Thesis: Ph. D., Joint Program in Oceanography/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. Vita. / Includes bibliographical references (pages 203-213). / The capabilities of autonomous underwater vehicles (AUVs) and their ability to perform tasks both autonomously and adaptively are rapidly improving, and the desire to quickly and efficiently sample the ocean environment as Earth's climate changes and natural disasters occur has increased significantly in the last decade. As such, this thesis proposes to develop a method for single and multiple AUVs to collaborate autonomously underwater while autonomously adapting their motion to changes in their local environments, allowing them to sample and track various features of interest with greater efficiency and synopticity than previously possible with preplanned AUV or ship-based surveys. This concept is demonstrated to work in field testing on multiple occasions: with a single AUV autonomously and adaptively tracking the depth range of a thermocline or acousticline, and with two AUVs coordinating their motion to collect a data set in which internal waves could be detected. This research is then taken to the next level by exploring the problem of adaptively and autonomously tracking spatiotemporally dynamic underwater fronts and plumes using individual and autonomously collaborating AUVs. / by Stephanie Marie Petillo. / 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), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 151-163). / Population connectivity is a fundamental process that governs the spatial and temporal dynamics of marine ecosystems. For many marine species, population connectivity is driven by dispersal during a planktonic larval phase. The ability to obtain accurate, affordable, and meaningful estimates of larval dispersal patterns is therefore a key aspect of understanding marine ecosystems. Although field observations provide insight into dispersal processes, they do not provide a comprehensive assessment. Individual-based models (IBMs) that couple ocean circulation and particle-tracking models provide a unique ability to examine larval dispersal patterns with high spatial and temporal resolution. Obtaining accurate results with IBMs requires simulating a sufficient number of particles, and the sequential Bayesian procedure presented in chapter 2 identifies when the number of particles is adequate to address predefined research objectives. In addition, this method optimizes the particle release locations to minimize the requisite number of particles. Even after applying this method, the computational expense of IBM studies is still large. The model in chapter 3 seeks to increase the affordability of IBM studies by transferring some of the calculations to graphics processing units. Chapter 4 describes three algorithms that assist in interpreting IBM output by identifying coherent geographic clusters from population connectivity data. The first two algorithms have existed for nearly a decade and recently been applied separately to marine ecology, and we provide a direct comparison of the results from each. Additionally, we develop and present a new algorithm that simultaneously considers multiple species. Finally, in chapter 5, we apply these tools and a trait-based modeling framework to assess which species traits are most likely to impact dispersal success and patterns in the Gulf of Maine. We conclude that the traits influencing spawning distributions and habitat requirements for settlement are most likely to influence dispersal. / by Benjamin Thomas Jones. / 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. / Quorum sensing (QS) via acylated homoserine lactones (AHLs) was discovered in the ocean, yet little is known about its role in the ocean beyond its involvement in certain symbiotic interactions. The objectives of this thesis were to constrain the chemical stability of AHLs in seawater, explore the production of AHLs in marine particulate environments, and probe selected behaviors which might be controlled by AHL-QS. I established that AHLs are more stable in seawater than previously expected and are likely to accumulate within biofilms. Based on this result, I chose to study AHLQS in the bacterial communities inhabiting biofilms attached to Trichodesmium spp. and detrital (photosynthetically-derived sinking particulate organic carbon, POC) particles. These hot spots of microbial activity are primary sites of interaction between marine primary producers and heterotrophs and crucial components of the biological pump. Biofilm communities associated with Trichodesmium thiebautii colonies in the Sargasso Sea differed considerably from seawater microbial communities. In addition, there was no overlap between the communities associated with tuft and puff colonies. These results suggest that bacterial communities associated with Trichodesmium are not random; rather, Trichodesmium selects for specific microbial flora. Novel 16S rRNA gene sequences are present both in clone libraries constructed from DNA extracted from colonies of Trichodesmium spp. and in culture collections derived from wild and laboratory cultivated Trichodesmium spp., supporting the idea that the phycosphere of Trichodesmium is a unique microenvironment. Using high performance liquid chromatography-mass spectrometry, I demonstrated that bacteria isolated from Trichodesmium synthesize AHLs. In addition, I detected AHLs in sinking particles collected from a site off of Vancouver Island, Canada. AHLs were subsequently added to laboratory cultures of non-axenic Trichodesmium colonies and sinking POC samples. This is the first time AHLs have been detected in POC and indicates that AHL-QS was occurring in POC. Further, I showed that AHLs enhanced certain organic-matter degrading hydrolytic enzyme activities. My results suggest that AHL-QS is a factor regulating biogeochemically relevant enzyme activities on sinking POC and within the biofilms attached to Trichodesmium colonies and thereby may impact the timing and magnitude of biogeochemical fluxes in the ocean. / by Laura Robin Hmelo. / 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), 2005. / Includes bibliographical references. / Minor and trace element records of planktic and benthic foraminifera from Atlantic sediment cores, as well as output from a coupled OAGCM, were used to investigate the magnitude and distribution of the oceanic response to abrupt climate events of the past 20 kyr. The study addressed three major questions: 1) What is the magnitude of high-latitude sea surface temperature and salinity variability during abrupt climate events? 2) Does intermediate depth ventilation change in conjunction with high-latitude climate variability? 3) Are the paleoclimate data consistent with the response of a coupled OAGCM to a freshwater perturbation? To address these questions, analytical methods were implemented for the simultaneous measurement of Mg/Ca, Zn/Ca, Cd/Ca, Mn/Ca and Al/Ca in foraminiferal samples using inductively-coupled plasma mass spectrometry. Paired records of planktic foraminiferal [delta]¹⁸O and Mg/Ca from the subpolar North Atlantic reveal trends of increasing temperatures ([approx.] 3⁰C) and salinities over the course of the Holocene, which were punctuated by abrupt events. The variability does not appear to be periodic, but tends to recur within a broad millennial band. The records provide the first evidence of open-ocean cooling (nearly 2⁰C) and freshening during the 8.2 kyr event, and suggest similar conditions at 9.3 ka. / (cont.) However, the two largest temperature oscillations ([approx.] 2⁰C) occurred during the last 4,000 years, suggesting a recent increase in temperature variability relative to the mid-Holocene. Benthic foraminiferal Cd/Ca from an intermediate depth, western South Atlantic core provides insights into changes in the southward penetration of North Atlantic Intermediate Water (NAIW). Cd seawater estimates (Cdw) for the last glacial are consistent with the production of NAIW and its export into the South Atlantic. At [approx.] 14.5 ka, the NAIW contribution to the South Atlantic began to decrease, marking a transition from a glacial subsurface geometry to a Younger Dryas geometry, which occurred concurrently with the onset of the Bolling-Allerod to Younger Dryas cooling. High Cdw in both the deep North Atlantic and the intermediate South Atlantic imply reduced export of deep and intermediate water during the Younger Dryas, and a major decrease in northward heat transport. Modern subsurface geometry was established at [approx.] 9 ka, concurrently with the establishment of Holocene warmth in the North Atlantic region, further supporting a close linkage between subsurface circulation and North Atlantic climate. / (cont.) Paired benthic foraminiferal Mg/Ca and [delta]¹⁸O data from two intermediate depth low latitude western Atlantic sites - one from the Florida Current and one from the Little Bahama Bank- provide insights into the spatial distribution of intermediate depth temperature and salinity variability during the Younger Dryas. The Florida site lies within the deeper portion of the Florida Current; the Little Bahama Bank site lies within the deeper, unventilated portion of the North Atlantic subtropical gyre. During the Younger Dryas, temperatures increased at the Florida Current site and temperatures decreased at the Little Bahama Bank site. The temperature increase within the Florida Current is consistent with the reduced northward heat transport associated with a reduction in the Atlantic meridional overturning circulation (MOC); the temperature decrease at Little Bahama Bank is consistent with a cooling of high latitude surface waters. To test the possibility that a freshening of the surface North Atlantic caused the terrestrial and oceanographic changes during the Younger Dryas, the GFDL R30 coupled ocean-atmosphere general circulation model was forced using a North Atlantic freshwater perturbation of 0.1 Sv for a period of 100 years. The freshwater flux causes an overall reduction in the Atlantic overturning from 25 Sv to 13 Sv. / (cont.) However, at [approx.] 1,100 meters water depth, ventilation increases, causing decreases in both temperature and salinity throughout much of the intermediate depth North Atlantic. In the open North Atlantic, intermediate depth temperatures decrease by approximately 1⁰C; at the eastern side, intermediate depth temperatures decrease by less than 0.4⁰C. Intermediate depth temperatures at the western boundary, however, increase due to a reduction in northward heat transport, and also due to a shift in the location of the Intertropical Convergence Zone, which causes a reduction in surface salinity and a decrease in the upwelling of colder, deeper waters. Benthic foraminiferal Cd/Ca from an intermediate depth Florida Current core documents the history of the northward penetration of southern source waters within the return flow of the Atlantic meridional overturning circulation (MOC). Cd seawater estimates (Cdw) for the last glacial are consistent with the reduced influence of southern source waters at this location relative to the present. / (cont.) At [approx.] 18.5 ka, the southern source contribution to the Florida Current began to increase significantly, marking the onset of a transition from a glacial circulation pattern to a deglacial pattern, which lasted from [approx.] 17 ka to [approx.] 14 ka. At [approx.] 12.5 ka, following the onset of the Younger Dryas cooling in the North Atlantic and the reduction in North Atlantic Deep Water (NADW) production, the influence of southern source waters within the Florida Current decreased abruptly. A renewed influence of southern source waters occurred at [approx.] 9 ka, concurrent with the establishment of Holocene warmth in the North Atlantic region. / by Rosemarie Evangeline Came. / Ph.D.

Thesis (S.M.)--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 (p. 40-41). / The purpose of this study is to understand the interactions of tropical cyclones with ocean eddies. In particular we examine the influence of a cold-core eddy on the cold wake formed during the passage of Typhoon Fanapi (2010). The three-dimensional version of the numerical Price-Weller-Pinkel (PWP) vertical mixing model has previously been used to simulate and study the cold wakes of Atlantic hurricanes. The model has not been used in comparison with observations of typhoons in the Western Pacific Ocean. In 2010 several typhoons were studied during the Impact of Typhoons on the Ocean in the Pacific (ITOP) field campaign and Fanapi was particularly well observed. We use these observations and the 3DPWP to understand the ocean cold wake generated by Fanapi. The cold wake of Fanapi was advected by a cyclonic eddy that was south of the typhoon track. The 3DPWP model outputs with and without an eddy are compared with observations made during the field campaign. These observations are compared to model outputs with eddies in a series of positions right and left of the storm track in order to study effects of mesoscale eddies on ocean vertical mixing in the cold wake of typhoons. / by Alexander Reid Miltenberger. / S.M.

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), June 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 55-56). / Throughout this thesis we will discuss the theoretical background and empirical observation of a swell band shore normal flux divergence reversal. Specifically, we will demonstrate the existence and persistence of the energy flux divergence reversal in the nearshore region of Atchafalaya Bay, Gulf of Mexico, across storms during the March through April 2010 deployment. We will show that the swell band offshore component of energy flux is rather insignificant during the periods of interest, and as such we will neglect it during the ensuing analysis. The data presented will verify that the greatest flux divergence reversal is seen with winds from the East to Southeast, which is consistent with theories which suggest shoreward energy flux as well as estuarine sediment transport and resuspension prior to passage of a cold front. Employing the results of theoretical calculations and numerical modeling we will confirm that a plausible explanation for this phenomena can be found in situations where temporally varying wind input may locally balance or overpower bottom induced dissipation, which may also contravene the hypothesis that dissipation need increase shoreward due to nonlinear wave-wave interactions and maturation of the spectrum. Lastly, we will verify that the data presented is consistent with other measures collected during the same deployment in the Atchafalaya Bay during March - April 2010. / by Shmuel G. Link. / 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), 2011. / "June 2011." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 253-293). / Sampling the vast volumes of the ocean requires tools capable of observing from a distance while retaining detail necessary for biology and ecology, ideal for optical methods. Algorithms that work with existing SeaBED AUV imagery are developed, including habitat classification with bag-of-words models and multi-stage boosting for rock sh detection. Methods for extracting images of sh from videos of long-line operations are demonstrated. A prototype digital holographic imaging device is designed and tested for quantitative in situ microscale imaging. Theory to support the device is developed, including particle noise and the effects of motion. A Wigner-domain model provides optimal settings and optical limits for spherical and planar holographic references. Algorithms to extract the information from real-world digital holograms are created. Focus metrics are discussed, including a novel focus detector using local Zernike moments. Two methods for estimating lateral positions of objects in holograms without reconstruction are presented by extending a summation kernel to spherical references and using a local frequency signature from a Riesz transform. A new metric for quickly estimating object depths without reconstruction is proposed and tested. An example application, quantifying oil droplet size distributions in an underwater plume, demonstrates the efficacy of the prototype and algorithms. / by Nicholas C. Loomis. / 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 (pages 321-351). / Many chemical constituents are removed from the ocean by attachment to settling particles, a process referred to as "scavenging." Radioisotopes of thorium, a highly particle-reactive element, have been used extensively to study scavenging in the ocean. However, this process is complicated by the highly variable chemical composition and concentration of particles in oceanic waters. This thesis focuses on understanding the cycling of thorium as affected by particle concentration and particle composition in the North Atlantic. This objective is addressed using (i) the distributions 228,230,234 Th, their radioactive parents, particle composition, and bulk particle concentration, as measured or estimated along the GEOTRACES North Atlantic Transect (GA03) and (ii) a model for the reversible exchange of thorium with particles. Model parameters are either estimated by inversion (chapter 2-4), or prescribed in order to simulate 230Th in a circulation model (chapter 5). The major findings of this thesis follow. In chapters 2 and 3, I find that the rate parameters of the reversible exchange model show systematic variations along GA03. In particular, k1 , the apparent first-order rate "constant" of Th adsorption onto particles, generally presents maxima in the mesopelagic zone and minima below. A positive correlation between k, and bulk particle concentration is found, consistent with the notion that the specific rate at which a metal in solution attaches to particles increases with the number of surface sites available for adsorption. In chapter 4, I show that Mn (oxyhydr)oxides and biogenic particles most strongly influence k1 west of the Mauritanian upwelling, but that biogenic particles dominate ki in this region. In chapter 5, I find that dissolved 230Th data are best represented by a model that assumes enhanced values of k, near the seafloor. Collectively, my findings suggest that spatial variations in Th radioisotope activities observed in the North Atlantic reflect at least partly variations in the rate at which Th is removed from the water column. / by Paul Lerner. / 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 (pages [191]-201). / Submesoscale flows, current systems 1-100 km in horizontal extent, are increasingly coming into focus as an important component of upper-ocean dynamics. A range of processes have been proposed to energize submesoscale flows, but which process dominates in reality must be determined observationally. We diagnose from observed flow statistics that in the thermocline the dynamics in the submesoscale range transition from geostrophic turbulence at large scales to inertia-gravity waves at small scales, with the transition scale depending dramatically on geographic location. A similar transition is shown to occur in the atmosphere, suggesting intriguing similarities between atmospheric and oceanic dynamics. We furthermore diagnose from upper-ocean observations a seasonal cycle in submesoscale turbulence: fronts and currents are more energetic in the deep wintertime mixed layer than in the summertime seasonal thermocline. This seasonal cycle hints at the importance of baroclinic mixed layer instabilities in energizing submesoscale turbulence in winter. To better understand this energization, three aspects of the dynamics of baroclinic mixed layer instabilities are investigated. First, we formulate a quasigeostrophic model that describes the linear and nonlinear evolution of these instabilities. The simple model reproduces the observed wintertime distribution of energy across scales and depth, suggesting it captures the essence of how the submesoscale range is energized in winter. Second, we investigate how baroclinic instabilities are affected by convection, which is generated by atmospheric forcing and dominates the mixed layer dynamics at small scales. It is found that baroclinic instabilities are remarkably resilient to the presence of convection and develop even when rapid overturns keep the mixed layer unstratified. Third, we discuss the restratification induced by baroclinic mixed layer instabilities. We show that the rate of restratification depends on characteristics of the baroclinic eddies themselves, a dependence not captured by a previously proposed parameterization. These insights sharpen our understanding of submesoscale dynamics and can help focus future inquiry into whether and how submesoscale flows influence the ocean's role in climate. / by Jörn Callies. / 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), June 2011. / "June 2011." Cataloged from PDF version of thesis. / Includes bibliographical references. / Atmospheric nitrous oxide N₂O concentrations have been rising steadily for the past century as a result of human activities. In particular, human perturbation of the nitrogen cycle has increased the N₂O production rates of the two major sources of this greenhouse gas, soil and the ocean. Nitrification, and particularly ammonia oxidation, is one of the major processes that produces N₂O in the ocean. In this thesis, a series of stable isotopic methods have been used to characterize the biogeochemical controls on N₂O production by marine nitrification as well as the natural abundance stable isotopic signatures of N₂O produced by marine nitrifiers. This thesis shows that in addition to chemical controls on N₂O production rates such as oxygen (O₂) and nitrite (NO₂- ) concentrations, there are also biological controls such as nitrifier cell abundances and coastal phytoplankton blooms that may influence N₂O production by ammonia oxidizers as well. Ammonia oxidizers can produce N₂O through two separate biochemical mechanisms that have unique isotopic signatures. Using culture-based measurements of these signatures, we conclude that one of these pathways, nitrifier-denitrification, may be a significant source of N₂O produced in the South Atlantic Ocean and possibly the global ocean. / by Caitlin Frame. / Ph.D.