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  • 1
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    A blueprint for an inclusive, global deep-sea ocean decade field program (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Howell, K. L., Hilario, A., Allcock, A. L., Bailey, D. M., Baker, M., Clark, M. R., Colaco, A., Copley, J., Cordes, E. E., Danovaro, R., Dissanayake, A., Escobar, E., Esquete, P., Gallagher, A. J., Gates, A. R., Gaudron, S. M., German, C. R., Gjerde, K. M., Higgs, N. D., Le Bris, N., Levin, L. A., Manea, E., McClain, C., Menot, L., Mestre, N. C., Metaxas, A., Milligan, R. J., Muthumbi, A. W. N., Narayanaswamy, B. E., Ramalho, S. P., Ramirez-Llodra, E., Robson, L. M., Rogers, A. D., Sellanes, J., Sigwart, J. D., Sink, K., Snelgrove, P. V. R., Stefanoudis, P., V., Sumida, P. Y., Taylor, M. L., Thurber, A. R., Vieira, R. P., Watanabe, H. K., Woodall, L. C., & Xavier, J. R. A blueprint for an inclusive, global deep-sea ocean decade field program. Frontiers in Marine Science, 7, (2020): 584861, doi:10.3389/fmars.2020.584861.
    Description: The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four objectives (Os). It specifically recognizes the scarcity of biological data for deep-sea biomes, and challenges the global scientific community to conduct research to advance understanding of deep-sea ecosystems to inform sustainable management. In this paper, we map four key scientific questions identified by the academic community to the Ocean Decade SOs: (i) What is the diversity of life in the deep ocean? (ii) How are populations and habitats connected? (iii) What is the role of living organisms in ecosystem function and service provision? and (iv) How do species, communities, and ecosystems respond to disturbance? We then consider the design of a global-scale program to address these questions by reviewing key drivers of ecological pattern and process. We recommend using the following criteria to stratify a global survey design: biogeographic region, depth, horizontal distance, substrate type, high and low climate hazard, fished/unfished, near/far from sources of pollution, licensed/protected from industry activities. We consider both spatial and temporal surveys, and emphasize new biological data collection that prioritizes southern and polar latitudes, deeper (〉 2000 m) depths, and midwater environments. We provide guidance on observational, experimental, and monitoring needs for different benthic and pelagic ecosystems. We then review recent efforts to standardize biological data and specimen collection and archiving, making “sampling design to knowledge application” recommendations in the context of a new global program. We also review and comment on needs, and recommend actions, to develop capacity in deep-sea research; and the role of inclusivity - from accessing indigenous and local knowledge to the sharing of technologies - as part of such a global program. We discuss the concept of a new global deep-sea biological research program ‘Challenger 150,’ highlighting what it could deliver for the Ocean Decade and UN Sustainable Development Goal 14.
    Description: Development of this paper was supported by funding from the Scientific Committee on Oceanic Research (SCOR) awarded to KH and AH as working group 159 co-chairs. KH, BN, and KS are supported by the UKRI funded One Ocean Hub NE/S008950/1. AH work is supported by the CESAM (UIDP/50017/2020 + 1432 UIDB/50017/2020) that is funded by Fundação para a Ciência e a Tecnologia (FCT)/MCTES through national funds. AA is supported by Science Foundation Ireland and the Marine Institute under the Investigators Program Grant Number SFI/15/IA/3100 co-funded under the European Regional Development Fund 2014–2020. AC is supported through the FunAzores -ACORES 01-0145-FEDER-000123 grant and by FCT through strategic project UID/05634/2020 and FCT and Direção-Geral de Politica do Mar (DGPM) through the project Mining2/2017/005. PE is funded by national funds (OE), through FCT in the scope of the framework contract foreseen in the numbers 4, 5 and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19. SG research is supported by CNRS funds. CG is supported by an Independent Study Award and the Investment in Science Fund at WHOI. KG gratefully acknowledges support from Synchronicity Earth. LL is funded by the NOAA Office of Ocean Exploration and Research (NA19OAR0110305) and the US National Science Foundation (OCE 1634172). NM is supported by FCT and DGPM, through the project Mining2/2017/001 and the FCT grants CEECIND/00526/2017, UIDB/00350/2020 + UIDP/00350/2020. SR is funded by the FCTgrant CEECIND/00758/2017. JS is supported by ANID FONDECYT #1181153 and ANID Millennium Science Initiative Program #NC120030. JX research is funded by the European Union’s Horizon 2020 research and innovation program through the SponGES project (grant agreement no. 679849) and further supported by national funds through FCT within the scope of UIDB/04423/2020 and UIDP/04423/2020. The Natural Sciences and Engineering Council of Canada supports AM and PVRS. MB and the Deep-Ocean Stewardship Initiative are supported by Arcadia - A charitable fund of Lisbet Rausing and Peter Baldwin. BN work is supported by the NERC funded Arctic PRIZE NE/P006302/1.
    Keywords: Deep sea ; Blue economy ; Ocean Decade ; Biodivercity ; Essential ocean variables
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  • 2
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    Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeiner, C. A., Purvine, S. O., Zink, E., Wu, S., Pasa-Tolic, L., Chaput, D. L., Santelli, C. M., & Hansel, C. M. Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition. Frontiers in Microbiology, 12, (2021): 610497, https://doi.org/10.3389/fmicb.2021.610497.
    Description: Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.
    Description: This work was supported by the National Science Foundation, grant numbers EAR-1249489 and CBET-1336496, both awarded to CH, by a JGI-EMSL Collaborative Science Initiative grant (proposal number 48100) awarded to CH and CS, and by the University of St. Thomas. Personal support for CZ was also provided by Harvard University and by a Ford Foundation Predoctoral Fellowship administered by the National Academies. A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program and used resources at the DOE Joint Genome Institute and the Environmental Molecular Sciences Laboratory (grid.436923.9), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Biological and Environmental Research Program and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). Part of this research was performed at the Bauer Core Facility of the FAS Center for Systems Biology at Harvard University. A portion of the bioinformatics analysis was performed at Harvard’s FAS Research Computing facility.
    Keywords: Manganese oxides ; Filamentous fungi ; Geomicrobiology ; Proteomics ; Biomineralization ; Secretome
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  • 3
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    Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Meiling, S. S., Muller, E. M., Lasseigne, D., Rossin, A., Veglia, A. J., MacKnight, N., Dimos, B., Huntley, N., Correa, A. M. S., Smith, T. B., Holstein, D. M., Mydlarz, L. D., Apprill, A., & Brandt, M. E. Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure. Frontiers in Marine Science, 8, (2021): 670829, https://doi.org/10.3389/fmars.2021.670829.
    Description: Stony coral tissue loss disease (SCTLD) was initially documented in Florida in 2014 and outbreaks with similar characteristics have since appeared in disparate areas throughout the northern Caribbean, causing significant declines in coral communities. SCTLD is characterized by focal or multifocal lesions of denuded skeleton caused by rapid tissue loss and affects at least 22 reef-building species of Caribbean corals. A tissue-loss disease consistent with the case definition of SCTLD was first observed in the U.S. Virgin Islands (USVI) in January of 2019 off the south shore of St. Thomas at Flat Cay. The objective of the present study was to characterize species susceptibility to the disease present in St. Thomas in a controlled laboratory transmission experiment. Fragments of six species of corals (Colpophyllia natans, Montastraea cavernosa, Orbicella annularis, Porites astreoides, Pseudodiploria strigosa, and Siderastrea siderea) were simultaneously incubated with (but did not physically contact) SCTLD-affected colonies of Diploria labyrinthiformis and monitored for lesion appearance over an 8 day experimental period. Paired fragments from each corresponding coral genotype were equivalently exposed to apparently healthy colonies of D. labyrinthiformis to serve as controls; none of these fragments developed lesions throughout the experiment. When tissue-loss lesions appeared and progressed in a disease treatment, the affected coral fragment, and its corresponding control genet, were removed and preserved for future analysis. Based on measures including disease prevalence and incidence, relative risk of lesion development, and lesion progression rates, O. annularis, C. natans, and S. siderea showed the greatest susceptibility to SCTLD in the USVI. These species exhibited earlier average development of lesions, higher relative risk of lesion development, greater lesion prevalence, and faster lesion progression rates compared with the other species, some of which are considered to be more susceptible based on field observations (e.g., P. strigosa). The average transmission rate in the present study was comparable to tank studies in Florida, even though disease donor species differed. Our findings suggest that the tissue loss disease affecting reefs of the USVI has a similar epizootiology to that observed in other regions, particularly Florida.
    Description: This work was supported by the National Science Foundation (Biological Oceanography) award number 1928753 to MB and TS, 1928609 to AC, 1928817 to EM, 19228771 to LM, 1927277 to DH, and 1928761 to AA as well as by VI EPSCoR (NSF #0814417 and NSF #1946412).
    Keywords: Stony coral tissue loss disease ; Coral disease ; Transmission experiment ; Susceptibility ; Lesion progression rate ; Caribbean ; United States Virgin Islands ; Histopathology
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  • 4
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    International Quality-Controlled Ocean Database (IQuOD) v0.1: the temperature uncertainty specification (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cowley, R., Killick, R. E., Boyer, T., Gouretski, V., Reseghetti, F., Kizu, S., Palmer, M. D., Cheng, L., Storto, A., Le Menn, M., Simoncelli, S., Macdonald, A. M., & Domingues, C. M. International Quality-Controlled Ocean Database (IQuOD) v0.1: the temperature uncertainty specification. Frontiers in Marine Science, 8, (2021): 689695, https://doi.org/10.3389/fmars.2021.689695.
    Description: Ocean temperature observations are crucial for a host of climate research and forecasting activities, such as climate monitoring, ocean reanalysis and state estimation, seasonal-to-decadal forecasts, and ocean forecasting. For all of these applications, it is crucial to understand the uncertainty attached to each of the observations, accounting for changes in instrument technology and observing practices over time. Here, we describe the rationale behind the uncertainty specification provided for all in situ ocean temperature observations in the International Quality-controlled Ocean Database (IQuOD) v0.1, a value-added data product served alongside the World Ocean Database (WOD). We collected information from manufacturer specifications and other publications, providing the end user with uncertainty estimates based mainly on instrument type, along with extant auxiliary information such as calibration and collection method. The provision of a consistent set of observation uncertainties will provide a more complete understanding of historical ocean observations used to examine the changing environment. Moving forward, IQuOD will continue to work with the ocean observation, data assimilation and ocean climate communities to further refine uncertainty quantification. We encourage submissions of metadata and information about historical practices to the IQuOD project and WOD.
    Description: This work was supported by the Scientific Committee on Oceanic Research (SCOR) Working Group 148, funded by national SCOR committees and a grant to SCOR from the U.S. National Science Foundation (Grant OCE-1546580); and the Intergovernmental Oceanographic Commission of UNESCO/International Oceanographic Data and Information Exchange (IOC/IODE) IQuOD Steering Group. RC was supported through funding from the Earth Systems and Climate Change Hub of the Australian Government's National Environmental Science Program. RK and MP were supported by the Met Office Hadley Centre Climate Programme funded by BEIS and Defra. CD was supported by the Australian Research Council (Discovery Grant DP160103130), ARC Centre of Excellence for Climate Extremes (CE170100023) and by the Natural Environment Research Council (TICTOC, NE/P019293/1). AM's contribution was supported by National Science Foundation grant OCE#-1923387 and National Oceanographic and Atmospheric Administration grant #NA16OAR4310172.
    Keywords: XBT ; Ocean temperature profiles ; Ocean data assimilation ; Ocean climate ; Accuracy ; Uncertainty ; Bias correction
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  • 5
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    Tau: a signaling hub protein (2021)
    Frontiers Media
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mueller, R. L., Combs, B., Alhadidy, M. M., Brady, S. T., Morfini, G. A., & Kanaan, N. M. Tau: a signaling hub protein. Frontiers in Molecular Neuroscience, 14, (2021): 647054, https://doi.org/10.3389/fnmol.2021.647054.
    Description: Over four decades ago, in vitro experiments showed that tau protein interacts with and stabilizes microtubules in a phosphorylation-dependent manner. This observation fueled the widespread hypotheses that these properties extend to living neurons and that reduced stability of microtubules represents a major disease-driving event induced by pathological forms of tau in Alzheimer’s disease and other tauopathies. Accordingly, most research efforts to date have addressed this protein as a substrate, focusing on evaluating how specific mutations, phosphorylation, and other post-translational modifications impact its microtubule-binding and stabilizing properties. In contrast, fewer efforts were made to illuminate potential mechanisms linking physiological and disease-related forms of tau to the normal and pathological regulation of kinases and phosphatases. Here, we discuss published work indicating that, through interactions with various kinases and phosphatases, tau may normally act as a scaffolding protein to regulate phosphorylation-based signaling pathways. Expanding on this concept, we also review experimental evidence linking disease-related tau species to the misregulation of these pathways. Collectively, the available evidence supports the participation of tau in multiple cellular processes sustaining neuronal and glial function through various mechanisms involving the scaffolding and regulation of selected kinases and phosphatases at discrete subcellular compartments. The notion that the repertoire of tau functions includes a role as a signaling hub should widen our interpretation of experimental results and increase our understanding of tau biology in normal and disease conditions.
    Description: This work was supported by NIH grants (R01AG067762 and R01AG044372 to NK, R01NS082730 to NK and SB, R01NS118177 and R21NS120126 to GM, R01NS023868 and R01NS041170 to SB), a gift from Neurodegenerative Research Inc. (GM), a Zenith Award from the Alzheimer’s Association (SB), a grant from the Secchia Family Foundation (NK), NIH/National Institute on Aging (NIA) funded Michigan Alzheimer’s Disease Research Center 5P30AG053760 (BC), the Office of the Assistant Secretary of Defense for Health Affairs through the Peer-Reviewed Alzheimer’s Research Program (Award No. W81XWH-20-1-0174 to BC), and an Alzheimer’s Association Research Grant 20-682085 (BC).
    Keywords: Tauopathy ; Kinase ; Phosphatase ; Scaffold protein ; Axon ; Synpase ; Nucleus ; Oligodendrocyte
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  • 6
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    Marine genetic resources in areas beyond national jurisdiction: promoting marine scientific research and enabling equitable benefit sharing (2021)
    Frontiers Media
    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 Rogers, A. D., Baco, A., Escobar-Briones, E., Gjerde, K., Gobin, J., Jaspars, M., Levin, L., Linse, K., Rabone, M., Ramirez-Llodra, E., Sellanes, J., Shank, T. M., Sink, K., Snelgrove, P. V. R., Taylor, M. L., Wagner, D., & Harden-Davies, H. Marine genetic resources in areas beyond national jurisdiction: promoting marine scientific research and enabling equitable benefit sharing. Frontiers in Marine Science, 8, (2021): 667274, https://doi.org/10.3389/fmars.2021.667274.
    Description: Growing human activity in areas beyond national jurisdiction (ABNJ) is driving increasing impacts on the biodiversity of this vast area of the ocean. As a result, the United Nations General Assembly committed to convening a series of intergovernmental conferences (IGCs) to develop an international legally-binding instrument (ILBI) for the conservation and sustainable use of marine biological diversity of ABNJ [the biodiversity beyond national jurisdiction (BBNJ) agreement] under the United Nations Convention on the Law of the Sea. The BBNJ agreement includes consideration of marine genetic resources (MGR) in ABNJ, including how to share benefits and promote marine scientific research whilst building capacity of developing states in science and technology. Three IGCs have been completed to date with the fourth delayed by the Covid pandemic. This delay has allowed a series of informal dialogues to take place between state parties, which have highlighted a number of areas related to MGR and benefit sharing that require technical guidance from ocean experts. These include: guiding principles on the access and use of MGR from ABNJ; the sharing of knowledge arising from research on MGR in ABNJ; and capacity building and technology transfer for developing states. In this paper, we explain what MGR are, the methods required to collect, study and archive them, including data arising from scientific investigation. We also explore the practical requirements of access by developing countries to scientific cruises, including the sharing of data, as well as participation in research and development on shore whilst promoting rather than hindering marine scientific research. We outline existing infrastructure and shared resources that facilitate access, research, development, and benefit sharing of MGR from ABNJ; and discuss existing gaps. We examine international capacity development and technology transfer schemes that might facilitate or complement non-monetary benefit sharing activities. We end the paper by highlighting what the ILBI can achieve in terms of access, utilization, and benefit sharing of MGR and how we might future-proof the BBNJ Agreement with respect to developments in science and technology.
    Description: We would like to thank the Governments of The Kingdom of Belgium, The Principality of Monaco and Costa Rica, as well as The Prince Albert II Monaco Foundation, The Norwegian Nobel Institute, The Nobel Institute, The High Seas Alliance, The Pew Charitable Trusts, Ocean Unite and REV Ocean for supporting the High Seas Treaty Dialogues which have allowed informal discussions between States representatives on the Biodiversity Beyond National Jurisdiction agreement.
    Keywords: high seas ; marine genetic resources ; access and benefit sharing ; UNCLOS ; developing states
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  • 7
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    A 70 3-component sensor deployment to monitor the 2020 EGS stimulation in Espoo/Helsinki, southern Finland - Dataset (2021)
    GFZ Data Services
    Details
    Publication Date: 2022-11-28
    Description: Abstract
    Description: The stations are part of a seismic network in the Helsinki capital area of Finland in 2020. The stations recorded the response to a second stimulation of a ∼ 6 km deep enhanced geothermal system in the Otaniemi district of Espoo that followed on the first larger stimulation in 2018. The second stimulation from 6 May to 24 May 2020 established a geothermal doublet system. The Institute of Seismology, University of Helsinki (ISUH), installed the 70 GIPP-provided geophones in addition to surface broadband sensors, ISUH-owned short-period instruments, and a borehole satellite network deployed by the operating company. The data set consists of raw CUBE-recorder data and converted MSEED data. The data set has been collected to underpin a wide range of seismic analysis techniques for complementary scientific studies of the evolving reservoir processes and the induced event properties. These should inform the legislation and educate the public for transparent decision making around geothermal power generation in Finland. The full 2020 network and with it the deployment of the CUBE stations is described in a Seismological Research Letter Data Mine Column by A. Rintamäki et al. (2021).
    Description: Other
    Description: The Geophysical Instrument Pool Potsdam (GIPP) provides field instruments for (temporary) seismological studies (both controlled source and earthquake seismology) and for magnetotelluric (electromagnetic) experiments. The GIPP is operated by the GFZ German Research Centre for Geosciences. The instrument facility is open for academic use. Instrument applications are evaluated and ranked by an external steering board. See Haberland and Ritter (2016) and https://www.gfz-potsdam.de/gipp for more information.
    Keywords: Geothermal system ; geothermal reservoir ; stimulation ; induced seismicity ; induced earthquakes ; Fennoscandian shield ; earthquake monitoring ; seismic arrays ; array seismology ; array of arrays ; Finland ; Helsinki] ; EARTH SCIENCE 〉 SOLID EARTH ; EARTH SCIENCE 〉 SOLID EARTH 〉 TECTONICS 〉 EARTHQUAKES ; EARTH SCIENCE 〉 SOLID EARTH 〉 TECTONICS 〉 EARTHQUAKES 〉 SEISMIC PROFILE ; geology
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  • 8
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    Assessing the skill of a high-resolution marine biophysical model using geostatistical analysis of mesoscale ocean chlorophyll variability from field observations and remote sensing (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creaive Commons Attribution License. The definitive version was published in Eveleth, R., Glover, D. M., Long, M. C., Lima, I. D., Chase, A. P., & Doney, S. C. . Assessing the skill of a high-resolution marine biophysical model using geostatistical analysis of mesoscale ocean chlorophyll variability from field observations and remote sensing. Frontiers in Marine Science, 8, (2021): 612764, https://doi.org/10.3389/fmars.2021.612764.
    Description: High-resolution ocean biophysical models are now routinely being conducted at basin and global-scale, opening opportunities to deepen our understanding of the mechanistic coupling of physical and biological processes at the mesoscale. Prior to using these models to test scientific questions, we need to assess their skill. While progress has been made in validating the mean field, little work has been done to evaluate skill of the simulated mesoscale variability. Here we use geostatistical 2-D variograms to quantify the magnitude and spatial scale of chlorophyll a patchiness in a 1/10th-degree eddy-resolving coupled Community Earth System Model simulation. We compare results from satellite remote sensing and ship underway observations in the North Atlantic Ocean, where there is a large seasonal phytoplankton bloom. The coefficients of variation, i.e., the arithmetic standard deviation divided by the mean, from the two observational data sets are approximately invariant across a large range of mean chlorophyll a values from oligotrophic and winter to subpolar bloom conditions. This relationship between the chlorophyll a mesoscale variability and the mean field appears to reflect an emergent property of marine biophysics, and the high-resolution simulation does poorly in capturing this skill metric, with the model underestimating observed variability under low chlorophyll a conditions such as in the subtropics.
    Description: This work was supported in part by the National Aeronautics and Space Administration (NASA) as part of the North Atlantic Aerosol and Marine Ecosystems Study (NAAMES; NASA grant 80NSSC18K0018). The CESM project is supported by the National Science Foundation and the Office of Science (BER) of the United States Department of Energy. Computing resources were provided by the Climate Simulation Laboratory at NCAR’s Computational and Information Systems Laboratory (CISL), sponsored by the National Science Foundation and other agencies. This research was enabled by CISL compute and storage resources.
    Keywords: Geostatistical analysis ; North Atlantic Ocean ; Community Earth System Model ; Model validataion ; Chlorophyll
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  • 9
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    Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry (2021)
    Frontiers Media
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    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 Li, J., Boiteau, R. M., Babcock-Adams, L., Acker, M., Song, Z., McIlvin, M. R., & Repeta, D. J. Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry. Frontiers in Marine Science, 8, (2021): 630494, https://doi.org/10.3389/fmars.2021.630494.
    Description: Metabolites that incorporate elements other than carbon, nitrogen, hydrogen and oxygen can be selectively detected by inductively coupled mass spectrometry (ICPMS). When used in parallel with chromatographic separations and conventional electrospray ionization mass spectrometry (ESIMS), ICPMS allows the analyst to quickly find, characterize and identify target metabolites that carry nutrient elements (P, S, trace metals; “nutrient metabolites”), which are of particular interest to investigations of microbial biogeochemical cycles. This approach has been applied to the study of siderophores and other trace metal organic ligands in the ocean. The original method used mass search algorithms that relied on the ratio of stable isotopologues of iron, copper and nickel to assign mass spectra collected by ESIMS to metabolites carrying these elements detected by ICPMS. However, while isotopologue-based mass assignment algorithms were highly successful in characterizing metabolites that incorporate some trace metals, they do not realize the whole potential of the ICPMS/ESIMS approach as they cannot be used to assign the molecular ions of metabolites with monoisotopic elements or elements for which the ratio of stable isotopes is not known. Here we report a revised ICPMS/ESIMS method that incorporates a number of changes to the configuration of instrument hardware that improves sensitivity of the method by a factor of 4–5, and allows for more accurate quantitation of metabolites. We also describe a new suite of mass search algorithms that can find and characterize metabolites that carry monoisotopic elements. We used the new method to identify siderophores in a laboratory culture of Vibrio cyclitrophicus and a seawater sample collected in the North Pacific Ocean, and to assign molecular ions to monoisotopic cobalt and iodine nutrient metabolites in extracts of a laboratory culture of the marine cyanobacterium Prochorococcus MIT9215.
    Description: This work was generously supported by the National Science Foundation grant OCE-1829761 to RB and OCE-1356747 and -1736280 to DR. DR also received generous support from the Simons Foundation Life Sciences Project Award 49476.
    Keywords: LC-MS ; Algorithm ; Environmental metabolomics ; Trace metal ; Siderophores
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  • 10
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    Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bernhard, J. M., Wit, J. C., Starczak, V. R., Beaudoin, D. J., Phalen, W. G., & McCorkle, D. C. Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming. Frontiers in Marine Science, 8, (2021): 643339, https://doi.org/10.3389/fmars.2021.643339.
    Description: Ocean chemistry is changing as a result of human activities. Atmospheric carbon dioxide (CO2) concentrations are increasing, causing an increase in oceanic pCO2 that drives a decrease in oceanic pH, a process called ocean acidification (OA). Higher CO2 concentrations are also linked to rising global temperatures that can result in more stratified surface waters, reducing the exchange between surface and deep waters; this stronger stratification, along with nutrient pollution, contributes to an expansion of oxygen-depleted zones (so called hypoxia or deoxygenation). Determining the response of marine organisms to environmental changes is important for assessments of future ecosystem functioning. While many studies have assessed the impact of individual or paired stressors, fewer studies have assessed the combined impact of pCO2, O2, and temperature. A long-term experiment (∼10 months) with different treatments of these three stressors was conducted to determine their sole or combined impact on the abundance and survival of a benthic foraminiferal community collected from a continental-shelf site. Foraminifera are well suited to such study because of their small size, relatively rapid growth, varied mineralogies and physiologies. Inoculation materials were collected from a ∼77-m deep site south of Woods Hole, MA. Very fine sediments (〈53 μm) were used as inoculum, to allow the entire community to respond. Thirty-eight morphologically identified taxa grew during the experiment. Multivariate statistical analysis indicates that hypoxia was the major driving factor distinguishing the yields, while warming was secondary. Species responses were not consistent, with different species being most abundant in different treatments. Some taxa grew in all of the triple-stressor samples. Results from the experiment suggest that foraminiferal species’ responses will vary considerably, with some being negatively impacted by predicted environmental changes, while other taxa will tolerate, and perhaps even benefit, from deoxygenation, warming and OA.
    Description: This work was supported by the US NSF SEES-OA grant OCE-1219948 to JB and the Investment in Science Program at WHOI. DM also received support from the NSF Independent Research and Development Program.
    Keywords: Deoxygenation ; Ocean acidification ; Benthic communities ; Benthic foraminifera ; Climate change ; Propagule bank ; Global warming
    Repository Name: Woods Hole Open Access Server
    Type: Article
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