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), 2014. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from PDF student-submitted version of thesis. "September 2014." / Includes bibliographical references (pages 191-201). / Synechococcus is a ubiquitous marine primary producer. Our understanding of the factors that determine its abundance has been limited by available observational tools, which have not been able to resolve population dynamics at timescales that match response times of cells (hours-days). Development of an automated flow cytometer (FlowCytobot) has enabled hourly observation of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) since 2003. In order to ascribe changes in cell abundances to either growth or loss processes, information on division rate is needed. I refined a matrix population model that relates diel changes in the distribution of cell volume to division rate and demonstrated that it provides accurate estimates of daily division rate for both cultured and natural populations. Application of the model to the 11-year MVCO time series reveals that division rate is temperature limited during winter and spring, but light limited during fall. Inferred loss rates closely follow division rate in magnitude over the entire seasonal cycle, suggesting that losses are mainly generated by biological processes. While Synechococcus cell abundance, division rate, and loss rate demonstrate striking seasonal patterns, there are also significant shorter timescale variations and important multi-year trends that may be linked to climate. Interpretation of population dynamic patterns is complicated by the diversity found within marine Synechococcus, which is partitioned into 20 genetically distinct clades. Each clade may represent an ecotype, with a distinct ecological niche. To understand how diversity may affect population dynamics, I assessed the diversity at MVCO over annual cycles with culture-independent and dependent approaches. The population at MVCO is diverse, but dominated by clade I representatives throughout the year. Other clades were only found during summer and fall. High through-put sequencing of a diversity marker allowed a more quantitative investigation into these patterns. Five main Synechococcus oligotypes that comprise the population showed seasonal abundance patterns: peaking either during the spring bloom or during late summer and fall. This pattern strongly suggests that features of seasonal abundance are affected by the underlying diversity structure. Synechococcus abundance patterns result from a complex interplay among seasonal environmental changes, diversity, and biological losses. / by Kristen Rachell Hunter-Cevera. / Ph. D.

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. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 87-92). / Observations, theoretical models, and a numerical model (ADCIRC) are used to investigate the effects of tides, waves, bay bathymetry, and changing inlet geometry on the hydrodynamics of the multiple-inlet Katama system, Martha's Vineyard, MA. Momentum fluxes from breaking waves drive water into the inlet, nearly stopping the 2 m/s ebb currents during a hurricane. The evolving morphology of Katama Inlet has a dominant effect on tidal distortion and bay circulation. As Katama inlet lengthened, narrowed, and shoaled between 2011 and 2014, the relative effects of friction (observed and simulated) increased greatly, resulting in reduced circulation energy, an increase in the M6 tidal constituent, and changes in velocity asymmetries that are consistent with an evolution from flood to ebb dominance. The effects of changing inlet parameters (e.g., inlet geometry, bay bathymetry, friction, tidal forcing) are quantified via a lumped element model that accounts for the presence of a shallow flood shoal that limits flow from the ocean into the bay. As the difference in depth between inlet and flood shoal increases, the amplitude and phase of the incoming tide are increasingly modified from predictions without a flood shoal, and flows into the bay are further hindered. / by Mara S. M. Orescanin. / 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. / Driven by increasingly heavy oil reserves and more efficient refining technologies, use of heavy fuel oils for power generation is rising. Unlike other refined products and crude oils, a large portion of these heavy oils is undetectable using the traditional gas chromatography-based techniques on which oil spill science has been based. In the current study, samples collected after the 2007 M/V Cosco Busan heavy fuel oil spill (San Francisco, CA) were analyzed using gas chromatography (GC)-based techniques, numerical modeling and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to examine natural weathering of the oil over a one and a half year period. Traditional GC techniques detected variable evidence of evaporation/ dissolution, biodegradation and photodegradation. Petroleum hydrocarbon compounds smaller than -n-C 16 were rapidly lost due to evaporation and dissolution. Significant biodegradation was not detected until one month post spill while photodegradation was only observed at one field site. To further examine the processes of evaporation and dissolution, samples were analyzed with comprehensive two-dimensional GC (GCxGC) and a physiochemical model developed to approximate quantitative apportionment of compounds lost to the atmosphere and water. Model results suggest temperature is the primary control of evaporation. Finally, to examine the prominent non-GC amenable component of the oil, samples were analyzed with FT-ICR MS. Results showed expected clustering of samples, with those samples collected sooner after the spill having the most compositional similarity to the unweathered oil. Analysis of dominant heteroatom classes within the oil showed losses of high molecular weight species and the formation of stable core structures with time. These results highlight the susceptibility to weathering of these higher molecular weight components, previously believed to be recalcitrant in the environment. Research findings indicate that environmental weathering results in removal or alteration of larger alkylated compounds as well as loss of lower molecular weight species through evaporation/dissolution, biodegradation and photodegradation, with a resultant fraction of stable compounds likely to remain in the environment years after the spill. This research demonstrates the advantages of combining multiple analytical and modeling approaches for a fuller understanding of oil spill chemistry. / by Karin Lydia Lemkau. / 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), 2011. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 63-65). / Remote sensing and in situ observations are used to investigate the ocean response to the Tokar Wind Jet in the Red Sea. The wind jet blows down the pressure gradient through the Tokar Gap on the Sudanese coast, at about 18°N, during the summer monsoon season. It disturbs the prevailing along-sea (southeastward) winds with strong cross-sea (northeastward) winds that can last from days to weeks and reach amplitudes of 20-25 m/s. By comparing scatterometer winds with along-track and gridded sea level anomaly observations, it is shown that an intense dipolar eddy spins up in less than seven days in response to the wind jet. The eddy pair has a horizontal scale of 140 km. Maximum ocean surface velocities can reach 1 m/s and eddy currents extend at least 200 m into the water column. The eddy currents appear to cover the width of the sea, providing a pathway for rapid transport of marine organisms and other drifting material from one coast to the other. Interannual variability in the strength of the dipole is closely matched with variability in the strength of the wind jet. The dipole is observed to be quasi-stationary, although there is some evidence for slow eastward propagation-simulation of the dipole in an idealized high-resolution numerical model suggests that this is the result of self-advection. These and other recent in situ observations in the Red Sea show that the upper ocean currents are dominated by mesoscale eddies rather than by a slow overturning circulation. / by Ping Zhai. / S.M.

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), 2010. / Includes bibliographical references (p. 54-56). / This paper begins to explore a previously neglected mechanism for abyssal ocean mixing using bottom boundary layer dynamics. Abyssal mixing and the associated upward buoyancy fluxes are necessary to balance the sinking of dense waters at high latitudes and to close the global overturning circulation. Previous studies have concentrated on the hypothesis that the primary mechanism for this mixing is breaking internal waves generated by tidal flows over rough topography. However, intriguing observations, particularly from the Brazil Basin Tracer Release Experiment, suggest that mixing in the flank canyons of the Mid-Atlantic Ridge generated when strong mean flows interact with the many sills and constrictions within the canyons may represent a dynamically important amount of abyssal mixing. The energy pathways and mechanisms of this mixing are much less clear than in the case of breaking internal waves. This study attempts to clarify this by suggesting an analogy with an idealized diffusive boundary layer over a sloping bottom. This boundary layer is characterized by up-slope flows powered by the buoyancy flux in the fluid far from the boundary. Here we explore the energy budget of the boundary layer, and find that the diffusive boundary layer provides flows that are generally consistent with those observed in submarine canyons. In addition, we derive the vertical velocity in the far-field fluid, analogous to an Ekman pumping velocity, that these boundary layers can induce when the bottom slope is not constant. Finally, we present both theoretical and numerical models of exchange flows between the bottom boundary and the far-field flow when the bottom slope is not constant. These exchange flows provide a mechanism by which boundary-driven mixing can affect the overall stratification and buoyancy fluxes of the basin interior. / by Rebecca Walsh Dell. / S.M.

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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 68-74). / Coastal barriers are particularly susceptible to the predicted effects of accelerated of sea-level rise and the potential for increased impacts of intense storms. Over centennial scales, barriers are maintained via overtopping during storms, causing deposition of washover fans on their landward sides. This study examines three washover fans on the south shore of Martha's Vineyard using a suite of data including vibracores, ground penetrating radar, high resolution dGPS, and LiDAR data. From these data, the volumes of the deposits were determined and range from 2.1-2.4 x 10⁴ m³. Two overwashes occurred during Hurricane Bob in 1991. The water levels produced by this storm have a return interval of ~28 years, resulting in an onshore sediment flux of 2.4-3.4 m³/m/yr. The third washover was deposited by a nor'easter in January 1997, which has a water level return interval of ~6 years, resulting in a flux of 8.5 m³/m/yr. These fluxes are smaller than the flux of sediment needed to maintain a geometrically stable barrier estimated from shoreline retreat rates, suggesting that the barrier is not in long-term equilibrium, a result supported by the thinning of the barrier over this time interval. / by Emily A. Carruthers. / 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), February 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 327-334). / In the present work, we study the statistics of wavefields obtained from non-linear phase-resolved simulations. The numerical model used to generate the waves models wave-wave interactions based on the fully non-linear Zakharov equations. We vary the simulated wavefield's input spectral properties: directional spreading function, Phillips parameter and peak shape parameter. We then investigate the relationships between a wavefield's input spectral properties and its output physical properties via statistical analysis. We investigate surface elevation distribution, wave definition methods in a nonlinear wavefield with a two-dimensional wavenumber, defined waves' distributions, and the occurrence and spacing of large wave events. / by Legena Albertha Henry. / S.M.

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 (pages 185-213). / In this thesis, I use coastal measurements of dissolved O₂ and inert gases to provide insight into the chemical, biological, and physical processes that impact the oceanic cycles of carbon and dissolved gases. Dissolved O₂ concentration and triple isotopic composition trace net and gross biological productivity. The saturation states of inert gases trace physical processes, such as air-water gas exchange, temperature change, and mixing, that affect all gases. First, I developed a field-deployable system that measures Ne, Ar, Kr, and Xe gas ratios in water. It has precision and accuracy of 1 % or better, enables near-continuous measurements, and has much lower cost compared to existing laboratory-based methods. The system will increase the scientific community's access to use dissolved noble gases as environmental tracers. Second, I measured O₂ and five noble gases during a cruise in Monterey Bay, California. I developed a vertical model and found that accurately parameterizing bubble-mediated gas exchange was necessary to accurately simulate the He and Ne measurements. I present the first comparison of multiple gas tracer, incubation, and sediment trap-based productivity estimates in the coastal ocean. Net community production estimated from ¹⁵NO₃⁻ uptake and 02 /Ar gave equivalent results at steady state. Underway O₂/Ar measurements revealed submesoscale variability that was not apparent from daily incubations. Third, I quantified productivity by O₂ mass balance and air-water gas exchange by dual tracer (³He/SF₆ ) release during ice melt in the Bras d'Or Lakes, a Canadian estuary. The gas transfer velocity at >90 % ice cover was 6 % of the rate for nearly ice-free conditions. Rates of volumetric gross primary production were similar when the estuary was completely ice-covered and ice-free, and the ecosystem was on average net autotrophic during ice melt and net heterotrophic following ice melt. I present a method for incorporating the isotopic composition of H₂O into the O₂ isotope-based productivity calculations, which increases the estimated gross primary production in this study by 46-97 %. In summary, I describe a new noble gas analysis system and apply O₂ and inert gas observations in new ways to study chemical, biological, and physical processes in coastal waters. / by Cara Charlotte Marie Manning. / Ph. D.

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 (S.M. in Biology)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references (leaves 23-30). / Phytoplankton mortality (herbivory) and bacterivory were examined experimentally in West Neck Bay and Coecles Harbor, Long Island, NY from April through September, 1998. Small algae (<5 [tm diameter) dominated phytoplankton communities in both ecosystems throughout the summer, and zooplankton were also small (mostly <40 tm). Generally, plankton abundances were indicative of eutrophic ecosystems. Oscillations in standing stocks and mortality of prey indicated tight coupling of growth and grazing mortality in both bays. Phytoplankton mortality rates accounted for the removal of 14% to 65% of total phytoplankton standing stocks daily, while bacterivory accounted for the removal of 14% to 88% of total bacterial standing stocks daily. Estimates of carbon consumption revealed high energy flux through the nano- and microzooplankton assemblages of these estuarine environments. / by Katie Rose Boissonneault Cellineri. / S.M.in Biology