Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Zooplankton, such as copepods, are highly abundant environmental reservoirs of many bacterial pathogens. Although copepods are known to support diverse and productive bacterial communities, little is understood about whether copepods are affected by bacterial attachment and whether they can regulate these associations through mechanisms such as the innate immune response. This thesis investigates the potential role that copepod physiology may play in regulating Vibrio association and the community structure of its microbiome. To this end, the intrinsic ability of oceanic copepod hosts to transcriptionally respond to mild stressors was first investigated. Specifically, the transcriptional regulation of several heat shock proteins (Hsps), a highly conserved superfamily of molecular chaperones, in the copepod Calanusfinmarchicus was examined and demonstrated that Hsps are a conserved element of the copepod's transcriptional response to stressful conditions and diapause regulation. To then investigate whether copepod hosts respond to and regulate their microbiota, the transcriptomic response of an estuarine copepod Eurytemora affinis to two distinct Vibric species, a free-living strain (V. ordalii 12B09) and a zooplankton specialist (V. sp. F10 9ZB36), was examined with RNA-Seq. Our findings provide evidence that the copepod E. affinis does distinctly recognize and respond to colonizing vibrios via transcriptional regulation of innate immune response elements and transcripts involved in maintaining cuticle integrity. Our work also suggests that association with E. affinis can significantly impact the physiology of Vibrio colonists. Finally, the inter-individual variability of the C.finmarchicus microbiome was examined to identify how specifically and predictably bacterial communities assemble on copepods and whether host physiology influences the bacterial community structure. Our findings suggest that copepods have a predictable "core microbiome" that persists throughout the host's entrance into diapause, a dormancy period characterized by dramatic physiological changes in the host. However, diapausing and active populations harbor distinct flexible microbiomes which may be driven by factors such including the copepod's feeding history, body size, and bacterial interactions. This thesis work highlights the role of copepods as dynamic reservoirs of diverse bacterial communities and implicates copepod host physiology as an important contributor to the activity, abundance, and community structure of its microbiome. / by Amalia Aruda Almada. / 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. / The mechanisms of faunal dispersal across ocean basins are key unknowns toward understanding of the modern biogeography and biodiversity of deep-sea fauna. Seamounts are considered to play a defining role in faunal evolution, acting as regional centers of speciation, "stepping-stones" for dispersal, and/or refugia for deep-sea populations. The overarching goal of this dissertation was to examine the role of seamounts in structuring marine biodiversity and biogeography. This study focused on North Atlantic seamounts, specifically the New England seamount chain, the Corner Rise seamounts, and Muir seamount, areas damaged and threatened by deep-sea fisheries and currently a focus of conservation efforts. Videographic analyses of biological community structure revealed distinct faunal assemblages, dominated by the Porifera, Cnidaria, and Echinodermata and structured by geographic region, depth regions (with apparent taxonomic breaks at 1300 m, 2300 m, and 2600 m), and substrate type (including natural/anthropogenic and abiotic substrates and biotic substrates). Amongst these assemblages, seven highly specific coral host- invertebrate associate relationships were identified. To investigate whether or not these broad community patterns were discernible at a genetic level, the 16S mtDNA gene was utilized as a genetic "barcode" within the Class Ophiuroidea, through which 22 putative species were identified, including four target species (Asteroschema clavigera, Ophiocreas oedipus, Ophioplinthaca abyssalis, and Ophioplinthaca chelys) for subsequent population genetic studies. Analyses of mitochondrial 16S and COI gene sequences revealed evidence for recent population expansion and estimates of recent high gene flow across all four species throughout the North Atlantic seamount region. / (cont.) However, genetic differentiation within populations of A. clavigera and 0. chelys within seamount regions was significant, suggesting that historical diversification has been mediated by a long-distance dispersal mechanism that homogenizes this genetic signal on a regional scale. In addition, comparisons of all ophiuroid populations revealed no congruent pattern of historical migration amongst seamounts, which may also be attributed to the varying levels of host specificity and reproductive strategy of each ophiuroid species. These results will guide future studies and conservation efforts to protect seamount communities vulnerable to deep-sea fishery activities. / by Walter W. Cho. / 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), 2000. / Vita. / Includes bibliographical references. / by Robert P. Ackert, Jr. / 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. / As the only low-latitude connection between ocean basins, the Indonesian Throughflow allows the direct transmission of heat and salinity between the Pacific and Indian Oceans. Despite its potential importance, the role of the Indonesian Throughflow in global ocean circulation and regional climate is still not clear due to sparse measurements and the relative difficulty of modeling the region. The Mg/Ca and [delta]¹⁸0 of calcite of the calcitic planktic foraminifera Globigerinoides ruber (G. ruber) were used to estimate the sea surface temperature and [delta]¹⁸0 of water, an indicator of hydrologic conditions, over the past 20,000 years. I also attempted to estimate thermocline structure using the foraminifera, Pulleniatina obliquiloculata, but the Mg/Ca and [delta]¹⁸0 of calcite data yield conflicting interpretations, indicating further work on this proxy is required. The G. ruber Mg/Ca results suggest that the sea surface temperature of the outflow passages was influenced by high latitude Southern Hemisphere temperature. This connection is likely via intermediate waters that upwell in the Banda Sea. At approximately 10,000 years before present, there was a warming in the Makassar Strait. This local warming was coincident with the flooding of the Sunda Shelf, which opened a connection between the South China Sea and the Indonesian Throughflow. Regional [delta]¹⁸0 of seawater reconstructions show that during the last glacial maximum the [delta]¹⁸0 of seawater pattern was very similar to modern, but there were relatively enriched values over the equatorial IndoPacific during high latitude Northern Hemisphere cold events (Heinrich Stadial 1 and the Younger Dryas). From these results we postulate that the mean position of the Intertropical Convergence Zone was approximately the same as modern at the last glacial maximum and was likely displaced to the south during the Younger Dryas and Heinrich Stadial 1, suggesting the Intertropical Convergence Zone primarily responds to changes in the interhemispheric temperature gradient. These results shed light on the primary controls of the temperature and hydrology of Indonesian Throughflow region. / by Fern Tolley Gibbons. / Ph.D.

Thesis: Ph. D., Joint Program in Marine Chemistry and Geochemistry (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Hydrophobic organic chemicals (HOCs) are a class of environmental contaminants responsible for numerous acute and chronic health effects in humans and wildlife. This thesis illustrates three applications of polyethylene (PE) passive sampling, which enhance our toolbox for estimating environmental hazards associated with HOCs. First, we present a methodology that can be used to estimate the bioaccumulation potential of numerous organic chemicals based on passive sampling and comprehensive two dimensional gas chromatography (GC x GC). Using GC x GC retention times, we show that lipid-water and samplerwater partition coefficients can be estimated within a factor of 2 and 3, respectively. The method was then applied to estimate body burdens of various HOCs in benthic organisms from GC x GC analysis of PE equilibrated with contaminated sediment. Empirical observations of accumulation in the Nereis virens polychaete were in good agreement with PE-based predictions for PCBs, but were lower by at least an order of magnitude for other classes of HOCs (such as PAHs) presumably due to metabolism. Second, we applied the same methodology to a set of contaminated sediments and estimated the cumulative baseline toxicity associated with environmental mixtures of HOCs. The predictions were compared against empirical measurements of baseline toxicity using the water flea Daphnia magna. The estimated total body burdens of HOCs were in good agreement with measured toxicity, with toxicity occurring at body burdens larger than 30 mg/gipid. In contrast, the toxicity estimated based on priority pollutants severely underestimated the observed toxicity, emphasizing the importance of cumulative effects. Lastly, to advance our understanding of the processes that affect passive sampling results in situ (when they are operating away from equilibrium), a mathematical model was developed for reactive chemicals transferring between PE and sediment beds. The reaction diffusion model was used to infer in situ degradation rates of dichlorodiphenyltrichloroethane (DDT), which in the sediments of a freshwater lake were found to be between 0.09 and 0.9 d-1. A second mathematical model describing the kinetics of exchange between passive samplers and water was also developed, which can be used in both field (infinite baths) and laboratory (finite baths) conditions. / by Alexandra Patricia Tcaciuc. / Ph. D.

Thesis: Ph. D., Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 169-190). / Terrestrial organic carbon (OC) erosion, remineralization, transport through river networks, and burial in marine sediments is a major pathway of the global carbon cycle. However, our ability to constrain these processes and fluxes is largely limited by (i) analytical capability and (ii) temporal sampling resolution. To address issue (i), here I discuss methodological advancements and data analysis techniques for the Ramped PyrOx serial oxidation isotope method developed at WHOI. Ramped-temperature pyrolysis/oxidation coupled with the stable carbon (¹²C, ¹³C) and radiocarbon (¹⁴C) analysis of evolved CO₂ is a promising tool for understanding and separating complex OC mixtures. To quantitatively investigate distributions of OC source, reservoir age, and chemical structure contained within a single sample, I developed a kinetic model linking RPO-derived activation energy, ¹³C composition, and radiocarbon content. This tool provides a novel method to fundamentally address the unknown relationship between OC remineralization rates and chemical structure in various environmental settings. To address issue (ii), I additionally present results from time-series sample sets collected on two end-member systems: the Congo River (Central Africa) and the LiWu River (Taiwan). For the Congo River, bulk and plant-wax-lipid ¹³C compositions indicate that a majority of particulate OC is consistently derived from downstream, C₃-dominated rainforest ecosystems. Furthermore, bulk radiocarbon content and microbial lipid molecular distributions are strongly correlated with discharge, suggesting that pre-aged, swamp-forest-derived soils are preferentially exported when northern hemisphere discharge is highest. Combined, these results provide insight into the relationship between hydrological processes and fluvial carbon export. Lastly, I examined the processes controlling carbon source and flux in a set of soils and time-series fluvial sediments from the LiWu River catchment located in Taiwan. A comparison between bedrock and soil OC content reveals that soils can contain significantly less carbon than the underlying bedrock, suggesting that this material is remineralized to CO₂ prior to soil formation. Both the presence of bacterial lipids and a shift toward lower activation energy of ¹⁴C-free OC contained in soil saprolite layers indicate that this process is microbially mediated and that microbial respiration of rock-derived OC likely represents a larger geochemical flux than previously thought. The results presented in this thesis therefore provide novel insight into the role of rivers in the global carbon cycle as well as their response to environmental perturbations. / by Jordon Dennis Hemingway / 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), 2005. / Includes bibliographical references (p. 131-149). / This thesis evaluates the nature and magnitude of tropical climate variability from the Last Glacial Maximum to the present. The temporal variability of two specific tropical climate phenomena is examined. The first is the position of the Intertropical Convergence Zone (ITCZ) in the Atlantic basin, which affects sea surface temperature (SST) and precipitation patterns throughout the tropical Atlantic. The second is the strength of the Indian Monsoon, an important component of both tropical and global climate. Long-term variations in the position of the ITCZ in the Atlantic region are determined using both organic geochemical techniques and climate modeling. Upwelling in Cariaco Basin is reconstructed using chlorin steryl esters as proxies for phytoplankton community structure. We find that the diatom population was larger during the Younger Dryas cold event, indicating that upwelling was enhanced and the mean position of the ITCZ was farther south during the Younger Dryas than it is today. A climate simulation using an ocean-atmosphere general circulation model confirms these results by demonstrating that the ITCZ shifts southward in response to high-latitude cooling. The climate of the Arabian Sea region is dominated by the Indian Monsoon. / (cont.) Results from modern sediments from a suite of cores located throughout the Arabian Sea suggest that wind strength is well represented by the accumulation rate and carbon isotopic composition of terrestrially-derived plant waxes in sediments. Arabian Sea SST patterns, reconstructed from a suite of sediment cores representing four time slices utilizing the Mg/Ca SST proxy, suggest that both the summer and winter monsoons were enhanced 8,000 yr BP relative to today while the summer monsoon was weaker and the winter monsoon stronger at 15,000 and 20,000 yr. These results are confirmed by a time-series reconstruction of SST on the Oman Margin that reveals that SST at this site is sensitive to both regional and global climate processes. The results of this thesis demonstrate that tropical climate, as evaluated by a number of different proxies as well as climate models, has varied substantially over the past 20,000 years and is closely coupled to climate at high-latitudes. / by Kristina Ariel Dahl. / 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), 2004. / Includes bibliographical references (p. 188-198). / Relatively little is known about the role of eddies in controlling subduction in the eastern half of the subtropical gyre. Here, a new tool to study the eastern North Atlantic Ocean is created by combining a regional, eddy-resolving numerical model with observations to produce a state estimate of the ocean circulation. The estimate is a synthesis of a variety of in-situ observations from the Subduction Experiment, TOPEX/POSEIDON altimetry, and the MIT General Circulation Model. A novel aspect of this work is the search for an initial eddy field and eddy-scale open boundary conditions by the use of an adjoint model. The adjoint model for this region of the ocean is stable and yields useful information despite concerns about the chaotic nature of eddy-resolving models. The method is successful because the dynamics are only weakly nonlinear in the eastern region of the subtropical gyre. Therefore, no fundamental obstacle exists to constraining the model to both the large scale circulation and the eddy scale in this region of the ocean. Individual eddy trajectories can also be determined. The state estimate is consistent with observations, self-consistent with the equations of motion, and it explicitly resolves eddy-scale motions with a 1/6⁰ grid. Therefore, subduction rates, volume budgets, and buoyancy budgets are readily diagnosed in a physically interpretable context. Estimates of eddy subduction for the eastern subtropical gyre of the North Atlantic are larger than previously calculated from parameterizations in coarse-resolution models. Eddies contribute up to 40 m/yr of subduction locally. Furthermore, eddy subduction rates have typical magnitudes of 15% of the total subduction rate. To evaluate the net effect of eddies on an individual density class, / (cont.) volume budgets are diagnosed. Eddies contribute as much as 1 Sv to diapycnal flux, and hence subduction, in the density range 25.5 < [sigma] < 26.5. Eddies have a integrated impact which is sizable relative to the 2.5 Sv of diapycnal flux by the mean circulation. A combination of Eulerian and isopycnal maps suggest that the North Equatorial Current and the Azores Current are the geographical centers of eddy subduction. The findings of this thesis imply that the inability to resolve or accurately parameterize eddy subduction in climate models would lead to an accumulation of error in the structure of the main thermocline, even in the eastern subtropical gyre, which is a region of comparatively weak eddy motions. / by Geoffrey Alexander Gebbie. / 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), 2007. / Includes bibliographical references. / Basaltic ocean crust has the potential to host one of the largest endolithic communities on Earth. This portion of the biosphere, however, remains largely unexplored. In this study, we utilize molecular biological, microscopic, and geochemical tools to gain a better understanding of the geomicrobiology of the ocean crust. Specifically, we examine the phylogenetic diversity of microorganisms inhabiting basaltic lavas, the activities and abundances of these microorganisms, the spatial extent of the biosphere, and the potential effect that microbial activity has on the geochemistry of the ocean crust and overlying water column. Our study demonstrates that young, fresh volcanic lavas near mid-ocean ridges host an incredibly diverse and dense population of microorganisms dominated by Bacteria, quite distinct from the microbial communities found in surrounding deep seawater and hydrothermal vents. Furthermore, these communities may contribute to the elemental cycling of Fe, S, Mn, N, and C in this environment. The inability to definitively identify microorganisms in drill-cores of old (> 15 Ma) ocean crust, however, implies that these once prolific communities may become scarce as the crust ages and moves further away from the ridge axis. Finally, we provide evidence suggesting that these communities are fueled by oxidative alteration reactions occurring in the basaltic crust. / by Cara M. Santelli. / 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), 2007. / Includes bibliographical references. / A 225-year old coral from the south shore of Bermuda (64°W, 320N) provides a record of decadal-to-centennial scale climate variability. The coral was collected live, and sub-annual density bands seen in x-radiographs delineate cold and warm seasons allowing for precise dating. Coral skeletons incorporate strontium (Sr) and calcium (Ca) in relative proportions inversely to the sea surface temperature (SST) in which the skeleton is secreted. [Delta]180 of the coral skeleton changes based on both temperature and the [delta]180 of sea water ([delta]Ow), and 6Ow is proportional to sea surface salinity (SSS). Understanding long-term climate variability requires the reconstruction of key climate parameters, such as sea surface temperature (SST) and salinity, in records extending beyond the relatively short instrumental period. The high accretion rates, longevity, and skeletal growth bands found in coral skeletons make them an ideal resource for well-dated, seasonal climate reconstructions. Growing between 2 and 6 mm/year and reaching more than im in length, slow-growing corals provide multi-century records from one colony. Additionally, unlike the fast growing (10-20 mm/year) species Porites, slow-growing species are generally found in both tropical and sub-tropical locations greatly expanding the geographical location of these records. A high resolution record (HRR, ~11 samples per year) was drilled for the entire length of the coral record (218 years). Samples were split and Sr/Ca, [delta]180, and [delta]13C were measured for each sample. Sr/Ca was used to reconstruct winter time and mean-annual SST. Oxygen isotopic measurements were used to determine directional salinity changes, in conjunction with Sr/Ca based SST reconstructions. / (cont.) Winter-time and mean annual SSTs show SSTs -1.5 'C colder during the end of the Little Ice Age (LIA) relative to today. Simultaneously, SSS is fresher during that time. Sr/Ca based climate reconstructions from coral skeletons have been met with some skepticism because some reconstructions show temperature changes back in time that are 2-4 times greater than the reconstructions of other marine proxies. In this study, we show that when using bulk-sampled, slow-growing corals, two steps are critical to producing accurate reconstructions: 1) incorporating growth rate into multi-variant regressions with SST and Sr/Ca and 2) using multiple colonies that grew at the same time with varying average growth rates and Sr/Ca. Application of these novel methods over the period of the instrumental record from Hydrostation S (monthly since 1954, 32°10'N, 64°30'W) reduces the root mean square of the residuals between the reconstructed SST and the instrumental SST by as much as 1.52'C to 0.460C for three coral colonies. Winter-time SSTs at Bermuda are correlated to phases of the North Atlantic Oscillation (NAO), a meridional oscillation in atmospheric mass. Much uncertainty remains about the relationship between the NAO and the ocean, and one critical outstanding question is whether anthropogenic changes are perturbing the system. Using winter Sr/Ca as a proxy for temperature, we show strong coherence to the NAO at multi-decadal and inter-annual frequencies. These coral records show significant changes in variance in the NAO during the late 20th century compared to the cooler LIA, but limited changes in the mean phase (positive or negative) of the NAO, implying that climate change may be pushing the NAO to extremes but not to a new mean position. / by Nathalie Fairbank Goodkin. / Ph.D.