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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 189-202). / Over the past several decades, the West Antarctic Peninsula (WAP) has undergone physical and ecological changes at a rapid pace, with warming surface ocean and a sharp decrease in the duration of the sea ice season. The impact of these changes in the ocean chemistry and ecosystem are not fully understood and have been investigated by the Palmer-LTER since 1991. Given the data acquisition constraints imposed by weather conditions in this region, an ocean circulation, sea ice and biogeochemistry model was implemented to help fill the gaps in the dataset. The results with the present best case from the suite of sensitivity experiments indicate that the model is able to represent the seasonal and interannual variations observed in the circulation, water mass distribution and sea ice observed in the WAP, and has identified gaps in the observations that could guide improvement of the simulation of the regional biogeochemistry. Comparison of model results with data from the Palmer-LTER project suggests that the large spatial and temporal variability observed in the phytoplankton bloom in the WAP is influenced by variability in the glacial sources of dissolved iron. Seasonal progression of the phytoplankton bloom is well represented in the model, and values of vertically integrated net primary production (NPP) are largely consistent with observations. Although a bias towards lower surface dissolved inorganic carbon (DIC) and alkalinity was identified in the model results, interannual variability was similar to the observed in the Palmer-LTER cruise data. / by Cristina Schultz. / Ph. D. / 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)

Thesis (M.S.)--Joint Program in Oceanography and Oceanographic Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), June 1996. / "May 1996." / Includes bibliographical references (leaves 66-68). / This thesis details two years of research conducted with the guidance and support of three advisors: Dr. J. K. Whelan, Dr. J. S. Seewald and Dr. T. I. Eglinton. Each of the three chapters represents a different, self-contained research project. All of the projects are related to the organic geochemistry of marine sediments, however, this is a fairly encompassing area of study. Chapters 1 and 2 stem from the same experimental study -- the use of hydrous-pyrolysis to investigate mechanisms leading to the production of petroleum-related products during kerogen maturation. Chapter 3, on the other hand, utilizes a recently developed technique of isolating and AMS-14C dating individual compounds from complex sedimentary organic mixtures. The samples used in each investigation came from all over the world. The first two chapters utilize ancient marine sediment samples obtained from an outcrop in California (Chpts. 1 and 2) and from a well in Alabama (Chpt. 2). In contrast, recent marine sediment samples were obtained from the Arabian and Black Seas for the third chapter. Several preparative and analytical methods are common to all three studies. Nevertheless, each employ techniques totally unique from one another and from previous investigations. In Chapter 1, for example, X-ray absorption spectroscopy (XANES) is used to determine the speciation of organic sulfur present in kerogen, bitumen, and bulk sediment samples. While Chapter 3 represents the first study in which the "4C ages of individual, known hydrocarbon biomarkers are determined after isolation by Preparative Capillary Gas Chromatography (PCGC). The insights gained by these investigations are discussed in detail in the following chapters. The common thread between the three chapters is that the source of organic matter, the rate at which it is delivered to marine sediments and the depositional environment, all set the stage for kerogen formation and eventual petroleum generation. / by Bryan C. Benitez-Nelson. / M.S.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), February 2002. / Vita. / Includes bibliographical references (leaves 153-161). / I used direct measurements of nitrogen gas (N₂ fluxes and a ¹⁵N stable isotope tracer to determine the contribution of denitrification to salt marsh sediment N cycling. Denitrification in salt marsh tidal creekbottoms is a major sink for groundwater nitrate of terrestrial origin. I studied creekbottom denitrification by direct measurements of N₂ fluxes in closed chambers against a low-N₂ background. I undertook experiments and simulation modeling of sediment N₂ fluxes in closed chambers to optimize the key experimental parameters of this approach. Denitrification in these sediments was driven by the degradation of labile organic matter pools which are depleted during long incubations. Sediment thickness was the most important parameter controlling the required incubation time. Errors of up to 13% with gas headspaces and 80% with water headspaces resulted from headspace N2 accumulation and the resulting collapse of the sediment-water diffusion gradient. These errors could be eliminated by using headspaces of sufficient thickness. Headspace flushing to reduce ammonium accumulation did not affect denitrification rates, but caused transient disturbance of N₂ flux rates. Direct measurements of 0₂, C0₂, N₂, and inorganic N fluxes from the sediments of a salt marsh tidal creek were made in order to examine the interaction of denitrification with the carbon, oxygen, and N cycles. Organic carbon concentration and lability were the primary controls on metabolic rates. C0₂/N flux ratios averaged 6.1, indicating respiration driven by algal biomass. / (cont.) Allochthonous denitrification accounted for 39% of total sediment denitrification (2.7 mol N m⁻² yr⁻¹). 46% of remineralized ammonium was denitrified, while the contribution of autochthonous denitrification to 0₂ and C0₂ fluxes was 18% and 10%, respectively. A ¹⁵N-ammonium tracer was used to study competition between plants and nitrifying bacteria for remineralized ammonium. In undisturbed sediments of Spartina alterniflora, plant uptake out-competed nitrification-denitrification, with plant uptake accounting for 66% of remineralized ammonium during the growing season. Under N fertilization (15.5 mol m⁻² yr⁻¹), both plant N uptake and denitrification increased, but denitrification dominated, accounting for 72% of the available N. When plant uptake was hydrologically suppressed, nitrification-denitrification was stimulated by the excess N, shifting the competitive balance toward denitrification. / by Michael Robert Hamersley. / 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. 160-163). / Physical oceanographers have known for several decades the total amount of abyssal mixing and upwelling required to balance the deep-water formation, but are still working to understand the mechanisms and locations-how and where it happens. From observational studies, we know that areas of rough topography are important and the hundreds of Grand-Canyon sized canyons that line mid-ocean ridges have particularly energetic mixing. To better understand the mechanisms by which rough topography translates into energetic currents and mixing, I studied diffusive boundary layers over varying topography using theoretical approaches and idealized numerical simulations using the ROMS model. In this dissertation, I show a variety of previously unidentified characteristics of diffusive boundary layers that are likely relevant for understanding the circulation of the abyssal ocean. These boundary layers share many important properties with observed flows in abyssal canyons, like increased kinetic energy near topographic sills and strong currents running from the abyssal plains up the slopes of the mid-ocean ridges toward their crests. They also have a previously unknown capacity to accelerate into overflows for a variety of oceanographically relevant shapes and sizes of topography. This acceleration happens without external forcing, meaning such overflows may be ubiquitous in the deep ocean. These boundary layers also can force exchange of large volumes of fluid between the relatively unstratified boundary layer and the stratified far-field fluid, altering the stratification far from the boundary. We see these effects in boundary layers in two- and three-dimensions, with and without rotation. In conclusion, these boundary layer processes, though previously neglected, may be a source of a dynamically important amount of abyssal upwelling, profoundly affecting predictions of the basin-scale circulation. This type of mechanism cannot be captured by the kind of mixing parameterizations used in current global climate models, based on a bottom roughness. Therefore, there is much work still to do to better understand how these boundary layers behave in more realistic contexts and how we might incorporate that understanding into climate models. / by Rebecca Walsh Dell. / 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. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Halogenated 1'-methyl-1,2'-bipyrroles (MBPs) are a distinctive class of marine organic compounds. They are naturally produced, they have a unique carbon structure, they are highly halogenated, and they bioaccumulate in upper trophic levels. MBPs share many characteristics with persistent organic pollutants (POPs), and may prove to be useful natural analogues for these anthropogenic compounds. Further, their unique structure suggests that their biosynthetic organism(s) may have new genes to add to current knowledge of biosynthetic chemistry. The objectives of this dissertation were to further clarify the environmental distribution of MBPs, to examine whether MBPs biomagnify, and to investigate possible origins of these compounds through their stable nitrogen isotopic signatures. Results from these investigations have shown that over 40 highly brominated MBP congeners are present in marine mammals, fish, and squid from the Northwestern Atlantic Ocean. The most abundant MBPs do appear to biomagnify through the food web to reach the concentrations observed in marine mammals. This additional evidence affords greater confidence in the use of MBPs as natural analogues for POPs. However, differences in the environmental chemistry of MBPs and anthropogenic compounds are also evident, and may be due to these compounds' different origins, or to the capacity of degradative enzymes to act upon them. / (cont.) Finally, compound-specific nitrogen isotope analyses on MBPs isolated from dolphin blubber show that these compounds are dramatically enriched in 15N relative to other biosynthetic organic compounds. This enrichment is likely a signal imparted during biosynthesis, and may assist in elucidating the organism(s) and mechanism(s) responsible for the biosynthesis of MBPs. / by Kristin C. Pangallo. / Ph.D.

Thesis (Ocean E.)--Joint program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering and Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references (p. 127-128). / Acoustic coded signaling offers potentially significant improvements over traditional "toneburst" methods in many underwater applications where error due to noise and multipath interference is a problem. In this thesis, the use of these spread spectrum techniques is analyzed for navigation of the REMUS autonomous underwater vehicle. The accuracy of the current system using Turyn and Barker sequences, as well as toneburst, is quantified, and the sources of the remaining error are examined. / by Benjamin Kerbin Evans. / Ocean E.

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), 2005. / Includes bibliographical references. / The geographic distribution and dynamics of coastal benthic populations are shaped by physical - biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short term (i.e. days) small- scale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus g-landula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. / (cont.) Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation of nauplii and cyprids. Differences in survival, growth rate, size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics of benthic populations at multiple spatial-temporal scales, and the usefulness of small scale high- frequency observations of nearshore phenomena, especially in relation with the dispersal of larvae. / by Fabián J. Tapia. / 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. / Trichodesmium spp. are considered the dominant nitrogen (N) fixing cyanobacteria in tropical and subtropical oceans, regimes frequently characterized by low iron (Fe). Limited information exists about what levels of Fe limit Trichodesmium N fixation. I developed a diagnostic for Fe limitation using quantitative reverse transcription PCR (qRT-PCR) of the Fe stress response gene isiB, which encodes for flavodoxin a non-Fe containing substitute for ferredoxin. I determined that high isiB gene expression corresponded to cell-specific reductions in N fixation rates in both phylogenetic clades of Trichodesmium grown on varying levels of Fe. Using these laboratory-determined thresholds, I assessed Fe limitation of Trichodesmium from the Sargasso Sea, equatorial Atlantic Ocean and Western Pacific Warm Pool in conjunction with other analytical measurements (N, phosphorus (P) and dissolved Fe (<0.4[mu]m filtered)). I found widespread Fe limitation in Trichodesmium from the Pacific Ocean and minimal expression in the North Atlantic Ocean. I also found an inverse correlation between isiB expression and dissolved Fe:P ratios in seawater and data suggesting that most dissolved Fe in seawater, including organic ligand-bound Fe, is available to Trichodesmium. These data support and refine previous model predictions and demonstrate, in situ, the importance of Fe to the marine N cycle. / by Phoebe Dreux Chappell. / S.M.

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), 2006. / Includes bibliographical references. / Two years of moored oceanographic and automatic weather station data which span the winter ice seasons of 2001-2003 within Marguerite Bay on the western Antarctic Peninsula (wAP) shelf were collected as part of the Southern Ocean Global Ocean Ecosystems Dynamics program. In order to characterize the ice environment in the region, a novel methodology is developed for determining ice coverage, draft and velocity from moored upward-looking acoustic Doppler current profiler data. A linear momentum balance shows the importance of internal ice stresses in the observed motion of the ice pack. Strong inertial, not tidal, motions were observed in both the sea ice and upper ocean. Estimates of upward diapycnal fluxes of heat and salt from the Upper Circumpolar Deep Water to the surface mixed layer indicate almost no contribution from double diffusive convection. A one-dimensional vertical mixed layer model adapted for investigation of mixing beneath an ice-covered ocean indicates that the initial wind event, rather than subsequent inertial shear, causes the majority of the mixing. This work points towards episodic wind-forced shear at the base of the mixed layer coupled with static instability from brine rejection due to ice production as a major factor in mixing on the wAP shelf. / by Jason Hyatt. / 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), February 2013. / "February 2013." Cataloged from PDF version of thesis. / Includes bibliographical references. / Intact polar diacylglycerolipids (IP-DAGs) were used to study microbial dynamics in the surface ocean. IP-DAGs from surface ocean seawater were quantified using high performance liquid chromatography-mass spectrometry (HPLC-MS), after first developing a sensitive, high throughput molecular ion independent triple quadrupole MS method for quantification. Using this analytical technique I examined the distribution of the nine most abundant classes of IPDAGs across the Mediterranean, and found that phospholipids as a percent of total IP-DAGs correlated with phosphate concentration. Furthermore, phospholipids were a higher percent of total particulate phosphorus where phosphate was higher, ranging from 1-14%. Thus IP-DAGs can play not only a significant but also a dynamic role in defining planktonic nutrient needs and cellular C:N:P ratios in the environment. Additionally, microcosm incubations were amended with phosphate and ammonium, and in the course of several days this elicited a shift in the ratios of IP-DAGs. This study was the first to demonstrate the dynamic response of membrane lipid composition to changes in nutrients in a natural, mixed planktonic community, and indicated that the change in IP-DAG ratios in response to changing nutrients may be a useful indicator of microbial nutrient stress. In the surface waters of the western North Atlantic I used three experimental approaches to identify the microbial sources of the nine most abundant classes of IP-DAGs. Phytoplankton are the primary source of one class of sulfolipid, sulfoquinovosyldiacylglycerol, and one class of betaine lipid, diacylglyceryl-trimethyl-homoserine, while heterotrophic bacteria are the dominant source of the phospholipids phosphatidylglycerol and phosphatidylethanolamine. In regrowth experiments in the Sargasso Sea and the North Pacific I demonstrated that phospholipid specific production rate is representative of heterotrophic bacterial cell specific growth rate. I measured phospholipid specific production rate and bacterial production rate using uptake of 3H-leucine (³H-Leu) and 3H-thymidine (³H-TdR) across the North Atlantic, across the Mediterranean, and in the North Pacific subtropical gyre. I found that phospholipid specific production rates estimate heterotrophic bacterial cell specific growth rates that are on the order of 1 per day, an order of magnitude faster than cell specific growth rates suggested by uptake of ³H-Leu and ³H-TdR. / by Kimberly J. Popendorf. / Ph.D.