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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / To maintain the benefits of group membership, social animals need mechanisms to stay together and reunite if separated. This thesis explores the acoustic signals that dolphins use to overcome this challenge and mediate their complex relationships in a dynamic 3D environment. Bottlenose dolphins are the most extensively studied toothed whale, but research on acoustic behavior has been limited by an inability to identify the vocalizing individual or measure inter-animal distances in the wild. This thesis resolves these problems by simultaneously deploying acoustic tags on closely-associated pairs of known animals. These first reported deployments of acoustic tags on dolphins allowed me to characterize temporal patterns of vocal behavior on an individual level, uncovering large variation in vocal rates and inter-call waiting time between animals. Looking more specifically at signature whistles, a type of call often linked to cohesion, I found that when one animal produced its own signature whistle, its partner was more likely to respond with its own whistle. To better evaluate potential cohesion functions for signature whistles, I then modeled the probability of an animal producing a signature whistle at different times during a temporary separation and reunion from its partner. These data suggest that dolphins use signature whistles to signal a motivation to reunite and to confirm identity prior to rejoining their partner. To examine how cohesion is maintained during separations that do not include whistles, I then investigated whether dolphins could keep track of their partners by passively listening to conspecific echolocation clicks. Using a multi-pronged approach, I demonstrated that the passive detection range of echolocation clicks overlaps with the typical separation ranges of Sarasota mother-calf pairs and that the amount of time since an animal was last able to detect a click from its partner helped explain its probability of producing a signature whistle. Finally, this thesis developed a portable stereo camera system to study cohesion in situations where tagging is not possible. Integrating a GPS receiver, an attitude sensor and 3D stereo photogrammetry, the system rapidly positions multiple animals, grounding behavioral observations in quantitative metrics and characterizing fine-scale changes that might otherwise be missed. / by Nicholas Blair Wootton Macfarlane. / 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), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Although over a dozen elements are needed to support phytoplankton growth, only a few are considered to be growth-limiting. As the central atom in vitamin B12, cobalt is crucial for metabolism, but its status as a limiting nutrient is uncertain. This thesis investigates the geochemical controls on oceanic cobalt scarcity and their biological consequences. Analysis of over 1000 samples collected in the Tropical Pacific Ocean reveals a dissolved cobalt distribution that is strongly coupled to dissolved oxygen, with peak concentrations where oxygen is lowest. Large cobalt plumes within anoxic waters are maintained by three processes: 1) a cobalt supply from organic matter remineralization, 2) an amplified sedimentary source from oxygen-depleted coastlines, and 3) low-oxygen inhibition of manganese oxidation, which scavenges cobalt from the water column. Rates of scavenging are calculated from a global synthesis of recent GEOTRACES data and agree with cobalt accumulation rates in pelagic sediments. Because both sources and sinks are tied to the extent of oxygen minimum zones, oceanic cobalt inventories are likely dynamic on the span of decades. Despite extremely low cobalt in the South Pacific gyre, the cyanobacterium Prochlorococcus thrives. Minimum cobalt and iron requirements of a Prochlorococcus strain isolated from the Equatorial Pacific are quantified. Cobalt quotas are related to demand for ribonucleotide reductase and methionine synthase enzymes, which catalyze critical steps in DNA and protein biosynthesis, respectively. Compared to other cyanobacteria, a streamlined metal physiology makes Prochlorococcus susceptible to competitive inhibition of cobalt uptake by low levels of zinc. Although phytoplankton in the Equatorial Pacific are subject to chronic iron-limitation, widespread cobalt scarcity and vulnerability to zinc inhibition observed in culture imply that wild Prochlorococcus are not far from a cobalt-limitation threshold. / by Nicholas James Hawco. / 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), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The mechanisms involved in the formation of coral skeletons are examined using a laboratory model for coral calcification and the growth of living corals under different environmental conditions. Abiogenic aragonite was precipitated from seawater over a range of saturation states (Chapter 1). Abiogenic aragonite formed at high saturation state ([Omega]>~20) had a granular appearance and was enriched in trace elements, similar to the crystals found within the centers of calcification and dark bands in coral skeletons. Abiogenic aragonite formed fibrous crystals at lower saturation states, similar to the crystals which radiate out from the centers of calcification. These similarities suggest that the internal calcifying environment of the coral experiences a wide range of saturation states. To estimate when periods of high or low saturation state occur within the coral, corals were stained to mark the skeleton deposited during specific time intervals (Chapter 2). Dark bands are shown to form between dusk and dawn. A conceptual model is proposed in which daytime saturation state is limited by the availability of CO₂ due to the uptake of CO₂ by photosynthesis. To test the potential for photosynthesis to limit CO₂ availability to calcification, corals were grown under experimentally manipulated CO₂ and nutrient levels. Elevated CO₂ levels were found to decrease calcification in zooxanthellate colonies of the coral Astrangia poculata, however the addition of inorganic nutrients reduced the negative impact of CO₂ (Chapter 3), while reduced calcification rates were associated with elevated nutrients at ambient CO₂ levels. Together these results suggest that nutrient availability may limit photosynthesis under elevated pCO₂ conditions, while at ambient conditions additional stimulation of photosynthesis may limit the CO₂ supply to calcification. To further test the interaction of photosynthesis with calcification, the effects of nutrients, CO₂, and temperature were tested on both zooxanthellate and azooxanthellate coral colonies (Chapter 4). No clear pattern of nutrient enhancement of photosynthesis or calcification was found. However, a pronounced gender difference was found in the effect of CO₂ on calcification in spawning corals, with female corals being more sensitive to elevated CO₂. / (cont.) Coral calcification is examined using a laboratory model and living corals. In the laboratory model, abiogenic aragonite formed at high saturation state ([Omega]>~20) had a granular appearance and was enriched in trace elements, similar to centers of calcification and dark bands in corals. Abiogenic aragonite formed fibrous crystals at lower saturation states, similar to crystals which radiate out from centers of calcification. These similarities suggest the calcifying environment of the coral experiences a range of saturation states. To estimate when high or low saturation states occur within the coral, living corals were stained, staining patterns suggest dark bands form between dusk and dawn. A model is proposed in which daytime saturation state is limited by the availability of CO₂. To test the potential for photosynthesis to limit CO₂ availability to calcification, corals were grown under altered CO₂ and nutrient levels. Elevated CO₂ levels decreased calcification in zooxanthellate corals, however addition of nutrients reduced the negative impact of CO₂. This suggests nutrient availability may limit photosynthesis under elevated pCO₂2 conditions. The effects of nutrients, CO₂, and temperature were further tested on both zooxanthellate and azooxanthellate coral colonies. Unexpectedly, a gender difference was found in the effect of CO₂ on calcification. / by Michael Holcomb. / Ph.D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2015 / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 183-193). / This thesis is motivated by a series of biological experiments that display the harbor seal's extraordinary ability to track the wake of an object several seconds after it has swum by. They do so despite having auditory and visual cues blocked, pointing to use of their whiskers as sensors of minute water movements. In this work, I elucidate the basic uid mechanisms that seals may employ to accomplish this detection. Key are the unique ow-induced vibration properties resulting from the geometry of the harbor seal whisker, which is undulatory and elliptical in cross-section. First, the vortex-induced vibration (VIV) characteristics of the whisker geometry are tested. Direct force measurements and ow visualizations on a rigid whisker model undergoing a range of 1-D imposed oscillations show that the geometry passively reduces VIV (factor of > 10), despite contributions from eective added mass and damping. Next, a biomimetic whisker sensor is designed and fabricated. The rigid whisker model is mounted on a four-armed flexure, allowing it to freely vibrate in both in-line and crossflow directions. Strain gauges on the flexure measure deflections at the base. Finally, this device is tested in a simplified version of the sh wake { seal whisker interaction scenario. The whisker is towed behind an upstream cylinder with larger diameter. Whereas in open water the whisker exhibits very low vibration when its long axis is aligned with the incoming ow, once it enters the wake it oscillates with large amplitude and its frequency coincides with the Strouhal frequency of the upstream cylinder. This makes the detection of an upstream wake as well as an estimation of the size of the wake-generating body possible. A slaloming motion among the wake vortices causes the whisker to oscillate in this manner. The same mechanism has been previously observed in energy-extracting foils and trout actively swimming behind bluff cylinders in a stream. / by Heather Rachel Beem. / 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), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / This thesis investigates the timing and source(s) of water and volatile elements to the inner solar system by studying the basaltic meteorites angrites and eucrites. In chapters 2 and 3, I present the results from angrite meteorites. Chapter 2 examines the water and volatile element content of the angrite parent body and I suggest that some water and other volatile elements accreted to inner solar system bodies by ~2 Myr after the start of the solar system. Chapter 3 examines the D/H of this water and I suggest it is derived from carbonaceous chondrites. Chapter 4, 5, 6, and 7 addresses eucrite meteorites. Chapter 4 expands on existing models to explain geochemical trends observed in eucrites. In Chapter 5, I examine the water and F content of the eucrite parent body, 4 Vesta. In chapter 6, I determine the source of water for 4 Vesta and determine that carbonaceous chondrites delivered water to this body. Chapter 7 discusses degassing on 4 Vesta while it was forming. / by Adam Robert Sarafian. / Ph. D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references (p. 177-190). / Our ability to image extended underwater scenes is severely limited by attenuation and backscatter. Generating a composite view from multiple overlapping images is usually the most practical and flexible way around this limitation. In this thesis we look at the general constraints associated with imaging from underwater vehicles for scientific applications - low overlap, non-uniform lighting and unstructured motion - and present a methodology for dealing with these constraints toward a solution of the problem of large area 3D reconstruction. Our approach assumes navigation data is available to constrain the structure from motion problem. We take a hierarchical approach where the temporal image sequence is broken into subsequences that are processed into 3D reconstructions independently. These submaps are then registered to infer their overall layout in a global frame. From this point a bundle adjustment refines camera and structure estimates. We demonstrate the utility of our techniques using real data obtained during a SeaBED AUV coral reef survey. Test tank results with ground truth are also presented to validate the methodology. / by Oscar Pizarro. / 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. / Corals are increasingly threatened by warming sea surface temperatures and other anthropogenic changes. The delicate symbiosis between corals and their algal endosymbionts (zooxanthellae) is easily disrupted by thermal stress, leading to bleaching and eventual mortality. The use of lipid ratios as biomarkers of environmental conditions is well established. Coral biomass contains abundant lipids, and the potential of lipid parameters to diagnose thermal tolerance in zooxanthellae has been previously suggested. In this thesis, I explore the response of specific fatty acids, sterols, and thylakoid membrane lipids to thermal and disease stress in zooxanthellae grown in culture, as well as those isolated from living corals. I present the discovery of a bioactive thylakoid lipid within zooxanthellae cells, and show how this compound is selectively mobilized in thermally stressed cells. I present a plausible mechanism for the breakdown of this compound into products that may cause apoptosis and disrupt the coral-algal symbiosis, eventually causing bleaching. I present two new lipid biomarkers of thermal stress in zooxanthellae, the C18 fatty acid unsaturation ratio, and the fatty acid to sterol ratio. I calibrate the decline of these two parameters to levels of thermal stress comparable to those needed to cause bleaching. I further show that these parameters are sensitive to pathogen stress as well. In several case studies of diseased and thermally stressed corals, I demonstrate that these lipid biomarkers of coral stress may be applied to zooxanthellae isolated from environmental samples. I show that these same compounds are preserved within coral aragonite, which opens up the potential to retrieve lipid-based historical records of coral health from annual layers of coral skeleton. This work demonstrates the value of using lipid biomarkers to assess coral health and better understand the biochemical mechanisms of coral bleaching. / by Jessie Mary Kneeland. / 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), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / In the ocean, chromium (Cr) is a redox-sensitive trace metal. The reduction of Cr(VI) to Cr(III) occurs in oxygen deficient zones (ODZs), and Cr reduction in general has been identified as a significant Cr isotope fractionation mechanism. This thesis presents the first Cr isotope variations (653 Cr) in ODZs of the ocean and adds to the sparse Cr isotope data published for modern seawater. I developed a precise and accurate Cr isotope method for seawater samples. Seawater acidification converts total Cr to Cr(III) which is preconcentrated by Mg(OH) 2 coprecipitation. A three-column anion exchange chromatography scheme separates Cr from isobaric and polyatomic interferences present in the seawater and reagent matrixes. Isotope analysis is performed on a MC-ICP-MS IsoProbe. The addition of a 50Cr-54Cr double spike allows for accurate correction of procedural and instrumental Cr mass fractionations. The first Cr isotope ratio data for a full water column profile in the Pacific Ocean is presented. This station serves as a fully oxic counterpart to stations located within the ODZ of the Eastern Tropical North Pacific. At one station, Cr concentrations are lower and [delta]53Cr values are heavier within the ODZ. This is consistent with Cr reduction resulting in isotopically lighter, particle-reactive Cr(III), which is scavenged and exported from the water column. A strong correlation of [delta]53Cr and [delta]15 NNo3- at this station suggests that Cr reduction may be microbially mediated instead of simply being a product of thermodynamic equilibrium. Alternatively, Cr may be reduced by Fe(II). In the anoxic bottom waters of the Santa Barbara Basin a strong Cr reduction signal (lower [Cr], heavier [delta]53Cr) is observed, which may result from the same aforementioned Cr reduction mechanisms. A shift to the heaviest seawater Cr isotope signatures yet observed was detected in the oxic bottom waters of the shallow Arctic Chukchi shelf, while Cr concentrations decreased. This extreme isotope signal may result from Cr reduction by a reduced species (e.g. Fe(II)), which was released from the underlying anoxic shelf sediments. Cr in the Atlantic layer and in the bottom water of a central Arctic station appears to be shaped by a novel, unidentified process. / by Simone Beatrice Moos. / 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. / 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.