some sampling occasions and that individuals become unobservable during some life-stages. I introduce a stage-structure that permits simple conversion of estimated transition probabilities into a matrix population model. I describe an algorithm to simplify programming for parameter estimation. I also introduce a method to estimate the distribution of dispersal displacements (a dispersal kernel) from mark-recapture data. I apply some of the methods described above to data of the North Atlantic right whale (Eubalaena glacialis). The right whales are considered one of the most endangered mammals. The current population size is about 300 in the northwestern Atlantic, and the number is declining. I applied the multi-stage mark-recapture statistics to the 17-year in- dividual sighting history data. / (cont.) Using the estimated transition probabilities, I constructed a population projection matrix, which was used for further demographic analyses. I found that the population was slowly increasing in 1980, but it started to decline slowly around 1992. I show that (1) this change was caused by increased mortality of females that have just given birth, (2) protecting two females a year from the deaths is enough to prevent the declining trend, and (3) demographic stochasticity is a more important factor influencing their long-term viability than environmental stochasticity. / by Masami Fujiwara. / 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), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / At the land-ocean interface, terrestrial groundwater interacts with seawater to form a subterranean estuary, which can play host to dynamic biogeochemical cycling of nutrients, trace metals and radionuclides. This chemically altered groundwater enters the ocean through submarine groundwater discharge (SGD), a process that is driven by a number of physical processes acting on aquifers and the coastal ocean. In this thesis, seasonal variability in chemical cycling and associated loading to the coastal ocean was observed in a monthly time series within the Waquoit Bay (MA, USA) subterranean estuary. The position of the aquifer mixing zone moved seaward with an increase in hydraulic gradient, resulting in low salinity conditions and reduced mixing, while a decrease in gradient led to landward movement, high salinity groundwater and enhanced mixing. At this location, seasonal variability in sea level, not groundwater level, was the dominant variable driving the hydraulic gradient and therefore SGD. Fluxes of sediment bound cations to the ocean increased coincidently with sea level rise due to desorption. There was enhanced nitrogen attenuation during winter, potentially due to longer groundwater residence times, with greater nutrient delivery to coastal waters during the spring and summer bloom. Interannual climate fluctuations that control sea level and precipitation may ultimately control the timing and magnitude of chemical and water flux via SGD. In addition to temporal variability, aquifer lithology influences chemical export. This thesis also demonstrates that SGD from karst subterranean estuaries may play a role in local and global element budgets. The potential for the chemical signature of SGD to be recorded in the coral record was tested through a combination of coral culture experiments and field and modeling studies in the Yucatan Peninsula. Coral barium was well correlated with precipitation for a twelve-year record, with coral geochemistry reflecting the passage of a hurricane in 2002. While additional complexities in deciphering coral records remain, this proxy offers the potential to extend SGD records into the past. / by Meagan Joan Eagle Gonneea. / Ph. D.