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. / Compound-specific carbon isotopic (613C and A14C) data are reported for lipid biomarkers isolated from Santa Monica Basin (SMB) and Santa Barbara Basin (SBB) surface sediments. These organic compounds represent phytoplanktonic, zooplanktonic, bacterial, archaeal, terrestrial, and fossil carbon sources. The lipids include long-chain n-alkanes, fatty acids (as FAMEs), n-alcohols, C30 mid-chain ketols and diols, sterols, hopanols, and ether-linked C40-biphytanes of Archaea. The data show that the carbon source for most of the biomarkers is marine euphotic zone primary production or subsequent heterotrophic consumption of this biomass. Two lipid classes represent exceptions to this finding. A14C values for the n-alkanes are consistent with mixed fossil and contemporary terrestrial plant sources. The archaeal isoprenoid data reflect chemoautotrophic growth below the euphotic zone. The biomarker class most clearly representing marine phytoplanktonic production is the sterols. It is suggested, therefore, that the sterols could serve as paleoceanographic tracers for surface-water DIC. The isotopic data are used to construct two algebraic models. The first calculates the contributions of fossil and modern vascular plant carbon to SMB n-alkanes. This model indicates that the A14C of the modern component is +235%o (post-bomb) or 0%o (pre-bomb). The second model uses these values to determine the origin of sedimentary TOC. The results are comparable to estimates based on other approaches and suggest that -60% of SMB TOC is of marine origin, modern terrestrial and fossil sources contribute -10% each, and the remaining -20% is of unknown origin. / by Ann Pearson. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Marine mammals possess high body burdens of persistent organic pollutants, including PCBs and dioxin-like compounds (DLC). Chronic environmental or dietary exposure to these chemicals can disrupt the function of reproductive and immune systems, as well as cause developmental defects in laboratory animals. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, mediating the expression of a suite of genes in response to exposure to DLC and structurally related chemicals. Species-specific differences in AHR structure can affect an organism's susceptibility to the effects of DLC. The structures and functions of several cetacean AHRs were investigated using in vitro molecular cloning and biochemical techniques. Using a novel combination of remote biopsy and molecular cloning methods, RNA was extracted from small integument samples from living North Atlantic right whales to identify the cDNA sequence for AHR and other genes of physiological importance. Biopsy-derived RNA was found to be of higher quality than RNA extracted from stranded cetaceans, and proved a good source for identifying cDNA sequences for expressed genes. / (cont.) The molecular sequences, binding constants, and transcriptional activities for North Atlantic right whale and humpback whale AHRs cDNAs were determined using in vitro and cell culture methods. Whale AHRs are capable of specifically binding dioxin and initiating transcription of reporter genes. The properties of these AHRs were compared with those from other mammalian species, including human, mouse, hamster, and guinea pig, and other novel marine mammal AHRs, using biochemical, phylogenetic, and homology modeling analyses. The relative binding affinities for some marine mammal AHRs fall between those for the high-affinity mouse AHRb-1 and the lower affinity human AHR. Species-specific variability in two regions of the AHR ligand binding domain were identified as having the greatest potential impact on AHR tertiary structure, yet does not sufficiently explain differences observed in ligand binding assays. Additional studies are necessary to link exposure to environmental contaminants with potential reproductive effects in marine mammals, especially via interactions with steroid hormone receptor pathways. / by Joy M. Lapseritis. / 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. / Includes bibliographical references (leaves 137-143). / Predictions of deposition rate are integral to the transport of many constituents including contaminants, organic matter, and larvae. Review of the literature demonstrates a general appreciation for the potential control of deposition by bed roughness, but no direct tests involving flat sediment beds. Understanding the mechanisms at work for flat sediment beds would provide the basis for exploring more complicated bed conditions and the incorporation of other transport processes, such as bioturbation and bedload transport. Generally, fine particle deposition rates are assumed to be equivalent to the suspension settling velocity, therefore, deposition rates in excess of settling are considered enhanced. Flume observations of deposition were made using treatments that covered a wide range of flow, particle, and bed conditions. Specific treatments demonstrated large enhancements (up to eight times settling). Delivery of particles to the interface is important, but models based on delivery alone failed to predict the observed enhancement. This necessitated the development of a new model based on a balance between delivery and filtration in the bed. Interfacial diffusion was chosen as a model for particle delivery. Filtration of particles by the bed is a useful framework for retention, but the shear in the interstitial flow may introduce additional factors not included in traditional filtration experiments. / (cont.) The model performed well in prediction of flow conditions, but there remained a discrepancy between predictions and observed deposition rate, especially for treatments with significant enhancement. Fluid flow predictions by the model, such as slip at the sediment water interface and fluid penetration into the sediment, appeared to be supported by flume experiments. Therefore, failure to predict the magnitude of enhancement was attributed to far greater filtration efficiencies for the sediment water interface than those measured in sediment columns. Emerging techniques to directly measure fluid and particle motion at the interface could reveal these mechanisms. The observation of enhanced deposition to flat sediment beds reinforces the importance of permeable sediments to the mediation of transport from the water column to the sediment bed. / by Jerry Stephen Fries. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology, and the Woods Hole Oceanographic Institution), 2001. / Includes bibliographical references. / This thesis presents methods to analyze the function of vocalizations of the bottlenose dolphin, Tursiops truncatus. The thesis uses the social interaction as the basic unit of analysis, and maintains a deliberate focus on quantitative and replicable analyses throughout. A method for determining identity of the vocalizing animal in a lagoon was developed. This method combined passive acoustic localization with video sampling to determine which animal vocalized. It fills an urgent need for unbiased identification of vocalizations of undisturbed dolphins where details of social interactions can be followed without affecting the behavior of the subjects. This method was implemented in a captive lagoon with 6 dolphins: two adult females, their two male calves, and a juvenile male and a juvenile female. This thesis also reviews the current state of analysis of the bottlenose dolphin acoustic repertoire, highlighting the need for a detailed, quantitative, and consistent study of the entire vocal repertoire. It does not attempt to do a comprehensive repertoire study, but uses several new quantitative methods to parameterize vocalizations and relate these to behavior from dolphins. Vocalizations within the lagoon tended to occur around the time of onset of behaviors produced by the focal dolphin. A comparison of vocalizations during affiliative and agonistic interactions revealed that the association of group vocalizations with the behavior of a focal animal was related to agonistic but not affiliative interactions. / Using the localization/video method, vocalizations in a time window around submissive behaviors were localized and classified as having come from either dolphins engaged in the interaction or dolphins not engaged in the interaction. Vocalizations were emitted by interactants more often than expected, and by non-interactants less often than expected. Use of different vocalization types was found to vary depending on the context of the agonistic interaction. In addition, the sequence of vocalizations with respect to behaviors within the interaction mattered, with more vocalizations occurring after than before submissive behaviors. These results demonstrated that group-based analyses of vocalizations are insufficient and one must use techniques designed to focus on the level of the interaction in order to study communication and social behavior in dolphins. / by Rebecca Elizabeth Thomas. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology, and the Woods Hole Oceanographic Institution), 2001. / Includes bibliographical references. / In recent years, the use of clay minerals has emerged as one of the most promising strategies for directly controlling harmful algal blooms (HABs). Its principle is based on the mutual aggregation of algal cells and mineral particles, leading to the formation of large flocs that rapidly settle to the ocean floor. This work investigated the effectiveness of various domestic clays against a number of bloom-forming species from the United States. Twenty-five clays were tested against the dinoflagellate, Karenia brevis (formerly Gymnodinium breve), and the chrysophyte, Aureococcus anophagefferens. In general, the highest removal efficiencies (RE>90% at 0.25 g l-1 of clay) against K brevis were found using montmorillonite, bentonite and phosphatic clays (i.e. a product of phosphate mining containing large amounts of montmorillonite). The RE of phosphatic clays remained high (>80%) even at 0.03 g l-1. Kaolinite and zeolite were mostly ineffective against K brevis. Removal with clay exceeded those for alum, polyaluminum chloride (PAC) and several other polymeric flocculants by a factor of two. However, the combination of phosphatic clay and PAC (at 5 mg l-1) decreased the amount of clay needed to maintain 80% RE by one order of magnitude. Cell viability and recovery remained high when clay loading stayed below 0.03 g l-1 with or without resuspension of the sediment. However, cell mortality approached 100% with 0.50 g l-1 even with daily resuspension. Between 0.10 and 0.25 g l-1, K brevis survival and recovery depended on the interplay of clay loading, the frequency of resuspension, and duration of contact prior to the first resuspension event. / (cont.) For A. anophagefferens, the RE did not exceed 40% for any clay at 0.25 g l-1 even in combination with coagulants and flocculants. The highest removal was achieved by thoroughly mixing the clay slurry (e.g. phosphatic clay) into the cell culture. The RE by phosphatic clay varied significantly in a survey consisting of 17 different species from five algal classes. Moreover, the removal trends varied substantially with increasing cell concentration. For example, cell removal increased with increasing clay loading and cell concentration for K. brevis. However, RE dropped below 70% when cell concentration was <1000 cell ml-1 for clay loadings up to 0.50 g l-1. This suggested that a critical number of organisms should be present for clays to remain effective. Similarly, enhanced removal with increasing cell concentration was also found in Akashiwo sanguinea (formerly Gymnodinium sanguineum), Heterosigma akashiwo and Heterocapsa triquetra. In the six remaining species, RE initially increased then decreased, or RE remained constant as more cells were treated. The removal pattern among the species at comparable cell numbers did not correlate with the cross-sectional area (R2=0.23), swimming speed (R2=0.04), or a type of cell covering (i.e. theca, silica frustule) ... / by Mario Rhuel Sengco. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Magnetotactic bacteria (MTB) biomineralize intracellular membrane-bound crystals of magnetite (Fe3O4) or greigite (Fe3S4), and are abundant in the suboxic to anoxic zones of stratified marine environments worldwide. Their population densities (up to 105 cells ml-1) and high intracellular iron content suggest a potentially significant role in iron cycling, but very little is known about their population dynamics and regulation by environmental geochemistry. The MTB community in Salt Pond (Falmouth, MA), a small stratified marine basin, was used as a model system for quantitative community studies. Magnetiteproducing MTB predominate slightly above the oxic-anoxic interface and greigiteproducing MTB predominate in sulfidic waters. A quantitative PCR (QPCR) assay was developed and applied to enumerate four major groups of MTB in Salt Pond: magnetite-producing cocci, barbells, the greigite-producing many-celled magnetotactic prokaryote (MMP), and a greigite-producing rod. The barbells were identified as [delta]-Proteobacteria while the rod was identified as the first MTB in the [gamma]-Proteobacteria. / (cont.) The previously thought to be a single species, consists of at least five clades with greater than 5% divergence in their 16s rRNA. Fluorescent in situ hybridization probes showed significant variation in clade abundances across a seasonal cycle in salt marsh productivity. FISH also showed that aggregates consist of genetically identical cells. QPCR data indicated that populations are finely layered around the oxic-anoxic interface: cocci immediately above the dissolved Fe(II) peak, barbells immediately below, the MMP in microsulfidic waters, and the greigite-producing rod in low numbers (100 cells ml-1) below the gradient region. The barbell reached 1-10% of total eubacteria in the late season, and abundances of cocci and barbells appeared to vary inversely. Calculations based on qPCR data suggest that MTB are significant unrecognized contributors to iron flux in stratified environments. Barbells can respond to high oxygen levels by swimming toward geomagneticsouth, the opposite of all previously reported magnetotactic behavior. This behavior is at least partially dependent on environmental oxidation-reduction potential. The co-existence of MTB with opposing polarities in the same redox environment conflicts with current models of the adaptive value of magnetotaxis. / by Sheri Lynn Simmons. / Ph.D.

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 (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Coastal and estuarine environments experience large variability and rapid shifts in pCO₂ levels. Elevated pCO², or ocean acidification, often negatively affects early life stages of calcifying marine invertebrates, including bivalves, but it is unclear which developmental stage is most sensitive. I hypothesized that initial calcification is a critical stage during which high pCO₂ exposure has severe effects on larval growth and development of bay scallop (Argopecten irradians). Using five experiments varying the timing of exposure of embryonic and larval bay scallops to high CO₂, this thesis identifies two distinct stages of development during which exposure to high CO₂/low pH causes different effects on bay scallop larvae. I show that any exposure to high CO₂ consistently reduces survival of bay scallop larvae. I also show that high CO₂ exposure during initial calcification (12-24 h post-fertilization) results in significantly smaller shells, relative to ambient conditions, and this size decrease persists through the first week of development. High CO₂ exposure at 2-12 h post-fertilization (pre-calcification), does not impact shell size, suggesting that the CO₂ impact on size is a consequence of water chemistry during calcification. However, high CO₂ exposure prior to shell formation (2-12 h post-fertilization) causes a high incidence of larval shell deformity, regardless of CO₂ conditions during initial calcification. This impact does not occur in response to high CO₂ exposure after the 2-12 h period. The observations of two critical stages in early development has implications for both field and hatchery populations. If field populations were able to time their spawning to occur during the night, larvae would undergo initial calcification during the daytime, when CO₂ conditions are more favorable, resulting in larger veliger larvae. Hatcheries could invest minimal resources to monitor and modify water chemistry only during the first day of development to ensure larva are exposed to favorable conditions during that critical period. / by Meredith Megan White. / Ph.D.