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  • Massachusetts Institute of Technology and Woods Hole Oceanographic Institution  (60)
  • American Physical Society (APS)
  • Springer Nature
  • 2020-2023  (96)
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  • 1
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    Enabling human-robot cooperation in scientific exploration of bandwidth-limited environments (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Aeronautics and Astronautics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2020.
    Description: Contemporary scientific exploration most often takes place in highly remote and dangerous environments, such as in the deep sea and on other planets. These environments are very hostile to humans, which makes robotic exploration the first and often the only option. However, they also impose restrictive limits on how much communication is possible, creating challenges in implementing remote command and control. We propose an approach to enable more efficient autonomous robot-based scientific exploration of remote environments despite these limits on human-robot communication. We find this requires the robot to have a spatial observation model that can predict where to find various phenomena, a reward model which can measure how relevant these phenomena are to the scientific mission objectives, and an adaptive path planner which can use this information to plan high scientific value paths. We identified and addressed two main gaps: the lack of a general-purpose means for spatial observation modelling, and the challenge in learning a reward model based on images online given the limited bandwidth constraints. Our first key contribution is enabling general-purpose spatial observation modelling through spatio-temporal topic models, which are well suited for unsupervised scientific exploration of novel environments. Our next key contribution is an active learning criterion which enables learning an image-based reward model during an exploration mission by communicating with the science team efficiently. We show that using these together can result in a robotic explorer collecting up to 230% more scientifically relevant observations in a single mission than when using lawnmower trajectories.
    Description: This work was partially supported by the National Science Foundation (NSF) Award #1734400, as well as by the Woods Hole Oceanographic Institution (WHOI). The author would like to thank both organizations for their support.
    Keywords: Robotics ; Autonomous ; Exploration
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 2
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    Finescale abyssal turbulence: sources and modeling (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2020.
    Description: A detailed understanding of the intensity and three-dimensional spatial distribution of diabatic abyssal turbulence is germane to understanding the abyssal branch of the global overturning circulation. This thesis addresses the issue through 1) an investigation of the dynamics of an abyssal boundary layer and through 2) the construction of a probabilistic finescale parameterization using mixture density networks (MDNs). A boundary layer, formed by the interaction of heaving isopycnals by the tide and viscous/adiabatic boundary conditions, is investigated through direct numerical simulations (DNS) and Floquet analysis. Turbulence is sustained throughout the tidal period in the DNS on extra-critical slopes characterized by small slope Burger numbers, leading to the formation of turbulent stratified Stokes-Ekman layers. Floquet analysis suggests that the boundary layers are unstable to disturbances to the vorticity component aligned with the across-isobath tidal velocity on extra-critical slopes. MDNs, trained on microstructure observations, are used to construct probabilistic finescale parameterization dependent on the finescale vertical kinetic energy (VKE), N2f2, , and both variables. The MDN model predictions are as accurate as conventional parameterizations, but also predict the underlying probability density function of the dissipation rate as a function of the dependent parameters.
    Description: My doctoral studies in the WHOI/MIT Joint Program were funded by the National Science Foundation (OCE-1657870) and the National Science Foundation Graduate Research Fellowship Program.
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 3
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    Stochastic acoustic ray tracing with dynamically orthogonal equations (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2020.
    Description: Developing accurate and computationally efficient models for ocean acoustics is inherently challenging due to several factors including the complex physical processes and the need to provide results on a large range of scales. Furthermore, the ocean itself is an inherently dynamic environment within the multiple scales. Even if we could measure the exact properties at a specific instant, the ocean will continue to change in the smallest temporal scales, ever increasing the uncertainty in the ocean prediction. In this work, we explore ocean acoustic prediction from the basics of the wave equation and its derivation. We then explain the deterministic implementations of the Parabolic Equation, Ray Theory, and Level Sets methods for ocean acoustic computation. We investigate methods for evolving stochastic fields using direct Monte Carlo, Empirical Orthogonal Functions, and adaptive Dynamically Orthogonal (DO) differential equations. As we evaluate the potential of Reduced-Order Models for stochastic ocean acoustics prediction, for the first time, we derive and implement the stochastic DO differential equations for Ray Tracing (DO-Ray), starting from the differential equations of Ray theory. With a stochastic DO-Ray implementation, we can start from non-Gaussian environmental uncertainties and compute the stochastic acoustic ray fields in a reduced order fashion, all while preserving the complex statistics of the ocean environment and the nonlinear relations with stochastic ray tracing. We outline a deterministic Ray-Tracing model, validate our implementation, and perform Monte Carlo stochastic computation as a basis for comparison. We then present the stochastic DO-Ray methodology with detailed derivations. We develop varied algorithms and discuss implementation challenges and solutions, using again direct Monte Carlo for comparison. We apply the stochastic DO-Ray methodology to three idealized cases of stochastic sound-speed profiles (SSPs): constant-gradients, uncertain deep-sound channel, and a varied sonic layer depth. Through this implementation with non-Gaussian examples, we observe the ability to represent the stochastic ray trace field in a reduced order fashion.
    Description: Office of Naval Research Grants N00014-19-1-2664 (Task Force Ocean: DEEP-AI) and N00014-19-1-2693 (INBDA)
    Keywords: Stochastic Processes ; Acoustic Wave Propagation ; Acoustic Rays
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 4
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    Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ferrer-González, F. X., Widner, B., Holderman, N. R., Glushka, J., Edison, A. S., Kujawinski, E. B., & Moran, M. A. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME Journal, (2020), doi:10.1038/s41396-020-00811-y.
    Description: The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
    Description: This work was supported by grants from the Gordon and Betty Moore Foundation (5503) and the National Science Foundation (IOS-1656311) to MAM, ASE, and EBK, and by the Simons Foundation grant 542391 to MAM within the Principles of Microbial Ecosystems (PriME) Collaborative.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Exploring Employee Perceptions towards Smart Working during the COVID-19 Pandemic: a Comparative Analysis of Two Italian Public Research Organizations (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Of all the socio-economic changes caused by the Covid-19 pandemic, the disruption to workforce organizations will probably leave the largest indelible mark. The way work will be organized in the future will be closely linked to the experience of work-ing under the same institution’s response to the pandemic. This paper aims to fill the gap in knowledge about smart working (SW) in public organizations, with a focus on the experience of the employees of two Italian research organizations, CNR and INGV. Analysing primary data, it explored and assessed how SW had been experi-enced following the implementation of governmental measures aimed at limiting the spread of COVID-19
    Description: Published
    Description: 815–833
    Description: 2TM. Divulgazione Scientifica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Combining audio and visual displays to highlight temporal and spatial seismic patterns (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Data visualization, and to a lesser extent data sonification, are classic tools to the scientific community. However, these two approaches are very rarely combined, although they are highly complementary: our visual system is good at recognizing spatial patterns, whereas our auditory system is better tuned for temporal patterns. In this article, data representation methods are proposed that combine visualization, sonification, and spatial audio techniques, in order to optimize the user’s perception of spatial and temporal patterns in a single display, to increase the feeling of immersion, and to take advantage of multimodal integration mechanisms. Three seismic data sets are used to illustrate the methods, covering different physical phenomena, time scales, spatial distributions, and spatio-temporal dynamics. The methods are adapted to the specificities of each data set, and to the amount of information that the designer wants to display. This leads to further developments, namely the use of audification with two time scales, the switch from pure audification to time-modulated noise, and the switch from pure audification to sonic icons. First user feedback from live demonstrations indicates that the methods presented in this article seem to enhance the perception of spatio-temporal patterns, which is a key parameter to the understanding of seismically active systems, and a step towards apprehending the processes that drive this activity.
    Description: Published
    Description: 125–142
    Description: 7T. Variazioni delle caratteristiche crostali e "precursori"
    Description: JCR Journal
    Keywords: 04.06. Seismology
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  • 7
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    Deep water inflow slowed offshore expansion of the West Antarctic Ice Sheet at the Eocene-Oligocene transition (2022)
    Springer Nature
    In:  EPIC3Nature Communications Earth & Environment, Springer Nature, 3(1)
    Details
    Publication Date: 2022-02-21
    Description: The stability of the West Antarctic Ice Sheet is threatened by the incursion of warm Circumpolar Deepwater which flows southwards via cross-shelf troughs towards the coast there melting ice shelves. However, the onset of this oceanic forcing on the development and evolution of the West Antarctic Ice Sheet remains poorly understood. Here, we use single- and multichannel seismic reflection profiles to investigate the architecture of a sediment body on the shelf of the Amundsen Sea Embayment. We estimate the formation age of this sediment body to be around the Eocene-Oligocene Transition and find that it possesses the geometry and depositional pattern of a plastered sediment drift. We suggest this indicates a southward inflow of deep water which probably supplied heat and, thus, prevented West Antarctic Ice Sheet advance beyond the coast at this time. We conclude that the West Antarctic Ice Sheet has likely experienced a strong oceanic influence on its dynamics since its initial formation.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
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    Short-term clustering modeling of seismicity in Eastern Aegean Sea (Greece): a retrospective forecast test of the 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos earthquake sequences (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-03
    Description: Short-term earthquake clustering properties in the Eastern Aegean Sea (Greece) area investigated through the application of an epidemic type stochastic model (Epidemic Type Earthquake Sequence; ETES). The computations are performed in an earthquake catalog covering the period 2008 to 2020 and including 2332 events with a completeness threshold of Mc = 3.1 and separated into two subcatalogs. The first subcatalog is employed for the learning period, which is between 2008/01/01 and 2016/12/31 (N = 1197 earthquakes), and used for the model’s parameters estimation. The second subcatalog from 2017/01/01 to 2020/11/10 (1135 earthquakes), in which the sequences of 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos main shocks are included, and used for a retrospective forecast testing based on the constructed model. The estimated model parameters imply a swarm like behavior, indicating the ability of earthquakes of small to moderate magnitude above Mc to produce their own offsprings, along with the stronger earthquakes. The retrospective evaluation of the model is examined in the three aftershock sequences, where lack of foreshocks resulted in low predictability of the mainshocks, with estimated daily probabilities around 10– 5. Immediately after the mainshocks occurrence the model adjusts with notable resemblance between the expected and observed aftershock rates, particularly for earthquakes with M ≥ 3.5.
    Description: Published
    Description: 1085–1099
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
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  • 9
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    Simulation of non-stationary stochastic ground motions based on recent Italian earthquakes (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: This work presents an up-to-date model for the simulation of non-stationary ground motions, including several novelties compared to the original study of Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996). The selection of the input motion in the framework of earthquake engineering has become progressively more important with the growing use of nonlinear dynamic analyses. Regardless of the increasing availability of large strong motion databases, ground motion records are not always available for a given earthquake scenario and site condition, requiring the adoption of simulated time series. Among the different techniques for the generation of ground motion records, we focused on the methods based on stochastic simulations, considering the time- frequency decomposition of the seismic ground motion. We updated the non-stationary stochastic model initially developed in Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996) and later modified by Pousse et al. (Bull Seism Soc Am 96:2103–2117, 2006) and Laurendeau et al. (Nonstationary stochastic simulation of strong ground-motion time histories: application to the Japanese database. 15 WCEE Lisbon, 2012). The model is based on the S-transform that implicitly considers both the amplitude and frequency modulation. The four model parameters required for the simulation are: Arias intensity, significant duration, central frequency, and frequency bandwidth. They were obtained from an empirical ground motion model calibrated using the accelerometric records included in the updated Italian strong-motion database ITACA. The simulated accelerograms show a good match with the ground motion model prediction of several amplitude and frequency measures, such as Arias intensity, peak acceleration, peak velocity, Fourier spectra, and response spectra.
    Description: Published
    Description: 3287–3315
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 10
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    Insights on the Italian Seismic Network from location uncertainties (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-01
    Description: Probabilistic earthquake locations provide confidence intervals for the hypocentre solutions such as errors encountered in the position, the origin time, and in magnitude. If the relationship of the parameters relative to the local arrangement of the seismic network is considered, such as the node distance, the number of stations, the seismic gap, and the quality of phase readings), the uncertainties can then provide insights on the location capability of the network. In this paper, we collect the earthquake data recorded from the Italian Seismic Network for a time span of 5 years. The data pertain to three different catalogues according to the progressive refinement phases of the location procedure: automatic location, revised location, and published location. By means of spatial analysis,we assess the distribution of the location-related and network-related estimators across the study area. These estimators are subsequently combined to assess the existence of spatial correlations at a local scale. The results indicate that the Italian network is generally able to provide robust locations at the national scale and for smaller earthquakes, and the elongated shape of Italy (and of its network) does not cause systematic bias in the locations. However, we highlight the existence of subregions in which the performance of the network is weaker. At present, a unique 2D, 3-layer velocity model is used for the earthquake location procedure, and this could represent the main limitation for the improvement of the locations. Therefore, the assessment of locally optimized velocity models is the priority for the homogenization and the improvement of the Italian Seismic Network performance.
    Description: Published
    Description: 1061–1076
    Description: 1IT. Reti di monitoraggio e sorveglianza
    Description: JCR Journal
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  • 11
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    New trenching results along the İznik segment of the central strand of the North Anatolian Fault (Turkey): an integration with preexisting data (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-06
    Description: This paper provides a new contribution to the construction of the complex and fragmentary mosaic of the Late Holocene earthquakes history of the İznik segment of the central strand of the North Anatolian Fault (CNAF) in Turkey. The CNAF clearly displays lower dextral slip rates with respect to the northern strand however, surface rupturing and large damaging earthquakes (M 〉 7) occurred in the past, leaving clear signatures in the built and natural environments. The association of these historical events to specific earthquake sources (e.g., Gemlik, İznik, or Geyve fault segments) is still a matter of debate. We excavated two trenches across the İznik fault trace near Mustafali, a village about 10 km WSW of İznik where the morphological fault scarp was visible although modified by agricultural activities. Radiocarbon and TL dating on samples collected from the trenches show that the displaced deposits are very recent and span the past 2 millennia at most. Evidence for four surface faulting events was found in the Mustafali trenches. The integration of these results with historical data and previous paleoseismological data yields an updated Late Holocene history of surface-rupturing earthquakes along the İznik Fault in 1855, 740 (715), 362, and 121 CE. Evidence for the large M7 + historical earthquake dated 1419 CE generally attributed to this fault, was not found at any trench site along the İznik fault nor in the subaqueous record. This unfit between paleoseismological, stratigraphic, and historical data highlights one more time the urge for extensive paleoseismological trenching and offshore campaigns because of the high potential to solve the uncertainties on the seismogenic history (age, earthquake location, extent of the rupture and size) of this portion of NAFZ and especially on the attribution of historical earthquakes to the causative fault.
    Description: Published
    Description: 115–128
    Description: 2T. Deformazione crostale attiva
    Description: N/A or not JCR
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  • 12
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    Checking the site categorization criteria and amplification factors of the 2021 draft of Eurocode 8 Part 1–1 (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: In this paper the site categorization criteria and the corresponding site amplification factors proposed in the 2021 draft of Part 1 of Eurocode 8 (2021-draft, CEN/TC250/SC8 Working Draft N1017) are first introduced and compared with the current version of Eurocode 8, as well as with site amplification factors from recent empirical ground motion prediction equations. Afterwards, these values are checked by two approaches. First, a wide dataset of strong motion records is built, where recording stations are classified according to 2021-draft, and the spectral amplifications are empirically estimated computing the site-to-site residuals from regional and global ground motion models for reference rock conditions. Second, a comprehensive parametric numerical study of one-dimensional (1D) site amplification is carried out, based on randomly generated shear-wave velocity profiles, classified according to the new criteria. A reasonably good agreement is found by both approaches. The most relevant discrepancies occur for the shallow soft soil conditions (soil category E) that, owing to the complex interaction of shear wave velocity, soil deposit thickness and frequency range of the excitation, show the largest scatter both in terms of records and of 1D numerical simulations. Furthermore, 1D numerical simulations for soft soil conditions tend to provide lower site amplification factors than 2021-draft, as well as lower than the corresponding site-to-site residuals from records, because of higher impact of non-linear (NL) site effects in the simulations. A site-specific study on NL effects at three KiK-net stations with a significantly large amount of high-intensity recorded ground motions gives support to the 2021-draft NL reduction factors, although the very limited number of recording stations allowing such analysis prevents deriving more general implications. In the presence of such controversial arguments, it is reasonable that a standard should adopt a prudent solution, with a limited reduction of the site amplification factors to account for NL soil response, while leaving the possibility to carry out site-specific estimations of such factors when sufficient information is available to model the ground strain dependency of local soil properties.
    Description: Published
    Description: 4199–4234
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 13
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    Exceedance of design actions in epicentral areas: insights from the ShakeMap envelopes for the 2016–2017 central Italy sequence (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: ShakeMap is the tool to evaluate the ground motion effect of earthquakes in vast areas. It is useful to delimit the zones where the shaking is expected to have been most significant, for civil defense rapid response. From the earthquake engineering point of view, it can be used to infer the seismic actions on the built environment to calibrate vulnerability models or to define the reconstruction policies based on observed damage vs shaking. In the case of long-lasting seismic sequences, it can be useful to develop ShakeMap envelopes, that is, maps of the largest ground intensity among those from the ShakeMap of (selected) events of a seismic sequence, to delimit areas where the effects of the whole sequence have been of structural engineering relevance. This study introduces ShakeMap envelopes and discusses them for the central Italy 2016–2017 seismic sequence. The specific goals of the study are: (i) to compare the envelopes and the ShakeMap of the main events of the sequence to make the case for sequence-based maps; (ii) to quantify the exceedance of design seismic actions based on the envelopes; (iii) to make envelopes available for further studies and the reconstruction planning; (iv) to gather insights on the (repeated) exceedance of design seismic actions at some sites. Results, which include considerations of uncertainty in ShakeMap, show that the sequence caused exceedance of design hazard in thousands of square kilometers. The most relevant effects of the sequence are, as expected, due to the mainshock, yet seismic actions larger than those enforced by the code for structural design are found also around the epicenters of the smaller magnitude events. At some locations, the succession of ground-shaking that has excited structures, provides insights on structural damage accumulation that has likely taken place; something that is not accounted for explicitly in modern seismic design. The envelopes developed are available as supplemental material.
    Description: Published
    Description: 5391–5414
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 14
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    Automatic inspection and analysis of digital waveform images by means of convolutional neural networks (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-13
    Description: Analyzing seismic data to get information about earthquakes has always been a major task for seismologists and, more in general, for geophysicists. Recently, thanks to the technological development of observation systems, more and more data are available to perform such tasks. However, this data “grow up” makes “human possibility” of data processing more complex in terms of required efforts and time demanding. That is why new technological approaches such as artificial intelligence are becoming very popular and more and more exploited. In this paper, we explore the possibility of interpreting seismic waveform segments by means of pre-trained deep learning. More specifically, we apply convolutional networks to seismological waveforms recorded at local or regional distances without any pre-elaboration or filtering. We show that such an approach can be very successful in determining if an earthquake is “included” in the seismic wave image and in estimating the distance between the earthquake epicenter and the recording station.
    Description: Published
    Description: 1347–1359
    Description: 1T. Struttura della Terra
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
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  • 15
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    Midlatitude climatology of the ionospheric equivalent slab thickness over two solar cycles (2021)
    Springer Nature
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    Publication Date: 2021-10-25
    Description: Themain climatological features of the ionospheric equivalent slab thickness (τ ) for the Northern hemispheremidlatitudes are analyzed. F2-layer peak electron density values recorded at three midlatitude ionospheric stations (Chilton 51.5° N, 0.6° W, U.K.; Roquetes 40.8° N, 0.5° E, Spain;Wallops Island 37.9° N, 75.5°W, USA) and vertical total electron content values from colocated ground-based Global Navigation Satellite System receivers are used to calculate a dataset of τ values for the last two solar cycles, considering only magnetically quiet periods. Results are presented both as grids of binned medians and as boxplots as a function of local time and month of the year, for different solar activity levels. Corresponding trends are first compared to those output by the midlatitude empirical model developed by Fox et al. (Radio Sci 26:429–438, 1991) and then discussed in the light of what is known so far. From this investigation, the strong need to implement an improved empirical model of τ has emerged. Both Space Weather and Space Geodesy applications might benefit from such model. Therefore, both the dataset and the methodology described in the paper represent a first fundamental step aimed at implementing an empirical climatological model of the ionospheric equivalent slab thickness. The study highlighted also that at midlatitudes τ shows the following main patterns: daytime values considerably smaller than nighttime ones (except in summer); well-defined maxima at solar terminator hours; a greater dispersion during nighttime and solar terminator hours; no clear and evident solar activity dependence.
    Description: Published
    Description: 124
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
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  • 16
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    Fracturing and healing of basaltic magmas during explosive volcanic eruptions (2021)
    Springer Nature
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    Publication Date: 2021-11-26
    Description: The eruption of basaltic magmas dominates explosive volcanism on Earth and other planets within the Solar System. The mechanism through which continuous magma fragments into volcanic particles is central in governing eruption dynamics and the ensuing hazards. However, the mechanism of fragmentation of basaltic magmas is still disputed, with both viscous and brittle mechanisms having been proposed. Here we carry out textural analysis of the products of ten eruptions from seven volcanoes by scanning electron microscopy. We find broken crystals surrounded by intact glass that testify to the brittle fragmentation of basaltic magmas during explosive activity worldwide. We then replicated the natural textures of broken crystals in laboratory experiments where variably crystallized basaltic melt was fragmented by rapid deformation. The experiments reveal that crystals are broken by the propagation of a network of fractures through magma, and that afterwards the fractures heal by viscous flow of the melt. Fracturing and healing affect gas mobility, stress distribution, and bubble and crystal size distributions in magma. Our results challenge the idea that the grain size distribution of basaltic eruption products reflects the density of fractures that initially fragmented the magma and ultimately indicate that brittle fracturing and viscous healing of magma may underlie basaltic explosive eruptions globally.
    Description: Published
    Description: 248–254
    Description: 4V. Processi pre-eruttivi
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
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  • 17
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    Catching the Main Ethiopian Rift evolving towards plate divergence (2022)
    Springer Nature
    Details
    Publication Date: 2022-02-11
    Description: Magmatism accompanies rifting along divergent plate boundaries, although its role before continental breakup remains poorly understood. For example, the magma-assisted Northern Main Ethiopian Rift (NMER) lacks current volcanism and clear tectono-magmatic relationships with its contiguous rift portions. Here we define its magmatic behaviour, identifying the most recent eruptive fissures (EF) whose aphyric basalts have a higher Ti content than those of older monogenetic scoria cones (MSC), which are porphyritic and plagioclase-dominated. Despite these differences, calculations highlight a similar parental melt for EF and MSC products, suggesting only a different evolutionary history after melt generation. While MSC magmas underwent a further step of storage at intermediate crustal levels, EF magmas rose directly from the base of the crust without contamination, even below older polygenetic volcanoes, suggesting rapid propagation of transcrustal dikes across solidified magma chambers. Whether this recent condition in the NMER is stable or transient, it indicates a transition from central polygenetic to linear fissure volcanism, indicative of increased tensile conditions and volcanism directly fed from the base of the crust, suggesting transition towards mature rifting.
    Description: Published
    Description: 21821
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Neapolitan volcanoes (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-24
    Description: This book serves as a guide to discovering the most interesting volcano sites in Italy. Accompanied by some extraordinary contemporary images of active Neapolitan volcanoes, it explains the main volcanic processes that have been shaping the landscape of the Campania region and influencing human settlements in this area since Greek and Roman times and that have prompted leading international scientists to visit and study this natural volcanology laboratory. While volcanology is the central topic, the book also addresses other aspects related to the area’s volcanism and is divided into three sections: 1) Neapolitan volcanic activity and processes (with a general introduction to volcanology and its development around Naples together with descriptions of the landscape and the main sites worth visiting); 2) Volcanoes and their interactions with local human settlements since the Bronze Age, recent population growth and the transformation of the territory; 3) The risks posed by Neapolitan Volcanoes, their recent activity and the problem of forecasting any future eruption.
    Description: Published
    Description: 2TM. Divulgazione Scientifica
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Northern Hemisphere drought risk in a warming climate (2021)
    Springer Nature
    In:  EPIC3npj Climate and Atmospheric Science, Springer Nature, 4(1), ISSN: 2397-3722
    Details
    Publication Date: 2022-02-15
    Repository Name: EPIC Alfred Wegener Institut
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    Energy threshold changes in volcanic activity at Mt. Etna (Italy) inferred from volcanic tremor (2022)
    Springer Nature
    Details
    Publication Date: 2022-10-28
    Description: From the 2010s on, pattern classification has proven an effective method for flagging alerts of volcano unrest before eruptive activity at Mt. Etna, Italy. The analysis has been applied online to volcanic tremor data, and has supported the surveillance activity of the volcano that provides timely information to Civil Protection and other authorities. However, after declaring an alert, no one knows how long the volcano unrest will last and if a climactic eruptive activity will actually begin. These are critical aspects when considering the effects of a prolonged state of alert. An example of longstanding unrest is related to the Christmas Eve eruption in 2018, which was heralded by several months of almost continuous Strombolian activity. Here, we discuss the usage of thresholds to detect conditions leading to paroxysmal activity, and the challenges associated with defining such thresholds, leveraging a dataset of 52 episodes of lava fountains occurring in 2021. We were able to identify conservative settings regarding the thresholds, allowing for an early warning of impending paroxysm in almost all cases (circa 85% for the first 4 months in 2021, and over 90% for the whole year). The chosen thresholds also proved useful to predict that a paroxysmal activity was about to end. Such information provides reliable numbers for volcanologists for their assessments, based on visual information, which may not be available in bad weather or cloudy conditions.
    Description: Project IMPACT (A multidisciplinary Insight on the kinematics and dynamics of Magmatic Processes at Mt. Etna Aimed at identifying preCursor phenomena and developing early warning sysTems). IMPACT belongs to the Progetti Dipartimentali INGV [DIP7], https://progetti.ingv.it/index.php/it/progetti-dipartimentali/vulcani/impact#informazioni-sul-progetto.
    Description: Published
    Description: 17895
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: Volcanic tremor ; Volcano monitoring ; Pattern recognition ; Self Organizing maps ; Fuzzy clustering ; Mt. Etna ; 04.06. Seismology ; 04.08. Volcanology ; 05.01. Computational geophysics
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    Evidence for late glacial oceanic carbon redistribution and discharge from the Pacific Southern Ocean (2022)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 13, 12 p., ISSN: 2041-1723
    Details
    Publication Date: 2022-11-14
    Description: Southern Ocean deep-water circulation plays an important role in the global carbon cycle. On geological time-scales, upwelling along the Chilean continental margin likely contributed to the deglacial atmospheric carbon dioxide rise, but little quantitative evidence exists of carbon storage. Here, we use a new X-ray Micro-Computer-Tomography method to assess foraminiferal test dissolution as proxy for paleo-carbonate ion concentrations [CO3^2−]. Our subantarctic Southeast Pacific sediment core depth transect shows significant deep-water [CO3^2−] variations during the Last Glacial Maximum and Deglaciation (10 – 22 ka BP). We provide evidence for an increase in [CO3^2−] during the early deglacial period (15-19 ka BP), followed by a ca. 40 µmol kg^-1 reduction in Lower Circumpolar Deepwater (CDW). This decreased Pacific to Atlantic export of low-carbon CDW contributed to significantly lowered carbon storage within the Southern Ocean, highlighting the importance of a dynamic Pacific–Southern Ocean deep-water reconfiguration for shaping late-glacial oceanic carbon storage, and subsequent deglacial oceanic-atmospheric CO2 transfer.
    Repository Name: EPIC Alfred Wegener Institut
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    Southern Ocean biogenic blooms freezing-in Oligocene colder climates (2022)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 13(1), pp. 1-10, ISSN: 2041-1723
    Details
    Publication Date: 2022-11-24
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Crossing a key atmospheric CO〈jats:sub〉2〈/jats:sub〉 threshold triggered a fundamental global climate reorganisation ~34 million years ago (Ma) establishing permanent Antarctic ice sheets. Curiously, a more dramatic CO〈jats:sub〉2〈/jats:sub〉 decline (~800–400 ppm by the Early Oligocene(~27 Ma)), postdates initial ice sheet expansion but the mechanisms driving this later, rapid drop in atmospheric carbon during the early Oligocene remains elusive and controversial. Here we use marine seismic reflection and borehole data to reveal an unprecedented accumulation of early Oligocene strata (up to 2.2 km thick over 1500 × 500 km) with a major biogenic component in the Australian Southern Ocean. High-resolution ocean simulations demonstrate that a tectonically-driven, one-off reorganisation of ocean currents, caused a unique period where current instability coincided with high nutrient input from the Antarctic continent. This unrepeated and short-lived environment favoured extreme bioproductivity and enhanced sediment burial. The size and rapid accumulation of this sediment package potentially holds ~1.067 × 10〈jats:sup〉15〈/jats:sup〉 kg of the ‘missing carbon’ sequestered during the decline from an Eocene high CO〈jats:sub〉2〈/jats:sub〉-world to a mid-Oligocene medium CO〈jats:sub〉2〈/jats:sub〉-world, highlighting the exceptional role of the Southern Ocean in modulating long-term climate.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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    Environmental stability and phenotypic plasticity benefit the cold-water coral Desmophyllum dianthus in an acidified fjord (2022)
    Springer Nature
    In:  EPIC3Communications Biology, Springer Nature, 5(683)
    Details
    Publication Date: 2022-07-13
    Description: The stratified Chilean Comau Fjord sustains a dense population of the cold-water coral (CWC) Desmophyllum dianthus in aragonite supersaturated shallow and aragonite under- saturated deep water. This provides a rare opportunity to evaluate CWC fitness trade-offs in response to physico-chemical drivers and their variability. Here, we combined year-long reciprocal transplantation experiments along natural oceanographic gradients with an in situ assessment of CWC fitness. Following transplantation, corals acclimated fast to the novel environment with no discernible difference between native and novel (i.e. cross-transplanted) corals, demonstrating high phenotypic plasticity. Surprisingly, corals exposed to lowest ara- gonite saturation (Ωarag 〈 1) and temperature (T 〈 12.0 °C), but stable environmental condi- tions, at the deep station grew fastest and expressed the fittest phenotype. We found an inverse relationship between CWC fitness and environmental variability and propose to consider the high frequency fluctuations of abiotic and biotic factors to better predict the future of CWCs in a changing ocean.
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    Mid-Pliocene El Niño/Southern Oscillation suppressed by Pacific intertropical convergence zone shift (2022)
    Springer Nature
    In:  EPIC3Nature Geoscience, Springer Nature, ISSN: 1752-0908
    Details
    Publication Date: 2022-08-16
    Description: The El Niño/Southern Oscillation (ENSO), the dominant driver of year-to-year climate variability in the equatorial Pacific Ocean, impacts climate pattern across the globe. However, the response of the ENSO system to past and potential future temperature increases is not fully understood. Here we investigate ENSO variability in the warmer climate of the mid-Pliocene (~3.0–3.3 Ma), when surface temperatures were ~2–3 °C above modern values, in a large ensemble of climate models—the Pliocene Model Intercomparison Project. We show that the ensemble consistently suggests a weakening of ENSO variability, with a mean reduction of 25% (±16%). We further show that shifts in the equatorial Pacific mean state cannot fully explain these changes. Instead, ENSO was suppressed by a series of off-equatorial processes triggered by a northward displacement of the Pacific intertropical convergence zone: weakened convective feedback and intensified Southern Hemisphere circulation, which inhibit various processes that initiate ENSO. The connection between the climatological intertropical convergence zone position and ENSO we find in the past is expected to operate in our warming world with important ramifications for ENSO variability.
    Repository Name: EPIC Alfred Wegener Institut
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    New insights into the marine oxygen cycle from manganese oxide minerals and reactive oxygen species (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanography and Applied Ocean Science and Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2020.
    Description: The redox cycling of oxygen between O2, water, and intermediate redox states including hydrogen peroxide and superoxide, has profound impact on the availability and distribution of dissolved O2, the habitability of the marine biosphere, and cellular metabolic and physiological reactions that utilize O2. The sum total of processes that produce, consume, and exchange atoms with O2 in the atmosphere, oceans, and subsurface leave their isotopic fingerprints on the abundance of the three stable isotopes of O2 in the environment. In this thesis, I explore two aspects of the oxygen cycle in the past and present. First, I investigate the ability of manganese (Mn) oxide minerals to capture and retain the oxygen isotopic signature of dissolved O2 during the oxidation of aqueous Mn(II) to Mn-oxide minerals. I determine that approximately half of the oxygen atoms in Mn(III,IV) oxides are directly incorporated from dissolved oxygen, and use isotope labeling techniques to further constrain how the dissolved oxygen isotope signature may be determined from that of Mn oxides. I perform an in-depth characterization of a ferromanganese crust from the central Pacific and, using triple oxygen isotope measurements, demonstrate that Mn oxides in ferromanganese crusts from around the world retain signatures of dissolved oxygen for at least 30 million years. I next turn to a previously unconsidered aspect of the global oxygen cycle: dark, extracellular superoxide production by marine microbes. I measure extracellular superoxide production rates by some of the ocean’s most abundant organisms. I use these rates along with previous measurements to estimate that extracellular superoxide production yields a net sink of 5-19% of marine dissolved oxygen. Ultimately, the degree to which superoxide production is a sink of oxygen lies in the fate of its primary decay product, hydrogen peroxide. I determine the range of oxidative and reductive decay of hydrogen peroxide across a range of environmental conditions in a meromictic pond, thus validating several assumptions from our global estimate. Altogether, this thesis illuminates a path toward investigating the oxygen cycle on million-year timescales in Earth’s recent past and demonstrates the importance of microbial superoxide production in the biogeochemical cycling of O2.
    Description: This work was funded by the following grants and organizations: NASA Earth and Space Science Fellowship (NNX15AR62H), MIT Praecis Presidential Graduate Fellowship, NASA Exobiology (NNX15AM046), NSF-OCE grant 1355720, WHOI Ocean Ventures Fund, MIT Student Assistance Fund, WHOI Academic Programs Office, and the Stanford Synchrotron Radiation Lightsource. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DEAC02-76SF00515.
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    Protein regulation in Trichodesmium and other marine bacteria: observational and interpretive biomarkers of biogeochemical processes (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography and Microbial Biogeochemistry at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2020.
    Description: Marine microbes play key roles in global biogeochemistry by mediating chemical transformations and linking nutrient cycles to one another. A major goal in oceanography is to predict the activity of marine microbes across disparate ocean ecosystems. Towards this end, molecular biomarkers are important tools in chemical oceanography because they allow for both the observation and interpretation of microbial behavior. In this thesis, I use molecular biomarkers to develop a holistic, systems biology approach to the study of marine microbes. I begin by identifying unique patterns in the biochemical sensory systems of marine bacteria and suggest that these represent a specific adaptation to the marine environment. Building from this, I focus on the prevalent marine nitrogen fixer Trichodesmium, whose activity affects global nitrogen, carbon, phosphorus, and trace metal cycles. A metaproteomic survey of Trichodesmium populations identified simultaneous iron and phosphate co-stress throughout the tropical and subtropical oceans, demonstrating that this is caused by the biophysical limits of membrane space and nutrient diffusion. Tackling the problem at a smaller scale, I investigated the metaproteomes of individual Trichodesmium colonies captured from a single field site, and identified significant variability related to iron acquisition from mineral particles. Next, I investigated diel proteomes of cultured Trichodesmium erythraeum sp. IMS101 to highlight its physiological complexity and understand how and why nitrogen fixation occurs in the day, despite the incompatibly of the nitrogenase enzyme with oxygen produced in photosynthesis. This thesis develops a fundamental understanding of how Trichodesmium and other organisms affect, and are affected by, their surroundings. It indicates that a reductionist approach in which environmental drivers are considered independently may not capture the full complexity of microbechemistry interactions. Future work can focus on benchmarking and calibration of the protein biomarkers identified here, as well as continued connection of systems biology frameworks to the study of ocean chemistry.
    Description: This work was supported by an MIT Walter A. Rosenblith Presidential Fellowship and a National Science Foundation Graduate Research Program Fellowship under grant number 1122274 [N.Held]. This work was also supported by the WHOI Ocean Ventures fund [N.Held], Gordon and Betty Moore Foundation grant number 3782 [M.Saito], National Science Foundation grant numbers OCE-1657766 [M.Saito], EarthCube-1639714 [M.Saito], OCE-1658030 [M.Saito], and OCE-1260233 [M.Saito], and funding from the UK Natural Environment Research Council (NERC) under grants awarded to C.M. (NE/N001079/1) and M.L. (NE/N001125/1). This thesis was completed during a writing residency at the Turkeyland Cove Foundation.
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    Stable aerobic and anaerobic coexistence in anoxic marine zones (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zakem, E. J., Mahadevan, A., Lauderdale, J. M., & Follows, M. J. Stable aerobic and anaerobic coexistence in anoxic marine zones. ISME Journal, 14, (2019): 288–301, doi: 10.1038/s41396-019-0523-8.
    Description: Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
    Description: We are grateful for the thorough and thoughtful comments of two anonymous reviewers. We also thank Andrew Babbin for helpful comments. EJZ was supported by the Simons Foundation (Postdoctoral Fellowship in Marine Microbial Ecology). AM was supported by the Office of Naval Research (ONR #N000-14-15-1-2555). JML was supported by U.S. National Science Foundation (NSF #OCE-1259388). MJF was supported by the Gordon and Betty Moore Foundation (GBMF #3778) and the Simons Foundation: the Simons Collaboration on Ocean Processes and Ecology (SCOPE #329108) and the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES #549931).
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    Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ponnudurai, R., Heiden, S. E., Sayavedra, L., Hinzke, T., Kleiner, M., Hentschker, C., Felbeck, H., Sievert, S. M., Schlüter, R., Becher, D., Schweder, T., & Markert, S. Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions. ISME Journal, 14, (2019): 649–656, doi: 10.1038/s41396-019-0517-6.
    Description: Deep-sea Bathymodiolus mussels and their chemoautotrophic symbionts are well-studied representatives of mutualistic host–microbe associations. However, how host–symbiont interactions vary on the molecular level between related host and symbiont species remains unclear. Therefore, we compared the host and symbiont metaproteomes of Pacific B. thermophilus, hosting a thiotrophic symbiont, and Atlantic B. azoricus, containing two symbionts, a thiotroph and a methanotroph. We identified common strategies of metabolic support between hosts and symbionts, such as the oxidation of sulfide by the host, which provides a thiosulfate reservoir for the thiotrophic symbionts, and a cycling mechanism that could supply the host with symbiont-derived amino acids. However, expression levels of these processes differed substantially between both symbioses. Backed up by genomic comparisons, our results furthermore revealed an exceptionally large repertoire of attachment-related proteins in the B. thermophilus symbiont. These findings imply that host–microbe interactions can be quite variable, even between closely related systems.
    Description: Thanks to captain, crew, and pilots of the research vessels Atlantis (ROV Jason cruise AT26–10 in 2014) and Meteor (cruise M82–3 in 2010). We thank Jana Matulla, Sebastian Grund, and Annette Meuche for excellent technical assistance during sample preparation, MS measurements in the Orbitrap Classic, and TEM imaging preparation, respectively. We appreciate Nikolaus Leisch’s help with TEM image interpretation, Inna Sokolova’s advice on bivalve physiology, and Marie Zühlke’s support during manuscript revision. RP was supported by the EU-funded Marie Curie Initial Training Network ‘Symbiomics’ (project no. 264774) and by a fellowship of the Institute of Marine Biotechnology e.V. TH was supported by the German Research Foundation DFG (grant MA 6346/2–1 to SM). The Atlantis cruise was funded by a grant of the US National Science Foundation’s Dimensions of Biodiversity program to SMS (OCE-1136727).
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    Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Miller, C. A., Holm, H. C., Horstmann, L., George, J. C., Fredricks, H. F., Van Mooy, B. A. S., & Apprill, A. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. ISME Journal, 14, (2019): 688-701, doi: 10.1038/s41396-019-0549-y.
    Description: Whale digestion plays an integral role in many ocean ecosystems. By digesting enormous quantities of lipid-rich prey, whales support their energy intensive lifestyle, but also excrete nutrients important to ocean biogeochemical cycles. Nevertheless, whale digestion is poorly understood. Gastrointestinal microorganisms play a significant role in vertebrate digestion, but few studies have examined them in whales. To investigate digestion of lipids, and the potential contribution of microbes to lipid digestion in whales, we characterized lipid composition (lipidomes) and bacterial communities (microbiotas) in 126 digesta samples collected throughout the gastrointestinal tracts of 38 bowhead whales (Balaena mysticetus) harvested by Alaskan Eskimos. Lipidomes and microbiotas were strongly correlated throughout the gastrointestinal tract. Lipidomes and microbiotas were most variable in the small intestine and most similar in the large intestine, where microbiota richness was greatest. Our results suggest digestion of wax esters, the primary lipids in B. mysticetus prey representing more than 80% of total dietary lipids, occurred in the mid- to distal small intestine and was correlated with specific microorganisms. Because wax esters are difficult to digest by other marine vertebrates and constitute a large reservoir of carbon in the ocean, our results further elucidate the essential roles that whales and their gastrointestinal microbiotas play in the biogeochemical cycling of carbon and nutrients in high-latitude seas.
    Description: Devonshire Foundation (to CAM), Marine Mammal Center, Woods Hole Oceanographic Institution (WHOI; to CAM), WHOI Ocean Life Institute (to AA and CAM), Dalio Foundation’s Dalio Ocean Initiative (now ‘OceanX’) (to AA), National Science Foundation (OCE-1756254 and OPP-1543328 to BASVM). Samples were collected under Department of Commerce National Oceanic and Atmospheric Administration National Marine Fisheries Service permit numbers 17350-00, 17350-01, and 17350-02 to North Slope Borough Department of Wildlife Management.
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    Wave-driven geomorphology of Pacific carbonate coastlines: from landscape to wavelength scale (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2020.
    Description: The shallow marine ecosystems of coral atolls and the human communities they support are among the most vulnerable to anthropogenic climate change. Sea-level rise threatens to inundate low-lying reef islands, tropical cyclone intensification threatens islands with flooding and erosion, and ocean warming and acidification threaten the health of coral reefs. Unfortunately, the sediment dynamics that shape the morphology of coral reefs and atoll reef islands are poorly understood, hindering predictions of coral atoll responses to climate change forcing. Here, I apply an eclectic set of methods, including numerical modeling, physical lab experiments, and sedimentological analysis, to produce insights into the ways tropical cyclones and waves move sediment on fringing reefs. First, I use a numerical model of hydrodynamics to predict the influence of sea-level rise and wave climate change on sediment transport across a coral atoll fringing reef. I demonstrate that by the end of the century, sea-level rise will reduce sediment transport rates from the fore reef to the beach, but increase transport rates from the reef flat to the beach. Wave climate change will have relatively negligible influence on cross-reef sediment transport. Additionally, I use the weathering of foraminifera tests to produce a sediment proxy of transport duration and direction across atoll reef flats, but demonstrate that the proxy does not clearly identify storm deposits. Second, I execute a series of experiments in an oscillating flow tunnel to constrain the rate at which sediment erodes reef surfaces under waves. I find that the erosion rate increases as a power law of wave orbital velocity, and that amount of sediment has a second-order influence. Finally, I establish grain size in a sediment core retrieved from a blue hole in the Marshall Islands as a proxy for tropical cyclone genesis and, using the results from an ensemble of climate models, demonstrate that enhanced tropical cyclogenesis during the Little Ice Age may have been driven by an anomalously negative Pacific Meridional Mode. This thesis demonstrates the importance of sediment dynamics on the morphology of fringing reefs and atoll reef islands and the sensitivity of those dynamics to centennial climate variability.
    Description: Funding for this project was provided by the Strategic Environmental Research and Development Program (SERDP RC-2336).
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    A method for on-line water current velocity estimation using low-cost autonomous underwater vehicles (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Advances in the miniaturization of microelectronics has greatly contributed to the proliferation of small, low cost autonomous underwater vehicles (AUVs). These affordable vehicles offer organizations a flexible platform that can be adapted to support a multitude of research goals. The small size and low entry cost come with a trade off of simple navigation systems, typically dead reckoning (DR) using a speed determined via propeller counts and heading from a low cost micro-electromechanical system (MEMS) inertial measurement unit (IMU), whose error grows unbounded without the availability of a ground referenced fix source and is compounded by the bias present in the speed measurement due to the change in hydrodynamics from the addition of sensors to the hull form. Additionally, some capabilities such as water current velocity measurement traditionally requires the addition of equipment that is not only expensive, but also whose size and power consumption can adversely affect operating characteristics and deployment times. This thesis expands on previous research using one-way travel time inverted USBL (OWTT-iUSBL) to calculate the local current velocity without the addition of a Doppler velocity log (DVL) or acoustic Doppler current profiler (ADCP). A novel extended Kalman filter (EKF) is proposed that, in addition to calculating the current velocity, estimates and corrects for the bias present in the speed measurement as determined by the main vehicle computer. Using data collected on the Charles River at the Massachusetts Institute of Technology (MIT) Sailing Pavilion, it is shown that current velocities can be reasonably calculated using OWTT-iUSBL data as compared to the values calculated using long baseline (LBL) data.
    Description: Funding for this thesis research was provided the US Navy Civilian Institutions Office through the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program.
    Keywords: EKF ; low-cost ; AUV
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    Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gazitua, M. C., Vik, D. R., Roux, S., Gregory, A. C., Bolduc, B., Widner, B., Mulholland, M. R., Hallam, S. J., Ulloa, O., & Sullivan, M. B. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. Isme Journal, (2020), doi:10.1038/s41396-020-00825-6.
    Description: Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
    Description: We thank Sullivan Lab members and Heather Maughan for comments on the paper, Bess Ward for her contribution in the N-cycle context of our story, Kurt Hanselmann for his assistance in the calculations of the Gibbs-free energies, and the scientific party and crew of the R/V Atlantis (grant OCE-1356056 to MRM) for the sampling opportunity and support at sea. This work was funded in part by awards from the Agouron Institute to OU and MBS, a Gordon and Betty Moore Foundation Investigator Award (#3790) and NSF Biological Oceanography Awards (#1536989 and #1829831) to MBS, and the Millennium Science Initiative (grant ICN12_019-IMO) to OU. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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    Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Babbin, A. R., Tamasi, T., Dumit, D., Weber, L., Rodríguez, M. V. I., Schwartz, S. L., Armenteros, M., Wankel, S. D., & Apprill, A. Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. ISME Journal, (2020), doi:10.1038/s41396-020-00845-2.
    Description: Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm−2 d−1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
    Description: Research was conducted in the Gardens of the Queen, Cuba in accordance with the requirements of the Republic of Cuba, conducted under permit NV2370 and NV2568 issued by the Ministerio de Relaciones Exteriores. We gratefully acknowledge funding for this research by MIT Sea Grant award #2018-DOH-49-LEV, Simons Foundation award #622065, and MIT ESI seed funding to ARB, the MIT Montrym, Ferry, and mTerra Seed Grant Funds, and the generous contributions by Dr Bruce L. Heflinger.
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    Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Trembath-Reichert, E., Tully, B. J., & Huber, J. A. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. Isme Journal, (2020), doi:10.1038/s41396-020-00843-4.
    Description: The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
    Description: The Gordon and Betty Moore Foundation sponsored most of the observatory components at North Pond through grant GBMF1609. This work was supported by NSF OCE-1062006, OCE-1745589 and OCE-1635208 to J.A.H. E.T.R. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute and a L’Oréal USA For Women in Science Fellowship. The Center for Dark Energy Biosphere Investigations (C-DEBI OCE-0939564) also supported the participation of J.A.H. and B.T. This is C-DEBI contribution number 548.
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    The heterogeneity and volatile content of Earth’s mantle, magmas and crust (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: This thesis explores the volatile content of the mantle, subducted oceanic crust, and arc magmas as well as the structure of slow spreading ocean crust and the heterogeneity of Earth’s upper mantle. In Chapter 2, I directly explore the halogen (F and Cl) content of mantle minerals in situ, then use these measurements to assess the halogen content of the upper mantle. In Chapter 3, I investigate the volatile content of Raspas eclogites (SW Ecuador), a proxy for deeply subducted oceanic crust, to evaluate volatile transfer from crustal generation at divergent plate boundaries (e.g., mid-ocean ridges) to recycling of ocean crust at subduction zones. In Chapter 4, I use the H2O content of nominally anhydrous minerals in plutonic arc cumulates to elucidate the H2O content of the melts from which the rocks crystallized. In this way, I assert that primitive arc magmas may contain 4–10 wt.% H2O and through fractional crystallization up to ~20 wt.% H2O, making them far more hydrous than traditional methods (i.e., olivine-hosted melt inclusions) surmise. In Chapter 5, I show that mantle peridotite exposed along the 16ºN region of the Mid-Atlantic Ridge originated in an arc setting and has been remixed into subridge mantle, indicating that the sub-ridge mantle is more heterogeneous and depleted than inferences made from mid-ocean ridge basalts suggest. Chapter 6 surveys the life cycle of oceanic core complexes through zircon geochronology and posits an updated framework for understanding the termination of oceanic core complexes, and more broadly oceanic detachment faults. Together, this contribution highlights the chemical heterogeneity of the mantle, and quantifies the full extent of volatiles hosted by mantle and crustal reservoirs.
    Description: The Stanley Watson Fellowship (WHOI) provided financial support during my first year of graduate school. The Academic Programs Office Ocean Venture Fund (WHOI) provided seed funding which initiated Chapters 3 and 4, and ultimately led to two funded NSF proposals. These resources are vital to JP students, and I am incredibly grateful for them. Primary support was provided by the National Science Foundation grants to Veronique Le Roux (EAR P&G #1524311, #1839128, #1855302) and Henry Dick (MG&G #1637130, #1657983).
    Keywords: Geochemistry of the crust and mantle ; Volatile elements ; Tectonics
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    Towards basin-scale in-situ characterization of sea-ice using an Autonomous Underwater Glider (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-19
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: This thesis presents an Autonomous Underwater Glider (AUG) architecture that is intended for basin-scale unattended survey of Arctic sea-ice. The distinguishing challenge for AUG operations in the Arctic environment is the presence of year-round sea-ice cover which prevents vehicle surfacing for localization updates and shore-side communication. Due to the high cost of operating support vessels in the Arctic, the proposed AUG architecture minimizes external infrastructure requirements to brief and infrequent satellite updates on the order of once per day. This is possible by employing onboard acoustic sensing for sea-ice observation and navigation, along with intelligent management of onboard resources. To enable unattended survey of Arctic sea-ice with an AUG, this thesis proposes a hierarchical acoustics-based sea-ice characterization scheme to perform science data collection and assess environment risk, a multi-factor terrain-aided navigation method that leverages bathymetric features and active ocean current sensing to limit localization error, and a set of energy-optimal propulsive and hotel policies that react to evolving environmental conditions to improve AUG endurance. These methods are evaluated with respect to laboratory experiments and preliminary field data, and future Arctic sea-ice survey mission concepts are discussed.
    Description: Support for this research was provided through the National Science Foundation Navigating the New Arctic Grant #1839063 and the NASA PSTAR Grant #NNX16AL08G. Additionally, this research was supported by the Walter A. Rosenblith Presidential Fellowship.
    Keywords: Autonomous Underwater Glider (AUG) ; Sea-ice ; Energy efficient
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    Modifiable Stability and Maneuverability of High Speed Unmanned Underwater Vehicles (UUVs) Through Bioinspired Control Fins (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-19
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Oceanography/Applied Ocean Science and Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Underwater Vehicles generally have control fins located only near their aft end, for making controllable changes in directions. This design allows for stability of control; but, the turns are typically large in comparison to the vehicle’s body length. Some bony fish, such as tuna, however, have deployable fins located towards the front of their body, in addition to their other fins. Their deployable fins allow them to modulate their hydrodynamic behavior in response to their environment. Tunas keep these fins retracted during steady cruising, and then deploy them during rapid maneuvers. However, the details of these hydrodynamic effects are not well understood. To investigate this phenomena, using a REMUS 100 as a model, a pair of vertical fins was added at different hull positions, to investigate the effects of fin location on the horizontal plane hydrodynamics, through: stability parameters, nonlinear simulation, and towing tank experiments. Depending on the added fin location, the vehicle stability changed, thereby affecting the maneuverability. As fins were placed forward on the vehicle, maneuverability increased, with effects tapering off at 0.2 BL ahead of the vehicle's center of buoyancy. This investigation explored how rigid underwater vehicles could benefit from added fins, without drastically changing the design of current vehicles.
    Keywords: Maneuverability ; UUVs ; Bioinspiration
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    Morphological approaches to understanding Antarctic Sea ice thickness (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-19
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Sea ice thickness has long been an under-measured quantity, even in the satellite era. The snow surface elevation, which is far easier to measure, cannot be directly converted into sea ice thickness estimates without knowledge or assumption of what proportion of the snow surface consists of snow and ice. We do not fully understand how snow is distributed upon sea ice, in particular around areas with surface deformation. Here, we show that deep learning methods can be used to directly predict snow depth, as well as sea ice thickness, from measurements of surface topography obtained from laser altimetry. We also show that snow surfaces can be texturally distinguished, and that texturally-similar segments have similar snow depths. This can be used to predict snow depth at both local (sub-kilometer) and satellite (25 km) scales with much lower error and bias, and with greater ability to distinguish inter-annual and regional variability than current methods using linear regressions. We find that sea ice thickness can be estimated to ∼20% error at the kilometer scale. The success of deep learning methods to predict snow depth and sea ice thickness suggests that such methods may be also applied to temporally/spatially larger datasets like ICESat-2.
    Description: This research was funded by National Aeronautics and Space Administration grant numbers NNX15AC69G and 80NSSC20K0972, the US National Science Foundation grant numbers ANT-1341513, ANT-1341606, ANT-1142075 and ANT-1341717, and the WHOI Academic Programs Office.
    Keywords: Sea ice ; Antarctic ; Snow depth
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    Vertical fluxes in the upper ocean (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Oceanic fronts at the mesoscale and submesoscale are associated with enhanced vertical motion, which strengthens their role in global biogeochemical cycling as hotspots of primary production and subduction of carbon from the surface to the interior. Using process study models, theory, and field observations of biogeochemical tracers, this thesis improves understanding of submesoscale vertical tracer fluxes and their influence on carbon cycling. Unlike buoyancy, vertical transport of biogeochemical tracers can occur both due to the movement of isopycnals and due to motion along sloping isopycnals. We decompose the vertical velocity below the mixed layer into two components in a Lagrangian frame: vertical velocity along sloping isopycnal surfaces and the adiabatic vertical velocity of isopycnal surfaces and demonstrate that vertical motion along isopycnal surfaces is particularly important at submesoscales (1-10 km). The vertical flux of nutrient, and consequently the new production of phytoplankton depends not just on the vertical velocity but on the relative time scales of vertical transport and nutrient uptake. Vertical nutrient flux is maximum when the biological timescale of phytoplankton growth matches the vertical velocity frequency. Export of organic matter from the surface and the interior requires water parcels to cross the mixed layer base. Using Lagrangian analysis, we study the dynamics of this process and demonstrate that geostrophic and ageostrophic frontogenesis drive subduction along density surfaces across the mixed layer base. Along-front variability is an important factor in subduction. Both the physical and biological modeling studies described above are used to interpret observations from three research cruises in the Western Mediterranean. We sample intrusions of high chlorophyll and particulate organic carbon below the euphotic zone that are advected downward by 100 meters on timescales of days to weeks. We characterize the community composition in these subsurface intrusions at a lateral resolution of 1–10 km. We observe systematic changes in community composition due to the changing light environment and differential decay of the phytoplankton communities in low-light environments, along with mixing. We conclude that advective fluxes could make a contribution to carbon export in subtropical gyres that is equal to the sinking flux.
    Description: The work in this dissertation was funded by a NDSEG fellowship, Martin Fellowship, Grassle fellowship, Montrym grant, WHOI Academic Programs Office, and Office of Naval Research CALYPSO DRI grant N00014-16-1-3130.
    Keywords: Vertical velocity ; Submesoscale dynamics ; Biophysical interactions
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    Environmental effects of the Beaufort Lens on underwater acoustic communications during Arctic operations (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Operations in the Arctic Ocean are increasingly important due to the changing environment and the resulting global implications. These changes range from the availability of new global trade routes, accessibility of newly available resources in the area, and national security interests of the United States in the region. It’s necessary to build a greater understanding of the undersea environment and how it’s changing since these environmental changes have a direct impact on adjusting future operations in the region and looming global changes as less Arctic ice is present. The recent presence of the Beaufort Lens is changing the acoustic propagation paths throughout the Arctic region. Here a network of buoys were employed to communicate with an Autonomous Undersea Vehicle (AUV) while it operated under the ice throughout the Beaufort Lens with the goal of achieving near GPS quality navigation. The acoustic communications paths were compared using a vertical array throughout the Beaufort Lens. This beam forming was compared to the prediction from BELLHOP. As well, since acoustic communications are affected by multi-path, attenuation and interference from other sources it was interesting to note that bottom bounce was sometimes a reliable acoustic path.
    Keywords: Arctic ; Beaufort Lens ; Acoustic communications
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    Investigating chromium cycling in global oxygen deficient zones with chromium isotopes (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Chromium (Cr) isotopes have shown great potential as a paleo-redox proxy to trace the redox conditions of ancient oceans and atmosphere. However, its cycling in modern environments is poorly constrained. In my thesis, I attempt to fill in the gap of our understanding of chromium cycling in the modern ocean, with a focus on the redox processes in global oxygen deficient zones (ODZs). Firstly, we developed a method to analyze Cr isotopes of different Cr redox species. Tests on processing conditions demonstrated its robustness in obtaining accurate Cr isotope data. It is applicable to both frozen and fresh samples. This method allows us to investigate the redox cycling of Cr that is hard to unravel by existing total Cr methods. Secondly, in the Eastern Tropical North Pacific (ETNP), Eastern Tropical South Pacific (ETSP) and Arabian Sea ODZs, their total dissolved Cr profiles show preferential reduction of isotopically light Cr(VI) to Cr(III), which is scavenged and exported to deeper oceans. Applying our new method to ETNP and ETSP ODZ seawater samples, we observed Cr(VI) reduction in both ODZs with a similar fractionation factor. This indicates similar mechanisms may be controlling Cr(VI) reduction in the two ODZs. Cr(III) maximum coincides with Fe(II) and secondary nitrite maximums in the upper core of both ODZs. Shipboard incubations with spiked Fe(II) showed fast Cr(VI) reduction occurring in the ETNP ODZ. But neither Fe(II) nor microbes were reducing Cr(VI) directly. Thirdly, we calculated the isotope effects of Cr scavenging in the ETNP and ETSP ODZs. Thetwo ODZs show a similar isotope partitioning during Cr scavenging. And spatial variability is observed in the ETNP ODZ. Our calculated scavenged Cr isotope ratio is lighter than that of the total dissolved Cr from the same depth. It is also comparable to that of reducing or anoxic sediments, which implies that Cr isotopes can be used as an archive for local redox conditions.
    Description: This research was supported by an anonymous MIT Fellowship, Praceis Presidential Fellowship, Frederick A. Middleton Fellowship, the US National Science Foundation (NSF Award No. OCE-1459287, OCE-1736996, OCE-1924050 and DEB-1542240) and the Center for Microbial Oceanography: Research and Education (C-MORE, NSF-OIA Award No. EF-0424599).
    Keywords: Chromium isotopes ; Oxygen deficient zones ; Redox cycling
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    Advances in passive acoustic detection, localization, and tracking applied to unmanned underwater vehicles (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Detection, classification, localization, and tracking (DCLT) of unmanned underwater vehicles (UUVs) in the presence of shipping traffic is a critical task for passive acoustic harbor security systems. In general, vessels can be tracked by their unique acoustic signature due to machinery vibration and cavitation noise. However, cavitation noise of UUVs is considerably quieter than ships and boats, making detection significantly more challenging. In this thesis, I demonstrated that it is possible to passively track a UUV from its highfrequency motor noise using a stationary array in shallow-water experiments with passing boats. First, causes of high frequency tones were determined through direct measurements of two UUVs at a range of speeds. From this analysis, common and dominant features of noise were established: strong tones at the motor’s pulse-width modulated frequency and its harmonics. From the unique acoustic signature of the motor, I derived a high-precision, remote sensing method for estimating propeller rotation rate. In shallow-water UUV field experiments, I demonstrated that detecting a UUV from motor noise, in comparison to broadband noise from the vehicle, reduces false alarms from 45% to 8.4% for 90% true detections. Beamforming on the motor noise, in comparison to broadband noise, improved the bearing accuracy by a factor of 3.2×. Because the signal is also high-frequency, the Doppler effect on motor noise is observable and I demonstrate that range rate can be measured. Furthermore, measuring motor noise was a superior method to the “detection of envelope modulation on noise” algorithm for estimating the propeller rotation rate. Extrapolating multiple measurements from the motor signature is significant because Bearing-Doppler-RPM measurements outperform traditional bearing-Doppler target motion analysis. In the unscented Kalman filter implementation, the tracking solution accuracy for bearing, bearing rate, range, and range rate improved by a factor 2.2×, 15.8×, 3.1×, and 6.2× respectively. These findings are significant for improving UUV localization and tracking, and for informing the next-generation of quiet UUV propulsion systems.
    Keywords: Autonomy ; Passive sonar ; Tracking
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    Anthropogenic and natural radioisotopes as tracers for contaminant sources and particulate fluxes (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Radioactive isotopes act as nuclear clocks that are utilized to trace and measure rates of chemical, biological, physical, and geological oceanographic processes. This thesis seeks to utilize both artificial (e.g., released from anthropogenic sources) and natural radioisotopes as tracers within the Pacific Ocean basin. Artificial radioisotopes released as a result of the 2011 Fukushima Daiichi nuclear power plants accident have the potential to negatively impact human and environmental health. This study evaluates 137Cs, 90Sr, and 129I concentrations in seawater off the coast of Japan, reconciles the sources of contaminated waters, and assesses the application of 137Cs/90Sr, 129I/137Cs, and 129I/90Sr as oceanic tracers. The analysis of activity ratios suggests a variety of sources, including ongoing sporadic and independent releases of radiocontaminants. Though decreasing, concentrations remain elevated compared to preaccident levels. Future planned releases of stored water from the reactor site may affect the surrounding environment; and thus, continued efforts to understand the distribution and fate of these radionuclides are warranted. Naturally-occurring radioisotopes (e.g., the 238U-234Th series used in this thesis) can give insight into surface export and remineralization of particulate organic carbon (POC) and trace metals (TMs). POC and TMs play a vital role in regulating the biological carbon pump (BCP), which in turn helps to moderate atmospheric CO2 levels by transporting carbon to the deep ocean, where it can be sequestered on timescales of centuries to millennia. Through this thesis we utilize the 238U:234Th disequilibrium method throughout the GEOTRACES GP15 Pacific Meridional Transect in order o provide basin-scale estimates of POC export and remineralization. There is only limited, recent use of this method to constrain TM fluxes, and as such this study also seeks to further develop this method for use in understanding TM cycling through comparative flux studies in the North Pacific.
    Description: Funding sources for this thesis include the Gordon and Betty Moore Foundation, the Deerbrook Charitable Trust, NSF OCE award no. 1356630 and no. 1735445, and the NSF GRFP.
    Keywords: Radioactive tracers ; Carbon cycling ; Trace metal cycling
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    Characterizing cobalamin cycling by Antarctic marine microbes across multiple scales (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2020.
    Description: Highly productive marine microbial communities in the coastal Southern Ocean sustain the broader Antarctic ecosystem and play a key role in Earth’s climate via the biological pump. Regional phytoplankton growth is primarily limited by iron and co-limited by cobalamin (vitamin B12), a trace cobalt-containing organometallic compound only synthesized by some bacteria and archaea. These micronutrients impact primary production and the microbial ecology of the two keystone phytoplankton types: diatoms and Phaeocystis antarctica. This thesis investigates microbe-driven cobalamin cycling in Antarctic seas across multiple spatiotemporal scales. I conducted laboratory culture experiments with complementary proteomics and transcriptomics to investigate the B12-ecophysiology of P. antarctica strain CCMP 1871 morphotypes under iron-B12 co-limitation. We observed colony formation under higher iron treatments, and a facultative use of B12-dependent (MetH) and B12-independent (MetE) methionine synthase isoforms in response to vitamin availability, demonstrating that this strain is not B12-auxotrophic. Through comparative ’omics, we identified a putative MetE protein in P. antarctica abundant under low B12, which is also found in other marine microbes. Across Antarctic seas, community-scale cobalt and B12 uptake rates were measured by 57Co radiotracer incubation experiments and integrated with hydrographic and phytoplankton pigment data. I observed significant correlations between uptake fluxes and environmental variables, providing evidence for predominantly diatom-driven uptake of these micronutrients in warmer, fresher surface waters with notable regional differences. To date, this work is the most comprehensive attempt to elucidate the processes governing the co-cycling of cobalt and B12 in any marine system. At the ecosystem-scale, I developed and tested a hypothesis of micronutrient-driven community dynamics through a trait-based model with cross-feeding interactions. The model demonstrates how the observed seasonal succession of springtime P. antarctica from solitary to colonial cells, bacterioplankton, and summertime diatoms may be explained by the microbial cycling of iron, dissolved organic carbon, and B12. Overall, this dissertation provides new information about the micronutrient-driven ecology of Antarctic marine microbes and adds to our understanding of the interconnections between organismal life cycle, trace metals, and trace organics in marine environments.
    Description: My training as a scientist during my time in the MIT–WHOI Joint Program (2014-2020) and the work presented in this dissertation were financially supported by the Academic Programs Office (APO) at the Woods Hole Oceanographic Institution (WHOI) and various funding agencies. My first semester was supported by the WHOI Von Damm Fellowship (2014). Subsequent years and endeavors were supported by awards from the Gordon and Betty Moore Foundation to Professor Michael Follows (Award 3778, M.J.F.) and Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (Award 549931, M.J.F.); National Science Foundation (NSF) grant to Dr. Stephanie Dutkiewicz (Grant number 1434007, S.D.), and NSF Office of Polar Program (OPP) grant to Dr. Makoto Saito (M.S.) for the CICLOPS research expedition (OPP-1643684, OPP-1643845, and OPP-1644073).
    Keywords: Antarctica ; Cobalamin ; Microbes
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    High resolution sedimentary archives of past millennium hurricane activity in the Bahama Archipelago (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Little is known about how Atlantic hurricane activity changes on long timescales. This thesis uses proxy development and proxy-model integration to constrain the spatiotemporal variability in hurricane activity in the Bahama Archipelago over the past millennium. I present annually-resolved archives of storm activity derived from sediment cores from blue holes on three islands in the Bahama Archipelago: South Andros, Long Island, and Middle Caicos. Dramatic differences between these records suggest localized controls on the hurricane patterns observed by each island. Thus, compiling these records together more accurately captures regional variations in hurricane strikes. Integrating our new Bahama Archipelago compilation with compiled paleohurricane records from the U.S. coastline indicates shifting patterns of hurricane activity over the past millennium between the Gulf Coast and the Bahama Archipelago/New England. Finally, I address whether variability in hurricane strikes observed in Bahamian paleohurricane records is related to climate or random variability using hurricane model output. The signal observed in any individual record of paleohurricane activity from the Bahama Archipelago is driven more by random variability in hurricane tracks than by climate. This thesis lays the groundwork for creating high-resolution paleohurricane records from blue holes and using hurricane models to inform our interpretations of these records.
    Description: This work was funded by the National Science Foundation Graduate Research Fellowship (to E.J.W.), National Science Foundation grant OCE-1356708 (to J.P.D. and P.J.vH.) and the Dalio Explore Foundation.
    Keywords: Paleohurricanes ; Carbonate sediment ; Blue holes
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    Investigating Mexican paleoclimate with precisely dated speleothems (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Speleothems, or sedimentary rocks formed in caves, act as valuable archives of past climate change due to their suitability for U-series dating and high-resolution proxy analysis. These records can provide insights into water availability and controls on hydrology prior to the instrumental record. In this thesis, I present three records from newly-analyzed Mexican stalagmites using stable isotope (oxygen and carbon) and trace element to calcium (Mg/Ca and Sr/Ca) ratios as proxies for changing hydroclimate. Chapter 2 presents a precisely dated, mid-Holocene record of high rainfall and limited precipitation variability in the Yucatan Peninsula, Mexico. Chapters 3 and 4 present novel climate records from northeastern Mexico, an understudied region of North America. Both records come from cave sites within the Mexican arid zone, which is simultaneously experiencing increased water scarcity and a rapidly growing population. In Chapter 3, I examine a speleothem from the first millennium of the Common Era, which showed that there is a precipitation dipole between northern and southern Mexico. Chapter 4 highlights, for the first time at decadal resolution, the northeast Mexican response to the 8.2 ka event and the Younger Dryas. These chapters show that the San Luis Potosí region is vulnerable to droughts under multiple climate mean states, and is subject to drying as Atlantic Meridional Overturning Circulation weakens due to anthropogenic climate change. The climate records detailed in this thesis improve our understanding of controls on Mexican hydroclimate and can serve as benchmarks for climate models.
    Description: This work was funded by US National Science Foundation (NSF) grants AGS-1702848 (M. Medina-Elizalde), AGS–1502877 (S. Burns), AGS-1804512 and AGS-1806090 (K. Johnson and D. McGee). I was also supported by the NSF Graduate Research Fellowship and the MIT School of Science Dean’s Fellowship. Fieldwork and analysis were funded by the WHOI Ocean Ventures Fund, the MIT EAPS Student Research Fund, and the MIT International Science and Technology Initiatives (MISTI) Mexico program. Initial work for this project was also supported by UC MEXUS-CONACYT Collaborative Grant from the University of California Institute for Mexico and the United States (UC MEXUS CN-16-120). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation.
    Keywords: Stalagmite ; Drought ; Holocene
    Repository Name: Woods Hole Open Access Server
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  • 47
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    Assessing the potential for Zn limitation of marine primary production: proteomic characterization of the low Zn stress response in marine diatoms (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: Marine diatoms are abundant photoautotrophic algae that contribute significantly to photosynthetic carbon fixation and export throughout the oceans. Zinc is an important micronutrient in algal metabolism, with scarce dissolved concentrations in the upper euphotic zone reflecting high biological demand. In this thesis, I investigated the response of marine diatoms to Zn scarcity to characterize metabolic mechanisms used to combat Zn stress. I began by assaying the ability to metabolically substitute cobalt (Co) in place of Zn in four diatom species and found that enhanced abilities to use Co are likely an adaptation to high surface dCo:dZn ratios in the native environment. I next demonstrated that Zn/Co metabolic substitution in diatoms is not universal using culture studies of Chaetoceros neogracile RS19, which has an absolute Zn requirement. Using global proteomic analysis, I then identified and characterized diatom ZCRP-A and ZCRP-B, a putative Zn-chaperone and membrane-tethered Zn acquisition protein, respectively, as two proteins involved in the low-Zn response. I demonstrated that these proteins are widespread in marine phytoplankton and can be deployed as protein biomarkers of Zn stress in the field. I furthermore documented both the detection of ZCRPs in the Southern Ocean and the existence of Zn/Fe co-limitation within the natural phytoplankton population in Terra Nova Bay, demonstrating that Zn co-limitation can indeed occur in the field, even in high macronutrient waters. Lastly, I explored the relative demand of Zn and cadmium (Cd) within the Southern Ocean community using stable 67Zn and 110Cd tracers, documenting a high demand for both metals during the austral 2017-2018 summer season and investigating the cycling of these elements within this important region. Overall, this dissertation provides new information regarding Zn acquisition and homeostasis mechanisms within marine algae and demonstrates that Zn co-limitation in the field is not only possible, but detectable via protein biomarkers.
    Description: I am very fortunate to have been financially supported over the course of my PhD by awards granted to the Saito Lab, specifically by National Institutes of Health (NIH) grant R01GM135709, Gordon and Betty Moore Foundation grant 3782, and National Science Foundation (NSF) grants OCE-1657766, OCE-1658030, OCE-1736599, OCE-1850719, and OCE-1924554.
    Keywords: Zinc ; Diatoms ; Proteomic
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  • 48
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    Phosphonate biogeochemical cycling in the marine environment: from an ocean scale to a molecular scale (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: The existence of a marine phosphorus (P) redox cycle was recently confirmed when phosphonates, organophosphorus compounds with P in the (III) oxidation state, were found in high molecular weight dissolved organic matter. Although some features of the P redox cycle have come to light since the discovery of phosphonates, many aspects of phosphonate production, cycling and fate remain unknown. To address these gaps in our understanding, we studied phosphonate cycling in the Eastern Mediterranean Sea, a chronically P-limited basin, using 33P and enzymatic assays. We showed that phosphonate production was low but consumption was high, suggesting that phosphonate production and consumption may be spatially or temporally decoupled. We also explored phosphonate production in the model marine cyanobacterium Prochlorococcus SB. Using 31P NMR, we found Prochlorococcus SB allocates ~50% of its cellular P to phosphonates. Allocation of P to phosphonates was conserved under P-limitation, and further investigation revealed phosphonates were associated with proteins. The discovery of phosphonoproteins in Prochlorococcus SB opens new perspectives on the biochemical function of phosphonates and their role in P-cycling. Finally, we developed a new P-targeted method to characterize marine organophosphorus compounds using liquid chromatography coupled to electrospray ionization and inductively coupled plasma mass spectrometry.
    Description: This work was supported by the Simons Foundation under grant numbers POP49476 and 721227 [D. Repeta], the Gordon and Betty Moore Foundation under the grant number 6000 [D. Repeta] and the National Science Foundation OCE under the grant number 1634080 [D. Repeta].
    Keywords: Phosphorus ; Phosphonate ; Biogeochemical cycling
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  • 49
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    Inferring the thermomechanical state of the lithosphere using geophysical and geochemical observables (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Geophysics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: This thesis focuses on interpreting geophysical and geochemical observables in terms of the thermomechanical state of the lithosphere. In Chapter 1, I correlate lower crustal rheology with seismic wave speed. Compositional variation is required to explain half of the total variability in predicted lower crustal stress, implying that constraining regional lithology is important for lower crustal geodynamics. In Chapter 2, I utilize thermobarometry, diffusion models, and thermodynamic modelling to constrain the ultra-high formation conditions and cooling rates of the Gore Mountain Garnet Amphibolite in order to understand the rheology of the lower crust during orogenic collapse. In Chapter 3, I interpret geophysical data along a 74 Myr transect in the Atlantic to the temporal variability and relationship of crustal thickness and normal faults. In Chapter 4, I constrain the error present in the forward-calculation of seismic wave speed from ultramafic bulk composition. I also present a database and toolbox to interpret seismic wave speeds in terms of temperature and composition. Finally, in Chapter 5 I apply the methodology from Chapter 4 to interpret a new seismic tomographic model in terms of temperature, density, and composition in order to show that the shallow lithospheric roots are density unstable.
    Description: Funding for this research was provided by an MIT Presidential Fellowship, MIT Student Research Funds, the National Science Foundation Division of Earth Sciences (EAR) and Ocean Sciences (OCE) grants EAR-16-24109, EAR-17-22932, EAR-17-22935, OCE-14-58201, and SCEC Awards 16106 and 17202., SCEC, Geological Society of America Graduate Student Research Fellowship, WHOI Ocean Venture Fund, and the WHOI Academic Programs Office.
    Keywords: Lithosphere ; Seismic wave speed ; Rheology
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    Diagnosing the variability in temperature and velocity in the Middle Atlantic Bight (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Observations of hydrographic and dynamical properties on the Middle Atlantic Bight shelf document strong variability at time scales spanning events that last a few days to century long trends. This thesis studies individual processes which impact shelf temperature and velocity structure, and quantifies the mean velocity conditions at the shelf break. Chapter 2 uses model output to study the dynamics that lead to the breakdown of summertime thermal stratification, and how the processes which reduce stratification vary from year to year. In summer, the atmosphere heats the surface of the ocean, leading to strong thermal stratification with warm water overlying cool water. During fall, strong storm events with downwelling-favorable winds are found to be the primary process by which stratification is reduced. The timing of these events and the associated destratification varies from year to year. In Chapter 3, the velocity structure of the New Jersey shelf break is examine, with a focus on the Shelfbreak Jet. Using 25 years of velocity measurements, mean velocity sections of the Shelfbreak Jet are created in both Eulerian and stream coordinate frameworks. The jet exhibits strong seasonal variability, with maximum velocities observed in spring and minimum velocities in summer. Evidence is found that Warm Core Rings, originating from the Gulf Stream and passing through the Slope Sea adjacent to the New Jersey shelf, tend to shift the Shelfbreak Jet onshore of its mean position or entirely shutdown the Shelfbreak Jet’s flow. At interannual timescales, variability in the Shelfbreak Jet velocity is correlated with the temperature on the New Jersey Shelf, with temperature lagging by about 2 months. Chapter 4 focuses on the impact of Warm Core Rings on the velocity and temperature structure on the New Jersey shelf. Warm Core Rings that have higher azimuthal velocities and whose cores approach closer to the shelf are found to exert greater influence on the shelf’s along-shelf velocities, with the fastest and closest rings reversing the direction of flow at the shelf break. Warm Core Rings are also observed to exert long-lasting impacts on the shelf temperature, with faster rings cooling the shelf and slower rings warming the shelf. Seasonal changes in thermal stratification strongly affect how rings alter the shelf temperature. Rings in summer tend to cool the shelf, and rings throughout the rest of the year generally warm the shelf.
    Description: This research was funded under WHOI Academic Programs Endowed Funds, NSF #OCE-1634094, and NSF #OCE-1924041.
    Keywords: Temperature variability ; Velocity variability ; Middle Atlantic Bight
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    Environmental drivers of the abundance and distribution of forage fishes on the Northeast US shelf, with a particular emphasis on northern sand lance (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Small pelagic fishes, also termed forage fishes, represent a critical link between secondary production and myriad top predators in marine ecosystems, including the Northeast US shelf. In this dissertation, I analyze the drivers of forage fish distribution throughout the Northeast US shelf and the drivers of the abundance of the ecologically important northern sand lance. Chapter 2 examines the basic ecology of northern sand lance and uses these insights to identify mechanistic drivers of their abundance. I then explore different scenarios of these drivers to project sand lance abundance through the end of the 21st century, which appears precarious for adult sand lance unless current trajectories change. Chapter 3 analyzes the environmental drivers of the distribution of the six dominant, offshore forage fish species (northern sand lance, Atlantic herring, alewife, blueback herring, Atlantic mackerel, and Atlantic butterfish) on the Northeast US shelf to elucidate the role of environmental covariates in shelf occupancy by these taxa. The results of this chapter indicate shelf occupancy of butterfish and Atlantic mackerel are increasing through time while occupancy of sand lance is decreasing with time. The occurrence of most of these species is also moving deeper and northward with time. Chapter 4 assesses the source-sink dynamics of three sand lance hotspots through Lagrangian particle tracking models simulating larval sand lance transport. Connectivity varies among these hotspots with Georges Bank and Stellwagen Bank having notable retention while the Great South Channel relies on larvae from other hotspots. Retention on Stellwagen Bank and Georges Bank are linked to strong wind events during the larval period of sand lance. Collectively, this dissertation improves our understanding of the dynamics driving variability in the Northeast US shelf forage fish complex, particularly for northern sand lance.
    Description: The research within this dissertation was funded by a National Science Foundation Graduate Research Fellowship (awarded to JJS), Woods Hole Sea Grant (NA18OAR4170104, Project No. R/O-57), the Bureau of Ocean Energy Management (IA agreement M17PG0019), and the National Marine Sanctuary Foundation.
    Keywords: Forage fish ; Northwest Atlantic ; Fisheries oceanography
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  • 52
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    Control of the abyssal ocean overturning circulation by mixing-driven bottom boundary layers (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: An emerging paradigm posits that the abyssal overturning circulation is driven by bottom-enhanced mixing, which results in vigorous upwelling in the bottom boundary layer (BBL) along the sloping seafloor and downwelling in the stratified mixing layer (SML) above; their residual is the overturning circulation. This boundary-controlled circulation fundamentally alters abyssal tracer distributions, with implications for global climate. Chapter 1 describes how a basin-scale overturning circulation arises from the coupling between the ocean interior and mixing-driven boundary layers over rough topography, such as the sloping flanks of mid-ocean ridges. BBL upwelling is well predicted by boundary layer theory, whereas the compensation by SML downwelling is weakened by the upward increase of the basin-wide stratification, which supports a finite net overturning. These simulated watermass transformations are comparable to best-estimate diagnostics but are sustained by a crude parameterization of boundary layer restratification processes. In Chapter 2, I run a realistic simulation of a fracture zone canyon in the Brazil Basin to decipher the non-linear dynamics of abyssal mixing layers and their interactions with rough topography. Using a hierarchy of progressively idealized simulations, I identify three physical processes that set the stratification of abyssal mixing layers (in addition to the weak buoyancy-driven cross-slope circulation): submesoscale baroclinic eddies on the ridge flanks, enhanced up-canyon flow due to inhibition of the cross-canyon thermal wind, and homogenization of canyon troughs below the level of blocking sills. Combined, these processes maintain a sufficiently large near-boundary stratification for mixing to drive globally significant BBL upwelling. In Chapter 3, simulated Tracer Release Experiments illustrate how passive tracers are mixed, stirred, and advected in abyssal mixing layers. Exact diagnostics reveal that while a tracer’s diapycnal motion is directly proportional to the mean divergence of mixing rates, its diapycnal spreading depends on both the mean mixing rate and an additional non-linear stretching term. These simulations suggest that the theorized boundary-layer control on the abyssal circulation is falsifiable: downwelling in the SML has already been confirmed by the Brazil Basin Tracer Release Experiment, while an upcoming experiment in the Rockall Trough will confirm or deny the existence of upwelling in the BBL.
    Description: This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 174530. I also acknowledge funding support from National Science Foundation Awards OCE-1536515 and OCE-1736109. This work was partially supported by MIT’s Rosenblith Presidential Fellowship.
    Keywords: Abyss ; Circulation ; Mixing
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    Assessing anthropogenic noise impacts and relevant soundscape cues for marine invertebrates: leveraging squid and coral reefs as model systems (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Sound is utilized by marine animal taxa for many ecologically important functions, and these taxa are vulnerable to adverse effects of anthropogenic noise on hearing and behavior. However, little is known about marine invertebrates’ responses to anthropogenic noise, and the ambient environmental sounds (“soundscapes”) they detect and respond to. Most acoustic studies report sound pressure (detected by mammals and some fish), but few report particle motion, the back-and-forth vibratory component of sound detected by marine invertebrates. I investigated invertebrate use of and response to sounds in two facets: 1) behavioral responses of longfin squid, Doryteuthis pealeii to anthropogenic noise, and 2) particle motion of coral reef soundscapes in the U.S. Virgin Islands. In laboratory-based experiments I exposed D. pealeii to construction noise originally recorded from an offshore wind farm. I found significant increases in squids’ alarm responses and in failed prey capture attempts during noise. Conversely, noise exposure had no significant effects on reproductive behaviors of groups of D. pealeii, indicating high motivation of these squid to reproduce during this stressor. Collectively, these experiments revealed the importance of considering behavioral context in studies and regulatory decisions regarding invertebrates’ susceptibility to anthropogenic noise impacts. In studying coral reef soundscapes, I reported particle motion trends over several months for coral reefs varying in habitat quality, including coral cover and fish abundance. I found acoustic properties over which particle motion closely scaled with pressure, and others over which it did not. I compared soundscape data with particle motion hearing thresholds, and found that invertebrates may only detect high amplitude and low frequency transient sound cues on reefs, such as those produced by fishes. My research bring new insights on natural and anthropogenic sound cues detectable by marine invertebrates, and how and when invertebrates will be vulnerable to anthropogenic noise pollution.
    Description: My graduate work was funded in part by the US Department of Interior, Bureau of Ocean Energy Management Environmental Studies Program through Interagency Agreement Number M17PG00029 with the U.S. Department of Commerce, National Oceanic and Atmospheric Administration (funding to Aran Mooney and Jenni Stanley). My work was also supported by the NSF Biological Oceanography award OCE-1536782 (funding to Aran Mooney). I received tuition and stipend support from the National Science Foundation Graduate Research Fellowship Program [Grant No. 2388357]. The Academic Program Office at the Woods Hole Oceanographic Institution provided tuition and stipend support as well as travel support. The MIT Student Assistance Fund, the Aquatic Noise 2019 Organizing Committee, and the Acoustical Society of America also provided travel support.
    Keywords: Cephalopod ; Renewable energy ; Ecoacoustics
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    Multi-path Penalty metric in underwater acoustic communication for autonomy and human decision-making (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: A novel performance metric to improve underwater digital acoustic communication, called Multipath Penalty (MPP), is proposed as an alternative to traditional signal-to-noise ratio (SNR) methods in the context of the Arctic Beaufort Sea. MPP and SNR are compared alongside a third performance metric, Minimum Achievable Error (MAE), which replicates the operation of a channel estimate-based decision feedback equalizer in an acoustic modem. The three metrics are then tested in a hardware-in-the-loop Virtual Ocean simulator for an autonomous undersea vehicle (AUV) communicating with a collaborator. Using field data of modem statistics obtained duringICEX20 and expanded data supplied by the simulator, calibration of the three metrics to modem packet success is evaluated, resulting in a proposed recalibration for MAE. The AUV’s ability to communicate when adaptively choosing its depth is analyzed above and below the Beaufort Lens, and settings for MPP’s engineering variables are obtained. The results show MPP generally improves reception and demodulation of acoustic transmissions over SNR by approximately 5% within an operational range of 8 km, while achieving similar results to the more robust metric MAE. MPP is an improved utility for underwater digital acoustic communication in both marine autonomy and as a tactical decision aid.
    Description: This work would not be possible without the extraordinary support of the United States Navy, which provided funding for this research, my degree, and my livelihood as an active duty submarine officer.
    Keywords: Multi-path Penalty ; Acoustics ; Metric
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    Reduced order modeling for stochastic prediction and data assimilation onboard autonomous platforms at sea (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: There are many significant challenges for unmanned autonomous platforms at sea including predicting the likely scenarios for the ocean environment, quantifying regional uncertainties, and updating forecasts of the evolving dynamics using their observations. Due to the operational constraints such as onboard power, memory, bandwidth, and space limitations, efficient adaptive reduced order models (ROMs) are needed for onboard predictions. In the first part, several reduced order modeling schemes for regional ocean forecasting onboard autonomous platforms at sea are described, investigated, and evaluated. We find that Dynamic Mode Decomposition (DMD), a data-driven dimensionality reduction algorithm, can be used for accurate predictions for short periods in ocean environments. We evaluate DMD methods for ocean PE simulations by comparing and testing several schemes including domain splitting, adjusting training size, and utilizing 3D inputs. Three new approaches that combine uncertainty with DMD are also investigated and found to produce practical and accurate results, especially if we employ either an ensemble of DMD forecasts or the DMD of an ensemble of forecasts. We also demonstrate some results from projecting / compressing high-fidelity forecasts using schemes such as POD projection and K-SVD for sparse representation due to showing promise for distributing forecasts efficiently to remote vehicles. In the second part, we combine DMD methods with the GMM-DO filter to produce DMD forecasts with Bayesian data assimilation that can quickly and efficiently be computed onboard an autonomous platform. We compare the accuracy of our results to traditional DMD forecasts and DMD with Ensemble Kalman Filter (EnKF) forecast results and show that in Root Mean Square Error (RMSE) sense as well as error field sense, that the DMD with GMM-DO errors are smaller and the errors grow slower in time than the other mentioned schemes. We also showcase the DMD of the ensemble method with GMM-DO. We conclude that due to its accurate and computationally efficient results, it could be readily applied onboard autonomous platforms. Overall, our contributions developed and integrated stochastic DMD forecasts and efficient Bayesian GMM-DO updates of the DMD state and parameters, learning from the limited gappy observation data sets.
    Description: I wish to thank the U.S. Navy’s Civilian Institution Program along with the MITWHOI Joint Program for providing the funding and resources that made this research and continuing my education possible.
    Keywords: Data assimilation ; Reduced order models ; Stochastic prediction
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    The stratification maxima of the seasonally varying Surface layer in the Arctic Ocean’s Beaufort Gyre (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: The Beaufort Gyre region of the Arctic Ocean is strongly stratified at the base of the wintertime mixed layer, which impedes the vertical transport of heat, energy, and other tracers. Ice-Tethered Profiler observations during 2004-2018 were used to characterize and investigate the seasonal and interannual variability of the strength, depth, density, and thickness of this highly stratified layer at the base of the mixed layer. This includes investigating the remnant stratification maximum, which formed when the summer mixed layer shoaled. Seasonally, the stratification maximum was never in a steady state. It was largest in October (4.8 × 10−3 rad2/sec2) and decreased during all winter months (to 2.3 × 10−3rad2/sec2 in June), indicating that surface forcing and interior vertical mixing were never in equilibrium during the year. Interannually, the period from 2011-2018 had a higher stratification maximum than then the period from 2005-2010 regardless of the season. The remnant stratification maximum was consistently weaker than the winter stratification maximum from which it formed. The initial evolution of the remnant stratification maximum is used to estimate an effective vertical diffusivity of order 10−6m2/s. No significant geographic variability was found, in part due to high temporal and small scale variability of the stratification maximum layer. Implications for heat transport through to the sea ice cover are discussed.
    Keywords: Beaufort Gyre ; Stratification ; Remnant layer
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  • 57
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    Trojan horses in the marine realm: characterizing protistan parasite ecology in coastal waters (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Protists are taxonomically and metabolically diverse drivers of energy and nutrient flow in the marine environment, with recent research suggesting significant roles in global carbon cycling throughout the water column. Top-down controls on planktonic protists include grazing and parasitism, processes that both contribute to nutrient transfer and biogeochemical cycling in the global ocean. Recent global surveys of eukaryotic small subunit ribosomal RNA molecular signatures have highlighted the fact that parasites belonging to the marine alveolate order Syndiniales are both abundant and ubiquitous in coastal and open ocean environments, suggesting a major role for this taxon in marine food webs. Two coastal sites, Saanich Inlet (Vancouver Island, BC) and Salt Pond (Falmouth, MA, USA) were selected as model ecosystems to examine the impacts of Syndinian parasitism on protist communities. Data presented in this thesis combines high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, and modeling to address key knowledge gaps regarding syndinian ecology. Information is presented on previously undescribed putative host taxa, the prevalence of syndinian parasites and infections on different hosts in coastal waters, and a framework for modeling host-parasite interactions based on field observations.
    Description: Research was supported by the WHOI Ocean Venture Fund, the National Science Foundation Biological Oceanography OCE-1851012, and the National Science Foundation Graduate Research Fellowship under Grant No. 1745302.
    Keywords: Syndiniales ; Parasitism ; Protist
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    Structure, variability, and dynamics of the West Greenland Boundary Current System (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: The ventilation of intermediate waters in the Labrador Sea has important implications for the strength of the Atlantic Meridional Overturning Circulation. Boundary current-interior interactions regulate the exchange of properties between the slope and the basin, which in turn regulates the magnitude of interior convection and the export of ventilated waters from the subpolar gyre. This thesis characterizes theWest Greenland Boundary Current System near Cape Farewell across a range of spatio-temporal scales. The boundary current system is composed of three velocity cores: (1) the West Greenland Coastal Current (WGCC), transporting Greenland and Arctic meltwaters on the shelf; (2) the West Greenland Current (WGC), which advects warm, saline Atlantic-origin water at depth, meltwaters at the surface, and newly-ventilated Labrador Sea Water (LSW); and (3) the Deep Western Boundary Current, which carries dense overflow waters ventilated in the Nordic Seas. The seasonal presence of the LSW and Atlantic-origin water are dictated by air-sea buoyancy forcing, while the seasonality of the WGCC is governed by remote wind forcing and the propagation of coastally trapped waves from East Greenland. Using mooring data and hydrographic surveys, we demonstrate mid-depth intensified cyclones generated at Denmark Strait are found offshore of the WGC and enhance the overflow water transport at synoptic timescales. Using mooring, hydrographic, and satellite data, we demonstrate that the WGC undergoes extensive meandering due to baroclinic instability that is enhanced in winter due to LSW formation adjacent to the current. This leads to the production of small-scale, anticyclonic eddies that can account for the entirety of wintertime heat loss within the Labrador Sea. The meanders are shown to trigger the formation of Irminger Rings downstream. Using mooring, hydrographic, atmospheric, and Lagrangian data, and a mixing model, we find that strong atmospheric storms known as forward tip jets cause upwelling at the shelfbreak that triggers offshore export of freshwater. This freshwater flux can explain the observed lack of ventilation in the eastern Labrador Sea. Together, this thesis documents previously unobserved interannual, seasonal, and synoptic-scale variability and dynamics within the West Greenland boundary current system that must be accounted for in future modeling.
    Description: The work in this dissertation was funded by the National Science Foundation grants OCE-1259618 and OCE-1756361.
    Keywords: Boundary current dynamics ; Labrador sea water formation ; Eddies
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    Radium isotopes and radon-222 as tracers of sediment-water interaction in Arctic coastal and lacustrine environments (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Arctic marine and lacustrine systems are experiencing rapid warming due to climate change. These changes are especially important at the interface between sediments and surface waters because they are hotspots for biogeochemical transformations such as redox reactions, nutrient consumption and regeneration, organic matter leaching and degradation, and mineral weathering. Radium isotopes (223Ra, 224Ra, 226Ra, 228Ra) and radon-222, naturally occurring radioactive isotopes produced in sediments, are well-suited as tracers of nutrients, trace metals, and organic matter cycling processes at the sediment-water interface. In this thesis, I have applied radon-222 and the quartet of radium isotopes to study fundamental processes in subarctic lakes and on the Arctic continental shelf. First, radon-222 is used to quantify groundwater discharge into a shallow, tundra lake on the Yukon-Kuskokwim Delta in Alaska in summer of 2017. Radon-derived groundwater fluxes were then paired with methane (CH4) measurements to determine delivery rates of methane into the lake via groundwater. Groundwater CH4 fluxes significantly exceeded diffusive air-water fluxes from the lake to the atmosphere, suggesting that groundwater is an important source of CH4 to Arctic lakes and may drive observed CH4 emissions. Higher CH4 emissions were observed compared to those reported previously in high latitude lakes, like due to higher CH4 concentrations in groundwater. These findings indicate that deltaic lakes across warmer permafrost regions may act as important hotspots for methane release across Arctic landscapes. Then, the quartet of radium isotopes is used to study the impacts of storms and sea ice formation as drivers of sediment-water interaction on the Alaskan Beaufort shelf. The timeseries presented in this study is among the first to document the combined physical and chemical signals of winter water formation in the Beaufort Sea, made possible by repeat occupations of the central Beaufort shelf. Radium measurements are combined with inorganic nitrogen and hydrographic measurements to elucidate the episodic behavior of winter water formation and its ability to drive exchange with bottom sediments during freeze-up.
    Description: Financial support for Chapter 2 was funded by National Science Foundation awards OCE-1458305 to M.A.C., 1561437 to S.M.N, J.D.S., and R.M.H and 1624927 to S.M.N., P.J.M. and R.M.H. The work completed for Chapter 3 was funded by the Montrym Fund at the Massachusetts Institute of Technology, the Academic Programs Office at Woods Hole Oceanographic Institution, and the NSF Arctic GEOTRACES (OCE-1458305), Pacific GEOTRACES (OCE-1736277), and Arctic Observing Network programs (OPP-1733564).
    Keywords: Arctic ; Sediment ; Radionuclides
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    Signal Absorption-Based Range Estimator for Undersea Swarms (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Robotic swarms are increasingly complex above the waterline due to reliable communication links. However, the limited propagation of similar signals in the ocean has impacted advances in undersea robotics. Underwater vehicles often rely on acoustics for navigation solutions; however, this presents challenges for robotic swarms. Many localization methods rely on precision time synchronization or two-way communication to estimate ranges. The cost of Chip-scale Atomic Clocks (CSACs) and acoustic modems is limiting for large-scale swarms due to the cost-per-vehicle and communications structure. We propose a single vehicle with reliable navigation as a "leader" for a scalable swarm of lower-cost vehicles that receive signals via a single hydrophone. This thesis outlines range estimation methods for sources with known signal content, including frequency and power at its origin. Transmission loss is calculated based on sound absorption in seawater and geometric spreading loss to estimate range through the Signal Absorption-Based Range Estimator (SABRE). SABRE's objective is to address techniques that support low-cost undersea swarming. This thesis's contributions include a novel method for range estimation onboard underwater vehicles that supports relative navigation through Doppler-shift methods for target bearing. This thesis develops the theory, algorithms, and analytical tools for real-world data range estimation.
    Keywords: Absorption ; Single-hydrophone ; Swarm
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    A planned approach to high collision risk area (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: This thesis examines the transition of a vessel from the open ocean, where collisions are rare, to a high risk and heavy traffic area such as a Traffic Separation Scheme (TSS). Previous autonomy approaches generally view path planning and collision avoidance as two separate functions, i.e. a vessel will follow the planned path until conditions are met for collision avoidance algorithms to take over. Here an intermediate phase is proposed with the goal of adjusting the time of arrival to a high vessel density area so that the risk of collision is reduced. A general algorithm that calculates maximum future traffic density for all choices in the speed domain is proposed and implemented as a MOOS-IvP behavior. This behavior gives the vessel awareness of future collision risks and aids the collision avoidance process. This new approach improves the safety of the vessel by reducing the number of risky encounters that will likely require the vessel to maneuver for safety.
    Keywords: Collision avoidance ; MOOS-IvP ; COLREGs
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    Distribution, growth, and transport of larval fishes and implications for population dynamics (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: The early life stages of marine fishes play a critical role in population dynamics, largely due to their high abundance, high mortality, and ease of transport in ocean currents. This dissertation demonstrates the value of combining larval data, collected in the field and the laboratory, with model simulations. In Chapter 2, analyses of field observations of ontogenetic vertical distributions of coral reef fish revealed a diversity of behaviors both between and within families. In Caribbean-wide particle-tracking simulations of representative behaviors, surface-dwelling larvae were generally transported longer distances with greater population connectivity amongst habitat patches, while the evenly-distributed vertical behavior and downward ontogenetic vertical migration were similar to one another and led to greater retention near natal sites. However, hydrodynamics and habitat vailability created some local patterns that contradicted the overall expectation. Chapter 3 presents evidence of tuna spawning inside a large no-take marine protected area, the Phoenix Islands Protected Area (PIPA). Despite variation in temperature and chlorophyll, the larval tuna distributions were similar amongst years, with skipjack (Katsuwonus pelamis) and Thunnus spp. tunas observed in all three years. Backtracking simulations indicated that spawning occurred inside PIPA in all 3 study years, demonstrating that PIPA is protecting viable tuna spawning habitat. In Chapter 4, several lines of larval evidence support the classification of the Slope Sea as a major spawning ground for Atlantic bluefin tuna with conditions suitable for larval growth. The abundance of bluefin tuna larvae observed in the Slope Sea aligns with typical observations on the other two spawning grounds. Age and growth analyses of bluefin tuna larvae collected in the Slope Sea and the Gulf of Mexico in 2016 did not show a growth rate difference between regions, but did suggest that Slope Sea larvae are larger at the onset of exogenous feeding. Collected larvae were backtracked to locations north of Cape Hatteras and forward tracked to show that they would have been retained within the Slope Sea until the onset of swimming. As a whole, this thesis presents valuable contributions to the study of larval fishes and the attendant implications for marine resource management.
    Description: National Science Foundation Graduate Research Fellowship Program (to C.M.H.), the Woods Hole Oceanographic Institution Ocean Life Institute (Grant 22569.01 to J. Llopiz and C.M.H.), the Adelaide and Charles Link Foundation, the Phoenix Islands Protected Area Trust, the J. Seward Johnson Endowment in support of the Woods Hole Oceanographic Institution's Marine Policy Center, and the WHOI Academic Programs Office.
    Keywords: Marine protected area ; Trait-based ; Biophysical model
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    Structure and mechanics of the subducted Gorda plate: constrained by afterslip simulations and scattered seismic waves (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Subduction zones host the greatest earthquakes on earth and pose great threat to human society. The largest slip in megathrust earthquakes often occurs in the 10–50 km depth range, yet seismic imaging of the material properties in this region has proven difficult. This thesis focuses on developing methods to utilize high frequency (2–12 Hz) seismic waves scattered from the megathrust plate interface to constrain its fine-scale velocity structures and to investigate the relationship between velocity structures and megathrust slip behaviors. Chapter 2 investigates the locking condition of the subducted Gorda plate by simulating afterslip that would be expected as a result of the stress changes from offshore strike-slip earthquakes. Chapter 3 develops array analysis methods to identify P-to-S and S-to-P seismic converted phases that convert at the subducted Gorda plate interface from local earthquakes and uses them to constrain the geometry and material properties of the plate boundary fault of the subducted Gorda plate between 5–20 km depth. Chapters 4 and 5 use a dense nodal array and numerical modeling methods to study the seismic guided waves that propagate along the thin low velocity layer at the boundary of the subducted Gorda plate. Taken together, our results indicate that material properties of the subduction plateboundary fault is highly heterogeneous and the plate-boundary fault is potentially contained in a low velocity layer with significant porosity and fluid content at seismogenic depths.
    Description: Funding for this research was provided by National Science Foundation Division of Earth Sciences (EAR) award #1520690 and the WHOI Academic Programs Office.
    Keywords: Subduction zone ; Scattered seismic waves ; Plate boundary
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    Coral reefs in the Anthropocene Ocean: novel insights from skeletal proxies of climate change, impacts, and resilience (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Anthropogenic emissions of greenhouse gases are driving rapid changes in ocean conditions. Shallow-water coral reefs are experiencing the brunt of these changes, including intensifying marine heatwaves (MHWs) and rapid ocean acidification (OA). Consequently, coral reefs are in broad-scale decline, threatening the livelihoods of hundreds of millions of people. Ensuring survival of coral reefs in the 21st century will thus require a new management approach that incorporates robust understanding of reef-scale climate change, the mechanisms by which these changes impact corals, and their potential for adaptation. In this thesis, I extract information from within coral skeletons to 1) Quantify the climate changes occurring on coral reefs and the effects on coral growth, 2) Identify differences in the sensitivity of coral reefs to these changes, and 3) Evaluate the adaptation potential of the keystone reef-building coral, Porites. First, I develop a mechanistic Porites growth model and reveal the physicochemical link between OA and skeletal formation. I show that the thickening (densification) of coral skeletal framework is most vulnerable to OA and that, under 21st century climate model projections, OA will reduce Porites skeletal density globally, with greatest impact in the Coral Triangle. Second, I develop an improved metric of thermal stress, and use a skeletal bleaching proxy to quantify coral responses to intensifying heatwaves in the central equatorial Pacific (CEP) since 1982. My work reveals a long history of bleaching in the CEP, and reef-specific differences in thermal tolerance linked to past heatwave exposure implying that, over time, reef communities have adapted to tolerate their unique thermal regimes. Third, I refine the Sr-U paleo-thermometer to enable monthly-resolved sea surface temperatures (SST) generation using laser ablation ICPMS. I show that laser Sr-U accurately captures CEP SST, including the frequency and amplitude of MHWs. Finally, I apply laser Sr-U to reconstruct the past 100 years of SST at Jarvis Island in the CEP, and evaluate my proxy record of bleaching severity in this context. I determine that Porites coral populations on Jarvis Island have not yet adapted to the pace of anthropogenic climate change.
    Description: This research was supported by US National Science Foundation Awards OCE-1220529, ANT-1246387, OCE-1737311, CE-1601365, OCE-1805618, OCE-1537338, OCE-2016133, and from the Woods Hole Oceanographic Institution through the Ocean Life Institute, the Ocean Ventures Fund, the Grassle Fellowship Fund, and the MIT-WHOI Academic Programs Office. Additional funding was provided by the Taiwan MOST Grant 104-2628-M-001-007-MY3, the Robertson Foundation, the Leverhulme Trust in UK, the Atlantic Donor Advised Fund, The Prince Albert 2 of Monaco Foundation, the Akiko Shiraki Dynner Fund, the New England Aquarium, the Martin Family Society Fellowship for Sustainability, the Gates Millenium Scholarship, the Arthur Vining Davis Foundation, the NOAA Coral Reef Conservation Program, and from the Woods Hole Oceanographic Institution through Investment in Science Fund, the Early Career Award, and the Access to the Sea Award.
    Keywords: Coral reef ; Climate ; Proxy
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    Computational approaches for sub-meter ocean color remote sensing (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Mechanical and Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: The satellite ocean color remote sensing paradigm developed by government space agencies enables the assessment of ocean color products on global scales at kilometer resolutions. A similar paradigm has not yet been developed for regional scales at sub-meter resolutions, but it is essential for specific ocean color applications (e.g., mapping algal biomass in the marginal ice zone). While many aspects of the satellite ocean color remote sensing paradigm are applicable to sub-meter scales, steps within the paradigm must be adapted to the optical character of the ocean at these scales and the opto-electronics of the available sensing instruments. This dissertation adapts the three steps of the satellite ocean color remote sensing paradigm that benefit the most from reassessment at sub-meter scales, namely the correction for surface-reflected light, the design and selection of the opto-electronics and the post-processing of over-sampled regions. First, I identify which surface-reflected light removal algorithm and view angle combination are optimal at sub-meter scales, using data collected during a field deployment to the Martha’s Vineyard Coastal Observatory. I find that of the three most widely used glint correction algorithms, a spectral optimization based approach applied to measurements with a 40∘ view angle best recovers the remotesensing reflectance and chlorophyll concentration despite centimeter scale variability in the surface-reflected light. Second, I develop a simulation framework to assess the impact of higher optical and electronics noise on ocean color product retrieval from unique ocean color scenarios. I demonstrate the framework’s power as a design tool by identifying hardware limitations, and developing potential solutions, for estimating algal biomass from high dynamic range sensing in the marginal ice zone. Third, I investigate a spectral super-resolution technique for application to spatially over-sampled oceanic regions. I determine that this technique more accurately represents spectral frequencies beyond the Nyquist and that it can be trained to be invariant to noise sources characteristic of ocean color remote sensing on images with similar statistics as the training dataset. Overall, the developed and critically assessed sub-meter ocean color remote sensing paradigm enables researchers to collect high fidelity sub-meter data from imaging spectrometers in unique ocean color scenarios.
    Description: Ryan O’Shea was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. This research was funded by Woods Hole Oceanographic Institution’s Edwin W. Hiam Ocean Science and Technology Award Fund, its Ocean Venture Funds, its Academic Programs Office, and the National Aeronautics and Space Administration via grant number CCE NNX17AI72G to Dr. Samuel Laney. The raw data for Figures 3-3 and 3-4 were provided through Australian Antarctic Science grants 2678 and 4390.
    Keywords: Ocean color ; Hyperspectral ; Remote sensing
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    Estimating atmospheric boundary layer turbulence in the marine environment using lidar systems with applications for offshore wind energy (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Estimating turbulence in the marine-atmospheric boundary layer is critical to many industrial, commercial and scientific fields, but of particular importance to the wind energy industry. Contributing to both the efficiency of energy extraction and the life-cycle cost of the turbine itself, turbulence in the atmospheric boundary layer is estimated within the wind energy industry as Turbulence Intensity (TI) and more recently by Turbulent Kinetic Energy (TKE). Traditional in-situ methods to measure turbulence are extremely difficult to deploy in the marine environment, resulting in a recent movement to and dependence on remote sensing methods. One type of remote sensing instrument, Doppler lidars, have shown to reliably estimate the wind speed and atmospheric turbulence while being cost effective and easily deployable, and hence are being increasingly utilized as a standard for wind energy assessments. In this thesis, the ability of lidars to measure turbulence up to a height of 200 m above mean sea level in the marine-atmospheric boundary layer was tested using a 7-month data set spanning winter to early summer. Lidar-based TI and TKE were estimated by three methods using observations from a highly validated lidar system and compared under both convective and stable atmospheric stability conditions. Convective periods were found to have higher turbulence at all the heights compared to stable conditions, while mean wind speed and shear were higher during stable conditions. The study period was characterized by generally low turbulent conditions with high turbulence events occurring at timescales of a few days. Mean vertical profiles of TKE were non-uniformly distributed in height during low turbulent conditions. During highly turbulent events, TKE increased more strongly with height. The definition of TI– following the industry or meteorology conventions – had no real effect on the results, and differences between cup or sonic anemometers and lidar TI values were small except at low wind speeds. All the three lidar-based TKE methods tested corresponded closely to independent estimates, and differences between the methods were small relative to the temporal variability of TKE observed at the offshore site.
    Keywords: Turbulence ; Wind engery ; Lidar
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    Pseudo-nitzschia in the Gulf of Maine: investigating bloom dynamics, species introduction, and climate change implications with observations and models (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: The apparent global increase in harmful algal blooms (HABs) includes Pseudo-nitzschia blooms in the Gulf of Maine, where shellfishery closures can cost millions of dollars. Temperatures in the gulf are warming, which can affect the severity of some HABs. Yet Pseudo-nitzschia in the region are understudied. Pseudo-nitzschia bloom dynamics, P. australis introduction, and potential future changes thereof were investigated in the Gulf of Maine. Data from ship surveys and moorings were used, as well as hydrodynamic, climate, and Lagrangian particle tracking models. Pseudonitzschia bloom toxicity was driven primarily by species composition, not environmental factors. P. australis was introduced to the region in 2016 via a coastal current from the Scotian Shelf. Climate change might intensify Pseudo-nitzschia blooms, shift bloom timing 1–2 weeks earlier in the spring or 4–6 weeks later in the fall, or lengthen the growing season by 3 weeks. It might also affect species composition and connectivity within the gulf. This work has implications for the monitoring of current and future blooms in the Gulf of Maine and for our understanding of HAB introduction to the region. It can also be used to develop predictive models for Pseudo-nitzschia, which could be applied to other HABs.
    Description: This research was funded by the National Science Foundation (Grants OCE-1314642 and OCE-1840381), the National Institute of Environmental Health Sciences (Grants 1P01ES021923-01 and P01 ES028938-01), the Woods Hole Center for Oceans and Human Health, WHOI Academic Programs Funds, the Vannevar Bush Faculty Fellowship, and the National Oceanic and Atmospheric Administration’s HAB Event Response Program (2012 and 2016).
    Keywords: Harmful algal blooms ; Modeling ; Gulf of Maine
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    Ambient acoustics as indicator of environmental change in the Beaufort Sea: experiments & methods for analysis (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: The Arctic Ocean is a vital component of Earth’s climate system experiencing dramatic environmental changes. The changes are reflected in its underwater ambient soundscape as its origin and propagation are primarily dependent on properties of the ice cover and water column. The first component of this work examines the effect on ambient noise characteristics due to changes to the Beaufort Sea sound speed profile (SSP) and ice cover. Specifically, the emergence of a warm water intrusion near 70 m depth has altered the historical Arctic SSP while the ice cover has become thinner and younger due to the rise in average global temperature. Hypothesized shifts to the ambient soundscape and surface noise generation due to these changes are verified by comparing the measured noise data during two experiments to modeled results. These changes include a broadside notch in noise vertical directionality as well as a shift from uniform surface noise generation to discrete generation at specific ranges. Motivated by our data analyses, the second component presents several tools to facilitate ambient noise characterization and generation monitoring. One is a convolutional neural network (CNN) approach to noise range estimation. Its robustness to SSP and bottom depth mismatch is compared with conventional matched field processing. We further explore how the CNN approach achieves its performance by examining its intermediate outputs. Another tool is a frequency domain, transient event detection algorithm that leverages image processing and hierarchical clustering to identify and categorize noise transients in data spectrograms. The spectral content retained by this method enables insight into the generation mechanism of the detected events by the ice cover. Lastly, we present the deployment of a seismo-acoustic system to localize transient events. Two forward approaches that utilize time-difference-ofarrival are described and compared with a more conventional, inverse technique. The examination of this system’s performance prompts recommendations for future deployments. With our ambient noise analysis and algorithm development, we hope these contributions provide a stronger foundation for continued study of the Arctic ambient soundscape as the region continues to grow in significance.
    Description: Office of Naval Research (ONR) via the University of California - San Diego (UCSD) under award number N00014-16-1-2129. Defense Advanced Research Projects Agency (DARPA) via Applied Physical Sciences Corp. (APS) under award number HR0011-18-C-0008. Office of Naval Research (ONR) under award number N00014-17-1-2474. Office of Naval Research (ONR) under award number N00014-19-1-2741. National Science Foundation (NSF) under grant number 2389237.
    Keywords: Ambient noise ; Arctic change ; Noise analysis
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    Barrier island groundwater dynamics (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: Nearly 1.5 million people inhabit barrier islands along the U.S. Atlantic and Gulf Coasts and coastal groundwater dynamics influence the availability of freshwater, ecosystem health, pollutant transport, and flooding in these densely populated communities. However, groundwater dynamics, including the aquifer head distribution and subsurface salinity structure, in coastal aquifers are affected by multiple environmental forcings, such as waves, tides, storm surges, and precipitation that act on a variety of spatial and temporal scales, making coastal groundwater dynamics complex and difficult to predict. Here, measurements of groundwater heads, salinities, and temperatures collected for 3 years across a 550-m-wide barrier island are used in conjunction with observations of ocean tides, surge, waves, sound level, and rainfall to characterize the dynamics of the surface aquifer. Infiltration from surge, tides, and waves during storms caused up to 2 m increases in the groundwater level under the dune. The head gradients owing to these storm-induced groundwater bulges suggest flows become inland directed on the ocean-side of the island during storms. An upper saline plume (20-30 PSU) was observed above fresher (10 PSU) water up to 30 m inland of the dune face, which was the maximum wave runup location. Differences in inland propagation between tidal- and storm-induced groundwater head fluctuations are explained using analytical theories for intermediate depth aquifers. Additionally, a separate analytical water-table evolution model driven with estimated ocean shoreline water levels (based on the 36-hr-averaged offshore tide, surge, and wave height) and measured precipitation is validated by citizen-science flood reports and predicts the maximum water-table height within 0.1 m of the observed levels across the barrier island.
    Description: Funding for this research was provided by the U.S. Coastal Research Program, the National Science Foundation, a National Science Foundation Graduate Research Fellowship, the Woods Hole Oceanographic ISP program, and National Security Science & Engineering and Vannevar Bush Faculty Fellowships.
    Keywords: Groundwater ; Storms ; Coastal aquifer
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    A Virtual Ocean framework for environmentally adaptive, embedded acoustic navigation on autonomous underwater vehicles (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Autonomous underwater vehicles (AUVs) are an increasingly capable robotic platform, with embedded acoustic sensing to facilitate navigation, communication, and collaboration. The global positioning system (GPS), ubiquitous for air- and terrestrial-based drones, cannot position a submerged AUV. Current methods for acoustic underwater navigation employ a deterministic sound speed to convert recorded travel time into range. In acoustically complex propagation environments, however, accurate navigation is predicated on how the sound speed structure affects propagation. The Arctic’s Beaufort Gyre provides an excellent case study for this relationship via the Beaufort Lens, a recently observed influx of warm Pacific water that forms a widespread yet variable sound speed lens throughout the gyre. At short ranges, the lens intensifies multipath propagation and creates a dramatic shadow zone, deteriorating acoustic communication and navigation performance. The Arctic also poses the additional operational challenge of an ice-covered, GPSdenied environment. This dissertation demonstrates a framework for a physics-based, model-aided, real-time conversion of recorded travel time into range—the first of its kind—which was essential to the successful AUV deployment and recovery in the Beaufort Sea, in March 2020. There are three nominal steps. First, we investigate the spatio-temporal variability of the Beaufort Lens. Second, we design a human-in-the-loop graphical decision-making framework to encode desired sound speed profile information into a lightweight, digital acoustic message for onboard navigation and communication. Lastly, we embed a stochastic, ray-based prediction of the group velocity as a function of extrapolated source and receiver locations. This framework is further validated by transmissions among GPS-aided modem buoys and improved upon to rival GPS accuracy and surpass GPS precision. The Arctic is one of the most sensitive regions to climate change, and as warmer surface temperatures and shrinking sea ice extent continue to deviate from historical conditions, the region will become more accessible and navigable. Underwater robotic platforms to monitor these environmental changes, along with the inevitable rise in human traffic related to trade, fishing, tourism, and military activity, are paramount to coupling national security with international climate security.
    Description: Office of Naval Research (N00014-14-1-0214) — GOATS’14 Adaptive and Collaborative Exploitation of 3-Dimensional Environmental Acoustics in Distributed Undersea Networks Draper Laboratory Incorporated (SC001-0000001039) — Positioning System for Deep Ocean Navigation (POSYDON) Office of Naval Research (N00014-16-1-2129) — MURI: The Information Content of Ocean Noise: Theory and Experiment Office of Naval Research (N00014-17-1-2474) — Environmentally Adaptive Acoustic Communication and Navigation in the New Arctic Office of Naval Research (N00014-19-1-2716) — TFO: Assessing Realism and Uncertainties in Navy Decision Aids Department of Defense, Office of Naval Research — National Defense, Science, and Engineering Graduate Fellowship
    Keywords: Beaufort Lens ; GPS-denied underwater navigation ; Marine robotics
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    Field-Portable dissolved gas sensing and perspectives in aqueous microplastic detection (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Aeronautics and Astronautics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: Global temperature rise and increased atmospheric carbon dioxide (CO2) levels have affected the health of the world’s ocean and water ecosystems, impacting the balances of natural carbon cycling and causing ocean acidification. Additionally, as global temperatures rise, thawing permafrost has stimulated increased release of methane (CH4), a gas with a shorter lifetime in the atmosphere but with even more heat trapping ability than CO2. In situ analysis of dissolved gas content in surface waters is currently performed with large, expensive instruments, such as spectrometers, which are coupled with gas equilibration systems, which extract dissolved gas from water and feed it to the sensor. Accurate, low cost, and portable sensors are needed to measure the dissolved CH4 and CO2 concentration in water systems to quantify their release and understand their relationship to the global carbon budget. At the same time, while greenhouse gases are well established threats to water ecosystems, the ubiquity and potential consequences of microplastics in aqueous environments are just beginning to be recognized by the environmental research community. Microplastics (MPs) are small particles of polymer debris, commonly defined as being between 1 μm and 1000 μm. Despite the pervasiveness of MPs, our ability to characterize MPs in the environment is limited by the lack of technologies for rapidly and accurately identifying and quantifying MPs. This thesis is concerned with the engineering challenges prompted by the need for high quality and quantity environmental data to better study and the impact, cycling, and prevalence of these pollutants in aqueous environments. Three distinct investigations are presented here. First, the design of the Low-Cost Gas Extraction and Measurement System (LC-GEMS) for dissolved CO2 is presented. At just under $600 dollar to build, the LC-GEMS is an ultra-portable, toolbox-sized instrument for dissolved gas sensing in near-surface waters. The LCGEMS was characterized in the lab and demonstrated linear relationships with dissolved CO2 as well as temperature. Lab calibrations and subsequent field testing in the Little Sippewissett Marsh, in Falmouth, Massachusetts showed that the LCGEMS captures both diurnal and minute-time scale trends in dissolved CO2. Second, this thesis presents the novel design of three simple and low-cost planar nanophotonic and plasmonic structures as optical transducers for measuring dissolved CH4. Through simulations, the sensitivity of the structures are evaluated and found to exhibit superior performance in the reflectance intensity readout mode to that of the standard surface-plasmon-polariton-mode Spreeta sensor. A practical, small, and low-cost implementation of this chip with a simple intensity-based measurement scheme is proposed. This design is novel in the space of dissolved gas monitoring because it shows potential to measure directly in the water phase while being robust and low-cost to implement. Finally, this thesis presents a literature review and perspective to motivate the development of field-deployable microplastic sensing techniques. A framework for field-deployable microplastic sensing is presented and seeks to inform the MP community of the potential in both traditional MP analysis techniques and unconventional methods for creating rapid and automated MP sensors. The field-deployabilty framework addresses a full scope of practical/technological trade-offs to be considered for portable MP detection.
    Keywords: Dissolved gas ; Microplastics ; Instrumentation
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    Characterizing the impact of underwater glider observations on the Navy Coastal Ocean Model (NCOM) in the Gulf Stream Region (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: As the western boundary current of the North Atlantic, the Gulf Stream is a well established area of interest for the United States Navy, predominately due to its proximity to the continental shelf and the associated challenges of acoustic propagation across large property gradients. Autonomous underwater gliders conduct routine, high-resolution surveys along the U.S. East Coast, including within the Gulf Stream. These observations are assimilated into the operational Navy Coastal Ocean Model (NCOM). An investigation of the forecast-to-nowcast changes in the model for 2017 demonstrates the impact of the observations on the model. The magnitude of model change as a function of distance from nearest new observation reveals relatively large impact of glider observations within a radius of 𝒪(100) km. Glider observations are associated with larger local impact than Argo data, likely due to glider sampling focusing on large spatial gradients. Due to the advective nature of the Gulf Stream system, the impact of glider observations in the model is anisotropic with larger impacts extending downstream from observation locations. Forecast-to-nowcast changes in modeled temperature, salinity, and density result in improved agreement between observed and modeled ocean structure within the upper 200 m over the 24 hours between successive model runs.
    Description: This research was funded via the United States Navy’s Civilian Institution Program with the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program (MIT/WHOI JP). Glider observations and analyses have been generously supported by the National Science Foundation (OCE-0220769, OCE-1558521, OCE-1633911, OCE-1923362), NOAA’s Global Ocean Monitoring and Observing Program (NA14OAR4320158, NA19OAR4320074), the Office of Naval Research (N000141713040), Eastman Chemical Corporation, WHOI’s Oceans and Climate Change Institute, and the W. Van Alan Clark, Jr. Chair for Excellence in Oceanography at WHOI (awarded to Breck Owens).
    Keywords: Model ; Glider ; Gulf Stream
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    Observing and quantifying kinematic properties and lagrangian coherent structures of ocean flows using drifter experiments (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: This thesis analyzes data from two types of unique drifter experiments in order to characterize two aspects of ocean flows that are often difficult to study. First, vertical velocities and their associated transport processes are often challenging to observe in the real ocean since vertical velocities are typically orders of magnitude smaller than horizontal velocities in mesoscale and submesoscale flows. Second, Lagrangian coherent structures (LCS) are features which categorize ocean flows into regimes of distinct behavior. These structures are also difficult to quantify in the real ocean, since sets of gridded trajectories from real ocean data (rather than model fields) are rarely available. The first experiment uses drifters drogued at multiple depths in the Alboran Sea to observe and characterize the ocean’s vertical structure, particularly near a strong front where vertical velocities are expected to be much stronger than other regions of the Ocean. The second experiment uses a roughly gridded pattern of surface drifters in the Gulf of Mexico to study LCSs as quantified by methods from dynamical systems such as finitetime Lyapunov exponents (FTLEs), trajectory arc-length, correlation dimension, dilation, Lagrangian-averaged vorticity deviation (LAVD), and spectral clustering. This thesis includes the first attempt to apply these dynamical systems techniques to real drifters for LCS detection. Overall, these experiments and the methods used in this paper are shown to be promising new techniques for quantifying both the vertical structure of ocean flows and Lagrangian Coherent Structures of flows using real drifter data. Future work may involve modified versions of the experiments, with denser sets of ocean drifters in the horizontal and/or vertical directions.
    Description: My Masters studies in the MIT/WHOI Joint Program were funded by the US Navy Civilian Institution Office.
    Keywords: Lagrangian coherent structures ; Finite-time Lyapunov exponents ; Vertical transport
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    A metabolic lens on phytoplankton physiology (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Phytoplankton are communities of diverse groups of prokaryotic and eukaryotic single-celled organisms responsible for nearly 50% of global primary production. The relative abundance of individual groups changes dynamically in response to environmental perturbations. Recent studies suggest that such changes are primarily driven by the distinct physiological responses employed by each group towards a particular perturbation. Although knowledge of some of these responses has come to light in recent years, many aspects of their metabolisms remain unknown. We attempt to address this gap by studying the metabolism of several phytoplankton groups using metabolomics. Firstly, we developed a method to enhance the analysis of untargeted metabolomics data. Secondly, we constructed two conceptual models describing how metabolism of the raphidophyte Heterosigma akashiwo responds to phosphorus and nitrogen stress. These conceptual models revealed several new stress response mechanisms not previously reported in other phytoplankton. Finally, we compared the metabolic changes of several distinct phytoplankton groups to uncover possible adaptation and acclimations that distinguish them. This analysis revealed several pathways and metabolites that represent the studied groups. The contributions of these pathways and metabolites towards physiology may support the ecological fitness of these organisms.
    Description: None of this work would have been possible without a variety of funding sources. I was supported for three years by a National Science Foundation Graduate Research Fellowship and one year with a GEM fellowship. The research was carried out with grants from the MIT Microbiome Center (Award ID #6936800, EBK), the Simons Foundation (Award ID #509034, EBK), the Gordon and Betty Moore Foundation (Award ID #3304 EBK), the National Science Foundation (Award ID #OCE-0619608 to EBK and OCE-1057447 to EBK and MCKS) and the WHOI Ocean Ventures Fund.
    Keywords: Phytoplankton ; Metabolism ; Metbolomics
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    Human-autonomy teaming for improved diver navigation (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Diving operations are inherently complex due to navigation and communication limitations. Until recently, fixed-beacon acoustic localization techniques have served as the primary means of improving diver navigation. However, modern artificial intelligence and acoustic modem technologies have enabled accurate relative navigation methods between a diver and an autonomous vehicle. Human-robot collaboration takes advantage of each member’s strengths to create the most effective team. This concept proves especially advantageous within the ocean domain, where humans are naturally deficient navigators. Yet humans serve as the team’s creative spirit, offering the critical thinking and flexibility needed to succeed in an unpredictable and dynamic environment. Recent underwater human-robot cooperative navigation systems typically rely on autonomous surface vehicles (ASVs), specially designed underwater vehicles, or stereo cameras. This thesis proposes a diver navigation method exhibiting significantly improved accuracy over dead reckoning without relying on a surface presence, cameras, or fixed acoustic beacons. Specifically, we develop and evaluate the communication architecture and autonomous behaviors required to guide a diver to a target location using subsurface humanautonomous underwater vehicle (AUV) teaming with no requirement for ocean current data or exact diver speeds. By depending on acoustic communication and commercial AUV navigation capabilities, our method has increased accessibility, applicability, and robustness over former techniques. We utilize the Woods Hole Oceanographic Institution (WHOI) Micromodem 2’s twoway-travel-time (TWTT) capability to enable range-only single-beacon navigation between two kayaks serving as proxies for the diver and Remote Environmental Monitoring Units (REMUS) 100 AUV. During processing, a nonlinear least-squares (NLS) method, called incremental smoothing and mapping 2 (iSAM2), utilizes odometry and range measurements to provide real-time diver position estimates given unknown ocean currents. Field experiments demonstrate an average online endpoint error of 4.53 meters after transits four hundred meters long. Additionally, simulations test our method’s performance in more challenging situations than those experienced in the field. Overall, this research progresses the interoperability of divers and AUVs.
    Description: The United States Navy funded my graduate education. The Office of Naval Research also partially supported this work under grant N00014-18-1-2832.
    Keywords: Human-autonomy teaming ; Autonomous underwater vehicle ; Diver navigation
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    Molecular characterization of organically bound copper in the marine environment (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: Marine microbes require copper (Cu) for a variety of key enzymes and can therefore experience limitation when concentrations are low. However, when Cu concentrations are too high, it becomes toxic causing decreased cell growth and even cell death. Laboratory culture experiments have shown that a diverse array of microbes produce organic ligands that complex Cu (CuL) and buffer the free ion concentration, which is the most bioavailable fraction. In this way, the microbes impose a control on the speciation of Cu, decreasing the toxic effects of Cu and making seawater conditions favorable for growth. Studies have shown that CuL complexes produced in laboratory cultures have similar complexation strengths to those found in seawater samples, which suggests a biological source of CuLs in seawater where dissolved Cu is almost entirely bound by organic ligands. However, information about individual CuL complexes is lacking which limits our understanding of the sources, sinks, and cycling of dissolved Cu. In order to fill this gap in knowledge, molecular level information about CuL complexes produced in culture and found in seawater must be obtained. To investigate this, liquid chromatography (LC) was coupled to two mass spectrometers (MS), an inductively coupled plasma (ICP) MS and an electrospray ionization (ESI) MS. By using data supplied by both techniques, the molecular charateristics of CuLs were determined laboratory cultures of the marine diatom Phaeodactylum tricornutum and the cyanobacterium Synechococcus, as well as investigating the distribution of CuLs in natural seawater samples along a line from 56°N to 20°S, along 152°W through the north and central Pacific Ocean. The CuLs identified in laboratory cultures had molecular formulae and fragmentation patterns characteristic of linear tetrapyrroles, a group of organic compounds commonly found in biological systems. This identification was further supported by absorbance and nuclear magnetic resonance spectroscopy. The distribution of CuLs in the Pacific Ocean showed a highly dynamic and complex mixture of ligands, closely tied to biological cycles.
    Description: Funding for this work was provided by the National Science Foundation Graduate Research Fellowship Program (NSF award 1122374) for providing three years of funding. Thank you to the National Science Foundation Chemical Oceanography Program (NSF award OCE-1736280 and OCE-2045223) and the Simons Collaboration on Ocean Processes and Ecology (award P49476). A portion of this work was performed at the National High Magnetic Field Laboratory in Tallahassee, Florida, which is supported through NSF DMR 11-57490, and the State of Florida.
    Keywords: Organic ligands ; Copper ; LC-MS
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    Barium isotope cycling in the marine environment: pathways of fractionation and implications for paleoceanographic applications (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: Removal of particulate organic carbon (POC) from sunlit surface waters into the deep ocean represents a climatically important sink of atmospheric carbon dioxide (CO2), linking the biogeochemical cycling of POC to CO2-driven climate change. As POC is not well preserved in the sediment record, other proxies, including the chemistry of barium (Ba) in the ocean and through the sedimentary record, offer an avenue to investigate oceanic carbon export through Earth’s history. This thesis seeks to constrain the controls on the formation, cycling, and isotopic signature of the main particulate phase of marine barium, the mineral barite (BaSO4) through its inception in the water column, during deposition, and ultimately into the rock record. To that end, I characterize the depth, spatial region, and general controls on particulate Ba formation in the South Pacific Ocean through shipboard experimentation and find that particulate Ba forms mainly in the surface of the Polar Frontal Zone in the presence of large particles and microbial activity. Next, I characterize the effect of ion exchange on BaSO4, a process previously unstudied under marine conditions, in a laboratory setting. Ion exchange occurs rapidly between dissolved Ba and BaSO4 and imparts a characteristic net offset between the Ba isotope composition of the dissolved and solid phase, which arises through a combination of Ba isotope fractionation during both precipitation and dissolution. Finally, I investigate the role of ion exchange in marine settings using co-located pore fluids and sedimented BaSO4. Modeling constrained by data from natural samples produce results that are consistent with the laboratory study, suggesting that this mode of isotopic fractionation impacts Ba isotopes in the environment and must be accounted for when applying Ba based climate proxies.
    Description: Funding for this work was provided by the National Science Foundation (OCE-2023456 & OCE-1827401), the Woods Hole Oceanographic Institution Ocean Ventures Fund, a National Science Foundation Graduate Research Fellowship (2017250048), and Woods Hole Oceanographic Institution.
    Keywords: Barium isotopes ; Geochemistry ; Paleoceanography
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    The Gulf Stream: along-stream evolution of volume transport and water properties observed by underwater gliders (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: The Gulf Stream, the western boundary current of the subtropical North Atlantic, plays a key role in the Earth’s climate system with its poleward volume and heat transports being major components of the upper limb of the Atlantic Meridional Overturning Circulation. Extensive observations collected using Spray autonomous underwater gliders from 2004 through 2020 fill a 1500-km-long gap in longer-term sustained subsurface measurements of the Gulf Stream. The gliders provide concurrent, high-resolution measurements of Gulf Stream hydrography and velocity over more than 15 degrees of latitude between Florida and New England. These observations are used to characterize the along-stream evolution of Gulf Stream volume transport; its long-known poleward increase is shown to result primarily from entrainment of subthermocline waters. Antarctic Intermediate Water, which makes up the deepest waters within the Gulf Stream in the Florida Strait, is eroded through both vertical mixing and lateral stirring as it flows downstream. Satellite-based observations of sea surface height coincident with the glider observations are used to evaluate the efficacy of inferring Gulf Stream transport from remotely sensed measurements. The detailed analyses of Gulf Stream transport and water property evolution herein provide targets for regional and global circulation models to replicate.
    Description: We gratefully acknowledge funding from the National Science Foundation (OCE-0220769, OCE-1633911, OCE-1923362, OCE-1558521), NOAA’s Global Ocean Monitoring and Observing Program (NA14OAR4320158, NA19OAR4320074), the Office of Naval Research (N000141713040), WHOI’s Oceans and Climate Change Institute, Eastman Chemical Company, and the W. Van Alan Clark, Jr. Chair for Excellence in Oceanography at WHOI (awarded to Breck Owens).
    Keywords: Gulf Stream ; Autonomous underwater gliders ; Volume transport
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    Constraining natural and anthropogenic disturbances in the delivery of coastal ecosystem services (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Coastal ecosystems provide key services that benefit human wellbeing yet are undergoing rapid degradation due to natural and anthropogenic pressures. This thesis seeks to understand how disturbances impact salt marsh and estuarine ecosystem functioning in order to refine their role in coastal ecosystem service delivery and predict future resilience. Salt marsh survival relative to sealevel rise increasingly relies on the accumulation and preservation of soil organic carbon (SOC). Firstly, I characterized SOC development and turnover in a New England salt marsh and found that salt marsh soils typically store marsh grass-derived compounds that are reworked over centuries-to-millennia. Next, I assessed how two common marsh disturbances – natural ponding and anthropogenic mosquito ditching – affect salt marsh carbon cycling and storage. Salt marsh ponds deepen through soil erosion and decomposition of long-buried marsh peat. Further, the SOC lost during pond development is not fully recouped once drained ponds are revegetated and virtually indistinguishable from the surrounding marsh. Mosquito ditches, which were installed in ~ 90% of New England salt marshes during the Great Depression, did not significantly alter marsh carbon storage. In Buzzards Bay, Massachusetts, a US National Estuary, we tested relationships among measures of estuarine water quality, recreational activity, and local socioeconomic conditions to understand how the benefits of cultural ecosystem services are affected by shifts in water quality associated with global change and anthropogenic activity. Over a 24-year period, water quality degradation coinciding with increases in Chlorophyll a is associated with declines in fishery abundance and cultural ecosystem service values ($0.08 – 0.67 million USD). In combination, incorporation of both anthropogenic and natural disturbances to coastal ecosystem functioning and service delivery can produce improved estimates of ecosystem service valuation for effective resource decision-making under future climate scenarios.
    Description: Funding for this work was provided by John D. and Catherine T. MacArthur Foundation (Grant no. 14-106159-000-CFP), National Science Foundation (OCE1233678), National Oceanic and Atmospheric Administration, National Oceanic and Atmospheric Administration – National Estuaries Research Reserve Collaborative (NA14OAR4170104 and NA- 14NOS4190145), Woods Hole Sea Grant (NA14OAR4170104), MIT Sea Grant (subaward number 5710004045), Ocean Ventures Fund, the Marine Policy Center Johnson Endowment, and Woods Hole Oceanographic Institution.
    Keywords: Salt marsh ; Geochemistry ; Carbon storage
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    Questions and clarity: insights from applying computational methods to paleoclimate archives (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Marine Geology & Geophysics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: It is a scientifically accepted fact that the Earth’s climate is presently undergoing significant changes with the potential for immense negative impacts on human society. As evidence of these impacts become clear and common, it becomes ever more important to constrain the nature, magnitude, and speed of changes to Earth systems. A fundamentally important tool to this understanding is the Earth’s past, recorded in the geologic record. There, lie examples of climate change under various forcings: important data for understanding the fundamental dynamics of climate change on our planet. However, when a climate signal is written in the geologic record, it is coded into the language of proxies and distorted by time. This thesis endeavors to decode that record using a variety of computational methods on a number of challenging proxies, to draw more information from the climate past than has previously been possible. First, machine learning and computer vision are used to decipher the primary, centimeter-scale textures of carbonate deposits in Searles Valley and Mono Lake, California. This work is able to connect facies in the tufa at Searles, grown during the Last Glacial Period, and those forming presently at Mono Lake. Next, the tracks of icebergs purged during Heinrich Events are simulated using the MIT General Circulation Model. This work, running multiple experiments exploring different aspects internal and external to the icebergs, reveals wind and sediment partitioning as centrally important to the spatial extent of Heinrich Layers. Each of these works considers a traditional geologic archive – a carbonate facies, a marine sediment layer – and uses computational methods to approach that archive from a different perspective. By applying these new methods, more information can be gleaned from the geologic record, building a richer narrative of the Earth’s climate history. The final chapter of this thesis discusses effective teaching and strategies for building communities to support teaching practice in Earth Science departments.
    Description: This thesis work was funded by the MIT EAPS Rasmussen and Whiteman Fellowships, NSF Project Number NSF-EAR-1903544, and the WHOI Academic Programs Office.
    Keywords: Paleoclimate ; Iceberg ; Modeling
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    Residual overturning circulation and its connection to Southern Ocean dynamics (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Over the last 20 years, our understanding of the meridional overturning circulation has improved, but primarily in a two-dimensional, zonally-averaged framework. In this thesis, I have pushed beyond this simplification and shown that the additional complexity of meanders, storm tracks, and other zonal asymmetries is necessary to reproduce the lowest-order behavior of the overturning circulation. First I examined the role of basin width for determining whether the Atlantic or Pacific oceans experience deep convection. I used a two layered model and a rectangular single-basin model to show that the basin width, in combination with scalings for the overturning circulation make the overturning relatively weaker in the wider basin, priming it for a convection shut down. In addition to this large-scale work, I have examined Southern Ocean-like meanders using a hierarchy of idealized models to understand the role of bottom topography in determining how the large-scale circulation responds to climate change scenarios. These are useful because they preserve the lowest-order behavior, while remaining simple enough to understand. I tested the response of the stratification and transport in the Southern Ocean to changes in wind using a highly-idealized two-layer quasi-geostrophic model. In addition to showing that meanders are necessary to reproduce the behavior of the Southern Ocean, I found that strong winds concentrate the baroclinic and barotropic instabilities downstream of the bottom topography and weaken the instabilities elsewhere due to a form-drag process. With weak winds, however, the system is essentially symmetric in longitude, like a flat-bottomed ocean. This result is consistent with observations of elevated turbulence downstream of major topography in the Southern Ocean. My next study investigated a more realistic Southern Ocean-like channel, with and without bottom topography, and examined the three-dimensional circulation in order to understand where vertical transport occurs and develop a picture of the pathways taken by each individual water parcel. I found that the vertical transport happens in very isolated locations, just downstream of topography. Finally, I added a biogeochemical model to my simulations and found that carbon fluxes are enhanced near topography, again highlighting the role of zonal asymmetries.
    Description: I have been funded by the American Meteorological Society’s Graduate Fellowship, as well as the National Defense Science and Engineering Graduate Fellowship. I have also been supported by NSF OCE-1536515 and NCAR Large Scale Computing Award UMIT0025.
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    Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coskun, O. K., Vuillemin, A., Schubotz, F., Klein, F., Sichel, S. E., Eisenreich, W., & Orsi, W. D. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. Isme Journal. (2021), https://doi.org/10.1038/s41396-021-01066-x.
    Description: Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
    Description: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 364653263—TRR 235 to WDO and WE, and under Germany’s Excellence Strategy—EXC 2077-390741603. The work was also supported by the Dalio Explore Fund and LMU Mentoring Program. Open Access funding enabled and organized by Projekt DEAL.
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    An analysis of Atlantic Water in the Arctic Ocean using the Arctic Subpolar Gyre State Estimate and observations (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: The Atlantic Water (AW) Layer in the Arctic Subpolar gyre sTate Estimate (ASTE), a regional, medium-resolution coupled ocean-sea ice state estimate, is analyzed for the first time using bounding isopycnals. A surge of AW, marked by rapid increases in mean AW Layer potential temperature and AW Layer thickness, begins two years into the state estimate (2004) and traverses the Arctic Ocean along boundary current pathways at approximately 2 cm/s. The surge also alters AW flow direction and speed including a significant reversal in flow direction along the Lomonosov Ridge. The surge results in a new quasi-steady AW flow from 2010 through the end of the state estimate period in 2017. The time-mean AW circulation during this time period indicates a significant amount of AW spreads over the Lomonosov Ridge rather than directly returning along the ridge to Fram Strait. A three-layer depiction of ASTE’s overturning circulation within the AO indicates AW is converted to colder, fresher Surface Layer water at a faster rate than is transformed to Bottom Water (1.2 Sv vs. 0.4 Sv). Observed AW properties compared to ASTE output indicate increasing misfit during the simulated period with ASTE’s AW Layer generally being warmer and thicker than in observations.
    Description: This research was funded via the United States Navy’s Civilian Institution Program with the MIT/WHOI Joint Program (JP). The thesis supervisor’s participation in this project was supported by National Science Foundation-Grant #PLR-1603660 and by Office of Naval Research-Grant #N000141612381. This project, specifically ASTE developed by Dr. An T. Nguyen, is also supported by National Science Foundation-Grant #PLR-1603903.
    Keywords: Atlantic water ; Arctic Ocean ; Arctic Subpolar Gyre State Estimate
    Repository Name: Woods Hole Open Access Server
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    The effect of attenuation from fish on long-range active and passive acoustic sensing in the ocean (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Attenuation from fish can reduce the intensity of acoustic signals and significantly decrease detection range for long-range active and passive sensing in the ocean. This makes it important to understand the relevant mechanisms and accurately predict attenuation from fish in underwater acoustic sensing. Formulations for predicting attenuation from fish, however, depend on the accurate characterization of population density and spatial distribution of fish groups along long-range propagation paths, which is difficult to achieve using conventional survey methods. In previous investigations of attenuation from fish, population densities were inferred from reductions in the intensity of long-range acoustic signals caused by diel or seasonal shoaling patterns of fish groups. Here, Ocean Acoustic Waveguide Remote Sensing (OAWRS) is used to instantaneously image massive Norwegian herring shoals that stretch for thousands of square kilometers and simultaneously measure attenuation from these shoals within the active OAWRS transmissions, as well as attenuation to ship-radiated tonals detected by Passive Ocean Acoustic Waveguide Remote Sensing (POAWRS). Reductions in signal intensity are predicted using a normal-mode-based analytical theory derived from first principles for acoustic propagation and scattering through inhomogeneities in an ocean waveguide. The predictions of the waveguide attenuation formulation are in agreement with measured reductions from attenuation, where the position, size, and population density of the fish groups are characterized using OAWRS imagery as well as in situ echosounder measurements of the specific shoals occluding the propagation path. Common heuristic formulations that employ free space scattering assumptions for attenuation from fish groups are not in agreement with measurements here, and waveguide scattering theory is found to be necessary for accurate predictions. It is experimentally and theoretically shown that attenuation can be significant when the sensing frequency is near the resonance frequency of the shoaling fish, where scattering losses from the fish swimbladders and damping from fish flesh is most significant. Negligible attenuation was observed in previous OAWRS and POAWRS surveys because the frequency of the acoustic signals was sufficiently far from the swimbladder resonance peak of the shoaling fish or the packing densities of the fish shoals were not sufficiently high.
    Description: This work was supported by: • Office of Naval Research under grant number N00014-17-1-2197. • Office of Naval Research via the Graduate Traineeship Award under grant number N00014-18-1-2085.
    Keywords: Attenuation ; Fish ; Acoustic
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  • 85
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    Sea ice surface temperatures from helicopter-borne thermal infrared imaging during the MOSAiC expedition (2022)
    Springer Nature
    In:  EPIC3Scientific Data, Springer Nature, 9(1), ISSN: 2052-4463
    Details
    Publication Date: 2022-06-27
    Description: The sea ice surface temperature is important to understand the Arctic winter heat budget. We conducted 35 helicopter flights with an infrared camera in winter 2019/2020 during the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. The flights were performed from a local, 5 to 10 km scale up to a regional, 20 to 40 km scale. The infrared camera recorded thermal infrared brightness temperatures, which we converted to surface temperatures. More than 150000 images from all flights can be investigated individually. As an advanced data product, we created surface temperature maps for every flight with a 1 m resolution. We corrected image gradients, applied an ice drift correction, georeferenced all pixels, and corrected the surface temperature by its natural temporal drift, which results in time-fixed surface temperature maps for a consistent analysis of one flight. The temporal and spatial variability of sea ice characteristics is an important contribution to an increased understanding of the Arctic heat budget and, in particular, for the validation of satellite products.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 86
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    U-Th Dating of lacustrine carbonates (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-09-14
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanography and Applied Ocean Science and Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2020.
    Description: Carbonates are prevalent in many modern and ancient lacustrine settings, but reconstructions of past lake levels or environments from such materials have been hindered by poor chronology. Uranium-thorium (U-Th) dating has the potential to fill a gap in current geochronological tools for such archives, but past attempts have been confounded by poor understanding of the complex makeup of lacustrine carbonates, leading to misguided conclusions on both the utility of certain geochronological tools as well as the age of these deposits. This thesis showcases strategies for the successful application of U-Th geochronology to two types of lacustrine carbonates: lake bottom sediments and tufa deposits. Chapter 2 presents a systematic approach to U-Th dating carbonate-rich lake sediments using the ICDP sediment core from Lake Junín, Peru. Chapters 3–5 seek to demonstrate the descriptive power of combining precise U-Th dates on tufas and other carbonates with geologic observations of their depositional context at all scales—from the outcrop to the microscale. Here, the tufas originate from a transect of closed-basin lakes in the central Andes of northern Chile. With improved sample selection and leveraging of the incontrovertible constraints of stratigraphy and coevality, we are able to test the validity of U-Th data. Combining quality-controlled geochronological constraints with careful characterization of different carbonate facies can yield new insight on the character of lake level changes. These case studies offer frameworks for interpreting scattered geochronologic data of any size or system. By embracing the noise in our data, we now have a richer understanding of the controls on uranium in these deposits. Of all the lessons learned, we hold the following as most important: for the determination of the age of lacustrine carbonates, geologic context—in the form of sedimentological observations, additional geochemical data, and paleoecological descriptions—is of equal importance to the numerical accuracy and precision of geochronological measurements.
    Description: Funding sources: National Science Foundation, Massachusetts Institute of Technology, Geological Society of America, MIT MISTI, Comer Foundation, American Philosophical Society, National Geographic Society, Explorers Club.
    Keywords: Carbonates ; Tufa ; Geochronology
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    Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean (2022)
    Springer Nature
    Details
    Publication Date: 2022-06-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.
    Description: Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
    Description: This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016).
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    Intracellular nitrate storage by diatoms can be an important nitrogen pool in freshwater and marine ecosystems (2022)
    Springer Nature
    In:  EPIC3Communications Earth & Environment, Springer Nature, 3(1), ISSN: 2662-4435
    Details
    Publication Date: 2022-07-06
    Description: Identifying and quantifying nitrogen pools is essential for understanding the nitrogen cycle in aquatic ecosystems. The ubiquitous diatoms represent an overlooked nitrate pool as they can accumulate nitrate intracellularly and utilize it for nitrogen assimilation, dissipation of excess photosynthetic energy, and Dissimilatory Nitrate Reduction to Ammonium (DNRA). Here, we document the global co-occurrence of diatoms and intracellular nitrate in phototrophic microbial communities in freshwater (n = 69), coastal (n = 44), and open marine (n = 4) habitats. Diatom abundance and total intracellular nitrate contents in water columns, sediments, microbial mats, and epilithic biofilms were highly significantly correlated. In contrast, diatom community composition had only a marginal influence on total intracellular nitrate contents. Nitrate concentrations inside diatom cells exceeded ambient nitrate concentrations ∼100–4000-fold. The collective intracellular nitrate pool of the diatom community accounted for 〈1% of total nitrate in pelagic habitats and 65–95% in benthic habitats. Accordingly, nitrate-storing diatoms are emerging as significant contributors to benthic nitrogen cycling, in particular through Dissimilatory Nitrate Reduction to Ammonium activity under anoxic conditions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed , info:eu-repo/semantics/article
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  • 89
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    Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.
    Description: Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.
    Description: We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB).
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    Development and testing of the AXBT Realtime Editing System (ARES) (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Airborne eXpendable BathyThermographs (AXBTs) are air-launched, single use temperature-depth probes that telemeter temperature observations as a VHF-modulated frequency. This study describes the AXBT Realtime Editing System (ARES), which was developed to receive and quality control temperature-depth profiles with no external hardware other than a VHF radio receiver. The ARES Data Acquisition System performs fast Fourier transforms on windowed segments of demodulated signal transmitted from the AXBT and uses the resulting spectra to identify valid temperature-depth observations. When evaluated using 389 profiles, the ARES data acquisition system produced temperature-depth profiles nearly identical to those generated using a Sippican MK-21 processor, while reducing the amount of noise from VHF interference included in those profiles. The ARES Profile Editor applies a series of automated checks to identify and correct common profile discrepancies, before displaying the profile on an editing interface that provides simple user controls to make additional corrections. When evaluated against 1,177 tropical Atlantic and Pacific AXBT profiles, the ARES automated quality control system successfully corrected 87% of the profiles without any manual intervention necessary. The ARES Data Acquisition and Profile Editing Systems performed exceptionally well when operationally tested with 44 AXBTs during Hurricane Dorian (2019), enabling high resolution observations across key oceanic features including Dorian’s cold wake and the Gulf Stream. Necessary future work includes improvements on the automated quality control algorithm and evaluation against a more diverse dataset of temperature-depth profiles.
    Description: This research was funded by the U.S. Navy’s Civilian Institution (CIVINS) Office with the MIT-WHOI Joint Program. Additionally, this work was funded by the Office of Naval Research, grant number N000141812819.
    Keywords: Airborne Expendable Bathythermograph ; AXBT ; Upper Ocean Observations
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  • 91
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    High resolution, in-situ studies of seawater carbonate chemistry and carbon cycling in coastal systems using CHANnelized Optical System II (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: Study of the marine CO2 system is critical for understanding global carbon cycling and the impacts of changing ocean chemistry on marine ecosystems. This thesis describes the development of a near-continuous, in-situ dissolved inorganic carbon (DIC) sensor, CHANnelized Optical System (CHANOS) II, suitable for deployment from both mobile and stationary platforms. The system delivers DIC measurements with an accuracy of 2.9 (laboratory) or 9.0 (field) μmol kg-1, at a precision of ~4.9-5.5 μmol kg-1. Time-series field deployments in the Pocasset River, MA, revealed seasonal and episodic biogeochemical shifts in DIC, including two different responses to tropical storm and nor’easter systems. Towed surface mapping deployments across Waquoit Bay, MA, highlighted the export of DIC from salt marshes through tidal water. High resolution (〈100 m) data collected during ROV deployments over deep coral mounds on the West Florida Slope revealed a much wider DIC range (~1900 – 2900 μmol kg-1) across seafloor and coral habitats than was observed through the few bottle samples collected during the dives (n = 5, 2190.9 ± 1.0 μmol kg-1). These deployments highlight the need to investigate deep sea biogeochemistry at high spatial scales in order to understand the range of environmental variation encountered by benthic communities.
    Description: Funding for this work was provided by the National Science Foundation (OCE Award No. 1233654, OCE 1635388, OCE 1841092), National Oceanic and Atmospheric Administration Office of Ocean Exploration and Research (NA18OAR0110352), MIT Seagrant (2017-R/RCM-51), and Woods Hole Oceanographic Institution (Ocean Ventures Fund, Grassle Fellowship).
    Keywords: DIC ; sensor ; ROV
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    The Role of Zooplankton in Regulating Carbon Export and Phytoplankton Community Structure: Integrating Models and Observations (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: In this thesis, I explore two topics in plankton ecology with a combination of models and observations. First, I investigate the contribution of zooplankton diel vertical migration (DVM) to the vertical flux of carbon as part of the biological pump. I do this by constructing and analyzing a global model that includes DVM and is driven by satellite-based estimates of primary productivity. There has long been speculation about the significance of DVM to the biological pump, but quantitative estimates of its impact are rare. I estimate that DVM constitutes approximately 16% of the global carbon export flux associated with the biological pump and that the relative contribution of DVM is higher in subtropical latitudes. In later chapters, I build two nutrient-hytoplankton-zooplankton (NPZ) models with different levels of complexity to evaluate the role of nutrient supply and grazing in promoting phytoplankton diversity. Zooplankton switching plays a significant role in promoting diversity because it allows competing phytoplankton types to coexist in situations that would otherwise lead to competitive exclusion. When implemented in a size-structured NPZ model, stronger switching increases the evenness of the distribution of biomass between coexisting size classes, which is used as a proxy for taxonomic diversity. I also describe a particular characteristic of the Kill-the-Winner functional response (used in the NPZ models), which I have termed synergistic grazing. Synergistic grazing occurs when the grazing rate on one phytoplankton type increases as the biomass of an alternative phytoplankton type increases. This characteristic can result in unintuitive model dynamics. Finally, I describe patterns in phytoplankton community size structure in the shelfbreak region of the Northeast U.S. Shelf using high-resolution flow-cytometry measurements. I find that enhancement of phytoplankton biovolume at the shelfbreak front is common during the springtime, but these enhancement events are not associated with consistent changes in community size structure. I evaluate these results in the context of hypotheses generated based on my analysis of the NPZ models.
    Description: The research in this thesis was supported by the National Science Foundation (NSF, OCE-1434000 and OCE-1657803) and the National Aeronautics and Space Administration (NASA) as part of the EXport Processes in the global Ocean from RemoTe Sensing (EXPORTS) field campaign (grant 80NSSC17K0692) and the North Atlantic Aerosol and MarineEcosystems Study (NAAMES, grantsNNX15AE72G and 80NSSC18K0018). Additional support came from NSF (OCE-1655686 and OCE-1657803) and the Simons Foundation (561126).
    Keywords: zooplankton ; grazing ; diversity
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    Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castro, S. P., Borton, M. A., Regan, K., de Angelis, I. H., Wrighton, K. C., Teske, A. P., Strous, M., & Ruff, S. E. Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. Isme Journal. (2021), https://doi.org/10.1038/s41396-021-01026-5.
    Description: Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.
    Description: We are grateful to the captain and crew of the R/V Atlantis AT37-06 as well as the crew of the human occupied vehicle Alvin for their tireless support. Sampling at Guaymas Basin was supported by NSF (OCE-1357238).
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    Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mara, P., Vik, D., Pachiadaki, M. G., Suter, E. A., Poulos, B., Taylor, G. T., Sullivan, M. B., & Edgcomb, V. P. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME Journal, (2020), doi:10.1038/s41396-020-00739-3.
    Description: Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.
    Description: This work was supported by the National Science Foundation grant OCE-1336082 to VPE, OCE-1335436 to GTT, OCE-1536989, a Moore Foundation Award (#3790) to MBS, and WHOI subaward A101259 to MP. The sequencing conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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    Sediment dynamics of a divergent bay-marsh complex (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © Springer Nature , 2020. This article is posted here by permission of Springer Nature for personal use, not for redistribution. The definitive version was published in Nowacki, D. J., & Ganju, N. K. Sediment dynamics of a divergent bay-marsh complex. Estuaries and Coasts, (2020), doi:10.1007/s12237-020-00855-5.
    Description: Bay–marsh systems, composed of an embayment surrounded by fringing marsh incised by tidal channels, are widely distributed coastal environments. External sediment availability, marsh-edge erosion, and sea-level rise acting on such bay–marsh complexes may drive diverse sediment-flux regimes. These factors reinforce the ephemeral and dynamic nature of fringing marshes: material released by marsh-edge erosion becomes part of a bay–marsh exchange that fuels the geomorphic evolution of the coupled system. The dynamics of this sediment exchange determine the balance among seaward export, deposition on the embayment seabed, flux into tidal channels, and import to the marsh platform. In this work, we investigate the sediment dynamics of a transgressive bay–marsh complex and link them to larger-scale considerations of its geomorphic trajectory. Grand Bay, Alabama/Mississippi, is a shallow microtidal embayment surrounded by salt marshes with lateral erosion rates of up to 5 m year−1. We collected 6 months of oceanographic data at four moorings within Grand Bay and its tidal channels to assess hydrographic conditions and net sediment-flux patterns and augmented the observations with numerical modeling. The observations imply a divergent sedimentary system in which a majority of the suspended sediment is exported seaward, while a smaller fraction is imported landward via tidal channels, assisting in vertical marsh-plain accumulation, maintenance of channel and intertidal-flat morphologies, and landward transgression. These results describe a dynamic system that is responsive to episodic atmospheric forcing in the absence of a strong tidal signal and the presence of severe lateral marsh loss.
    Description: We thank the staff of the Grand Bay NERR for their role in facilitating fieldwork within Grand Bay. Jonathan Pitchford, also of the Grand Bay NERR, provided the SET data. Giulio Mariotti and an anonymous reviewer are acknowledged for their helpful comments.
    Keywords: Salt marsh ; Geomorphic trajectory ; Sediment flux
    Repository Name: Woods Hole Open Access Server
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    Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions (2021)
    Springer Nature
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bayer, B., Saito, M. A., McIlvin, M. R., Lucker, S., Moran, D. M., Lankiewicz, T. S., Dupont, C. L., & Santoro, A. E. (2020). Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. Isme Journal, doi:10.1038/s41396-020-00828-3.
    Description: The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
    Description: We thank John B. Waterbury and Frederica Valois for providing the culture of Nitrospira marina Nb-295T and for continued advice about cultivation. The N. marina genome was sequenced as part of US Department of Energy Joint Genome Institute Community Sequencing Project 1337 to CLD, AES, and MAS in collaboration with the user community. We thank Claus Pelikan for bioinformatic assistance. This research was supported by a Simons Foundation Early Career Investigator in Marine Microbiology and Evolution Award (345889) and US National Science Foundation (NSF) award OCE-1924512 to AES. Proteomics analysis was supported by NSF awards OCE-1924554 and OCE-1850719, and NIH award R01GM135709 to MAS. BB was supported by the Austrian Science Fund (FWF) Project Number: J4426-B (“The influence of nitrifiers on the oceanic carbon cycle”), SL by the Netherlands Organization for Scientific Research (NWO) grant 016.Vidi.189.050, and CLD by NSF award OCE-125999.
    Repository Name: Woods Hole Open Access Server
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