Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 229-238). / The fate of trace metals in contaminated coastal sediments is poorly understood, yet critical for effective coastal management. The aim of this thesis is to investigate and quantify the mechanisms leading to the release of silver, lead and copper across the sediment-water interface. Two contrasting sites were investigated, a heavily contaminated site in Boston Harbor and a less impacted, offshore site in Massachusetts Bay. High-resolution porewater and solid phase samples were collected in each season to determine the diagenetic cycles and chemistry controlling the fate of these metals. The trace metals are scavenged by iron oxyhydroxides and released to the porewaters when these oxides are reduced. At the strongly reducing site in Boston Harbor, there is seasonal transfer of trace metals from oxide phases in winter, to sulfides phase in summer. At the Massachusetts Bay site, due to the lack of sulfide, the metals are focused into the surface oxide layer, giving a solid phase enrichment. There is a diffusive flux of copper to the water column throughout the year, while silver is released only in winter. Lead is strongly scavenged and is rarely released to the overlying waters. / (cont.) Analysis of reduced sulfur compounds in the porewaters has shown that there is also a significant flux of these strong ligands to the overlying waters. Polysulfide species enhance the solubility of copper within the porewaters. Sediment resuspension fluxes were quantified using an erosion chamber. Sediment resuspension leads to enhanced release of dissolved metals and is especially important in redistributing contaminants as the first particles to be eroded are enriched in trace metals. The total release of dissolved metals from the sediments by diffusion and sediment resuspension is estimated to be 60% and 10% of the riverine flux for copper and lead respectively. With continued pollution control reducing the discharge of metals from other sources, the benthic release of metals will become increasingly important terms in the metal budget of Boston Harbor. / by Linda H. Kalnejais. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and, the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references. / The goal of this thesis is to investigate three different areas relating to the characterization of dissolved organic matter (DOM): further determination of the chemical compounds present in high molecular weight DOM (HMWDOM), the cycling of individual compounds within the HMWDOM pool, and the biological controls on DOM release. The first section of this thesis provided additional molecular level characterization of HMWDOM. While some individual components have been identified, the total yield of compounds isolated is much smaller than the amount expected by spectroscopic analysis by nuclear magnetic resonance (NMR) spectroscopy. Since the majority of the as-yet unidentified carbon was inferred to be carbohydrate, periodate over-oxidation was used to analyze this fraction. Analysis of both surface and deep water HMWDOM samples indicated that the majority of the carbon present was periodate over-oxidizable, including 70% of the aliphatic NMR signal. Comparison of the periodate demand for HMWDOM versus that for linear glucopolysaccharide standards indicated that HMWDOM had a greater degree of branching. Based on the changes in the H NMR spectra during the reaction, it was concluded that 6-deoxysugars were the primary compounds in the unidentified fraction of HMWDOM. Compound specific radiocarbon analysis can provide information about the cycling and relative ages for individual HMWDOM components. In the second section of this thesis, a new method was presented for the purification of individual underivatized amino acids hydrolyzed from HMWDOM. / (cont.) This new separation protocol utilized various chromatographic techniques, including cation exchange chromatography and high- pressure liquid chromatography (HPLC) using C18 and strong cation exchange (SCX) columns. Six amino acids were isolated from a HMWDOM sample with sufficient purity and quantity for radiocarbon analysis. These amino acids had a range of A'4C values, from 121%o to -454%o. The final section investigates biological controls on the dissolved organic nitrogen (DON) pool. Total hydrolyzable amino acids (THAA), and nucleic acids were measured for four incubations: a control incubation, a grazer added incubation, a zero virus incubation, and a 10 times virus incubation. Comparison to the control showed THAA and nucleic acid release were influenced by viruses but not grazers. / by Tracy M. Quan. / Ph.D.

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Zinc (Zn) stable isotopes can record information about important oceanographic processes. This thesis presents data on Zn isotopes in anthropogenic materials, hydrothermal fluids and minerals, cultured marine phytoplankton, natural plankton, and seawater. By measuring Zn isotopes in a diverse array of marine samples, we hope to understand how Zn isotopes are fractionated in the oceans and how Zn isotopes may be used as tracers of marine biogeochemical processes. Common forms of anthropogenic Zn had [delta]66Zn from +0.08 %o to +0.32 %o, a range similar to Zn ores and terrigenous materials. Larger variations were discovered in hydrothermal fluids and minerals, with hydrothermal fluids ranging in 666Zn from 0.02 %o to +0.93 %o, and chimney minerals ranging from -0.09 %o to +1.17 %o. Lower-temperature vent systems had higher [delta]666Zn values, suggesting that precipitation of isotopically light Zn sulfides drives much of the Zn isotope fractionation in hydrothermal systems. In cultured diatoms, a relationship was discovered between Zn transport by either high-affinity or low-affinity uptake pathways, and the magnitude of Zn isotope fractionation. We established isotope effects of [delta]66Zn = -0.2 %o for high-affinity uptake and [delta]66Zn = -0.8 %o for low-affinity uptake. This work is the first to describe the molecular basis for biological fractionation of transition metals. Biological fractionation of Zn isotopes under natural conditions was investigated by measuring Zn isotopes in plankton collected in the Peru Upwelling Region and around the world. / (cont.) Seawater dissolved Zn isotopes also reflect the chemical and biological cycling of Zn. The [delta]66Zn of deep seawater in the North Pacific and North Atlantic is about 0.5%0, and the dissolved [delta]66Zn gets lighter in the upper water column. This is unexpected based our observations of a biological preference for uptake of light Zn isotopes, and suggests that Zn transport to deep waters may occur by Zn adsorption to sinking particles rather than as primary biological Zn. The thesis, by presenting data on several important aspects of Zn isotope cycling in the oceans, lays the groundwork for further use of Zn isotopes as a marine biogeochemical tracer. / by Seth Greeley John. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), February 2000. / Includes bibliographical references. / Benthic foraminiferal δ13C, Cd/Ca, and Ba/Ca are important tools for reconstructing nutrient distributions, and thus ocean circulation, on glacial-interglacial timescales. However, each tracer has its own "artifacts" that can complicate paleoceanographic interpretations. It is therefore advantageous to measure multiple nutrient proxies with the aim of separating the various complicating effects. Zn/Ca is introduced as an important aid toward this goal. Benthic (Hoeglundina elegans) Cd/Ca ratios from the Bahama Banks indicate that the North Atlantic subtropical gyre was greatly depleted in nutrients during the last glacial maximum (LGM). A high-resolution Cd/Ca record from 965 m water depth suggests that Glacial North Atlantic Intermediate Water formation was strong during the LGM, weakened during the deglaciation, and strengthened again during the Younger Dryas cold period. Comparison of Cd/Ca and δ13C data reveals apparent short-term changes in carbon isotopic air-sea signatures. Benthic foraminiferal Zn/Ca could be a sensitive paleoceanographic tracer because deep water masses have characteristic Zn concentrations that increase about ten-fold from the deep North Atlantic to the deep North Pacific. A "core top calibration" shows that Zn/Ca is controlled by bottom water dissolved Zn concentration and, like Cd/Ca and BalCa, by bottom water saturation state with respect to calcite Since Zn/Ca responds to a different range of saturation states than Cd/Ca, the two may be used together to evaluate changes in deep water carbonate ion (CO32- ) concentration. Zn/Ca and Cd/Ca ratios in the benthic foraminifer Cibicidoides wuellerstorfi exhibit large fluctuations over the past 100,000 years in a deep (3851 m) eastern equatorial Pacific sediment core. The data imply that bottom water CO32- concentrations were lowest during glacial Marine Isotope Stage 4 and highest during the last deglaciation. LGM CO32- concentrations appear to have been within a few μmol kg-1 of modern values. Deep North Atlantic Cd/Ca ratios imply much higher nutrient concentrations during the LGM. Although such data have usually been explained by a northward penetration of Southern Ocean Water (SOW), it has been suggested that they could result from increased preformed nutrient levels in the high-latitude North Atlantic or by increased aging of lower North Atlantic Deep Water (NADW). Glacial Zn/Ca data, however, require a substantially increased mixing with SOW and thus a reduction in NADW formation. Large changes in carbon isotopic air-sea exchange are invoked to reconcile benthic δ13C and trace metal data. / by Thomas Mathew Marchitto, Jr. / Ph.D.

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references. / This thesis explores the potential of zinc, cobalt, and phosphorus to influence primary production in the subarctic North Pacific, the Bering Sea, and the North Atlantic Ocean. In the North Pacific and Bering Sea, total zinc concentrations were measured along a near-surface transect and in selected deep profiles. Zinc speciation was also measured with a novel anodic stripping voltammetry method, and the results were consistent with previous studies using different methods. The potential for zinc to impact primary production in the North Pacific was demonstrated in a shipboard incubation and by comparing two phytoplankton pigment markers to total zinc and free zinc ion concentrations. In the North Atlantic, total dissolved zinc and cobalt concentrations were measured and compared to concentrations of dissolved inorganic phosphorus and chlorophyll. In some areas of the North Atlantic the concentrations of zinc and cobalt were decoupled.The relationship between cobalt and inorganic phosphorus suggests that cobalt drawdown may be related to a high alkaline phosphatase related demand at low phosphorus concentrations. This trend compliments a shipboard incubation where alkaline phosphatase activities increased after cobalt addition. The presence of measurable alkaline phosphatase activity indicated that the phytoplankton community in the Sargasso Sea was experiencing phosphorus stress. Shipboard incubations generally confirmed this with inorganic phosphorus additions resulting in chlorophyll increases at 4 out of 5 stations. Further, the addition of dissolved organic phosphorus, as either a phosphate monoester or a phosphonate compound, resulted in a chlorophyll increase in 3 out of 3 incubations. This suggests that dissolved organic phosphorus may be an important phosphorus source for phytoplankton in low phosphorus environments and that the ability to use phosphonates may be more widespread than previously recognized. Overall, this thesis adds to our understanding of how the nutrients phosphorus, zinc, and cobalt may influence primary production. / by Rachel J. Wisniewski. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (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. / The sinking flux of particulate matter into the ocean interior is an oceanographic phenomenon that fuels much of the metabolic demand of the subsurface ocean and affects the distribution of carbon and other elements throughout the biosphere. In this thesis, I use a new suite of observations to study the dynamics of marine particulate matter at the contrasting sites of the subtropical Sargasso Sea near Bermuda and the waters above the continental shelf of the Western Antarctic Peninsula (WAP). An underwater digital camera system was employed to capture images of particles in the water column. The subsequent analysis of these images allowed for the determination of the particle concentration size distribution at high spatial, depth, and temporal resolutions. Drifting sediment traps were also deployed to assess both the bulk particle flux and determine the size distribution of the particle flux via image analysis of particles collected in polyacrylamide gel traps. The size distribution of the particle concentration and flux were then compared to calculate the average sinking velocity as a function of particle size. I found that the average sinking velocities of particles ranged from about 10-200 m d- and exhibited large variability with respect to location, depth, and date. Particles in the Sargasso Sea, which consisted primarily of small heterogeneous marine snow aggregates, sank more slowly than the rapidly sinking krill fecal pellets and diatom aggregates of the WAP. Moreover, the average sinking velocity did not follow a pattern of increasing velocities for the larger particles, a result contrary to what would be predicted from a simple formulation of Stokes' Law. At each location, I derived a best-fit fractal correlation between the flux size distribution and the total carbon flux. The use of this relationship and the computed average sinking velocities enabled the estimation of particle flux from measurements of the particle concentration size distribution. This approach offers greatly improved spatial and temporal resolution when compared to traditional sediment trap methods for measuring the downward flux of particulate matter. Finally, I deployed specialized in situ incubation chambers to assess the respiration rates of microbes attached to sinking particles. I found that at Bermuda, the carbon specific remineralization rate of sinking particulate matter ranged from 0.2 to 1.1 d', while along the WAP, these rates were very slow and below the detection limit of the instruments. The high microbial respiration rates and slow sinking velocities in the Sargasso Sea resulted in the strong attenuation of the flux with respect to depth, whereas the rapid sinking velocities and slow microbial degradation rates of the WAP resulted in nearly constant fluxes with respect to depth. / by Andrew M. P. McDonnell. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (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. / The distribution and magnitude of marine primary production helps determine the ocean's role in global carbon cycling. Constraining factors that impact this productivity and elucidating selective pressures that drive the composition of marine microbial communities are thus essential aspects of marine biogeochemistry. Vitamin B₁₂, also known as cobalamin, is a cobalt containing organometallic micronutrient produced by some bacteria and archaea and required by many eukaryotic phytoplankton for methionine biosynthesis and regeneration. Although the potential for vitamin B₁₂ availability to impact primary production and phytoplankton species composition has long been recognized, the lack of molecular-level tools for studying B₁₂ production, use and acquisition has limited inquiry into the role of the vitamin in marine biogeochemical processes. This thesis describes the development of such tools and implements them for the study of B₁₂ dynamics in an Antarctic shelf ecosystem. Nucleic acid probes for B₁₂ biosynthesis genes were designed and used to identify a potentially dominant group of B₁₂ producers in the Ross Sea. The activity of this group was then verified by mass spectrometry-based peptide measurements. Then, possible interconnections between iron and B₁₂ dynamics in this region were identified using field-based bottle incubation experiments and vitamin uptake measurements, showing that iron availability may impact both B₁₂ production and consumption. Changes in diatom proteomes induced by low B₁₂ and low iron availability were then examined and used to identify a novel B₁₂ acquisition protein, CBA1, in diatoms. This represents the first identification of a B₁₂ acquisition protein in eukaryotic phytoplankton. Transcripts encoding CBA 1 were detected in natural phytoplankton communities, confirming that B₁₂ acquisition is an important part of phytoplankton molecular physiology. Selected reaction monitoring mass spectrometry was used to measure the abundance of CBA1 and methionine synthase proteins in diatoms cultures, revealing distinct protein abundance patterns as a function of B₁₂ availability. These peptide measurements were implemented to quantify methionine synthase proteins in McMurdo Sound, revealing that there is both B₁₂ utilization and starvation in natural diatom communities and that these peptide measurements hold promise for revealing the metabolic status of marine ecosystems with respect to vitamin B₁₂. / by Erin Marie Bertrand. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 143-154). / The physical environment in the oceans dictates not only how phytoplankton cells are dispersed and their populations intermingled, but also mediates the supply of nutrients to the surface mixed layer. In this thesis I explore both of these aspects of the interaction between phytoplankton ecology and ocean physics, and have approached this topic in two distinct but complementary ways, working with a global ocean ecosystem model, and collecting data at sea. In the first half of the thesis, I examine the role of mesoscale physical features in shaping phytoplankton community structure and influencing rates of primary production. I compare the output of a complex marine ecosystem model coupled to coarse resolution and eddy-permitting physical models. Explicitly resolving eddies resulted in marked regional variations in primary production, zooplankton and phytoplankton biomass. The same phytoplankton phenotypes persisted in both cases, and were dominant in the same regions. Global phytoplankton diversity was unchanged. However, levels of local phytoplankton diversity were markedly different, with a large increase in local diversity in the higher resolution model. Increased diversity could be attributed to a combination of enhanced dispersal, environmental variability and nutrient supply in the higher resolution model. Diversity "hotspots" associated with western boundary currents and coastal upwelling zones are sustained through a combination of all of these factors. In the second half of the thesis I describe the results of a fine scale ecological and biogeochemical survey of the Kuroshio Extension Front. I found fine scale patterns in physical, chemical and biological properties that can be linked back to both the large scale horizontal and smaller scale vertical physical dynamics of the study region. A targeted genomic analysis of samples focused on the ecology of the picoeukaryote Ostreococcus clade distributions strongly supports the model derived hypotheses about the mechanisms supporting diversity hotspots. Strikingly, two distinct clades of Ostreococcus co-occur in more than half of the samples. A "hotspot" of Ostreococcus diversity appears to be supported by a confluence of water masses containing either clade, as well as a local nutrient supply at the front and the mesoscale variability of the region. / by Sophie Anne Clayton. / 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), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Many species of whales migrate annually between high-latitude feeding grounds and low-latitude breeding grounds. Yet, very little is known about how these animals navigate during these migrations. This thesis takes a first look at the roles of geomagnetic and acoustic cues in humpback whale navigation and orientation, in addition to documenting some effects of human-produced sound on beaked whales. The tracks of satellite-tagged humpback whales migrating from Hawaii to Alaska were found to have systematic deviations from the most direct route to their destination. For each whale, a migration track was modeled using only geomagnetic inclination and intensity as navigation cues. The directions in which the observed and modeled tracks deviated from the direct route were compared and found to match for 7 out of 9 tracks, which suggests that migrating humpback whales may use geomagnetic cues for navigation. Additionally, in all cases the observed tracks followed a more direct route to the destination than the modeled tracks, indicating that the whales are likely using additional navigational cues to improve their routes. There is a significant amount of sound available in the ocean to aid in navigation and orientation of a migrating whale. This research investigates the possibility that humpback whales migrating near-shore listen to sounds of snapping shrimp to detect the presence of obstacles, such as rocky islands. A visual tracking study was used, together with hydrophone recordings near a rocky island, to determine whether the whales initiated an avoidance reaction at distances that varied with the acoustic detection range of the island. No avoidance reaction was found. Propagation modeling of the snapping shrimp sounds suggested that the detection range of the island was beyond the visual limit of the survey, indicating that snapping shrimp sounds may be suited as a long-range indicator of a rocky island. Lastly, this thesis identifies a prolonged avoidance reaction of a Blainville's beaked whale to playbacks of Navy mid-frequency active sonar and orca predation calls. Navy sonar exercises have been linked to beaked whale strandings, and identifying whether these are the result of a mistaken predator avoidance reaction may help prevent future strandings. / by Ann Nichole Allen. / Ph.D.

Thesis: S.M. in Oceanographic Engineering, Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 83-87). / Recent advances in acoustic navigation methodologies are enabling the way for AUVs to extend their submerged mission time and maintain a bounded XY position error. Additionally, advances in inertial sensor technology have drastically lowered the size, power consumption, and cost of these sensors. Nonetheless, these sensors are still noisy and accrue error over time. This thesis builds on the research and recent developments in single beacon one-way-travel- time (OWTT) acoustic navigation and investigates the degree of bounding position error for small AUVs with a minimal navigation strap-down sensor suite, relying mostly on a consumer grade microelectromechanical system (MEMS) inertial measurement unit (IMU) and a vehicle's dynamic model velocity. An implementation of an Extended Kalman Filter (EKF) that includes IMU bias estimation and coupled with a range filter, is obtained in the field on two OceanServer Technology, Inc. Iver2 AUVs and one Bluefin Robotics SandShark [mu]AUV. Results from these field trials on Ashumet Pond of Falmouth, Massachusetts, the Charles River of Cambridge, Massachusetts, and Monterey Bay near Santa Cruz, California show a navigation solution accuracy comparable to current standard navigation techniques. / by James H. Kepper, IV. / S.M. in Oceanographic Engineering