Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references. / This thesis explores the potential of zinc, cobalt, and phosphorus to influence primary production in the subarctic North Pacific, the Bering Sea, and the North Atlantic Ocean. In the North Pacific and Bering Sea, total zinc concentrations were measured along a near-surface transect and in selected deep profiles. Zinc speciation was also measured with a novel anodic stripping voltammetry method, and the results were consistent with previous studies using different methods. The potential for zinc to impact primary production in the North Pacific was demonstrated in a shipboard incubation and by comparing two phytoplankton pigment markers to total zinc and free zinc ion concentrations. In the North Atlantic, total dissolved zinc and cobalt concentrations were measured and compared to concentrations of dissolved inorganic phosphorus and chlorophyll. In some areas of the North Atlantic the concentrations of zinc and cobalt were decoupled.The relationship between cobalt and inorganic phosphorus suggests that cobalt drawdown may be related to a high alkaline phosphatase related demand at low phosphorus concentrations. This trend compliments a shipboard incubation where alkaline phosphatase activities increased after cobalt addition. The presence of measurable alkaline phosphatase activity indicated that the phytoplankton community in the Sargasso Sea was experiencing phosphorus stress. Shipboard incubations generally confirmed this with inorganic phosphorus additions resulting in chlorophyll increases at 4 out of 5 stations. Further, the addition of dissolved organic phosphorus, as either a phosphate monoester or a phosphonate compound, resulted in a chlorophyll increase in 3 out of 3 incubations. This suggests that dissolved organic phosphorus may be an important phosphorus source for phytoplankton in low phosphorus environments and that the ability to use phosphonates may be more widespread than previously recognized. Overall, this thesis adds to our understanding of how the nutrients phosphorus, zinc, and cobalt may influence primary production. / by Rachel J. Wisniewski. / 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: S.M. in Oceanographic Engineering, Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 83-87). / Recent advances in acoustic navigation methodologies are enabling the way for AUVs to extend their submerged mission time and maintain a bounded XY position error. Additionally, advances in inertial sensor technology have drastically lowered the size, power consumption, and cost of these sensors. Nonetheless, these sensors are still noisy and accrue error over time. This thesis builds on the research and recent developments in single beacon one-way-travel- time (OWTT) acoustic navigation and investigates the degree of bounding position error for small AUVs with a minimal navigation strap-down sensor suite, relying mostly on a consumer grade microelectromechanical system (MEMS) inertial measurement unit (IMU) and a vehicle's dynamic model velocity. An implementation of an Extended Kalman Filter (EKF) that includes IMU bias estimation and coupled with a range filter, is obtained in the field on two OceanServer Technology, Inc. Iver2 AUVs and one Bluefin Robotics SandShark [mu]AUV. Results from these field trials on Ashumet Pond of Falmouth, Massachusetts, the Charles River of Cambridge, Massachusetts, and Monterey Bay near Santa Cruz, California show a navigation solution accuracy comparable to current standard navigation techniques. / by James H. Kepper, IV. / S.M. in Oceanographic Engineering

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 Marine Geology and Geophysics (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. / Here I use a simple numerical model of reef profile evolution to show that the present-day morphology of carbonate islands has developed largely in response to late Pleistocene sea level oscillations in addition to variable vertical motion and reef accretion rates. In particular, large amplitude 'ice-house' sea-level variability resulted in long lagoonal depositional hiatuses, producing the morphology characteristic of modern-day barrier reefs. Reactivation of carbonate factories, transport of coarse reef material and rapid infilling of shallow water accommodation space since deglaciation makes these unique sites for reconstructing Holocene climate. Integration of new tropical cyclone reconstructions from both back-barrier reef (central Pacific) and carbonate bank (the Bahamas) settings with existing storm archives suggests a coordinated pattern of cyclone activity across storm basins since the late Holocene. Seesawing of intense tropical cyclone activity between the western Pacific (-0- 1000 yrs BP) and North Atlantic/Central Pacific (~1000 ~2500 yrs BP) appears closely tied with hydrographic patterns in the tropical Pacific and El Niflo-like variability. Decoupling of North Atlantic (inactive) and South Pacific (active) tropical cyclone patterns during the mid-Holocene suggests precession driven changes in storm season insolation may constrain ocean-atmosphere thermal gradients and therefore cyclone potential intensity on orbital timescales. / by Michael Toomey. / 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.