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 Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 139-150). / Many benthic marine invertebrates have two-phase life histories, relying on planktonic larval stages for dispersal and exchange of individuals between adult populations. Historically, larvae were considered passive drifters in prevailing ocean currents. More recently, however, the paradigm has shifted toward active larval behavior mediating transport in the water column. Larvae in the plankton encounter a variety of physical, chemical, and biological cues, and their behavioral responses to these cues may directly impact transport, survival, settlement, and successful recruitment. In this thesis, I investigated the effects of turbulence, light, and conspecific adult exudates on larval swimming behavior. I focused on two invertebrate species of distinct morphologies: the purple urchin Arbacia punctulata, which was studied in pre-settlement planktonic stages, and the Eastern oyster Crassostrea virginica, which was studied in the competent-to-settle larval stage. From this work, I developed a conceptual framework within which larval behavior is understood as being driven simultaneously by external environmental cues and by larval age. As no a priori theory for larval behavior is derivable from first principles, it is only through experimental work that we are able to access behaviors and tie them back to specific environmental triggers. In this work, I studied the behavioral responses of larvae at the individual level, but those dynamics are likely playing out at larger scales in the ocean, impacting population connectivity, community structure, and resilience. In this way, my work represents progress in understanding how the ocean environment and larval behavior couple to influence marine ecological processes. / by Jeanette Danielle Wheeler. / Ph. D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2004. / Also issued in pages. / Includes bibliographical references. / The marine cyanobacteria Prochlorococcus and Synechococcus are numerically dominant primary producers in the oceans. Each genera consists of multiple physiologically and genetically distinct groups (termed "ecotypes" in Prochlorococcus). Cyanobacterial viruses (cyanophages) that infect Synechococcus are abundant (to 104-106 phage ml-1) in the oceans and calculations suggest that they play a small but significant role in host mortality. Cyanophages are also thought to shape their host populations through regulation of sub-populations and through transfer of genes. Here we describe the isolation of Prochlorococcus cyanophages and the assembly of a culture collection established using a broadly diverse suite of Prochlorococcus and Synechococcus hosts. The collection contains three morphological families, Myoviridae, Podoviridae and Siphoviridae, known to infect marine bacteria and cyanobacteria. Host strains of similar ecotypes often yielded cyanophages of the same family. Host-range analyses of these isolates demonstrated varying levels of specificity among the different morphological types, ranging from infection of a single strain to infection across ecotypes and even across both cyanobacterial genera. Strain-specific cyanophage titers were low in open ocean waters where total cyanobacterial abundances were high, suggesting low phage titers might be a feature of open oceans. Investigations of the underlying cause(s) of this trend require culture-independent assays for quantifying phage that infect particular hosts. / (cont.) We used the phage g20 gene, which encodes the portal protein, to examine the diversity of Myoviridae isolates and found that g20 sequences from our isolates had high similarity to those from other cultured isolates, but not to six phylogenetic clusters of environmental g20 sequences that lacked cultured representatives. Three Prochlorococcus cyanophage genomes were sequenced and analysis of these genomes show striking similarity to the well-studied T7- and T4-like phages, but additionally suggest that these Prochlorococcus cyanophages are modified for infection of photosynthetic hosts, that live in nutrient-limited environments. All three cyanophage genomes contain, among other novel genes of interest, photosynthetic genes that are full-length, conserved, and clustered in the genome suggesting they are functional during infection. Phylogenetic inference suggests that some of these genes were horizontally transferred between host and phage influencing the evolution and ecology of both host and phage. / by Matthew Brian Sullivan. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1999. / Vita. / Includes bibliographical references. / by Deborah Redish Fripp. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Biology (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references. / How do larval cod, Gadus morhua, balance foraging effort against the high cost of swimming in a viscous hydrodynamic regime? A respirometry system was developed to measure the activity metabolism of individual larvae. The cost of swimming was modeled as a power-performance relationship (energy expenditure as a function of swimming speed) and as the cost of transport (the cost to travel a given distance). The cost of transport was high relative to juvenile and adult fish, but larvae swam more efficiently as they grew and became better able to overcome viscous drag. A large-volume observation system was developed to record foraging behavior in three dimensions. There are two phases of the saltatory search cycle used by larval cod: the burst which serves to position larvae within a new search volume and the pause when larvae search for prey. Burst characteristics did not change under different prey treatments, but pause duration increased while foraging capacity and swimming activity decreased when prey were absent. Longer pause durations could reflect greater effort to visually process each search volume when prey were difficult to find. Reduced swimming activity could also be an energy conservation strategy under unfavorable foraging conditions. By applying the cost of swimming model to the observed swimming intensity of freely foraging larvae, foraging activity was estimated to account for up to 80% of routine metabolism. A trophodynamic model was developed incorporating observed foraging behavior and swimming costs to estimate the prey density required to cover all metabolic demands. / (cont.) Small larvae (5mm) can survive on typical mean Georges Bank prey densities in mildly turbulent conditions. Larger larvae (>6mm) can survive even at high turbulence levels. Simulated alternative foraging strategies predict that when predator-prey contact rates are high, the greatest net energy gain is realized with short pause durations. When predator-prey contact rates are low, larvae should achieve greater net energy gains by remaining at rest for extended periods. Larvae observed foraging in the absence of prey do not change behavior as much as the simulation model predicts, suggesting that they use a prey encounter maximization strategy rather than an energy conservation strategy. / by James Joseph Ruzicka. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography, Massachusetts Institute of Technology/Woods Hole Oceanographic Institution, 1988. / Bibliography: p. 182-187. / by John Alexander Barth. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and, the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references (leaves 169-180). / Toxic algae are a growing concern in the marine environment. One unique marine diatom, Pseudo-nitzschia multiseries (Hasle) Hasle, produces the neurotoxin domoic acid, which is the cause of amnesic shellfish poisoning. The molecular characterization of this organism has been limited to date. Therefore, the focus of this thesis was to identify and initiate characterization of actively expressed genes that control cell growth and physiology in P. multiseries, with the specific goal of identifying genes that may play a significant role in toxin production. The first step in gene discovery was to establish a complementary DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries. 2552 cDNAs were sequenced, generating a set of 1955 unique contigs, of which 21% demonstrated significant similarity with known protein coding sequences. Among the genes identified by sequence similarity were several involved in photosynthetic pathways, including fucoxanthin-chlorophyll a/c light harvesting protein and a C4-specific pyruvate, orthophosphate dikinase. Several genes that may be involved in domoic acid synthesis were also revealed through sequence similarity, for example, glutamate dehydrogenase and 5-oxo-L-prolinase. In addition, the identification of sequences that appear novel to Pseudo-nitzschia may provide insight into unique aspects of Pseudo-nitzschia biology, such as toxin production. Genes whose expression patterns were correlated with toxin production were identified by hybridization to a microarray manufactured from 5376 cDNAs. 121 cDNAs, representing 12 unique cDNA contigs or non-redundant cDNAs, showed significantly increased expression levels in P. multiseries cell populations that were actively producing toxin. / (cont.) The up-regulated transcripts included cDNAs with sequence similarity to 3-carboxymuconate cyclase, phosphoenolpyruvate carboxykinase, an amino acid transporter, a small heat shock protein, a long- chain fatty acid Co-A ligase, and an aldo/keto reductase. These results provide a framework for investigating the control of toxin production in P. multiseries. These transcripts may also be useful in ecological field studies in which they may serve as signatures of toxin production. Prospects for further application of molecular genetic technology to the understanding of the physiology and ecology of P. multiseries is discussed. / by Katie Rose Boissonneault. / Ph.D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. / 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 (p. 125-127). / In this thesis, I expand a spatially-explicit bioeconomic fishery model to include the negative effects of fishing effort on habitat quality. I consider two forms of effort driven habitat damage: First, fishing effort may directly increase individual mortality rates. Second, fishing effort may increase competition between individuals, thereby increasing density-dependent mortality rates. I then optimize effort distribution and fish stock density according to three management cases: (1) a sole owner, with jurisdiction over the entire fishery, who seeks to maximize profit by optimizing effort distribution; (2) a manager with limited control of effort and stock distributions, who seeks to maximize tax revenue by setting the length of a single, central reserve and a uniform tax per unit effort outside it; and (3) a manager with even more limited enforcement power, who can only set a tax per unit effort everywhere in the habitat space. I demonstrate that the economic efficiency of reserves depends upon model parameterization. In particular, reserves are most likely to increase profit (or tax revenue) when density-dependent fish mortality rates are affected. Interestingly, for large habitats that are sufficiently sensitive to density-dependent fish mortality effects, reserve networks (alternating fished and unshed areas of fixed periodicity) emerge. These results suggest that spatial forms of management which include marine reserves may enable signicant economic gains over nonspatial management strategies, in addition to the well-established conservation benefits provided by closed areas. / by Holly Villacorta Moeller. / S.M.