Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) - a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean. / by Oscar Abraham Sosa. / 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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Holes and channels were excavated in the surf zone on an ocean beach near Duck, NC, and observations of the subsequent evolution of waves, currents, and the modified seafloor were used to investigate nearshore dynamics. In one set of seafloor perturbation experiments, deep holes with steeply sloping sides were excavated in the inner surfzone seafloor. Observations of the infilling holes were used to make the first field estimates of the surfzone morphological diffusivity, which describes the rate of seafloor smoothing by downslope sediment transport. To improve the temporal resolution of bathymetric estimates, a mapping method was developed to combine infrequent, spatially dense watercraft surveys with continuous, spatially sparse in situ altimeter estimates of the seafloor location. In another set of seafloor perturbation experiments, channels were dredged across the surf zone with the propellers of a landing craft. Alongshore variations in wave breaking caused by the perturbed bathymetry resulted in strong rip currents in the channels under some conditions, whereas alongshore currents bypassed the channels under other conditions. The dynamics of the circulation response for changing wave forcing, bathymetry, and tidal elevation are investigated using the observations, a numerical model, and a parameter based on wave properties and bathymetry. / by Melissa Moulton. / 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), 2007. / Includes bibliographical references. / Paralytic shellfish poisoning (PSP) is a human intoxication associated with the consumption of shellfish contaminated with a family of neurotoxins called saxitoxins. Many species in the dinoflagellate genus Alexandrium have been shown to produce these toxins. Here I report the first case of a culture of Alexandrium that has completely lost the ability to produce saxitoxins. The loss of toxicity was accompanied by a reduction in growth capability. A subculture of this isolate maintains the ability to produce toxins and to grow at rates and to cell abundances that were characteristic of the original Alexandrium culture. The growth and toxicity differences in the two isolates were demonstrated to be a property of the dinoflagellate itself and were not dependent on the different bacterial symbionts associated with each culture. The pair of subcultures is a novel experimental system to study gene expression related to toxin production and growth in dinoflagellates. The products of gene expression were analyzed in the two subcultures of Alexandrium grown under the same conditions, but where toxicity and growth differ. At the metabolome level, compounds were identified that were unique to the non-toxic isolate; their emergence may be correlated to a disruption of the biosynthetic pathway for PSP toxins. / (cont.) These compounds share some characteristics and potential structural similarities with saxitoxins, though they are not any of the known toxin derivatives. Difference gel electrophoresis (DIGE) identified proteins differentially expressed between the two subcultures. Identification of some of these proteins was possible by searching the expressed sequence tag (EST) database for dinoflagellates. Proteins shown to be down-regulated in the non-toxic, slower growing subculture are all enzymes from the Calvin cycle, which may explain the limited growth of the non-toxic isolate. Other unknown, differentially expressed proteins may relate to the loss of toxicity, but their identity and function remain unresolved. / by Claudia A. Martins. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / To understand how waves and sea level shape sandy shoreline profiles, I use existing energetics-based equations of cross-shore sediment flux to describe shoreface evolution and equilibrium profiles, utilizing linear Airy wave theory instead of shallow-water wave assumptions. By calculating a depth-dependent characteristic diffusivity timescale, I develop a morphodynamic depth of shoreface closure for a given time envelope, with depth increasing as temporal scale increases. To assess which wave events are most important in shaping the shoreface in terms of occurrence and severity, I calculate the characteristic effective wave conditions for both cross-shore and alongshore shoreline evolution. Extreme events are formative in the cross-shore shoreface evolution, while alongshore shoreline evolution scales linearly with the mean wave climate. Bimodal distributions of weighted wave heights are indicative of a site impacted more frequently by tropical storms rather than extra-tropical storms. To understand how offshore wave climate and underlying geometry of a carbonate reef platform shapes evolution of atolls, I simulate the hydrodynamics of a simplified reef flat, using XBeach, a two-dimensional model of infragravity wave propagation. The reef flat self-organizes to a specific width and water depth depending on the offshore wave climate and characteristics of the available sediment. Formation of a sub-aerial landmass, like a motu, can be initiated by a change in offshore wave climate (like a storm), which can create a nucleation site from mobilization and deposition of coarse sediment on the reef flat. Once a motu is present, the shoreline should prograde until reaching a critical reef-flat width. Our conceptual model of reef-flat evolution and motu formation is governed by understanding the hydrodynamics of the system and subsequent response of sediment transport. / by Alejandra C. Ortiz. / Ph. D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (leaf 75). / This thesis explores the feasibility of making wind speed profile measurements from an oceanographic buoy using a Doppler sodar. In the fall of 2005, we deployed a Scintec SFAS sodar on an ASIS buoy. Roughly one week of buoy motion data and one day of sodar observations were collected. Data from both this deployment, and the Martha's Vineyard Coastal Observatory, were used in conjunction with models to predict sodar performance. Results are compared for an ASIS and a 3-meter discus buoy. We also predict the yearly average probability of sodar data availability in the presence of buoy motion. We show that buoy tilting in response to wave forcing is the main factor affecting sodar performance. Our results strongly suggest that ASIS is a suitable platform for sodar measurements at sea. / by Allison M. Berg. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references (leaves 209-213). / In this thesis, an innovative architecture for real-time adaptive and cooperative control of autonomous sensor platforms in a marine sensor network is described in the context of the autonomous oceanographic network scenario. This architecture has three major components, an intelligent, logical sensor that provides high-level environmental state information to a behavior-based autonomous vehicle control system, a new approach to behavior-based control of autonomous vehicles using multiple objective functions that allows reactive control in complex environments with multiple constraints, and an approach to cooperative robotics that is a hybrid between the swarm cooperation and intentional cooperation approaches. The mobility of the sensor platforms is a key advantage of this strategy, allowing dynamic optimization of the sensor locations with respect to the classification or localization of a process of interest including processes which can be time varying, not spatially isotropic and for which action is required in real-time. Experimental results are presented for a 2-D target tracking application in which fully autonomous surface craft using simulated bearing sensors acquire and track a moving target in open water. / (cont.) In the first example, a single sensor vehicle adaptively tracks a target while simultaneously relaying the estimated track to a second vehicle acting as a classification platform. In the second example, two spatially distributed sensor vehicles adaptively track a moving target by fusing their sensor information to form a single target track estimate. In both cases the goal is to adapt the platform motion to minimize the uncertainty of the target track parameter estimates. The link between the sensor platform motion and the target track estimate uncertainty is fully derived and this information is used to develop the behaviors for the sensor platform control system. The experimental results clearly illustrate the significant processing gain that spatially distributed sensors can achieve over a single sensor when observing a dynamic phenomenon as well as the viability of behavior-based control for dealing with uncertainty in complex situations in marine sensor networks. / by Donald Patrick Eickstedt. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and, the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references. / This study is a geochemical investigation into the accretion of lower oceanic crust and processes of shallow melt-rock reaction at mid-ocean ridges. Major-, trace-elements, and isotopes from whole-rocks and minerals from the Lyngen Gabbro, a 480-My old dismembered ophiolite from the Scandinavian Caledonides, indicate that this igneous complex was produced from hydrous supra-subduction zone magmas, a remnant of an incipient ocean-arc. Such ophiolites are better models for the structural evolution than the geochemical evolution of the lower oceanic crust at mid-ocean ridges. Minerals in gabbros from Atlantis Bank, Southwest Indian Ridge, a modern, in-situ example of lower ocean-crust, were analyzed for major and trace-elements. The MELTS algorithm indicates that these gabbros formed by near-fractional crystallization at mid-crustal pressures. The gabbroic crust is more evolved than the lavas and represents melts fractionated 50-95% relative to a mantle-derived melt-composition, supported by trace-element models. This argues against the often-cited gabbro-glacier accretion model, where mantle-derived melts are transported to a shallow melt-lens and fractionates there before eruption. There remain >770-m of additional primitive cumulates below 1500-m deep Hole 735B or within the underlying mantle. Thus, the seismic Moho, beneath Hole 735B, could be the crust-mantle boundary, rather than an alteration front as suggested elsewhere. The Atlantis Bank gabbros have augites that are more primitive than plagioclases and olivines with which they coexist. Melt-rock interaction, where ascending melts dissolve the pre-existing gabbroic rocks and create hybrid magma may have caused this. Dissolution-experiments for plagioclase-olivine and plagioclase-augite mineral pairs / (cont.) were performed at 1180⁰-1330⁰C and 20-min - 24hrs. Dissolution occurs rapidly and out of equilibrium, with the dissolution rates dependent on the [delta]T above the solidus. Rocks with small grain-boundary areas (coarse grained or nearly mono-mineralic) heat internally when enclosed in hot magma, causing xenoliths or wall-rock to melt and disaggregate. The dissolution-derived magma crystallizes minerals more refractory-looking than the melts that precipitated the original gabbroic rocks. Assimilation of gabbroic rocks increases the Na content and decreases the Fe content of the melt that digests it, thus basaltic glasses formed after this hybridization will falsely reflect a lower degree and pressure of mantle melting. / by Astri Jæger Sweetman Kvassnes. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (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 (p. 191-202). / Melting and crystallization processes on the Earth and Moon are explored in this thesis, and the topics of melt generation, transport, and crystallization are discussed in three distinct geologic environments: the Moon's mantle, the Greenland ice sheet, and the Earth's crust. Experiments have been conducted to determine the conditions of origin for two high-titanium magmas from the Moon. The lunar experiments (Chapter 2) were designed to explore the effects of variable oxygen fugacity (fo₂) on the high pressure and high temperature crystallization of olivine and orthopyroxene in high-Ti magmas. The results of these experiments showed that the source regions for the high-Ti lunar magmas are distributed both laterally and vertically within the lunar mantle, and that it is critical to estimate the pre-eruptive oxygen fugacity in order to determine true depth of origin for these magmas within the lunar mantle. Chapter 3 models the behavior of water flow through the Greenland ice sheet driven by hydrofracture of water through ice. The results show that melt water in the ablation zone of Greenland has almost immediate access to the base of the ice sheet in areas with up two kilometers of ice. Chapter 4 is an experimental study of two hydrous high-silica mantle melts from the Mt. Shasta, CA region. Crystallization is simulated at H₂O saturated conditions at all crustal depths, and a new geobarometer-hygrometer based on amphibole magnesium number is calibrated. In Chapter 5 I use the new barometer to study a suite of mafic enclaves from the Mt. Shasta region, and apply it to amphiboles in these enclaves. Evidence for pre-eruptive H₂O contents of up to 14 wt% is presented, and bulk chemical analyses of the inclusions are used to show that extensive magma mixing has occurred at all crustal depths up to 35 km beneath Mt. Shasta. / by Michael James Krawczynski. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / 122 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 149-158). / Understanding the fate of primary production in the ocean is a challenging task because once produced, organic material is oxidized over timescales which range from minutes, to millions of years. This timescale diversity is matched by an equal heterogeneity in both the local physical and chemical environment. In this thesis we explore the relationship between the distinct reservoirs of organic carbon in the ocean and their underlying complexity. First, we show how the heterogeneity of portions of the carbon cycle can be packaged in terms of age structured models and their accompanying age and rate distributions. We further relate the moments of the rate distributions to bulk reservoir properties like average age and flux. Explicit relationships are then derived for the specific case of a single turnover time and a lognormal distribution. We apply these ideas to the problem of dissolved organic carbon (DOC) cycling in the ocean. Current models of bulk concentration and isotope data suggest a microbially sourced DOC reservoir consisting of two components. A nearly homogeneous background component with a long turnover time (> 6000 years) is joined by a component of fast turnover time (~ 1 year) and equal concentration in the surface ocean. We confirm the presence of isotopically enriched, modern DOC co-cycling with an isotopically depleted older fraction in the upper ocean. However, our results show that up to 30% of the deep DOC reservoir is modern and supported by a 1 Pg per year carbon flux, ten times higher than inferred from bulk isotope measurements. Isotopically depleted material turns over at an apparent time scale of 30, 000 years, far slower than indicated by bulk isotope measurements. These results are consistent with global DOC measurements and explain both the fluctuations in deep DOC concentration and the anomalous radiocarbon values of DOC in the Southern Ocean. Finally, the thesis explores methods for determining the validity of diffusion limitation as the mechanism behind the power-law slowdown in organic remineralization in sediment. We find that diffusion limitation connects the decay behavior of organic material to the correlations found between mineral surface area and organic matter content in sediments. / by Christopher L. Follett. / 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), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 173-186). / This thesis investigates the long-term evolution of rift-bounding normal faults. To first order, the observed diversity of extensional tectonic styles reflects differences in the maximum offset that can be accommodated on individual faults during their life span. My main objective is to develop a theoretical framework that explains these differences in terms of a few key mechanical and geological controls. I start by laying out the energy cost associated with slip on a normal fault, which consists of (1) overcoming the frictional resistance on the fault, (2) bending the faulted layer and (3) sustaining the growth of topography. In Chapter 2, I propose that flexural rotation of the active fault plane enables faults to evolve along a path of minimal energy, thereby enhancing their life span. Flexural rotation occurs more rapidly in thinner faulted layers, and can potentially explain the wide range of normal fault dips documented with focal mechanisms. In Chapter 3, I show that surface processes can enhance the life span of continental normal faults by reducing the energy cost associated with topography buildup. In Chapter 4, I focus on lithospheric bending induced by fault growth, which is well described by elasto-plastic flexure models. I demonstrate that numerical models that treat the lithosphere as a visco-plastic solid can properly predict fault evolution only when the rate-dependent viscous flexural wavelength of the lithosphere is accommodated within the numerical domain. In Chapter 5, I consider the interplay of faulting and crustal emplacement at a slow mid-ocean ridge. I show that a depth-variable rate of magma emplacement can reconcile the formation of long-lived detachment faults, which requires a moderate melt supply, and the exhumation of large volumes of lower crustal material. Finally, in Chapter 6 I investigate the three-dimensional interactions between normal faults in a lithosphere of varying thickness. I suggest that large along-axis gradients in lithospheric thickness can prevent the growth of continuous faults along-axis, and instead decouple the modes of faulting at the segment center and at the segment end. / by Jean-Arthur Louis Olive. / Ph. D.