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  • Wiley  (7,813)
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  • Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
  • Nature Research
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  • 101
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    The Angola Gyre is a hotspot of dinitrogen fixation in the South Atlantic Ocean (2022)
    Nature Research
    Details
    Publication Date: 2022-10-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marshall, T., Granger, J., Casciotti, K. L., Dahnke, K., Emeis, K.-C., Marconi, D., McIlvin, M. R., Noble, A. E., Saito, M. A., Sigman, D. M., & Fawcett, S. E. The Angola Gyre is a hotspot of dinitrogen fixation in the South Atlantic Ocean. Communications Earth & Environment, 3(1), (2022): 151, https://doi.org/10.1038/s43247-022-00474-x.
    Description: Biological dinitrogen fixation is the major source of new nitrogen to marine systems and thus essential to the ocean’s biological pump. Constraining the distribution and global rate of dinitrogen fixation has proven challenging owing largely to uncertainty surrounding the controls thereon. Existing South Atlantic dinitrogen fixation rate estimates vary five-fold, with models attributing most dinitrogen fixation to the western basin. From hydrographic properties and nitrate isotope ratios, we show that the Angola Gyre in the eastern tropical South Atlantic supports the fixation of 1.4–5.4 Tg N.a−1, 28-108% of the existing (highly uncertain) estimates for the basin. Our observations contradict model diagnoses, revealing a substantial input of newly-fixed nitrogen to the tropical eastern basin and no dinitrogen fixation west of 7.5˚W. We propose that dinitrogen fixation in the South Atlantic occurs in hotspots controlled by the overlapping biogeography of excess phosphorus relative to nitrogen and bioavailable iron from margin sediments. Similar conditions may promote dinitrogen fixation in analogous ocean regions. Our analysis suggests that local iron availability causes the phosphorus-driven coupling of oceanic dinitrogen fixation to nitrogen loss to vary on a regional basis.
    Description: This work was supported by the South African National Research Foundation (114673 and 130826 to T.M., 115335, 116142 and 129320 to S.E.F.); the US National Science Foundation (CAREER award, OCE-1554474 to J.G., OCE-1736652 to D.M.S. and K.L.C., OCE-05-26277 to K.L.C.); the German Federal Agency for Education and Research (DAAD-SPACES 57371082 to T.M.); the Royal Society (FLAIR fellowship to S.E.F.); and the University of Cape Town (T.M., J.G., S.E.F.). The authors also recognize the support of the South African Department of Science and Innovation’s Biogeochemistry Research Infrastructure Platform (BIOGRIP).
    Repository Name: Woods Hole Open Access Server
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  • 102
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    A deep Tasman outflow of Pacific waters during the last glacial period (2022)
    Nature Research
    Details
    Publication Date: 2022-10-12
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Struve, T., Wilson, D., Hines, S., Adkins, J., & van de Flierdt, T. A deep Tasman outflow of Pacific waters during the last glacial period. Nature Communications, 13(1), (2022): 3763, https://doi.org/10.1038/s41467-022-31116-7.
    Description: The interoceanic exchange of water masses is modulated by flow through key oceanic choke points in the Drake Passage, the Indonesian Seas, south of Africa, and south of Tasmania. Here, we use the neodymium isotope signature (εNd) of cold-water coral skeletons from intermediate depths (1460‒1689 m) to trace circulation changes south of Tasmania during the last glacial period. The key feature of our dataset is a long-term trend towards radiogenic εNd values of ~−4.6 during the Last Glacial Maximum and Heinrich Stadial 1, which are clearly distinct from contemporaneous Southern Ocean εNd of ~−7. When combined with previously published radiocarbon data from the same corals, our results indicate that a unique radiogenic and young water mass was present during this time. This scenario can be explained by a more vigorous Pacific overturning circulation that supported a deeper outflow of Pacific waters, including North Pacific Intermediate Water, through the Tasman Sea.
    Description: The authors acknowledge financial support from the Grantham Institute of Climate Change and the Environment (T.v.d.F. and T.S.), the Ministry for Science and Culture of the State of Lower Saxony (T.S.), Marie Curie Reintegration grant IRG 230828 (T.v.d.F.), Leverhulme Trust grant RPG-398 (T.v.d.F.), Natural Environment Research Council grants NE/F016751/1 (T.v.d.F.), NE/N001141/1 (T.v.d.F. and D.J.W.), and NE/T011440/1 (D.J.W.), and National Science Foundation grant OCE-1503129 (J.F.A. and S.K.V.H.). Open Access funding is enabled by the DFG open access publication fund and the Carl von Ossietzky University Oldenburg.
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  • 103
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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
    Repository Name: Woods Hole Open Access Server
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  • 104
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    Inferring the thermomechanical state of the lithosphere using geophysical and geochemical observables (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Geophysics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: This thesis focuses on interpreting geophysical and geochemical observables in terms of the thermomechanical state of the lithosphere. In Chapter 1, I correlate lower crustal rheology with seismic wave speed. Compositional variation is required to explain half of the total variability in predicted lower crustal stress, implying that constraining regional lithology is important for lower crustal geodynamics. In Chapter 2, I utilize thermobarometry, diffusion models, and thermodynamic modelling to constrain the ultra-high formation conditions and cooling rates of the Gore Mountain Garnet Amphibolite in order to understand the rheology of the lower crust during orogenic collapse. In Chapter 3, I interpret geophysical data along a 74 Myr transect in the Atlantic to the temporal variability and relationship of crustal thickness and normal faults. In Chapter 4, I constrain the error present in the forward-calculation of seismic wave speed from ultramafic bulk composition. I also present a database and toolbox to interpret seismic wave speeds in terms of temperature and composition. Finally, in Chapter 5 I apply the methodology from Chapter 4 to interpret a new seismic tomographic model in terms of temperature, density, and composition in order to show that the shallow lithospheric roots are density unstable.
    Description: Funding for this research was provided by an MIT Presidential Fellowship, MIT Student Research Funds, the National Science Foundation Division of Earth Sciences (EAR) and Ocean Sciences (OCE) grants EAR-16-24109, EAR-17-22932, EAR-17-22935, OCE-14-58201, and SCEC Awards 16106 and 17202., SCEC, Geological Society of America Graduate Student Research Fellowship, WHOI Ocean Venture Fund, and the WHOI Academic Programs Office.
    Keywords: Lithosphere ; Seismic wave speed ; Rheology
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  • 105
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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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  • 106
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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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  • 107
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    Control of the abyssal ocean overturning circulation by mixing-driven bottom boundary layers (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: An emerging paradigm posits that the abyssal overturning circulation is driven by bottom-enhanced mixing, which results in vigorous upwelling in the bottom boundary layer (BBL) along the sloping seafloor and downwelling in the stratified mixing layer (SML) above; their residual is the overturning circulation. This boundary-controlled circulation fundamentally alters abyssal tracer distributions, with implications for global climate. Chapter 1 describes how a basin-scale overturning circulation arises from the coupling between the ocean interior and mixing-driven boundary layers over rough topography, such as the sloping flanks of mid-ocean ridges. BBL upwelling is well predicted by boundary layer theory, whereas the compensation by SML downwelling is weakened by the upward increase of the basin-wide stratification, which supports a finite net overturning. These simulated watermass transformations are comparable to best-estimate diagnostics but are sustained by a crude parameterization of boundary layer restratification processes. In Chapter 2, I run a realistic simulation of a fracture zone canyon in the Brazil Basin to decipher the non-linear dynamics of abyssal mixing layers and their interactions with rough topography. Using a hierarchy of progressively idealized simulations, I identify three physical processes that set the stratification of abyssal mixing layers (in addition to the weak buoyancy-driven cross-slope circulation): submesoscale baroclinic eddies on the ridge flanks, enhanced up-canyon flow due to inhibition of the cross-canyon thermal wind, and homogenization of canyon troughs below the level of blocking sills. Combined, these processes maintain a sufficiently large near-boundary stratification for mixing to drive globally significant BBL upwelling. In Chapter 3, simulated Tracer Release Experiments illustrate how passive tracers are mixed, stirred, and advected in abyssal mixing layers. Exact diagnostics reveal that while a tracer’s diapycnal motion is directly proportional to the mean divergence of mixing rates, its diapycnal spreading depends on both the mean mixing rate and an additional non-linear stretching term. These simulations suggest that the theorized boundary-layer control on the abyssal circulation is falsifiable: downwelling in the SML has already been confirmed by the Brazil Basin Tracer Release Experiment, while an upcoming experiment in the Rockall Trough will confirm or deny the existence of upwelling in the BBL.
    Description: This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 174530. I also acknowledge funding support from National Science Foundation Awards OCE-1536515 and OCE-1736109. This work was partially supported by MIT’s Rosenblith Presidential Fellowship.
    Keywords: Abyss ; Circulation ; Mixing
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  • 108
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    Assessing anthropogenic noise impacts and relevant soundscape cues for marine invertebrates: leveraging squid and coral reefs as model systems (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Sound is utilized by marine animal taxa for many ecologically important functions, and these taxa are vulnerable to adverse effects of anthropogenic noise on hearing and behavior. However, little is known about marine invertebrates’ responses to anthropogenic noise, and the ambient environmental sounds (“soundscapes”) they detect and respond to. Most acoustic studies report sound pressure (detected by mammals and some fish), but few report particle motion, the back-and-forth vibratory component of sound detected by marine invertebrates. I investigated invertebrate use of and response to sounds in two facets: 1) behavioral responses of longfin squid, Doryteuthis pealeii to anthropogenic noise, and 2) particle motion of coral reef soundscapes in the U.S. Virgin Islands. In laboratory-based experiments I exposed D. pealeii to construction noise originally recorded from an offshore wind farm. I found significant increases in squids’ alarm responses and in failed prey capture attempts during noise. Conversely, noise exposure had no significant effects on reproductive behaviors of groups of D. pealeii, indicating high motivation of these squid to reproduce during this stressor. Collectively, these experiments revealed the importance of considering behavioral context in studies and regulatory decisions regarding invertebrates’ susceptibility to anthropogenic noise impacts. In studying coral reef soundscapes, I reported particle motion trends over several months for coral reefs varying in habitat quality, including coral cover and fish abundance. I found acoustic properties over which particle motion closely scaled with pressure, and others over which it did not. I compared soundscape data with particle motion hearing thresholds, and found that invertebrates may only detect high amplitude and low frequency transient sound cues on reefs, such as those produced by fishes. My research bring new insights on natural and anthropogenic sound cues detectable by marine invertebrates, and how and when invertebrates will be vulnerable to anthropogenic noise pollution.
    Description: My graduate work was funded in part by the US Department of Interior, Bureau of Ocean Energy Management Environmental Studies Program through Interagency Agreement Number M17PG00029 with the U.S. Department of Commerce, National Oceanic and Atmospheric Administration (funding to Aran Mooney and Jenni Stanley). My work was also supported by the NSF Biological Oceanography award OCE-1536782 (funding to Aran Mooney). I received tuition and stipend support from the National Science Foundation Graduate Research Fellowship Program [Grant No. 2388357]. The Academic Program Office at the Woods Hole Oceanographic Institution provided tuition and stipend support as well as travel support. The MIT Student Assistance Fund, the Aquatic Noise 2019 Organizing Committee, and the Acoustical Society of America also provided travel support.
    Keywords: Cephalopod ; Renewable energy ; Ecoacoustics
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  • 109
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    Multi-path Penalty metric in underwater acoustic communication for autonomy and human decision-making (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: A novel performance metric to improve underwater digital acoustic communication, called Multipath Penalty (MPP), is proposed as an alternative to traditional signal-to-noise ratio (SNR) methods in the context of the Arctic Beaufort Sea. MPP and SNR are compared alongside a third performance metric, Minimum Achievable Error (MAE), which replicates the operation of a channel estimate-based decision feedback equalizer in an acoustic modem. The three metrics are then tested in a hardware-in-the-loop Virtual Ocean simulator for an autonomous undersea vehicle (AUV) communicating with a collaborator. Using field data of modem statistics obtained duringICEX20 and expanded data supplied by the simulator, calibration of the three metrics to modem packet success is evaluated, resulting in a proposed recalibration for MAE. The AUV’s ability to communicate when adaptively choosing its depth is analyzed above and below the Beaufort Lens, and settings for MPP’s engineering variables are obtained. The results show MPP generally improves reception and demodulation of acoustic transmissions over SNR by approximately 5% within an operational range of 8 km, while achieving similar results to the more robust metric MAE. MPP is an improved utility for underwater digital acoustic communication in both marine autonomy and as a tactical decision aid.
    Description: This work would not be possible without the extraordinary support of the United States Navy, which provided funding for this research, my degree, and my livelihood as an active duty submarine officer.
    Keywords: Multi-path Penalty ; Acoustics ; Metric
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  • 110
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    Reduced order modeling for stochastic prediction and data assimilation onboard autonomous platforms at sea (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: There are many significant challenges for unmanned autonomous platforms at sea including predicting the likely scenarios for the ocean environment, quantifying regional uncertainties, and updating forecasts of the evolving dynamics using their observations. Due to the operational constraints such as onboard power, memory, bandwidth, and space limitations, efficient adaptive reduced order models (ROMs) are needed for onboard predictions. In the first part, several reduced order modeling schemes for regional ocean forecasting onboard autonomous platforms at sea are described, investigated, and evaluated. We find that Dynamic Mode Decomposition (DMD), a data-driven dimensionality reduction algorithm, can be used for accurate predictions for short periods in ocean environments. We evaluate DMD methods for ocean PE simulations by comparing and testing several schemes including domain splitting, adjusting training size, and utilizing 3D inputs. Three new approaches that combine uncertainty with DMD are also investigated and found to produce practical and accurate results, especially if we employ either an ensemble of DMD forecasts or the DMD of an ensemble of forecasts. We also demonstrate some results from projecting / compressing high-fidelity forecasts using schemes such as POD projection and K-SVD for sparse representation due to showing promise for distributing forecasts efficiently to remote vehicles. In the second part, we combine DMD methods with the GMM-DO filter to produce DMD forecasts with Bayesian data assimilation that can quickly and efficiently be computed onboard an autonomous platform. We compare the accuracy of our results to traditional DMD forecasts and DMD with Ensemble Kalman Filter (EnKF) forecast results and show that in Root Mean Square Error (RMSE) sense as well as error field sense, that the DMD with GMM-DO errors are smaller and the errors grow slower in time than the other mentioned schemes. We also showcase the DMD of the ensemble method with GMM-DO. We conclude that due to its accurate and computationally efficient results, it could be readily applied onboard autonomous platforms. Overall, our contributions developed and integrated stochastic DMD forecasts and efficient Bayesian GMM-DO updates of the DMD state and parameters, learning from the limited gappy observation data sets.
    Description: I wish to thank the U.S. Navy’s Civilian Institution Program along with the MITWHOI Joint Program for providing the funding and resources that made this research and continuing my education possible.
    Keywords: Data assimilation ; Reduced order models ; Stochastic prediction
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  • 111
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    The stratification maxima of the seasonally varying Surface layer in the Arctic Ocean’s Beaufort Gyre (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: The Beaufort Gyre region of the Arctic Ocean is strongly stratified at the base of the wintertime mixed layer, which impedes the vertical transport of heat, energy, and other tracers. Ice-Tethered Profiler observations during 2004-2018 were used to characterize and investigate the seasonal and interannual variability of the strength, depth, density, and thickness of this highly stratified layer at the base of the mixed layer. This includes investigating the remnant stratification maximum, which formed when the summer mixed layer shoaled. Seasonally, the stratification maximum was never in a steady state. It was largest in October (4.8 × 10−3 rad2/sec2) and decreased during all winter months (to 2.3 × 10−3rad2/sec2 in June), indicating that surface forcing and interior vertical mixing were never in equilibrium during the year. Interannually, the period from 2011-2018 had a higher stratification maximum than then the period from 2005-2010 regardless of the season. The remnant stratification maximum was consistently weaker than the winter stratification maximum from which it formed. The initial evolution of the remnant stratification maximum is used to estimate an effective vertical diffusivity of order 10−6m2/s. No significant geographic variability was found, in part due to high temporal and small scale variability of the stratification maximum layer. Implications for heat transport through to the sea ice cover are discussed.
    Keywords: Beaufort Gyre ; Stratification ; Remnant layer
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  • 112
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    Trojan horses in the marine realm: characterizing protistan parasite ecology in coastal waters (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Protists are taxonomically and metabolically diverse drivers of energy and nutrient flow in the marine environment, with recent research suggesting significant roles in global carbon cycling throughout the water column. Top-down controls on planktonic protists include grazing and parasitism, processes that both contribute to nutrient transfer and biogeochemical cycling in the global ocean. Recent global surveys of eukaryotic small subunit ribosomal RNA molecular signatures have highlighted the fact that parasites belonging to the marine alveolate order Syndiniales are both abundant and ubiquitous in coastal and open ocean environments, suggesting a major role for this taxon in marine food webs. Two coastal sites, Saanich Inlet (Vancouver Island, BC) and Salt Pond (Falmouth, MA, USA) were selected as model ecosystems to examine the impacts of Syndinian parasitism on protist communities. Data presented in this thesis combines high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, and modeling to address key knowledge gaps regarding syndinian ecology. Information is presented on previously undescribed putative host taxa, the prevalence of syndinian parasites and infections on different hosts in coastal waters, and a framework for modeling host-parasite interactions based on field observations.
    Description: Research was supported by the WHOI Ocean Venture Fund, the National Science Foundation Biological Oceanography OCE-1851012, and the National Science Foundation Graduate Research Fellowship under Grant No. 1745302.
    Keywords: Syndiniales ; Parasitism ; Protist
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  • 113
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    Structure, variability, and dynamics of the West Greenland Boundary Current System (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: The ventilation of intermediate waters in the Labrador Sea has important implications for the strength of the Atlantic Meridional Overturning Circulation. Boundary current-interior interactions regulate the exchange of properties between the slope and the basin, which in turn regulates the magnitude of interior convection and the export of ventilated waters from the subpolar gyre. This thesis characterizes theWest Greenland Boundary Current System near Cape Farewell across a range of spatio-temporal scales. The boundary current system is composed of three velocity cores: (1) the West Greenland Coastal Current (WGCC), transporting Greenland and Arctic meltwaters on the shelf; (2) the West Greenland Current (WGC), which advects warm, saline Atlantic-origin water at depth, meltwaters at the surface, and newly-ventilated Labrador Sea Water (LSW); and (3) the Deep Western Boundary Current, which carries dense overflow waters ventilated in the Nordic Seas. The seasonal presence of the LSW and Atlantic-origin water are dictated by air-sea buoyancy forcing, while the seasonality of the WGCC is governed by remote wind forcing and the propagation of coastally trapped waves from East Greenland. Using mooring data and hydrographic surveys, we demonstrate mid-depth intensified cyclones generated at Denmark Strait are found offshore of the WGC and enhance the overflow water transport at synoptic timescales. Using mooring, hydrographic, and satellite data, we demonstrate that the WGC undergoes extensive meandering due to baroclinic instability that is enhanced in winter due to LSW formation adjacent to the current. This leads to the production of small-scale, anticyclonic eddies that can account for the entirety of wintertime heat loss within the Labrador Sea. The meanders are shown to trigger the formation of Irminger Rings downstream. Using mooring, hydrographic, atmospheric, and Lagrangian data, and a mixing model, we find that strong atmospheric storms known as forward tip jets cause upwelling at the shelfbreak that triggers offshore export of freshwater. This freshwater flux can explain the observed lack of ventilation in the eastern Labrador Sea. Together, this thesis documents previously unobserved interannual, seasonal, and synoptic-scale variability and dynamics within the West Greenland boundary current system that must be accounted for in future modeling.
    Description: The work in this dissertation was funded by the National Science Foundation grants OCE-1259618 and OCE-1756361.
    Keywords: Boundary current dynamics ; Labrador sea water formation ; Eddies
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    Radium isotopes and radon-222 as tracers of sediment-water interaction in Arctic coastal and lacustrine environments (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Arctic marine and lacustrine systems are experiencing rapid warming due to climate change. These changes are especially important at the interface between sediments and surface waters because they are hotspots for biogeochemical transformations such as redox reactions, nutrient consumption and regeneration, organic matter leaching and degradation, and mineral weathering. Radium isotopes (223Ra, 224Ra, 226Ra, 228Ra) and radon-222, naturally occurring radioactive isotopes produced in sediments, are well-suited as tracers of nutrients, trace metals, and organic matter cycling processes at the sediment-water interface. In this thesis, I have applied radon-222 and the quartet of radium isotopes to study fundamental processes in subarctic lakes and on the Arctic continental shelf. First, radon-222 is used to quantify groundwater discharge into a shallow, tundra lake on the Yukon-Kuskokwim Delta in Alaska in summer of 2017. Radon-derived groundwater fluxes were then paired with methane (CH4) measurements to determine delivery rates of methane into the lake via groundwater. Groundwater CH4 fluxes significantly exceeded diffusive air-water fluxes from the lake to the atmosphere, suggesting that groundwater is an important source of CH4 to Arctic lakes and may drive observed CH4 emissions. Higher CH4 emissions were observed compared to those reported previously in high latitude lakes, like due to higher CH4 concentrations in groundwater. These findings indicate that deltaic lakes across warmer permafrost regions may act as important hotspots for methane release across Arctic landscapes. Then, the quartet of radium isotopes is used to study the impacts of storms and sea ice formation as drivers of sediment-water interaction on the Alaskan Beaufort shelf. The timeseries presented in this study is among the first to document the combined physical and chemical signals of winter water formation in the Beaufort Sea, made possible by repeat occupations of the central Beaufort shelf. Radium measurements are combined with inorganic nitrogen and hydrographic measurements to elucidate the episodic behavior of winter water formation and its ability to drive exchange with bottom sediments during freeze-up.
    Description: Financial support for Chapter 2 was funded by National Science Foundation awards OCE-1458305 to M.A.C., 1561437 to S.M.N, J.D.S., and R.M.H and 1624927 to S.M.N., P.J.M. and R.M.H. The work completed for Chapter 3 was funded by the Montrym Fund at the Massachusetts Institute of Technology, the Academic Programs Office at Woods Hole Oceanographic Institution, and the NSF Arctic GEOTRACES (OCE-1458305), Pacific GEOTRACES (OCE-1736277), and Arctic Observing Network programs (OPP-1733564).
    Keywords: Arctic ; Sediment ; Radionuclides
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    Signal Absorption-Based Range Estimator for Undersea Swarms (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Robotic swarms are increasingly complex above the waterline due to reliable communication links. However, the limited propagation of similar signals in the ocean has impacted advances in undersea robotics. Underwater vehicles often rely on acoustics for navigation solutions; however, this presents challenges for robotic swarms. Many localization methods rely on precision time synchronization or two-way communication to estimate ranges. The cost of Chip-scale Atomic Clocks (CSACs) and acoustic modems is limiting for large-scale swarms due to the cost-per-vehicle and communications structure. We propose a single vehicle with reliable navigation as a "leader" for a scalable swarm of lower-cost vehicles that receive signals via a single hydrophone. This thesis outlines range estimation methods for sources with known signal content, including frequency and power at its origin. Transmission loss is calculated based on sound absorption in seawater and geometric spreading loss to estimate range through the Signal Absorption-Based Range Estimator (SABRE). SABRE's objective is to address techniques that support low-cost undersea swarming. This thesis's contributions include a novel method for range estimation onboard underwater vehicles that supports relative navigation through Doppler-shift methods for target bearing. This thesis develops the theory, algorithms, and analytical tools for real-world data range estimation.
    Keywords: Absorption ; Single-hydrophone ; Swarm
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    A planned approach to high collision risk area (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Mechanical Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: This thesis examines the transition of a vessel from the open ocean, where collisions are rare, to a high risk and heavy traffic area such as a Traffic Separation Scheme (TSS). Previous autonomy approaches generally view path planning and collision avoidance as two separate functions, i.e. a vessel will follow the planned path until conditions are met for collision avoidance algorithms to take over. Here an intermediate phase is proposed with the goal of adjusting the time of arrival to a high vessel density area so that the risk of collision is reduced. A general algorithm that calculates maximum future traffic density for all choices in the speed domain is proposed and implemented as a MOOS-IvP behavior. This behavior gives the vessel awareness of future collision risks and aids the collision avoidance process. This new approach improves the safety of the vessel by reducing the number of risky encounters that will likely require the vessel to maneuver for safety.
    Keywords: Collision avoidance ; MOOS-IvP ; COLREGs
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  • 117
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    Distribution, growth, and transport of larval fishes and implications for population dynamics (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: The early life stages of marine fishes play a critical role in population dynamics, largely due to their high abundance, high mortality, and ease of transport in ocean currents. This dissertation demonstrates the value of combining larval data, collected in the field and the laboratory, with model simulations. In Chapter 2, analyses of field observations of ontogenetic vertical distributions of coral reef fish revealed a diversity of behaviors both between and within families. In Caribbean-wide particle-tracking simulations of representative behaviors, surface-dwelling larvae were generally transported longer distances with greater population connectivity amongst habitat patches, while the evenly-distributed vertical behavior and downward ontogenetic vertical migration were similar to one another and led to greater retention near natal sites. However, hydrodynamics and habitat vailability created some local patterns that contradicted the overall expectation. Chapter 3 presents evidence of tuna spawning inside a large no-take marine protected area, the Phoenix Islands Protected Area (PIPA). Despite variation in temperature and chlorophyll, the larval tuna distributions were similar amongst years, with skipjack (Katsuwonus pelamis) and Thunnus spp. tunas observed in all three years. Backtracking simulations indicated that spawning occurred inside PIPA in all 3 study years, demonstrating that PIPA is protecting viable tuna spawning habitat. In Chapter 4, several lines of larval evidence support the classification of the Slope Sea as a major spawning ground for Atlantic bluefin tuna with conditions suitable for larval growth. The abundance of bluefin tuna larvae observed in the Slope Sea aligns with typical observations on the other two spawning grounds. Age and growth analyses of bluefin tuna larvae collected in the Slope Sea and the Gulf of Mexico in 2016 did not show a growth rate difference between regions, but did suggest that Slope Sea larvae are larger at the onset of exogenous feeding. Collected larvae were backtracked to locations north of Cape Hatteras and forward tracked to show that they would have been retained within the Slope Sea until the onset of swimming. As a whole, this thesis presents valuable contributions to the study of larval fishes and the attendant implications for marine resource management.
    Description: National Science Foundation Graduate Research Fellowship Program (to C.M.H.), the Woods Hole Oceanographic Institution Ocean Life Institute (Grant 22569.01 to J. Llopiz and C.M.H.), the Adelaide and Charles Link Foundation, the Phoenix Islands Protected Area Trust, the J. Seward Johnson Endowment in support of the Woods Hole Oceanographic Institution's Marine Policy Center, and the WHOI Academic Programs Office.
    Keywords: Marine protected area ; Trait-based ; Biophysical model
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    Structure and mechanics of the subducted Gorda plate: constrained by afterslip simulations and scattered seismic waves (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Subduction zones host the greatest earthquakes on earth and pose great threat to human society. The largest slip in megathrust earthquakes often occurs in the 10–50 km depth range, yet seismic imaging of the material properties in this region has proven difficult. This thesis focuses on developing methods to utilize high frequency (2–12 Hz) seismic waves scattered from the megathrust plate interface to constrain its fine-scale velocity structures and to investigate the relationship between velocity structures and megathrust slip behaviors. Chapter 2 investigates the locking condition of the subducted Gorda plate by simulating afterslip that would be expected as a result of the stress changes from offshore strike-slip earthquakes. Chapter 3 develops array analysis methods to identify P-to-S and S-to-P seismic converted phases that convert at the subducted Gorda plate interface from local earthquakes and uses them to constrain the geometry and material properties of the plate boundary fault of the subducted Gorda plate between 5–20 km depth. Chapters 4 and 5 use a dense nodal array and numerical modeling methods to study the seismic guided waves that propagate along the thin low velocity layer at the boundary of the subducted Gorda plate. Taken together, our results indicate that material properties of the subduction plateboundary fault is highly heterogeneous and the plate-boundary fault is potentially contained in a low velocity layer with significant porosity and fluid content at seismogenic depths.
    Description: Funding for this research was provided by National Science Foundation Division of Earth Sciences (EAR) award #1520690 and the WHOI Academic Programs Office.
    Keywords: Subduction zone ; Scattered seismic waves ; Plate boundary
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    Coral reefs in the Anthropocene Ocean: novel insights from skeletal proxies of climate change, impacts, and resilience (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Anthropogenic emissions of greenhouse gases are driving rapid changes in ocean conditions. Shallow-water coral reefs are experiencing the brunt of these changes, including intensifying marine heatwaves (MHWs) and rapid ocean acidification (OA). Consequently, coral reefs are in broad-scale decline, threatening the livelihoods of hundreds of millions of people. Ensuring survival of coral reefs in the 21st century will thus require a new management approach that incorporates robust understanding of reef-scale climate change, the mechanisms by which these changes impact corals, and their potential for adaptation. In this thesis, I extract information from within coral skeletons to 1) Quantify the climate changes occurring on coral reefs and the effects on coral growth, 2) Identify differences in the sensitivity of coral reefs to these changes, and 3) Evaluate the adaptation potential of the keystone reef-building coral, Porites. First, I develop a mechanistic Porites growth model and reveal the physicochemical link between OA and skeletal formation. I show that the thickening (densification) of coral skeletal framework is most vulnerable to OA and that, under 21st century climate model projections, OA will reduce Porites skeletal density globally, with greatest impact in the Coral Triangle. Second, I develop an improved metric of thermal stress, and use a skeletal bleaching proxy to quantify coral responses to intensifying heatwaves in the central equatorial Pacific (CEP) since 1982. My work reveals a long history of bleaching in the CEP, and reef-specific differences in thermal tolerance linked to past heatwave exposure implying that, over time, reef communities have adapted to tolerate their unique thermal regimes. Third, I refine the Sr-U paleo-thermometer to enable monthly-resolved sea surface temperatures (SST) generation using laser ablation ICPMS. I show that laser Sr-U accurately captures CEP SST, including the frequency and amplitude of MHWs. Finally, I apply laser Sr-U to reconstruct the past 100 years of SST at Jarvis Island in the CEP, and evaluate my proxy record of bleaching severity in this context. I determine that Porites coral populations on Jarvis Island have not yet adapted to the pace of anthropogenic climate change.
    Description: This research was supported by US National Science Foundation Awards OCE-1220529, ANT-1246387, OCE-1737311, CE-1601365, OCE-1805618, OCE-1537338, OCE-2016133, and from the Woods Hole Oceanographic Institution through the Ocean Life Institute, the Ocean Ventures Fund, the Grassle Fellowship Fund, and the MIT-WHOI Academic Programs Office. Additional funding was provided by the Taiwan MOST Grant 104-2628-M-001-007-MY3, the Robertson Foundation, the Leverhulme Trust in UK, the Atlantic Donor Advised Fund, The Prince Albert 2 of Monaco Foundation, the Akiko Shiraki Dynner Fund, the New England Aquarium, the Martin Family Society Fellowship for Sustainability, the Gates Millenium Scholarship, the Arthur Vining Davis Foundation, the NOAA Coral Reef Conservation Program, and from the Woods Hole Oceanographic Institution through Investment in Science Fund, the Early Career Award, and the Access to the Sea Award.
    Keywords: Coral reef ; Climate ; Proxy
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    Computational approaches for sub-meter ocean color remote sensing (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Mechanical and Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: The satellite ocean color remote sensing paradigm developed by government space agencies enables the assessment of ocean color products on global scales at kilometer resolutions. A similar paradigm has not yet been developed for regional scales at sub-meter resolutions, but it is essential for specific ocean color applications (e.g., mapping algal biomass in the marginal ice zone). While many aspects of the satellite ocean color remote sensing paradigm are applicable to sub-meter scales, steps within the paradigm must be adapted to the optical character of the ocean at these scales and the opto-electronics of the available sensing instruments. This dissertation adapts the three steps of the satellite ocean color remote sensing paradigm that benefit the most from reassessment at sub-meter scales, namely the correction for surface-reflected light, the design and selection of the opto-electronics and the post-processing of over-sampled regions. First, I identify which surface-reflected light removal algorithm and view angle combination are optimal at sub-meter scales, using data collected during a field deployment to the Martha’s Vineyard Coastal Observatory. I find that of the three most widely used glint correction algorithms, a spectral optimization based approach applied to measurements with a 40∘ view angle best recovers the remotesensing reflectance and chlorophyll concentration despite centimeter scale variability in the surface-reflected light. Second, I develop a simulation framework to assess the impact of higher optical and electronics noise on ocean color product retrieval from unique ocean color scenarios. I demonstrate the framework’s power as a design tool by identifying hardware limitations, and developing potential solutions, for estimating algal biomass from high dynamic range sensing in the marginal ice zone. Third, I investigate a spectral super-resolution technique for application to spatially over-sampled oceanic regions. I determine that this technique more accurately represents spectral frequencies beyond the Nyquist and that it can be trained to be invariant to noise sources characteristic of ocean color remote sensing on images with similar statistics as the training dataset. Overall, the developed and critically assessed sub-meter ocean color remote sensing paradigm enables researchers to collect high fidelity sub-meter data from imaging spectrometers in unique ocean color scenarios.
    Description: Ryan O’Shea was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. This research was funded by Woods Hole Oceanographic Institution’s Edwin W. Hiam Ocean Science and Technology Award Fund, its Ocean Venture Funds, its Academic Programs Office, and the National Aeronautics and Space Administration via grant number CCE NNX17AI72G to Dr. Samuel Laney. The raw data for Figures 3-3 and 3-4 were provided through Australian Antarctic Science grants 2678 and 4390.
    Keywords: Ocean color ; Hyperspectral ; Remote sensing
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    Estimating atmospheric boundary layer turbulence in the marine environment using lidar systems with applications for offshore wind energy (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2021.
    Description: Estimating turbulence in the marine-atmospheric boundary layer is critical to many industrial, commercial and scientific fields, but of particular importance to the wind energy industry. Contributing to both the efficiency of energy extraction and the life-cycle cost of the turbine itself, turbulence in the atmospheric boundary layer is estimated within the wind energy industry as Turbulence Intensity (TI) and more recently by Turbulent Kinetic Energy (TKE). Traditional in-situ methods to measure turbulence are extremely difficult to deploy in the marine environment, resulting in a recent movement to and dependence on remote sensing methods. One type of remote sensing instrument, Doppler lidars, have shown to reliably estimate the wind speed and atmospheric turbulence while being cost effective and easily deployable, and hence are being increasingly utilized as a standard for wind energy assessments. In this thesis, the ability of lidars to measure turbulence up to a height of 200 m above mean sea level in the marine-atmospheric boundary layer was tested using a 7-month data set spanning winter to early summer. Lidar-based TI and TKE were estimated by three methods using observations from a highly validated lidar system and compared under both convective and stable atmospheric stability conditions. Convective periods were found to have higher turbulence at all the heights compared to stable conditions, while mean wind speed and shear were higher during stable conditions. The study period was characterized by generally low turbulent conditions with high turbulence events occurring at timescales of a few days. Mean vertical profiles of TKE were non-uniformly distributed in height during low turbulent conditions. During highly turbulent events, TKE increased more strongly with height. The definition of TI– following the industry or meteorology conventions – had no real effect on the results, and differences between cup or sonic anemometers and lidar TI values were small except at low wind speeds. All the three lidar-based TKE methods tested corresponded closely to independent estimates, and differences between the methods were small relative to the temporal variability of TKE observed at the offshore site.
    Keywords: Turbulence ; Wind engery ; Lidar
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    Diel differences in blue whale (Balaenoptera musculus) dive behavior increase nighttime risk of ship strikes in northern Chilean Patagonia (2021)
    Wiley
    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 Caruso, F., Hickmott, L., Warren, J. D., Segre, P., Chiang, G., Bahamonde, P., Español-Jiménez, S., Li, S., & Bocconcelli, A. Diel differences in blue whale (Balaenoptera musculus) dive behavior increase nighttime risk of ship strikes in northern Chilean Patagonia. Integrative Zoology, (2020): 1-18, doi:10.1111/1749-4877.12501.
    Description: The northern Chilean Patagonia region is a key feeding ground and a nursing habitat in the southern hemisphere for blue whales (Balaenoptera musculus). From 2014 to 2019, during 6 separate research cruises, the dive behavior of 28 individual blue whales was investigated using bio‐logging tags (DTAGs), generating ≈190 h of data. Whales dove to significantly greater depths during the day compared to nighttime (day: 32.6 ± 18.7 m; night: 6.2 ± 2.7 m; P 〈 0.01). During the night, most time was spent close to the surface (86% ± 9.4%; P 〈 0.01) and at depths of less than 12 m. From 2016 to 2019, active acoustics (scientific echosounders) were used to record prey (euphausiids) density and distribution simultaneously with whale diving data. Tagged whales appeared to perform dives relative to the vertical migration of prey during the day. The association between diurnal prey migration and shallow nighttime dive behavior suggests that blue whales are at increased risk of ship collisions during periods of darkness since the estimated maximum ship draft of vessels operating in the region is also ≈12 m. In recent decades, northern Chilean Patagonia has seen a large increase in marine traffic due to a boom in salmon aquaculture and the passenger ship industry. Vessel strike risks for large whales are likely underestimated in this region. Results reported in this study may be valuable for policy and mitigation decisions regarding conservation of the endangered blue whale.
    Description: This work was conducted under Chilean research permit PINV 38–2014 Ballena Azul, Golfo Corcovado, from the Ministerio de Economia, Fomento y Turismo, Subsecreteria de Pesca y Acuicultura. We would like to thank the crews of the vessels Centinela, Khronos and Solidaridad for their involvement in the fieldwork. Special thanks to Rafaela Landea‐Briones, Gloria Howes, Esteban Tapia Brunet, Pepe Montt, Thomas Montt, and Daniel Casado for helping and welcoming us in Patagonia. Thanks to MERI Foundation and their students Carlos Cantergiani, Andrea Hirmas and Elvira Vergara for their support and contributions to field efforts. We extend our gratitude to our collaborators Laela Sayigh, Michael Moore, Daniel Zitterbart, Frants Jensen, Aran Mooney, John Durban, Jeremy Goldbogen, and Dave Cade. Thanks to WHOI for financial and technical support. The data analysis and paper writing was financially supported by the National Key Research and Development Program of China (Grant number 2016YFC0300802); the biodiversity investigation, observation and assessment program (2019‐2023) of the Ministry of Ecology and Environment of China; and Indian Ocean Ninety‐east Ridge Ecosystem and Marine Environment Monitoring and Protection, supported by the China Ocean Mineral Resources R&D Association (no. DY135‐E2‐4). Additionally, FC thanks the President's International Fellowship Initiative (PIFI) of the Chinese Academy of Sciences.
    Keywords: Bio‐logging tags ; Blue whale ; Diving profile ; Ocean conservation ; Prey distribution
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    Pseudo-nitzschia in the Gulf of Maine: investigating bloom dynamics, species introduction, and climate change implications with observations and models (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: The apparent global increase in harmful algal blooms (HABs) includes Pseudo-nitzschia blooms in the Gulf of Maine, where shellfishery closures can cost millions of dollars. Temperatures in the gulf are warming, which can affect the severity of some HABs. Yet Pseudo-nitzschia in the region are understudied. Pseudo-nitzschia bloom dynamics, P. australis introduction, and potential future changes thereof were investigated in the Gulf of Maine. Data from ship surveys and moorings were used, as well as hydrodynamic, climate, and Lagrangian particle tracking models. Pseudonitzschia bloom toxicity was driven primarily by species composition, not environmental factors. P. australis was introduced to the region in 2016 via a coastal current from the Scotian Shelf. Climate change might intensify Pseudo-nitzschia blooms, shift bloom timing 1–2 weeks earlier in the spring or 4–6 weeks later in the fall, or lengthen the growing season by 3 weeks. It might also affect species composition and connectivity within the gulf. This work has implications for the monitoring of current and future blooms in the Gulf of Maine and for our understanding of HAB introduction to the region. It can also be used to develop predictive models for Pseudo-nitzschia, which could be applied to other HABs.
    Description: This research was funded by the National Science Foundation (Grants OCE-1314642 and OCE-1840381), the National Institute of Environmental Health Sciences (Grants 1P01ES021923-01 and P01 ES028938-01), the Woods Hole Center for Oceans and Human Health, WHOI Academic Programs Funds, the Vannevar Bush Faculty Fellowship, and the National Oceanic and Atmospheric Administration’s HAB Event Response Program (2012 and 2016).
    Keywords: Harmful algal blooms ; Modeling ; Gulf of Maine
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    Ambient acoustics as indicator of environmental change in the Beaufort Sea: experiments & methods for analysis (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: The Arctic Ocean is a vital component of Earth’s climate system experiencing dramatic environmental changes. The changes are reflected in its underwater ambient soundscape as its origin and propagation are primarily dependent on properties of the ice cover and water column. The first component of this work examines the effect on ambient noise characteristics due to changes to the Beaufort Sea sound speed profile (SSP) and ice cover. Specifically, the emergence of a warm water intrusion near 70 m depth has altered the historical Arctic SSP while the ice cover has become thinner and younger due to the rise in average global temperature. Hypothesized shifts to the ambient soundscape and surface noise generation due to these changes are verified by comparing the measured noise data during two experiments to modeled results. These changes include a broadside notch in noise vertical directionality as well as a shift from uniform surface noise generation to discrete generation at specific ranges. Motivated by our data analyses, the second component presents several tools to facilitate ambient noise characterization and generation monitoring. One is a convolutional neural network (CNN) approach to noise range estimation. Its robustness to SSP and bottom depth mismatch is compared with conventional matched field processing. We further explore how the CNN approach achieves its performance by examining its intermediate outputs. Another tool is a frequency domain, transient event detection algorithm that leverages image processing and hierarchical clustering to identify and categorize noise transients in data spectrograms. The spectral content retained by this method enables insight into the generation mechanism of the detected events by the ice cover. Lastly, we present the deployment of a seismo-acoustic system to localize transient events. Two forward approaches that utilize time-difference-ofarrival are described and compared with a more conventional, inverse technique. The examination of this system’s performance prompts recommendations for future deployments. With our ambient noise analysis and algorithm development, we hope these contributions provide a stronger foundation for continued study of the Arctic ambient soundscape as the region continues to grow in significance.
    Description: Office of Naval Research (ONR) via the University of California - San Diego (UCSD) under award number N00014-16-1-2129. Defense Advanced Research Projects Agency (DARPA) via Applied Physical Sciences Corp. (APS) under award number HR0011-18-C-0008. Office of Naval Research (ONR) under award number N00014-17-1-2474. Office of Naval Research (ONR) under award number N00014-19-1-2741. National Science Foundation (NSF) under grant number 2389237.
    Keywords: Ambient noise ; Arctic change ; Noise analysis
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    Barrier island groundwater dynamics (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: Nearly 1.5 million people inhabit barrier islands along the U.S. Atlantic and Gulf Coasts and coastal groundwater dynamics influence the availability of freshwater, ecosystem health, pollutant transport, and flooding in these densely populated communities. However, groundwater dynamics, including the aquifer head distribution and subsurface salinity structure, in coastal aquifers are affected by multiple environmental forcings, such as waves, tides, storm surges, and precipitation that act on a variety of spatial and temporal scales, making coastal groundwater dynamics complex and difficult to predict. Here, measurements of groundwater heads, salinities, and temperatures collected for 3 years across a 550-m-wide barrier island are used in conjunction with observations of ocean tides, surge, waves, sound level, and rainfall to characterize the dynamics of the surface aquifer. Infiltration from surge, tides, and waves during storms caused up to 2 m increases in the groundwater level under the dune. The head gradients owing to these storm-induced groundwater bulges suggest flows become inland directed on the ocean-side of the island during storms. An upper saline plume (20-30 PSU) was observed above fresher (10 PSU) water up to 30 m inland of the dune face, which was the maximum wave runup location. Differences in inland propagation between tidal- and storm-induced groundwater head fluctuations are explained using analytical theories for intermediate depth aquifers. Additionally, a separate analytical water-table evolution model driven with estimated ocean shoreline water levels (based on the 36-hr-averaged offshore tide, surge, and wave height) and measured precipitation is validated by citizen-science flood reports and predicts the maximum water-table height within 0.1 m of the observed levels across the barrier island.
    Description: Funding for this research was provided by the U.S. Coastal Research Program, the National Science Foundation, a National Science Foundation Graduate Research Fellowship, the Woods Hole Oceanographic ISP program, and National Security Science & Engineering and Vannevar Bush Faculty Fellowships.
    Keywords: Groundwater ; Storms ; Coastal aquifer
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    A Virtual Ocean framework for environmentally adaptive, embedded acoustic navigation on autonomous underwater vehicles (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Autonomous underwater vehicles (AUVs) are an increasingly capable robotic platform, with embedded acoustic sensing to facilitate navigation, communication, and collaboration. The global positioning system (GPS), ubiquitous for air- and terrestrial-based drones, cannot position a submerged AUV. Current methods for acoustic underwater navigation employ a deterministic sound speed to convert recorded travel time into range. In acoustically complex propagation environments, however, accurate navigation is predicated on how the sound speed structure affects propagation. The Arctic’s Beaufort Gyre provides an excellent case study for this relationship via the Beaufort Lens, a recently observed influx of warm Pacific water that forms a widespread yet variable sound speed lens throughout the gyre. At short ranges, the lens intensifies multipath propagation and creates a dramatic shadow zone, deteriorating acoustic communication and navigation performance. The Arctic also poses the additional operational challenge of an ice-covered, GPSdenied environment. This dissertation demonstrates a framework for a physics-based, model-aided, real-time conversion of recorded travel time into range—the first of its kind—which was essential to the successful AUV deployment and recovery in the Beaufort Sea, in March 2020. There are three nominal steps. First, we investigate the spatio-temporal variability of the Beaufort Lens. Second, we design a human-in-the-loop graphical decision-making framework to encode desired sound speed profile information into a lightweight, digital acoustic message for onboard navigation and communication. Lastly, we embed a stochastic, ray-based prediction of the group velocity as a function of extrapolated source and receiver locations. This framework is further validated by transmissions among GPS-aided modem buoys and improved upon to rival GPS accuracy and surpass GPS precision. The Arctic is one of the most sensitive regions to climate change, and as warmer surface temperatures and shrinking sea ice extent continue to deviate from historical conditions, the region will become more accessible and navigable. Underwater robotic platforms to monitor these environmental changes, along with the inevitable rise in human traffic related to trade, fishing, tourism, and military activity, are paramount to coupling national security with international climate security.
    Description: Office of Naval Research (N00014-14-1-0214) — GOATS’14 Adaptive and Collaborative Exploitation of 3-Dimensional Environmental Acoustics in Distributed Undersea Networks Draper Laboratory Incorporated (SC001-0000001039) — Positioning System for Deep Ocean Navigation (POSYDON) Office of Naval Research (N00014-16-1-2129) — MURI: The Information Content of Ocean Noise: Theory and Experiment Office of Naval Research (N00014-17-1-2474) — Environmentally Adaptive Acoustic Communication and Navigation in the New Arctic Office of Naval Research (N00014-19-1-2716) — TFO: Assessing Realism and Uncertainties in Navy Decision Aids Department of Defense, Office of Naval Research — National Defense, Science, and Engineering Graduate Fellowship
    Keywords: Beaufort Lens ; GPS-denied underwater navigation ; Marine robotics
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    Field-Portable dissolved gas sensing and perspectives in aqueous microplastic detection (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Aeronautics and Astronautics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2021.
    Description: Global temperature rise and increased atmospheric carbon dioxide (CO2) levels have affected the health of the world’s ocean and water ecosystems, impacting the balances of natural carbon cycling and causing ocean acidification. Additionally, as global temperatures rise, thawing permafrost has stimulated increased release of methane (CH4), a gas with a shorter lifetime in the atmosphere but with even more heat trapping ability than CO2. In situ analysis of dissolved gas content in surface waters is currently performed with large, expensive instruments, such as spectrometers, which are coupled with gas equilibration systems, which extract dissolved gas from water and feed it to the sensor. Accurate, low cost, and portable sensors are needed to measure the dissolved CH4 and CO2 concentration in water systems to quantify their release and understand their relationship to the global carbon budget. At the same time, while greenhouse gases are well established threats to water ecosystems, the ubiquity and potential consequences of microplastics in aqueous environments are just beginning to be recognized by the environmental research community. Microplastics (MPs) are small particles of polymer debris, commonly defined as being between 1 μm and 1000 μm. Despite the pervasiveness of MPs, our ability to characterize MPs in the environment is limited by the lack of technologies for rapidly and accurately identifying and quantifying MPs. This thesis is concerned with the engineering challenges prompted by the need for high quality and quantity environmental data to better study and the impact, cycling, and prevalence of these pollutants in aqueous environments. Three distinct investigations are presented here. First, the design of the Low-Cost Gas Extraction and Measurement System (LC-GEMS) for dissolved CO2 is presented. At just under $600 dollar to build, the LC-GEMS is an ultra-portable, toolbox-sized instrument for dissolved gas sensing in near-surface waters. The LCGEMS was characterized in the lab and demonstrated linear relationships with dissolved CO2 as well as temperature. Lab calibrations and subsequent field testing in the Little Sippewissett Marsh, in Falmouth, Massachusetts showed that the LCGEMS captures both diurnal and minute-time scale trends in dissolved CO2. Second, this thesis presents the novel design of three simple and low-cost planar nanophotonic and plasmonic structures as optical transducers for measuring dissolved CH4. Through simulations, the sensitivity of the structures are evaluated and found to exhibit superior performance in the reflectance intensity readout mode to that of the standard surface-plasmon-polariton-mode Spreeta sensor. A practical, small, and low-cost implementation of this chip with a simple intensity-based measurement scheme is proposed. This design is novel in the space of dissolved gas monitoring because it shows potential to measure directly in the water phase while being robust and low-cost to implement. Finally, this thesis presents a literature review and perspective to motivate the development of field-deployable microplastic sensing techniques. A framework for field-deployable microplastic sensing is presented and seeks to inform the MP community of the potential in both traditional MP analysis techniques and unconventional methods for creating rapid and automated MP sensors. The field-deployabilty framework addresses a full scope of practical/technological trade-offs to be considered for portable MP detection.
    Keywords: Dissolved gas ; Microplastics ; Instrumentation
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    Characterizing the impact of underwater glider observations on the Navy Coastal Ocean Model (NCOM) in the Gulf Stream Region (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: As the western boundary current of the North Atlantic, the Gulf Stream is a well established area of interest for the United States Navy, predominately due to its proximity to the continental shelf and the associated challenges of acoustic propagation across large property gradients. Autonomous underwater gliders conduct routine, high-resolution surveys along the U.S. East Coast, including within the Gulf Stream. These observations are assimilated into the operational Navy Coastal Ocean Model (NCOM). An investigation of the forecast-to-nowcast changes in the model for 2017 demonstrates the impact of the observations on the model. The magnitude of model change as a function of distance from nearest new observation reveals relatively large impact of glider observations within a radius of 𝒪(100) km. Glider observations are associated with larger local impact than Argo data, likely due to glider sampling focusing on large spatial gradients. Due to the advective nature of the Gulf Stream system, the impact of glider observations in the model is anisotropic with larger impacts extending downstream from observation locations. Forecast-to-nowcast changes in modeled temperature, salinity, and density result in improved agreement between observed and modeled ocean structure within the upper 200 m over the 24 hours between successive model runs.
    Description: This research was funded via the United States Navy’s Civilian Institution Program with the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program (MIT/WHOI JP). Glider observations and analyses have been generously supported by the National Science Foundation (OCE-0220769, OCE-1558521, OCE-1633911, OCE-1923362), NOAA’s Global Ocean Monitoring and Observing Program (NA14OAR4320158, NA19OAR4320074), the Office of Naval Research (N000141713040), Eastman Chemical Corporation, WHOI’s Oceans and Climate Change Institute, and the W. Van Alan Clark, Jr. Chair for Excellence in Oceanography at WHOI (awarded to Breck Owens).
    Keywords: Model ; Glider ; Gulf Stream
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    Observing and quantifying kinematic properties and lagrangian coherent structures of ocean flows using drifter experiments (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: This thesis analyzes data from two types of unique drifter experiments in order to characterize two aspects of ocean flows that are often difficult to study. First, vertical velocities and their associated transport processes are often challenging to observe in the real ocean since vertical velocities are typically orders of magnitude smaller than horizontal velocities in mesoscale and submesoscale flows. Second, Lagrangian coherent structures (LCS) are features which categorize ocean flows into regimes of distinct behavior. These structures are also difficult to quantify in the real ocean, since sets of gridded trajectories from real ocean data (rather than model fields) are rarely available. The first experiment uses drifters drogued at multiple depths in the Alboran Sea to observe and characterize the ocean’s vertical structure, particularly near a strong front where vertical velocities are expected to be much stronger than other regions of the Ocean. The second experiment uses a roughly gridded pattern of surface drifters in the Gulf of Mexico to study LCSs as quantified by methods from dynamical systems such as finitetime Lyapunov exponents (FTLEs), trajectory arc-length, correlation dimension, dilation, Lagrangian-averaged vorticity deviation (LAVD), and spectral clustering. This thesis includes the first attempt to apply these dynamical systems techniques to real drifters for LCS detection. Overall, these experiments and the methods used in this paper are shown to be promising new techniques for quantifying both the vertical structure of ocean flows and Lagrangian Coherent Structures of flows using real drifter data. Future work may involve modified versions of the experiments, with denser sets of ocean drifters in the horizontal and/or vertical directions.
    Description: My Masters studies in the MIT/WHOI Joint Program were funded by the US Navy Civilian Institution Office.
    Keywords: Lagrangian coherent structures ; Finite-time Lyapunov exponents ; Vertical transport
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    A metabolic lens on phytoplankton physiology (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Phytoplankton are communities of diverse groups of prokaryotic and eukaryotic single-celled organisms responsible for nearly 50% of global primary production. The relative abundance of individual groups changes dynamically in response to environmental perturbations. Recent studies suggest that such changes are primarily driven by the distinct physiological responses employed by each group towards a particular perturbation. Although knowledge of some of these responses has come to light in recent years, many aspects of their metabolisms remain unknown. We attempt to address this gap by studying the metabolism of several phytoplankton groups using metabolomics. Firstly, we developed a method to enhance the analysis of untargeted metabolomics data. Secondly, we constructed two conceptual models describing how metabolism of the raphidophyte Heterosigma akashiwo responds to phosphorus and nitrogen stress. These conceptual models revealed several new stress response mechanisms not previously reported in other phytoplankton. Finally, we compared the metabolic changes of several distinct phytoplankton groups to uncover possible adaptation and acclimations that distinguish them. This analysis revealed several pathways and metabolites that represent the studied groups. The contributions of these pathways and metabolites towards physiology may support the ecological fitness of these organisms.
    Description: None of this work would have been possible without a variety of funding sources. I was supported for three years by a National Science Foundation Graduate Research Fellowship and one year with a GEM fellowship. The research was carried out with grants from the MIT Microbiome Center (Award ID #6936800, EBK), the Simons Foundation (Award ID #509034, EBK), the Gordon and Betty Moore Foundation (Award ID #3304 EBK), the National Science Foundation (Award ID #OCE-0619608 to EBK and OCE-1057447 to EBK and MCKS) and the WHOI Ocean Ventures Fund.
    Keywords: Phytoplankton ; Metabolism ; Metbolomics
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    Human-autonomy teaming for improved diver navigation (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Diving operations are inherently complex due to navigation and communication limitations. Until recently, fixed-beacon acoustic localization techniques have served as the primary means of improving diver navigation. However, modern artificial intelligence and acoustic modem technologies have enabled accurate relative navigation methods between a diver and an autonomous vehicle. Human-robot collaboration takes advantage of each member’s strengths to create the most effective team. This concept proves especially advantageous within the ocean domain, where humans are naturally deficient navigators. Yet humans serve as the team’s creative spirit, offering the critical thinking and flexibility needed to succeed in an unpredictable and dynamic environment. Recent underwater human-robot cooperative navigation systems typically rely on autonomous surface vehicles (ASVs), specially designed underwater vehicles, or stereo cameras. This thesis proposes a diver navigation method exhibiting significantly improved accuracy over dead reckoning without relying on a surface presence, cameras, or fixed acoustic beacons. Specifically, we develop and evaluate the communication architecture and autonomous behaviors required to guide a diver to a target location using subsurface humanautonomous underwater vehicle (AUV) teaming with no requirement for ocean current data or exact diver speeds. By depending on acoustic communication and commercial AUV navigation capabilities, our method has increased accessibility, applicability, and robustness over former techniques. We utilize the Woods Hole Oceanographic Institution (WHOI) Micromodem 2’s twoway-travel-time (TWTT) capability to enable range-only single-beacon navigation between two kayaks serving as proxies for the diver and Remote Environmental Monitoring Units (REMUS) 100 AUV. During processing, a nonlinear least-squares (NLS) method, called incremental smoothing and mapping 2 (iSAM2), utilizes odometry and range measurements to provide real-time diver position estimates given unknown ocean currents. Field experiments demonstrate an average online endpoint error of 4.53 meters after transits four hundred meters long. Additionally, simulations test our method’s performance in more challenging situations than those experienced in the field. Overall, this research progresses the interoperability of divers and AUVs.
    Description: The United States Navy funded my graduate education. The Office of Naval Research also partially supported this work under grant N00014-18-1-2832.
    Keywords: Human-autonomy teaming ; Autonomous underwater vehicle ; Diver navigation
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    Molecular characterization of organically bound copper in the marine environment (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: Marine microbes require copper (Cu) for a variety of key enzymes and can therefore experience limitation when concentrations are low. However, when Cu concentrations are too high, it becomes toxic causing decreased cell growth and even cell death. Laboratory culture experiments have shown that a diverse array of microbes produce organic ligands that complex Cu (CuL) and buffer the free ion concentration, which is the most bioavailable fraction. In this way, the microbes impose a control on the speciation of Cu, decreasing the toxic effects of Cu and making seawater conditions favorable for growth. Studies have shown that CuL complexes produced in laboratory cultures have similar complexation strengths to those found in seawater samples, which suggests a biological source of CuLs in seawater where dissolved Cu is almost entirely bound by organic ligands. However, information about individual CuL complexes is lacking which limits our understanding of the sources, sinks, and cycling of dissolved Cu. In order to fill this gap in knowledge, molecular level information about CuL complexes produced in culture and found in seawater must be obtained. To investigate this, liquid chromatography (LC) was coupled to two mass spectrometers (MS), an inductively coupled plasma (ICP) MS and an electrospray ionization (ESI) MS. By using data supplied by both techniques, the molecular charateristics of CuLs were determined laboratory cultures of the marine diatom Phaeodactylum tricornutum and the cyanobacterium Synechococcus, as well as investigating the distribution of CuLs in natural seawater samples along a line from 56°N to 20°S, along 152°W through the north and central Pacific Ocean. The CuLs identified in laboratory cultures had molecular formulae and fragmentation patterns characteristic of linear tetrapyrroles, a group of organic compounds commonly found in biological systems. This identification was further supported by absorbance and nuclear magnetic resonance spectroscopy. The distribution of CuLs in the Pacific Ocean showed a highly dynamic and complex mixture of ligands, closely tied to biological cycles.
    Description: Funding for this work was provided by the National Science Foundation Graduate Research Fellowship Program (NSF award 1122374) for providing three years of funding. Thank you to the National Science Foundation Chemical Oceanography Program (NSF award OCE-1736280 and OCE-2045223) and the Simons Collaboration on Ocean Processes and Ecology (award P49476). A portion of this work was performed at the National High Magnetic Field Laboratory in Tallahassee, Florida, which is supported through NSF DMR 11-57490, and the State of Florida.
    Keywords: Organic ligands ; Copper ; LC-MS
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    Barium isotope cycling in the marine environment: pathways of fractionation and implications for paleoceanographic applications (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: Removal of particulate organic carbon (POC) from sunlit surface waters into the deep ocean represents a climatically important sink of atmospheric carbon dioxide (CO2), linking the biogeochemical cycling of POC to CO2-driven climate change. As POC is not well preserved in the sediment record, other proxies, including the chemistry of barium (Ba) in the ocean and through the sedimentary record, offer an avenue to investigate oceanic carbon export through Earth’s history. This thesis seeks to constrain the controls on the formation, cycling, and isotopic signature of the main particulate phase of marine barium, the mineral barite (BaSO4) through its inception in the water column, during deposition, and ultimately into the rock record. To that end, I characterize the depth, spatial region, and general controls on particulate Ba formation in the South Pacific Ocean through shipboard experimentation and find that particulate Ba forms mainly in the surface of the Polar Frontal Zone in the presence of large particles and microbial activity. Next, I characterize the effect of ion exchange on BaSO4, a process previously unstudied under marine conditions, in a laboratory setting. Ion exchange occurs rapidly between dissolved Ba and BaSO4 and imparts a characteristic net offset between the Ba isotope composition of the dissolved and solid phase, which arises through a combination of Ba isotope fractionation during both precipitation and dissolution. Finally, I investigate the role of ion exchange in marine settings using co-located pore fluids and sedimented BaSO4. Modeling constrained by data from natural samples produce results that are consistent with the laboratory study, suggesting that this mode of isotopic fractionation impacts Ba isotopes in the environment and must be accounted for when applying Ba based climate proxies.
    Description: Funding for this work was provided by the National Science Foundation (OCE-2023456 & OCE-1827401), the Woods Hole Oceanographic Institution Ocean Ventures Fund, a National Science Foundation Graduate Research Fellowship (2017250048), and Woods Hole Oceanographic Institution.
    Keywords: Barium isotopes ; Geochemistry ; Paleoceanography
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    The Gulf Stream: along-stream evolution of volume transport and water properties observed by underwater gliders (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: The Gulf Stream, the western boundary current of the subtropical North Atlantic, plays a key role in the Earth’s climate system with its poleward volume and heat transports being major components of the upper limb of the Atlantic Meridional Overturning Circulation. Extensive observations collected using Spray autonomous underwater gliders from 2004 through 2020 fill a 1500-km-long gap in longer-term sustained subsurface measurements of the Gulf Stream. The gliders provide concurrent, high-resolution measurements of Gulf Stream hydrography and velocity over more than 15 degrees of latitude between Florida and New England. These observations are used to characterize the along-stream evolution of Gulf Stream volume transport; its long-known poleward increase is shown to result primarily from entrainment of subthermocline waters. Antarctic Intermediate Water, which makes up the deepest waters within the Gulf Stream in the Florida Strait, is eroded through both vertical mixing and lateral stirring as it flows downstream. Satellite-based observations of sea surface height coincident with the glider observations are used to evaluate the efficacy of inferring Gulf Stream transport from remotely sensed measurements. The detailed analyses of Gulf Stream transport and water property evolution herein provide targets for regional and global circulation models to replicate.
    Description: We gratefully acknowledge funding from the National Science Foundation (OCE-0220769, OCE-1633911, OCE-1923362, OCE-1558521), NOAA’s Global Ocean Monitoring and Observing Program (NA14OAR4320158, NA19OAR4320074), the Office of Naval Research (N000141713040), WHOI’s Oceans and Climate Change Institute, Eastman Chemical Company, and the W. Van Alan Clark, Jr. Chair for Excellence in Oceanography at WHOI (awarded to Breck Owens).
    Keywords: Gulf Stream ; Autonomous underwater gliders ; Volume transport
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    Constraining natural and anthropogenic disturbances in the delivery of coastal ecosystem services (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Coastal ecosystems provide key services that benefit human wellbeing yet are undergoing rapid degradation due to natural and anthropogenic pressures. This thesis seeks to understand how disturbances impact salt marsh and estuarine ecosystem functioning in order to refine their role in coastal ecosystem service delivery and predict future resilience. Salt marsh survival relative to sealevel rise increasingly relies on the accumulation and preservation of soil organic carbon (SOC). Firstly, I characterized SOC development and turnover in a New England salt marsh and found that salt marsh soils typically store marsh grass-derived compounds that are reworked over centuries-to-millennia. Next, I assessed how two common marsh disturbances – natural ponding and anthropogenic mosquito ditching – affect salt marsh carbon cycling and storage. Salt marsh ponds deepen through soil erosion and decomposition of long-buried marsh peat. Further, the SOC lost during pond development is not fully recouped once drained ponds are revegetated and virtually indistinguishable from the surrounding marsh. Mosquito ditches, which were installed in ~ 90% of New England salt marshes during the Great Depression, did not significantly alter marsh carbon storage. In Buzzards Bay, Massachusetts, a US National Estuary, we tested relationships among measures of estuarine water quality, recreational activity, and local socioeconomic conditions to understand how the benefits of cultural ecosystem services are affected by shifts in water quality associated with global change and anthropogenic activity. Over a 24-year period, water quality degradation coinciding with increases in Chlorophyll a is associated with declines in fishery abundance and cultural ecosystem service values ($0.08 – 0.67 million USD). In combination, incorporation of both anthropogenic and natural disturbances to coastal ecosystem functioning and service delivery can produce improved estimates of ecosystem service valuation for effective resource decision-making under future climate scenarios.
    Description: Funding for this work was provided by John D. and Catherine T. MacArthur Foundation (Grant no. 14-106159-000-CFP), National Science Foundation (OCE1233678), National Oceanic and Atmospheric Administration, National Oceanic and Atmospheric Administration – National Estuaries Research Reserve Collaborative (NA14OAR4170104 and NA- 14NOS4190145), Woods Hole Sea Grant (NA14OAR4170104), MIT Sea Grant (subaward number 5710004045), Ocean Ventures Fund, the Marine Policy Center Johnson Endowment, and Woods Hole Oceanographic Institution.
    Keywords: Salt marsh ; Geochemistry ; Carbon storage
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    Questions and clarity: insights from applying computational methods to paleoclimate archives (2022)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Marine Geology & Geophysics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 2022.
    Description: It is a scientifically accepted fact that the Earth’s climate is presently undergoing significant changes with the potential for immense negative impacts on human society. As evidence of these impacts become clear and common, it becomes ever more important to constrain the nature, magnitude, and speed of changes to Earth systems. A fundamentally important tool to this understanding is the Earth’s past, recorded in the geologic record. There, lie examples of climate change under various forcings: important data for understanding the fundamental dynamics of climate change on our planet. However, when a climate signal is written in the geologic record, it is coded into the language of proxies and distorted by time. This thesis endeavors to decode that record using a variety of computational methods on a number of challenging proxies, to draw more information from the climate past than has previously been possible. First, machine learning and computer vision are used to decipher the primary, centimeter-scale textures of carbonate deposits in Searles Valley and Mono Lake, California. This work is able to connect facies in the tufa at Searles, grown during the Last Glacial Period, and those forming presently at Mono Lake. Next, the tracks of icebergs purged during Heinrich Events are simulated using the MIT General Circulation Model. This work, running multiple experiments exploring different aspects internal and external to the icebergs, reveals wind and sediment partitioning as centrally important to the spatial extent of Heinrich Layers. Each of these works considers a traditional geologic archive – a carbonate facies, a marine sediment layer – and uses computational methods to approach that archive from a different perspective. By applying these new methods, more information can be gleaned from the geologic record, building a richer narrative of the Earth’s climate history. The final chapter of this thesis discusses effective teaching and strategies for building communities to support teaching practice in Earth Science departments.
    Description: This thesis work was funded by the MIT EAPS Rasmussen and Whiteman Fellowships, NSF Project Number NSF-EAR-1903544, and the WHOI Academic Programs Office.
    Keywords: Paleoclimate ; Iceberg ; Modeling
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    Towards automated sample collection and return in extreme underwater environments (2022)
    Wiley
    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 Billings, G., Walter, M., Pizarro, O., Johnson-Roberson, M., & Camilli, R. Towards automated sample collection and return in extreme underwater environments. Journal of Field Robotics, 2(1), (2022): 1351–1385, https://doi.org/10.55417/fr.2022045.
    Description: In this report, we present the system design, operational strategy, and results of coordinated multivehicle field demonstrations of autonomous marine robotic technologies in search-for-life missions within the Pacific shelf margin of Costa Rica and the Santorini-Kolumbo caldera complex, which serve as analogs to environments that may exist in oceans beyond Earth. This report focuses on the automation of remotely operated vehicle (ROV) manipulator operations for targeted biological sample-collection-and-return from the seafloor. In the context of future extraterrestrial exploration missions to ocean worlds, an ROV is an analog to a planetary lander, which must be capable of high-level autonomy. Our field trials involve two underwater vehicles, the SuBastian ROV and the Nereid Under Ice (NUI) hybrid ROV for mixed initiative (i.e., teleoperated or autonomous) missions, both equipped seven-degrees-of-freedom hydraulic manipulators. We describe an adaptable, hardware-independent computer vision architecture that enables high-level automated manipulation. The vision system provides a three-dimensional understanding of the workspace to inform manipulator motion planning in complex unstructured environments. We demonstrate the effectiveness of the vision system and control framework through field trials in increasingly challenging environments, including the automated collection and return of biological samples from within the active undersea volcano Kolumbo. Based on our experiences in the field, we discuss the performance of our system and identify promising directions for future research.
    Description: This work was funded under a NASA PSTAR grant, number NNX16AL08G, and by the National Science Foundation under grants IIS-1830660 and IIS-1830500. The authors would like to thank the Costa Rican Ministry of Environment and Energy and National System of Conservation Areas for permitting research operations at the Costa Rican shelf margin, and the Schmidt Ocean Institute (including the captain and crew of the R/V Falkor and ROV SuBastian) for their generous support and making the FK181210 expedition safe and highly successful. Additionally, the authors would like to thank the Greek Ministry of Foreign Affairs for permitting the 2019 Kolumbo Expedition to the Kolumbo and Santorini calderas, as well as Prof. Evi Nomikou and Dr. Aggelos Mallios for their expert guidance and tireless contributions to the expedition.
    Keywords: Underwater robotics ; Mobile manipulation ; Marine robotics ; Exploration
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    Evaluation of alkenones, a renewably sourced, plant-derived wax as a structuring agent for lipsticks (2020)
    Wiley
    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 Huynh, A., Maktabi, B., Reddy, C. M., O'Neil, G. W., Chandler, M., & Baki, G. Evaluation of alkenones, a renewably sourced, plant-derived wax as a structuring agent for lipsticks. International Journal of Cosmetic Science, (2020), doi:10.1111/ics.12597.
    Description: OBJECTIVE Waxes are used as structuring agents in lipsticks. There are a variety of waxes combined in a single lipstick to provide good stability, pleasant texture and good pay‐off. Due to a significant growth for natural, green and sustainable products, there is a constant search for alternatives to animal‐derived and petroleum‐derived ingredients. In this study, a green, non‐animalderived wax, namely long‐chain ketones (referred to as alkenones), sourced from marine microalgae was formulated into lipsticks and evaluated as a structuring agent. METHODS Alkenones were used as a substitute for microcrystalline wax, ozokerite and candelilla wax, typical structuring agents. In total, 384 lipsticks were formulated: L1 (control, no alkenones), L2 (alkenones as a substitute for ozokerite), L3 (alkenones as a substitute for microcrystalline wax) and L4 (alkenones as a substitute for candelilla wax). Products were tested for hardness (bending force), stiffness, firmness (needle penetration), pay‐off (using a texture analyser and a consumer panel), friction, melting point and stability for 12 weeks at 25 and 45°C. RESULTS Alkenones influenced each characteristic evaluated. In general, lipsticks with alkenones (L2‐L4) became softer and easier to bend compared to the control (L1). In terms of firmness, lipsticks were similar to the control, except for L4, which was significantly (P 〈 0.05) firmer. The effect on pay‐off was not consistent. L2 and L3 had higher pay‐off to skin and fabric than L1. In addition, L4 had the lowest amount transferred, but it still had the highest colour intensity on skin. Alkenones influenced friction (glide) positively; the average friction decreased for L2‐L4. The lowest friction (i.e. best glide) was shown in L4. Melting point of the lipsticks was lower when alkenones were present. Overall, L4, containing 7% of 4 alkenones in combination with microcrystalline wax, ozokerite and carnauba wax, was found to have the most desirable attributes, including ease of bending, high level of firmness, low pay‐off in terms of amount, high colour intensity on skin and low friction (i.e. better glide). Consumers preferred L4 the most overall. CONCLUSION Results of this study indicate that alkenones offer a sustainable, non‐animal and non‐petroleum‐derived choice as a structuring agent for lipsticks.
    Description: The authors would like to thank Texture Technologies for the technical assistance provided during this project. This research was funded by the Washington Research Foundation and a private donor from friends of the Woods Hole Oceanographic Institution, grant number N‐127244.
    Keywords: Colour cosmetics ; Formulation/stability ; Statistics ; Alkenones ; Lipstick
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  • 139
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    Albatrosses respond adaptively to climate variability by changing variance in a foraging trait (2021)
    Wiley
    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 Patrick, S. C., Martin, J. G. A., Ummenhofer, C. C., Corbeau, A., & Weimerskirch, H. Albatrosses respond adaptively to climate variability by changing variance in a foraging trait. Global Change Biology, (2021), https://doi.org/10.1111/gcb.15735.
    Description: The ability of individuals and populations to adapt to a changing climate is a key determinant of population dynamics. While changes in mean behaviour are well studied, changes in trait variance have been largely ignored, despite being assumed to be crucial for adapting to a changing environment. As the ability to acquire resources is essential to both reproduction and survival, changes in behaviours that maximize resource acquisition should be under selection. Here, using foraging trip duration data collected over 7 years on black-browed albatrosses (Thalassarche melanophris) on the Kerguelen Islands in the southern Indian Ocean, we examined the importance of changes in the mean and variance in foraging behaviour, and the associated effects on fitness, in response to the El Niño Southern Oscillation (ENSO). Using double hierarchical models, we found no evidence that individuals change their mean foraging trip duration in response to a changing environment, but found strong evidence of changes in variance. Younger birds showed greater variability in foraging trip duration in poor conditions as did birds with higher fitness. However, during brooding, birds showed greater variability in foraging behaviour under good conditions, suggesting that optimal conditions allow the alteration between chick provisioning and self-maintenance trips. We found weak correlations between sea surface temperature and the ENSO, but stronger links with sea-level pressure. We suggest that variability in behavioural traits affecting resource acquisition is under selection and offers a mechanism by which individuals can adapt to a changing climate. Studies which look only at effects on mean behaviour may underestimate the effects of climate change and fail to consider variance in traits as a key evolutionary force.
    Description: The authors thank the Institut Polaire Français Paul Emile Victor (IPEV, programme 109 to HW) for providing financial and logistical support for the field work at Kerguelen, and to the Terres Australes et Antarctique Francaises (TAAF). The usage of the following data sets is gratefully acknowledged: SOI, NCEP/NCAR SLP and NOAA OISST v2, all provided by NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, through https://www.esrl.noaa.gov/psd. CCU acknowledges support from the Joint Initiative Awards Fund from the Andrew W. Mellon Foundation and the James E. and Barbara V. Moltz Fellowship for Climate-Related Research.
    Keywords: Bet-hedging ; Intra-individual variability ; Resource acquisition ; Salt-water immersion logger ; Seabirds ; Southern Oscillation Index
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    Residual overturning circulation and its connection to Southern Ocean dynamics (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: Over the last 20 years, our understanding of the meridional overturning circulation has improved, but primarily in a two-dimensional, zonally-averaged framework. In this thesis, I have pushed beyond this simplification and shown that the additional complexity of meanders, storm tracks, and other zonal asymmetries is necessary to reproduce the lowest-order behavior of the overturning circulation. First I examined the role of basin width for determining whether the Atlantic or Pacific oceans experience deep convection. I used a two layered model and a rectangular single-basin model to show that the basin width, in combination with scalings for the overturning circulation make the overturning relatively weaker in the wider basin, priming it for a convection shut down. In addition to this large-scale work, I have examined Southern Ocean-like meanders using a hierarchy of idealized models to understand the role of bottom topography in determining how the large-scale circulation responds to climate change scenarios. These are useful because they preserve the lowest-order behavior, while remaining simple enough to understand. I tested the response of the stratification and transport in the Southern Ocean to changes in wind using a highly-idealized two-layer quasi-geostrophic model. In addition to showing that meanders are necessary to reproduce the behavior of the Southern Ocean, I found that strong winds concentrate the baroclinic and barotropic instabilities downstream of the bottom topography and weaken the instabilities elsewhere due to a form-drag process. With weak winds, however, the system is essentially symmetric in longitude, like a flat-bottomed ocean. This result is consistent with observations of elevated turbulence downstream of major topography in the Southern Ocean. My next study investigated a more realistic Southern Ocean-like channel, with and without bottom topography, and examined the three-dimensional circulation in order to understand where vertical transport occurs and develop a picture of the pathways taken by each individual water parcel. I found that the vertical transport happens in very isolated locations, just downstream of topography. Finally, I added a biogeochemical model to my simulations and found that carbon fluxes are enhanced near topography, again highlighting the role of zonal asymmetries.
    Description: I have been funded by the American Meteorological Society’s Graduate Fellowship, as well as the National Defense Science and Engineering Graduate Fellowship. I have also been supported by NSF OCE-1536515 and NCAR Large Scale Computing Award UMIT0025.
    Repository Name: Woods Hole Open Access Server
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  • 141
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    Isotopic evidence for the formation of the moon in a canonical giant impact (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nielsen, S. G., Bekaert, D. V., & Auro, M. Isotopic evidence for the formation of the moon in a canonical giant impact. Nature Communications, 12(1), (2021): 1817, https://doi.org/10.1038/s41467-021-22155-7.
    Description: Isotopic measurements of lunar and terrestrial rocks have revealed that, unlike any other body in the solar system, the Moon is indistinguishable from the Earth for nearly every isotopic system. This observation, however, contradicts predictions by the standard model for the origin of the Moon, the canonical giant impact. Here we show that the vanadium isotopic composition of the Moon is offset from that of the bulk silicate Earth by 0.18 ± 0.04 parts per thousand towards the chondritic value. This offset most likely results from isotope fractionation on proto-Earth during the main stage of terrestrial core formation (pre-giant impact), followed by a canonical giant impact where ~80% of the Moon originates from the impactor of chondritic composition. Our data refute the possibility of post-giant impact equilibration between the Earth and Moon, and implies that the impactor and proto-Earth mainly accreted from a common isotopic reservoir in the inner solar system.
    Description: This study was funded by NASA Emerging Worlds grant NNX16AD36G to S.G.N. We thank NASA-JSC, Tony Irving, and Thorsten Kleine for access to meteorite and Apollo mission samples. US Antarctic meteorite samples are recovered by the Antarctic Search for Meteorites (ANSMET) program, which has been funded by NSF and NASA, and characterized and curated by the Astromaterials Curation Office at NASA Johnson Space Center and the Department of Mineral Sciences of the Smithsonian Institution. J. Blusztajn is thanked for help with mass spectrometry support at WHOI.
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  • 142
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    Possible limitations of dolphin echolocation: a simulation study based on a cross-modal matching experiment (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wei, C., Hoffmann-Kuhnt, M., Au, W. W. L., Ho, A. Z. H., Matrai, E., Feng, W., Ketten, D. R., & Zhang, Y. Possible limitations of dolphin echolocation: a simulation study based on a cross-modal matching experiment. Scientific Reports, 11(1), (2021): 6689, https://doi.org/10.1038/s41598-021-85063-2.
    Description: Dolphins use their biosonar to discriminate objects with different features through the returning echoes. Cross-modal matching experiments were conducted with a resident bottlenose dolphin (Tursiops aduncus). Four types of objects composed of different materials (water-filled PVC pipes, air-filled PVC pipes, foam ball arrays, and PVC pipes wrapped in closed-cell foam) were used in the experiments, respectively. The size and position of the objects remained the same in each case. The data collected in the experiment showed that the dolphin’s matching accuracy was significantly different across the cases. To gain insight into the underlying mechanism in the experiments, we used finite element methods to construct two-dimensional target detection models of an echolocating dolphin in the vertical plane, based on computed tomography scan data. The acoustic processes of the click’s interaction with the objects and the surrounding media in the four cases were simulated and compared. The simulation results provide some possible explanations for why the dolphin performed differently when discriminating the objects that only differed in material composition in the previous matching experiments.
    Description: One of the authors, Wei. C is supported by a Forrest Research Foundation Fellowship. Support for D. Ketten for this effort was provided by the Joint Industry Programme and by the Helmholtz Foundation. This work was also supported by the Hawaii Institute of Marine Biology (HIMB) contribution No. 1630 and School of Ocean and Earth Science and Technology (SOEST) contribution No. 9452.
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    Postnatal structural development of mammalian basilar membrane provides anatomical basis for the maturation of tonotopic maps and frequency tuning (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tani, T., Koike-Tani, M., Tran, M. T., Shribak, M., & Levic, S. Postnatal structural development of mammalian basilar membrane provides anatomical basis for the maturation of tonotopic maps and frequency tuning. Scientific Reports, 11(1), (2021): 7581, https://doi.org/10.1038/s41598-021-87150-w.
    Description: The basilar membrane (BM) of the mammalian cochlea constitutes a spiraling acellular ribbon that is intimately attached to the organ of Corti. Its graded stiffness, increasing from apex to the base of the cochlea provides the mechanical basis for sound frequency analysis. Despite its central role in auditory signal transduction, virtually nothing is known about the BM’s structural development. Using polarized light microscopy, the present study characterized the architectural transformations of freshly dissected BM at time points during postnatal development and maturation. The results indicate that the BM structural elements increase progressively in size, becoming radially aligned and more tightly packed with maturation and reach the adult structural signature by postnatal day 20 (P20). The findings provide insight into structural details and developmental changes of the mammalian BM, suggesting that BM is a dynamic structure that changes throughout the life of an animal.
    Description: This work was supported by Medical Research Council grant MR/ N004299/1 (to SL), University of Sussex Research Innovation Funds (to SL), Brighton and Sussex Medical School research funds (to SL), National Institute of General Medical Sciences, NIH grant R01 GM101701 (to MS), NIH R01 GM100160 (to TT) and KAKENHI JP18K19962 (to TT).
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  • 144
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    A warm jet in a cold ocean (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MacKinnon, J. A., Simmons, H. L., Hargrove, J., Thomson, J., Peacock, T., Alford, M. H., Barton, B., Boury, S., Brenner, S. D., Couto, N., Danielson, S. L., Fine, E. C., Graber, H. C., Guthrie, J., Hopkins, J. E., Jayne, S. R., Jeon, C., Klenz, T., Lee, C. M., Lenn, Y-D., Lucas, A. J., Lund, B., Mahaffey, C., Norman, L., Rainville, L., Smith, M. M., Thomas, L. N., Torres-Valdés, S., & Wood, K. R. A warm jet in a cold ocean. Nature Communications, 12(1), (2021): 2418, https://doi.org/10.1038/s41467-021-22505-5.
    Description: Unprecedented quantities of heat are entering the Pacific sector of the Arctic Ocean through Bering Strait, particularly during summer months. Though some heat is lost to the atmosphere during autumn cooling, a significant fraction of the incoming warm, salty water subducts (dives beneath) below a cooler fresher layer of near-surface water, subsequently extending hundreds of kilometers into the Beaufort Gyre. Upward turbulent mixing of these sub-surface pockets of heat is likely accelerating sea ice melt in the region. This Pacific-origin water brings both heat and unique biogeochemical properties, contributing to a changing Arctic ecosystem. However, our ability to understand or forecast the role of this incoming water mass has been hampered by lack of understanding of the physical processes controlling subduction and evolution of this this warm water. Crucially, the processes seen here occur at small horizontal scales not resolved by regional forecast models or climate simulations; new parameterizations must be developed that accurately represent the physics. Here we present novel high resolution observations showing the detailed process of subduction and initial evolution of warm Pacific-origin water in the southern Beaufort Gyre.
    Description: Support for this work was provided by the US Office of Naval Research Stratified Ocean Dynamics of the Arctic program (grant numbers N000141512903, N000141612378, N000141612377, N000141612379, N0001416123450, N000141612360, N000141612349, N000141812007, N000141812475, and N000141912514). Additional support for biogeochemistry sampling was provided by UK (NERC) and Germany (BMBF) through the Changing Arctic Ocean Program’s ARISE (NE/P006035/1, NE/P006000/2), PEANUTS (NE/R01275X/1, NE/R012547/2, and BMBF 03F0804) projects and the UK-France PhD program DGA/Dstl. Float deployments and hydrographic data compilations were supported in part by North Pacific Research Board grants A91-99a and A91-00a. The deployment of autonomous ocean profilers was supported by ONR, NOAA Research, and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA15OAR4320063.
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    Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sivaguru, M., Todorov, L. G., Fouke, C. E., Munro, C. M. O., Fouke, K. W., Fouke, K. E., Baughman, M. E., & Fouke, B. W. Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature. Scientific Reports, 11(1), (2021): 2230, https://doi.org/10.1038/s41598-021-81520-0.
    Description: The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.
    Description: Financial support for this work was provided by the Office of Naval Research (N00014-00-1-0609), the Illinois Carl R. Woese Institute for Genomic Biology Undergraduate Summer Research Fellowship, the Illinois Carl R. Woese Institute for Genomic Biology Mark Tracy Fellowship for Translational Research, and the Illinois Department of Molecular and Cellular Biology Jenner Family Summer Research Fellowship and the Edward and Barbara Weil Research Fund provided to the University of Illinois Urbana-Champaign.
    Keywords: Autofluorescence ; Two-photon microscopy ; X-ray Micro CT ; Water Depth ; Bathymetry ; Sea surface temperature ; Symbiodiniaceae symbiont ; chromatophores ; calmodulin ; carbonic anhydrase ; mucus ; Scleractinian corals ; Orbicella annularis ; Orbicella faveolata
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    The call of the emperor penguin: legal responses to species threatened by climate change (2021)
    Wiley
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jenouvrier, S., Judy, C.-C., Wolf, S., Holland, M., Labrousse, S., LaRue, M., Wienecke, B., Fretwell, P., Barbraud, C., Greenwald, N., Stroeve, J., & Trathan, P. N. The call of the emperor penguin: legal responses to species threatened by climate change. Global Change Biology, 27, (2021): 5008– 5029, https://doi.org/10.1111/gcb.15806.
    Description: Species extinction risk is accelerating due to anthropogenic climate change, making it urgent to protect vulnerable species through legal frameworks in order to facilitate conservation actions that help mitigate risk. Here, we discuss fundamental concepts for assessing climate change risks to species using the example of the emperor penguin (Aptenodytes forsteri), currently being considered for protection under the US Endangered Species Act (ESA). This species forms colonies on Antarctic sea ice, which is projected to significantly decline due to ongoing greenhouse gas (GHG) emissions. We project the dynamics of all known emperor penguin colonies under different GHG emission scenarios using a climate-dependent meta-population model including the effects of extreme climate events based on the observational satellite record of colonies. Assessments for listing species under the ESA require information about how species resiliency, redundancy and representation (3Rs) will be affected by threats within the foreseeable future. Our results show that if sea ice declines at the rate projected by climate models under current energy system trends and policies, the 3Rs would be dramatically reduced and almost all colonies would become quasi-extinct by 2100. We conclude that the species should be listed as threatened under the ESA.
    Description: We acknowledge support of NASA (80NSSC20K1289) to SJ, MH, and of NSF—OPP (1744794) to SJ, ML.
    Keywords: climate risk assessments ; Endangered Species Act ; foreseeable future ; population projections ; resiliency, redundancy and representation (3Rs) ; sea ice projections ; species distribution ; treatment of scientific uncertainty
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    Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, M. D., Scott, J. J., Leray, M., Lucey, N., Bravo, L. M. R., Wied, W. L., & Altieri, A. H. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nature Communications, 12(1), (2021): 4522, https://doi.org/10.1038/s41467-021-24777-3.
    Description: Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.
    Description: M.D.J. was funded by postdoctoral fellow awards from the Smithsonian Institution’s Marine Global Earth Observatory (MarineGEO) and the Smithsonian Tropical Research Institute (STRI); M.L. and N.L. were funded by postdoctoral support from the STRI Office of Fellowships. J.J.S. was funded by a grant from the Gordon and Betty Moore Foundation awarded to STRI and UC Davis (doi:10.37807/GBMF5603). L.M.R.B., W.L.W., and A.H.A. were supported by MarineGEO, a private funder, and STRI funds to A.H.A. Many of the computations were conducted on the Smithsonian High-Performance Cluster (SI/HPC), Smithsonian Institution (doi:10.25572/SIHPC). We thank Rachel Collin for facilities support at the Bocas del Toro Research Station, Plinio Gondola and the research station staff for logistical support, Roman Barco for insight into the functional analyses, Sherly Castro for informative feedback, and Mike Fox for assistance with community analyses. Research permits were provided by the Autoridad Nacional del Ambiente de Panamá. This paper is the result of research funded by the National Oceanic and Atmospheric Administration’s National Centers for Coastal Ocean Science Competitive Research Program under award NA18NOS4780170 to A.H.A. and M.D.J. through the University of Florida. This is contribution 257 from the Coastal Hypoxia Research Program and 86 from the Smithsonian’s MarineGEO and Tennenbaum Marine Observatories Network.
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    An intermittent detachment faulting system with a large sulfide deposit revealed by multi-scale magnetic surveys (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wu, T., Tivey, M. A., Tao, C., Zhang, J., Zhou, F., & Liu, Y. An intermittent detachment faulting system with a large sulfide deposit revealed by multi-scale magnetic surveys. Nature Communications, 12(1), (2021): 5642, https://doi.org/10.1038/s41467-021-25880-1.
    Description: Magmatic and tectonic processes can contribute to discontinuous crustal accretion and play an important role in hydrothermal circulation at ultraslow-spreading ridges, however, it is difficult to accurately describe the processes without an age framework to constrain crustal evolution. Here we report on a multi-scale magnetic survey that provides constraints on the fine-scale evolution of a detachment faulting system that hosts hydrothermal activity at 49.7°E on the Southwest Indian Ridge. Reconstruction of the multi-stage detachment faulting history shows a previous episode of detachment faulting took place 0.76~1.48 My BP, while the present fault has been active for the past ~0.33 My and is just in the prime of life. This fault sustains hydrothermal circulation that has the potential for developing a large sulfide deposit. High resolution multiscale magnetics allows us to constrain the relative balance between periods of detachment faulting and magmatism to better describe accretionary processes on an ultraslow spreading ridge.
    Description: This work was supported by National Key R&D Program of China under contract no. 2018YFC0309901, National Natural Science Foundation of China (41906065), National Key R&D Program of China (2017YFC0306803) and COMRA Major Project under contract no. DY135-S1-01-06 and no. DY135-S1-01-01.
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    Asynchronous release sites align with NMDA receptors in mouse hippocampal synapses (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Li, S., Raychaudhuri, S., Lee, S. A., Brockmann, M. M., Wang, J., Kusick, G., Prater, C., Syed, S., Falahati, H., Ramos, R., Bartol, T. M., Hosy, E., & Watanabe, S. Asynchronous release sites align with NMDA receptors in mouse hippocampal synapses. Nature Communications, 12(1), (2021): 677, https://doi.org/10.1038/s41467-021-21004-x.
    Description: Neurotransmitter is released synchronously and asynchronously following an action potential. Our recent study indicates that the release sites of these two phases are segregated within an active zone, with asynchronous release sites enriched near the center in mouse hippocampal synapses. Here we demonstrate that synchronous and asynchronous release sites are aligned with AMPA receptor and NMDA receptor clusters, respectively. Computational simulations indicate that this spatial and temporal arrangement of release can lead to maximal membrane depolarization through AMPA receptors, alleviating the pore-blocking magnesium leading to greater activation of NMDA receptors. Together, these results suggest that release sites are likely organized to activate NMDA receptors efficiently.
    Description: e also thank the Marine Biological Laboratory and their Neurobiology course for supporting the initial set of experiments (course supported by National Institutes of Health grant R25NS063307). S.W. and this work were supported by start-up funds from the Johns Hopkins University School of Medicine, Johns Hopkins Discovery funds, and the National Science Foundation (1727260), the National Institutes of Health (1DP2 NS111133-01 and 1R01 NS105810-01A1) awarded to S.W. S.W. is an Alfred P. Sloan fellow, McKnight Foundation Scholar, and Klingenstein and Simons Foundation scholar. G.K. was supported by a grant from the National Institutes of Health to the Biochemistry, Cellular and Molecular Biology Program of the Johns Hopkins University School of Medicine (T32 GM007445) and is a National Science Foundation Graduate Research Fellow (2016217537). E.H. and T.M.B. are supported by CRCNS-NIH-ANR grant AMPAR-T. The EM ICE high-pressure freezer was purchased partly with funds from an equipment grant from the National Institutes of Health (S10RR026445) awarded to Scot C Kuo.
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    Shifting seasonality of cyclones and western boundary current interactions in Bay of Bengal as observed during Amphan and Fani (2022)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sil, S., Gangopadhyay, A., Gawarkiewicz, G., & Pramanik, S. Shifting seasonality of cyclones and western boundary current interactions in Bay of Bengal as observed during Amphan and Fani. Scientific Reports, 11(1), (2021): 22052 https://doi.org/10.1038/s41598-021-01607-6.
    Description: In recent years, the seasonal patterns of Tropical Cyclones (TC) in the Bay of Bengal have been shifting. While tropical depressions have been common in March–May (spring), they typically have been relatively weaker than the TCs during October–December. Here we show that the spatial pattern of recent warming trends during the last two decades in the southwestern Bay has allowed for stronger springtime pre-monsoon cyclones such as Amphan (May 2020, Super Cyclone) and Fani (April–May 2019, Extremely Severe Cyclone). The tracks of the pre-monsoon cyclones shifted westward, concurrent with an increasing rate of warming. This shift allowed both Fani and Amphan tracks to cross the northeastward warm Western Boundary Current (WBC) and associated warm anti-cyclonic eddies, while the weaker Viyaru (April 2013, Cyclonic Storm) did not interact with the WBC. A quantitative model linking the available along-track heat potential to cyclone’s intensity is developed to understand the impact of the WBC on cyclone intensification. The influence of the warming WBC and associated anti-cyclonic eddies will likely result in much stronger springtime TCs becoming relatively common in the future.
    Description: The authors gratefully acknowledge the financial and infrastructural support from the Indian Institute of Technology Bhubaneswar to carry out this research. SS acknowledges the financial assistance from Science and Engineering Research Board (SERB), Government of India (Grant No. CRG/2019/005842). All the figures are prepared using MATLAB. AG and SS appreciate the support of SERB's VAJRA Faculty Scheme (VJR/2018/000108) for the initiation of this collaborative work between SMAST and IITBBS. AG also acknowledges partial support from NSF (OCE 1851242) in completing this manuscript. GG was supported by a Grant from the Office of Naval Research as part of the Task Force Ocean initiative.
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    Detecting climate signals in populations across life histories (2022)
    Wiley
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jenouvrier, S., Long, M. C., Coste, C. F. D., Holland, M., Gamelon, M., Yoccoz, N., & Saether, B.-E. Detecting climate signals in populations across life histories. Global Change Biology, 28, (2022): 2236– 2258, https://doi.org/10.1111/gcb.16041.
    Description: Climate impacts are not always easily discerned in wild populations as detecting climate change signals in populations is challenged by stochastic noise associated with natural climate variability, variability in biotic and abiotic processes, and observation error in demographic rates. Detection of the impact of climate change on populations requires making a formal distinction between signals in the population associated with long-term climate trends from those generated by stochastic noise. The time of emergence (ToE) identifies when the signal of anthropogenic climate change can be quantitatively distinguished from natural climate variability. This concept has been applied extensively in the climate sciences, but has not been explored in the context of population dynamics. Here, we outline an approach to detecting climate-driven signals in populations based on an assessment of when climate change drives population dynamics beyond the envelope characteristic of stochastic variations in an unperturbed state. Specifically, we present a theoretical assessment of the time of emergence of climate-driven signals in population dynamics (ToEpop). We identify the dependence of (ToEpop)on the magnitude of both trends and variability in climate and also explore the effect of intrinsic demographic controls on (ToEpop). We demonstrate that different life histories (fast species vs. slow species), demographic processes (survival, reproduction), and the relationships between climate and demographic rates yield population dynamics that filter climate trends and variability differently. We illustrate empirically how to detect the point in time when anthropogenic signals in populations emerge from stochastic noise for a species threatened by climate change: the emperor penguin. Finally, we propose six testable hypotheses and a road map for future research.
    Description: We acknowledge the support of NASA 80NSSC20K1289 to SJ, ML, and MH; NSF OPP 1744794 to SJ and NSF OPP 2037561 to SJ and MH.
    Keywords: climate change ; emperor penguin ; life histories ; population trend ; population variability ; signal to noise ; time of emergence
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    Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lenz, P. H., Roncalli, V., Cieslak, M. C., Tarrant, A. M., Castelfranco, A. M., & Hartline, D. K. Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod. Communications Biology, 4(1), (2021): 426, https://doi.org/10.1038/s42003-021-01946-0.
    Description: Many arthropods undergo a seasonal dormancy termed “diapause” to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses to identify program-specific genes and biological processes. These analyses elucidated physiological differences and established protocols that distinguish between programs. Differences in gene expression were associated with maturation of individuals on the reproductive program, while those on the diapause program showed little change over time. Only two of six filters effectively separated copepods by developmental program. The first one included all genes annotated to RNA metabolism and this was confirmed using differential gene expression analysis. The second filter identified 54 differentially expressed genes that were consistently up-regulated in individuals on the diapause program in comparison with those on the reproductive program. Annotated to oogenesis, RNA metabolism and fatty acid biosynthesis, these genes are both indicators for diapause preparation and good candidates for functional studies.
    Description: This work was supported by National Science Foundation Grants (NSF) OCE-1459235 and OCE-1756767 to P.H.L., D.K.H. and AE Christie and OPP-1746087 to A.M.T.
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    The chemical defensome of five model teleost fish (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Eide, M., Zhang, X., Karlsen, O. A., Goldstone, J., Stegeman, J., Jonassen, I., & Goksoyr, A. The chemical defensome of five model teleost fish. Scientific Reports, 11(1), (2021): 10546, https://doi.org/10.1038/s41598-021-89948-0.
    Description: How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.
    Description: The work was supported by the Norwegian Research Council as part of the iCOD and iCOD 2.0 projects (Grant Nos. 192441/I30 and 244654/E40), and the dCod 1.0 project (Grant No. 248840) which is part of Centre for Digital Life Norway. The American collaborators were funded by the National Institute of Health (USA) NIH P42ES007381 (Boston University Superfund Center to JJS and JVG), NIH R21HD073805 (JVG) and NHI R01ES029917 (JVG) grants. The Ocean Outlook exchange program funded the trans-Atlantic collaboration.
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    Nutrient content and stoichiometry of pelagic Sargassum reflects increasing nitrogen availability in the Atlantic Basin (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lapointe, B. E., Brewton, R. A., Herren, L. W., Wang, M., Hu, C., McGillicuddy, D. J., Lindell, S., Hernandez, F. J., & Morton, P. L. Nutrient content and stoichiometry of pelagic Sargassum reflects increasing nitrogen availability in the Atlantic Basin. Nature Communications, 12(1), (2021): 3060, https://doi.org/10.1038/s41467-021-23135-7.
    Description: The pelagic brown macroalgae Sargassum spp. have grown for centuries in oligotrophic waters of the North Atlantic Ocean supported by natural nutrient sources, such as excretions from associated fishes and invertebrates, upwelling, and N2 fixation. Using a unique historical baseline, we show that since the 1980s the tissue %N of Sargassum spp. has increased by 35%, while %P has decreased by 44%, resulting in a 111% increase in the N:P ratio (13:1 to 28:1) and increased P limitation. The highest %N and δ15N values occurred in coastal waters influenced by N-rich terrestrial runoff, while lower C:N and C:P ratios occurred in winter and spring during peak river discharges. These findings suggest that increased N availability is supporting blooms of Sargassum and turning a critical nursery habitat into harmful algal blooms with catastrophic impacts on coastal ecosystems, economies, and human health.
    Description: This work was funded by the US NASA Ocean Biology and Biogeochemistry Program (80NSSC20M0264, NNX16AR74G) and Ecological Forecast Program (NNX17AF57G), NOAA RESTORE Science Program (NA17NOS4510099), National Science Foundation (NSF-OCE 85–15492 and OCE 88–12055), “Save Our Seas” Specialty License Plate funds, granted through the Harbor Branch Oceanographic Institute Foundation, Ft. Pierce, FL, and a Red Wright Fellowship from the Bermuda Biological Station. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. D.J.M. gratefully acknowledges the Holger W. Jannasch and Columbus O’Donnell Iselin Shared Chairs for Excellence in Oceanography, as well as support from the Mill Reef Fund.
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    Large-scale shift in the structure of a kelp forest ecosystem co-occurs with an epizootic and marine heatwave (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McPherson, M. L., Finger, D. J., I., Houskeeper, H. F., Bell, T. W., Carr, M. H., Rogers-Bennett, L., & Kudela, R. M. Large-scale shift in the structure of a kelp forest ecosystem co-occurs with an epizootic and marine heatwave. Communications Biology, 4(1), (2021): 298, https://doi.org/10.1038/s42003-021-01827-6.
    Description: Climate change is responsible for increased frequency, intensity, and duration of extreme events, such as marine heatwaves (MHWs). Within eastern boundary current systems, MHWs have profound impacts on temperature-nutrient dynamics that drive primary productivity. Bull kelp (Nereocystis luetkeana) forests, a vital nearshore habitat, experienced unprecedented losses along 350 km of coastline in northern California beginning in 2014 and continuing through 2019. These losses have had devastating consequences to northern California communities, economies, and fisheries. Using a suite of in situ and satellite-derived data, we demonstrate that the abrupt ecosystem shift initiated by a multi-year MHW was preceded by declines in keystone predator population densities. We show strong evidence that northern California kelp forests, while temporally dynamic, were historically resilient to fluctuating environmental conditions, even in the absence of key top predators, but that a series of coupled environmental and biological shifts between 2014 and 2016 resulted in the formation of a persistent, altered ecosystem state with low primary productivity. Based on our findings, we recommend the implementation of ecosystem-based and adaptive management strategies, such as (1) monitoring the status of key ecosystem attributes: kelp distribution and abundance, and densities of sea urchins and their predators, (2) developing management responses to threshold levels of these attributes, and (3) creating quantitative restoration suitability indices for informing kelp restoration efforts.
    Description: M.H.C. received support from the National Science Foundation (OCE‐1538582).
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    Hydraulic transmissivity inferred from ice-sheet relaxation following Greenland supraglacial lake drainages (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lai, C.-Y., Stevens, L. A., Chase, D. L., Creyts, T. T., Behn, M. D., Das, S. B., & Stone, H. A. Hydraulic transmissivity inferred from ice-sheet relaxation following Greenland supraglacial lake drainages. Nature Communications, 12(1), (2021): 3955, https://doi.org/10.1038/s41467-021-24186-6.
    Description: Surface meltwater reaching the base of the Greenland Ice Sheet transits through drainage networks, modulating the flow of the ice sheet. Dye and gas-tracing studies conducted in the western margin sector of the ice sheet have directly observed drainage efficiency to evolve seasonally along the drainage pathway. However, the local evolution of drainage systems further inland, where ice thicknesses exceed 1000 m, remains largely unknown. Here, we infer drainage system transmissivity based on surface uplift relaxation following rapid lake drainage events. Combining field observations of five lake drainage events with a mathematical model and laboratory experiments, we show that the surface uplift decreases exponentially with time, as the water in the blister formed beneath the drained lake permeates through the subglacial drainage system. This deflation obeys a universal relaxation law with a timescale that reveals hydraulic transmissivity and indicates a two-order-of-magnitude increase in subglacial transmissivity (from 0.8 ± 0.3 mm3 to 215 ± 90.2 mm3) as the melt season progresses, suggesting significant changes in basal hydrology beneath the lakes driven by seasonal meltwater input.
    Description: C.-Y.L. and L.A.S thank Lamont-Doherty Earth Observatory for funding through the Lamont Postdoctoral Fellowships. D.L.C acknowledges support from the National Science Foundation (NSF) Graduate Research Fellowship. T.T.C. was supported by NSF’s Office of Polar Programs (NSF-OPP) through OPP-1643970, the National Aeronautics and Space Administration (NASA) through NNX16AJ95G, and a grant from the Vetlesen Foundation. S.B.D. and M.D.B. acknowledge funding from NSF-OPP and NASA’s Cryospheric Sciences Program through OPP-1838410, ARC-1023364, ARC-0520077, and NNX10AI30G. H.A.S. thanks the High Meadows Environmental Institute and the Carbon Mitigation Initiative at Princeton University. This publication was supported by the Princeton University Library Open Access Fund.
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    Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, Y., Moreno, C., Marchetti, A., Ducklow, H., Schofield, O., Delage, E., Meredith, M., Li, Z., Eveillard, D., Chaffron, S., & Cassar, N. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula. Nature Communications, 12(1), (2021): 4948, https://doi.org/10.1038/s41467-021-25235-w.
    Description: Since the middle of the past century, the Western Antarctic Peninsula has warmed rapidly with a significant loss of sea ice but the impacts on plankton biodiversity and carbon cycling remain an open question. Here, using a 5-year dataset of eukaryotic plankton DNA metabarcoding, we assess changes in biodiversity and net community production in this region. Our results show that sea-ice extent is a dominant factor influencing eukaryotic plankton community composition, biodiversity, and net community production. Species richness and evenness decline with an increase in sea surface temperature (SST). In regions with low SST and shallow mixed layers, the community was dominated by a diverse assemblage of diatoms and dinoflagellates. Conversely, less diverse plankton assemblages were observed in waters with higher SST and/or deep mixed layers when sea ice extent was lower. A genetic programming machine-learning model explained up to 80% of the net community production variability at the Western Antarctic Peninsula. Among the biological explanatory variables, the sea-ice environment associated plankton assemblage is the best predictor of net community production. We conclude that eukaryotic plankton diversity and carbon cycling at the Western Antarctic Peninsula are strongly linked to sea-ice conditions.
    Description: This work is supported by NSF OPP-1643534 to N.C., NSF OPP-1341479 to A.M., and NSF PLR-1440435 to H.D. and O.S. (Palmer LTER).
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    Real-time polarization microscopy of fibrillar collagen in histopathology (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keikhosravi, A., Shribak, M., Conklin, M. W., Liu, Y., Li, B., Loeffler, A., Levenson, R. M., & Eliceiri, K. W. Real-time polarization microscopy of fibrillar collagen in histopathology. Scientific Reports, 11(1), (2021): 19063, https://doi.org/10.1038/s41598-021-98600-w.
    Description: Over the past two decades, fibrillar collagen reorganization parameters such as the amount of collagen deposition, fiber angle and alignment have been widely explored in numerous studies. These parameters are now widely accepted as stromal biomarkers and linked to disease progression and survival time in several cancer types. Despite all these advances, there has not been a significant effort to make it possible for clinicians to explore these biomarkers without adding steps to the clinical workflow or by requiring high-cost imaging systems. In this paper, we evaluate previously described polychromatic polarization microscope (PPM) to visualize collagen fibers with an optically generated color representation of fiber orientation and alignment when inspecting the sample by a regular microscope with minor modifications. This system does not require stained slides, but is compatible with histological stains such as H&E. Consequently, it can be easily accommodated as part of regular pathology review of tissue slides, while providing clinically useful insight into stromal composition.
    Description: This work was supported by NIH R01 CA238191 (KWE), NIH P41GM135019 (KWE), NIH R01 GM101701 (MS), funding from the Morgridge Institute for Research (KWE), the Semiconductor Research Corporation (SRC) (KWE), and the William T. Golden Endowment (MS).
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    Developmental exposure to non-dioxin-like polychlorinated biphenyls promotes sensory deficits and disrupts dopaminergic and GABAergic signaling in zebrafish (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brun, N. R., Panlilio, J. M., Zhang, K., Zhao, Y., Ivashkin, E., Stegeman, J. J., & Goldstone, J. Developmental exposure to non-dioxin-like polychlorinated biphenyls promotes sensory deficits and disrupts dopaminergic and GABAergic signaling in zebrafish. Communications Biology, 4(1), (2021): 1129, https://doi.org/10.1038/s42003-021-02626-9.
    Description: The most abundant polychlorinated biphenyl (PCB) congeners found in the environment and in humans are neurotoxic. This is of particular concern for early life stages because the exposure of the more vulnerable developing nervous system to neurotoxic chemicals can result in neurobehavioral disorders. In this study, we uncover currently unknown links between PCB target mechanisms and neurobehavioral deficits using zebrafish as a vertebrate model. We investigated the effects of the abundant non-dioxin-like (NDL) congener PCB153 on neuronal morphology and synaptic transmission linked to the proper execution of a sensorimotor response. Zebrafish that were exposed during development to concentrations similar to those found in human cord blood and PCB contaminated sites showed a delay in startle response. Morphological and biochemical data demonstrate that even though PCB153-induced swelling of afferent sensory neurons, the disruption of dopaminergic and GABAergic signaling appears to contribute to PCB-induced motor deficits. A similar delay was observed for other NDL congeners but not for the potent dioxin-like congener PCB126. The effects on important and broadly conserved signaling mechanisms in vertebrates suggest that NDL PCBs may contribute to neurodevelopmental abnormalities in humans and increased selection pressures in vertebrate wildlife.
    Description: This work was supported by the Swiss National Science Foundation P2EZP2_165200 (NRB), the Boston University Superfund Research Program NIH 5P42ES007381 (J.J.S. and J.V.G.), the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381) (N.R.B., J.M.P., and J.J.S.), and the National Natural Science Foundation of China 22006099 (K.Z. and Y.Z.) and the Shanghai Pujiang Program 19PJ1404900 (K.Z. and Y.Z.).
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    Placozoan fiber cells: mediators of innate immunity and participants in wound healing (2022)
    Nature Research
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mayorova, T. D., Hammar, K., Jung, J. H., Aronova, M. A., Zhang, G., Winters, C. A., Reese, T. S., & Smith, C. L. Placozoan fiber cells: mediators of innate immunity and participants in wound healing. Scientific Reports, 11(1), (2021): 23343, https://doi.org/10.1038/s41598-021-02735-9.
    Description: Placozoa is a phylum of non-bilaterian marine animals. These small, flat organisms adhere to the substrate via their densely ciliated ventral epithelium, which mediates mucociliary locomotion and nutrient uptake. They have only six morphological cell types, including one, fiber cells, for which functional data is lacking. Fiber cells are non-epithelial cells with multiple processes. We used electron and light microscopic approaches to unravel the roles of fiber cells in Trichoplax adhaerens, a representative member of the phylum. Three-dimensional reconstructions of serial sections of Trichoplax showed that each fiber cell is in contact with several other cells. Examination of fiber cells in thin sections and observations of live dissociated fiber cells demonstrated that they phagocytose cell debris and bacteria. In situ hybridization confirmed that fiber cells express genes involved in phagocytic activity. Fiber cells also are involved in wound healing as evidenced from microsurgery experiments. Based on these observations we conclude that fiber cells are multi-purpose macrophage-like cells. Macrophage-like cells have been described in Porifera, Ctenophora, and Cnidaria and are widespread among Bilateria, but our study is the first to show that Placozoa possesses this cell type. The phylogenetic distribution of macrophage-like cells suggests that they appeared early in metazoan evolution.
    Description: Open Access funding provided by the National Institutes of Health (NIH).
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    Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish (2022)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brun, N. R., Salanga, M. C., Mora-Zamorano, F. X., Lamb, D. C., Goldstone, J. V., & Stegeman, J. J. Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish. Scientific Reports, 11(1), (2021): 23892, https://doi.org/10.1038/s41598-021-03068-3.
    Description: Orphan cytochrome P450 (CYP) enzymes are those for which biological substrates and function(s) are unknown. Cytochrome P450 20A1 (CYP20A1) is the last human orphan P450 enzyme, and orthologs occur as single genes in every vertebrate genome sequenced to date. The occurrence of high levels of CYP20A1 transcripts in human substantia nigra and hippocampus and abundant maternal transcripts in zebrafish eggs strongly suggest roles both in the brain and during early embryonic development. Patients with chromosome 2 microdeletions including CYP20A1 show hyperactivity and bouts of anxiety, among other conditions. Here, we created zebrafish cyp20a1 mutants using CRISPR/Cas9, providing vertebrate models with which to study the role of CYP20A1 in behavior and other neurodevelopmental functions. The homozygous cyp20a1 null mutants exhibited significant behavioral differences from wild-type zebrafish, both in larval and adult animals. Larval cyp20a1-/- mutants exhibited a strong increase in light-simulated movement (i.e., light–dark assay), which was interpreted as hyperactivity. Further, the larvae exhibited mild hypoactivity during the adaptation period of the optomotor assays. Adult cyp20a1 null fish showed a pronounced delay in adapting to new environments, which is consistent with an anxiety paradigm. Taken together with our earlier morpholino cyp20a1 knockdown results, the results described herein suggest that the orphan CYP20A1 has a neurophysiological role.
    Description: These studies were supported in part by the Boston University Superfund Research Program NIH 5P42ES007381 (MCS, NRB, FXM, JVG, JJS), the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381; NRB and JJS), and EBI/EMBL Medakatox NIEHS R01ES029917 (JVG). DCL was funded by a UK-US Fulbright Scholarship.
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    Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones (2022)
    Nature Research
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beman, J. M., Vargas, S. M., Wilson, J. M., Perez-Coronel, E., Karolewski, J. S., Vazquez, S., Yu, A., Cairo, A. E., White, M. E., Koester, I., Aluwihare, L. I., & Wankel, S. D. Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones. Nature Communications, 12(1), (2021): 7043, https://doi.org/10.1038/s41467-021-27381-7.
    Description: Oceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations 〈20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and 15N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation can account for all DO consumption only under DO concentrations 〈393 nM found in and below the secondary chlorophyll maximum. These patterns are consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizing Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results demonstrate that nitrite oxidation plays a pivotal role in the maintenance and biogeochemical dynamics of OMZs.
    Description: This work was supported by NSF CAREER Grant OCE-1555375 to J.M.B. Metagenome sequencing was supported by the UCMEXUS-CONACyT Collaborative Grants Program (joint awards to J.M.B. and José García Maldonado).
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    Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment (2022)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Remple, K. L., Silbiger, N. J., Quinlan, Z. A., Fox, M. D., Kelly, L. W., Donahue, M. J., & Nelson, C. E. Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment. Npj Biofilms and Microbiomes, 7(1), (2021): 84, https://doi.org/10.1038/s41522-021-00252-1.
    Description: Work on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.
    Description: This work was supported through grants from the National Science Foundation for Biological Oceanography (1923877 to C.E.N. and M.J.D., 1949033 to C.E.N. and 2118687 to L.W.K., and 1924281 to N.J.S.) and the National Fish and Wildlife Foundation (grant no. 44447 to C.E.N.). This paper is funded in part by the National Oceanic and Atmospheric Administration, Project A/AS-1, which is sponsored by the University of Hawaii Sea Grant College Program, SOEST, under Institutional Grant No. NA18OAR4170076 from NOAA Office of Sea Grant, Department of Commerce. This is CSUN marine biology contribution #365, UH Sea Grant contribution UNIHI-SEAGRANT-JC-21-06, and UH SOEST contribution 11435.
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  • 164
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    Attachment of zebra and quagga mussel adhesive plaques to diverse substrates (2022)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in James, B. D., Kimmins, K. M., Nguyen, M.-T., Lausch, A. J., & Sone, E. D. Attachment of zebra and quagga mussel adhesive plaques to diverse substrates. Scientific Reports, 11(1), (2021): 23998, https://doi.org/10.1038/s41598-021-03227-6.
    Description: Like marine mussels, freshwater zebra and quagga mussels adhere via the byssus, a proteinaceous attachment apparatus. Attachment to various surfaces allows these invasive mussels to rapidly spread, however the adhesion mechanism is not fully understood. While marine mussel adhesion mechanics has been studied at the individual byssal-strand level, freshwater mussel adhesion has only been characterized through whole-mussel detachment, without direct interspecies comparisons on different substrates. Here, adhesive strength of individual quagga and zebra mussel byssal plaques were measured on smooth substrates with varying hydrophobicity—glass, PVC, and PDMS. With increased hydrophobicity of substrates, adhesive failures occurred more frequently, and mussel adhesion strength decreased. A new failure mode termed 'footprint failure' was identified, where failure appeared to be adhesive macroscopically, but a microscopic residue remained on the surface. Zebra mussels adhered stronger and more frequently on PDMS than quagga mussels. While their adhesion strengths were similar on PVC, there were differences in the failure mode and the plaque-substrate interface ultrastructure. Comparisons with previous marine mussel studies demonstrated that freshwater mussels adhere with comparable strength despite known differences in protein composition. An improved understanding of freshwater mussel adhesion mechanics may help explain spreading dynamics and will be important in developing effective antifouling surfaces.
    Description: This work was supported by Discovery grant (#342455) to EDS from the National Sciences and Engineering Research Council (NSERC) of Canada (RGPIN-2019-06210).
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    Differential susceptibility of reef-building corals to deoxygenation reveals remarkable hypoxia tolerance (2022)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, M. D., Swaminathan, S. D., Nixon, E. N., Paul, V. J., & Altieri, A. H. Differential susceptibility of reef-building corals to deoxygenation reveals remarkable hypoxia tolerance. Scientific Reports, 11(1), (2021): 23168, https://doi.org/10.1038/s41598-021-01078-9.
    Description: Ocean deoxygenation threatens the persistence of coastal ecosystems worldwide. Despite an increasing awareness that coastal deoxygenation impacts tropical habitats, there remains a paucity of empirical data on the effects of oxygen limitation on reef-building corals. To address this knowledge gap, we conducted laboratory experiments with ecologically important Caribbean corals Acropora cervicornis and Orbicella faveolata. We tested the effects of continuous exposure to conditions ranging from extreme deoxygenation to normoxia (~ 1.0 to 6.25 mg L−1 dissolved oxygen) on coral bleaching, photophysiology, and survival. Coral species demonstrated markedly different temporal resistance to deoxygenation, and within a species there were minimal genotype-specific treatment effects. Acropora cervicornis suffered tissue loss and mortality within a day of exposure to severe deoxygenation (~ 1.0 mg L−1), whereas O. faveolata remained unaffected after 11 days of continuous exposure to 1.0 mg L−1. Intermediate deoxygenation treatments (~ 2.25 mg L−1, ~ 4.25 mg L−1) elicited minimal responses in both species, indicating a low oxygen threshold for coral mortality and coral resilience to oxygen concentrations that are lethal for other marine organisms. These findings demonstrate the potential for variability in species-specific hypoxia thresholds, which has important implications for our ability to predict how coral reefs may be affected as ocean deoxygenation intensifies. With deoxygenation emerging as a critical threat to tropical habitats, there is an urgent need to incorporate deoxygenation into coral reef research, management, and action plans to facilitate better stewardship of coral reefs in an era of rapid environmental change.
    Description: This research was funded by an award from the National Oceanic and Atmospheric Administration’s National Centers for Coastal Ocean Science Competitive Research Program to AA, MJ, and VP (NA18NOS4780170) through the University of Florida. MJ was funded by postdoctoral fellow awards from the Smithsonian Institution's Marine Global Earth Observatory (MarineGEO), the Smithsonian Marine Station, and Woods Hole Oceanographic Institution. This material is based on work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1842473. This is contribution 259 from the Coastal Hypoxia Research Program, 93 from the Smithsonian’s MarineGEO and Tennenbaum Marine Observatories Network, and 1167 from the Smithsonian Marine Station at Fort Pierce.
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    Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs (2022)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tyne, R. L., Barry, P. H., Lawson, M., Byrne, D. J., Warr, O., Xie, H., Hillegonds, D. J., Formolo, M., Summers, Z. M., Skinner, B., Eiler, J. M., & Ballentine, C. J. Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs. Nature, 600(7890), (2021): 670-674, https://doi.org/10.1038/s41586-021-04153-3.
    Description: Carbon capture and storage (CCS) is a key technology to mitigate the environmental impact of carbon dioxide (CO2) emissions. An understanding of the potential trapping and storage mechanisms is required to provide confidence in safe and secure CO2 geological sequestration1,2. Depleted hydrocarbon reservoirs have substantial CO2 storage potential1,3, and numerous hydrocarbon reservoirs have undergone CO2 injection as a means of enhanced oil recovery (CO2-EOR), providing an opportunity to evaluate the (bio)geochemical behaviour of injected carbon. Here we present noble gas, stable isotope, clumped isotope and gene-sequencing analyses from a CO2-EOR project in the Olla Field (Louisiana, USA). We show that microbial methanogenesis converted as much as 13–19% of the injected CO2 to methane (CH4) and up to an additional 74% of CO2 was dissolved in the groundwater. We calculate an in situ microbial methanogenesis rate from within a natural system of 73–109 millimoles of CH4 per cubic metre (standard temperature and pressure) per year for the Olla Field. Similar geochemical trends in both injected and natural CO2 fields suggest that microbial methanogenesis may be an important subsurface sink of CO2 globally. For CO2 sequestration sites within the environmental window for microbial methanogenesis, conversion to CH4 should be considered in site selection.
    Description: R.L.T. was supported by a Natural Environment Research Council studentship (grant reference NE/L002612/1). C.J.B. and P.H.B. acknowledge A. Regberg and B. Meurer for their support of the project and help with sample collection. C.J.B. was part supported by an Earth4D CIFAR fellowship. P.H.B. was supported by NSF awards 1923915 and 2015789. O.W. was supported by Natural Sciences and Engineering Research Council of Canada Discovery and Accelerator grants awarded to the Sherwood Lollar research group and acknowledges B. Sherwood Lollar’s support for the project. Z.M.S. acknowledges J. Biddle and G. Christman for their help in generating the microbial data.
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    An analysis of Atlantic Water in the Arctic Ocean using the Arctic Subpolar Gyre State Estimate and observations (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2020.
    Description: The Atlantic Water (AW) Layer in the Arctic Subpolar gyre sTate Estimate (ASTE), a regional, medium-resolution coupled ocean-sea ice state estimate, is analyzed for the first time using bounding isopycnals. A surge of AW, marked by rapid increases in mean AW Layer potential temperature and AW Layer thickness, begins two years into the state estimate (2004) and traverses the Arctic Ocean along boundary current pathways at approximately 2 cm/s. The surge also alters AW flow direction and speed including a significant reversal in flow direction along the Lomonosov Ridge. The surge results in a new quasi-steady AW flow from 2010 through the end of the state estimate period in 2017. The time-mean AW circulation during this time period indicates a significant amount of AW spreads over the Lomonosov Ridge rather than directly returning along the ridge to Fram Strait. A three-layer depiction of ASTE’s overturning circulation within the AO indicates AW is converted to colder, fresher Surface Layer water at a faster rate than is transformed to Bottom Water (1.2 Sv vs. 0.4 Sv). Observed AW properties compared to ASTE output indicate increasing misfit during the simulated period with ASTE’s AW Layer generally being warmer and thicker than in observations.
    Description: This research was funded via the United States Navy’s Civilian Institution Program with the MIT/WHOI Joint Program (JP). The thesis supervisor’s participation in this project was supported by National Science Foundation-Grant #PLR-1603660 and by Office of Naval Research-Grant #N000141612381. This project, specifically ASTE developed by Dr. An T. Nguyen, is also supported by National Science Foundation-Grant #PLR-1603903.
    Keywords: Atlantic water ; Arctic Ocean ; Arctic Subpolar Gyre State Estimate
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  • 168
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    The contribution of water radiolysis to marine sedimentary life (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sauvage, J. F., Flinders, A., Spivack, A. J., Pockalny, R., Dunlea, A. G., Anderson, C. H., Smith, D. C., Murray, R. W., & D'Hondt, S. The contribution of water radiolysis to marine sedimentary life. Nature Communications, 12(1), (2021): 1297, https://doi.org/10.1038/s41467-021-21218-z.
    Description: Water radiolysis continuously produces H2 and oxidized chemicals in wet sediment and rock. Radiolytic H2 has been identified as the primary electron donor (food) for microorganisms in continental aquifers kilometers below Earth’s surface. Radiolytic products may also be significant for sustaining life in subseafloor sediment and subsurface environments of other planets. However, the extent to which most subsurface ecosystems rely on radiolytic products has been poorly constrained, due to incomplete understanding of radiolytic chemical yields in natural environments. Here we show that all common marine sediment types catalyse radiolytic H2 production, amplifying yields by up to 27X relative to pure water. In electron equivalents, the global rate of radiolytic H2 production in marine sediment appears to be 1-2% of the global organic flux to the seafloor. However, most organic matter is consumed at or near the seafloor, whereas radiolytic H2 is produced at all sediment depths. Comparison of radiolytic H2 consumption rates to organic oxidation rates suggests that water radiolysis is the principal source of biologically accessible energy for microbial communities in marine sediment older than a few million years. Where water permeates similarly catalytic material on other worlds, life may also be sustained by water radiolysis.
    Description: This project was funded by the US National Science Foundation (through grant NSF-OCE-1130735 and the Center for Deep Dark Energy Biosphere Investigations [C-DEBI; grant NSF-OCE-0939564]); the National Aeronautics and Space Administration (grant NNX12AD65G); the U.S. Science Support Program, IODP; and a Schlanger Ocean Drilling Fellowship to J.F.S. This is a contribution to the Deep Carbon Observatory (DCO). It is C-DEBI publication 553.
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    Large subglacial source of mercury from the southwestern margin of the Greenland Ice Sheet (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hawkings, J. R., Linhoff, B. S., Wadham, J. L., Stibal, M., Lamborg, C. H., Carling, G. T., Lamarche-Gagnon, G., Kohler, T. J., Ward, R., Hendry, K. R., Falteisek, L., Kellerman, A. M., Cameron, K. A., Hatton, J. E., Tingey, S., Holt, A. D., Vinsova, P., Hofer, S., Bulinova, M., Větrovský, T., Meire, L., Spencer, R. G. M. Large subglacial source of mercury from the southwestern margin of the Greenland Ice Sheet. Nature Geoscience, 14, (2021): 496-502, https://doi.org/10.1038/s41561-021-00753-w.
    Description: The Greenland Ice Sheet is currently not accounted for in Arctic mercury budgets, despite large and increasing annual runoff to the ocean and the socio-economic concerns of high mercury levels in Arctic organisms. Here we present concentrations of mercury in meltwaters from three glacial catchments on the southwestern margin of the Greenland Ice Sheet and evaluate the export of mercury to downstream fjords based on samples collected during summer ablation seasons. We show that concentrations of dissolved mercury are among the highest recorded in natural waters and mercury yields from these glacial catchments (521–3,300 mmol km−2 year−1) are two orders of magnitude higher than from Arctic rivers (4–20 mmol km−2 year−1). Fluxes of dissolved mercury from the southwestern region of Greenland are estimated to be globally significant (15.4–212 kmol year−1), accounting for about 10% of the estimated global riverine flux, and include export of bioaccumulating methylmercury (0.31–1.97 kmol year−1). High dissolved mercury concentrations (~20 pM inorganic mercury and ~2 pM methylmercury) were found to persist across salinity gradients of fjords. Mean particulate mercury concentrations were among the highest recorded in the literature (~51,000 pM), and dissolved mercury concentrations in runoff exceed reported surface snow and ice values. These results suggest a geological source of mercury at the ice sheet bed. The high concentrations of mercury and its large export to the downstream fjords have important implications for Arctic ecosystems, highlighting an urgent need to better understand mercury dynamics in ice sheet runoff under global warming.
    Description: This research is part of a European Commission Horizon 2020 Marie Skłodowska-Curie Actions fellowship ICICLES (grant agreement #793962) to J.R.H. Greenland terrestrial research campaigns were funded by a UK NERC standard grant (NE/I008845/1) and a Leverhulme Trust Research Grant (RPG-2016-439) to J.L.W., with additional support provided by a Royal Society Wolfson Merit Award to J.L.W. Additional funding came from Czech Science Foundation grants (GACR; 15-17346Y and 18-12630S) to M.S. Fjord fieldwork was supported by European Research Council grant ICY-LAB (grant agreement 678371) and Royal Society Enhancement Award (grant RGF\EA\181036) to K.R.H. L.M. was funded by research programme VENI (0.16.Veni.192.150, NWO). T.J.K. was supported by Charles University Research Centre program no. 204069. The authors thank the captain and crew of the RV Kisaq and staff at the Greenland Institute of Natural Resources for assistance during fjord fieldwork, and all those involved with fieldwork at Leverett Camp during the 2012 and 2015 field campaigns. M. Cooper is thanked for providing the geological overview file for Extended Data Fig. 1a, and K. Mankoff for help in generating the modelled GrIS discharge datasets. The authors also thank G. White in the geochemistry group at the National High Magnetic Field Geochemistry Laboratory, which is supported by NSF DMR-1644779 and the State of Florida, for analytical support.
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    Subpolar North Atlantic western boundary density anomalies and the Meridional Overturning Circulation (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Li, F., Lozier, M. S., Bacon, S., Bower, A. S., Cunningham, S. A., de Jong, M. F., DeYoung, B., Fraser, N., Fried, N., Han, G., Holliday, N. P., Holte, J., Houpert, L., Inall, M. E., Johns, W. E., Jones, S., Johnson, C., Karstensen, J., Le Bras, I. A., P. Lherminier, X. Lin, H. Mercier, M. Oltmanns, A. Pacini, T. Petit, R. S. Pickart, D. Rayner, F. Straneo, V. Thierry, M. Visbeck, I. Yashayaev & Zhou, C. Subpolar North Atlantic western boundary density anomalies and the Meridional Overturning Circulation. Nature Communications, 12(1), (2021): 3002, https://doi.org/10.1038/s41467-021-23350-2.
    Description: Changes in the Atlantic Meridional Overturning Circulation, which have the potential to drive societally-important climate impacts, have traditionally been linked to the strength of deep water formation in the subpolar North Atlantic. Yet there is neither clear observational evidence nor agreement among models about how changes in deep water formation influence overturning. Here, we use data from a trans-basin mooring array (OSNAP—Overturning in the Subpolar North Atlantic Program) to show that winter convection during 2014–2018 in the interior basin had minimal impact on density changes in the deep western boundary currents in the subpolar basins. Contrary to previous modeling studies, we find no discernable relationship between western boundary changes and subpolar overturning variability over the observational time scales. Our results require a reconsideration of the notion of deep western boundary changes representing overturning characteristics, with implications for constraining the source of overturning variability within and downstream of the subpolar region.
    Description: We acknowledge funding from the Physical Oceanography Program of the U.S. National Science Foundation (OCE-1259398, OCE-1756231, OCE-1948335); the U.K. Natural Environment Research Council (NERC) National Capability programs the Extended Ellett Line and CLASS (NE/R015953/1), and NERC grants UK-OSNAP (NE/K010875/1, NE/K010875/2, NE/K010700/1) and U.K. OSNAP Decade (NE/T00858X/1, NE/T008938/1). Additional support was received from the European Union 7th Framework Program (FP7 2007-2013) under grant 308299 (NACLIM), the Horizon 2020 research and innovation program under grants 727852 (Blue-Action), 862626 (EuroSea). We also acknowledge support from the Royal Netherlands Institute for Sea Research, the Surface Water and Ocean Topography-Canada (SWOT-C), Canadian Space Agency, the Aquatic Climate Change Adaptation Services Program (ACCASP), Fisheries and Oceans Canada, an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant, and from the China’s national key research and development projects (2016YFA0601803), the National Natural Science Foundation of China (41925025) and the Fundamental Research Funds for the Central Universities (201424001). Support for the 53°N array by the RACE program of the German Ministry BMBF is acknowledged, as is the contribution from Fisheries and Oceans Canada’s Atlantic Zone Monitoring Program.
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    The cytochrome P450 (CYP) superfamily in cnidarians (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pankov, K., McArthur, A. G., Gold, D. A., Nelson, D. R., Goldstone, J., & Wilson, J. Y. The cytochrome P450 (CYP) superfamily in cnidarians. Scientific Reports, 11(1), (2021): 9834, https://doi.org/10.1038/s41598-021-88700-y.
    Description: The cytochrome P450 (CYP) superfamily is a diverse and important enzyme family, playing a central role in chemical defense and in synthesis and metabolism of major biological signaling molecules. The CYPomes of four cnidarian genomes (Hydra vulgaris, Acropora digitifera, Aurelia aurita, Nematostella vectensis) were annotated; phylogenetic analyses determined the evolutionary relationships amongst the sequences and with existing metazoan CYPs. 155 functional CYPs were identified and 90 fragments. Genes were from 24 new CYP families and several new subfamilies; genes were in 9 of the 12 established metazoan CYP clans. All species had large expansions of clan 2 diversity, with H. vulgaris having reduced diversity for both clan 3 and mitochondrial clan. We identified potential candidates for xenobiotic metabolism and steroidogenesis. That each genome contained multiple, novel CYP families may reflect the large evolutionary distance within the cnidarians, unique physiology in the cnidarian classes, and/or different ecology of the individual species.
    Description: This study was supported by grants from the Natural Science Engineering Research Council of Canada in the form of a Discovery Grant (RGPIN-328204-2011 and RGPIN-05767-2016) to J.Y.W. A.G.M. held a Cisco Research Chair in Bioinformatics, supported by Cisco Systems Canada, Inc. K.V.P. was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Undergraduate Student Research Award (USRA). Computer resources were supplied by the McMaster Service Lab and Repository computing cluster, funded in part by grants to A.G.M. from the Canadian Foundation for Innovation (34531 to A.G.M.).
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    The effect of attenuation from fish on long-range active and passive acoustic sensing in the ocean (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-27
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.
    Description: Attenuation from fish can reduce the intensity of acoustic signals and significantly decrease detection range for long-range active and passive sensing in the ocean. This makes it important to understand the relevant mechanisms and accurately predict attenuation from fish in underwater acoustic sensing. Formulations for predicting attenuation from fish, however, depend on the accurate characterization of population density and spatial distribution of fish groups along long-range propagation paths, which is difficult to achieve using conventional survey methods. In previous investigations of attenuation from fish, population densities were inferred from reductions in the intensity of long-range acoustic signals caused by diel or seasonal shoaling patterns of fish groups. Here, Ocean Acoustic Waveguide Remote Sensing (OAWRS) is used to instantaneously image massive Norwegian herring shoals that stretch for thousands of square kilometers and simultaneously measure attenuation from these shoals within the active OAWRS transmissions, as well as attenuation to ship-radiated tonals detected by Passive Ocean Acoustic Waveguide Remote Sensing (POAWRS). Reductions in signal intensity are predicted using a normal-mode-based analytical theory derived from first principles for acoustic propagation and scattering through inhomogeneities in an ocean waveguide. The predictions of the waveguide attenuation formulation are in agreement with measured reductions from attenuation, where the position, size, and population density of the fish groups are characterized using OAWRS imagery as well as in situ echosounder measurements of the specific shoals occluding the propagation path. Common heuristic formulations that employ free space scattering assumptions for attenuation from fish groups are not in agreement with measurements here, and waveguide scattering theory is found to be necessary for accurate predictions. It is experimentally and theoretically shown that attenuation can be significant when the sensing frequency is near the resonance frequency of the shoaling fish, where scattering losses from the fish swimbladders and damping from fish flesh is most significant. Negligible attenuation was observed in previous OAWRS and POAWRS surveys because the frequency of the acoustic signals was sufficiently far from the swimbladder resonance peak of the shoaling fish or the packing densities of the fish shoals were not sufficiently high.
    Description: This work was supported by: • Office of Naval Research under grant number N00014-17-1-2197. • Office of Naval Research via the Graduate Traineeship Award under grant number N00014-18-1-2085.
    Keywords: Attenuation ; Fish ; Acoustic
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    Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, M., Guo, Z., Xu, S., Barry, P. H., Sano, Y., Zhang, L., Halldorsson, S. A., Chen, A.-T., Cheng, Z., Liu, C.-Q., Li, S.-L., Lang, Y.-C., Zheng, G., Li, Z., Li, L., & Li, Y. Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau. Nature Communications, 12(1), (2021): 4157, https://doi.org/10.1038/s41467-021-24415-y.
    Description: The episodic growth of high-elevation orogenic plateaux is controlled by a series of geodynamic processes. However, determining the underlying mechanisms that drive plateau growth dynamics over geological history and constraining the depths at which growth originates, remains challenging. Here we present He-CO2-N2 systematics of hydrothermal fluids that reveal the existence of a lithospheric-scale fault system in the southeastern Tibetan Plateau, whereby multi-stage plateau growth occurred in the geological past and continues to the present. He isotopes provide unambiguous evidence for the involvement of mantle-scale dynamics in lateral expansion and localized surface uplift of the Tibetan Plateau. The excellent correlation between 3He/4He values and strain rates, along the strike of Indian indentation into Asia, suggests non-uniform distribution of stresses between the plateau boundary and interior, which modulate southeastward growth of the Tibetan Plateau within the context of India-Asia convergence. Our results demonstrate that deeply-sourced volatile geochemistry can be used to constrain deep dynamic processes involved in orogenic plateau growth.
    Description: This work was supported by China Seismic Experimental Site (CSES) (2019CSES0104), the Strategic Priority Research Program (B) of Chinese Academy of Sciences (XDB26000000), the National Key Research and Development Program of China (2020YFA0607700), the National Natural Science Foundation of China (41930642, 41602341, 41772355, and 41702361), the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) (2019QZKK0702), and the United Laboratory of High-Pressure Physics and Earthquake Science (2019HPPES02). P.H.B. was supported by the US National Science Foundation EAR Grant 1144559 during a portion of this work.
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    Understanding physical drivers of the 2015/16 marine heatwaves in the Northwest Atlantic (2021)
    Nature Research
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Perez, E., Ryan, S., Andres, M., Gawarkiewicz, G., Ummenhofer, C. C., Bane, J., & Haines, S. Understanding physical drivers of the 2015/16 marine heatwaves in the Northwest Atlantic. Scientific Reports, 11(1), (2021): 17623, https://doi.org/10.1038/s41598-021-97012-0.
    Description: The Northwest Atlantic, which has exhibited evidence of accelerated warming compared to the global ocean, also experienced several notable marine heatwaves (MHWs) over the last decade. We analyze spatiotemporal patterns of surface and subsurface temperature structure across the Northwest Atlantic continental shelf and slope to assess the influences of atmospheric and oceanic processes on ocean temperatures. Here we focus on MHWs from 2015/16 and examine their physical drivers using observational and reanalysis products. We find that a combination of jet stream latitudinal position and ocean advection, mainly due to warm core rings shed by the Gulf Stream, plays a role in MHW development. While both atmospheric and oceanic drivers can lead to MHWs they have different temperature signatures with each affecting the vertical structure differently and horizontal spatial patterns of a MHW. Northwest Atlantic MHWs have significant socio-economic impacts and affect commercially important species such as squid and lobster.
    Description: The work was supported by a Woods Hole Oceanographic Institution Summer Student Fellowship (to E.P.) through the National Science Foundation (NSF) REU under grant OCE-1852460, a Feodor-Lynen Fellowship by the Alexander von Humboldt Foundation and the WHOI Postdoctoral Scholar program (to S.R.), NSF grants OCE-1924041 (to M.A.) and OCE-1851261 (to G.G.) and OCE-1558920 (to J.B. and H. Seim at the Univ. of North Carolina), ONR grant N-14-19-1-2646 (to G.G.), and the James E. and Barbara V. Moltz Fellowship for Climate-Related Research (to C.C.U.).
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    A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo (2021)
    Nature Research
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hawk, J. D., Wisdom, E. M., Sengupta, T., Kashlan, Z. D., & Colon-Ramos, D. A. A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo. Nature Communications, 12(1), (2021): 4795, https://doi.org/10.1038/s41467-021-24690-9.
    Description: Chemogenetic and optogenetic tools have transformed the field of neuroscience by facilitating the examination and manipulation of existing circuits. Yet, the field lacks tools that enable rational rewiring of circuits via the creation or modification of synaptic relationships. Here we report the development of HySyn, a system designed to reconnect neural circuits in vivo by reconstituting synthetic modulatory neurotransmission. We demonstrate that genetically targeted expression of the two HySyn components, a Hydra-derived neuropeptide and its receptor, creates de novo neuromodulatory transmission in a mammalian neuronal tissue culture model and functionally rewires a behavioral circuit in vivo in the nematode Caenorhabditis elegans. HySyn can interface with existing optogenetic, chemogenetic and pharmacological approaches to functionally probe synaptic transmission, dissect neuropeptide signaling, or achieve targeted modulation of specific neural circuits and behaviors.
    Description: This work was initiated in the Grass Laboratory at the Marine Biological Laboratories (MBL) with funding through a Grass Fellowship awarded to J.D.H. Thanks to Richard Goodman (OHSU) for encouragement during the conceptualization of the fellowship application, and the 2019 Grass Fellows, Mel Coleman (Grass Director), and Christophe Dupré (Associate Director) for advice and support during the summer fellowship. We thank the MBL Division of Education and participants in the Vendor Equipment Loan Program. Special thanks to Sutter Instruments, who generously provided all electrophysiology equipment and substantial on-site assistance, and Zeiss, who provided on-site assistance at MBL. We thank Zhao-Wen Wang and Ping Liu (UConn) for guidance and training in patch-clamp electrophysiology, as well as providing Neuro2a cells. We thank Rob Steele (UCI) for supplying Hydra, as well as advice and inspiration on Hydra biology. We thank members of the Colón-Ramos lab and Hari Shroff (NIH) for thoughtful comments on the manuscript. We thank Michael Koelle and Andrew Olson (Yale University) for advice and reagents regarding serotonin rewiring experiments. We also thank Steve Flavell (MIT) for ideas and reagents regarding the experiments associated with del-7. We thank Life Science Editors for editing assistance. D.A.C.-R. is an MBL Fellow. Research in the D.A.C.-R. lab was supported by NIH R01NS076558, DP1NS111778, and by an HHMI Scholar Award.
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    Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization (2022)
    Nature Research
    Details
    Publication Date: 2022-08-03
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schmidbaur, H., Kawaguchi, A., Clarence, T., Fu, X., Hoang, O. P., Zimmermann, B., Ritschard, E. A., Weissenbacher, A., Foster, J. S., Nyholm, S., Bates, P. A., Albertin, C. B., Tanaka, E., & Simakov, O. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature Communications, 13(1), (2022): 2172, https://doi.org/10.1038/s41467-022-29694-7.
    Description: Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations.
    Description: H.S., O.P.H., E.R., and O.S. were supported by the Austrian Science Fund (FWF) grant P30686-B29. O.S. was supported by Whitman Center Early Career Fellowship (Frank R. Lillie Quasi-Endowment Fund, L. & A. Colwin Summer Research Fellowship, Bell Research Award in Tissue Engineering). H.S. was supported by the short-term grant abroad (KWA) of the University of Vienna. H.S. and O.S. were supported by the University of Chicago/Vienna Strategic Partnership Programme Mobility Grant. A.K. was supported by the JSPS Postdoctoral Fellowship for Overseas Researchers program from Japan. C.B.A. was supported by the Hibbitt Early Career Fellowship. Eggs and paralarvae of E. scolopes were generated in part by support by the NASA Space Biology 80NSSC18K1465 awarded to J.S.F. S.V.N. was supported by the National Science Foundation IOS-1557914. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003).
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    A strategic framework for community engagement in oceans and human health (2022)
    Wiley
    Details
    Publication Date: 2022-07-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carson, M., Doberneck, D., Hart, Z., Kelsey, H., Pierce, J., Porter, D., Richlen, M., Schandera, L., & Triezenberg, H. A strategic framework for community engagement in oceans and human health, Community Science, 1(1), (2022): e2022CSJ000001, https://doi.org/10.1029/2022csj000001.
    Description: Over the past two decades, scientific research on the connections between the health and resilience of marine ecosystems and human health, well-being, and community prosperity has expanded and evolved into a distinct “metadiscipline” known as Oceans and Human Health (OHH), recognized by the scientific community as well as policy makers. OHH goals are diverse and seek to improve public health outcomes, promote sustainable use of aquatic systems and resources, and strengthen community resilience. OHH research has historically included some level of community outreach and partner involvement; however, the increasing disruption of aquatic environments and urgency of public health impacts calls for a more systematic approach to effectively identify and engage with community partners to achieve project goals and outcomes. Herein, we present a strategic framework developed collaboratively by community engagement personnel from the four recently established U.S. Centers for Oceans and Human Health (COHH). This framework supports researchers in defining levels of community engagement and in aligning partners, purpose, activities, and approaches intentionally in their community engagement efforts. Specifically, we describe: (a) a framework for a range of outreach and engagement approaches; (b) the need for identifying partners, purpose, activities, and approaches; and (c) the importance of making intentional alignment among them. Misalignment across these dimensions may lead to wasting time or resources, eroding public trust, or failing to achieve intended outcomes. We illustrate the framework with examples from current COHH case studies and conclude with future directions for strategic community engagement in OHH and other environmental health contexts.
    Description: This publication was prepared by Heather Triezenberg and the team under award NA180AR4170102 from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce through the Regents of the University of Michigan, and supported by funding from the NIH (1P01ES028939-01) and the NSF (1840715) to the Bowling Green State University Great Lakes Center for Fresh Waters and Human Health. Funding for M. L. Richlen was provided by the NSF (OCE1840381) and NIH (1P01-ES028938-01) through the Woods Hole Center for Oceans and Human Health. Research at the Center for Oceans and Human Health and Climate Change Interactions (OHHC2I) at the University of South Carolina is supported by the NIH Award Number P01ES028942, granted to Principal Investigators Geoffrey Scott and Paul Sandifer. M. A. Carson, Z. Hart, H. Kelsey, D. E. Porter, and L. Schandera are Community Engagement Core investigators at this Center. Funding for J. Pierce is provided by the NSF (grant number OCE-1841811) and the NIH (P01ES028949) through the Greater Caribbean Center for Ciguatera Research at the Florida Gulf Coast University.
    Keywords: harmful algal blooms ; human health ; pollutants ; ocean health
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    Turbulence-induced bubble nucleation in hydrothermal fluids beneath Yellowstone Lake (2022)
    Nature Research
    Details
    Publication Date: 2022-08-04
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caudron, C., Vandemeulebrouck, J., & Sohn, R. A. Turbulence-induced bubble nucleation in hydrothermal fluids beneath Yellowstone Lake. Communications Earth & Environment, 3(1), (2022): 103, https://doi.org/10.1038/s43247-022-00417-6.
    Description: Volcanic systems generate large amounts of gas, and understanding gas fluxes is a fundamental aspect of volcanology and hazard mitigation. Volcanic gases can be challenging to measure, but acoustic methods hold promise in underwater environments because gas bubbles are powerful sound sources. We deployed an acoustic system to study the nature of gas discharge at a large (~30 MW) thermal field on the floor of Yellowstone Lake, which has experienced numerous hydrothermal explosions since the last glaciation (~13.4 ka). We find that small (〈10 Pa) turbulent flow instabilities trigger the nucleation of CO2 bubbles in the saturated fluids. The observation of CO2 bubbles nucleating in hydrothermal fluids due to small pressure perturbations informs our understanding of hydrothermal explosions in Yellowstone Lake, and demonstrates that acoustic data in underwater environments can provide insight into the stability of gas-rich systems, as well as gas fluxes.
    Description: This research was supported by the National Science Foundation grant EAR-1516361 to R.A.S. All work in Yellowstone National Park was completed under an authorized research permit (YELL-2018-SCI-7018). We also acknowledge the IRGA 2021 Volquan project (funded by Université Grenoble Alpes) and Thomas Jefferson Fund Face Foundation (project TJF20_009 ‘Quantifying underwater volcano degassing using novel seismo-acoustic approaches’).
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    PANGAEA Data Publisher for Earth & Environmental Science - INTERACT Workshop 2022 (2022)
    PANGAEA
    In:  EPIC3INTERACT Webinar on Data Repositories, Online, 2022-05-12Bremerhaven, PANGAEA
    Details
    Publication Date: 2022-10-04
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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    Open ocean particle flux variability from surface to seafloor (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(9), pp. e2021GL092895, ISSN: 0094-8276
    Details
    Publication Date: 2022-08-15
    Description: The sinking of carbon fixed via net primary production (NPP) into the ocean interior is an important part of marine biogeochemical cycles. NPP measurements follow a log-normal probability distribution, meaning NPP variations can be simply described by two parameters despite NPP's complexity. By analyzing a global database of open ocean particle fluxes, we show that this log-normal probability distribution propagates into the variations of near-seafloor fluxes of particulate organic carbon (POC), calcium carbonate, and opal. Deep-sea particle fluxes at subtropical and temperate time-series sites follow the same log-normal probability distribution, strongly suggesting the log-normal description is robust and applies on multiple scales. This log-normality implies that 29% of the highest measurements are responsible for 71% of the total near-seafloor POC flux. We discuss possible causes for the dampening of variability from NPP to deep-sea POC flux, and present an updated relationship predicting POC flux from mineral flux and depth.
    Repository Name: EPIC Alfred Wegener Institut
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    Arctic observations identify phytoplankton community composition as driver of carbon flux attenuation (2020)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 47(14), pp. e2020GL087465, ISSN: 0094-8276
    Details
    Publication Date: 2022-08-15
    Description: The attenuation coefficient b is one of the most common ways to describe how strong the carbon flux is attenuated throughout the water column. Therefore, b is an essential input variable in many carbon flux and climate models. Marsay et al. (2015, https://doi.org/10.1073/pnas.1415311112) proposed that the median surface water temperature (0–500 m) may be a predictor of b, but our observations from Arctic waters challenge this hypothesis. We found a highly variable attenuation coefficient (b = 0.43–1.84) in cold Arctic waters (〈4.1 °C). Accordingly, we suggest that water temperature is not a globally valid predictor of the attenuation coefficient. We advocate instead that the phytoplankton composition and especially the relative abundance of diatoms can be used to parametrize the carbon flux attenuation in local and global carbon flux models.
    Repository Name: EPIC Alfred Wegener Institut
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  • 182
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    Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments (2022)
    Nature Research
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sievert, S. M., Buehring, S., Gulmann, L. K., Hinrichs, K.-U., Ristova, P. P., & Gomez-Saez, G. Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments. Communications Earth & Environment, 3(1), (2022): 96, https://doi.org/10.1038/s43247-022-00426-5.
    Description: Hydrothermalism in coastal sediments strongly impacts biogeochemical processes and supports chemoautotrophy. Yet, the effect of fluid flow on microbial community composition and rates of chemoautotrophic production is unknown because rate measurements under natural conditions are difficult, impeding an assessment of the importance of these systems. Here, in situ incubations controlling fluid flow along a transect of three geochemically distinct locations at a shallow-water hydrothermal system off Milos (Greece) show that Campylobacteria dominated chemoautotrophy in the presence of fluid flow. Based on injected 13C-labelled dissolved inorganic carbon and its incorporation into fatty acids, we constrained carbon fixation to be as high as 12 µmol C cm−3 d−1, corresponding to areal rates up to 10-times higher than previously reported for coastal sediments, and showed the importance of fluid flow for supplying the necessary substrates to support chemoautotrophy. Without flow, rates were substantially lower and microbial community composition markedly shifted. Our results highlight the importance of fluid flow in shaping the composition and activity of microbial communities of shallow-water hydrothermal vents, identifying them as hotspots of microbial productivity.
    Description: Open Access funding enabled and organized by Projekt DEAL.
    Repository Name: Woods Hole Open Access Server
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    Arctic drainage of Laurentide Ice Sheet meltwater throughout the past 14,700 years (2022)
    Nature Research
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sufke, F., Gutjahr, M., Keigwin, L. D., Reilly, B., Giosan, L., & Lippold, J. Arctic drainage of Laurentide Ice Sheet meltwater throughout the past 14,700 years. Communications Earth & Environment, 3(1), (2022): 98, https://doi.org/10.1038/s43247-022-00428-3.
    Description: During the last deglaciation substantial volumes of meltwater from the decaying Laurentide Ice Sheet were supplied to the Arctic, Gulf of Mexico and North Atlantic along different drainage routes, sometimes as catastrophic flood events. These events are suggested to have impacted global climate, for example initiating the Younger Dryas cold period. Here we analyze the authigenic Pb isotopic composition of sediments in front of the Arctic Mackenzie Delta, a sensitive tracer for elevated freshwater runoff of the retreating Laurentide Ice Sheet. Our data reveal continuous meltwater supply to the Arctic along the Mackenzie River since the onset of the Bølling–Allerød. The strongest Lake Agassiz outflow event is observed at the end of the Bølling–Allerød close to the onset of the Younger Dryas. In context of deglacial North American runoff records from the southern and eastern outlets, our findings provide a detailed reconstruction of the deglacial drainage chronology of the disintegrating Laurentide Ice Sheet.
    Description: Open Access funding enabled and organized by Projekt DEAL.
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    Ciliary flows in corals ventilate target areas of high photosynthetic oxygen production (2022)
    Cell Press
    In:  EPIC3Current Biology, Cell Press, ISSN: 09609822
    Details
    Publication Date: 2022-08-30
    Description: Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O2) may lead to excess O2 in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O2 and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O2-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O2 in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O2 in the DBL and Chla in the underlying tissue, with patches of high O2 in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O2 concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O2 is related to ciliary-induced flows, causing a lateral redistribution of O2 in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O2 transport allocates parts of the O2 surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.
    Repository Name: EPIC Alfred Wegener Institut
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    Genome and transcriptome mechanisms driving cephalopod evolution (2022)
    Nature Research
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Albertin, C. B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z. Y., Grimwood, J., Rosenthal, J. J. C., Ragsdale, C. W., Simakov, O., & Rokhsar, D. S. Genome and transcriptome mechanisms driving cephalopod evolution. Nature Communications, 13(1), (2022): 2427, https://doi.org/10.1038/s41467-022-29748-w.
    Description: Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing.
    Description: We thank the Marine Resources Center and the Cephalopod program at the Marine Biological Laboratory for supplying D. pealeii, R. Hanlon for the image in Fig. 1a, R. Hanlon and S. Senft for help with tissue dissection, Dr. Chuck Winkler for supplying O. bimaculoides, B. Burford and W. Gilly for assistance with D. opalescens collection, and the Vienna Zoo (Tiergarten Schönbrunn), particularly R. Halbauer, A. Weissenbacher, and the aquarist team for E. scolopes husbandry. Computation was done using the Life Science Cluster at the University of Vienna. This project began with generous funding from the Grass Foundation, administered by the MBL through J.J.R. It was also supported by Austrian Science fund FWF (P30686-B29) to H.S. and O.S., the Whitman Center Early Career Fellowship to O.S., the Okinawa Institute of Science and Technology Molecular Genetics Unit, Chan-Zuckerberg BioHub, and the Marthella Foskett Brown Chair in Computational Biology to D.S.R, NSF grant (IOS-1354898) to C.W.R, and the Hibbitt Early Career Fellowship to C.B.A. Sequencing at the University of Chicago Functional Genomics Facility was partially supported by the NIH (5UL1TR002389-02 and UL1 TR000430).
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    A Maluku Sea intermediate western boundary current connecting Pacific Ocean circulation to the Indonesian Throughflow (2022)
    Nature Research
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yuan, D., Yin, X., Li, X., Corvianawatie, C., Wang, Z., Li, Y., Yang, Y., Hu, X., Wang, J., Tan, S., Surinati, D., Purwandana, A., Wardana, A., Ismail, M., Budiman, A., Bayhaqi, A., Avianto, P., Santoso, P., Kusmanto, E., Dirhamsyah, Arifin, Z., & Pratt, L. A Maluku Sea intermediate western boundary current connecting Pacific Ocean circulation to the Indonesian Throughflow. Nature Communications, 13(1), (2022): 2093, https://doi.org/10.1038/s41467-022-29617-6.
    Description: The Indonesian Throughflow plays an important role in the global ocean circulation and climate. Existing studies of the Indonesian Throughflow have focused on the Makassar Strait and the exit straits, where the upper thermocline currents carry North Pacific waters to the Indian Ocean. Here we show, using mooring observations, that a previous unknown intermediate western boundary current (with the core at ~1000 m depth) exists in the Maluku Sea, which transports intermediate waters (primarily the Antarctic Intermediate Water) from the Pacific into the Seram-Banda Seas through the Lifamatola Passage above the bottom overflow. Our results suggest the importance of the western boundary current in global ocean intermediate circulation and overturn. We anticipate that our study is the beginning of more extensive investigations of the intermediate circulation of the Indo-Pacific ocean in global overturn, which shall improve our understanding of ocean heat and CO2 storages significantly.
    Description: This study is supported by NSFC (D.Y., Z.W., Y.L., Y.Y., S.T., J.W., and X.L.: 41720104008; D.Y., J.W., Y.L., X.L., Y.Y., S.T., X.H., and X.Y.: 91858204), the National Key Research and Development Program of China (D.Y. and X.L.: 2020YFA0608800), CAS (D.Y., Z.W., J.W., and Y.L.: XDB42000000), projects. Affiliations 1 and 2 share the first position. D.Y. is supported by QMSNL (2018SDKJ0104-02), and Shandong Provincial (U1606402) and the “Kunpeng Outstanding Scholar Program” of the FIO/NMR of China, J.W. supported by NSFC (41776011), Z.W. by NSFC (41876025).
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    Integrated on‐land‐offshore stratigraphy of the Campi Flegrei caldera: new insights into the volcano‐tectonic evolution in the last 15 kyr (2021)
    Wiley
    Details
    Publication Date: 2022-06-22
    Description: Silicic calderas are volcanic systems whose unrest evolution is more unpredictable than other volcano types because they often do not culminate in an eruption. Their complex structure strongly influences the post-collapse volcano-tectonic evolution, usually coupling volcanism and ground deformation. Among such volcanoes, the Campi Flegrei caldera (southern Italy) is one of the most studied. Significant long- and short-term ground deformations characterize this restless volcano. Several studies performed on the marinecontinental succession exposed in the central sector of the Campi Flegrei caldera provided a reconstruction of ground deformation during the last 15 kyr. However, considering that over one-third of the caldera is presently submerged beneath the Pozzuoli Gulf, a comprehensive stratigraphic on-land-offshore framework is still lacking. This study aims at reconstructing the offshore succession through analysis of high-resolution single and multichannel reflection seismic profiles and correlates the resulting seismic stratigraphic framework with the stratigraphy reconstructed on-land. Results provide new clues on the causative relations between the intra-caldera marine and volcaniclastic sedimentation and the alternating phases of marine transgressions and regressions originated by the interplay between ground deformation and sea-level rise. The volcano-tectonic reconstruction, provided in this work, connects the major caldera floor movements to the large Plinian eruptions of Pomici Principali (12 ka) and Agnano Monte Spina (4.55 ka), with the onset of the first post-caldera doming at ~10.5 ka. We emphasize that ground deformation is usually coupled with volcanic activity, which shows a self-similar pattern, regardless of its scale. Thus, characterizing the long-term deformation history becomes of particular interest and relevance for hazard assessment and definition of future unrest scenarios.
    Description: Published
    Description: 855-882
    Description: 1V. Storia eruttiva
    Description: JCR Journal
    Keywords: offshore stratigraphy ; seismic units ; La Starza succession ; volcanism, ; 04.08. Volcanology ; 04.04. Geology ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Benthic Carbon Remineralization and Iron Cycling in Relation to Sea Ice Cover along the Eastern Continental Shelf of the Antarctic Peninsula (2022)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Oceans, Wiley, ISSN: 0148-0227
    Details
    Publication Date: 2022-06-29
    Description: Rapid and profound climatic and environmental changes have been predicted for the Antarctic Peninsula with so far unknown impact on the biogeochemistry of the continental shelves. In this study, we investigate benthic carbon sedimentation, remineralization and iron cycling using sediment cores retrieved on a 400 mile transect with contrasting sea ice conditions along the eastern shelf of the Antarctic Peninsula. Sediments at comparable water depths of 330-450 m showed sedimentation and remineralization rates of organic carbon, ranging from 2.5-13 and 1.8-7.2 mmol C m-2 d-1, respectively. Both rates were positively correlated with the occurrence of marginal sea ice conditions (5-35% ice cover) along the transect, suggesting a favorable influence of the corresponding light regime and water column stratification on algae growth and sedimentation rates. From south to north, the burial efficiency of organic carbon decreased from 58% to 27%, while bottom water temperatures increased from -1.9 to -0.1 °C. Net iron reduction rates, as estimated from pore-water profiles of dissolved iron, were significantly correlated with carbon degradation rates and contributed 0.7-1.2% to the total organic carbon remineralization. Tightly coupled phosphate-iron recycling was indicated by significant covariation of dissolved iron and phosphate concentrations, which almost consistently exhibited P/Fe flux ratios of 0.26. Iron efflux into bottom waters of 0.6-4.5 µmol Fe m-2 d-1 was estimated from an empirical model. Despite the deep shelf waters, a clear bentho-pelagic coupling is indicated, shaped by the extent and duration of marginal sea ice conditions during summer, and likely to be affected by future climate change.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 189
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    Robust but weak winter atmospheric circulation response to future Arctic sea ice loss (2022)
    Nature Research
    In:  EPIC3Nature Communications, Nature Research, 13, pp. 727, ISSN: 2041-1723
    Details
    Publication Date: 2022-06-29
    Description: The possibility that Arctic sea ice loss weakens mid-latitude westerlies, promoting more severe cold winters, has sparked more than a decade of scientific debate, with apparent support from observations but inconclusive modelling evidence. Here we show that sixteen models contributing to the Polar Amplification Model Intercomparison Project simulate a weakening of mid-latitude westerlies in response to projected Arctic sea ice loss. We develop an emergent constraint based on eddy feedback, which is 1.2 to 3 times too weak in the models, suggesting that the real-world weakening lies towards the higher end of the model simulations. Still, the modelled response to Arctic sea ice loss is weak: the North Atlantic Oscillation response is similar in magnitude and offsets the projected response to increased greenhouse gases, but would only account for around 10% of variations in individual years. We further find that relationships between Arctic sea ice and atmospheric circulation have weakened recently in observations and are no longer inconsistent with those in models.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed , info:eu-repo/semantics/article
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  • 190
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    Ocean Model Formulation Influences Transient Climate Response (2021)
    Wiley
    In:  EPIC3Journal of Geophysical Research-Oceans, Wiley, 126(12), pp. e2021JC017633, ISSN: 0148-0227
    Details
    Publication Date: 2022-06-29
    Description: The transient climate response (TCR) is 20% higher in the Alfred Wegener Institute Climate Model (AWI-CM) compared to the Max Planck Institute Earth System Model (MPI-ESM) whereas the equilibrium climate sensitivity (ECS) is by up to 10% higher in AWI-CM. These results are largely independent of the two considered model resolutions for each model. The two coupled CMIP6 models share the same atmosphere-land component ECHAM6.3 developed at the Max Planck Institute for Meteorology (MPI-M). However, ECHAM6.3 is coupled to two different ocean models, namely the MPIOM sea ice-ocean model developed at MPI-M and the FESOM sea ice-ocean model developed at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI). A reason for the different TCR is related to ocean heat uptake in response to greenhouse gas forcing. Specifically, AWI-CM simulations show stronger surface heating than MPI-ESM simulations while the latter accumulate more heat in the deeper ocean. The vertically integrated ocean heat content is increasing slower in AWI-CM model configurations compared to MPI-ESM model configurations in the high latitudes. Weaker vertical mixing in AWI-CM model configurations compared to MPI-ESM model configurations seems to be key for these differences. The strongest difference in vertical ocean mixing occurs inside the Weddell and Ross Gyres and the northern North Atlantic. Over the North Atlantic, these differences materialize in a lack of a warming hole in AWI-CM model configurations and the presence of a warming hole in MPI-ESM model configurations. All these differences occur largely independent of the considered model resolutions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 191
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    Rotation at subduction margins: How complexity at fault‐scale (the 2019 Albanian Mw 6.4 earthquake) mirrors the regional deformation (2022)
    Wiley
    Details
    Publication Date: 2022-06-24
    Description: A variety of tectonic processes spread along the circum-Mediterranean orogenic belts driven by the convergence of major plates, episodes of slab retreat and lateral and vertical mantle flows. Here, we provide an updated view of crustal stress and strain-rate fields for the Albanides belt in the eastern Adria-Eurasia convergence boundary. We framed a new geodetic-based source model for the 2019 Mw6.4 Durrёs earthquake in light of the regional deformation, propending for a transpressional west-dipping seismogenic fault. Our results highlight a fault-scale complexity which mirrors the long-time scale deformation of the Albanides plate boundary, where the rotation induced by the fast Hellenic rollback is accommodated also by transpression on inherited structures.
    Description: Published
    Description: 244–252
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 192
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    Energy facies : A global view of pyroclastic currents from vent to deposit (2022)
    Wiley
    Details
    Publication Date: 2022-05-24
    Description: Pyroclastic currents are described as gravity currents, and the classic conceptual model gives a first-order importance to the density of such currents. This directs quantitative models to assume specific flow structures (shallow water or equilib rium turbulent boundary layer), which may apply to restricted volcanic areas inde pendently of source dynamics or may correspond to source dynamics separate from topographic interaction. The recent introduction of two end-members of pyroclastic currents, inertial and forced, is further developed here, leading to a global conceptual model in which source dynamics and topographic interaction are both taken into account. The concept of energy facies is defined here as the ensemble of the first order indicators of pyroclastic currents (topological aspect ratio, competence ratio and emplacement temperature) that are proxies of the energy of such currents. Nine energy facies are introduced with general applicability and with the goal to globally characterize pyroclastic currents from vent to deposit.
    Description: Published
    Description: 1-11
    Description: 4V. Processi pre-eruttivi
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Keywords: Energy facies ; pyroclastic currents
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 193
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    Petrographical and geochemical criteria for a chronology of Roman mortars between the 1st century BC and the 2nd century AD: the Curia of Pompey the Great (2021)
    Wiley
    Details
    Publication Date: 2022-06-22
    Description: Thirteen samples of mortar collected from different masonry structures of the Curia of Pompey the Great and from three mixtilinear basins located within the Sacred Area of Largo Argentina were studied. Despite the use of the same volcanic deposit, known as "Pozzolane Rosse", to produce the fine aggregate in all these mortars, it was possible to highlight some distinctive features through the combination of geochemical analyses on selected trace elements and petrographic analysis under an optical microscope, allowing us to distinguish among the three groups of mortars. These types of mortars reflect a perfect coincidence between the diversity of the volcanic materials used and the different construction phases identified and documented by the analysis of the stratigraphic units: a first construction phase of Pompeian age, a second one of Augustan age and, finally, one of the medieval period. Furthermore, it was possible to ascertain two phases of construction of the basins, the second coeval with the interventions of the Augustan period. Finally, this study increases the knowledge on the methods of exploitation and selection of volcanic materials used to produce mortars in Roman times, identifying additional elements useful to establish their origin and chronology of use.
    Description: Published
    Description: 597-610
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: JCR Journal
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  • 194
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    Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states (2021)
    Wiley
    In:  EPIC3Microbiology Open, Wiley, 6
    Details
    Publication Date: 2022-07-10
    Description: The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.
    Repository Name: EPIC Alfred Wegener Institut
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  • 195
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    Differential effects of elevated 〈scp〉 〈i〉p〈/i〉 CO 〈sub〉2〈/sub〉 〈/scp〉 and warming on marine phytoplankton stoichiometry (2022)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, 67(3), pp. 598-607, ISSN: 0024-3590
    Details
    Publication Date: 2022-09-15
    Description: Phytoplankton stand at the base of the marine food-web, and play a major role in global carbon cycling. Rising CO2 levels and temperatures are expected to enhance growth and alter carbon:nutrient stoichiometry of marine phytoplankton, with possible consequences for the functioning of marine food-webs and the oceanic carbon pump. To date, however, the consistency of phytoplankton stoichiometric responses remains unclear. We therefore performed a meta-analysis on data from experimental studies on stoichiometric responses of marine phytoplankton to elevated pCO2 and 3–5° warming under nutrient replete and limited conditions. Our results demonstrate that elevated pCO2 increased overall phytoplankton C:N (by 4%) and C:P (by 9%) molar ratios under nutrient replete conditions, as well as phytoplankton growth rates (by 6%). Nutrient limitation amplified the CO2 effect on C:N and C:P ratios, with increases to 27% and 17%, respectively. In contrast to elevated pCO2, warming did not consistently alter phytoplankton elemental composition. This could be attributed to species- and study-specific increases and decreases in stoichiometry in response to warming. While our observed moderate CO2-driven changes in stoichiometry are not likely to drive marked changes in food web functioning, they are in the same order of magnitude as current and projected estimations of oceanic carbon export. Therefore, our results may indicate a stoichiometric compensation mechanism for reduced oceanic carbon export due to declining primary production in the near future.
    Repository Name: EPIC Alfred Wegener Institut
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  • 196
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    U-Th Dating of lacustrine carbonates (2020)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-09-14
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanography and Applied Ocean Science and Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2020.
    Description: Carbonates are prevalent in many modern and ancient lacustrine settings, but reconstructions of past lake levels or environments from such materials have been hindered by poor chronology. Uranium-thorium (U-Th) dating has the potential to fill a gap in current geochronological tools for such archives, but past attempts have been confounded by poor understanding of the complex makeup of lacustrine carbonates, leading to misguided conclusions on both the utility of certain geochronological tools as well as the age of these deposits. This thesis showcases strategies for the successful application of U-Th geochronology to two types of lacustrine carbonates: lake bottom sediments and tufa deposits. Chapter 2 presents a systematic approach to U-Th dating carbonate-rich lake sediments using the ICDP sediment core from Lake Junín, Peru. Chapters 3–5 seek to demonstrate the descriptive power of combining precise U-Th dates on tufas and other carbonates with geologic observations of their depositional context at all scales—from the outcrop to the microscale. Here, the tufas originate from a transect of closed-basin lakes in the central Andes of northern Chile. With improved sample selection and leveraging of the incontrovertible constraints of stratigraphy and coevality, we are able to test the validity of U-Th data. Combining quality-controlled geochronological constraints with careful characterization of different carbonate facies can yield new insight on the character of lake level changes. These case studies offer frameworks for interpreting scattered geochronologic data of any size or system. By embracing the noise in our data, we now have a richer understanding of the controls on uranium in these deposits. Of all the lessons learned, we hold the following as most important: for the determination of the age of lacustrine carbonates, geologic context—in the form of sedimentological observations, additional geochemical data, and paleoecological descriptions—is of equal importance to the numerical accuracy and precision of geochronological measurements.
    Description: Funding sources: National Science Foundation, Massachusetts Institute of Technology, Geological Society of America, MIT MISTI, Comer Foundation, American Philosophical Society, National Geographic Society, Explorers Club.
    Keywords: Carbonates ; Tufa ; Geochronology
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 197
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    A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations (2022)
    Wiley
    Details
    Publication Date: 2022-09-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thomas, M., Jensen, F. H., Averly, B., Demartsev, V., Manser, M. B., Sainburg, T., Roch, M. A., & Strandburg-Peshkin, A. A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations. The Journal of Animal Ecology, 91(8), (2022): 1567– 1581, https://doi.org/10.1111/1365-2656.13754.
    Description: 1. Background: The manual detection, analysis and classification of animal vocalizations in acoustic recordings is laborious and requires expert knowledge. Hence, there is a need for objective, generalizable methods that detect underlying patterns in these data, categorize sounds into distinct groups and quantify similarities between them. Among all computational methods that have been proposed to accomplish this, neighbourhood-based dimensionality reduction of spectrograms to produce a latent space representation of calls stands out for its conceptual simplicity and effectiveness. 2. Goal of the study/what was done: Using a dataset of manually annotated meerkat Suricata suricatta vocalizations, we demonstrate how this method can be used to obtain meaningful latent space representations that reflect the established taxonomy of call types. We analyse strengths and weaknesses of the proposed approach, give recommendations for its usage and show application examples, such as the classification of ambiguous calls and the detection of mislabelled calls. 3. What this means: All analyses are accompanied by example code to help researchers realize the potential of this method for the study of animal vocalizations.
    Description: This work was supported by HFSP Research Grant RGP0051/2019 to ASP, MBM and MAR, and funded by the Deutsche Forschungsgemeinschaft (DFG) under Germany's Excellence Strategy (EXC-2117-422037984). ASP received additional funding from the Gips-Schüle Stiftung, the Zukunftskolleg at the University of Konstanz and the Max-Planck-Institute of Animal Behaviour. VD was funded by the Minerva Stiftung and Alexander von Humboldt Foundation.
    Keywords: animal sounds ; animal vocalizations ; bioacoustics ; call classification ; dimensionality reduction ; spectrogram ; UMAP ; unsupervised learning
    Repository Name: Woods Hole Open Access Server
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  • 198
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    Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse (2022)
    Nature Research
    Details
    Publication Date: 2022-09-23
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pattanayak, R., Underwood, R., Crowley, M. R., Crossman, D. K., Morgan, J. R., & Yacoubian, T. A. Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse. Scientific Reports, 12(1), (2022): 9837, https://doi.org/10.1038/s41598-022-13557-8.
    Description: We report an incidental 358.5 kb deletion spanning the region encoding for alpha-synuclein (αsyn) and multimerin1 (Mmrn1) in the Rab27a/Rab27b double knockout (DKO) mouse line previously developed by Tolmachova and colleagues in 2007. Western blot and RT-PCR studies revealed lack of αsyn expression at either the mRNA or protein level in Rab27a/b DKO mice. PCR of genomic DNA from Rab27a/b DKO mice demonstrated at least partial deletion of the Snca locus using primers targeted to exon 4 and exon 6. Most genes located in proximity to the Snca locus, including Atoh1, Atoh2, Gm5570, Gm4410, Gm43894, and Grid2, were shown not to be deleted by PCR except for Mmrn1. Using whole genomic sequencing, the complete deletion was mapped to chromosome 6 (60,678,870–61,037,354), a slightly smaller deletion region than that previously reported in the C57BL/6J substrain maintained by Envigo. Electron microscopy of cortex from these mice demonstrates abnormally enlarged synaptic terminals with reduced synaptic vesicle density, suggesting potential interplay between Rab27 isoforms and αsyn, which are all highly expressed at the synaptic terminal. Given this deletion involving several genes, the Rab27a/b DKO mouse line should be used with caution or with appropriate back-crossing to other C57BL/6J mouse substrain lines without this deletion.
    Description: This study was supported by NIH [R56NS115767 (TAY), RF1NS115767-01A1 (TAY), P50NS108675 (TAY), and NINDS/NIA RF1NS078165 (JRM)].
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    An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatan Peninsula, Mexico (2022)
    Nature Research
    Details
    Publication Date: 2022-07-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ballou, L., Brankovits, D., Chavez-Solis, E. M., Diaz, J. M. C., Gonzalez, B. C., Rohret, S., Salinas, A., Liu, A., Simoes, N., Alvarez, F., Miglietta, M. P., Iliffe, T. M., & Borda, E. An integrative re-evaluation of Typhlatya shrimp within the karst aquifer of the Yucatan Peninsula, Mexico. Scientific Reports, 12(1), (2022): 5302, https://doi.org/10.1038/s41598-022-08779-9.
    Description: The Yucatán Peninsula, Mexico is a carbonate platform well-known for extensive karst networks of densely stratified aquifer ecosystems. This aquifer supports diverse anchialine fauna, including species of the globally distributed anchialine shrimp genus Typhlatya (Atyidae). Four species (T. campecheae, T. pearsei, T. dzilamensis and T. mitchelli) are endemic to the Peninsula, of which three are federally listed in Mexico. This first integrative evaluation (i.e., molecular, morphological, broad geographic and type locality sampling, and environmental data) of Yucatán Typhlatya reveals considerable species identity conflict in prior phylogenetic assessments, broad species ranges, syntopy within cave systems and five genetic lineages (of which two are new to science). Despite sampling from the type locality of endangered T. campecheae, specimens (and molecular data) were indistinguishable from vulnerable T. pearsei. Ancestral/divergence reconstructions support convergent evolution of a low-salinity ancestor for a post-Paleogene arc Yucatán + Cuba Typhlatya clade within the anchialine Atyidae clade. A secondary adaptation for the coastal-restricted euryhaline (2–37 psu), Typhlatya dzilamensis (unknown conservation status) was identified, while remaining species lineages were low-salinity (〈 5 psu) adapted and found within the meteoric lens of inland and coastal caves. This study demonstrates the need for integrative/interdisciplinary approaches when conducting biodiversity assessments in complex and poorly studied aquifers.
    Description: Financial support for this study was provided by Texas A&M-CONACYT (TI, FA), TI, FA), PAPIIT IN208519 (DGAPA-UNAM) (FA), CONACYT Ciencia Básica A1-S-32846 (FA), Texas A&M University San Antonio (TAMUSA) Start-up Funds (EB), TAMUSA Research Council Grant (EB), TAMUSA Summer Faculty Grant and Fellowship (EB). NSF-REU/OCE: 1560242 supported AL and EB, and TAMU-Louis Stokes Alliance for Minority Participation (HRD: 1612776) supported SR, LS. This work was also supported by the NSF Graduate Research Fellowship Program (M1703014) and the Cave Conservancy Foundation (LB). Typhlatya sampling was sanctioned under collection permits SEMARNAT/SGPA/DGVS 05263/14, 004471/18, 05996/19.
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    Tropical origins of the record-breaking 2020 summer rainfall extremes in East Asia (2022)
    Nature Research
    Details
    Publication Date: 2022-07-21
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, S., Park, J.-H., & Kug, J.-S. Tropical origins of the record-breaking 2020 summer rainfall extremes in East Asia. Scientific Reports, 12(1), (2022): 5366, https://doi.org/10.1038/s41598-022-09297-4.
    Description: The East Asian countries have experienced heavy rainfalls in boreal summer 2020. Here, we investigate the dynamical processes driving the rainfall extremes in East Asia during July and August. The Indian Ocean basin warming in June can be responsible for the anticyclonic anomalies in the western North Pacific (WNP), which modulate the zonally-elongated rainfalls in East Asia during July through an atmospheric Rossby wave train. In August, the East Asian rainfall increase is also related to the anticyclonic anomalies in the subtropical WNP, although it is located further north. The north tropical Atlantic warming in June partly contributes to the subtropical WNP rainfall decrease in August through a subtropical teleconnection. Then the subtropical WNP rainfall decrease drives the local anticyclonic anomalies that cause the rainfall increase in East Asia during August. The tropical Indian Ocean anomalously warmed in June and the subtropical WNP rainfall decreased in August 2020, which played a role in modulating the WNP anticyclonic anomalies. Therefore, the record-breaking rainfall extremes in East Asia that occurred during summer 2020 can be explained by the teleconnections associated with the tropical origins among the Indian, Pacific, and Atlantic Oceans and their interbasin interactions.
    Description: This work is supported by the National Research Foundation of Korea (NRF-2018R1A5A1024958 & NRF-2021M3I6A1086808).
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