Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / "June 2009." / Includes bibliographical references. / Marine cyanobacteria in the genus Synechococcus are widely distributed and contribute significantly to global primary productivity. In many parts of the ocean their growth is limited by a lack of iron, an essential nutrient that is virtually insoluble in seawater. To overcome this, Synechococcus have evolved a number of strategies to acquire iron. Gene distribution, metagenomics and a novel immunological flow cytometry assay in the Costa Rica Upwelling Dome were used to estimate the importance of Fe stress. Genomic and metagenomic measures suggest that iron limitation is, paradoxically, more severe in coastal and upwelling areas than in the open ocean, where iron is less abundant. A serological assay found significant differences in the vertical distribution of the Fe stress protein IdiA over just a few meters. Despite average surface ocean iron concentrations of just 0.07 nM, most marine oligotrophic cyanobacteria lack iron-binding siderophores that are present in many heterotrophic marine bacteria. Siderophores are widely distributed in the surface ocean and compose an important portion of the pool of natural ligands that bind >99% of all soluble Fe. In bottle incubations from the Sargasso Sea we found the addition of Fe complexed to an excess of the siderophore desferrioxamine B (DFB) limited Synechococcus growth and stimulated the growth of heterotrophic bacteria in a concentration dependent manner. / (cont.) Laboratory work revealed that excess DFB decreased Synechococcus growth beyond Fe-limited controls at concentrations as low as 20-40 nM. The inhibition was aggravated by light but it could be reversed by the addition of Fe. The DFB inhibition could not be explained by thermodynamic or kinetic models of Fe' or co-limitation with other metals. DFB may interact with some aspect of cellular physiology to directly inhibit cyanobacterial growth. / by Adam R. Rivers. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, and the Woods Hole Oceanographic Institution), 2002. / Vita. / Includes bibliographical references. / Photochemical transformations of chromophoric dissolved organic matter (CDOM) are one of the principal processes controlling its fate in coastal waters. The photochemical decomposition of CDOM leads to the formation of a variety of biologically available carbon substrates. Photomineralization of CDOM to dissolved inorganic carbon may constitute a significant flux in the global carbon cycle. Photoreactions ultimately lead to the destruction of the chromophores and hence to the loss of absorption and fluorescence (bleaching), thus acting as a sink for CDOM. Photodecomposition may proceed both via direct photochemical reactions, following absorption of photons by CDOM, or via indirect processes, involving DOM reactions with photochemically generated intermediates such as reactive oxygen species (ROS). The reactions of CDOM with two important ROS, superoxide (02-) and hydroxyl radical (OH), have different consequences. Superoxide reactions with CDOM did not appear to degrade the CDOM. Instead, CDOM catalysed the dismutation of 02- to 02 and HOOH. This reactivity has the effect of limiting the steady-state concentration of 02- in most coastal waters. In contrast, reactions of CDOM with radiolytically produced OH formed CO2 and several low molecular weight carboxylic acids, as well as bleached both the absorption and fluorescence at slow rates. These reactions did not increase the bioavailability of this material to a microbial consortium. Both direct and indirect photochemical processes are expected to be accelerated by the presence of iron. / (cont.) However, addition of iron to several coastal seawater samples neither increased the rate of photobleaching nor the apparent quantum yield (AQY) of CO. Similarly, the addition of the siderophore desferrioxamine B did not change the photobleaching rates or the CO AQYs. The addition of 2[mu]M Fe to solutions of Suwannee River Fulvic Acid did not increase the photobleaching rates. In combination with prior results, these findings suggest that indirect photoreactions do not increase the photobleaching rates of CDOM in coastal systems. A model of CDOM photobleaching based on the assumption of negligible indirect photobleaching processes and multiple non-interacting chromophores was created utilizing photobleaching data produced with monochromatic light to calculate the spectra and exponential decay rates of independent components. These components were then used to calculate bleaching spectra for broadband light and compared with actual bleaching spectra. / by Jared Verrill Goldstone. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references. / The marine cyanobacteria Synechococcus and Prochlorococcus are important primary producers in oligotrophic oceans. The abundance and cell division rates of these cyanobacteria can be influenced by trace metals such as iron and copper. Iron is an essential trace metal that is present in the high nutrient, low chlorophyll waters of the equatorial Pacific in extremely low concentrations. When these waters were enriched with iron, Prochlorococcus chlorophyll fluorescence per cell and cell size increased. Cell division rates doubled inside the iron enriched patch and reached two divisions per day in bottle incubations with additional iron, indicating that Prochlorococcus were iron limited. However, cell numbers remained constant because mortality rates nearly doubled after the addition of iron and essentially matched the increases in cell division rate. Trace metals can also be present in toxic, rather than limiting concentrations. Copper is an essential trace element that is toxic to cyanobacteria in pM quantities. In stratified water columns in the Sargasso Sea, free Cu2+ concentrations are high in the mixed layer (up to 6pM) and most of the Prochlorococcus population is located below the thermocline where free Cu2+ concentrations are lower. The distribution of Synechococcus is more uniform with depth. Prochlorococcus isolates were more sensitive to copper than Synechococcus, but members of the low chi BIA (high light adapted) ecotype were less sensitive than strains with high chi BIA ratios (low light adapted). In the field, the in situ concentration of free Cu2+ had a strong effect on the copper sensitivity of Prochlorococcus. Net growth rates were substantially reduced when Prochlorococcus from environments where the in situ free Cu2+ was low (deep mixed layers and below the thermocline in stratified water) were exposed to copper. Prochlorococcus in shallow mixed layers where in situ Cu2 + was high were less sensitive to copper and may have been members of the copper resistant low chi B/ A ecotype. Synechococcus were relatively copper resistant across a range of environments. These data are consistent with the hypothesis that ambient copper levels may influence the relative abundance of Prochlorococcus and Synechococcus in the Sargasso Sea. / by Elizabeth Lowell Mann. / Ph.D.

Thesis (S.M.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references. / Paleoclimate records with sufficient length and temporal resolution to study the occurrence and causal mechanisms of abrupt climate change are exceedingly rare. Rapidly deposited ocean sediments provide the best archive for studying these events through geologic time, but such sites in the open ocean are limited to sediment drift deposits such as the Bermuda Rise in the northwest Atlantic. Using multiple climate proxies in a single core is becoming more common in high-resolution paleoclimate investigations, but a major potential concern for this approach arises from the possibility that the fine fraction of sediment (< 63 [micro]m), and the climate proxies within it, may represent conditions far from the deposition site. We hypothesize that hydrogen isotope ratios of alkenones, a class of lipids from phytoplankton, may provide insight into the source of fine fraction sediment. Because of their restricted sources, broad geographic distribution, and excellent preservation properties, alkenones are of particular interest in the emerging field of' compound-specific hydrogen isotopic analysis, and the sedimentary abundances, extents of unsaturations, and isotopic compositions of alkenones provide quantitative and near-continuous records. We isolated alkenones from cultured unicellular algae (haptophyte Emiliania huxleyi), surface ocean particulate material, and open ocean sediments to determine the extent and variability of hydrogen isotopic fractionation in the di-, tri-, and tetraunsaturated C₃₇ compounds. We then compared the [delta]D of the alkenones in surface sediments between the Bermuda Rise and the Scotian Margin above which a large ([approximately]20%) [delta]D gradient exists. We determined the fractionation between alkenones / (cont.) from suspended particulate samples and the water in which the phytoplanton lived, and examined the variability of alkenone 6D during key climate transitions at the Bermuda Rise. / by Amy C. Englebrecht. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences and the Woods Hole Oceanographic Institution, 1986. / Microfiche copy available in Archives and Science. / Vita. / Bibliography: leaves 271-297. / by Bruce J. Brownawell. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanographic Engineering (Massachusetts Institute of Technology, Dept. of Civil Engineering; and the Woods Hole Oceanographic Institution), 1989. / Includes bibliographical references (leaves 140-145). / The relationship between depth-averaged velocity and bottom stress for wind-driven flow in unstratified coastal waters is examined here. The adequacy of traditional linear and quadratic drag laws is addressed by comparison with a 2 1/2-D model. A 2 1/2-D model is one in which a simplified 1-D depth-resolving model (DRM) is used to provide an estimate of the relationship between the flow and bottom stress at each grid point of a depth-averaged model (DAM). Bottom stress information is passed from the DRM to the DAM in the form of drag tensor with two components: one which scales the flow and one which rotates it. This eliminates the problem of traditional drag laws requiring the flow and bottom stress to be collinear. In addition, the drag tensor field is updated periodically so that the relationship between the velocity and bottom stress can be time-dependent. However, simplifications in the 2 1/2-D model that render it computationally efficient also impose restrictions on the time-scale of resolvable processes. Basically, they must be much longer than the vertical diffusion time scale. Four progressively more complicated scenarios are investigated. The important factors governing the importance of bottom friction in each are found to be 1) non-dimensional surface Ekman depth ... is the surface shear velocity, f is the Coriolis parameter and h is the water depth 2) the non-dimensional bottom roughness, zo/h where zo is the roughness length and 3) the angle between the wind stress and the shoreline. Each has significant influence on the drag law. The drag tensor magnitude, r, and the drag tensor angle, 0 are functions of all three, while a drag tensor which scales with the square of the depth-averaged velocity has a magnitude, Cd, that only depends on zo/h. The choice of drag law is found to significantly affect the response of a domain. Spin up times and phase relationships vary between models. In general, the 2 1/2-D model responds more quickly than either a constant r or constant Cd model. Steady-state responses are also affected. The two most significant results are that failure to account for 0 in the drag law sometimes leads to substantial errors in estimating the sea surface height and to extremely poor resolution of cross-shore bottom stress. The latter implies that cross-shore near-bottom transport is essentially neglected by traditional DAMs. / by Harry Leonard Jenter, II. / 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), 2009. / Includes bibliographical references. / Tropical cyclone activity over the last 5000 years is investigated using overwash sediments from coastal lagoons on the islands of Vieques, Puerto Rico and Koshikijima, Japan. A simple sediment transport model can reproduce the landward fining deposits observed at Vieques, and reveals that although the record exhibits centennial-tomillennial changes in hurricane overwash frequency, the magnitude of these flooding events has remained relatively constant. Stochastic simulations of hurricane overwash show that breaks in activity at Vieques are extremely long and unlikely to occur under the current hurricane climatology and the present barrier morphology. Periods of less frequent hurricane deposition at Vieques are contemporaneous with intervals of increased El Nifio occurrences and reduced precipitation in West Africa, suggesting a dominant influence by these two climatic phenomena. Hiatuses in overwash activity between 3600-to-2500 and 1000-500 years ago are longer than what is generated by overwash simulations under a constant El Niflo-like state, indicating that mechanisms in addition to variability in the El Nifio/Southern Oscillation are required to completely produce the overwash variability at Vieques. Periods of low overwash activity at Vieques are concurrent with increased overwash activity at Kamikoshiki and may indicate a correspondence between tropical cyclone activity in the western Northern Atlantic and the western North Pacific. / by Jonathan D. Woodruff. / 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), 2008. / Includes bibliographical references. / In this thesis, I provide quantitative descriptions of toothed whale echolocation and foraging behavior, including assessment of the effects of noise on foraging behavior and the potential influence of ocean acoustic propagation conditions on biosonar detection ranges and whale noise exposure. In addition to presenting some novel basic science findings, the case studies presented in this thesis have implications for future work and for management. In Chapter 2, I describe the application of a modified version of the Dtag to studies of harbor porpoise echolocation behavior. The study results indicate how porpoises vary the rate and level of their echolocation clicks during prey capture events; detail the differences in echolocation behavior between different animals and in response to differences in prey fish; and show that, unlike bats, porpoises continue their echolocation buzz after the moment of prey capture. Chapters 3-4 provide case studies that emphasize the importance of applying realistic models of ocean acoustic propagation in marine mammal studies. These chapters illustrate that, although using geometric spreading approximations to predict communication/target detection ranges or noise exposure levels is appropriate in some cases, it can result in large errors in other cases, particularly in situations where refraction in the water column or multi-path acoustic propagation are significant. Finally, in Chapter 5, I describe two methods for statistical analysis of whale behavior data, the rotation test and a semi-Markov chain model. I apply those methods to test for changes in sperm whale foraging behavior in response to airgun noise exposure. Test results indicate that, despite the low-level exposures experienced by the whales in the study, some (but not all) of them reduced their buzz production rates and altered other foraging behavior parameters in response to the airgun exposure. / by Stacy Lynn DeRuiter. / Ph.D.

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), 2009. / Includes bibliographical references (p. 271-277). / The Basin Acoustic Seamount Scattering Experiment (BASSEX) of 2004 was conducted to measure forward-scattering around the Kermit-Roosevelt Seamount Complex in the Northeast Pacific. The BASSEX experiment was focused on the bathymetric effects on acoustic propagation, in particular, on direct blockage, horizontal refraction, diffraction, and scattering by the seamounts. A towed hydrophone array, with 64 sensors cut for 250Hz (3m spacing), was used to measure the signals transmitted from the aforementioned broadband sources at many locations around the Kermit-Roosevelt and Elvis seamounts. Utilizing the measured broadband signals from the towed array, the size of the shadow zone was obtained. The measured data in the BASSEX experiment strongly support the understanding of the complicated phenomena of sound propagation around the seamounts. In addition, the experimental data could be used to validate current 2D and 3D theoretical models and develop new models to properly realize the sound propagation with such complicated phenomena. In this thesis, the reconciliation between the measured pulse arrivals from the BASSEX experiment and various two-dimensional (2D) and three-dimensional (3D) theoretical models is carried out to investigate the physical characteristics of the sound propagation around seamounts: First, the 2D Parabolic Equation (PE) model and the 2D ray tracing model are used to reconcile each ray arrival with the BASSEX experiment in terms of arrival time and grazing angle. / (cont.) We construct a sound speed field database based on the sound speed profiles from the BASSEX experiment, World Ocean Atlas (WOA) 2005, and CTD casts using the objective analysis. Second, 3D broadband sound propagation around a conical seamount is investigated numerically using the 3D spectral coupled-mode model (W. Luo, PhD Thesis, MIT, 2007). Since the calculation of 3D broadband pulses with the spectral coupled-mode model requires extensive computation time, a parallel program is developed with a clustered computing system to obtain results in reasonable time. The validation of the 3D spectral coupled-mode model is performed by a series of comparisons between the various 2D and 3D models for a shallow-water waveguide. The Kermit-Roosevelt seamount is modeled by a simple conical seamount for the 3D model. The computed 3D broadband pulses for the modeled conical seamount are compared with those from the BASSEX experiment and the 2D PE simulation. Through this analysis, we examine the limit of the application of the sound propagation models and improve the efficiency of the 3D sound propagation model using parallel computing to obtain a broadband pulse in a reasonable amount of time. / by Hyun Joe Kim. / 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), 2008. / Page 362 blank. / Includes bibliographical references. / Understanding how organisms deal with potentially toxic or fitness-reducing allelochemicals is important for understanding patterns of predation and herbivory in the marine environment. The ability of marine consumers to tolerate dietary toxins may involve biochemical resistance mechanisms, which increase the hydrophilicity of compounds and facilitate their active efflux out of sensitive cells and tissues. While several allelochemical-responsive detoxification enzymes have been sequenced and functionally characterized in terrestrial invertebrates feeding on chemically defended host plants, there is virtually no information concerning the role of these biotransformation enzymes that may mediate feeding tolerance in marine invertebrates. The objective of this research was to assess the diversity and dietary regulation of cytochrome P450s (CYP), glutathione S-transferases (GST) and ABC transporters in the generalist marine gastropod Cyphoma gibbosum feeding on a variety of chemically defended gorgonian corals, and to identify those dietary natural products that act as substrates for these proteins. Molecular and proteomic techniques identified both allelochemically-responsive CYPs, and constitutively expressed GSTs and transporters in Cyphoma digestive glands. Inhibition of Cyphoma GST activity by gorgonian extracts and selected allelochemicals (i.e., prostaglandins) indicated that gorgonian diets are likely to contain substrates for molluscan detoxification enzymes. In vitro metabolism studies with recombinant CYPs suggested those Cyphoma enzymes most closely related to vertebrate fatty acid hydroxylating enzymes may contribute to the detoxification ofichthyodeterrent cyclopentenone prostaglandins found in abundance in selected gorgonian species. / (cont.) Finally, the presence and activity of multixenobiotic resistance transporters in Cyphoma and the co-occurring specialist nudibranch, Tritonia hamnerorum, suggests these efflux transporters could function as a first line of defense against dietary intoxication. Together, these results suggest marine consumers that regularly exploit allelochemical-rich prey have evolved both general (GST and ABC transporters) and allelochemical-specific (CYP) detoxification mechanisms to tolerate prey chemical defenses. / by Kristen Elizabeth Whalen. / Ph.D.