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. / The role of oxylipins in ocean biogeochemistry was investigated using microcosm amendment experiments, environmental lipidomics, and culture based studies. Oxylipins are a bioactive class of secondary metabolites produced by diatoms and other eukaryotic phytoplankton. Previous research has focused mainly on one class of oxylipins, polyunsaturated aldehydes (PUAs), and their impacts on copepods. And few studies have looked at the impacts of oxylipins in situ. Here I show that oxylipins have the potential to impact carbon flux attenuation, oxylipin production in situ is linked to diatom bloom decline and viruses, and oxylipins deter microzooplankton grazing. Sinking particles collected in the North Atlantic were determined to be hot spots for PUAs with concentrations in the micromolar range. Natural particle associated microbial communities exhibited a dose dependent response to PUAs. Stimulatory PUA concentrations ranged from 1-10 ptM, resulting in enhanced remineralization of organic matter by particle associated microbes. Thus, PUAs produced during bloom decline may lead to greater flux attenuation and nutrient recycling. A novel lipidomics approach was applied along a cruise track in the California Coastal System revealing that canonical diatom free fatty acids and oxylipins dominated the dissolved lipidome and oxylipin abundance was correlated with diatom bloom demise as assessed by phaeophytin and biogenic Si. RNA viruses were likely the cause of diatom bloom demise and may have induced oxylipin production. The link between viruses and oxylipins represents a new infochemical signaling pathway in the ocean. Many oxylipins that are novel to the marine environment were also identified. The dissolved lipidome was sampled during grazing experiments with the microzooplankton grazer Oxyrrhis marina and both wild type Phaeodactylum tricornutum and a chronically stressed, transgenic strain (PtNOA). Grazing was suppressed in the PtNOA treatments compared to the WT, likely due to upregulation of small unknown lipophilic molecules. This suggests that cellular stress and oxylipin production may deter microzooplankton grazing in the environment potentially altering the transfer of energy through the microbial food web. By employing interdisciplinary approaches, we have learned that oxylipins production in situ is linked to bloom decline and the bioactivity of these compounds has significant implications for ocean biogeochemical cycles. / by Bethanie Rachele Edwards. / 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. / Ocean waves are a powerful sediment transport mechanism in the coastal zone. This thesis investigates how waves shape deltaic landforms and how small scale river mouth processes affect large-scale delta morphology. I have developed and applied models of plan-view delta shape and their channel dynamics. Simple parameterizations and key insights from these models have allowed us to transcend spatial scales from river mouths to delta plains and make morphologic predictions around the globe for every delta on Earth. I have applied models of delta morphology to backtrack the late Holocene evolution of the Ebro River delta in Spain and estimate timescales and magnitude of past climate change and human impacts. Currently, many deltas around the world face large sediment deficits because of river damming. I model deltaic response to reductions in sediment load and offer frameworks to predict future deltaic change in these dynamic and threatened coastal regions. / by Jaap H. Nienhuis / 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. / 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. / Includes bibliographical references. / This thesis examines the structure of Pacific oceanic lithosphere that has been modified by post-formation magmatism in order to better understand the processes of secondary magmatic evolution of the lithosphere, which can have global-scale implications for oceanic and atmospheric chemistry. In the western Pacific, widespread Cretaceous magmatism has modified oceanic lithosphere over hundreds of millions of square kilometers. Seismic models of the upper crust from within the Jurassic Quiet Zone and the crust and upper mantle near the Mariana Trench reveal crust that is locally thickened via focused extrusive volcanism and crust that is modestly but uniformly thickened over broad regions. These distinct modes of magmatic emplacement suggest the operation of both focused and diffuse modes of melt transport through the lithosphere. Analysis of seismic observations from Guaymas Basin, in the Gulf of California, endeavor to advance our understanding of sill-driven alteration of sediments, an important consequence of secondary magmatism. We show that seismically imaged physical disruption to sediments due to igneous sill intrusion can be related to changes in sediment physical properties that reflect alteration processes. We also show how sill thickness can be estimated, enabling alteration intensity to be related to sill thickness in a variety of settings. / by Helen Shao-Hwa Feng. / Ph. D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and, the Woods Hole Oceanographic Institution), 2005. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Despite the importance of microorganisms for global and engineering processes, currently lacking is a theoretical framework to describe how the structure of a microbial assemblage translates an environmental condition into a system-level response. Prerequisite to developing such a framework is an understanding of how microbial diversity is partitioned into functional groups of organisms. This thesis has explored the organization and dynamics of microbial diversity within coastal bacterioplankton using the genus Vibrio as a model system. Vibrios are ubiquitous marine bacteria, and include a variety of pathogens. Quantification of Vibrio environmental dynamics by cultivation- independent quantitative PCR and constant denaturant capillary electrophoresis (CDCE), suggests that sea surface temperature is a driving factor in the distribution and abundance of Vibrio populations and that groups of organisms with >98-99% 16S rRNA sequence similarity maintain similar responses to temperature-mediated environmental change. Fine-scale analysis of the genetic structure within one Vibrio population (>99% rRNA similarity to V. splendidus) reveals vast co-occurring genomic diversity. The average concentration of unique genome-types is observed to be 1000-fold lower than the total population size and individual genomes vary in gene content by as much as 1.1 Mb (the equivalent of -1,000 genes). It is proposed that competition between individual genome variants is a weak driver of population genetic structure while stochastic interactions in the water column promote genetic heterogeneity rendering much of the observed diversity in natural populations neutral or effectively neutral. / (cont.) Quantification of Vibrio diversity and dynamics is critical to understanding the global factors that determine the prevalence and proliferation of disease-causing strains and their potential contribution to ecosystem-level processes such as organic matter degradation and macronutrient cycling. In addition, an understanding of how diversity is organized in natural assemblages is an important step in the effort to predict the characteristics of microbial systems based upon their component populations. / by Janelle Renée Thompson. / 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), 2005. / Handwritten on CDROMS: v. [1]. Appendix, histological images -- v. [2]. CT images. -- Table of contents refers to CDROMS as: Appendix and CT and histological images for all species, attached CD) / Includes bibliographical references (v. 2, leaves 216-247). / In this thesis, the relationships of olfactory sensitivity to three biological variables were tested. The sensitivity of a marine mammal, the sea otter (Enhydra lutris) was measured in order to determine whether a marine lifestyle results in impaired olfaction. The effect of dietary relevance on sensitivity to specific odorants was evaluated. Finally, a new morphometric model of olfactory uptake efficiency was developed and tested against behavioral measurements of olfactory sensitivity in twelve mammalian species from five orders. Olfactory thresholds were obtained for the first time from two sea otters for seven odorant compounds from various natural sources. Otters were trained using operant conditioning to participate in direct behavioral testing. Sea otter olfactory sensitivity was comparable to that of previously studied terrestrial mammals. The incidence of an odorant in the diet of the olfactor was found to influence specific sensitivity to that compound but to varying degrees among different mammalian orders. Nasal cavity specimens were measured using radiologic (CT scan) and histologic (light microscopy) techniques. Surface areas and volumes of the nasal cavity were used to calculate the Olfactory Uptake Efficiency (OUE). OUE is significantly related to olfactory bulb volume. A possible relationship was found between OUE and general olfactory sensitivity. / by Jennifer Hammock. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references. / The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. / (cont.) Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that selection operating at the post- settlement stage may be extremely important in structuring genetic differentiation between populations and life stages. Further, it demonstrates how combined genetic analysis of sub-adult and adult samples can provide more information about population dynamics than either could alone. / by Robert M. Jennings. / 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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Recurrent brown tide blooms caused by the harmful alga Alureococcus anophagefferens have decimated coastal ecosystems and shellfisheries along the Eastern U.S and South Africa. The exact mechanisms controlling bloom formation, sustenance, and decline are unclear, however bottom-up factors such as nutrient type and supply are thought to be critical. Traditional assays for studying algal nutrient physiology require bulk community measurements or in situ nutrient perturbations. Although useful, these techniques lack the ability to target individual species in complex, mixed microbial assemblages. The motivation for this thesis is to examine the metabolic strategies utilized by A. anophagefferens for meeting its nitrogen (N) and phosphorus (P) demand at the cellular level using molecular tools that, even in the presence of complex microbial assemblages, can be used to track how nutrients influence the bloom dynamics of A. anophageferens in the environment. Chapter two examines the global transcriptional responses of A. anophagefferens to N and P deficiency. Results demonstrate that A. anophagefferens has the capacity to utilize multiple forms of organic N and P when inorganic forms become unavailable. Chapter three analyzed the global protein changes in response to P deficiency and P re-supply. Consistent with transcript patterns, A. anophagefferens increases protein abundance for a number of genes involved in inorganic and organic P metabolism when inorganic P is deficient. Furthermore, increases in a sulfolipid biosynthesis protein combined with lipid data suggest A. anophagefferens can adjust its P requirement by switching from phospholipids to sulfolipids when inorganic P is unavailable. Analysis of protein abundances from Pdeficient cells that were re-fed inorganic P demonstrates variations in the timing of turnover among various proteins upon release from phosphate deficiency. Chapter four tests the expression patterns of candidate gene markers of nutrient physiology under controlled culture experiments. Results show that expression patterns of a phosphate transporter and xanthine/uracil/vitamin C permease are indicators of P and N deficiency, respectively. Taken together, these findings provide insight into the fundamental and ecological niche space of this harnful algal species with respect to N and P and provide a platform for assaying nutrient controls on natural brown tide blooms. / by Louie L. Wurch. / 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. / Global warming has led to a significant increase in Greenland ice sheet (GrIS) melt and runoff since 1990, resulting in escalated export of fresh water and associated sediment to the surrounding North Atlantic and Arctic Oceans. Similar to alpine glacial systems, surface meltwater on ice sheet surface drains to the base (subglacial) where it joins a drainage system and can become chemically enriched from its origin as dilute snow- and ice-melt. In this thesis, I examine the interdependence of glacial hydrology and biogeochemical cycling in terms of export of carbon and iron from the Greenland ice sheet. I develop a new isotope mixing-model to quantify water source contributions to the bulk meltwater discharge draining a GrIS outlet glacier. Results illustrate (a) the new application of a naturally occurring radioisotope (radon-222) as a quantitative tracer for waters stored at the glacier bed, and (b) the seasonal evolution of the subglacial drainage network from a delayed-flow to a quick-flow system. Model results also provide the necessary hydrological context to interpret and quantify glacially-derived organic carbon and iron fluxes. I combine bulk- and molecular-level studies of subglacial organic carbon to show that GrIS discharge exports old (radiocarbon depleted), labile organic matter. Similar investigations of dissolved and particulate iron reveal that GrIS discharge may be a significant flux of labile iron to the North Atlantic Ocean during the summer meltseason. Both carbon and iron are subject to proglacial processing prior to export to the marine environment, and exhibit strong seasonal variability in correlation with the subglacial drainage evolution. Low, chemically concentrated fluxes characterize the spring discharge, whereas higher, chemically dilute fluxes typify the summer discharge. Collectively, this thesis provides some of the first descriptions and flux estimates of carbon and iron, key elements in ocean biogeochemical cycles, in GrIS meltwater runoff. / by Maya Pilar Bhatia. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 155-181). / This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R² of 1.0), with a dynamic range from 10²-10⁶ cells/ml. Genotypes with >/=~80% average nucleotide identity to those targeted crosshybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R²=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions. / by Virginia Rich. / 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), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 147-160). / Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory cells accumulated to an order of magnitude greater cell densities than Tenacibaculum sp. cells on equivalent prey cell densities. Experiments were conducted to constrain the potential of the novel isolates to affect prey communities under more environmentally relevant conditions. An investigation of the minimum number of predatory cells needed to generate clearings of prey cells found that the inoculation of individual predatory flavobacteria cells can ultimately result in dense lytic swarms. In some cases, the susceptibility of particular prey species to lysis by a flavobacterial predator was found to vary based on the growth state of the prey cells or the presence of their spent growth media. A novel methodology for the experimental study of biofilms was used to assess the impact of exposure to predatory marine flavobacteria on the release of macronutrients from prey biofilms. The Olleya sp. predator had a stimulative effect on macronutrient release while the Tenacibaculum sp. did not, further suggesting the two groups of predators are adapted to different ecological niches. / by Erin C. Banning. / Ph.D.