Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / 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 (pages 169-182). / Protists play important roles in grazing and nutrient recycling, but quantifying these roles has been hindered by difficulties in collecting, culturing, and observing these often-delicate cells. During long-term deployments at the Martha's Vineyard Coastal Observatory (MVCO) (Massachusetts, USA), Imaging FlowCytobot (IFCB) made it possible to study live cells in situ without the need to culture or preserve. IFCB records images of cells with chlorophyll fluorescence above a trigger threshold, so taxonomically resolved analysis of protists is limited to mixotrophs and herbivores, which have eaten recently. To overcome this limitation, I coupled a broad-application 'live cell' fluorescent stain with a modified IFCB so that protists which do not contain chlorophyll (such as consumers of unpigmented bacteria and other heterotrophs) can also be recorded. Staining IFCB (IFCB-S) revealed higher abundances of grazers than the original IFCB, as well as some cell types not previously detected. To analyze a 10-year time series of herbivorous ciliates at MVCO and address broad patterns of seasonality of major ciliate classes and their components, I employed a statistical model that estimates a seasonal density pattern and simultaneously accounts for and separates any annual-scale effects. I describe the seasonality of three functional groups: a phototrophic ciliate, a mixotroph, and a group of strict heterotrophs, and comment on potential drivers of these patterns. DNA sequencing has also contributed to the study of protist communities, providing new insight into diversity, predator-prey interactions, and discrepancies between morphologically defined species and genotype. To explore how well IFCB images can be used to detect seasonal community change of the class Spirotrichea, an important and numerous group, I used high-throughput sequencing (HTS), which does not discriminate between chlorophyll-containing cells and the rest of the community. I report on species and genera of ciliates for which morphotype and genotype displayed high congruency. In comparing how well temporal aspects of genotypes and morphotypes correspond, I found that HTS was critical to detect and identify certain ciliates occupying a niche associated with warmer temperatures. I further showed that when these types of analyses are combined with IFCB results, they can provide hypotheses about food preferences. / by Emily Fay Brownlee. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 131-143). / Coral reefs are biodiverse ecosystems that are at risk of degradation as a result of environmental changes. Reefs are constantly in a state of flux: the resident species assemblages vary considerably in space and time. However, the drivers of this variability are poorly understood. Tracking these changes and studying how coral reefs respond to natural and anthropogenic disturbance can be challenging and costly, particularly for reefs that are located in remote areas. Because many reef animals produce and use sound, recording the ambient soundscape of a reef might be one way to efficiently study these habitats from afar. In this thesis, I develop and apply a suite of acoustics-based tools to characterize the biological and anthropogenic acoustic activity that largely comprises marine soundscapes. First, I investigate links between reef fauna and reef-specific acoustic signatures on coral reefs located in the U.S. Virgin Islands. Second, I compare those findings to a more expansive study that I conducted in Maui, Hawaii, in which the drivers of bioacoustic differences among reefs are explored. Third, I investigate the distances over which sounds of biological origin may travel away from the reef and consider the range within which these acoustic cues might be usable by pelagic larvae in search of a suitable adult habitat. Fourth, I assess the extent to which the presence of vessel noise in shallow-water habitats changes the ambient soundscape. Finally, I present the results of a modeling exercise that questions how ocean noise levels might change over the next two decades as a result of major projected increases in the number and size of and distance traveled by commercial ships. The acoustics-based tools presented here help provide insight into ecosystem function and the extent of human activity in a given habitat. Additionally, these tools can be used to inform an effective regulatory regime to improve coral reef ecosystem management. / by Maxwell Bernard Kaplan. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 113-127). / White sharks (Carcharodon carcharias) are highly migratory, ecologically important, vulnerable, and understudied marine predators. Ecogeochemistry, which takes advantage of natural variations in chemical signatures recorded in body tissues, can help determine lifetime movement, age, and ontogenetic diet history in difficult to study species. Shark vertebrae are constructed of distinct layers of tissue laid down sequentially over an individual's lifetime and may preserve a chemical record of environmental exposure. In this thesis, I investigate the ecology of the understudied northwest Atlantic (NWA) white shark population by applying several ecogeochemistry techniques to their vertebrae. I generate the first radiocarbon ([delta]¹⁴C) age estimates for adult white sharks, dramatically extending the maximum age and longevity compared to earlier age studies. [delta]¹⁴C results also verify a lack of reworking of vertebral material and hint at possible sexual dimorphism in growth rates. Using amino acid and bulk stable isotope analyses, I show that individual sharks have marked variation in feeding and movement, and that pinnipeds do not constitute a large portion of their diet. Finally, I explore the utility of elemental chemistry to retrospectively infer movement. This work provides an important informational baseline for future NWA white shark ecological studies and conservation and management efforts. / by Li Ling Hamady. / 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 (p. 147-166). / The ecological integrity of tropical habitats, including mangroves, seagrass beds and coral reefs, is coming under increasing pressure from human activities. Many coral reef fish species are thought to use mangroves and seagrass beds as juvenile nurseries before migrating to coral reefs as adults. Identifying essential habitats and preserving functional linkages among these habitats is likely necessary to promote ecosystem health and sustainable fisheries on coral reefs. This necessitates quantitative assessment of functional connectivity among essential habitats at the seascape level. This thesis presents the development and first application of a method for tracking fish migration using amino acid (AA) 13C analysis in otoliths. In a controlled feeding experiment with fish reared on isotopically distinct diets, we showed that essential AAs exhibited minimal trophic fractionation between consumer and diet, providing a 513C record of the baseline isoscape. We explored the potential for geochemical signatures in otoliths of snapper to act as natural tags of residency in seagrass beds, mangroves and coral reefs in the Red Sea, Caribbean Sea and Eastern Pacific Ocean. The 13C values of otolith essential AAs varied as a function of habitat type and provided a better tracer of residence in juvenile nursery habitats than conventional bulk stable isotope analyses (SIA). Using our otolith AA SIA approach, we quantified the relative contribution of coastal wetlands and reef habitats to Lutjanus ehrenbergii populations on coastal, shelf and oceanic coral reefs in the Red Sea. L. ehrenbergii made significant ontogenetic migrations, traveling more than 30 km from juvenile nurseries to coral reefs and across deep open water. Coastal wetlands were important nurseries for L. ehrenbergii; however, there was significant plasticity in L. ehrenbergii juvenile habitat requirements. Seascape configuration played an important role in determining the functional connectivity of L. ehrenbergii populations in the Red Sea. The compound-specific SIA approach presented in this thesis will be particularly valuable for tracking the movement of species and life-stages not amenable to conventional tagging techniques. This thesis provides quantitative scientific support for establishing realistic population connectivity models that can be used to design effective marine reserve networks. / by Kelton Wells McMahon. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / Page 242 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / Recent work has documented dramatic changes in the West Antarctic Ice Sheet (WAIS) over the past 30 years (e.g., mass loss, glacier acceleration, surface warming) due largely to the influence of the marine environment. WAIS is particularly vulnerable to large-scale atmospheric dynamics that remotely influence the transport of marine aerosols to the ice sheet. Understanding seasonal- to decadal-scale changes in the marine influence on WAIS (particularly sea-ice concentration) is vital to our ability to predict future change. In this thesis, I develop tools that enable us to reconstruct the source and transport variability of marine aerosols to West Antarctica in the past. I validate new firn-core sea-ice proxies over the satellite era; results indicate that firn-core glaciochemical records from this dynamic region may provide a proxy for reconstructing Amundsen Sea and Pine Island Bay polynya variability prior to the satellite era. I next investigate the remote influence of tropical Pacific variability on marine aerosol transport to West Antarctica. Results illustrate that both source and transport of marine aerosols to West Antarctica are controlled by remote atmospheric forcing, linking local dynamics (e.g., katabatic winds) with large-scale teleconnections to the tropics (e.g., Rossby waves). Oxygen isotope records allow me to further investigate the relationship between West Antarctic firn-core records and temperature, precipitation origin, sea-ice variability, and large-scale atmospheric circulation. I show that the tropical Pacific remotely influences the source and transport of the isotopic signal to the coastal ice sheet. The regional firm-core array reveals a spatially varying response to remote tropical Pacific forcing. Finally, I investigate longer-term (-200 year) ocean and ice-sheet changes using the methods and results gleaned from the previous work. I utilize sea-ice proxies to reconstruct long-term changes in sea-ice and polynya variability in the Amundsen Sea, and show that the tropics remotely influence West Antarctica over decadal timescales. This thesis utilizes some of the highest-resolution, most coastal records in the region to date, and provides some of the first analyses of the seasonal- to decadal-scale controls on source and transport of marine aerosols to West Antarctica. / by Alison Sara Criscitiello. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2013. / 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. 151-161). / Autonomous marine vehicles are increasingly used in clusters for an array of oceanographic tasks. The effectiveness of this collaboration is often limited by communications: throughput, latency, and ease of reconfiguration. This thesis argues that improved communication on intelligent marine robotic agents can be gained from acting on knowledge gained by improved awareness of the physical acoustic link and higher network layers by the AUV's decision making software. This thesis presents a modular acoustic networking framework, realized through a C++ library called goby-acomms, to provide collaborating underwater vehicles with an efficient short-range single-hop network. goby-acomms is comprised of four components that provide: 1) losslessly compressed encoding of short messages; 2) a set of message queues that dynamically prioritize messages based both on overall importance and time sensitivity; 3) Time Division Multiple Access (TDMA) Medium Access Control (MAC) with automatic discovery; and 4) an abstract acoustic modem driver. Building on this networking framework, two approaches that use the vehicle's "intelligence" to improve communications are presented. The first is a "non-disruptive" approach which is a novel technique for using state observers in conjunction with an entropy source encoder to enable highly compressed telemetry of autonomous underwater vehicle (AUV) position vectors. This system was analyzed on experimental data and implemented on a fielded vehicle. Using an adaptive probability distribution in combination with either of two state observer models, greater than 90% compression, relative to a 32-bit integer baseline, was achieved. The second approach is "disruptive," as it changes the vehicle's course to effect an improvement in the communications channel. A hybrid data- and model-based autonomous environmental adaptation framework is presented which allows autonomous underwater vehicles (AUVs) with acoustic sensors to follow a path which optimizes their ability to maintain connectivity with an acoustic contact for optimal sensing or communication. / by Toby Edwin Schneider. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 203-215). / Underwater wireless communication is quickly becoming a necessity for applications in ocean science, defense, and homeland security. Acoustics remains the only practical means of accomplishing long-range communication in the ocean. The acoustic communication channel is fraught with difficulties including limited available bandwidth, long delay-spread, time-variability, and Doppler spreading. These difficulties reduce the reliability of the communication system and make high data-rate communication challenging. Adaptive decision feedback equalization is a common method to compensate for distortions introduced by the underwater acoustic channel. Limited work has been done thus far to introduce the physics of the underwater channel into improving and better understanding the operation of a decision feedback equalizer. This thesis examines how to use physical models to improve the reliability and reduce the computational complexity of the decision feedback equalizer. The specific topics covered by this work are: how to handle channel estimation errors for the time varying channel, how to use angular constraints imposed by the environment into an array receiver, what happens when there is a mismatch between the true channel order and the estimated channel order, and why there is a performance difference between the direct adaptation and channel estimation based methods for computing the equalizer coefficients. For each of these topics, algorithms are provided that help create a more robust equalizer with lower computational complexity for the underwater channel. / by Ballard J. S. Blair. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Signaling pathways that respond to stress and sense nutrient availability are highly conserved throughout eukaryotes. In mammalian cells, these pathways have evolved to regulate immune responses, representing important therapeutic targets. Interestingly, components of these pathways can be found in plants, yeast and nematodes, where they also participate in response to abiotic and biotic stress. The Amino Acid Response (AAR) pathway, an ancient response to the cellular accumulation of uncharged tRNA, is part of the larger Integrated Stress Response (ISR) in mammals. The ISR consists of multiple branches, each one triggered by distinct stresses that produce phospho-eIF2x signal generation. Each ISR initiating stress results in a unique cellular response due to activation of both the ISR and additional parallel pathway(s) by the initiating stress, but, to date, no such alternate pathway has been identified for the AAR pathway. Despite its integral role in stress adaptation, the ISR has not been studied in early diverging animals. I have identified a highly conserved phosphorylation site in the protein eIF2a, the signature ISR effector, which allowed me to use a mammalian antibody to identify and characterize the ISR in the basal metazoan, Nematostella vectensis, revealing that the core components of the mammalian ISR were present over 550 million years ago in the common ancestor of cnidarians and bilaterians. Additionally, our lab has discovered a novel branch of the AAR pathway that regulates key tissue protective signals. Using evolutionary conservation of this pathway in model organisms, I have identified GCN1 as the branch point that links the signal generation components of the AAR pathway to downstream therapeutic effects. I then used transcriptomic and protein interaction analyses to begin to understand the scope of this pathway and identify key pathway regulators. / Funding for this research was provided by the National Science Foundation Graduate Research Fellowship Program, Allied Bristol Life Sciences (to Malcolm Whitman), the WHOI Academic Programs Office, and the WHOI Ocean Venture Fund / by Maja Lena Edenius. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 158-160). / Quantifying uncertainty and error bounds is a key outstanding challenge in ocean state estimation and climate research. It is particularly difficult due to the large dimensionality of this nonlinear estimation problem and the number of uncertain variables involved. The "Estimating the Circulation and Climate of the Oceans" (ECCO) consortium has developed a scalable system for dynamically consistent estimation of global time-evolving ocean state by optimal combination of ocean general circulation model (GCM) with diverse ocean observations. The estimation system is based on the "adjoint method" solution of an unconstrained least-squares optimization problem formulated with the method of Lagrange multipliers for fitting the dynamical ocean model to observations. The dynamical consistency requirement of ocean state estimation necessitates this approach over sequential data assimilation and reanalysis smoothing techniques. In addition, it is computationally advantageous because calculation and storage of large covariance matrices is not required. However, this is also a drawback of the adjoint method, which lacks a native formalism for error propagation and quantification of assimilated uncertainty. The objective of this dissertation is to resolve that limitation by developing a feasible computational methodology for uncertainty analysis in dynamically consistent state estimation, applicable to the large dimensionality of global ocean models. Hessian (second derivative-based) methodology is developed for Uncertainty Quantification (UQ) in large-scale ocean state estimation, extending the gradient-based adjoint method to employ the second order geometry information of the model-data misfit function in a high-dimensional control space. Large error covariance matrices are evaluated by inverting the Hessian matrix with the developed scalable matrix-free numerical linear algebra algorithms. Hessian-vector product and Jacobian derivative codes of the MIT general circulation model (MITgcm) are generated by means of algorithmic differentiation (AD). Computational complexity of the Hessian code is reduced by tangent linear differentiation of the adjoint code, which preserves the speedup of adjoint checkpointing schemes in the second derivative calculation. A Lanczos algorithm is applied for extracting the leading rank eigenvectors and eigenvalues of the Hessian matrix. The eigenvectors represent the constrained uncertainty patterns. The inverse eigenvalues are the corresponding uncertainties. The dimensionality of UQ calculations is reduced by eliminating the uncertainty null-space unconstrained by the supplied observations. Inverse and forward uncertainty propagation schemes are designed for assimilating observation and control variable uncertainties, and for projecting these uncertainties onto oceanographic target quantities. Two versions of these schemes are developed: one evaluates reduction of prior uncertainties, while another does not require prior assumptions. The analysis of uncertainty propagation in the ocean model is time-resolving. It captures the dynamics of uncertainty evolution and reveals transient and stationary uncertainty regimes. The system is applied to quantifying uncertainties of Antarctic Circumpolar Current (ACC) transport in a global barotropic configuration of the MITgcm. The model is constrained by synthetic observations of sea surface height and velocities. The control space consists of two-dimensional maps of initial and boundary conditions and model parameters. The size of the Hessian matrix is 0(1010) elements, which would require 0(60GB) of uncompressed storage. It is demonstrated how the choice of observations and their geographic coverage determines the reduction in uncertainties of the estimated transport. The system also yields information on how well the control fields are constrained by the observations. The effects of controls uncertainty reduction due to decrease of diagonal covariance terms are compared to dynamical coupling of controls through off-diagonal covariance terms. The correlations of controls introduced by observation uncertainty assimilation are found to dominate the reduction of uncertainty of transport. An idealized analytical model of ACC guides a detailed time-resolving understanding of uncertainty dynamics. Keywords: Adjoint model uncertainty, sensitivity, posterior error reduction, reduced rank Hessian matrix, Automatic Differentiation, ocean state estimation, barotropic model, Drake Passage transport. / by Alexander G. Kalmikov. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Marine phytoplankton are the principal producers of oceanic dissolved organic matter (DOM), the organic substrate responsible for secondary production by heterotrophic microbes in the sea. Despite the importance of DOM in marine food webs, details regarding how marine microbes cycle DOM are limited, and few definitive connections have been made between specific producers and consumers. Consumption is thought to depend on the source of the DOM as well as the identity of the consumer; however, it remains unclear how phytoplankton diversity and DOM composition are related, and the metabolic pathways involved in the turnover of DOM by different microbial taxa are largely unknown. The motivation for this thesis is to examine the role of microbial diversity in determining the composition, lability, and physiological consumption of marine DOM. The chemical composition of DOM produced by marine phytoplankton was investigated at the molecular level using mass spectrometry. Results demonstrate that individual phytoplankton strains release a unique suite of organic compounds. Connections between DOM composition and the phylogenetic identity of the producing organism were identified on multiple levels, revealing a direct relationship between phytoplankton diversity and DOM composition. Phytoplankton-derived DOM was also employed in growth assays with oligotrophic bacterioplankton strains to examine effects on heterotrophic growth dynamics. Reproducible responses ranged from suppressed to enhanced growth rates and cell yields, and depended both on the identity of the heterotroph and the source of the DOM. Novel relationships between specific bacterioplankton types and DOM from known biological sources were found, and targets for additional studies on reactive DOM components were identified. The physiology of DOM consumption by a marine Oceanospirillales strain was studied using a combined transcriptomic and untargeted metabolomic approach. The transcriptional response of this bacterium to Prochlorococcus-derived DOM revealed an increase in anabolic processes related to metabolism of carboxylic acids and glucosides, increased gene expression related to proteorhodopsin-based phototrophy, and decreased gene expression related to motility. Putative identification of compounds present in Prochlorococcus-derived DOM supported these responses. Collectively, these findings highlight the potential for linking detailed chemical analyses of labile DOM from a known biological source with bacterioplankton diversity and physiology. / by Jamie William Becker. / Ph.D.