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.

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. 91-99). / Trade-offs between filtration rate and swimming performance among several salp species with distinct morphologies and swimming styles were compared. Small-scale particle encounter at the salp filtering apparatus was also explored. Observations and experiments were conducted at the Liquid Jungle Lab, off the pacific coast of Panama in January 2006 through 2009. First, time-varying body volume was calculated by digitizing salp outlines from in situ video sequences. The resulting volume flow rates were higher than previous measurements, setting an upper limit on filtration capacity. Though each species possessed a unique combination of body kinematics, normalized filtration rates were comparable across species, with the exception of significantly higher rates in Weelia cylindrica aggregates, suggesting a tendency towards a flow optimum. Secondly, a combination of in situ dye visualization and particle image velocimetry (PIV) measurements were used to describe properties of the jet wake and swimming performance variables including thrust, drag and propulsive efficiency. All species investigated swam via vortex ring propulsion. Though Weelia cylindrica was the fastest swimmer, Pegea confoederata was the most efficient, producing the highest weight-specific thrust and wholecycle propulsive efficiency. Weak swimming performance parameters in Cyclosalpa afinis, including low weight-specific thrust and low propulsive efficiency, may be compensated by comparatively low energetic requirements. / (cont.) Finally, a low Reynolds number mathematical model using accurately measured parameters and realistic oceanic particle size concentrations showed that submicron particles are encountered at higher rates than larger particles. Results from feeding experiments with 0.5, 1 and 3 [mu]m po- lystyrene microspheres corroborated model predictions. Though 1 to 10 pm-sized particles (e.g. flagellates, small diatoms) are predicted to provide four times as much carbon as 0.1 to 1 pm- sized particles (e.g. bacteria, Prochlorococcus), particles smaller than the mesh size (1.4 [mu]m) can still fully satisfy salp energetic needs. / by Kelly Rakow Sutherland. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / Includes bibliographical references. / Iron availability and primary productivity in the oceans are intricately linked through photosynthesis. At the global scale we understand how iron addition induces phytoplankton blooms through meso-scale iron-addition experiments. At the atomic scale, we can describe the length and type of bonds that connect iron atoms to components of photosystem I, the most efficient light-harvesting complex in nature. Yet, we know little of how iron influences microbial diversity and distribution in the open ocean. In this study, we assess the influence of iron on the ecology of the numerically abundant marine cyanobacterium, Prochlorococcus. With its minimal genome and ubiquity in the global ocean, Prochlorococcus represents a model system in which to study the dynamics of the link between iron and primary productivity. To this end, we tested the iron physiology of two closely-related Prochlorococcus ecotypes. MED4 is adapted to high-light environments while MIT9313 lives best in low-light conditions. We determined that MIT9313 is capable of surviving at low iron concentrations that completely inhibit MED4. Furthermore, concentrations of Fe' that inhibit growth in culture are sufficient to support Prochlorococcus growth in the field, which raises questions about the species of iron available to Prochlorococcus. We then examined the molecular basis for the ability of MIT9313 to grow at lower iron concentrations than MED4 by assessing whole-genome transcription in response to changes in iron availability in the two ecotypes. / Genes that were differentially expressed fell into two categories: those that are shared by all (Prochlorococcus core genome) and those that are not (non-core genome). Only three genes shared between MED4 and MIT9313 were iron-responsive in both strains. We then tested the iron physiology of picocyanobacteria in the field and found that Synechococcus is iron-stressed in samples where Prochlorococcus is not. Finally, we propose a method to measure how iron stress in Prochlorococcus changes over natural gradients of iron in the oligotrophic ocean by quantifying transcription of the iron-stress induced gene, isiB. Taken together, our studies demonstrate that iron metabolism influences the ecology of Prochlorococcus both by contributing to its diversity and distinguishing it from other marine cyanobacteria. / by Anne Williford Thompson. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 149-162). / Trichodesmium is a colonial, N2-fixing cyanobacterium found in tropical oceans. Species of Trichodesmium are genetically similar but several species exist together in the same waters. In order to coexist, Trichodesmium spp. may occupy different niche spaces through differential utilization of resources such as nutrients and light, and through responses to physical characteristics such as temperature and turbulence. To investigate niche differentiation in Trichodesmium, I characterized cultured strains of Trichodesmium, identified and enumerated Trichodesmium clades in the field, and investigated P stress and N2 fixation in field populations. Species of Trichodesmium grouped into two clades based on sequences from 16S rDNA, the internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. Clade I contained Trichodesmium erythraeum and Trichodesmium contortum, and clade II contained Trichodesmium thiebautii, Trichodesmium tenue, Trichodesmium hildebrandtii, and Trichodesmium pelagicum. Each clade was morphologically diverse, but species within each clade had similar pigmentation. I developed a quantitative polymerase chain reaction (qPCR) method to distinguish between these two clades. In field populations of the Atlantic and Pacific Oceans, the qPCR method revealed that clade II Trichodesmium spp. were more prominent than clade I in the open ocean. Concentrations of Trichodesmium did not correlate with nutrient concentrations, but clade I had wider temperature and depth distributions than clade II. / (cont.) Temperature and light are physical characteristics that may define niche spaces for species of Trichodesmium. Clade I and II concentrations correlated with each other in the Pacific but not in the Atlantic, indicating that the two clades were limited by the same factors in the Pacific while different factors were limiting the abundance of the two clades in the Atlantic. Trichodesmium populations in the North Atlantic were more P stressed and had higher N2 fixation rates than populations in the western Pacific. While nutrient concentrations didn't directly correlate with Trichodesmium concentrations, the contrasting nutrient regimes found in the Atlantic and Pacific Oceans might influence distributions of the two clades differently. Unraveling the differences among species of Trichodesmium begins to explain their coexistence and enables us to understand factors controlling global N2 fixation. / by Annette Michelle Hynes. / Ph.D.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their interactions with bacteria are structured. This challenge arises because the diversity of both bacteria and viruses is exceedingly high and interactions between them are mediated by specific molecular interactions. This thesis uses heterotrophic bacteria of the genus Vibrio as a model to quantify virus-host interactions in light of host population structure and ecology. The methods developed in this thesis include streamlining of standard bacteriophage protocols, such as the agar overlay, and facilitate higher throughput in the isolation and characterization of novel environmental virus-host systems. Here, >1300 newly isolated Vibrio are assayed for infection by viral predators and susceptibility is found to be common, though total concentrations of predators are highly skewed, with most present at low abundance. The largest phylogenetically-resolved host range cross test available to date is conducted, using 260 viruses and 277 bacterial strains, and highly-specific viruses are found to be prevalent, with nearly half infecting only a single host in the panel. Observations of blocks of multiple viruses with nearly identical infection profiles infecting sets of highly-similar hosts suggest that increases in abundance of particular lineages of bacteria may be important in supporting the replication of highly specific viruses. The identification of highly similar virus genomes deriving from different sampling time points also suggests that interactions for some groups of viruses and hosts may be stable and persisting. Genome sequencing reveals that members of the largest broad host-range viral group recovered in the collection have sequence homology to non-tailed viruses, which have been shown to be dominant in the surface oceans but are underrepresented in culture collections. By integrating host population structure with sequencing of over 250 viral genomes it is found that viral groups are genomically cohesive and that closely-related and co-occurring populations of bacteria are subject to distinct regimes of viral predation. / by Anne Kathryn Marie Kauffman. / 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. / Larval supply is an important process linking reproductive output to recruitment of benthic marine invertebrates. Few species-specific studies of bivalve larvae have been performed due to the lack of suitable methods for species identification. This thesis focused on applying a method to identify larvae from field samples from Waquoit Bay, MA using shell birefringence patterns. This method was then used to address variability in larval supply for three bivalve species on weekly, tidal, and hourly scales. Sampling weekly for six months during two years showed large variability in larval concentrations on this time scale. Abundances of most species were related to bay temperature, and species distributions among sampling sites were indicative of transport potential and population coherence. Greater growth of larvae in 2009 compared to 2007 was attributed to more wind-induced mixing and better food availability in 2009. Integrative samples over each tidal event for a 14-day period demonstrated that larvae were mostly constrained by water masses. During a period when there were sharp tidal signals in temperature and salinity, larval concentrations were higher in bay water compared to coastal waters on incoming tides. After a storm event, water mass properties were less distinct between tidal events and a semidiurnal signal in larval concentrations was no longer apparent. The timing of periods of high larval concentrations did not always coincide with periods of highest water mass flux reducing net export in some cases. On an hourly scale, the vertical distribution of larvae affected by water column stratification and strength of tidal flow. Strong currents and a fresh upper layer both prevented larvae from concentrating at the surface. There was little evidence of peaks in larval concentrations associated with a given tidal period. Species-specific data can provide new perspectives on larval transport. For the three species studied, Anomia simplex, Guekensia demissa, and Mercenaria mercenaria, different source areas, patterns for growth, and potential for export were observed. Applying species-specific identification methods to future studies of bivalve larval transport has the potential to relate larval abundance to settlement patterns, an important component of larval ecology and shellfish management. / by Christine Mingione Thompson. / 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), 2003. / Includes bibliographical references (p. 132-139). / Iron (Fe) is an essential micronutrient for marine phytoplankton often limiting phytoplankton growth due to its low concentration in the ocean and thus playing a role in modulating the ocean's biological pump. In order to understand controls on global Fe distribution, the decoupling between Fe and P04 and the sensitivity of surface nutrient concentrations to changes in aeolian iron supply, I use a hierarchy of ocean circulation and biogeochemistry models. I formulate a mechanistic model of iron cycling which includes scavenging onto sinking particles and complexation with an organic ligand. The iron cycle is coupled to a model of the phosphorus cycle. The aeolian source of iron is prescribed. This system is examined in the context of a highly idealized box model. With appropriate choice of parameter values, the model can be brought into consistency with the relatively sparse ocean observations of iron in the oceans. I implement this biogeochemical scheme in a coarse resolution ocean general circulation model, guided by the box model sensitivity studies. This model is also able to reproduce the broad regional patterns of iron and phosphorus. In particular, the high macro-nutrient concentrations of the Southern Oceans result from iron limitation in the model. I define a tracer, Fe* that quantifies the degree to which a water mass is iron limited. Surface waters in high nutrient, low chlorophyll regions have negative Fe* values, indicating Fe limitation, because aeolian surface dust flux is not sufficient to / (cont.) compensate for the lack of iron in upwelled waters. The oceanic residence time of Fe is [approximately] 285 years in the model, confirming that transport plays an important role in controlling deep water [Fe[Tau]]. Globally, upwelling accounts for 40% of 'new' iron reaching the euphotic zone. Due to the potential ability of iron to change the efficiency of the carbon pump in the remote Southern Ocean, I study Southern Ocean surface P04 response to increased aeolian dust flux. My box model results suggest that a global ten fold increase in dust flux can support a P04 drawdown of [approximately]0.25[mu]M, while the GCM results suggest a P04 drawdown of 0.5 [mu]M. / by Payal Parekh. / Ph.D.