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.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 157-171). / Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10³¹ particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed phages (Caudovirales). These phages possess a distinctive icosehedral head, with a protein tail structure protruding from a single vertex. This organelle determines host specificity and provides the mechanism of passage of the phage genome into the host cell. Phages infecting differing microbial hosts may have access to a global pool of genes, albeit at different levels. Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are numerically dominant photosynthetic cells in the large oligotrophic gyres of the open oceans, and contribute an estimated 30% to the oceanic photosynthetic budget. Cyanophages have been isolated which propagate on many strains of Synechococcus and Prochlorococcus. Cyanophages can effect community structure and succession through lytic infection of their hosts, and have implications in lateral gene transfer, mediated through lysogeny, mixed infections, pseudolysogeny, and transduction. / (cont.) The broad host ranges (between genera) observed in some phages indicates that lateral gene transfer is not confined to cells of the same strain. These phage/host interactions begin by host recognition by the tail of the infecting phage. Few studies have examined the structural proteins of cyanophage, partially due to the lack of a robust protocol for the growth and purification of phage particles. Cyanophage Syn5 is a short-tailed phage isolated from the Sargasso Sea by Waterbury and Valois (1993) which infects Synechococcus strain WH8109. Methods of growing the host cells and the phage, and concentrating the phage by PEG precipitation were developed. These methods led to highly concentrated purified phage stocks, to titers of 1012 particles/ml. Preliminary characterization of the growth of Syn5 gave a burst size of approximately 30 phage/cell and a lytic period of approximately 10 hours when inoculated into exponentially growing host cells acclimated to a temperature of 26⁰C and a light intensity of 50[mu]E m⁻² s⁻¹. Isolation of the phage nucleic acid yielded dsDNA molecules of approximately 40kb. The Syn5 particles were comprised of twelve structural proteins, as determined by SDS-PAGE. / (cont.) The most intense band on the gel was assigned to the capsid protein of Syn5 ([approx.] 35kDa). However, it was not possible to distinguish putative tail proteins via this method. Purified Syn5 particles were sent to the Pittsburgh Bacteriophage Institute for genome sequencing. The completed Syn5 genome was 46,214 bp long with a 237bp terminal repeat. Annotation of the completed Syn5 genome identified 61 putative ORFs, and revealed that Syn5 appeared closely related to the enteric phage T7 and cyanophages P-SSP7 and P60, as determined by gene similarity and synteny, although the genome was [approx.] 10kb longer than T7. Syn5 appeared to possess a more extensive DNA replisome that T7, containing copies of genes that encoded proteins of known T7 host co-factors, such as thioredoxin, utilized by the T7 DNAP. Several large ORFs were identified between the gene encoding the putative tail fiber and the gene encoding the putative terminase. These ORFs encoded proteins similar to some fibrous sequences within the NCBI non- redundant (nr) gene sequence database as of March, 2005; but had unknown functions within the phage. Unlike other recently sequenced cyanophages, SynS did not contain any photosynthetic genes. / (cont.) The structural proteins of SynS, as visualized by SDS-PAGE, were characterized by mass-spectroscopy and N-terminal sequencing. This allowed the assignment of sequences to putative ORFs within the Syn5 genome. The Syn5 particle was comprised of eleven discreet protein chains of molecular weight 152kDa, 139kDa, 99kDa, 90kDa, 66kDa, 60kDa, 47kDa, 35kDa, 22kDa, 21kDa, and 16kDa. The identified proteins included the portal, capsid, two tail tube proteins, and three internal virion proteins. Each of the genes encoding these proteins were found in the same gene order in the Syn5 genome as the corresponding genes were ordered in the T7 genome. There were three unidentifiable proteins within the particle (66kDa, 47kDa, and 16kDa). These mapped to the area of the SynS genome between the gene encoding the putative tail fiber and the gene encoding the putative terminase. No minor capsid or decorative capsid proteins were detected. The copy numbers of the corresponding protein chains were similar to those known for T7, with the exception of the tail fiber, which was present at a number of three chains per particle in comparison to T7's eighteen per particle. / (cont.) Polyclonal antibodies were raised against Syn5 particles. A Western blot with these antibodies showed that the tail fiber and the two unknown fibrous sequences were highly antigenic. This evidence implies that the unknown structures may act as host recognition proteins in addition to the tail fiber. Characterization of these novel proteins may provide insight to the host recognition abilities of cyanophages. An additional study was also carried out, investigating the high temperature limit of the growth of phage P22. The results revealed that the production of infectious particles was limited by the temperature sensitivity of the folding and assembly of the P22 tailspike protein. This work has been published and is included in the Appendix. / by Welkin Hazel Pope. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references. / This study is a geochemical investigation of the evolution of the Kerguelen plume, on the basis of upper mantle and lower crustal xenoliths. Ultramafic xenoliths include harzburgites predominant, a lherzolite, dunites and pyroxenites, whereas lower crustal xenoliths are cumulate gabbros recrystallized under granulite facies conditions. On the basis of the whole rock major element characteristics and trace element abundance patterns in clinopyroxenes, the harzburgites were found to be residues of extensive melting at high pressures within the Kerguelen plume. These were then recrystallized at low pressures and metasomatized by plume generated melts. Details of the metasomatic process were determined from trace element variations in clinopyroxene in connection to texture. This demonstrated that meltrock reaction and the precipitation of new clinopyroxenes occurred by metasomatic carbonatitic melts. It was also found that some of the harzburgites had distinctly unradiogenic Os isotopic compositions and were identified as originating from the sub-Gondwanaland lithosphere. On the basis of major and trace element compositions, the granulite xenoliths were found to be originally gabbroic cumulates formed from plume-derived basaltic melts emplaced at the base of the crust by underplating and subsequently recrystallized isobarically under granulite conditions. The Sr, Nd and Os isotopic compositions of the peridotite and granulite xenoliths demonstrate that the Kerguelen plume is isotopically heterogeneous and displays a temporal progression toward more enriched Sr and Nd isotopic compositions from the Ninetyeast Ridge to granulite xenoliths to Kerguelen basalts and Heard Island basalts. / by Deborah Renee Hassler. / Ph.D.

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references. / The goal of this thesis was to use high resolution analytical techniques coupled with molecular level analyses to chemically characterize high molecular weight (> 1 k Da (HMW)) dissolved organic matter (DOM) isolated from seawater in an attempt to provide new insights in to the cycling of DOM in the ocean. While a variety of sites spanning different environments (fluvial, coastal and oceanic) and ocean basins were examined, the chemical structure of the isolated HMW DOM varied little at both the polymer and monomer levels. All samples show similar ratios of carbohydrate:acetate:lipid carbon (80±4:10±2:9±4) indicating that these biochemicals are present within a family of related polymers. The carbohydrate fraction shows a characteristic distribution of seven major neutral monosaccharides: rhamnose, fucose, arabinose, xylose, mannose, glucose and galactose; and additionally contains Nacetylated amino sugars as seen by Nuclear Magnetic Resonance Spectroscopy (NMR). This family of compounds, consisting of a specifically linked polysaccharide backbone that is acylated at several positions, has been termed acylated polysaccharides (APS) by our laboratory. APS accounts for 50% of the carbon in HMW DOM isolated from the surface ocean and 20% of the carbon in HMW DOM isolated from the deep ocean. In order to identify a possible source for APS three species of phytoplankton, Thalassiossira weissflogii, Emiliania huxleyi and Phaeocystis, were cultured in seawater and their HMW DOM exudates examined by variety of analytical techniques. Both the T. weissflogii and E. huxleyi exudates contain compounds that resemble APS indicating that phytoplankton are indeed a source of APS to the marine environment. Furthermore, the degradation of the T. weissflogii exudate by a natural assemblage of microorganisms indicates that the component resembling APS is more resistant to microbial degradation compared to other polysaccharides present in the culture. Molecular level analyses show the distribution of monosaccharides to be conservative in surface and deep waters suggesting that APS is present throughout the water column. In order to determine the mechanism by which APS is delivered to the deep ocean the [delta]14C value of APS in the deep ocean was compared to the A14C value of the dissolved inorganic carbon (DIC) at the same depth. If the formation of deep water is the dominant mode of transport then both the DIC and APS will have similar [delta]14C values. However, if APS is injected into the deep ocean from particles or marine snow then the [delta]14C value of APS will be higher than the DIC at the same depth. Our results indicate that APS in the deep Pacific Ocean carries a modem [delta]14C value and is substantially enriched in 14C relative to the total HMW DOM and the DIC at that depth. Thus, particle dissolution appears to be the most important pathway for the delivery of APS to the deep ocean. / by Lihini I. Aluwihare. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1998. / Includes bibliographical references (v. 2, leaves 423-433). / The goal of this thesis is to develop a methodology to interpret sound scattered from the seafloor in terms of seafloor structure and subseafloor geological properties. Specifically, this work has been directed towards the interpretation of matched-filtered, beam-formed monostatic acoustic reverberation data acquired on the west flank of the Mid-Atlantic Ridge when the seafloor is insonified by a band-limited, lowgrazing- angle acoustic pulse. This research is based on the hypothesis that observed backscatter signals are produced by a combination.of seafloor (interface) scattering and subseafloor (volume) scattering from structure having variations at scale lengths similar to the wavelength of the insonifying acoustic field. Analysis of monostatic reverberation data acquired during the Site A experiment (Run 1) of the Acoustic Reverberation Special Research Program 1993 Acoustics Cruise suggests that the scattered signals cannot be accounted for quantitatively in terms of large-scale slope, even though a strong correspondence between high intensity backscatter and seafloor ridges is observed. In order to investigate and quantify the actual sources of seafloor scattering, a numerical modeling study of seafloor models is undertaken using a finitedifference solution to the elastic wave equation. Geological data available at Site A and published reports describing geological properties of similar deep ocean crustal regions are used to develop a realistic seafloor model for the study area with realistic constraints on elastic parameters. Wavelength-scale heterogeneity in each model, in the form of seafloor roughness and subseafloor volume heterogeneity is defined using stochastic distributions with Gaussian autocorrelations. These distributions are quantified by their correlation lengths and standard deviation in amplitude. In order to incorporate all seafloor structure in a single parameterization of seafloor scattering, large-scale slope and wavelength-scale seafloor spatial parameters (rms height and correlation length), are included, along with the acoustic beam grazing-angle relative to a horizontal seafloor, in the definition of an 'effective grazing angle'. The Rayleigh roughness parameter, which depends on grazing angle of the insonification, is then redefined using the effective grazing angle and calculated for a variety of seafloor models. Scattering strengths are shown to vary systematically but nonlinearly with the 'effective Rayleigh roughness parameters' of horizontal rough seafloor models. This leads to an approximate interpretation scheme for backscatter intensity. In general, variation in backscattering is found to be dominated by the scattering from rough seafloor. If the seafloor is smooth or very low velocity (e.g., sediment), then scattering from volume heterogeneity becomes an important factor in the backscattered field. Both wavelength-scale seafloor roughness and volume heterogeneity are shown to be capable of producing the levels of variation in intensity observed in monostatic reverberation experiments. Variations in large-scale seafloor slope and subseafloor average velocity are shown to influence the backscatter response of seafloor models. / by Robert John Greaves. / Ph.D.