Symbiosis is one of the most widespread evolutionary strategies on Earth. In the deep-sea, symbioses between chemosynthetic bacteria and invertebrates are abundant at hydrothermal vents and cold seeps. These mutualisms, in which symbiont carbon fixation provides for host nutrition, are analogous to the ancient endosymbioses that resulted in the chloroplast and the eukaryotic mitochondrion. However, the evolutionary processes that led to the widespread dispersal of deep-sea organisms and the mechanisms by which symbioses are initiated and maintained are poorly characterized. This thesis examined the evolution of deep-sea mussels (Bathymodiolinae) and their chemosynthetic symbionts. Bathymodioline mussel taxonomy is in need of a comprehensive systematic revision because the majority of named genera do not constitute monophyletic groups. First, this thesis demonstrated that mussels found on the Northeast Pacific Ridges are members of Adipicola, a paraphyletic genus within Bathymodiolinae, refining the evolutionary history of this poorly characterized group. Second, an updated multi-locus phylogeny of bathymodiolines was presented and used to evaluate the statistical evidence for previously proposed hypotheses describing the directional evolution of bathymodioline traits. The results indicated that patterns of directional evolution in this group are not well supported and instead suggests that trait evolution has proceeded in a non-directional manner. Third, this thesis presented the first evidence of detection and abundance of bathymodioline symbionts in the deep-sea environment, providing direct evidence that these symbionts are environmentally acquired. Fourth, this thesis presented the first multi-locus phylogenies of bathymodioline symbionts and tested the hypothesis of environmental acquisition of symbionts in this group. The results demonstrated that symbiont and host lineages are decoupled, which is consistent with the environmental acquisition hypothesis. Finally, environmental acquisition implies that symbionts have opportunities to exchange genetic information with other bacterial strains and evidence for recombination in bathymodioline symbionts is also presented. This thesis advances our understanding of the evolutionary history of bathymodioline symbioses by clarifying host and symbiont evolutionary history and symbiont transmission strategy. In aggregate, these results suggest that bathymodiolines are more flexible with regard to the habitats they inhabit and the symbionts they harbor than previously understood.

abstract: Phytoplankton comprise the base of the marine food web, and, along with heterotrophic protists, they are key players in the biological pump that transports carbon from the surface to the deep ocean. In the world's subtropical oligotrophic gyres, plankton communities exhibit strong seasonality. Winter storms vent deep water into the euphotic zone, triggering a surge in primary productivity in the form of a spring phytoplankton bloom. Although the hydrographic trends of this "boom and bust" cycle have been well studied for decades, community composition and its seasonal and annual variability remains an integral subject of research. It is hypothesized here that proportions of different phytoplankton and protistan taxa vary dramatically between seasons and years, and that picoplankton represent an important component of this community and contributor to carbon in the surface ocean. Monthly samples from the Bermuda Atlantic Time-series Study (BATS) site were analyzed by epifluorescence microscopy, which permits classification by morphology, size, and trophic type. Epifluorescence counts were supplemented with flow cytometric quantification of Synechococcus, Prochlorococcus, and autotrophic pico- and nanoeukaryotes. Results from this study indicate Synechococcus and Prochlorococcus, prymnesiophytes, and hetero- and mixotrophic nano- and dinoflagellates were the major players in the BATS region plankton community. Ciliates, cryptophytes, diatoms, unidentified phototrophs, and other taxa represented rarer groups. Both flow cytometry and epifluorescence microscopy revealed Synechococcus to be most prevalent during the spring bloom. Prymnesiophytes likewise displayed distinct seasonality, with the highest concentrations again being noted during the bloom. Heterotrophic nano- and dinoflagellates, however, were most common in fall and winter. Mixotrophic dinoflagellates, while less abundant than their heterotrophic counterparts, displayed similar seasonality. A key finding of this study was the interannual variability revealed between the two years. While most taxa were more abundant in the first year, prymnesiophytes experienced much greater abundance in the second year bloom. Analyses of integrated carbon revealed further stark contrasts between the two years, both in terms of total carbon and the contributions of different groups. Total integrated carbon varied widely in the first study year but displayed less fluctuation after June 2009, and values were noticeably reduced in the second year. / Dissertation/Thesis / M.S. Microbiology 2010

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 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.

The deep ocean holds a diversity of life that remains to be discovered and described. Marine ecosystems fueled by chemosynthesis, such as hydrothermal vents and hydrocarbon seeps, represent biodiversity hotspots along the ocean floor. Yet, investigations into the diversity, genetic connectivity, and biogeography of life at such ecosystems are still ongoing. The present dissertation explores the diversity and biogeography of deep-sea gastropod mollusks from hydrocarbon seeps at the Pacific Costa Rica Margin to understand what factors lead to the generation and maintenance of novel biodiversity at chemosynthesis-based ecosystems in the ocean. The Pacific Costa Rica Margin was extensively sampled and explored between 2017 and 2019 and yielded an abundance and diversity of marine life. Gastropod mollusks were chosen as the model organisms for this research as they are taxonomically diverse, are found in high abundance, and occur at chemosynthesis-based ecosystems worldwide. Integrating taxonomic, phylogenetic, population genetic, and biogeographic methods, this dissertation contributes new species, occurrence records, genetic data, taxonomic tools, and biogeographic knowledge for deep-sea gastropods. As global biodiversity continues to be threatened by anthropogenic impacts such as overexploitation and climate change, documenting and understanding deep-sea biodiversity and the factors that influence it is of critical importance. / Biology

Polar regions impose harsh conditions, including low temperatures, and prolonged periods of darkness on resident microbial communities. Despite these challenges, the conditions in these environments can also create opportunities for organisms utilizing combined trophic strategies (Mixotrophy). Only a limited number of studies have identified mixotrophic behavior in polar microbial eukaryotes, and even fewer studies have quantified the response of mixotrophs to likely environmental drivers of trophic behavior (light and nutrients). The goal of this work is to provide an identification of mixotrophic behavior and elucidate of some of the factors that influence algae isolated from polar environments. First, a study of the Arctic prasinophyte, Micromonas pusilla is presented in the first species-specific identification of mixotrophy in a eukaryotic phytoflagellate of this size class. M. pusilla grazed on bacteria under all experimental conditions, responding to nutrient limitation with increased rates of bacterivory. M. pusilla also showed evidence of prey selection. In contrast to the phagotrophic response, photosynthetic production was decreased under low-nutrient conditions. In an additional study of microbial eukaryotes from the Antarctic environment, identification of phagotrophy in photosynthetic nanoflagellates representing multiple evolutionary lineages: Cryptophyceae (Geminigera cryophila) and Prasinophyceae (Pyramimonas tychotreta and Mantoniella antarctica), showed that mixotrophy is more widespread in the Southern ocean that previously thought. G. cryophila and M. antarctica increased ingestions in dark treatments, but did not respond to difference in nutrient concentrations. In contrast, no significant grazing activity was observed in P. tychotreta under high nutrient conditions. When nutrients were reduced, ingestion of bacteria by P. tychotreta was observed and grazing increased in dark as compared to illuminated treatments. Finally, through a series of experimental assays, the competitive advantages of mixotrophic flagellates as opposed to monotrophic specialists were evaluated, using organisms isolated from the Southern Ocean. In these experiments, G. cryophila is emerged as a dominant competitor against two solely autotrophic diatoms (Fragilaria sp. and Fragilariopsis sp.). In contrast, P. tychotreta was outcompeted by the solely heterotrophic chrysophyte Paraphysomonas antarctica. These results show that mixotrophic ability can confer advantages to organisms in some cases, while in other interactions the cost associated with maintenance of multiple trophic strategies results in competitive exclusion by a specialist. These results present novel identification as well as rigorous investigation of mixotrophic behaviors in phototrophic flagellates from both polar (Arctic and Antarctic) environments representing two evolutionary lineages. This work provides a significant contribution to our understanding of the versatile nature of the physiology and trophic ecology of microbial eukaryotic organisms occupying polar marine ecosystems. / Biology