Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), February 2000. / Includes bibliographical references. / Benthic foraminiferal δ13C, Cd/Ca, and Ba/Ca are important tools for reconstructing nutrient distributions, and thus ocean circulation, on glacial-interglacial timescales. However, each tracer has its own "artifacts" that can complicate paleoceanographic interpretations. It is therefore advantageous to measure multiple nutrient proxies with the aim of separating the various complicating effects. Zn/Ca is introduced as an important aid toward this goal. Benthic (Hoeglundina elegans) Cd/Ca ratios from the Bahama Banks indicate that the North Atlantic subtropical gyre was greatly depleted in nutrients during the last glacial maximum (LGM). A high-resolution Cd/Ca record from 965 m water depth suggests that Glacial North Atlantic Intermediate Water formation was strong during the LGM, weakened during the deglaciation, and strengthened again during the Younger Dryas cold period. Comparison of Cd/Ca and δ13C data reveals apparent short-term changes in carbon isotopic air-sea signatures. Benthic foraminiferal Zn/Ca could be a sensitive paleoceanographic tracer because deep water masses have characteristic Zn concentrations that increase about ten-fold from the deep North Atlantic to the deep North Pacific. A "core top calibration" shows that Zn/Ca is controlled by bottom water dissolved Zn concentration and, like Cd/Ca and BalCa, by bottom water saturation state with respect to calcite Since Zn/Ca responds to a different range of saturation states than Cd/Ca, the two may be used together to evaluate changes in deep water carbonate ion (CO32- ) concentration. Zn/Ca and Cd/Ca ratios in the benthic foraminifer Cibicidoides wuellerstorfi exhibit large fluctuations over the past 100,000 years in a deep (3851 m) eastern equatorial Pacific sediment core. The data imply that bottom water CO32- concentrations were lowest during glacial Marine Isotope Stage 4 and highest during the last deglaciation. LGM CO32- concentrations appear to have been within a few μmol kg-1 of modern values. Deep North Atlantic Cd/Ca ratios imply much higher nutrient concentrations during the LGM. Although such data have usually been explained by a northward penetration of Southern Ocean Water (SOW), it has been suggested that they could result from increased preformed nutrient levels in the high-latitude North Atlantic or by increased aging of lower North Atlantic Deep Water (NADW). Glacial Zn/Ca data, however, require a substantially increased mixing with SOW and thus a reduction in NADW formation. Large changes in carbon isotopic air-sea exchange are invoked to reconcile benthic δ13C and trace metal data. / by Thomas Mathew Marchitto, Jr. / 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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The sinking flux of particulate matter into the ocean interior is an oceanographic phenomenon that fuels much of the metabolic demand of the subsurface ocean and affects the distribution of carbon and other elements throughout the biosphere. In this thesis, I use a new suite of observations to study the dynamics of marine particulate matter at the contrasting sites of the subtropical Sargasso Sea near Bermuda and the waters above the continental shelf of the Western Antarctic Peninsula (WAP). An underwater digital camera system was employed to capture images of particles in the water column. The subsequent analysis of these images allowed for the determination of the particle concentration size distribution at high spatial, depth, and temporal resolutions. Drifting sediment traps were also deployed to assess both the bulk particle flux and determine the size distribution of the particle flux via image analysis of particles collected in polyacrylamide gel traps. The size distribution of the particle concentration and flux were then compared to calculate the average sinking velocity as a function of particle size. I found that the average sinking velocities of particles ranged from about 10-200 m d- and exhibited large variability with respect to location, depth, and date. Particles in the Sargasso Sea, which consisted primarily of small heterogeneous marine snow aggregates, sank more slowly than the rapidly sinking krill fecal pellets and diatom aggregates of the WAP. Moreover, the average sinking velocity did not follow a pattern of increasing velocities for the larger particles, a result contrary to what would be predicted from a simple formulation of Stokes' Law. At each location, I derived a best-fit fractal correlation between the flux size distribution and the total carbon flux. The use of this relationship and the computed average sinking velocities enabled the estimation of particle flux from measurements of the particle concentration size distribution. This approach offers greatly improved spatial and temporal resolution when compared to traditional sediment trap methods for measuring the downward flux of particulate matter. Finally, I deployed specialized in situ incubation chambers to assess the respiration rates of microbes attached to sinking particles. I found that at Bermuda, the carbon specific remineralization rate of sinking particulate matter ranged from 0.2 to 1.1 d', while along the WAP, these rates were very slow and below the detection limit of the instruments. The high microbial respiration rates and slow sinking velocities in the Sargasso Sea resulted in the strong attenuation of the flux with respect to depth, whereas the rapid sinking velocities and slow microbial degradation rates of the WAP resulted in nearly constant fluxes with respect to depth. / by Andrew M. P. McDonnell. / 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. / The distribution and magnitude of marine primary production helps determine the ocean's role in global carbon cycling. Constraining factors that impact this productivity and elucidating selective pressures that drive the composition of marine microbial communities are thus essential aspects of marine biogeochemistry. Vitamin B₁₂, also known as cobalamin, is a cobalt containing organometallic micronutrient produced by some bacteria and archaea and required by many eukaryotic phytoplankton for methionine biosynthesis and regeneration. Although the potential for vitamin B₁₂ availability to impact primary production and phytoplankton species composition has long been recognized, the lack of molecular-level tools for studying B₁₂ production, use and acquisition has limited inquiry into the role of the vitamin in marine biogeochemical processes. This thesis describes the development of such tools and implements them for the study of B₁₂ dynamics in an Antarctic shelf ecosystem. Nucleic acid probes for B₁₂ biosynthesis genes were designed and used to identify a potentially dominant group of B₁₂ producers in the Ross Sea. The activity of this group was then verified by mass spectrometry-based peptide measurements. Then, possible interconnections between iron and B₁₂ dynamics in this region were identified using field-based bottle incubation experiments and vitamin uptake measurements, showing that iron availability may impact both B₁₂ production and consumption. Changes in diatom proteomes induced by low B₁₂ and low iron availability were then examined and used to identify a novel B₁₂ acquisition protein, CBA1, in diatoms. This represents the first identification of a B₁₂ acquisition protein in eukaryotic phytoplankton. Transcripts encoding CBA 1 were detected in natural phytoplankton communities, confirming that B₁₂ acquisition is an important part of phytoplankton molecular physiology. Selected reaction monitoring mass spectrometry was used to measure the abundance of CBA1 and methionine synthase proteins in diatoms cultures, revealing distinct protein abundance patterns as a function of B₁₂ availability. These peptide measurements were implemented to quantify methionine synthase proteins in McMurdo Sound, revealing that there is both B₁₂ utilization and starvation in natural diatom communities and that these peptide measurements hold promise for revealing the metabolic status of marine ecosystems with respect to vitamin B₁₂. / by Erin Marie Bertrand. / 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), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 143-154). / The physical environment in the oceans dictates not only how phytoplankton cells are dispersed and their populations intermingled, but also mediates the supply of nutrients to the surface mixed layer. In this thesis I explore both of these aspects of the interaction between phytoplankton ecology and ocean physics, and have approached this topic in two distinct but complementary ways, working with a global ocean ecosystem model, and collecting data at sea. In the first half of the thesis, I examine the role of mesoscale physical features in shaping phytoplankton community structure and influencing rates of primary production. I compare the output of a complex marine ecosystem model coupled to coarse resolution and eddy-permitting physical models. Explicitly resolving eddies resulted in marked regional variations in primary production, zooplankton and phytoplankton biomass. The same phytoplankton phenotypes persisted in both cases, and were dominant in the same regions. Global phytoplankton diversity was unchanged. However, levels of local phytoplankton diversity were markedly different, with a large increase in local diversity in the higher resolution model. Increased diversity could be attributed to a combination of enhanced dispersal, environmental variability and nutrient supply in the higher resolution model. Diversity "hotspots" associated with western boundary currents and coastal upwelling zones are sustained through a combination of all of these factors. In the second half of the thesis I describe the results of a fine scale ecological and biogeochemical survey of the Kuroshio Extension Front. I found fine scale patterns in physical, chemical and biological properties that can be linked back to both the large scale horizontal and smaller scale vertical physical dynamics of the study region. A targeted genomic analysis of samples focused on the ecology of the picoeukaryote Ostreococcus clade distributions strongly supports the model derived hypotheses about the mechanisms supporting diversity hotspots. Strikingly, two distinct clades of Ostreococcus co-occur in more than half of the samples. A "hotspot" of Ostreococcus diversity appears to be supported by a confluence of water masses containing either clade, as well as a local nutrient supply at the front and the mesoscale variability of the region. / by Sophie Anne Clayton. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Many species of whales migrate annually between high-latitude feeding grounds and low-latitude breeding grounds. Yet, very little is known about how these animals navigate during these migrations. This thesis takes a first look at the roles of geomagnetic and acoustic cues in humpback whale navigation and orientation, in addition to documenting some effects of human-produced sound on beaked whales. The tracks of satellite-tagged humpback whales migrating from Hawaii to Alaska were found to have systematic deviations from the most direct route to their destination. For each whale, a migration track was modeled using only geomagnetic inclination and intensity as navigation cues. The directions in which the observed and modeled tracks deviated from the direct route were compared and found to match for 7 out of 9 tracks, which suggests that migrating humpback whales may use geomagnetic cues for navigation. Additionally, in all cases the observed tracks followed a more direct route to the destination than the modeled tracks, indicating that the whales are likely using additional navigational cues to improve their routes. There is a significant amount of sound available in the ocean to aid in navigation and orientation of a migrating whale. This research investigates the possibility that humpback whales migrating near-shore listen to sounds of snapping shrimp to detect the presence of obstacles, such as rocky islands. A visual tracking study was used, together with hydrophone recordings near a rocky island, to determine whether the whales initiated an avoidance reaction at distances that varied with the acoustic detection range of the island. No avoidance reaction was found. Propagation modeling of the snapping shrimp sounds suggested that the detection range of the island was beyond the visual limit of the survey, indicating that snapping shrimp sounds may be suited as a long-range indicator of a rocky island. Lastly, this thesis identifies a prolonged avoidance reaction of a Blainville's beaked whale to playbacks of Navy mid-frequency active sonar and orca predation calls. Navy sonar exercises have been linked to beaked whale strandings, and identifying whether these are the result of a mistaken predator avoidance reaction may help prevent future strandings. / by Ann Nichole Allen. / 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), 1988. / Vita. / Includes bibliographical references. / by John Paul Jasper. / 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), 1988. / Includes bibliographical references (v.2, leaves 339-351). / This study focuses on the zonal weakening, eastern termination and seasonal variations of the Atlantic equatorial undercurrent (EUC). The main and most original contribution of the dissertation is a detailed analysis of the Atlantic EUC simulated by Philander and Pacanowski's (1986)general circulation model (GCM), which provides a novel description of the dynamical regimes governing various regions of a nonlinear stratified undercurrent. Only in a narrow deep western region of the simulation does one find an approximately inertial regime corresponding to zonal acceleration. Elsewhere frictional processes cannot be ignored. The bulk of the mid-basin model EUC terminates in the overlying westward surface flow while only a small fraction (the deeper more inertial layers) terminates at the eastern coast. In agreement with observations, a robust feature of the GCM not present in simpler models is the apparent migration of the EUC core from above the thermocline in the west to below it in the east. In the GCM, this happens because the eastward flow is eroded more efficiently by vertical friction above the base of the thermocline than by lateral friction at greater depths. This mechanism is a plausible one for the observed EUC. A scale analysis using a depth scale which decreases with distance eastwards predicts the model zonal transition between western inertial and eastern inertio-frictional regimes. Historical and recent observations and simple models of the equatorial and coastal eastern undercurrents are reviewed, and a new analysis of current measurements in the eastern equatorial Atlantic is presented. Although the measurements are inadequate for definitive conclusions, they suggest that Lukas' (1981) claim of a spring surge of the Pacific EUC to the eastern coast and a seasonal branching of the EUC into a coastal southeastward undercurrent may also hold for the Atlantic Ocean. To improve the agreement between observed and modelled strength of the eastern undercurrent, it is suggested that the eddy coefficient of horizontal mixing should be reduced in future GCM simulations. / by Sophie Huguette Claire Wacongne. / 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), February 2000. / "September 1999." / Includes bibliographical references. / This dissertation discusses the experimental results designed to constrain the processes of MORB generation. The main focus of this study is to investigate the location and the related processes of the transformation boundary from spinel to garnet peridotite facies at subsolidus conditions, because the presence of garnet in melting residues has significant influence to the conclusion drawn from geochemical/geophysical observations. Using an approach that monitors the rate of reaction progresses, the experimental results confirmed the presence of a region that garnet and spinel coexist in peridotite compositions. The trace element distribution among the product phases (opx and cpx) subsequent to the garnet breakdown reaction is in disequilibrium, due to the differences of diffusivity between major and trace elements. The presence of disequilibrium distribution in nature may be used to infer time scales of geodynamic processes. Diffusion coefficients of Al in diopside are experimentally determined, and used for modeling the equilibration of major elements in pyroxene during MORB genesis. In summary, this dissertation contributes two major inferences: the location of the transformation boundaries of the garnet-spinel peridotite; the presence of disequilibrium trace elements distribution with equilibrium major elements distribution in mantle pyroxenes. / by Kenneth Tadao Koga. / 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 181-185). / This thesis presents an application of the Grant-Madsen-Glenn bottom boundary layer model (Grant and Madsen, 1979; Glenn and Grant, 1987) to predictions of sediment transport on the continental shelf. The analysis is a two-stage process. Via numerical experiment, we explore the sensitivity of sediment transport to variations in model parameters and assumptions. A notable result is the enhancement of suspended sediment stratification due to wave boundary layer effects. When sediment stratification is neglected under conditions of large wave bottom velocities (i.e. ,... ), concentration predictions can be more than an order of magnitude higher than any observed during storm conditions on the continental shelf. A number of limitations to application emerged from the analysis. Solutions to the stratified model are not uniquely determined under a number of cases of interest, potentially leading to gross inaccuracies in the prediction of sediment load and transport. Load and sediment transport in the outer Ekman Layer, beyond the region of emphasis for the model, can be as large or larger than the near-bottom estimates in some cases; such results suggest directions for improvements in the theoretical model. In the second step of the analysis, we test the ability of the model to make predictions of net sediment transport that are consistent with observed sediment depositional patterns. Data from the Mid-Atlantic Bight and the Northern California coast are used to define reasonable model input to represent conditions on two different types of shelves. In these examples, the results show how the intensification of wave bottom velocities with decreasing depth can introduce net transport over a region. The patterns of erosion/deposition are shown to be strongly influenced by sediment stratification and moveable bed roughness. Also predicted by the applications is a rapid winnowing out of fine grain size components when there is even a small variation of bed grain size texture in the along-flow direction. / by Margaret Redding Goud. / 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), 2004. / Includes bibliographical references. / The purpose of this thesis is to study campanulariid life cycle evolution and systematics. The Campanulariidae is a hydrozoan family with many life cycle variations, and provide an excellent model system to study life cycle evolution. Additionally, the unique campanulariid Obelia medusae may have been "re-invented" from ancestors without medusae. Chapter 1 reviews campanulariid life cycles and taxonomy. Chapter 2 presents a phylogeny based on 18S rDNA, calmodulin, 16S rDNA and cytochrome c oxidase I (COI). Ancestral life cycles are reconstructed using parsimony. Medusa loss is common, and Obelia may derive from ancestors with typical medusae. Taxonomic results are discussed in Chapter 3. Billardia, a nominal campanulariid, appears phylogenetically distant, while Bonneviella spp. (Bonneviellidae), are nested within the Campanulariidae. Campanulariid genera are not monophyletic. Orthopyxis integra and Clytia gracilis may represent cryptic species, while Obelia longissima may be cosmopolitan. Chapter 4 investigates Obelia geniculata phylogeography. Japanese and North Atlantic 16S rDNA and COI sequences are calibrated against the opening of the Bering Strait. Substitution rates are faster than in anthozoans and comparable to non-cnidarian invertebrates. Comparison of Pacific and Atlantic sequences suggests cryptic species exist. Finally, hydroids in New Brunswick, Canada and Iceland may have survived the last glaciation. / by Annette Frese Govindarajan. / Ph.D.