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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Recurrent brown tide blooms caused by the harmful alga Alureococcus anophagefferens have decimated coastal ecosystems and shellfisheries along the Eastern U.S and South Africa. The exact mechanisms controlling bloom formation, sustenance, and decline are unclear, however bottom-up factors such as nutrient type and supply are thought to be critical. Traditional assays for studying algal nutrient physiology require bulk community measurements or in situ nutrient perturbations. Although useful, these techniques lack the ability to target individual species in complex, mixed microbial assemblages. The motivation for this thesis is to examine the metabolic strategies utilized by A. anophagefferens for meeting its nitrogen (N) and phosphorus (P) demand at the cellular level using molecular tools that, even in the presence of complex microbial assemblages, can be used to track how nutrients influence the bloom dynamics of A. anophageferens in the environment. Chapter two examines the global transcriptional responses of A. anophagefferens to N and P deficiency. Results demonstrate that A. anophagefferens has the capacity to utilize multiple forms of organic N and P when inorganic forms become unavailable. Chapter three analyzed the global protein changes in response to P deficiency and P re-supply. Consistent with transcript patterns, A. anophagefferens increases protein abundance for a number of genes involved in inorganic and organic P metabolism when inorganic P is deficient. Furthermore, increases in a sulfolipid biosynthesis protein combined with lipid data suggest A. anophagefferens can adjust its P requirement by switching from phospholipids to sulfolipids when inorganic P is unavailable. Analysis of protein abundances from Pdeficient cells that were re-fed inorganic P demonstrates variations in the timing of turnover among various proteins upon release from phosphate deficiency. Chapter four tests the expression patterns of candidate gene markers of nutrient physiology under controlled culture experiments. Results show that expression patterns of a phosphate transporter and xanthine/uracil/vitamin C permease are indicators of P and N deficiency, respectively. Taken together, these findings provide insight into the fundamental and ecological niche space of this harnful algal species with respect to N and P and provide a platform for assaying nutrient controls on natural brown tide blooms. / by Louie L. Wurch. / 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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Global warming has led to a significant increase in Greenland ice sheet (GrIS) melt and runoff since 1990, resulting in escalated export of fresh water and associated sediment to the surrounding North Atlantic and Arctic Oceans. Similar to alpine glacial systems, surface meltwater on ice sheet surface drains to the base (subglacial) where it joins a drainage system and can become chemically enriched from its origin as dilute snow- and ice-melt. In this thesis, I examine the interdependence of glacial hydrology and biogeochemical cycling in terms of export of carbon and iron from the Greenland ice sheet. I develop a new isotope mixing-model to quantify water source contributions to the bulk meltwater discharge draining a GrIS outlet glacier. Results illustrate (a) the new application of a naturally occurring radioisotope (radon-222) as a quantitative tracer for waters stored at the glacier bed, and (b) the seasonal evolution of the subglacial drainage network from a delayed-flow to a quick-flow system. Model results also provide the necessary hydrological context to interpret and quantify glacially-derived organic carbon and iron fluxes. I combine bulk- and molecular-level studies of subglacial organic carbon to show that GrIS discharge exports old (radiocarbon depleted), labile organic matter. Similar investigations of dissolved and particulate iron reveal that GrIS discharge may be a significant flux of labile iron to the North Atlantic Ocean during the summer meltseason. Both carbon and iron are subject to proglacial processing prior to export to the marine environment, and exhibit strong seasonal variability in correlation with the subglacial drainage evolution. Low, chemically concentrated fluxes characterize the spring discharge, whereas higher, chemically dilute fluxes typify the summer discharge. Collectively, this thesis provides some of the first descriptions and flux estimates of carbon and iron, key elements in ocean biogeochemical cycles, in GrIS meltwater runoff. / by Maya Pilar Bhatia. / 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), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 147-160). / Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory cells accumulated to an order of magnitude greater cell densities than Tenacibaculum sp. cells on equivalent prey cell densities. Experiments were conducted to constrain the potential of the novel isolates to affect prey communities under more environmentally relevant conditions. An investigation of the minimum number of predatory cells needed to generate clearings of prey cells found that the inoculation of individual predatory flavobacteria cells can ultimately result in dense lytic swarms. In some cases, the susceptibility of particular prey species to lysis by a flavobacterial predator was found to vary based on the growth state of the prey cells or the presence of their spent growth media. A novel methodology for the experimental study of biofilms was used to assess the impact of exposure to predatory marine flavobacteria on the release of macronutrients from prey biofilms. The Olleya sp. predator had a stimulative effect on macronutrient release while the Tenacibaculum sp. did not, further suggesting the two groups of predators are adapted to different ecological niches. / by Erin C. Banning. / 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), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 91-99). / Trade-offs between filtration rate and swimming performance among several salp species with distinct morphologies and swimming styles were compared. Small-scale particle encounter at the salp filtering apparatus was also explored. Observations and experiments were conducted at the Liquid Jungle Lab, off the pacific coast of Panama in January 2006 through 2009. First, time-varying body volume was calculated by digitizing salp outlines from in situ video sequences. The resulting volume flow rates were higher than previous measurements, setting an upper limit on filtration capacity. Though each species possessed a unique combination of body kinematics, normalized filtration rates were comparable across species, with the exception of significantly higher rates in Weelia cylindrica aggregates, suggesting a tendency towards a flow optimum. Secondly, a combination of in situ dye visualization and particle image velocimetry (PIV) measurements were used to describe properties of the jet wake and swimming performance variables including thrust, drag and propulsive efficiency. All species investigated swam via vortex ring propulsion. Though Weelia cylindrica was the fastest swimmer, Pegea confoederata was the most efficient, producing the highest weight-specific thrust and wholecycle propulsive efficiency. Weak swimming performance parameters in Cyclosalpa afinis, including low weight-specific thrust and low propulsive efficiency, may be compensated by comparatively low energetic requirements. / (cont.) Finally, a low Reynolds number mathematical model using accurately measured parameters and realistic oceanic particle size concentrations showed that submicron particles are encountered at higher rates than larger particles. Results from feeding experiments with 0.5, 1 and 3 [mu]m po- lystyrene microspheres corroborated model predictions. Though 1 to 10 pm-sized particles (e.g. flagellates, small diatoms) are predicted to provide four times as much carbon as 0.1 to 1 pm- sized particles (e.g. bacteria, Prochlorococcus), particles smaller than the mesh size (1.4 [mu]m) can still fully satisfy salp energetic needs. / by Kelly Rakow Sutherland. / 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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Larval supply is an important process linking reproductive output to recruitment of benthic marine invertebrates. Few species-specific studies of bivalve larvae have been performed due to the lack of suitable methods for species identification. This thesis focused on applying a method to identify larvae from field samples from Waquoit Bay, MA using shell birefringence patterns. This method was then used to address variability in larval supply for three bivalve species on weekly, tidal, and hourly scales. Sampling weekly for six months during two years showed large variability in larval concentrations on this time scale. Abundances of most species were related to bay temperature, and species distributions among sampling sites were indicative of transport potential and population coherence. Greater growth of larvae in 2009 compared to 2007 was attributed to more wind-induced mixing and better food availability in 2009. Integrative samples over each tidal event for a 14-day period demonstrated that larvae were mostly constrained by water masses. During a period when there were sharp tidal signals in temperature and salinity, larval concentrations were higher in bay water compared to coastal waters on incoming tides. After a storm event, water mass properties were less distinct between tidal events and a semidiurnal signal in larval concentrations was no longer apparent. The timing of periods of high larval concentrations did not always coincide with periods of highest water mass flux reducing net export in some cases. On an hourly scale, the vertical distribution of larvae affected by water column stratification and strength of tidal flow. Strong currents and a fresh upper layer both prevented larvae from concentrating at the surface. There was little evidence of peaks in larval concentrations associated with a given tidal period. Species-specific data can provide new perspectives on larval transport. For the three species studied, Anomia simplex, Guekensia demissa, and Mercenaria mercenaria, different source areas, patterns for growth, and potential for export were observed. Applying species-specific identification methods to future studies of bivalve larval transport has the potential to relate larval abundance to settlement patterns, an important component of larval ecology and shellfish management. / by Christine Mingione Thompson. / 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), 2003. / Includes bibliographical references (p. 132-139). / Iron (Fe) is an essential micronutrient for marine phytoplankton often limiting phytoplankton growth due to its low concentration in the ocean and thus playing a role in modulating the ocean's biological pump. In order to understand controls on global Fe distribution, the decoupling between Fe and P04 and the sensitivity of surface nutrient concentrations to changes in aeolian iron supply, I use a hierarchy of ocean circulation and biogeochemistry models. I formulate a mechanistic model of iron cycling which includes scavenging onto sinking particles and complexation with an organic ligand. The iron cycle is coupled to a model of the phosphorus cycle. The aeolian source of iron is prescribed. This system is examined in the context of a highly idealized box model. With appropriate choice of parameter values, the model can be brought into consistency with the relatively sparse ocean observations of iron in the oceans. I implement this biogeochemical scheme in a coarse resolution ocean general circulation model, guided by the box model sensitivity studies. This model is also able to reproduce the broad regional patterns of iron and phosphorus. In particular, the high macro-nutrient concentrations of the Southern Oceans result from iron limitation in the model. I define a tracer, Fe* that quantifies the degree to which a water mass is iron limited. Surface waters in high nutrient, low chlorophyll regions have negative Fe* values, indicating Fe limitation, because aeolian surface dust flux is not sufficient to / (cont.) compensate for the lack of iron in upwelled waters. The oceanic residence time of Fe is [approximately] 285 years in the model, confirming that transport plays an important role in controlling deep water [Fe[Tau]]. Globally, upwelling accounts for 40% of 'new' iron reaching the euphotic zone. Due to the potential ability of iron to change the efficiency of the carbon pump in the remote Southern Ocean, I study Southern Ocean surface P04 response to increased aeolian dust flux. My box model results suggest that a global ten fold increase in dust flux can support a P04 drawdown of [approximately]0.25[mu]M, while the GCM results suggest a P04 drawdown of 0.5 [mu]M. / by Payal Parekh. / Ph.D.

Thesis: S.M., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2020 / Cataloged from the official PDF of thesis. / Includes bibliographical references (pages 119-126). / Developing accurate and computationally efficient models for ocean acoustics is inherently challenging due to several factors including the complex physical processes and the need to provide results on a large range of scales. Furthermore, the ocean itself is an inherently dynamic environment within the multiple scales. Even if we could measure the exact properties at a specific instant, the ocean will continue to change in the smallest temporal scales, ever increasing the uncertainty in the ocean prediction. In this work, we explore ocean acoustic prediction from the basics of the wave equation and its derivation. We then explain the deterministic implementations of the Parabolic Equation, Ray Theory, and Level Sets methods for ocean acoustic computation. We investigate methods for evolving stochastic fields using direct Monte Carlo, Empirical Orthogonal Functions, and adaptive Dynamically Orthogonal (DO) differential equations. / As we evaluate the potential of Reduced-Order Models for stochastic ocean acoustics prediction, for the first time, we derive and implement the stochastic DO differential equations for Ray Tracing (DO-Ray), starting from the differential equations of Ray theory. With a stochastic DO-Ray implementation, we can start from non-Gaussian environmental uncertainties and compute the stochastic acoustic ray fields in a reduced order fashion, all while preserving the complex statistics of the ocean environment and the nonlinear relations with stochastic ray tracing. We outline a deterministic Ray-Tracing model, validate our implementation, and perform Monte Carlo stochastic computation as a basis for comparison. We then present the stochastic DO-Ray methodology with detailed derivations. We develop varied algorithms and discuss implementation challenges and solutions, using again direct Monte Carlo for comparison. / We apply the stochastic DO-Ray methodology to three idealized cases of stochastic sound-speed profiles (SSPs): constant-gradients, uncertain deep-sound channel, and a varied sonic layer depth. Through this implementation with non-Gaussian examples, we observe the ability to represent the stochastic ray trace field in a reduced order fashion. / by Michael Jesus Humara. / S.M. / S.M. Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution)

Thesis: S.M., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), September, 2020 / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 97-102). / Robotic swarms are becoming increasingly complex on the surface and in air due to highspeed and reliable communication links, Global Positioning Satellites (GPS), and visual support to relative navigation. However, the limited propagation of these signals in the ocean has impacted similar advances in undersea robotics. Autonomous underwater vehicles (AUVs) often rely on acoustics to inform navigation solutions; however, this approach presents challenges for scalable robotic swarms. Acoustic navigation is a means to inform range and bearing to a target. Many methods for range and bearing estimation, including current low-cost solutions, rely on precision time synchronization or two-way communication to compute ranges as part of a full navigation solution. The high cost of reliable Chip-scale atomic clocks (CSACs) and acoustic modems relative to other vehicle components limits large-scale swarms due to the associated cost-per-vehicle and communications infrastructure. / We propose a single, high-cost vehicle with a reliable navigation solution as a "leader" for a scalable swarm of lower-cost vehicles that receive acoustic signals from a source onboard the lead vehicle using a single hydrophone. These lower-cost "followers" navigate relative to the leader according to the preferred behavioral pattern, but for simplicity, we will refer to a simple following behavior in this work. This thesis outlines a method to obtain range estimates to sound sources in which the signal content, including frequency and power at its origin, can be reasonably approximated. Total transmission loss is calculated based on empirical equations for the absorption of sound in seawater and combined with geometric spreading loss from environmental models to estimate range to a source based on the loss at differential frequencies. We refer to this calculation as the signal absorption-based range estimator (SABRE). / This method for obtaining range combines with Doppler-shift methods for target bearing based on the maximum frequency detected within a banded limit around a known source frequency. A primary objective for SABRE is to address techniques that support low-cost options for undersea swarming. This thesis's contributions include a novel method for range estimation onboard underwater autonomous vehicles that supports navigation relative to a known source when combined with Doppler-shift methods for target bearing. This thesis seeks to develop the theory, algorithms, and analytical tools required and apply those tools to real-world data sets to investigate the feasibility, sources of error, and accuracy of this new approach to range estimation for underwater swarms. / by Brendan O'Neill. / S.M. / S.M. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution)

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), 2020 / Cataloged from student-submitted PDF of thesis. "September 2020." / Includes bibliographical references. / Speleothems, or sedimentary rocks formed in caves, act as valuable archives of past climate change due to their suitability for U-series dating and high-resolution proxy analysis. These records can provide insights into water availability and controls on hydrology prior to the instrumental record. In this thesis, I present three records from newly-analyzed Mexican stalagmites using stable isotope (oxygen and carbon) and trace element to calcium (Mg/Ca and Sr/Ca) ratios as proxies for changing hydroclimate. Chapter 2 presents a precisely dated, mid- Holocene record of high rainfall and limited precipitation variability in the Yucatan Peninsula, Mexico. Chapters 3 and 4 present novel climate records from northeastern Mexico, an understudied region of North America. Both records come from cave sites within the Mexican arid zone, which is simultaneously experiencing increased water scarcity and a rapidly growing population. In Chapter 3, I examine a speleothem from the first millennium of the Common Era, which showed that there is a precipitation dipole between northern and southern Mexico. Chapter 4 highlights, for the first time at decadal resolution, the northeast Mexican response to the 8.2 ka event and the Younger Dryas. These chapters show that the San Luis Potosí region is vulnerable to droughts under multiple climate mean states, and is subject to drying as Atlantic Meridional Overturning Circulation weakens due to anthropogenic climate change. The climate records detailed in this thesis improve our understanding of controls on Mexican hydroclimate and can serve as benchmarks for climate models. / by Gabriela Serrato Marks. / Ph. D. / 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)

Thesis: S.M., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2020 / Cataloged from student-submitted PDF of thesis. / Includes bibliographical references (page 85). / Advances in the miniaturization of microelectronics has greatly contributed to the proliferation of small, low cost autonomous underwater vehicles (AUVs). These affordable vehicles offer organizations a flexible platform that can be adapted to support a multitude of research goals. The small size and low entry cost come with a trade off of simple navigation systems, typically dead reckoning (DR) using a speed determined via propeller counts and heading from a low cost micro-electromechanical system (MEMS) inertial measurement unit (IMU), whose error grows unbounded without the availability of a ground referenced fix source and is compounded by the bias present in the speed measurement due to the change in hydrodynamics from the addition of sensors to the hull form. Additionally, some capabilities such as water current velocity measurement traditionally requires the addition of equipment that is not only expensive, but also whose size and power consumption can adversely affect operating characteristics and deployment times. This thesis expands on previous research using one-way travel time inverted USBL (OWTT-iUSBL) to calculate the local current velocity without the addition of a Doppler velocity log (DVL) or acoustic Doppler current profiler (ADCP). A novel extended Kalman filter (EKF) is proposed that, in addition to calculating the current velocity, estimates and corrects for the bias present in the speed measurement as determined by the main vehicle computer. Using data collected on the Charles River at the Massachusetts Institute of Technology (MIT) Sailing Pavilion, it is shown that current velocities can be reasonably calculated using OWTT-iUSBL data as compared to the values calculated using long baseline (LBL) data. / by Christopher R. Dolan. / S.M. / S.M. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution)