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  • Frontiers Media  (145)
  • American Meteorological Society  (124)
  • Massachusetts Institute of Technology and Woods Hole Oceanographic Institution  (60)
  • American Chemical Society (ACS)
  • 2020-2023  (329)
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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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    Editorial: role of protein palmitoylation in synaptic plasticity and neuronal differentiation (2020)
    Frontiers Media
    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 Yoshii, A., & Green, W. N. Editorial: role of protein palmitoylation in synaptic plasticity and neuronal differentiation. Frontiers in Synaptic Neuroscience, 12(27), (2020), doi:10.3389/fnsyn.2020.00027.
    Description: Protein palmitoylation, the reversible addition of palmitate to proteins, is a dynamic post-translational modification. Both membrane (e.g., channels, transporters, and receptors) and cytoplasmic proteins (e.g., cell adhesion, scaffolding, cytoskeletal, and signaling molecules) are substrates. In mammals, palmitoylation is mediated by 23-24 palmitoyl acyltransferases (PATs), also called ZDHHCs for their catalytic aspartate-histidine-histidine-cysteine (DHCC) domain. PATs are integral membrane proteins found in cellular membranes. In the palmitoylation cycle, palmitate is removed by the depalmitoylation enzymes, acyl palmitoyl transferases (APT1 and 2), and α/β Hydrolase domain-containing protein 17 (ABHD17A-C). These are cytoplasmic proteins that are targeted to membranes where they are substrates for PATs. The second class of depalmitoylating enzymes are palmitoyl thioesterases, PPT1 and 2, discovered through their association with infantile neuronal ceroid lipofuscinosis. These are secreted proteins found in the lumen of intracellular organelles, primarily lysosomes, where their function as depalmitoylating enzymes is unclear.
    Description: This work was supported by University of Illinois start-up fund (to AY) and NIH/NIDA (grant DA044760 to WG).
    Keywords: palmitoylation and depalmitoylation ; synaptic plasticity ; axonal growth ; lysosome ; neurodegenerative disease ; neuronal ceroid lipofuscinoses (NCL) ; Huntington disease
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Ancestral absence of electron transport chains in Patescibacteria and DPANN (2020)
    Frontiers Media
    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 Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.
    Description: Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
    Description: This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548.
    Keywords: Bacteria ; Archaea ; evolution ; genomics fermentation ; respiration ; oxidoreductases
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Latitudinal structure of the meridional overturning circulation variability on interannual to decadal time scales in the North Atlantic Ocean (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 33(9), (2020): 3845-3862, doi:10.1175/JCLI-D-19-0215.1.
    Description: The latitudinal structure of the Atlantic meridional overturning circulation (AMOC) variability in the North Atlantic is investigated using numerical results from three ocean circulation simulations over the past four to five decades. We show that AMOC variability south of the Labrador Sea (53°N) to 25°N can be decomposed into a latitudinally coherent component and a gyre-opposing component. The latitudinally coherent component contains both decadal and interannual variabilities. The coherent decadal AMOC variability originates in the subpolar region and is reflected by the zonal density gradient in that basin. It is further shown to be linked to persistent North Atlantic Oscillation (NAO) conditions in all three models. The interannual AMOC variability contained in the latitudinally coherent component is shown to be driven by westerlies in the transition region between the subpolar and the subtropical gyre (40°–50°N), through significant responses in Ekman transport. Finally, the gyre-opposing component principally varies on interannual time scales and responds to local wind variability related to the annual NAO. The contribution of these components to the total AMOC variability is latitude-dependent: 1) in the subpolar region, all models show that the latitudinally coherent component dominates AMOC variability on interannual to decadal time scales, with little contribution from the gyre-opposing component, and 2) in the subtropical region, the gyre-opposing component explains a majority of the interannual AMOC variability in two models, while in the other model, the contributions from the coherent and the gyre-opposing components are comparable. These results provide a quantitative decomposition of AMOC variability across latitudes and shed light on the linkage between different AMOC variability components and atmospheric forcing mechanisms.
    Description: The authors gratefully acknowledge support from the Physical Oceanography Program of the U.S. National Science Foundation (Awards OCE-1756143 and OCE-1537136) and the Climate Program Office of the National Oceanic and Atmospheric Administration (Award NA15OAR4310088). Gratitude is extended to Claus Böning and Arne Biastoch who shared ORCA025 output. S. Zou thanks F. Li, M. Buckley, and L. Li for helpful discussions. We also thank three anonymous reviewers for helpful suggestions.
    Keywords: Deep convection ; Ocean circulation ; Thermocline circulation
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  • 7
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    Importance of Orography for Greenland cloud and melt response to atmospheric blocking (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Hahn, L. C., Storelvmo, T., Hofer, S., Parfitt, R., & Ummenhofer, C. C. Importance of Orography for Greenland cloud and melt response to atmospheric blocking. Journal of Climate, 33(10), (2020): 4187-4206, doi:10.1175/JCLI-D-19-0527.1.
    Description: More frequent high pressure conditions associated with atmospheric blocking episodes over Greenland in recent decades have been suggested to enhance melt through large-scale subsidence and cloud dissipation, which allows more solar radiation to reach the ice sheet surface. Here we investigate mechanisms linking high pressure circulation anomalies to Greenland cloud changes and resulting cloud radiative effects, with a focus on the previously neglected role of topography. Using reanalysis and satellite data in addition to a regional climate model, we show that anticyclonic circulation anomalies over Greenland during recent extreme blocking summers produce cloud changes dependent on orographic lift and descent. The resulting increased cloud cover over northern Greenland promotes surface longwave warming, while reduced cloud cover in southern and marginal Greenland favors surface shortwave warming. Comparison with an idealized model simulation with flattened topography reveals that orographic effects were necessary to produce area-averaged decreasing cloud cover since the mid-1990s and the extreme melt observed in the summer of 2012. This demonstrates a key role for Greenland topography in mediating the cloud and melt response to large-scale circulation variability. These results suggest that future melt will depend on the pattern of circulation anomalies as well as the shape of the Greenland Ice Sheet.
    Description: This research was supported by the Woods Hole Oceanographic Institution Summer Student Fellow program, by the U.S. National Science Foundation under AGS-1355339 to C.C.U., and by the European Research Council through Grant 758005.
    Keywords: Ice sheets ; Blocking ; Cloud cover ; Topographic effects ; Climate change ; Climate variability
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  • 8
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    Impacts of Arctic Sea Ice on Cold Season Atmospheric Variability and Trends Estimated from Observations and a Multi-model Large Ensemble (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-03-01
    Description: To examine the atmospheric responses to Arctic sea ice variability in the Northern Hemisphere cold season (from October to the following March), this study uses a coordinated set of large-ensemble experiments of nine atmospheric general circulation models (AGCMs) forced with observed daily varying sea ice, sea surface temperature, and radiative forcings prescribed during the 1979–2014 period, together with a parallel set of experiments where Arctic sea ice is substituted by its climatology. The simulations of the former set reproduce the near-surface temperature trends in reanalysis data, with similar amplitude, and their multimodel ensemble mean (MMEM) shows decreasing sea level pressure over much of the polar cap and Eurasia in boreal autumn. The MMEM difference between the two experiments allows isolating the effects of Arctic sea ice loss, which explain a large portion of the Arctic warming trends in the lower troposphere and drive a small but statistically significant weakening of the wintertime Arctic Oscillation. The observed interannual covariability between sea ice extent in the Barents–Kara Seas and lagged atmospheric circulation is distinguished from the effects of confounding factors based on multiple regression, and quantitatively compared to the covariability in MMEMs. The interannual sea ice decline followed by a negative North Atlantic Oscillation–like anomaly found in observations is also seen in the MMEM differences, with consistent spatial structure but much smaller amplitude. This result suggests that the sea ice impacts on trends and interannual atmospheric variability simulated by AGCMs could be underestimated, but caution is needed because internal atmospheric variability may have affected the observed relationship.
    Description: Published
    Description: 8419–8443
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Keywords: Arctic ; Sea ice ; Atmospheric circulation ; Climate models ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Atlantic Multidecadal Variability and North Atlantic Jet: A Multimodel View from the Decadal Climate Prediction Project (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-02-14
    Description: The influence of the Atlantic multidecadal variability (AMV) on the North Atlantic storm track and eddy-driven jet in the winter season is assessed via a coordinated analysis of idealized simulations with state-of-the-art coupled models. Data used are obtained from a multimodel ensemble of AMV± experiments conducted in the framework of the Decadal Climate Prediction Project component C. These experiments are performed by nudging the surface of the Atlantic Ocean to states defined by the superimposition of observed AMV± anomalies onto the model climatology. A robust extratropical response is found in the form of a wave train extending from the Pacific to the Nordic seas. In the warm phase of the AMV compared to the cold phase, the Atlantic storm track is typically contracted and less extended poleward and the low-level jet is shifted toward the equator in the eastern Atlantic. Despite some robust features, the picture of an uncertain and model-dependent response of the Atlantic jet emerges and we demonstrate a link between model bias and the character of the jet response.
    Description: Published
    Description: 347-360
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Temporal evolution of a geostrophic current under sea ice: analytical and numerical solutions (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-06-21
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(6),(2022): 1191-1204, https://doi.org/10.1175/jpo-d-21-0242.1.
    Description: A simplified quasigeostrophic (QG) analytical model together with an idealized numerical model are used to study the effect of uneven ice–ocean stress on the temporal evolution of the geostrophic current under sea ice. The tendency of the geostrophic velocity in the QG model is given as a function of the lateral gradient of vertical velocity and is further related to the ice–ocean stress with consideration of a surface boundary layer. Combining the analytical and numerical solutions, we demonstrate that the uneven stress between the ice and an initially surface-intensified, laterally sheared geostrophic current can drive an overturning circulation to trigger the displacement of isopycnals and modify the vertical structure of the geostrophic velocity. When the near-surface isopycnals become tilted in the opposite direction to the deeper ones, a subsurface velocity core is generated (via geostrophic setup). This mechanism should help understand the formation of subsurface currents in the edge of Chukchi and Beaufort Seas seen in observations. Furthermore, our solutions reveal a reversed flow extending from the bottom to the middepth, suggesting that the ice-induced overturning circulation potentially influences the currents in the deep layers of the Arctic Ocean, such as the Atlantic Water boundary current.
    Description: This work was funded by the National Key Research and Development Program of China (Grant 2017YFA0604600), the National Natural Science Foundation of China (Grant 41676019), the Fundamental Research Funds for the Central Universities (Grant 2019B81214), the Postgraduate Research and Practice Innovation Program of Jiangsu Province (Grant KYCX19_0384), and the National Science Foundation (MAS, Grants OPP-1822334, OCE-2122633).
    Keywords: Arctic ; Sea ice ; Channel flows ; Vertical motion ; Ekman pumping ; Idealized models ; Quasigeostrophic models
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  • 11
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    Effects of excess brain-derived human alpha-synuclein on synaptic vesicle trafficking (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Roman-Vendrell, C., Medeiros, A. T., Sanderson, J. B., Jiang, H., Bartels, T., & Morgan, J. R. Effects of excess brain-derived human alpha-synuclein on synaptic vesicle trafficking. Frontiers in Neuroscience, 15, (2021): 639414, https://doi.org/10.3389./fnins.2021.639414
    Description: α-Synuclein is a presynaptic protein that regulates synaptic vesicle trafficking under physiological conditions. However, in several neurodegenerative diseases, including Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy, α-synuclein accumulates throughout the neuron, including at synapses, leading to altered synaptic function, neurotoxicity, and motor, cognitive, and autonomic dysfunction. Neurons typically contain both monomeric and multimeric forms of α-synuclein, and it is generally accepted that disrupting the balance between them promotes aggregation and neurotoxicity. However, it remains unclear how distinct molecular species of α-synuclein affect synapses where α-synuclein is normally expressed. Using the lamprey reticulospinal synapse model, we previously showed that acute introduction of excess recombinant monomeric or dimeric α-synuclein impaired distinct stages of clathrin-mediated synaptic vesicle endocytosis, leading to a loss of synaptic vesicles. Here, we expand this knowledge by investigating the effects of native, physiological α-synuclein isolated from the brain of a neuropathologically normal human subject, which comprised predominantly helically folded multimeric α-synuclein with a minor component of monomeric α-synuclein. After acute introduction of excess brain-derived human α-synuclein, there was a moderate reduction in the synaptic vesicle cluster and an increase in the number of large, atypical vesicles called “cisternae.” In addition, brain-derived α-synuclein increased synaptic vesicle and cisternae sizes and induced atypical fusion/fission events at the active zone. In contrast to monomeric or dimeric α-synuclein, the brain-derived multimeric α-synuclein did not appear to alter clathrin-mediated synaptic vesicle endocytosis. Taken together, these data suggest that excess brain-derived human α-synuclein impairs intracellular vesicle trafficking and further corroborate the idea that different molecular species of α-synuclein produce distinct trafficking defects at synapses. These findings provide insights into the mechanisms by which excess α-synuclein contributes to synaptic deficits and disease phenotypes.
    Description: This work was supported by the NIH (NINDS/NIA R01NS078165 and R01NS078165-S1 to JM; NINDS U54-NS110435, R01-NS109209, and R21-NS107950 to TB); research funds from the Marine Biological Laboratory (to JM); grants from the UK Dementia Research Institute (DRI), which receives its funding from DRI Ltd., the UK Medical Research Council and Alzheimer’s Society, and Alzheimer’s Research UK (to TB); the Michael J. Fox Foundation (Ken Griffin Imaging Award to TB); a Parkinson’s Disease Foundation Stanley Fahn Award (PF-JFA-1884 to TB); the Eisai Pharmaceutical postdoctoral program to TB; and the Chan Zuckerberg Collaborative Pairs Initiative (to TB).
    Keywords: Clathrin mediated endocytosis ; Electron microscopy ; Endosome ; Lamprey ; Reticulospinal synapse
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    Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States (2021)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molino, G. D., Defne, Z., Aretxabaleta, A. L., Ganju, N. K., & Carr, J. A. Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States. Frontiers in Environmental Science, 9, (2021): 616319, https://doi.org/10.3389/fenvs.2021.616319.
    Description: Coastal salt marshes, which provide valuable ecosystem services such as flood mitigation and carbon sequestration, are threatened by rising sea level. In response, these ecosystems migrate landward, converting available upland into salt marsh. In the coastal-plain surrounding Chesapeake Bay, United States, conversion of coastal forest to salt marsh is well-documented and may offset salt marsh loss due to sea level rise, sediment deficits, and wave erosion. Land slope at the marsh-forest boundary is an important factor determining migration likelihood, however, the standard method of using field measurements to assess slope across the marsh-forest boundary is impractical on the scale of an estuary. Therefore, we developed a general slope quantification method that uses high resolution elevation data and a repurposed shoreline analysis tool to determine slope along the marsh-forest boundary for the entire Chesapeake Bay coastal-plain and find that less than 3% of transects have a slope value less than 1%; these low slope environments offer more favorable conditions for forest to marsh conversion. Then, we combine the bay-wide slope and elevation data with inundation modeling from Hurricane Isabel to determine likelihood of coastal forest conversion to salt marsh. This method can be applied to local and estuary-scale research to support management decisions regarding which upland forested areas are more critical to preserve as available space for marsh migration.
    Description: Funding for this study was provided by the United States Geological Survey’s Coastal/Marine Hazards and Resources Program and Ecosystems Mission Area.
    Keywords: Salt marsh ; Coastal forest ; Sea level rise ; Chesapeake Bay ; Marsh migration
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  • 13
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    Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum0 (2022)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stunz, E., Fetcher, N., Lavretsky, P., Mohl, J., Tang, J., & Moody, M. Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum. Frontiers in Plant Science, 13, (2022): 860439, https://doi.org/10.3389/fpls.2022.860439.
    Description: Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.
    Description: This research was made possible by funding provided by NSF/PLR-1417645 to MM. The Botanical Society of America Graduate Student Research Award and the Dodson Research Grant from the Graduate School of the University of Texas at El Paso provided assistance to ES. The grant 5U54MD007592 from the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH) provided bioinformatics resources and support of JM.
    Keywords: Arctic ; Climate change ; Eriophorum vaginatum ; Landscape genomics ; Environmental niche modeling ; Genotype-environment association analyses ; Refugia
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  • 14
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    Simulated estuary-wide response of seagrass (Zostera marina) to future scenarios of temperature and sea level (2020)
    Frontiers Media
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scalpone, C. R., Jarvis, J. C., Vasslides, J. M., Testa, J. M., & Ganju, N. K. Simulated estuary-wide response of seagrass (Zostera marina) to future scenarios of temperature and sea level. Frontiers in Marine Science, 7, (2020): 539946, doi:10.3389/fmars.2020.539946.
    Description: Seagrass communities are a vital component of estuarine ecosystems, but are threatened by projected sea level rise (SLR) and temperature increases with climate change. To understand these potential effects, we developed a spatially explicit model that represents seagrass (Zostera marina) habitat and estuary-wide productivity for Barnegat Bay-Little Egg Harbor (BB-LEH) in New Jersey, United States. Our modeling approach included an offline coupling of a numerical seagrass biomass model with the spatially variable environmental conditions from a hydrodynamic model to calculate above and belowground biomass at each grid cell of the hydrodynamic model domain. Once calibrated to represent present day seagrass habitat and estuary-wide annual productivity, we applied combinations of increasing air temperature and sea level following regionally specific climate change projections, enabling analysis of the individual and combined impacts of these variables on seagrass biomass and spatial coverage. Under the SLR scenarios, the current model domain boundaries were maintained, as the land surrounding BB-LEH is unlikely to shift significantly in the future. SLR caused habitat extent to decrease dramatically, pushing seagrass beds toward the coastline with increasing depth, with a 100% loss of habitat by the maximum SLR scenario. The dramatic loss of seagrass habitat under SLR was in part due to the assumption that surrounding land would not be inundated, as the model did not allow for habitat expansion outside the current boundaries of the bay. Temperature increases slightly elevated the rate of summer die-off and decreased habitat area only under the highest temperature increase scenarios. In combined scenarios, the effects of SLR far outweighed the effects of temperature increase. Sensitivity analysis of the model revealed the greatest sensitivity to changes in parameters affecting light limitation and seagrass mortality, but no sensitivity to changes in nutrient limitation constants. The high vulnerability of seagrass in the bay to SLR exceeded that demonstrated for other systems, highlighting the importance of site- and region-specific assessments of estuaries under climate change.
    Description: This research was supported by the National Science Foundation Research Experience for Undergraduates Program (OCE-1659463), the Woods Hole Oceanographic Institution Summer Student Fellowship Program, the Barnegat Bay Partnership (through a US EPA Clean Water Act grant to Ocean County College; CE98212313), and the USGS Coastal and Marine Hazards/Resources Program. Although this project has been funded in part by the United States Environmental Protection Agency pursuant to a grant agreement with Ocean County College, it has not gone through the Agency’s publications review process and may not necessarily reflect the views of the Agency; therefore, no official endorsement should be assumed. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
    Keywords: Seagrass (Zostera) ; Climate change ; Spatial model ; Sea level rise ; Temperature ; North American Atlantic Coast ; Regional ; Eelgrass (Zostera marina)
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  • 15
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    The lesser Pacific Striped Octopus, Octopus chierchiae: an emerging laboratory model (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Grearson, A. G., Dugan, A., Sakmar, T., Sivitilli, D. M., Gire, D. H., Caldwell, R. L., Niell, C. M., Doelen, G., Wang, Z. Y., & Grasse, B. The lesser Pacific Striped Octopus, Octopus chierchiae: an emerging laboratory model. Frontiers in Marine Science, 8, (2021): 753483, https://doi.org/10.3389/fmars.2021.753483.
    Description: Cephalopods have the potential to become useful experimental models in various fields of science, particularly in neuroscience, physiology, and behavior. Their complex nervous systems, intricate color- and texture-changing body patterns, and problem-solving abilities have attracted the attention of the biological research community, while the high growth rates and short life cycles of some species render them suitable for laboratory culture. Octopus chierchiae is a small octopus native to the central Pacific coast of North America whose predictable reproduction, short time to maturity, small adult size, and ability to lay multiple egg clutches (iteroparity) make this species ideally suited to laboratory culture. Here we describe novel methods for multigenerational culture of O. chierchiae, with emphasis on enclosure designs, feeding regimes, and breeding management. O. chierchiae bred in the laboratory grow from a 3.5 mm mantle length at hatching to an adult mantle length of approximately 20–30 mm in 250–300 days, with 15 and 14% survivorship to over 400 days of age in first and second generations, respectively. O. chierchiae sexually matures at around 6 months of age and, unlike most octopus species, can lay multiple clutches of large, direct-developing eggs every ∼30–90 days. Based on these results, we propose that O. chierchiae possesses both the practical and biological features needed for a model octopus that can be cultured repeatedly to address a wide range of biological questions.
    Description: The cephalopod program at the Marine Biological Laboratory (MBL) was supported by NSF 1827509 and NSF 1723141 grants. CN received funding from HFSP RGP0042. DG and DS received funding and research support from the University of Washington Friday Harbor Laboratories. ZYW was supported by funds from the Whitman Center at the MBL.
    Keywords: Iteroparity ; Cephalopod ; Model organism ; Aquaculture ; Reproduction – mollusk ; Developmental biology ; Neurobiology
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  • 16
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    How much marsh restoration is enough to deliver wave attenuation coastal protection benefits? (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castagno, K., Ganju, N., Beck, M., Bowden, A., & Scyphers, S. How much marsh restoration is enough to deliver wave attenuation coastal protection benefits? Frontiers in Marine Science, 8, (2022): 756670, https://doi.org/10.3389/fmars.2021.756670.
    Description: As coastal communities grow more vulnerable to sea-level rise and increased storminess, communities have turned to nature-based solutions to bolster coastal resilience and protection. Marshes have significant wave attenuation properties and can play an important role in coastal protection for many communities. Many restoration projects seek to maximize this ecosystem service but how much marsh restoration is enough to deliver measurable coastal protection benefits is still unknown. This question is critical to guiding assessments of cost effectiveness and for funding, implementation, and optimizing of marsh restoration for risk reduction projects. This study uses SWAN model simulations to determine empirical relationships between wave attenuation and marsh vegetation. The model runs consider several different common marsh morphologies (including systems with channels, ponds, and fringing mudflats), vegetation placement, and simulated storm intensity. Up to a 95% reduction in wave energy is seen at as low as 50% vegetation cover. Although these empirical relationships between vegetative cover and wave attenuation provide essential insight for marsh restoration, it is also important to factor in lifespan estimates of restored marshes when making overall restoration decisions. The results of this study are important for coastal practitioners and managers seeking performance goals and metrics for marsh restoration, enhancement, and creation.
    Keywords: Salt marsh ; Restoration ; Coastal protection ; UVVR ; Cost effectiveness ; Vegetation ; Numerical model ; Modeling
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  • 17
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    The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-31
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O’Brien, J., McParland, E. L., Bramucci, A. R., Ostrowski, M., Siboni, N., Ingleton, T., Brown, M. V., Levine, N. M., Laverock, B., Petrou, K., & Seymour, J. The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters. Frontiers in Microbiology, 13, (2022): 894026, https://doi.org/10.3389/fmicb.2022.894026.
    Description: The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and 〉2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
    Description: This research was supported by the Australian Research Council Grants FT130100218 and DP180100838 awarded to JS and DP140101045 awarded to JS and KP, as well as an Australian Government Research Training Program Scholarship awarded to JO’B.
    Keywords: DMSP ; DMS ; DLA ; Phytoplankton ; Bacteria ; qPCR ; 16S rRNA gene ; 18S rRNA gene
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  • 18
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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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  • 19
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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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  • 20
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    The Iceland Greenland Seas Project (2020)
    American Meteorological Society
    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 Renfrew, I. A., Pickart, R. S., Vage, K., Moore, G. W. K., Bracegirdle, T. J., Elvidge, A. D., Jeansson, E., Lachlan-Cope, T., McRaven, L. T., Papritz, L., Reuder, J., Sodemann, H., Terpstra, A., Waterman, S., Valdimarsson, H., Weiss, A., Almansi, M., Bahr, F., Brakstad, A., Barrell, C., Brooke, J. K., Brooks, B. J., Brooks, I. M., Brooks, M. E., Bruvik, E. M., Duscha, C., Fer, I., Golid, H. M., Hallerstig, M., Hessevik, I., Huang, J., Houghton, L., Jonsson, S., Jonassen, M., Jackson, K., Kvalsund, K., Kolstad, E. W., Konstali, K., Kristiansen, J., Ladkin, R., Lin, P., Macrander, A., Mitchell, A., Olafsson, H., Pacini, A., Payne, C., Palmason, B., Perez-Hernandez, M. D., Peterson, A. K., Petersen, G. N., Pisareva, M. N., Pope, J. O., Seidl, A., Semper, S., Sergeev, D., Skjelsvik, S., Soiland, H., Smith, D., Spall, M. A., Spengler, T., Touzeau, A., Tupper, G., Weng, Y., Williams, K. D., Yang, X., & Zhou, S. The Iceland Greenland Seas Project. Bulletin of the American Meteorological Society, 100(9), (2019): 1795-1817, doi:10.1175/BAMS-D-18-0217.1.
    Description: The Iceland Greenland Seas Project (IGP) is a coordinated atmosphere–ocean research program investigating climate processes in the source region of the densest waters of the Atlantic meridional overturning circulation. During February and March 2018, a field campaign was executed over the Iceland and southern Greenland Seas that utilized a range of observing platforms to investigate critical processes in the region, including a research vessel, a research aircraft, moorings, sea gliders, floats, and a meteorological buoy. A remarkable feature of the field campaign was the highly coordinated deployment of the observing platforms, whereby the research vessel and aircraft tracks were planned in concert to allow simultaneous sampling of the atmosphere, the ocean, and their interactions. This joint planning was supported by tailor-made convection-permitting weather forecasts and novel diagnostics from an ensemble prediction system. The scientific aims of the IGP are to characterize the atmospheric forcing and the ocean response of coupled processes; in particular, cold-air outbreaks in the vicinity of the marginal ice zone and their triggering of oceanic heat loss, and the role of freshwater in the generation of dense water masses. The campaign observed the life cycle of a long-lasting cold-air outbreak over the Iceland Sea and the development of a cold-air outbreak over the Greenland Sea. Repeated profiling revealed the immediate impact on the ocean, while a comprehensive hydrographic survey provided a rare picture of these subpolar seas in winter. A joint atmosphere–ocean approach is also being used in the analysis phase, with coupled observational analysis and coordinated numerical modeling activities underway.
    Description: The IGP has received funding from the U.S. National Science Foundation: Grant OCE-1558742; the U.K.’s Natural Environment Research Council: AFIS (NE/N009754/1); the Research Council of Norway: MOCN (231647), VENTILATE (229791), SNOWPACE (262710) and FARLAB (245907); and the Bergen Research Foundation (BFS2016REK01). We thank all those involved in the field work associated with the IGP, particularly the officers and crew of the Alliance, and the operations staff of the aircraft campaign.
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  • 21
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    On the steadiness and instability of the Intermediate Western Boundary Current between 24 degrees and 18 degrees S (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 49(12), (2019): 3127-3143, doi: 10.1175/JPO-D-19-0011.1.
    Description: The Intermediate Western Boundary Current (IWBC) transports Antarctic Intermediate Water across the Vitória–Trindade Ridge (VTR), a seamount chain at ~20°S off Brazil. Recent studies suggest that the IWBC develops a strong cyclonic recirculation in Tubarão Bight, upstream of the VTR, with weak time dependency. We herein use new quasi-synoptic observations, data from the Argo array, and a regional numerical model to describe the structure and variability of the IWBC and to investigate its dynamics. Both shipboard acoustic Doppler current profiler (ADCP) data and trajectories of Argo floats confirm the existence of the IWBC recirculation, which is also captured by our Regional Oceanic Modeling System (ROMS) simulation. An “intermediate-layer” quasigeostrophic (QG) model indicates that the ROMS time-mean flow is a good proxy for the IWBC steady state, as revealed by largely parallel isolines of streamfunction ψ⎯ and potential vorticity Q⎯; a ψ⎯−Q⎯ scatter diagram also shows that the IWBC is potentially unstable. Further analysis of the ROMS simulation reveals that remotely generated, westward-propagating nonlinear eddies are the main source of variability in the region. These eddies enter the domain through the Tubarão Bight eastern edge and strongly interact with the IWBC. As they are advected downstream and negotiate the local topography, the eddies grow explosively through horizontal shear production.
    Description: We thank Frank O. Smith for copy editing and proofreading this manuscript. This study was financed in part by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—CAPES, Brazil—Finance Code 001 and by Projeto REMARSUL (Processo CAPES 88882.158621/2014-01), Projeto VT-Dyn (Processo FAPESP 2015/21729-4) and Projeto SUBMESO (Processo CNPq 442926/2015-4). Rocha was supported by a WHOI Postdoctoral Scholarship.
    Description: 2020-06-06
    Keywords: South Atlantic Ocean ; Instability ; Mesoscale processes ; Intermediate waters ; In situ oceanic observations ; Quasigeostrophic models
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  • 22
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    Impact of multidecadal variability in Atlantic SST on winter atmospheric blocking (2020)
    American Meteorological Society
    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 Kwon, Y., Seo, H., Ummenhofer, C. C., & Joyce, T. M. Impact of multidecadal variability in Atlantic SST on winter atmospheric blocking. Journal of Climate, 33(3), (2020): 867-892, doi: 10.1175/JCLI-D-19-0324.1.
    Description: Recent studies have suggested that coherent multidecadal variability exists between North Atlantic atmospheric blocking frequency and the Atlantic multidecadal variability (AMV). However, the role of AMV in modulating blocking variability on multidecadal times scales is not fully understood. This study examines this issue primarily using the NOAA Twentieth Century Reanalysis for 1901–2010. The second mode of the empirical orthogonal function for winter (December–March) atmospheric blocking variability in the North Atlantic exhibits oppositely signed anomalies of blocking frequency over Greenland and the Azores. Furthermore, its principal component time series shows a dominant multidecadal variability lagging AMV by several years. Composite analyses show that this lag is due to the slow evolution of the AMV sea surface temperature (SST) anomalies, which is likely driven by the ocean circulation. Following the warm phase of AMV, the warm SST anomalies emerge in the western subpolar gyre over 3–7 years. The ocean–atmosphere interaction over these 3–7-yr periods is characterized by the damping of the warm SST anomalies by the surface heat flux anomalies, which in turn reduce the overall meridional gradient of the air temperature and thus weaken the meridional transient eddy heat flux in the lower troposphere. The anomalous transient eddy forcing then shifts the eddy-driven jet equatorward, resulting in enhanced Rossby wave breaking and blocking on the northern flank of the jet over Greenland. The opposite is true with the AMV cold phases but with much shorter lags, as the evolution of SST anomalies differs in the warm and cold phases.
    Description: We gratefully acknowledge support from the NSF Climate and Large-scale Dynamics Program (AGS-1355339) to Y-OK, HS, CCU, and TMJ, the NASA Physical Oceanography Program (NNX13AM59G) to Y-OK, HS, and TMJ, NOAA CPO Climate Variability and Predictability Program (NA13OAR4310139) and DOE CESD Regional and Global Model Analysis Program (DE-SC0019492) to Y-OK, and NSF Physical Oceanography Program (OCE-1419235) to HS. We are very grateful to the three anonymous reviewers and editor Dr. Mingfang Ting, for their thorough and insightful suggestions. The NOAA 20CR dataset was downloaded from the NOAA Earth System Research Laboratory Physical Science Division webpage (https://www.esrl.noaa.gov/psd/data/20thC_Rean/). Support for the 20CR Project version 2c dataset is provided by the U.S. Department of Energy, Office of Science Biological and Environmental Research (BER), and by the National Oceanic and Atmospheric Administration Climate Program Office. The HadISST dataset was downloaded from the U.K. Met Office Hadley Centre webpage (https://www.metoffice.gov.uk/hadobs/hadisst/). The ERA-20C dataset was downloaded from the ECMWF webpage (https://apps.ecmwf.int/datasets/data/era20c-daily/). The ERSST5 dataset was provided by the NOAA Earth System Research Laboratory Physical Science Division (https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.ersst.v5.html).
    Keywords: North Atlantic Ocean ; Atmosphere-ocean interaction ; Blocking ; Climate variability ; Multidecadal variability ; North Atlantic Oscillation
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  • 23
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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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  • 24
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    Dispersion in the open ocean seasonal pycnocline at scales of 1-10 km and 1-6 days (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(2), (2020): 415-437, doi:10.1175/JPO-D-19-0019.1.
    Description: Results are presented from two dye release experiments conducted in the seasonal thermocline of the Sargasso Sea, one in a region of low horizontal strain rate (~10−6 s−1), the second in a region of intermediate horizontal strain rate (~10−5 s−1). Both experiments lasted ~6 days, covering spatial scales of 1–10 and 1–50 km for the low and intermediate strain rate regimes, respectively. Diapycnal diffusivities estimated from the two experiments were κz = (2–5) × 10−6 m2 s−1, while isopycnal diffusivities were κH = (0.2–3) m2 s−1, with the range in κH being less a reflection of site-to-site variability, and more due to uncertainties in the background strain rate acting on the patch combined with uncertain time dependence. The Site I (low strain) experiment exhibited minimal stretching, elongating to approximately 10 km over 6 days while maintaining a width of ~5 km, and with a notable vertical tilt in the meridional direction. By contrast, the Site II (intermediate strain) experiment exhibited significant stretching, elongating to more than 50 km in length and advecting more than 150 km while still maintaining a width of order 3–5 km. Early surveys from both experiments showed patchy distributions indicative of small-scale stirring at scales of order a few hundred meters. Later surveys show relatively smooth, coherent distributions with only occasional patchiness, suggestive of a diffusive rather than stirring process at the scales of the now larger patches. Together the two experiments provide important clues as to the rates and underlying processes driving diapycnal and isopycnal mixing at these scales.
    Description: Results are presented from two dye release experiments conducted in the seasonal thermocline of the Sargasso Sea, one in a region of low horizontal strain rate (~10−6 s−1), the second in a region of intermediate horizontal strain rate (~10−5 s−1). Both experiments lasted ~6 days, covering spatial scales of 1–10 and 1–50 km for the low and intermediate strain rate regimes, respectively. Diapycnal diffusivities estimated from the two experiments were κz = (2–5) × 10−6 m2 s−1, while isopycnal diffusivities were κH = (0.2–3) m2 s−1, with the range in κH being less a reflection of site-to-site variability, and more due to uncertainties in the background strain rate acting on the patch combined with uncertain time dependence. The Site I (low strain) experiment exhibited minimal stretching, elongating to approximately 10 km over 6 days while maintaining a width of ~5 km, and with a notable vertical tilt in the meridional direction. By contrast, the Site II (intermediate strain) experiment exhibited significant stretching, elongating to more than 50 km in length and advecting more than 150 km while still maintaining a width of order 3–5 km. Early surveys from both experiments showed patchy distributions indicative of small-scale stirring at scales of order a few hundred meters. Later surveys show relatively smooth, coherent distributions with only occasional patchiness, suggestive of a diffusive rather than stirring process at the scales of the now larger patches. Together the two experiments provide important clues as to the rates and underlying processes driving diapycnal and isopycnal mixing at these scales.
    Description: 2020-08-06
    Keywords: Ocean ; Atlantic Ocean ; Diapycnal mixing ; Diffusion ; Dispersion ; Mixing
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  • 25
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    Improved statistical method for quality control of hydrographic observations (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 37(5), (2020): 789-806, doi:10.1175/JTECH-D-18-0244.1.
    Description: Realistic ocean state prediction and its validation rely on the availability of high quality in situ observations. To detect data errors, adequate quality check procedures must be designed. This paper presents procedures that take advantage of the ever-growing observation databases that provide climatological knowledge of the ocean variability in the neighborhood of an observation location. Local validity intervals are used to estimate binarily whether the observed values are considered as good or erroneous. Whereas a classical approach estimates validity bounds from first- and second-order moments of the climatological parameter distribution, that is, mean and variance, this work proposes to infer them directly from minimum and maximum observed values. Such an approach avoids any assumption of the parameter distribution such as unimodality, symmetry around the mean, peakedness, or homogeneous distribution tail height relative to distribution peak. To reach adequate statistical robustness, an extensive manual quality control of the reference dataset is critical. Once the data have been quality checked, the local minima and maxima reference fields are derived and the method is compared with the classical mean/variance-based approach. Performance is assessed in terms of statistics of good and bad detections. It is shown that the present size of the reference datasets allows the parameter estimates to reach a satisfactory robustness level to always make the method more efficient than the classical one. As expected, insufficient robustness persists in areas with an especially low number of samples and high variability.
    Description: This study has been conducted using EU Copernicus Marine Service Information and was supported by the European Union within the EU Copernicus Marine Service In Situ phase-I and phase-II contracts led by Ifremer. The publication was also supported by SOERE CTDO2 in France. The Argo data were collected and made freely available by the International Argo Program and the national programs that contribute to it (see http://www.argo.ucsd.edu, http://argo.jcommops.org). The Argo Program is part of the Global Ocean Observing System (http://doi.org/10.17882/42182). The marine mammal data were collected and made freely available by the International MEOP Consortium and the national programs that contribute to it (see http://www.meop.net; https://doi.org/10.17882/45461). Aleix Gelabert and Dídac Costa were the skippers of the OPOO, sponsored by the Intergovernmental Oceanographic Commission (UNESCO) and Pharmaton. The BWR is a periodic oceanic race organized by the Fundació Navegació Oceànica de Barcelona (FNOB). Reviewer D. Briand provided some useful comments on the final version of the draft paper before submission.
    Description: 2020-11-04
    Keywords: Ocean ; Climatology ; Salinity ; Temperature ; Data quality control ; Oceanic variability
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    Surface expression of a wall fountain: application to subglacial discharge plumes (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(5), (2020): 1245-1263, doi:10.1175/JPO-D-19-0213.1.
    Description: We use laboratory experiments and theoretical modeling to investigate the surface expression of a subglacial discharge plume, as occurs at many fjords around Greenland. The experiments consider a fountain that is released vertically into a homogeneous fluid, adjacent either to a vertical or a sloping wall, that then spreads horizontally at the free surface before sinking back to the bottom. We present a model that separates the fountain into two separate regions: a vertical fountain and a horizontal, negatively buoyant jet. The model is compared to laboratory experiments that are conducted over a range of volume fluxes, density differences, and ambient fluid depths. It is shown that the nondimensionalized length, width, and aspect ratio of the surface expression are dependent on the Froude number, calculated at the start of the negatively buoyant jet. The model is applied to observations of the surface expression from a Greenland subglacial discharge plume. In the case where the discharge plume reaches the surface with negative buoyancy the model can be used to estimate the discharge properties at the base of the glacier.
    Description: We gratefully acknowledge technical assistance from Anders Jensen and thank anonymous reviewers for improving the clarity of the manuscript. CM thanks the Weston Howard Jr. Scholarship for funding. Support to CC was given by NSF project OCE-1434041 and OCE-1658079.
    Description: 2020-10-27
    Keywords: Ocean ; Glaciers ; Ice sheets ; Convection ; Laboratory/physical models
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  • 27
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    Using the Helmholtz decomposition to define the Indian Ocean meridional overturning streamfunction (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(3), (2020): 679-694, doi:10.1175/JPO-D-19-0218.1.
    Description: The zonally integrated flow in a basin can be separated into the divergent/nondivergent parts, and a uniquely defined meridional overturning circulation (MOC) can be calculated. For a basin with significant volume exchange at zonal open boundaries, this method is competent in removing the components associated with the nonzero source terms due to zonal transports at open boundaries. This method was applied to the zonally integrated flow in the Indian Ocean basin extended all the way to the Antarctic by virtue of the ECCO dataset. The contributions due to two major zonal flow systems at open boundaries, the Indonesian Throughflow (ITF) and the Antarctic Circumpolar Current (ACC), were well separated from the rotational flow component, and a nondivergent overturning circulation pattern was identified. Comparisons with previous studies on the MOC of the Indian Ocean in different seasons showed overall consistency but with refinements in details to the south of the entry of the ITF, reflecting the influence of ITF on the MOC pattern in the domain. Other options of decomposition are also examined.
    Description: LH was supported by the National Basic Research Program of China through Grant 2019YFA0606703 and “The Fundamental Research Funds of Shandong University” (2019GN051). The authors thank the anonymous reviewers and the editor for their constructive comments. Code availability: The Matlab code that performs the decomposition and produces some figures in this paper is available at https://github.com/lei-han-SDU/IMOC/.
    Description: 2020-09-02
    Keywords: Meridional overturning circulation ; Ocean circulation ; Streamfunction
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  • 28
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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
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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    Potential vorticity dynamics of the arctic halocline (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(9), (2020): 2491-2506, doi:10.1175/JPO-D-20-0056.1.
    Description: An idealized two-layer shallow water model is applied to the study of the dynamics of the Arctic Ocean halocline. The model is forced by a surface stress distribution reflective of the observed wind stress pattern and ice motion and by an inflow representing the flow of Pacific Water through Bering Strait. The model reproduces the main elements of the halocline circulation: an anticyclonic Beaufort Gyre in the western basin (representing the Canada Basin), a cyclonic circulation in the eastern basin (representing the Eurasian Basin), and a Transpolar Drift between the two gyres directed from the upwind side of the basin to the downwind side of the basin. Analysis of the potential vorticity budget shows a basin-averaged balance primarily between potential vorticity input at the surface and dissipation at the lateral boundaries. However, advection is a leading-order term not only within the anticyclonic and cyclonic gyres but also between the gyres. This means that the eastern and western basins are dynamically connected through the advection of potential vorticity. Both eddy and mean fluxes play a role in connecting the regions of potential vorticity input at the surface with the opposite gyre and with the viscous boundary layers. These conclusions are based on a series of model runs in which forcing, topography, straits, and the Coriolis parameter were varied.
    Description: This study was supported by National Science Foundation Grant OPP-1822334. Comments and suggestions from two anonymous referees greatly helped to improve the paper.
    Description: 2021-02-17
    Keywords: Eddies ; Ekman pumping/transport ; Ocean circulation ; Ocean dynamics ; Potential vorticity ; Shallow-water equations
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    Tropical widening from global variations to regional impacts (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 101(6), (2020): E897-E904, doi:10.1175/BAMS-D-19-0047.1.
    Description: Over the past 15 years, numerous studies have suggested that the sinking branches of Earth’s Hadley circulation and the associated subtropical dry zones have shifted poleward over the late twentieth century and early twenty-first century. Early estimates of this tropical widening from satellite observations and reanalyses varied from 0.25° to 3° latitude per decade, while estimates from global climate models show widening at the lower end of the observed range. In 2016, two working groups, the U.S. Climate Variability and Predictability (CLIVAR) working group on the Changing Width of the Tropical Belt and the International Space Science Institute (ISSI) Tropical Width Diagnostics Intercomparison Project, were formed to synthesize current understanding of the magnitude, causes, and impacts of the recent tropical widening evident in observations. These working groups concluded that the large rates of observed tropical widening noted by earlier studies resulted from their use of metrics that poorly capture changes in the Hadley circulation, or from the use of reanalyses that contained spurious trends. Accounting for these issues reduces the range of observed expansion rates to 0.25°–0.5° latitude decade‒1—within the range from model simulations. Models indicate that most of the recent Northern Hemisphere tropical widening is consistent with natural variability, whereas increasing greenhouse gases and decreasing stratospheric ozone likely played an important role in Southern Hemisphere widening. Whatever the cause or rate of expansion, understanding the regional impacts of tropical widening requires additional work, as different forcings can produce different regional patterns of widening.
    Description: We thank U.S. CLIVAR and ISSI for funding the two working groups. We thank all members of the working groups for helpful discussions, and the U.S. CLIVAR and ISSI offices and their sponsoring agencies (NASA, NOAA, NSF, DOE, ESA, Swiss Confederation, Swiss Academy of Sciences, and University of Bern) for supporting these groups and activities.
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    The possession of coccoliths fails to deter microzooplankton grazers (2021)
    Frontiers Media
    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 Mayers, K. M. J., Poulton, A. J., Bidle, K., Thamatrakoln, K., Schieler, B., Giering, S. L. C., Wells, S. R., Tarran, G. A., Mayor, D., Johnson, M., Riebesell, U., Larsen, A., Vardi, A., & Harvey, E. L. The possession of coccoliths fails to deter microzooplankton grazers. Frontiers in Marine Science, 7, (2020): 562020, doi:10.3389/fmars.2020.569896.
    Description: Phytoplankton play a central role in the regulation of global carbon and nutrient cycles, forming the basis of the marine food webs. A group of biogeochemically important phytoplankton, the coccolithophores, produce calcium carbonate scales that have been hypothesized to deter or reduce grazing by microzooplankton. Here, a meta-analysis of mesocosm-based experiments demonstrates that calcification of the cosmopolitan coccolithophore, Emiliania huxleyi, fails to deter microzooplankton grazing. The median grazing to growth ratio for E. huxleyi (0.56 ± 0.40) was not significantly different among non-calcified nano- or picoeukaryotes (0.71 ± 0.31 and 0.55 ± 0.34, respectively). Additionally, the environmental concentration of E. huxleyi did not drive preferential grazing of non-calcified groups. These results strongly suggest that the possession of coccoliths does not provide E. huxleyi effective protection from microzooplankton grazing. Such indiscriminate consumption has implications for the dissolution and fate of CaCO3 in the ocean, and the evolution of coccoliths.
    Description: Mesocosm experiments in 2015 were supported by the Kiel Excellence Cluster “The Future Ocean” (CP1540) and the Leibniz Award to UR, in 2017 the MESOHUX experiment was supported by NSF (OCE-1559179) to KT and KB, NSF (OCE-1537951 and OCE-1459200) to KB, NSF (OCE-1459190, 1657808, and DBI-1624593) to EH, and in 2018 by AQUACOSM (EU H2020-INFRAIA-project No 731065). KM was supported by a NERC Doctoral Training Partnership (DTP) studentship as part of the Southampton Partnership for Innovative Training of Future Investigators Researching the Environment (SPITFIRE, grant number NE/L002531/1) and Research Council of Norway project (#280414) MIXsTRUCT.
    Keywords: coccolithophore ; phytoplankton ; microzooplankton ; biomineralisation ; predation ; evolution
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    Argo data 1999-2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats. (2020)
    Frontiers Media
    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 Wong, A. P. S., Wijffels, S. E., Riser, S. C., Pouliquen, S., Hosoda, S., Roemmich, D., Gilson, J., Johnson, G. C., Martini, K., Murphy, D. J., Scanderbeg, M., Bhaskar, T. V. S. U., Buck, J. J. H., Merceur, F., Carval, T., Maze, G., Cabanes, C., Andre, X., Poffa, N., Yashayaev, I., Barker, P. M., Guinehut, S., Belbeoch, M., Ignaszewski, M., Baringer, M. O., Schmid, C., Lyman, J. M., McTaggart, K. E., Purkey, S. G., Zilberman, N., Alkire, M. B., Swift, D., Owens, W. B., Jayne, S. R., Hersh, C., Robbins, P., West-Mack, D., Bahr, F., Yoshida, S., Sutton, P. J. H., Cancouet, R., Coatanoan, C., Dobbler, D., Juan, A. G., Gourrion, J., Kolodziejczyk, N., Bernard, V., Bourles, B., Claustre, H., D'Ortenzio, F., Le Reste, S., Le Traon, P., Rannou, J., Saout-Grit, C., Speich, S., Thierry, V., Verbrugge, N., Angel-Benavides, I. M., Klein, B., Notarstefano, G., Poulain, P., Velez-Belchi, P., Suga, T., Ando, K., Iwasaska, N., Kobayashi, T., Masuda, S., Oka, E., Sato, K., Nakamura, T., Sato, K., Takatsuki, Y., Yoshida, T., Cowley, R., Lovell, J. L., Oke, P. R., van Wijk, E. M., Carse, F., Donnelly, M., Gould, W. J., Gowers, K., King, B. A., Loch, S. G., Mowat, M., Turton, J., Rama Rao, E. P., Ravichandran, M., Freeland, H. J., Gaboury, I., Gilbert, D., Greenan, B. J. W., Ouellet, M., Ross, T., Tran, A., Dong, M., Liu, Z., Xu, J., Kang, K., Jo, H., Kim, S., & Park, H. Argo data 1999-2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats. Frontiers in Marine Science, 7, (2020): 700, doi:10.3389/fmars.2020.00700.
    Description: In the past two decades, the Argo Program has collected, processed, and distributed over two million vertical profiles of temperature and salinity from the upper two kilometers of the global ocean. A similar number of subsurface velocity observations near 1,000 dbar have also been collected. This paper recounts the history of the global Argo Program, from its aspiration arising out of the World Ocean Circulation Experiment, to the development and implementation of its instrumentation and telecommunication systems, and the various technical problems encountered. We describe the Argo data system and its quality control procedures, and the gradual changes in the vertical resolution and spatial coverage of Argo data from 1999 to 2019. The accuracies of the float data have been assessed by comparison with high-quality shipboard measurements, and are concluded to be 0.002°C for temperature, 2.4 dbar for pressure, and 0.01 PSS-78 for salinity, after delayed-mode adjustments. Finally, the challenges faced by the vision of an expanding Argo Program beyond 2020 are discussed.
    Description: AW, SR, and other scientists at the University of Washington (UW) were supported by the US Argo Program through the NOAA Grant NA15OAR4320063 to the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) at the UW. SW and other scientists at the Woods Hole Oceanographic Institution (WHOI) were supported by the US Argo Program through the NOAA Grant NA19OAR4320074 (CINAR/WHOI Argo). The Scripps Institution of Oceanography's role in Argo was supported by the US Argo Program through the NOAA Grant NA15OAR4320071 (CIMEC). Euro-Argo scientists were supported by the Monitoring the Oceans and Climate Change with Argo (MOCCA) project, under the Grant Agreement EASME/EMFF/2015/1.2.1.1/SI2.709624 for the European Commission.
    Keywords: global ; ocean ; pressure ; temperature ; salinity ; Argo ; profiling ; floats
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    Bifurcation and upwelling of the equatorial undercurrent west of the Galapagos Archipelago (2020)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(4), (2020): 887-905, doi:10.1175/JPO-D-19-0110.1.
    Description: The Equatorial Undercurrent (EUC) encounters the Galápagos Archipelago on the equator as it flows eastward across the Pacific. The impact of the Galápagos Archipelago on the EUC in the eastern equatorial Pacific remains largely unknown. In this study, the path of the EUC as it reaches the Galápagos Archipelago is measured directly using high-resolution observations obtained by autonomous underwater gliders. Gliders were deployed along three lines that define a closed region with the Galápagos Archipelago as the eastern boundary and 93°W from 2°S to 2°N as the western boundary. Twelve transects were simultaneously occupied along the three lines during 52 days in April–May 2016. Analysis of individual glider transects and average sections along each line show that the EUC splits around the Galápagos Archipelago. Velocity normal to the transects is used to estimate net horizontal volume transport into the volume. Downward integration of the net horizontal transport profile provides an estimate of the time- and areal-averaged vertical velocity profile over the 52-day time period. Local maxima in vertical velocity occur at depths of 25 and 280 m with magnitudes of (1.7 ± 0.6) × 10−5 m s−1 and (8.0 ± 1.6) × 10−5 m s−1, respectively. Volume transport as a function of salinity indicates that water crossing 93°W south (north) of 0.4°S tends to flow around the south (north) side of the Galápagos Archipelago. Comparisons are made between previous observational and modeling studies with differences attributed to effects of the strong 2015/16 El Niño event, the annual cycle of local winds, and varying longitudes between studies of the equatorial Pacific.
    Description: This work was supported by National Science Foundation (Grants OCE-1232971 and OCE-1233282) and the NASA Earth and Space Science Fellowship Program (Grant 80NSSC17K0443).
    Keywords: Tropics ; Boundary currents ; Topographic effects ; Transport ; Upwelling/downwelling ; In situ oceanic observations
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  • 34
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    Mean conditions and seasonality of the West Greenland boundary current system near Cape Farewell (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(10), (2020): 2849-2871, https://doi.org/10.1175/JPO-D-20-0086.1.
    Description: The structure, transport, and seasonal variability of the West Greenland boundary current system near Cape Farewell are investigated using a high-resolution mooring array deployed from 2014 to 2018. The boundary current system is comprised of three components: the West Greenland Coastal Current, which advects cold and fresh Upper Polar Water (UPW); the West Greenland Current, which transports warm and salty Irminger Water (IW) along the upper slope and UPW at the surface; and the Deep Western Boundary Current, which advects dense overflow waters. Labrador Sea Water (LSW) is prevalent at the seaward side of the array within an offshore recirculation gyre and at the base of the West Greenland Current. The 4-yr mean transport of the full boundary current system is 31.1 ± 7.4 Sv (1 Sv ≡ 106 m3 s−1), with no clear seasonal signal. However, the individual water mass components exhibit seasonal cycles in hydrographic properties and transport. LSW penetrates the boundary current locally, through entrainment/mixing from the adjacent recirculation gyre, and also enters the current upstream in the Irminger Sea. IW is modified through air–sea interaction during winter along the length of its trajectory around the Irminger Sea, which converts some of the water to LSW. This, together with the seasonal increase in LSW entering the current, results in an anticorrelation in transport between these two water masses. The seasonality in UPW transport can be explained by remote wind forcing and subsequent adjustment via coastal trapped waves. Our results provide the first quantitatively robust observational description of the boundary current in the eastern Labrador Sea.
    Description: A.P., R.S.P., F.B., D.J.T., and A.L.R. were funded by Grants OCE-1259618 and OCE-1756361 from the National Science Foundation. I.L.B, F.S., and J.H. were supported by U.S. National Science Foundation Grants OCE-1258823 and OCE-1756272. Mooring data from MA2 was funded by the European Union 7th Framework Programme (FP7 2007-2013) under Grant 308299 (NACLIM) and the Horizon 2020 research and innovation program under Grant 727852 (Blue-Action). J.K. and M.O. acknowledge EU Horizon 2020 funding Grants 727852 (Blue-action) and 862626 (EuroSea) and from the German Ministry of Research and Education (RACE Program). G.W.K.M. acknowledges funding from the Natural Sciences and Engineering Research Council.
    Keywords: Boundary currents ; Convection ; Deep convection ; Transport ; In situ oceanic observations ; Seasonal cycle
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  • 35
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    Coherent pathways for vertical transport from the Surface Ocean to Interior (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 101(11), (2020): E1996-E2004, https://doi.org/10.1175/BAMS-D-19-0305.1.
    Description: A long-standing challenge in oceanography is the observing, modeling, and prediction of vertical transport, which links the sunlit and atmospherically mediated surface boundary layer with the deeper ocean. Vertical motions play a critical role in the exchange of heat, freshwater, and biogeochemical tracers between the surface and the ocean interior. The most intense vertical velocities occur at horizontal scales less than 10 km, making them difficult to observe in the ocean and to resolve in models. Understanding how finescale turbulent motions and 0.1–10 km submesoscale processes contribute to the large-scale budgets of nutrients, oxygen, carbon, and heat and affect sea surface temperature, the air–sea exchange of gases, and the carbon cycle is one of the key challenges in oceanography.
    Description: CALYPSO is a Departmental Research Initiative (DRI) funded by the U.S. Office of Naval Research (ONR). It is a collaborative program involving more than 30 scientists and students and multiple institutions in the United States, Spain, and Italy. Measurements were conducted from the NRV Alliance, Pourquoi Pas?, and SOCIB. We are grateful to the captains and crews of these research vessels and the technical and scientific staff involved in making measurements, running models, analyzing data, and providing support.
    Description: 2021-05-01
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    Assessment of numerical simulations of deep circulation and variability in the Gulf of Mexico using recent observations (2020)
    American Meteorological Society
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    Publication Date: 2022-05-26
    Description: Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(4), (2020): 1045-1064, doi:10.1175/JPO-D-19-0137.1.
    Description: Three simulations of the circulation in the Gulf of Mexico (the “Gulf”) using different numerical general circulation models are compared with results of recent large-scale observational campaigns conducted throughout the deep (〉1500 m) Gulf. Analyses of these observations have provided new understanding of large-scale mean circulation features and variability throughout the deep Gulf. Important features include cyclonic flow along the continental slope, deep cyclonic circulation in the western Gulf, a counterrotating pair of cells under the Loop Current region, and a cyclonic cell to the south of this pair. These dominant circulation features are represented in each of the ocean model simulations, although with some obvious differences. A striking difference between all the models and the observations is that the simulated deep eddy kinetic energy under the Loop Current region is generally less than one-half of that computed from observations. A multidecadal integration of one of these numerical simulations is used to evaluate the uncertainty of estimates of velocity statistics in the deep Gulf computed from limited-length (4 years) observational or model records. This analysis shows that the main deep circulation features identified from the observational studies appear to be robust and are not substantially impacted by variability on time scales longer than the observational records. Differences in strengths and structures of the circulation features are identified, however, and quantified through standard error analysis of the statistical estimates using the model solutions.
    Description: This work was supported by the Gulf Research Program of the National Academy of Sciences under Awards 2000006422 and 2000009966. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Gulf Research Program or the National Academy of Sciences. The authors acknowledge the GLORYS project for providing the ocean reanalysis data used in the ROMS simulation. GLORYS is jointly conducted by MERCATOR OCEAN, CORIOLIS, and CNRS/INSU. Installation, recovery, data acquisition, and processing of the CANEK group current-meter moorings were possible because of CICESE-PetróleosMexicanos Grant PEP-CICESE 428229851 and the dedicated work of the crew of the B/O Justo Sierra and scientists of the CANEK group. The authors thank Dr. Aljaz Maslo, CICESE, for assistance with analysis of model data. The Bureau of Ocean Energy Management (BOEM), U.S. Dept. of the Interior, provided funding for the Lagrangian Study of the Deep Circulation in the Gulf of Mexico and the Observations and Dynamics of the Loop Current study. HYCOM simulation data are available from the HYCOM data server (https://www.hycom.org/data/goml0pt04/expt-02pt2), MITgcm data are available from the ECCO data server (http://ecco.ucsd.edu/gom_results2.html), and the ROMS simulation data are available from GRIIDC (NA.x837.000:0001).
    Keywords: Ocean circulation ; Abyssal circulation ; Bottom currents/bottom water ; Eddies ; Ocean models
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    Male alternative reproductive tactics and associated evolution of anatomical characteristics in loliginid squid (2020)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marian, J. E. A. R., Apostólico, L. H., Chiao, C. C., Hanlon, R. T., Hirohashi, N., Iwata, Y., Mather, J., Sato, N., & Shaw, P. W. Male alternative reproductive tactics and associated evolution of anatomical characteristics in loliginid squid. Frontiers in Physiology, 10, (2019): 1281, doi: 10.3389/fphys.2019.01281.
    Description: Loliginid squids provide a unique model system to explore male alternative reproductive tactics (ARTs) and their linkage to size, behavioral decision making, and possibly age. Large individuals fight one another and the winners form temporary consortships with females, while smaller individuals do not engage in male-male agonistic bouts but use various sneaker tactics to obtain matings, each with varying mating and fertilization success. There is substantial behavioral flexibility in most species, as smaller males can facultatively switch to the alternative consort behaviors as the behavioral context changes. These forms of ARTs can involve different: mating posture; site of spermatophore deposition; fertilization success; and sperm traits. Most of the traits of male dimorphism (both anatomical and behavioral) are consistent with traditional sexual selection theory, while others have unique features that may have evolved in response to the fertilization environment faced by each temporary or permanent male morph.
    Description: JM acknowledges the funding provided by FAPESP (São Paulo Research Foundation – proc. 2013/02653-1, 2014/11008-5, 2015/15447-6, 2017/16182-1, and 2018/19180-2), CNPq (National Council for Scientific and Technological Development – proc. 477233/2013–9), and CAPES (Coordination for the Improvement of Higher Education Personnel – Finance Code 001).
    Keywords: Sexual selection ; Alternative phenotypes ; ARTs ; ale dimorphism ; Consort ; Sneaker ; Cephalopoda ; Loliginidae
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    α-Synuclein-112 impairs synaptic vesicle recycling consistent with its enhanced membrane binding properties (2020)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Soll, L. G., Eisen, J. N., Vargas, K. J., Medeiros, A. T., Hammar, K. M., & Morgan, J. R. α-Synuclein-112 impairs synaptic vesicle recycling consistent with its enhanced membrane binding properties. Frontiers in Cell and Developmental Biology, 8, (2020): 405, doi:10.3389/fcell.2020.00405.
    Description: Synucleinopathies are neurological disorders associated with α-synuclein overexpression and aggregation. While it is well-established that overexpression of wild type α-synuclein (α-syn-140) leads to cellular toxicity and neurodegeneration, much less is known about other naturally occurring α-synuclein splice isoforms. In this study we provide the first detailed examination of the synaptic effects caused by one of these splice isoforms, α-synuclein-112 (α-syn-112). α-Syn-112 is produced by an in-frame excision of exon 5, resulting in deletion of amino acids 103–130 in the C-terminal region. α-Syn-112 is upregulated in the substantia nigra, frontal cortex, and cerebellum of parkinsonian brains and higher expression levels are correlated with susceptibility to Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple systems atrophy (MSA). We report here that α-syn-112 binds strongly to anionic phospholipids when presented in highly curved liposomes, similar to α-syn-140. However, α-syn-112 bound significantly stronger to all phospholipids tested, including the phosphoinositides. α-Syn-112 also dimerized and trimerized on isolated synaptic membranes, while α-syn-140 remained largely monomeric. When introduced acutely to lamprey synapses, α-syn-112 robustly inhibited synaptic vesicle recycling. Interestingly, α-syn-112 produced effects on the plasma membrane and clathrin-mediated synaptic vesicle endocytosis that were phenotypically intermediate between those caused by monomeric and dimeric α-syn-140. These findings indicate that α-syn-112 exhibits enhanced phospholipid binding and oligomerization in vitro and consequently interferes with synaptic vesicle recycling in vivo in ways that are consistent with its biochemical properties. This study provides additional evidence suggesting that impaired vesicle endocytosis is a cellular target of excess α-synuclein and advances our understanding of potential mechanisms underlying disease pathogenesis in the synucleinopathies.
    Description: This study was supported by a research grant from the National Institutes of Health (NIH NINDS/NIA R01 NS078165 to JM), as well as research funds from the Marine Biological Laboratory (to JM).
    Keywords: Clathrin ; Endocytosis ; Lamprey ; Phosphoinositide ; Synapse ; Synuclein ; Synaptic vesicle recycling
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    Modeling nitrous oxide emissions from large-scale intensive cropping systems in the southern Amazon (2022)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Costa Jr, C., Galford, G. L., Coe, M. T., Macedo, M., Jankowski, K., O’Connell, C., & Neill, C. Modeling nitrous oxide emissions from large-scale intensive cropping systems in the southern Amazon. Frontiers in Sustainable Food Systems, 5, (2021): 701416. https://doi.org/10.3389/fsufs.2021.701416.
    Description: Nitrogen (N) fertilizer use is rapidly intensifying on tropical croplands and has the potential to increase emissions of the greenhouse gas, nitrous oxide (N2O). Since about 2005 Mato Grosso (MT), Brazil has shifted from single-cropped soybeans to double-cropping soybeans with maize, and now produces 1.5% of the world's maize. This production shift required an increase in N fertilization, but the effects on N2O emissions are poorly known. We calibrated the process-oriented biogeochemical DeNitrification-DeComposition (DNDC) model to simulate N2O emissions and crop production from soybean and soybean-maize cropping systems in MT. After model validation with field measurements and adjustments for hydrological properties of tropical soils, regional simulations suggested N2O emissions from soybean-maize cropland increased almost fourfold during 2001–2010, from 1.1 ± 1.1 to 4.1 ± 3.2 Gg 1014 N-N2O. Model sensitivity tests showed that emissions were spatially and seasonably variable and especially sensitive to soil bulk density and carbon content. Meeting future demand for maize using current soybean area in MT might require either (a) intensifying 3.0 million ha of existing single soybean to soybean-maize or (b) increasing N fertilization to ~180 kg N ha−1 on existing 2.3 million ha of soybean-maize area. The latter strategy would release ~35% more N2O than the first. Our modifications of the DNDC model will improve estimates of N2O emissions from agricultural production in MT and other tropical areas, but narrowing model uncertainty will depend on more detailed field measurements and spatial data on soil and cropping management.
    Description: This work was supported by National Science Foundation (NSF#1257944) and CNPq-Ciências Sem Fronteiras Post-Doctoral Fellowship (249380/2013-7).
    Keywords: GHG emission ; Agriculture ; Nitrogen fertilization management ; Amazon ; Food system
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    Defined tau phosphospecies differentially inhibit fast axonal transport through activation of two independent signaling pathways (2021)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Morris, S. L., Tsai, M., Aloe, S., Bechberger, K., Konig, S., Morfini, G., & Brady, S. T. Defined tau phosphospecies differentially inhibit fast axonal transport through activation of two independent signaling pathways. Frontiers in Molecular Neuroscience, 13, (2021): 610037, https://doi.org/10.3389/fnmol.2020.610037.
    Description: Tau protein is subject to phosphorylation by multiple kinases at more than 80 different sites. Some of these sites are associated with tau pathology and neurodegeneration, but other sites are modified in normal tau as well as in pathological tau. Although phosphorylation of tau at residues in the microtubule-binding repeats is thought to reduce tau association with microtubules, the functional consequences of other sites are poorly understood. The AT8 antibody recognizes a complex phosphoepitope site on tau that is detectable in a healthy brain but significantly increased in Alzheimer’s disease (AD) and other tauopathies. Previous studies showed that phosphorylation of tau at the AT8 site leads to exposure of an N-terminal sequence that promotes activation of a protein phosphatase 1 (PP1)/glycogen synthase 3 (GSK3) signaling pathway, which inhibits kinesin-1-based anterograde fast axonal transport (FAT). This finding suggests that phosphorylation may control tau conformation and function. However, the AT8 includes three distinct phosphorylated amino acids that may be differentially phosphorylated in normal and disease conditions. To evaluate the effects of specific phosphorylation sites in the AT8 epitope, recombinant, pseudophosphorylated tau proteins were perfused into the isolated squid axoplasm preparation to determine their effects on axonal signaling pathways and FAT. Results from these studies suggest a mechanism where specific phosphorylation events differentially impact tau conformation, promoting activation of independent signaling pathways that differentially affect FAT. Implications of findings here to our understanding of tau function in health and disease conditions are discussed.
    Description: This research was funded by NIH grants R21NS096642 (GM); 1R01NS118177-01A1 (GM), R01 NS082730 (SB), a Zenith Award from the Alzheimer’s Association (SB), and a grant from the Tau Consortium/Rainwater Foundation (SB).
    Keywords: Tau phosphorylation ; Fast axonal transport ; Signal transduction ; GSK3 ; JNK ; PP1
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    Atmospheric and oceanographic forcing impact particle flux composition and carbon sequestration in the eastern Mediterranean Sea: a three-year time-series study in the deep Ierapetra Basin (2021)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pedrosa-Pamies, R., Parinos, C., Sanchez-Vidal, A., Calafat, A., Canals, M., Velaoras, D., Mihalopoulos, N., Kanakidou, M., Lampadariou, N., & Gogou, A. Atmospheric and oceanographic forcing impact particle flux composition and carbon sequestration in the eastern Mediterranean Sea: a three-year time-series study in the deep Ierapetra Basin. Frontiers in Earth Science, 9, (2021): 591948, https://doi.org/10.3389/feart.2021.591948.
    Description: Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling, little is known about the biotic composition and seasonal variability of sinking particles reaching abyssal depths. Herein, sinking particle flux data, collected in the deep Ierapetra Basin for a three-year period (June 2010 to June 2013), have been examined at the light of atmospheric and oceanographic parameters and main mass components (lithogenic, opal, carbonates, nitrogen, and organic carbon), stable isotopes of particulate organic carbon (POC) and source-specific lipid biomarkers. Our aim is to improve the current understanding of the dynamics of particle fluxes and the linkages between atmospheric dynamics and ocean biogeochemistry shaping the export of organic matter in the deep Eastern Mediterranean Sea. Overall, particle fluxes showed seasonality and interannual variability over the studied period. POC fluxes peaked in spring April–May 2012 (12.2 mg m−2 d−1) related with extreme atmospheric forcing. Summer export was approximately fourfold higher than mean wintertime, fall and springtime (except for the episodic event of spring 2012), fueling efficient organic carbon sequestration. Lipid biomarkers indicate a high relative contribution of natural and anthropogenic, marine- and land-derived POC during both spring (April–May) and summer (June–July) reaching the deep-sea floor. Moreover, our results highlight that both seasonal and episodic pulses are crucial for POC export, while the coupling of extreme weather events and atmospheric deposition can trigger the influx of both marine labile carbon and anthropogenic compounds to the deep Levantine Sea. Finally, the comparison of time series data of sinking particulate flux with the corresponding biogeochemical parameters data previously reported for surface sediment samples from the deep-sea shed light on the benthic–pelagic coupling in the study area. Thus, this study underscores that accounting the seasonal and episodic pulses of organic carbon into the deep sea is critical in modeling the depth and intensity of natural and anthropogenic POC sequestration, and for a better understanding of the global carbon cycle.
    Description: This research was supported by the REDECO (CTM2008-04973-E/MAR) and PERSEUS (GA 287600) projects. We further acknowledge support by the projects PANACEA—‘PANhellenic infrastructure for Atmospheric Composition and climatE chAnge’ (MIS 5021516) and ENIRISST—‘Intelligent Research Infrastructure for Shipping, Supply Chain, Transport and Logistics’ (MIS 5027930), which are implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020) and co-financed by Greece and EU; and by the Action “National Νetwork on Climate Change and its Impacts - Climpact” which is implemented under the sub-project 3 of the project “Infrastructure of national research networks in the fields of Precision Medicine, Quantum Technology and Climate Change,” funded by the Public Investment Program of Greece, General Secretary of Research and Technology/Ministry of Development and Investments.” Researchers from GRC Geociències Marines benefited from a Grups de Recerca Consolidats grant (2017 SGR 315) by Generalitat de Catalunya autonomous government.
    Keywords: Sinking particle fluxes ; Carbon cycle ; Lipid biomarkers ; Atmospheric forcing ; Eastern mediterranean sea ; Surface sediment ; Deep ocean ; Particulate organic carbon
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    Modeling marsh dynamics using a 3-D coupled wave-flow-sediment model (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kalra, T. S., Ganju, N. K., Aretxabaleta, A. L., Carr, J. A., Defne, Z., & Moriarty, J. M. Modeling marsh dynamics using a 3-D coupled wave-flow-sediment model. Frontiers in Marine Science, 8, (2021): 740921, https://doi.org/10.3389/fmars.2021.740921.
    Description: Salt marshes are dynamic biogeomorphic systems that respond to external physical factors, including tides, sediment transport, and waves, as well as internal processes such as autochthonous soil formation. Predicting the fate of marshes requires a modeling framework that accounts for these processes in a coupled fashion. In this study, we implement two new marsh dynamic processes in the 3-D COAWST (coupled-ocean-atmosphere-wave sediment transport) model. The processes added are the erosion of the marsh edge scarp caused by lateral wave thrust from surface waves and vertical accretion driven by biomass production on the marsh platform. The sediment released from the marsh during edge erosion causes a change in bathymetry, thereby modifying the wave-energy reaching the marsh edge. Marsh vertical accretion due to biomass production is considered for a single vegetation species and is determined by the hydroperiod parameters (tidal datums) and the elevation of the marsh cells. Tidal datums are stored at user-defined intervals as a hindcast (on the order of days) and used to update the vertical growth formulation. Idealized domains are utilized to verify the lateral wave thrust formulation and show the dynamics of lateral wave erosion leading to horizontal retreat of marsh edge. The simulations of Reedy and Dinner Creeks within the Barnegat Bay estuary system demonstrate the model capability to account for both lateral wave erosion and vertical accretion due to biomass production in a realistic marsh complex. The simulations show that vertical accretion is dominated by organic deposition in the marsh interior, whereas deposition of mineral estuarine sediments occurs predominantly along the channel edges. The ability of the model to capture the fate of the sediment can be extended to model to simulate the impacts of future storms and relative sea-level rise (RSLR) scenarios on salt-marsh ecomorphodynamics.
    Description: This work was supported by USGS Coastal and Marine Hazards and Resources Program.
    Keywords: Marsh morphology ; Sediment transport ; Numerical model ; COAWST model ; Marsh accretion
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    Recent nitrogen storage and accumulation rates in mangrove soils exceed historic rates in the urbanized San Juan Bay Estuary (Puerto Rico, United States) (2022)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wigand, C., Oczkowski, A. J., Branoff, B. L., Eagle, M., Hanson, A., Martin, R. M., Balogh, S., Miller, K. M., Huertas, E., Loffredo, J., & Watson, E. B. Recent nitrogen storage and accumulation rates in mangrove soils exceed historic rates in the urbanized San Juan Bay Estuary (Puerto Rico, United States). Frontiers in Forests and Global Change, 4, (2021): 765896, https://doi.org/10.3389/ffgc.2021.765896.
    Description: Tropical mangrove forests have been described as “coastal kidneys,” promoting sediment deposition and filtering contaminants, including excess nutrients. Coastal areas throughout the world are experiencing increased human activities, resulting in altered geomorphology, hydrology, and nutrient inputs. To effectively manage and sustain coastal mangroves, it is important to understand nitrogen (N) storage and accumulation in systems where human activities are causing rapid changes in N inputs and cycling. We examined N storage and accumulation rates in recent (1970 – 2016) and historic (1930 – 1970) decades in the context of urbanization in the San Juan Bay Estuary (SJBE, Puerto Rico), using mangrove soil cores that were radiometrically dated. Local anthropogenic stressors can alter N storage rates in peri-urban mangrove systems either directly by increasing N soil fertility or indirectly by altering hydrology (e.g., dredging, filling, and canalization). Nitrogen accumulation rates were greater in recent decades than historic decades at Piñones Forest and Martin Peña East. Martin Peña East was characterized by high urbanization, and Piñones, by the least urbanization in the SJBE. The mangrove forest at Martin Peña East fringed a poorly drained canal and often received raw sewage inputs, with N accumulation rates ranging from 17.7 to 37.9 g m–2 y–1 in recent decades. The Piñones Forest was isolated and had low flushing, possibly exacerbated by river damming, with N accumulation rates ranging from 18.6 to 24.2 g m–2 y–1 in recent decades. Nearly all (96.3%) of the estuary-wide mangrove N (9.4 Mg ha–1) was stored in the soils with 7.1 Mg ha–1 sequestered during 1970–2017 (0–18 cm) and 2.3 Mg ha–1 during 1930–1970 (19–28 cm). Estuary-wide mangrove soil N accumulation rates were over twice as great in recent decades (0.18 ± 0.002 Mg ha–1y–1) than historically (0.08 ± 0.001 Mg ha–1y–1). Nitrogen accumulation rates in SJBE mangrove soils in recent times were twofold larger than the rate of human-consumed food N that is exported as wastewater (0.08 Mg ha–1 y–1), suggesting the potential for mangroves to sequester human-derived N. Conservation and effective management of mangrove forests and their surrounding watersheds in the Anthropocene are important for maintaining water quality in coastal communities throughout tropical regions.
    Description: Some funding was provided by the United States Geological Coastal and Marine Hazards and Resources Program.
    Keywords: Nitrogen storage ; Nitrogen accumulation ; Mangrove forest ; Wastewater ; Anthropogenic stressors ; Peri-urban mangrove ; Urbanization
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    NLRP3 inflammasome assembly in neutrophils is supported by PAD4 and promotes NETosis under sterile conditions (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Muenzer, P., Negro, R., Fukui, S., di Meglio, L., Aymonnier, K., Chu, L., Cherpokova, D., Gutch, S., Sorvillo, N., Shi, L., Magupalli, V. G., Weber, A. N. R., Scharf, R. E., Waterman, C. M., Wu, H., & Wagner, D. D. NLRP3 inflammasome assembly in neutrophils is supported by PAD4 and promotes NETosis under sterile conditions. Frontiers in Immunology, 12, (2021): 683803, https://doi.org/10.3389/fimmu.2021.683803.
    Description: Neutrophil extracellular trap formation (NETosis) and the NLR family pyrin domain containing 3 (NLRP3) inflammasome assembly are associated with a similar spectrum of human disorders. While NETosis is known to be regulated by peptidylarginine deiminase 4 (PAD4), the role of the NLRP3 inflammasome in NETosis was not addressed. Here, we establish that under sterile conditions the cannonical NLRP3 inflammasome participates in NETosis. We show apoptosis-associated speck-like protein containing a CARD (ASC) speck assembly and caspase-1 cleavage in stimulated mouse neutrophils without LPS priming. PAD4 was needed for optimal NLRP3 inflammasome assembly by regulating NLRP3 and ASC protein levels post-transcriptionally. Genetic ablation of NLRP3 signaling resulted in impaired NET formation, because NLRP3 supported both nuclear envelope and plasma membrane rupture. Pharmacological inhibition of NLRP3 in either mouse or human neutrophils also diminished NETosis. Finally, NLRP3 deficiency resulted in a lower density of NETs in thrombi produced by a stenosis-induced mouse model of deep vein thrombosis. Altogether, our results indicate a PAD4-dependent formation of the NLRP3 inflammasome in neutrophils and implicate NLRP3 in NETosis under noninfectious conditions in vitro and in vivo.
    Description: This work was supported by a grant from National Heart, Lung, and Blood Institute of the National Institutes of Health (grant R35 HL135765) and a Steven Berzin family support to DDW, an Individual Erwin Deutsch fellowship by the German, Austrian and Swiss Society of Thrombosis and Hemostasis Research to RES, a Whitman fellowship (MBL) to DDW, and an Individual Marie Skłodowska-Curie Actions fellowship by the European Commission (796365 - COAGULANT) to PM. ANRW was funded by the Deutsche Forschungsgemeinschaft (TRR156/2 –246807620) and a research grant (We-4195/15-19). CMW was supported by the Division of Intramural Research, NHLBI, NIH.
    Keywords: Neutrophils ; NETs ; NLRP3 inflammasome ; MCC950 ; Deep vein thrombosis ; PAD4
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    Synuclein regulates synaptic vesicle clustering and docking at a vertebrate synapse (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fouke, K. E., Wegman, M. E., Weber, S. A., Brady, E. B., Roman-Vendrell, C., & Morgan, J. R. Synuclein regulates synaptic vesicle clustering and docking at a vertebrate synapse. Frontiers in Cell and Developmental Biology, 9, (2021): 774650, https://doi.org/10.3389/fcell.2021.774650.
    Description: Neurotransmission relies critically on the exocytotic release of neurotransmitters from small synaptic vesicles (SVs) at the active zone. Therefore, it is essential for neurons to maintain an adequate pool of SVs clustered at synapses in order to sustain efficient neurotransmission. It is well established that the phosphoprotein synapsin 1 regulates SV clustering at synapses. Here, we demonstrate that synuclein, another SV-associated protein and synapsin binding partner, also modulates SV clustering at a vertebrate synapse. When acutely introduced to unstimulated lamprey reticulospinal synapses, a pan-synuclein antibody raised against the N-terminal domain of α-synuclein induced a significant loss of SVs at the synapse. Both docked SVs and the distal reserve pool of SVs were depleted, resulting in a loss of total membrane at synapses. In contrast, antibodies against two other abundant SV-associated proteins, synaptic vesicle glycoprotein 2 (SV2) and vesicle-associated membrane protein (VAMP/synaptobrevin), had no effect on the size or distribution of SV clusters. Synuclein perturbation caused a dose-dependent reduction in the number of SVs at synapses. Interestingly, the large SV clusters appeared to disperse into smaller SV clusters, as well as individual SVs. Thus, synuclein regulates clustering of SVs at resting synapses, as well as docking of SVs at the active zone. These findings reveal new roles for synuclein at the synapse and provide critical insights into diseases associated with α-synuclein dysfunction, such as Parkinson’s disease.
    Description: Funding support for this project was provided by the National Institutes of Health NINDS/NIA R01 NS078165 (to JM); University of Chicago Jeff Metcalf Fellowship Grant (to SW).
    Keywords: Exocytosis ; Endocytosis ; Synapsin ; Lamprey ; Liquid phase separation ; VAMP2
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    Survival and axonal outgrowth of the Mauthner cell following spinal cord crush does not drive post-injury startle responses (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zottoli, S. J., Faber, D. S., Hering, J., Dannhauer, A. C., & Northen, S. Survival and axonal outgrowth of the Mauthner cell following spinal cord crush does not drive post-injury startle responses. Frontiers in Cell and Developmental Biology, 9, (2021): 744191, https://doi.org/10.3389/fcell.2021.744191.
    Description: A pair of Mauthner cells (M-cells) can be found in the hindbrain of most teleost fish, as well as amphibians and lamprey. The axons of these reticulospinal neurons cross the midline and synapse on interneurons and motoneurons as they descend the length of the spinal cord. The M-cell initiates fast C-type startle responses (fast C-starts) in goldfish and zebrafish triggered by abrupt acoustic/vibratory stimuli. Starting about 70 days after whole spinal cord crush, less robust startle responses with longer latencies manifest in adult goldfish, Carassius auratus. The morphological and electrophysiological identifiability of the M-cell provides a unique opportunity to study cellular responses to spinal cord injury and the relation of axonal regrowth to a defined behavior. After spinal cord crush at the spinomedullary junction about one-third of the damaged M-axons of adult goldfish send at least one sprout past the wound site between 56 and 85 days postoperatively. These caudally projecting sprouts follow a more lateral trajectory relative to their position in the fasciculus longitudinalis medialis of control fish. Other sprouts, some from the same axon, follow aberrant pathways that include rostral projections, reversal of direction, midline crossings, neuromas, and projection out the first ventral root. Stimulating M-axons in goldfish that had post-injury startle behavior between 198 and 468 days postoperatively resulted in no or minimal EMG activity in trunk and tail musculature as compared to control fish. Although M-cells can survive for at least 468 day (∼1.3 years) after spinal cord crush, maintain regrowth, and elicit putative trunk EMG responses, the cell does not appear to play a substantive role in the emergence of acoustic/vibratory-triggered responses. We speculate that aberrant pathway choice of this neuron may limit its role in the recovery of behavior and discuss structural and functional properties of alternative candidate neurons that may render them more supportive of post-injury startle behavior.
    Description: Support for this research came in part from NSF grant (BNS 8809445), NIH grant (2-P01-NS24707-09), and HHMI and Essel Foundation grants to Williams College.
    Keywords: Spinal cord regeneration ; Functional recovery ; Startle responses ; Mauthner cells ; Adult goldfish
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    Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ruff, S. E. Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers. Frontiers in Microbiology, 12, (2022): 802619, https://doi.org/10.3389/fmicb.2021.802619.
    Description: Most organic matter on Earth occurs in the form of macromolecules and complex biopolymers, which include the building blocks of every organism. Plant, animal, fungal, and microbial cells largely consist of macromolecules belonging to four compound classes: proteins, polysaccharides, nucleic acids, and lipids (Figure 1). The percentage of these compounds per dry weight can vary greatly between lineages, but also between individuals of the same species or developmental stages of the same organism. Living and lysing cells release a substantial quantity and variety of macromolecules to the environment. These compounds often contain nitrogen, phosphorus, and sulfur, in addition to carbon, and are thus ideal food sources for heterotrophic organisms. Although the degradation of biopolymers and macromolecules has received considerable attention, many knowledge gaps remain, particularly in very complex ecosystems such as soils and sediments.
    Keywords: Macromolecule ; Necromass ; Heterotrophic microorganism ; Protein ; Polysaccharide ; Carbohydrate ; Nucleic acid ; Lipid
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    Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Klein, S., Frazier, V., Readdean, T., Lucas, E., Diaz-Jimenez, E. P., Sogin, M., Ruff, E. S., & Echeverri, K. Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont. Frontiers in Ecology and Evolution, 9, (2021): 786037, https://doi.org/10.3389/fevo.2021.786037.
    Description: The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environments coupled with its genetic tractability render Nematostella a powerful model organism in which to study the effects of common pollutants on the natural development of these animals. Potassium nitrate, commonly used in fertilizers, and Phthalates, a component of plastics are frequent environmental stressors found in coastal and marsh waters. Here we present data showing how early exposure to these pollutants lead to dramatic defects in development of the embryos and eventual mortality possibly due to defects in feeding ability. Additionally, we examined the microbiome of the animals and identified shifts in the microbial community that correlated with the type of water that was used to grow the animals, and with their exposure to pollutants.
    Description: This work was funded by a Pilot Program award to ER and KE from the Microbiome Center at the University of Chicago. The microbiome sequencing was funded by a grant from the McDonnell Initiative to ER. KE was supported by a grant from NICHD R01 HD092451, start-up funds from the MBL and funding from the Owens Family Foundation. ER was supported by start-up funds from the MBL and MLS receives support from the Unger G. Vetlesen Foundation.
    Keywords: Nematostella ; Growth ; Microbiome ; Stressors ; Development
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    Activating transcription factor 3 (ATF3) is a highly conserved pro-regenerative transcription factor in the vertebrate nervous system (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Katz, H. R., Arcese, A. A., Bloom, O., & Morgan, J. R. Activating transcription factor 3 (ATF3) is a highly conserved pro-regenerative transcription factor in the vertebrate nervous system. Frontiers in Cell and Developmental Biology, 10, (2022): 824036, https://doi.org/10.3389/fcell.2022.824036.
    Description: The vertebrate nervous system exhibits dramatic variability in regenerative capacity across species and neuronal populations. For example, while the mammalian central nervous system (CNS) is limited in its regenerative capacity, the CNS of many other vertebrates readily regenerates after injury, as does the peripheral nervous system (PNS) of mammals. Comparing molecular responses across species and tissues can therefore provide valuable insights into both conserved and distinct mechanisms of successful regeneration. One gene that is emerging as a conserved pro-regenerative factor across vertebrates is activating transcription factor 3 (ATF3), which has long been associated with tissue trauma. A growing number of studies indicate that ATF3 may actively promote neuronal axon regrowth and regeneration in species ranging from lampreys to mammals. Here, we review data on the structural and functional conservation of ATF3 protein across species. Comparing RNA expression data across species that exhibit different abilities to regenerate their nervous system following traumatic nerve injury reveals that ATF3 is consistently induced in neurons within the first few days after injury. Genetic deletion or knockdown of ATF3 expression has been shown in mouse and zebrafish, respectively, to reduce axon regeneration, while inducing ATF3 promotes axon sprouting, regrowth, or regeneration. Thus, we propose that ATF3 may be an evolutionarily conserved regulator of neuronal regeneration. Identifying downstream effectors of ATF3 will be a critical next step in understanding the molecular basis of vertebrate CNS regeneration.
    Description: This work was supported by: a Morton Cure Paralysis Fund Research Grant (to HK); a NIH/NINDS R03 Research Grant (No. 1R03NS078519) and the New York State Spinal Cord Injury Research Board (to OB); and the Marine Biological Laboratory Eugene Bell Center Endowment, Rowe Endowment for Regenerative Biology, and Charles Evans Research Development award (to JM).
    Keywords: Regeneration ; Spinal cord injury ; Zebrafish ; Lamprey ; Dorsal root ganglia (DRG) neurons
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    Stochastic dispersal rather than deterministic selection explains the spatio-temporal distribution of soil bacteria in a temperate grassland (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Richter-Heitmann, T., Hofner, B., Krah, F., Sikorski, J., Wuest, P. K., Bunk, B., Huang, S., Regan, K. M., Berner, D., Boeddinghaus, R. S., Marhan, S., Prati, D., Kandeler, E., Overmann, J., & Friedrich, M. W. Stochastic dispersal rather than deterministic selection explains the spatio-temporal distribution of soil bacteria in a temperate grassland. Frontiers in Microbiology, 11, (2020): 1391, https://doi.org/10.3389/fmicb.2020.01391.
    Description: Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
    Description: The work has been funded by the DFG Priority Program 1374 “Infrastructure-Biodiversity-Exploratories” (Grants KA 1590/8-2, FR 1151/5-2, and OV 20/21-1). Field work permits were issued by the responsible state environmental office of Baden-Württemberg (according to § 72 BbgNatSchG).
    Keywords: Spatio-temporal analysis ; Soil bacteria communities ; Community assembly ; Variable selection ; Generalized additive model
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    Tau: a signaling hub protein (2021)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mueller, R. L., Combs, B., Alhadidy, M. M., Brady, S. T., Morfini, G. A., & Kanaan, N. M. Tau: a signaling hub protein. Frontiers in Molecular Neuroscience, 14, (2021): 647054, https://doi.org/10.3389/fnmol.2021.647054.
    Description: Over four decades ago, in vitro experiments showed that tau protein interacts with and stabilizes microtubules in a phosphorylation-dependent manner. This observation fueled the widespread hypotheses that these properties extend to living neurons and that reduced stability of microtubules represents a major disease-driving event induced by pathological forms of tau in Alzheimer’s disease and other tauopathies. Accordingly, most research efforts to date have addressed this protein as a substrate, focusing on evaluating how specific mutations, phosphorylation, and other post-translational modifications impact its microtubule-binding and stabilizing properties. In contrast, fewer efforts were made to illuminate potential mechanisms linking physiological and disease-related forms of tau to the normal and pathological regulation of kinases and phosphatases. Here, we discuss published work indicating that, through interactions with various kinases and phosphatases, tau may normally act as a scaffolding protein to regulate phosphorylation-based signaling pathways. Expanding on this concept, we also review experimental evidence linking disease-related tau species to the misregulation of these pathways. Collectively, the available evidence supports the participation of tau in multiple cellular processes sustaining neuronal and glial function through various mechanisms involving the scaffolding and regulation of selected kinases and phosphatases at discrete subcellular compartments. The notion that the repertoire of tau functions includes a role as a signaling hub should widen our interpretation of experimental results and increase our understanding of tau biology in normal and disease conditions.
    Description: This work was supported by NIH grants (R01AG067762 and R01AG044372 to NK, R01NS082730 to NK and SB, R01NS118177 and R21NS120126 to GM, R01NS023868 and R01NS041170 to SB), a gift from Neurodegenerative Research Inc. (GM), a Zenith Award from the Alzheimer’s Association (SB), a grant from the Secchia Family Foundation (NK), NIH/National Institute on Aging (NIA) funded Michigan Alzheimer’s Disease Research Center 5P30AG053760 (BC), the Office of the Assistant Secretary of Defense for Health Affairs through the Peer-Reviewed Alzheimer’s Research Program (Award No. W81XWH-20-1-0174 to BC), and an Alzheimer’s Association Research Grant 20-682085 (BC).
    Keywords: Tauopathy ; Kinase ; Phosphatase ; Scaffold protein ; Axon ; Synpase ; Nucleus ; Oligodendrocyte
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    The transcriptional response of soil bacteria to long-term warming and short-term seasonal fluctuations in a terrestrial forest (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chowdhury, P. R., Golas, S. M., Alteio, L., Stevens, J. T. E., Billings, A. F., Blanchard, J. L., Melillo, J. M., & DeAngelis, K. M. The transcriptional response of soil bacteria to long-term warming and short-term seasonal fluctuations in a terrestrial forest. Frontiers in Microbiology, 12, (2021): 666558, https://doi.org/10.3389/fmicb.2021.666558.
    Description: Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.
    Description: Funding for this study was provided by the Department of Energy Terrestrial Ecosystem Sciences program under contract number DE-SC0010740. Sites for sample collection were maintained with funding in part from the National Science Foundation (NSF) Long-Term Ecological Research (DEB 1237491) and the NSF Long-Term Research in Environmental Biology (DEB 1456528) programs.
    Keywords: Meta-transcriptomes ; Microbial ; Terrestrial ; Carbon cycle ; Global warming
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    Improved wetland soil organic carbon stocks of the conterminous U.S. through data harmonization (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Uhran, B., Windham-Myers, L., Bliss, N., Nahlik, A. M., Sundquist, E., & Stagg, C. L. Improved wetland soil organic carbon stocks of the conterminous U.S. through data harmonization. Frontiers in Soil Science, 1, (2021): 706701, https://doi.org/10.3389/fsoil.2021.706701.
    Description: Wetland soil stocks are important global repositories of carbon (C) but are difficult to quantify and model due to varying sampling protocols, and geomorphic/spatio-temporal discontinuity. Merging scales of soil-survey spatial extents with wetland-specific point-based data offers an explicit, empirical and updatable improvement for regional and continental scale soil C stock assessments. Agency-collected and community-contributed soil datasets were compared for representativeness and bias, with the goal of producing a harmonized national map of wetland soil C stocks with error quantification for wetland areas of the conterminous United States (CONUS) identified by the USGS National Landcover Change Dataset. This allowed an empirical predictive model of SOC density to be applied across the entire CONUS using relational %OC distribution alone. A broken-stick quantile-regression model identified %OC with its relatively high analytical confidence as a key predictor of SOC density in soil segments; soils 〈6% OC (hereafter, mineral wetland soils, 85% of the dataset) had a strong linear relationship of %OC to SOC density (RMSE = 0.0059, ~4% mean RMSE) and soils 〉6% OC (organic wetland soils, 15% of the dataset) had virtually no predictive relationship of %OC to SOC density (RMSE = 0.0348 g C cm−3, ~56% mean RMSE). Disaggregation by vegetation type or region did not alter the breakpoint significantly (6% OC) and did not improve model accuracies for inland and tidal wetlands. Similarly, SOC stocks in tidal wetlands were related to %OC, but without a mappable product for disaggregation to improve accuracy by soil class, region or depth. Our layered harmonized CONUS wetland soil maps revised wetland SOC stock estimates downward by 24% (9.5 vs. 12.5Pg C) with the overestimation being entirely an issue of inland organic wetland soils (35% lower than SSURGO-derived SOC stocks). Further, SSURGO underestimated soil carbon stocks at depth, as modeled wetland SOC stocks for organic-rich soils showed significant preservation downcore in the NWCA dataset (〈3% loss between 0 and 30 cm and 30 and 100 cm depths) in contrast to mineral-rich soils (37% downcore stock loss). Future CONUS wetland soil C assessments will benefit from focused attention on improved organic wetland soil measurements, land history, and spatial representativeness.
    Description: This project was funded through the U.S. Geological Survey's Land Carbon Program and a grant to ES through the U.S. Geological Survey's Community for Data Integration Program for generating cross-agency assessments.
    Keywords: Soil organic carbon ; Soil carbon density ; Wetland ; Organic matter ; Soil profile ; Soil carbon stock vulnerability
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    Modulation of G(q)/PLC-mediated signaling by acute lithium exposure (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sanchez Trivino, C. A., Landinez, M. P., Duran, S., Gomez, M. del P., & Nasi, E. Modulation of G(q)/PLC-mediated signaling by acute lithium exposure. Frontiers in Cellular Neuroscience, 16, (2022): 838939, https://doi.org/10.3389/fncel.2022.838939.
    Description: Although lithium has long been one of the most widely used pharmacological agents in psychiatry, its mechanisms of action at the cellular and molecular levels remain poorly understood. One of the targets of Li+ is the phosphoinositide pathway, but whereas the impact of Li+ on inositol lipid metabolism is well documented, information on physiological effects at the cellular level is lacking. We examined in two mammalian cell lines the effect of acute Li+ exposure on the mobilization of internal Ca2+ and phospholipase C (PLC)-dependent membrane conductances. We first corroborated by Western blots and immunofluorescence in HEK293 cells the presence of key signaling elements of a muscarinic PLC pathway (M1AchR, Gq, PLC-β1, and IP3Rs). Stimulation with carbachol evoked a dose-dependent mobilization of Ca, as determined with fluorescent indicators. This was due to release from internal stores and proved susceptible to the PLC antagonist U73122. Li+ exposure reproducibly potentiated the Ca response in a concentration-dependent manner extending to the low millimolar range. To broaden those observations to a neuronal context and probe potential Li modulation of electrical signaling, we next examined the cell line SHsy5y. We replicated the potentiating effects of Li on the mobilization of internal Ca, and, after characterizing the basic properties of the electrical response to cholinergic stimulation, we also demonstrated an equally robust upregulation of muscarinic membrane currents. Finally, by directly stimulating the signaling pathway at different links downstream of the receptor, the site of action of the observed Li effects could be narrowed down to the G protein and its interaction with PLC-β. These observations document a modulation of Gq/PLC/IP3-mediated signaling by acute exposure to lithium, reflected in distinct physiological changes in cellular responses.
    Description: This work was supported by DIB-Universidad Nacional de Colombia, grant Hermes No. 41821.
    Keywords: Lithium ; Phospholipase C ; Gq ; Calcium ; SHSY5Y ; HEK-293
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    Editorial: seagrasses under times of change (2022)
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Winters, G., Teichberg, M., Reuter, H., Viana, I. G., & Willette, D. A. Editorial: seagrasses under times of change. Frontiers in Plant Science, 13, (2022): 870478, https://doi.org/10.3389/fpls.2022.870478.
    Description: Awareness of the ecological importance of seagrasses is growing due to recent attention to their role in carbon sequestration as a potential blue carbon sink (Fourqurean et al., 2012; Bedulli et al.), as well as their role in nutrient cycling (Romero et al., 2006), sediment stabilization (James et al., 2019), pathogen filtration (Lamb et al., 2017), and the formation of essential habitats for economically important marine species (Jackson et al., 2001; Jones et al.). Despite their importance and the increasing public and scientific awareness of seagrasses, simultaneous global (e.g., ocean warming, increase in frequency and severity of extreme events, introduction and spread of invasive species) and local (e.g., physical disturbances, eutrophication, and sedimentation) anthropogenic stressors continue to be the main causes behind the ongoing global decline of seagrass meadows (Orth et al., 2006; Waycott et al., 2009).
    Description: This research was partially funded through the BMBF project SEANARIOS (Seagrass scenarios under thermal and nutrient stress: FKZ 03F0826A) to HR and MT. MT was partially funded through the DFG project SEAMAC (Seagrass and macroalgal community dynamics and performance under environmental change; TE 1046/3-1). IV was supported by a postdoctoral research grant Juan de la Cierva-Incorporación (IJC2019-040554-I) and from MCIN/AEI /10.13039/501100011033 (Spain).
    Keywords: Seagrasses ; Climate change ; Eutrophication ; Responses of seagrasses to single and combined stressors ; Spatial-temporal modeling
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    Editorial: Canopies in aquatic ecosystems: integrating form, function, and biophysical processes (2020)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Samson, J. E., Ghisalberti, M., Adams, M. P., Reidenbach, M. A., Long, M. H., Shavit, U., & Pasour, V. B. Editorial: Canopies in aquatic ecosystems: integrating form, function, and biophysical processes. Frontiers in Marine Science, 6, (2019): 697, doi: 10.3389/fmars.2019.00697.
    Description: This Research Topic presents new research investigating the coupling between physical (fluid dynamics, mass transport, and light availability) and biological (nutrient cycling, particle transport, ecosystem structure, and biodiversity) processes in aquatic canopies. The starting point for this topic was the observation that our notion of “canopy” in the aquatic sciences, in contrast to that of our terrestrially-focused colleagues, remains underdeveloped. Forest canopy studies have been considered a new field of science (Nadkarni et al., 2011) and the concept of forest canopy research is clearly documented in the literature (Barker and Pinard, 2001; Nadkarni, 2001; Lowman, 2009); we have not found similar mentions of the canopy concept in aquatic studies. Over the past decade, however, there has been an increase in the number of studies on underwater canopies, as well as a shift toward more multidisciplinary studies that consider more than just the physical impacts of the canopy's presence (Ackerman, 2007; Nepf et al., 2007; O'Brien et al., 2014).
    Description: MA acknowledges funding support from Australian Research Council (ARC) Linkage Grant LP160100496 and the National Environmental Science Programme (NESP) Tropical Water Quality Hub. Funding to MR provided by the National Science Foundation (DEB-1237733 and DEB-1832221) and by a NSF CAREER grant (OCE-1151314). ML was supported by NSF OCE grant 1633951.
    Keywords: Fluid dynamics ; Ecosystem engineering ; Coral ; Algae ; Canopy ; Mass transport ; Light availability ; Nutrient cycling
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    Exploring new frontiers in marine radioisotope tracing - adapting to new opportunities and challenges (2020)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cresswell, T., Metian, M., Fisher, N. S., Charmasson, S., Hansman, R. L., Bam, W., Bock, C., & Swarzenski, P. W. Exploring new frontiers in marine radioisotope tracing - adapting to new opportunities and challenges. Frontiers in Marine Science, 7, (2020): 406, doi:10.3389/fmars.2020.00406.
    Description: Radioisotopes have been used in earth and environmental sciences for over 150 years and provide unique tools to study environmental processes in great detail from a cellular level through to an oceanic basin scale. These nuclear techniques have been employed to understand coastal and marine ecosystems via laboratory and field studies in terms of how aquatic organisms respond to environmental stressors, including temperature, pH, nutrients, metals, organic anthropogenic contaminants, and biological toxins. Global marine issues, such as ocean warming, deoxygenation, plastic pollution, ocean acidification, increased duration, and intensity of toxic harmful algal blooms (HABs), and coastal contamination are all impacting marine environments, thereby imposing various environmental and economic risks. Being able to reliably assess the condition of coastal and marine ecosystems, and how they may respond to future disturbances, can provide vital information for society in the sustainable management of their marine environments. This paper summarizes the historical use of radiotracers in these systems, describes how existing techniques of radioecological tracing can be developed for specific current environmental issues and provides information on emerging issues that would benefit from current and new radiotracer methods. Current challenges with using radioecological tracers and opportunities are highlighted, as well as opportunities to maximize the application of these methods to greatly increase the ability of environmental managers to conduct evidence-based management of coastal and marine ecosystems.
    Description: The IAEA is grateful for the support provided to its Environment Laboratories by the Government of the Principality of Monaco. This contribution was made within the framework of the IAEA CRP on “Applied radioecological tracers to assess coastal and marine ecosystem health” (K41019).
    Keywords: Radionuclides ; Radiotracers ; Radioecology ; Ecosystem condition ; Marine ; Coastal
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    Lessening the hazards of Florida red tides: a common sense approach (2020)
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hoagland, P., Kirkpatrick, B., Jin, D., Kirkpatrick, G., Fleming, L. E., Ullmann, S. G., Beet, A., Hitchcock, G., Harrison, K. K., Li, Z. C., Garrison, B., Diaz, R. E., & Lovko, V. Lessening the hazards of Florida red tides: a common sense approach. Frontiers in Marine Science, 7, (2020): 538, doi:10.3389/fmars.2020.00538.
    Description: In the Gulf of Mexico, especially along the southwest Florida coast, blooms of the dinoflagellate Karenia brevis are a coastal natural hazard. The organism produces a potent class of toxins, known as brevetoxins, which are released following cell lysis into ocean or estuarine waters or, upon aerosolization, into the atmosphere. When exposed to sufficient levels of brevetoxins, humans may suffer from respiratory, gastrointestinal, or neurological illnesses. The hazard has been exacerbated by the geometric growth of human populations, including both residents and tourists, along Florida’s southwest coast. Impacts to marine organisms or ecosystems also may occur, such as fish kills or deaths of protected mammals, turtles, or birds. Since the occurrence of a severe Karenia brevis bloom off the southwest Florida coast three-quarters of a century ago, there has been an ongoing debate about the best way for humans to mitigate the impacts of this hazard. Because of the importance of tourism to coastal Florida, there are incentives for businesses and governments alike to obfuscate descriptions of these blooms, leading to the social amplification of risk. We argue that policies to improve the public’s ability to understand the physical attributes of blooms, specifically risk communication policies, are to be preferred over physical, chemical, or biological controls. In particular, we argue that responses to this type of hazard must emphasize maintaining the continuity of programs of scientific research, environmental monitoring, public education, and notification. We propose a common-sense approach to risk communication, comprising a simplification of the public provision of existing sources of information to be made available on a mobile website.
    Description: The research leading to these results was supported by the US National Science Foundation (NSF) under NSF Grant No. CNH 1009106. PH and DJ acknowledge the complementary support under NSF Grant No. PFI/BIC 1534054.
    Keywords: Harmful algal bloom ; Florida red tide ; Karenia brevis ; Economic effect ; Policy response ; Social amplification of risk ; Risk communication
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    Framework for a community health observing system for the Gulf of Mexico Region: preparing for future disasters (2020)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sandifer, P., Knapp, L., Lichtveld, M., Manley, R., Abramson, D., Caffey, R., Cochran, D., Collier, T., Ebi, K., Engel, L., Farrington, J., Finucane, M., Hale, C., Halpern, D., Harville, E., Hart, L., Hswen, Y., Kirkpatrick, B., McEwen, B., Morris, G., Orbach, R., Palinkas, L., Partyka, M., Porter, D., Prather, A. A., Rowles, T., Scott, G., Seeman, T., Solo-Gabriele, H., Svendsen, E., Tincher, T., Trtanj, J., Walker, A. H., Yehuda, R., Yip, F., Yoskowitz, D., & Singer, B. Framework for a community health observing system for the Gulf of Mexico Region: preparing for future disasters. Frontiers in Public Health, 8, (2020): 578463, doi:10.3389/fpubh.2020.578463.
    Description: The Gulf of Mexico (GoM) region is prone to disasters, including recurrent oil spills, hurricanes, floods, industrial accidents, harmful algal blooms, and the current COVID-19 pandemic. The GoM and other regions of the U.S. lack sufficient baseline health information to identify, attribute, mitigate, and facilitate prevention of major health effects of disasters. Developing capacity to assess adverse human health consequences of future disasters requires establishment of a comprehensive, sustained community health observing system, similar to the extensive and well-established environmental observing systems. We propose a system that combines six levels of health data domains, beginning with three existing, national surveys and studies plus three new nested, longitudinal cohort studies. The latter are the unique and most important parts of the system and are focused on the coastal regions of the five GoM States. A statistically representative sample of participants is proposed for the new cohort studies, stratified to ensure proportional inclusion of urban and rural populations and with additional recruitment as necessary to enroll participants from particularly vulnerable or under-represented groups. Secondary data sources such as syndromic surveillance systems, electronic health records, national community surveys, environmental exposure databases, social media, and remote sensing will inform and augment the collection of primary data. Primary data sources will include participant-provided information via questionnaires, clinical measures of mental and physical health, acquisition of biological specimens, and wearable health monitoring devices. A suite of biomarkers may be derived from biological specimens for use in health assessments, including calculation of allostatic load, a measure of cumulative stress. The framework also addresses data management and sharing, participant retention, and system governance. The observing system is designed to continue indefinitely to ensure that essential pre-, during-, and post-disaster health data are collected and maintained. It could also provide a model/vehicle for effective health observation related to infectious disease pandemics such as COVID-19. To our knowledge, there is no comprehensive, disaster-focused health observing system such as the one proposed here currently in existence or planned elsewhere. Significant strengths of the GoM Community Health Observing System (CHOS) are its longitudinal cohorts and ability to adapt rapidly as needs arise and new technologies develop.
    Description: This project was supported in part by contract # C-231826 between the Gulf of Mexico Alliance, on behalf of the Gulf of Mexico Research Initiative, and the College of Charleston. The content of this paper is solely the responsibility of the authors and does not necessarily represent the official views of the Gulf of Mexico Alliance, the Gulf of Mexico Research Initiative, the College of Charleston, or the Centers for Disease Control and Prevention. Mention of private companies, trade names, or products does not imply endorsement of any kind.
    Keywords: Health observing system ; Disasters ; Gulf of Mexico ; Cohort studies ; Stress ; COVID-19 ; Allostatic load ; Health surveillance
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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
    Repository Name: Woods Hole Open Access Server
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    A long-term geothermal observatory across subseafloor gas hydrates, IODP Hole U1364A, Cascadia accretionary prism (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in WHOI Becker, K., Davis, E. E., Heesemann, M., Collins, J. A., & McGuire, J. J. A long-term geothermal observatory across subseafloor gas hydrates, IODP Hole U1364A, Cascadia accretionary prism. Frontiers in Earth Science, 8, (2020): 568566, https://doi.org/10.3389/feart.2020.568566
    Description: We report 4 years of temperature profiles collected from May 2014 to May 2018 in Integrated Ocean Drilling Program Hole U1364A in the frontal accretionary prism of the Cascadia subduction zone. The temperature data extend to depths of nearly 300 m below seafloor (mbsf), spanning the gas hydrate stability zone at the location and a clear bottom-simulating reflector (BSR) at ∼230 mbsf. When the hole was drilled in 2010, a pressure-monitoring Advanced CORK (ACORK) observatory was installed, sealed at the bottom by a bridge plug and cement below 302 mbsf. In May 2014, a temperature profile was collected by lowering a probe down the hole from the ROV ROPOS. From July 2016 through May 2018, temperature data were collected during a nearly two-year deployment of a 24-thermistor cable installed to 268 m below seafloor (mbsf). The cable and a seismic-tilt instrument package also deployed in 2016 were connected to the Ocean Networks Canada (ONC) NEPTUNE cabled observatory in June of 2017, after which the thermistor temperatures were logged by Ocean Networks Canada at one-minute intervals until failure of the main ethernet switch in the integrated seafloor control unit in May 2018. The thermistor array had been designed with concentrated vertical spacing around the bottom-simulating reflector and two pressure-monitoring screens at 203 and 244 mbsf, with wider thermistor spacing elsewhere to document the geothermal state up to seafloor. The 4 years of data show a generally linear temperature gradient of 0.055°C/m consistent with a heat flux of 61–64 mW/m2. The data show no indications of thermal transients. A slight departure from a linear gradient provides an approximate limit of ∼10−10 m/s for any possible slow upward advection of pore fluids. In-situ temperatures are ∼15.8°C at the BSR position, consistent with methane hydrate stability at that depth and pressure.
    Description: KB was supported by NSF grant OCE-1259718 for construction and deployment of the thermistor cable in the hole. Construction of the seismic-strain-tilt instrumentation was supported by a Keck Foundation grant to WHOI, and deployment and recovery of the integrated sensor string was supported by NSF grant OCE-1259243 to JM and JC. Support for the pressure-monitoring instrumentation and 2014 CTD profile was provided by the Geological Survey of Canada and Ocean Networks Canada.
    Keywords: Heat flux ; Geothermal gradient ; Gas hydrates ; Bottom-simulating reflector ; Pore-fluid advection ; Borehole observatory ; Integrated Ocean Drilling Program
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    Migratory zooplankton excreta and its influence on prokaryotic communities (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Maas, A. E., Liu, S., Bolanos, L. M., Widner, B., Parsons, R., Kujawinski, E. B., Blanco-Bercial, L., & Carlson, C. A. Migratory zooplankton excreta and its influence on prokaryotic communities. Frontiers in Marine Science, 7, (2020): 573268, doi:10.3389/fmars.2020.573268.
    Description: Particulate organic matter (POM) (fecal pellets) from zooplankton has been demonstrated to be an important nutrient source for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12–16 h of incubation. We measured bulk dissolved organic carbon (DOC), dissolved free amino acids (DFAA) via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins, and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200 m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16S rRNA gene amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.
    Description: Funding for this research was provided by Simons Foundation International as part of the BIOS-SCOPE project to AM, LB-B, CC, and EK.
    Keywords: DOC ; Dissolved metabolites ; Diel vertical migration ; Biogeochemistry ; Copepod
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    Quantifying Po-210/Pb-210 disequilibrium in seawater: a comparison of two precipitation methods with differing results (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Roca-Marti, M., Puigcorbe, V., Castrillejo, M., Casacuberta, N., Garcia-Orellana, J., Kirk Cochran, J., & Masque, P. Quantifying Po-210/Pb-210 disequilibrium in seawater: a comparison of two precipitation methods with differing results. Frontiers in Marine Science, 8, (2021): 684484, https://doi.org/10.3389/fmars.2021.684484.
    Description: The disequilibrium between lead-210 (210Pb) and polonium-210 (210Po) is increasingly used in oceanography to quantify particulate organic carbon (POC) export from the upper ocean. This proxy is based on the deficits of 210Po typically observed in the upper water column due to the preferential removal of 210Po relative to 210Pb by sinking particles. Yet, a number of studies have reported unexpected large 210Po deficits in the deep ocean indicating scavenging of 210Po despite its radioactive mean life of ∼ 200 days. Two precipitation methods, Fe(OH)3 and Co-APDC, are typically used to concentrate Pb and Po from seawater samples, and deep 210Po deficits raise the question whether this feature is biogeochemically consistent or there is a methodological issue. Here, we present a compilation of 210Pb and 210Po studies that suggests that 210Po deficits at depths 〉300 m are more often observed in studies where Fe(OH)3 is used to precipitate Pb and Po from seawater, than in those using Co-APDC (in 68 versus 33% of the profiles analyzed for each method, respectively). In order to test whether 210Po/210Pb disequilibrium can be partly related to a methodological artifact, we directly compared the total activities of 210Pb and 210Po in four duplicate ocean depth-profiles determined by using Fe(OH)3 and Co-APDC on unfiltered seawater samples. While both methods produced the same 210Pb activities, results from the Co-APDC method showed equilibrium between 210Pb and 210Po below 100 m, whereas the Fe(OH)3 method resulted in activities of 210Po significantly lower than 210Pb throughout the entire water column. These results show that 210Po deficits in deep waters, but also in the upper ocean, may be greater when calculated using a commonly used Fe(OH)3 protocol. This finding has potential implications for the use of the 210Po/210Pb pair as a tracer of particle export in the oceans because 210Po (and thus POC) fluxes calculated using Fe(OH)3 on unfiltered seawater samples may be overestimated. Recommendations for future research are provided based on the possible reasons for the discrepancy in 210Po activities between both analytical methods.
    Description: MR-M was supported by an Endeavour Research Fellowship (6054) from the Australian Government, the Woods Hole Oceanographic Institution’s Ocean Twilight Zone study, and the Ocean Frontier Institute. VP received funding from the Edith Cowan University under the Early Career Researcher Grant Scheme (G1003456) and the Collaboration Enhancement Scheme (G1003362). MC is currently funded by an ETH Zurich Postdoctoral Fellowship Program (17-2 FEL-30), co-funded by the Marie Curie Actions for People COFUND Program. Support to JKC was provided by the National Science Foundation grant OCE-1736591. The authors acknowledge the financial support from the Spanish Ministry of Science, Innovation and Universities through the “María de Maeztu” program for Units of Excellence (CEX2019-000940-M), the Australian Research Council LIEF Project (LE170100219), and the Generalitat de Catalunya (MERS; 2017 SGR-1588).
    Keywords: Marine chemistry ; Radiochemistry ; Polonium isotopes ; Precipitation methods ; Co-APDC ; Fe(OH)3 ; 210Po/210Pb disequilibrium
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    Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suter, E. A., Pachiadaki, M., Taylor, G. T., & Edgcomb, V. P. Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters. Frontiers in Microbiology, 12, (2022): 764605, https://doi.org/10.3389/fmicb.2021.764605.
    Description: Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.
    Description: This work was supported by the National Science Foundation (NSF) grants (OCE-1336082 to VE and OCE-1335436 and OCE-1259110 to GT). The Cyverse infrastructure and resources are supported by the NSF under Award Numbers DBI-0735191, DBI-1265383, and DBI-1743442 (www.cyverse.org). Support was also provided by the Faculty Scholarship and Academic Advancement Committee at Molloy College.
    Keywords: 18S (SSU) rRNA gene ; Oxygen-depleted environment ; Oxygen minimum zone (OMZ) ; Protist ; Syndiniales ; Parasite ; Eukaryotes ; Network analysis
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    Oceanic crustal fluid single cell genomics complements metagenomic and metatranscriptomic surveys with orders of magnitude less sample volume (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in D’Angelo, T., Goordial, J., Poulton, N., Seyler, L., Huber, J., Stepanauskas, R., & Orcutt, B. Oceanic crustal fluid single cell genomics complements metagenomic and metatranscriptomic surveys with orders of magnitude less sample volume. Frontiers in Microbiology, 12, (2022): 738231, https://doi.org/10.3389/fmicb.2021.738231.
    Description: Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml–1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to ‘omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.
    Description: The borehole observatories that form the backbone of this project were funded by the Integrated Ocean Drilling Program (IODP, now the International Ocean Discovery Program), the United States National Science Foundation (NSF), and the Gordon and Betty Moore Foundation (grant GBMF1609). Cruise AT39-01 was funded by the NSF (OCE-1634025 to C. Geoff Wheat). Analyses were funded by the NSF (OCE-1536623 to BO; OIA-1826734 to RS, NP, and BO; and OCE-16435208 and OCE-1745589 to JH), the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) Science and Technology Center (via subawards from OIA-0939564 to BO and JH), and the NASA Exobiology program (80NSSC19K0466 to BO). This is C-DEBI publication 571.
    Keywords: Deep biosphere ; Oceanic crust ; Crustal fluid ; Single cell genomics ; Metatranscriptomics ; IODP ; CORKS ; North Pond
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    New opportunities and untapped scientific potential in the abyssal ocean (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marlow, J., Anderson, R., Reysenbach, A.-L., Seewald, J., Shank, T., Teske, A., Wanless, V., & Soule, S. New opportunities and untapped scientific potential in the abyssal ocean. Frontiers in Marine Science, 8, (2022): 798943, https://doi.org/10.3389./fmars.2021.798943
    Description: The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as silica and carbonate, and extremely high-temperature fluid-rock reactions in the shallow subsurface lead to distinctive and potentially unique geochemical profiles. Microbial residents range from low-abundance, low-energy communities on the abyssal plains to fast growing thermophiles at hydrothermal vents. Given its spatial extent and position as an intermediate zone between coastal and deep hadal settings, the abyss represents a lynchpin in global-scale processes such as nutrient and energy flux, population structure, and biogeographic diversity. Taken together, the abyssal ocean contributes critical ecosystem services while facing acute and diffuse anthropogenic threats from deep-sea mining, pollution, and climate change.
    Description: We would like to thank the National Science Foundation for their support through grants NSF 2009117 and 2129431 to SAS.
    Keywords: Abyssal ocean ; Geochemistry ; Microbiology ; Geology ; Ecology
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    Shale heavy metal isotope records of low environmental O2 between two Archean Oxidation Events (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ostrander, C. M., Kendall, B., Gordon, G. W., Nielsen, S. G., Zheng, W., & Anbar, A. D. Shale heavy metal isotope records of low environmental O2 between two Archean Oxidation Events. Frontiers in Earth Science, 10, (2022): 833609, https://doi.org/10.3389/feart.2022.833609.
    Description: Evidence of molecular oxygen (O2) accumulation at Earth’s surface during the Archean (4.0–2.5 billion years ago, or Ga) seems to increase in its abundance and compelling nature toward the end of the eon, during the runup to the Great Oxidation Event. Yet, many details of this late-Archean O2 story remain under-constrained, such as the extent, tempo, and location of O2 accumulation. Here, we present a detailed Fe, Tl, and U isotope study of shales from a continuous sedimentary sequence deposited between ∼2.6 and ∼2.5 Ga and recovered from the Pilbara Craton of Western Australia (the Wittenoom and Mt. Sylvia formations preserved in drill core ABDP9). We find a progressive decrease in bulk-shale Fe isotope compositions moving up core (as low as δ56Fe = –0.78 ± 0.08‰; 2SD) accompanied by invariant authigenic Tl isotope compositions (average ε205TlA = –2.0 ± 0.6; 2SD) and bulk-shale U isotope compositions (average δ238U = –0.30 ± 0.05‰; 2SD) that are both not appreciably different from crustal rocks or bulk silicate Earth. While there are multiple possible interpretations of the decreasing δ56Fe values, many, to include the most compelling, invoke strictly anaerobic processes. The invariant and near-crustal ε205TlA and δ238U values point even more strongly to this interpretation, requiring reducing to only mildly oxidizing conditions over ten-million-year timescales in the late-Archean. For the atmosphere, our results permit either homogenous and low O2 partial pressures (between 10−6.3 and 10−6 present atmospheric level) or heterogeneous and spatially restricted O2 accumulation nearest the sites of O2 production. For the ocean, our results permit minimal penetration of O2 in marine sediments over large areas of the seafloor, at most sufficient for the burial of Fe oxide minerals but insufficient for the burial of Mn oxide minerals. The persistently low background O2 levels implied by our dataset between ∼2.6 and ∼2.5 Ga contrast with the timeframes immediately before and after, where strong evidence is presented for transient Archean Oxidation Events. Viewed in this broader context, our data support the emerging narrative that Earth’s initial oxygenation was a dynamic process that unfolded in fits-and-starts over many hundreds-of-millions of years.
    Description: This work was supported financially by the NSF Frontiers in Earth System Dynamics program award NSF EAR-1338810 (AA), a Woods Hole Oceanographic Institution Postdoctoral Scholarship (CO), a NSERC Discovery Grant (RGPIN-435930) and the Canada Research Chair program (BK), and a NASA Exobiology award 80NSSC20K0615 (SN).
    Keywords: Archean ; Thallium ; Iron ; Uranium ; Isotopes ; Oxygen
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    Bacterioplankton diversity and distribution in relation to phytoplankton community structure in the Ross Sea surface waters (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cordone, A., D’Errico, G., Magliulo, M., Bolinesi, F., Selci, M., Basili, M., de Marco, R., Saggiomo, M., Rivaro, P., Giovannelli, D., & Mangoni, O. Bacterioplankton diversity and distribution in relation to phytoplankton community structure in the Ross Sea surface waters. Frontiers in Microbiology, 13, (2022): 722900, https://doi.org/10.3389/fmicb.2022.722900.
    Description: Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. However, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here, we report data on the bacterial diversity in relation to phytoplankton community structure in the surface waters of the Ross Sea during the Austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay (TNB) coastal waters and the Ross Sea Open Waters (RSOWs), with a dominance of members belonging to the bacterial phyla Bacteroidetes and Proteobacteria. In the TNB coastal area, microbial communities were characterized by a higher abundance of sequences related to heterotrophic bacterial genera such as Polaribacter spp., together with higher phytoplankton biomass and higher relative abundance of diatoms. On the contrary, the phytoplankton biomass in the RSOW were lower, with relatively higher contribution of haptophytes and a higher abundance of sequences related to oligotrophic and mixothrophic bacterial groups like the Oligotrophic Marine Gammaproteobacteria (OMG) group and SAR11. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provide new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters, suggesting that specific rather than random interaction contribute to the organic matter cycling in the Southern Ocean.
    Description: Samples were collected in the framework of Plankton biodiversity and functioning of the Ross Sea ecosystems in a changing Southern Ocean [P-ROSE – (PNRA16_00239)], and CDW Effects on glacial mElting and on Bulk of Fe in the Western Ross sea [CELEBeR – (PNRA16_00207)] projects – Italian National Antarctic Program – funded by the Ministry of Education, University and Research (MIUR), awarded to OM and PR, respectively. MM was supported by an Earth-Life Science Institute (Tokyo, Japan) visiting fellowship. This work was partially supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 948972) to DG.
    Keywords: Bacterial diversity ; Bacterioplankton ; Phytoplankton ; Ross Sea ; Antarctica
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    Making use of relicts: brisingid seastars aggregate on hydrothermally inactive sulfide chimneys near black smokers (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Woods, D., Cheadle, M., John, B., German, C., & Van Dover, C. Making use of relicts: brisingid seastars aggregate on hydrothermally inactive sulfide chimneys near black smokers. Frontiers in Marine Science, 9, (2022): 774628, https://doi.org/10.3389/fmars.2022.774628.
    Description: When hydrothermal activity ceases at black-smoker chimneys on mid-ocean ridges, populations of associated invertebrates hosting chemoautotrophic endosymbionts decline and then disappear, but the chimneys can persist on the seabed as relicts. Suspension-feeding brisingid seastars colonize hydrothermally inactive (relict) chimneys on the East Pacific Rise (EPR), though their distribution relative to available hard substrata and proximity to hydrothermal activity is poorly documented. In this study, brisingid abundance on sulfide and basalt substrata was assessed along an ∼3,700 m ROV Jason II transect at the summit of Pito Seamount (SE Pacific; ∼2,275 m). Brisingids were non-randomly distributed, with highest densities (up to ∼300 m–2) on relict sulfides chimneys near active black smokers. Brisingids were relatively uncommon on basalt substrata, and absent on black smokers. We infer that both relict sulfide structures and proximity to black smokers play key roles in the maintenance of dense brisingid populations on Pito Seamount and in similar environments on the EPR. Our observations suggest that experimental introduction of “artificial” relict chimneys providing microtopographic relief could test whether such an approach might mitigate potential impacts of mineral extraction on populations of suspension-feeding invertebrates.
    Description: his project was partially supported by the Global Ocean Biodiversity Initiative through the International Climate Initiative (IKI; grant no. 16_IV_049_Global_A_Global Ocean Biodiversity Initiative GOBI). The Federal Ministry for the Environment, Nature Conservation, and Nuclear Safety (BMU) supports IKI on the basis of a decision adopted by the German Bundestag. DW was supported by Duke University funds to CV. CG’s participation was funded through WHOI’s Deep Ocean Exploration Institute. The AT37-08 cruise was funded by NSF OCE-1459462 (MC and BJ) and OCE-1459387 (J Gee, Scripps Institution of Oceanography).
    Keywords: Brisingid seastar ; East Pacific Rise (EPR) ; Hydrothermal vent ; Pito Seamount ; Nautile Hydrothermal Field ; Deep-sea mining (DSM) ; Black smoker ; Hydrothermally inactive sulfide
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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
    Repository Name: Woods Hole Open Access Server
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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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    Using a Ladder of Seeps with computer decision processes to explore for and evaluate cold seeps on the Costa Rica active margin (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vrolijk, P., Summa, L., Ayton, B., Nomikou, P., Huepers, A., Kinnaman, F., Sylva, S., Valentine, D., & Camilli, R. Using a Ladder of Seeps with computer decision processes to explore for and evaluate cold seeps on the Costa Rica active margin. Frontiers in Earth Science, 9, (2021): 601019, https://doi.org/10.3389/feart.2021.601019.
    Description: Natural seeps occur at the seafloor as loci of fluid flow where the flux of chemical compounds into the ocean supports unique biologic communities and provides access to proxy samples of deep subsurface processes. Cold seeps accomplish this with minimal heat flux. While individual expertize is applied to locate seeps, such knowledge is nowhere consolidated in the literature, nor are there explicit approaches for identifying specific seep types to address discrete scientific questions. Moreover, autonomous exploration for seeps lacks any clear framework for efficient seep identification and classification. To address these shortcomings, we developed a Ladder of Seeps applied within new decision-assistance algorithms (Spock) to assist in seep exploration on the Costa Rica margin during the R/V Falkor 181210 cruise in December, 2018. This Ladder of Seeps [derived from analogous astrobiology criteria proposed by Neveu et al. (2018)] was used to help guide human and computer decision processes for ROV mission planning. The Ladder of Seeps provides a methodical query structure to identify what information is required to confirm a seep either: 1) supports seafloor life under extreme conditions, 2) supports that community with active seepage (possible fluid sample), or 3) taps fluids that reflect deep, subsurface geologic processes, but the top rung may be modified to address other scientific questions. Moreover, this framework allows us to identify higher likelihood seep targets based on existing incomplete or easily acquired data, including MBES (Multi-beam echo sounder) water column data. The Ladder of Seeps framework is based on information about the instruments used to collect seep information (e.g., are seeps detectable by the instrument with little chance of false positives?) and contextual criteria about the environment in which the data are collected (e.g., temporal variability of seep flux). Finally, the assembled data are considered in light of a Last-Resort interpretation, which is only satisfied once all other plausible data interpretations are excluded by observation. When coupled with decision-making algorithms that incorporate expert opinion with data acquired during the Costa Rica experiment, the Ladder of Seeps proved useful for identifying seeps with deep-sourced fluids, as evidenced by results of geochemistry analyses performed following the expedition.
    Description: Support for this research was provided through NASA PSTAR Grant #NNX16AL08G and National Science Foundation Navigating the New Arctic grant #1839063. Use of the R/V Falkor and ROV SuBastian were provided through a grant from the Schmidt Ocean Institute. The AUG Nemesis and the Aurora in-situ mass spectrometer was provided through in-kind support from Teledyne Webb Research and Navistry Corp, respectively.
    Keywords: Seep ; Autonomous exploration ; Costa Rica ; Geochemistry ; Water column data ; Temporal variability ; Decision-making algorithm
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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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    Physical characteristics and evolution of a long-lasting mesoscale cyclonic eddy in the Straits of Florida (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, Y., Hu, C., Kourafalou, V., Liu, Y., McGillicuddy, D., Barnes, B., & Hummon, J. Physical characteristics and evolution of a long-lasting mesoscale cyclonic eddy in the Straits of Florida. Frontiers in Marine Science, 9, (2022): 779450, https://doi.org/10.3389/fmars.2022.779450.
    Description: Ocean eddies along the Loop Current (LC)/Florida Current (FC) front have been studied for decades, yet studies of the entire evolution of individual eddies are rare. Here, satellite altimetry and ocean color observations, Argo profiling float records and shipborne acoustic Doppler current profiler (ADCP) measurements, together with high-resolution simulations from the global Hybrid Coordinate Ocean Model (HYCOM) are used to investigate the physical and biochemical properties, 3-dimensional (3-D) structure, and evolution of a long-lasting cyclonic eddy (CE) in the Straits of Florida (SoF) along the LC/FC front during April–August 2017. An Angular Momentum Eddy Detection Algorithm (AMEDA) is used to detect and track the CE during its evolution process. The long-lasting CE is found to form along the eastern edge of the LC on April 9th, and remained quasi-stationary for about 3 months (April 23 to July 15) off the Dry Tortugas (DT) until becoming much smaller due to its interaction with the FC and topography. This frontal eddy is named a Tortugas Eddy (TE) and is characterized with higher Chlorophyll (Chl) and lower temperature than surrounding waters, with a mean diameter of ∼100 km and a penetrating depth of ∼800 m. The mechanisms that contributed to the growth and evolution of this long-lasting TE are also explored, which reveal the significant role of oceanic internal instability.
    Description: This work was supported by the NASA student fellowship program “Future Investigators in NASA Earth and Space Science and Technology” (FINESST, 80NSSC19K1358), the National Academies of Sciences, Engineering and Medicine (NASEM) UGOS-1 (2000009918), the NOAA IOOS SECOORA Program [IOOS.21(097)USF.BW.OBS.1], and the NOAA RESTORE Science Program (NA17NOS4510099).
    Keywords: Satellite altimetry ; Ocean color ; Argo profiling float ; ADCP ; Global HYCOM ; Cyclonic eddy ; Straits of Florida ; Dry Tortugas
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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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  • 82
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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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    Improving resource management for unattended observation of the marginal ice zone using autonomous underwater gliders (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Duguid, Z., & Camilli, R. Improving resource management for unattended observation of the marginal ice zone using autonomous underwater gliders. Frontiers in Robotics and AI, 7, (2020): 579256, https://doi.org/10.3389/frobt.2020.579256.
    Description: We present control policies for use with a modified autonomous underwater glider that are intended to enable remote launch/recovery and long-range unattended survey of the Arctic's marginal ice zone (MIZ). This region of the Arctic is poorly characterized but critical to the dynamics of ice advance and retreat. Due to the high cost of operating support vessels in the Arctic, the proposed glider architecture minimizes external infrastructure requirements for navigation and mission updates to brief and infrequent satellite updates on the order of once per day. This is possible through intelligent power management in combination with hybrid propulsion, adaptive velocity control, and dynamic depth band selection based on real-time environmental state estimation. We examine the energy savings, range improvements, decreased communication requirements, and temporal consistency that can be attained with the proposed glider architecture and control policies based on preliminary field data, and we discuss a future MIZ survey mission concept in the Arctic. Although the sensing and control policies presented here focus on under ice missions with an unattended underwater glider, they are hardware independent and are transferable to other robotic vehicle classes, including in aerial and space domains.
    Description: Support for this research was provided through NASA PSTAR Grant #NNX16AL08G and the National Science Foundation Navigating the New Arctic grant #1839063.
    Keywords: Autonomous underwater glider ; Under-ice ; Long-range ; Onboard acoustic sensing ; Environment state estimation ; Marginal ice zone ; Adaptive control ; Energy efficiency
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  • 84
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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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    Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cadigan, J., Bekkaye, J., Jafari, N., Zhu, L., Booth, A., Chen, Q., Raubenheimer, B., Harris, B., O’Connor, C., Lane, R., Kemp, G., Day, J., Day, J., & Ulloa, H. Impacts of coastal infrastructure on shoreline response to major hurricanes in southwest Louisiana. Frontiers in Built Environment, 8, (2022): 885215. https://doi.org/10.3389/fbuil.2022.885215.
    Description: The Rockefeller Wildlife Refuge, located along the Chenier Plain in Southwest Louisiana, was the location of the sequential landfall of two major hurricanes in the 2020 hurricane season. To protect the rapidly retreating coastline along the Refuge, a system of breakwaters was constructed, which was partially completed by the 2020 hurricane season. Multi-institutional, multi-disciplinary rapid response deployments of wave gauges, piezometers, geotechnical measurements, vegetation sampling, and drone surveys were conducted before and after Hurricanes Laura and Delta along two transects in the Refuge; one protected by a breakwater system and one which was the natural, unprotected shoreline. Geomorphological changes were similar on both transects after Hurricane Laura, while after Delta there was higher inland sediment deposition on the natural shoreline. Floodwaters drained from the transect with breakwater protection more slowly than the natural shoreline, though topography profiles are similar, indicating a potential dampening or complex hydrodynamic interactions between the sediment—wetland—breakwater system. In addition, observations of a fluidized mud deposit in Rollover Bayou in the Refuge are presented and discussed in context of the maintenance of wetland elevation and stability in the sediment starved Chenier Plain.
    Description: Funding for the study has been partially provided by the National Science Foundation through grants NSF 2139882, 2139883, 1829136, 1848650, and 1939275, as well as through the United States Army Corps of Engineers Regional Sediment Management program. Student support provided through the National Science Foundation Graduate Research Fellowship Program and the Louisiana Coastal Science Assistantship Program.
    Keywords: Hurricane impact ; Wave attenuation and erosion control ; Storm surge ; Chenier plain ; Breakwater ; Field measured data ; Natural infrastructure ; Shoreline retreat
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  • 86
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    A three-dimensional inertial model for coastal upwelling along western boundaries (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-10-12
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(10), (2022): 2431-2444, https://doi.org/10.1175/jpo-d-22-0024.1.
    Description: A three-dimensional inertial model that conserves quasigeostrophic potential vorticity is proposed for wind-driven coastal upwelling along western boundaries. The dominant response to upwelling favorable winds is a surface-intensified baroclinic meridional boundary current with a subsurface countercurrent. The width of the current is not the baroclinic deformation radius but instead scales with the inertial boundary layer thickness while the depth scales as the ratio of the inertial boundary layer thickness to the baroclinic deformation radius. Thus, the boundary current scales depend on the stratification, wind stress, Coriolis parameter, and its meridional variation. In contrast to two-dimensional wind-driven coastal upwelling, the source waters that feed the Ekman upwelling are provided over the depth scale of this baroclinic current through a combination of onshore barotropic flow and from alongshore in the narrow boundary current. Topography forces an additional current whose characteristics depend on the topographic slope and width. For topography wider than the inertial boundary layer thickness the current is bottom intensified, while for narrow topography the current is wave-like in the vertical and trapped over the topography within the inertial boundary layer. An idealized primitive equation numerical model produces a similar baroclinic boundary current whose vertical length scale agrees with the theoretical scaling for both upwelling and downwelling favorable winds.
    Description: This research is supported in part by the China Scholarship Council (201906330102). H. G. is financially supported by the China Scholarship Council to study at WHOI for 2 years as a guest student. M.S. is supported by the National Science Foundation Grant OCE-1922538. Z. C. is supported by the ‘Taishan/Aoshan’ Talents program (2017ASTCPES05) the Fundamental Research Funds for the Central Universities (202072001).
    Description: 2023-03-30
    Keywords: Ekman pumping/transport ; Upwelling/downwelling ; Coastal flows
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  • 87
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    Shear turbulence in the high-wind Southern Ocean using direct measurements (2022)
    American Meteorological Society
    Details
    Publication Date: 2022-10-12
    Description: Author Posting. © American Meteorological Society, 2022. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 52(10), (2022): 2325–2341, https://doi.org/10.1175/jpo-d-21-0015.1.
    Description: The ocean surface boundary layer is a gateway of energy transfer into the ocean. Wind-driven shear and meteorologically forced convection inject turbulent kinetic energy into the surface boundary layer, mixing the upper ocean and transforming its density structure. In the absence of direct observations or the capability to resolve subgrid-scale 3D turbulence in operational ocean models, the oceanography community relies on surface boundary layer similarity scalings (BLS) of shear and convective turbulence to represent this mixing. Despite their importance, near-surface mixing processes (and ubiquitous BLS representations of these processes) have been undersampled in high-energy forcing regimes such as the Southern Ocean. With the maturing of autonomous sampling platforms, there is now an opportunity to collect high-resolution spatial and temporal measurements in the full range of forcing conditions. Here, we characterize near-surface turbulence under strong wind forcing using the first long-duration glider microstructure survey of the Southern Ocean. We leverage these data to show that the measured turbulence is significantly higher than standard shear-convective BLS in the shallower parts of the surface boundary layer and lower than standard shear-convective BLS in the deeper parts of the surface boundary layer; the latter of which is not easily explained by present wave-effect literature. Consistent with the CBLAST (Coupled Boundary Layers and Air Sea Transfer) low winds experiment, this bias has the largest magnitude and spread in the shallowest 10% of the actively mixing layer under low-wind and breaking wave conditions, when relatively low levels of turbulent kinetic energy (TKE) in surface regime are easily biased by wave events.
    Description: This paper is VIMS Contribution 4103. Computational resources were provided by the VIMS Ocean-Atmosphere and Climate Change Research Fund. AUSSOM was supported by the OCE Division of the National Science Foundation (1558639).
    Keywords: Turbulence ; Wind shear ; Boundary layer ; Parameterization
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  • 88
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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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  • 89
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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
    Repository Name: Woods Hole Open Access Server
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  • 90
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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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    Observations of shallow methane bubble emissions from Cascadia Margin (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Michel, A. P. M., Preston, V. L., Fauria, K. E., & Nicholson, D. P. Observations of shallow methane bubble emissions from Cascadia Margin. Frontiers in Earth Science, 9, (2021): 613234, https://doi.org/10.3389/feart.2021.613234.
    Description: Open questions exist about whether methane emitted from active seafloor seeps reaches the surface ocean to be subsequently ventilated to the atmosphere. Water depth variability, coupled with the transient nature of methane bubble plumes, adds complexity to examining these questions. Little data exist which trace methane transport from release at a seep into the water column. Here, we demonstrate a coupled technological approach for examining methane transport, combining multibeam sonar, a field-portable laser-based spectrometer, and the ChemYak, a robotic surface kayak, at two shallow (〈75 m depth) seep sites on the Cascadia Margin. We demonstrate the presence of elevated methane (above the methane equilibration concentration with the atmosphere) throughout the water column. We observe areas of elevated dissolved methane at the surface, suggesting that at these shallow seep sites, methane is reaching the air-sea interface and is being emitted to the atmosphere.
    Description: Funding for VP was provided by an NDSEG Fellowship. Funding for KF was provided by a WHOI Postdoctoral Scholar Fellowship. Ship time on the R/V Falkor was provided by the Schmidt Ocean Institute (FK180824).
    Keywords: Methane ; Bubbles ; Cascadia Margin ; Laser spectrometer ; Ocean sensing ; Surface vehicle ; Multibeam sonar ; Seeps
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  • 92
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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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    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
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 94
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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
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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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
    Repository Name: Woods Hole Open Access Server
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  • 96
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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
    Repository Name: Woods Hole Open Access Server
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  • 97
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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
    Repository Name: Woods Hole Open Access Server
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  • 98
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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
    Repository Name: Woods Hole Open Access Server
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  • 99
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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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    A review of the opportunities and challenges for using remote sensing for management of surface-canopy forming kelps (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cavanaugh, K. C., Bell, T., Costa, M., Eddy, N. E., Gendall, L., Gleason, M. G., Hessing-Lewis, M., Martone, R., McPherson, M., Pontier, O., Reshitnyk, L., Beas-Luna, R., Carr, M., Caselle, J. E., Cavanaugh, K. C., Miller, R. F., Hamilton, S., Heady, W. N., Hirsh, H. K., Hohman R., Lee L. C., Lorda J., Ray J., Reed D. C., Saccomanno V. R., Schroeder, S. B. A review of the opportunities and challenges for using remote sensing for management of surface-canopy forming kelps. Frontiers in Marine Science, 8, (2021): 753531, https://doi.org/10.3389/fmars.2021.753531.
    Description: Surface-canopy forming kelps provide the foundation for ecosystems that are ecologically, culturally, and economically important. However, these kelp forests are naturally dynamic systems that are also threatened by a range of global and local pressures. As a result, there is a need for tools that enable managers to reliably track changes in their distribution, abundance, and health in a timely manner. Remote sensing data availability has increased dramatically in recent years and this data represents a valuable tool for monitoring surface-canopy forming kelps. However, the choice of remote sensing data and analytic approach must be properly matched to management objectives and tailored to the physical and biological characteristics of the region of interest. This review identifies remote sensing datasets and analyses best suited to address different management needs and environmental settings using case studies from the west coast of North America. We highlight the importance of integrating different datasets and approaches to facilitate comparisons across regions and promote coordination of management strategies.
    Description: Funding was provided by the Nature Conservancy (Grant No. 02042019-5719), the U.S. National Science Foundation (Grant No. OCE 1831937), and the U.S. Department of Energy ARPA-E (Grant No. DE-AR0000922).
    Keywords: Kelp forest ; Remote sensing ; North America ; Coastal management ; Kelp management ; Bull kelp ; Giant kelp
    Repository Name: Woods Hole Open Access Server
    Type: Article
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