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 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. / Particulate organic carbon (POC) in the ocean and mobilized by rivers on land transfers -0. 1% of global primary productivity to the deep ocean sediments. This small fraction regulates the long-term carbon cycle by removing carbon dioxide from the atmosphere for centuries to millennia. This thesis investigates mechanisms of POC transfer to the deep ocean by analyzing particles collected in transit through two globally significant carbon reservoirs: the Southern Ocean and the Amazon River Basin. These endeavors test the hypothesis that organic matter composition controls the recycling and transfer efficiency of POC to the deep ocean, and illustrate new applications for ramped pyrolysis/oxidation (RPO), a growing method of POC characterization by thermal stability. By coupling RPO to stable and radiocarbon isotope analyses of riverine POC, I quantify three thermally distinct soil organic carbon pools mobilized by the Amazon River, and evaluate the degradability and fate of these different pools during transport to the coastal Atlantic Ocean. More directly, RPO analyses of marine samples suggest that POC transfer in the water column is in fact selective. Observations of consistent biomolecular changes that accompany transport of phytoplankton-derived organic matter to depth across the Southern Ocean support the argument for preferential degradation of specific POC pools in the water column. Combining discussions of POC recycling and transfer across both marine and terrestrial systems offer new perspectives of thermal stability as a proxy for diagenetic stability and POC degradation state. The challenges of interpreting RPO data in these two environments set the stage for applying the technique to more controlled experiments that trace POC from source to long-term sink. / by Sarah Zhou Rosengard. / 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), 2008. / Includes bibliographical references (p. 135-140). / Chapter 1 presents the first published measurements of Sr-isotope variability in olivine-hosted melt inclusions. Melt inclusions in just two Samoan basalt hand samples exhibit most of the total Sr-isotope variability observed in Samoan lavas. Chapter 3 deals with the largest possible scales of mantle heterogeneity, and presents the highest magmatic 3He/4He (33.8 times atmospheric) discovered in Samoa and the southern hemisphere. Along with Samoa, the highest 3He/4He sample from each southern hemisphere high 3He/4He hotspot exhibits lower 143Nd/144Nd ratios than their counterparts in the northern hemisphere. Chapter 2 presents geochemical data for a suite of unusually enriched Samoan lavas. These highly enriched Samoan lavas have the highest 87Sr/86Sr values (0.72163) measured in oceanic hotspot lavas to date, and along with trace element ratios (low Ce/Pb and Nb/U ratios), provide a strong case for ancient recycled sediment in the Samoan mantle. Chapter 4 explores whether the eclogitic and peridotitic portions of ancient subducted oceanic plates can explain the anomalous titanium, tantalum and niobium (TITAN) enrichment in high 3He/4He ocean island basalts (OIBs). The peridotitic portion of ancient subducted plates can contribute high 3He/4He and, after processing in subduction zones, a refractory, rutile-bearing eclogite may contribute the positive TITAN anomalies. / by Matthew G. Jackson. / 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), 2008. / Includes bibliographical references. / Segmentation and crustal accretion at oceanic transform fault systems are investigated through a combination of geophysical data analysis and geodynamical and geochemical modeling. Chapter 1 examines the effect of fault segmentation on the maximum predicted earthquake magnitude of an oceanic transform fault system. Results of thermal modeling suggest that fault segmentation by intra- transform spreading centers (ITSC) drastically reduces the available brittle area of a transform fault and thus limits the available earthquake rupture area. Coulomb stress models suggest that long ITSCs will prohibit static stress interaction between segments of a transform system and further limit the maximum possible magnitude of a given transform fault earthquake. In Chapter 2, gravity anomalies from a global set of oceanic transform fault systems are investigated. Surprisingly, negative residual mantle Bouguer gravity anomalies are found within fast-slipping transform fault domains. These gravity observations suggest a mass deficit within fast-slipping transform faults, which may result from porosity variations, mantle serpentinization, and/or crustal thickness variations. Two-dimensional forward modeling and the correlation of the negative gravity anomalies to bathymetric highs indicate crustal thickness excesses in these locations. Finally, in Chapter 3, mantle thermal and melting models for a visco-plastic rheology are developed to investigate the process of mantle melting and crustal accretion at ITSCs within segmented transform faults, and are applied to the Siqueiros transform fault system. Models in which melt migrates into the transform fault domain from a large region of the mantle best explain the gravity-derived crustal thickness variations observed at the Siqueiros transform. Furthermore, a mantle potential temperature of 1350⁰C and fractional crystallization at depths of 9 - 15.5 km best explain the major element composition variation observed at the Siqueiros transform. / by Patricia Michelle Marie Gregg. / Ph.D.

Thesis (M.S.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), February 1988. / "October 1987." / Includes bibliographical references (leaves 87-89). / Thermohaline staircases consisting of a series of well mixed layers approximately 30 m thick are found at depths of 300-500 m in a region of the tropical North Atlantic spanning 48° to 58°W, 8° to 17° N. Density ratios ( ... ) with values near 1 indicate a double diffusive origin for the structure (Schmitt, 1981,1986). Determining the importance of double-diffusive mixing to the regional advection - diffusion balance is the subject of this study. Using hydrographic and current meter data collected in the C-SALT program of 1985 (Schmitt, 1987), we construct inverse models in both cartesian and density coordinates and seek bounds on the cross isopycnal mixing in the staircase region. In cartesian coordinates, the role of diffusion was not well resolved, probably due to inadequacy of the steady state model in the presence of eddies. By reformulating the problem in boxes bounded by isopycnals which more closely follow the layers, and solving directly for cross isopycnal fluxes of salt and heat, the resolution of the diffusivities was improved. Inversions were done on data from the spring and fall CTD surveys. The average salt diffusivity in the step region was estimated from the isopycnal inversions to be ks = (2.8 + 1.3)cm2 /s in spring and ks = (3.9 ± 2.2)cm2 /s in fall. / by Joyce Marie Federiuk. / M.S.

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 (M.S.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1988. / Includes bibliographical references (leaves 82-85). / The sulfur content of planktonic and benthic foraminifera was measured in specimens recovered from deep-sea sediment cores and individuals grown in culture. A new method for measuring sulfur in foraminiferal calcium carbonate was developed, employing a high-resolution inductively coupled plasma-mass spectrometer. The sulfur measurements, expressed as sulfur-to-calcium (S/Ca) ratios in the foraminiferal shells, ranged from 0.26 to 6.0 mmol/mol. Most analyses fell in the range of 0.7 to 2.5 mmol/mol. Culturing experiments were conducted in the planktonic foraminifer G. sacculifer to test the hypothesis that S/Ca ratios in the foraminifer are inversely proportional to the carbonate ion concentration in the seawater in which they grow, and hence proportional to the pH of the seawater. The slope of the relationship between cultured G. sacculifer S/Ca and the pH of the seawater medium was -1.92 mmol mol-1/pH unit with a least squares linear correlation coefficient, r2=0.927. The S/Ca ratios of planktonic and benthic foraminifera from Holocene and last glacial period sediments were measured in an effort to use the established relationship of S/Ca and pH to calculate the ocean pH gradient between Holocene and glacial time. The results indicate the pH of global ocean deepwater was 0.10 to 0.15 pH units higher during glacial time than today. Smaller pH gradients were seen for some cores which may have been caused by circulation-induced water mass changes. Surface ocean changes in pH over the Holocene-glacial interval seem to vary from region to region, with up to an 0.2 pH unit increase at the Sierra Leone Rise in glacial time. Benthic foraminifera from coretops in the thermocline of the Little Bahama Bank were analyzed for S/Ca to examine the effects of hydrographic variables on S/Ca. The relationship of S/Ca to pH and [CO3=] has a positive slope, at odds with the expected negative slope from the previous results. The S/Ca results do correlate well with salinity, suggesting that salinity or other hydrographic parameters may also influence foraminiferal S/Ca ratios. / by Jeffrey Nicholas Berry. / M.S.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Page 296 blank. / Includes bibliographical references. / Marine thecate heterotrophic dinoflagellates likely play an important role in the consumption of primary productivity and in the trophic structure of the plankton, yet we know little about these species. This thesis expanded our understanding of the autecology and evolutionary history of the Protoperidinium and diplopsalids. The distributions of Protoperidinium species off the southwestern coast of Ireland were influenced by physical oceanographic conditions coupled with the availability of preferred prey. The distributions of individual Protoperidinium species varied widely from the distribution of total Protoperidinium, indicating differences in ecologies among species. Certain species of Protoperidinium co-occurred with known preferred phytoplankton prey species. Concentrations of other Protoperidinium species were not related to those of any particular phytoplankton species, indicating that these Protoperidinium may rely on phytoplankton or other food sources beyond those already known, may not be species specific selective feeders, or may have become uncoupled from their preferred prey. The description of the sexual and asexual life history of Protoperidinium steidingerae provided the first account of the life history of any Protoperidinium species. / (cont.) Asexual division occurred by eleutheroschisis within a temporary, immotile cyst, yielding two daughter cells. Daughter cells were initially round and half to two-thirds the size of parent cells, then rapidly increased in size, forming horns before separating. Sexual reproduction was constitutive in clonal cultures, indicating that the species may be homothallic. Fusing gametes were isogamous, and resulted in a planozygote with two longitudinal flagella. Hypnozygotes had a mandatory dormancy period of ca. 70 days. Germination resulted in planomeiocytes with two longitudinal flagella. Nuclear cyclosis may occur in the planomeiocyte stage. A high level of morphological diversity among life history stages of P. steidingerae has led to mis-classification and taxonomic inaccuracy of Protoperidinium species identified from field samples. The large subunit ribosomal DNA (LSU rDNA) molecular phylogeny of the heterotrophic dinoflagellates revealed that the genus Protoperidinium appeared to be recently diverged within the dinoflagellates. In maximum parsimony and neighbor joining analysis, Protoperidinium formed a monophyletic group, evolving from diplopsalid dinoflagellates. / (cont.) In maximum likelihood and Bayesian analyses, however, Protoperidinium was polyphyletic, as the lenticular, diplopsalid heterotroph, Diplopsalis lenticula Bergh, was inserted within the Protoperidinium clade basal to Protoperidinium excentricum (Paulsen) Balech, and Preperidinium meunieri (Pavillard) Elbrichter fell within a separate clade as a sister to the Oceanica section and Protoperidinium steidingerae Balech. In all analyses, the Protoperidinium were divided into two major clades, with members in the Oceanica group and subgenus Testeria in one clade, and the Excentrica, Conica, Pellucida, Pyriforme, and Divergens sections in another clade. The LSU rDNA molecular phylogeny supported the historical morphologically determined sections, but not a simple morphology-based model of evolution based on thecal plate shape. LSU rDNA gene sequences are frequently used to infer the phylogeny of organisms. The many copies of the LSU rDNA found in the genome are thought to be kept homogenous by concerted evolution. In Protoperidinium species, however, there was high intragenomic diversity in the D1-D6 region of the LSU rDNA. For each species, the clone library was usually comprised of one highly represented copy and many unique sequences. / (cont.) Sequence differences were primarily characterized by single base pair substitutions, single base pair insertion/deletions (indels), and/or large indels. Phylogenetic analysis of all clones gave strong support for monophyly of the polymorphic copies of each species, and recovered the same species tree as an analysis using just one sequence per species. Analysis of LSU rDNA gene expression in three species by RT-PCR indicated that copies with fewer substitutions and fewer and smaller indels are expressed, and that 50% or more of the copies are pseudogenes. High intraspecific and intraindividual LSU rDNA sequence variability could lead to inaccurate species phylogenies and over-estimation of species diversity in environmental sequencing studies. This thesis has explored the ecology, life history, molecular phylogeny, and intraspecific DNA sequence variability of marine thecate heterotrohic dinoflagellates using a wide range of methodologies, including field sampling, culturing, microscopy, morphological analyses, histological staining, and molecular biology. The work here has broadened our understanding of the Protoperidinium and diplopsalids, providing new insights into the ecological and evolutionary relationships of these heterotrophs with other plankton species. / by Kristin Elizabeth Gribble. / 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), 1987. / Includes bibliographical references (leaves 179-201). / by Bernward Josef Hay. / 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.