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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bundy, R. M., Tagliabue, A., Hawco, N. J., Morton, P. L., Twining, B. S., Hatta, M., Noble, A. E., Cape, M. R., John, S. G., Cullen, J. T., & Saito, M. A. Elevated sources of cobalt in the Arctic Ocean. Biogeosciences, 17(19), (2020): 4745-4767, doi:10.5194/bg-17-4745-2020.
    Description: Cobalt (Co) is an important bioactive trace metal that is the metal cofactor in cobalamin (vitamin B12) which can limit or co-limit phytoplankton growth in many regions of the ocean. Total dissolved and labile Co measurements in the Canadian sector of the Arctic Ocean during the U.S. GEOTRACES Arctic expedition (GN01) and the Canadian International Polar Year GEOTRACES expedition (GIPY14) revealed a dynamic biogeochemical cycle for Co in this basin. The major sources of Co in the Arctic were from shelf regions and rivers, with only minimal contributions from other freshwater sources (sea ice, snow) and eolian deposition. The most striking feature was the extremely high concentrations of dissolved Co in the upper 100 m, with concentrations routinely exceeding 800 pmol L−1 over the shelf regions. This plume of high Co persisted throughout the Arctic basin and extended to the North Pole, where sources of Co shifted from primarily shelf-derived to riverine, as freshwater from Arctic rivers was entrained in the Transpolar Drift. Dissolved Co was also strongly organically complexed in the Arctic, ranging from 70 % to 100 % complexed in the surface and deep ocean, respectively. Deep-water concentrations of dissolved Co were remarkably consistent throughout the basin (∼55 pmol L−1), with concentrations reflecting those of deep Atlantic water and deep-ocean scavenging of dissolved Co. A biogeochemical model of Co cycling was used to support the hypothesis that the majority of the high surface Co in the Arctic was emanating from the shelf. The model showed that the high concentrations of Co observed were due to the large shelf area of the Arctic, as well as to dampened scavenging of Co by manganese-oxidizing (Mn-oxidizing) bacteria due to the lower temperatures. The majority of this scavenging appears to have occurred in the upper 200 m, with minimal additional scavenging below this depth. Evidence suggests that both dissolved Co (dCo) and labile Co (LCo) are increasing over time on the Arctic shelf, and these limited temporal results are consistent with other tracers in the Arctic. These elevated surface concentrations of Co likely lead to a net flux of Co out of the Arctic, with implications for downstream biological uptake of Co in the North Atlantic and elevated Co in North Atlantic Deep Water. Understanding the current distributions of Co in the Arctic will be important for constraining changes to Co inputs resulting from regional intensification of freshwater fluxes from ice and permafrost melt in response to ongoing climate change.
    Description: This work was supported by National Science Foundation Ocean Sciences (NSF OCE) grants (grant nos. 1435056, 1736599, and 1924554) to Mak A. Saito, as well as by a Woods Hole Oceanographic Institution Postdoctoral Scholar grant to Randelle M. Bundy and Mattias R. Cape. Mariko Hatta was supported by NSF OCE grant no. 1439253. Alessandro Tagliabue was supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (BYONIC, grant no. 724289). Benjamin S. Twining was supported by NSF OCE grant no. 1435862. Peter L. Morton was supported by NSF OCE grant no. 1436019, and a portion of the work was completed at the NHMFL, which is supported by the National Science Foundation through DMR-1644779 and the State of Florida. Jay T. Cullen was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and an International Polar Year (IPY) Canada grant.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-25
    Description: Dataset: Dissolved Trace Metals
    Description: Concentrations of total dissolved trace metals (Fe, Mn, Zn, Ni, Cd) obtained using seaFAST preconcentration and ICP-MS from the R/V Kilo Moana cruise KM1128. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/836347
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1031271
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 3
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Inomura, K., Deutsch, C., Wilson, S. T., Masuda, T., Lawrenz, E., Lenka, B., Sobotka, R., Gauglitz, J. M., Saito, M. A., Prášil, O., & Follows, M. J. Quantifying oxygen management and temperature and light dependencies of nitrogen fixation by Crocosphaera watsonii. Msphere, 4(6), (2019): e00531-19, doi: 10.1128/msphere.00531-19.
    Description: Crocosphaera is a major dinitrogen (N2)-fixing microorganism, providing bioavailable nitrogen (N) to marine ecosystems. The N2-fixing enzyme nitrogenase is deactivated by oxygen (O2), which is abundant in marine environments. Using a cellular scale model of Crocosphaera sp. and laboratory data, we quantify the role of three O2 management strategies by Crocosphaera sp.: size adjustment, reduced O2 diffusivity, and respiratory protection. Our model predicts that Crocosphaera cells increase their size under high O2. Using transmission electron microscopy, we show that starch granules and thylakoid membranes are located near the cytoplasmic membranes, forming a barrier for O2. The model indicates a critical role for respiration in protecting the rate of N2 fixation. Moreover, the rise in respiration rates and the decline in ambient O2 with temperature strengthen this mechanism in warmer water, providing a physiological rationale for the observed niche of Crocosphaera at temperatures exceeding 20°C. Our new measurements of the sensitivity to light intensity show that the rate of N2 fixation reaches saturation at a lower light intensity (∼100 μmol m−2 s−1) than photosynthesis and that both are similarly inhibited by light intensities of 〉500 μmol m−2 s−1. This suggests an explanation for the maximum population of Crocosphaera occurring slightly below the ocean surface.
    Description: We thank Stephanie Dutkiewicz and Sallie W. Chisholm for useful discussion, Martin Lukeš for technical assistance for the N2 fixation measurement, and the members of Writing and Communication Center at MIT for their advice on writing. This research was supported by the Japan Student Service Organization (JASSO) (grant L11171020001 to K.I.), the Gordon and Betty Moore Foundation (grant GBMF 3775 to C.D. and grant GBMF 3778 to M.J.F.), the U.S. National Science Foundation (grant OCE-1756524 to S.T.W., grant OCE-1558702 to M.J.F., and grant OCE-PRF 1421196 to J.M.G), the Simons Foundation (Simons Postdoctoral Fellowship in Marine Microbial Ecology award 544338 to K.I., Simons Collaboration on Ocean Processes and Ecology award 329108 to M.J.F., Simons Collaboration on Computational BIOgeochemical Modeling of Marine EcosystemS [CBIOMES] award 549931 to M.J.F.), the Czech Science Foundation (GAČR) (grant 16-15467S to O.P.), and the National Sustainability Programme (NPU) (grant LO1416 Algatech plus to O.P.).
    Keywords: Crocosphaera ; Carbon ; Cell flux model ; Daily cycle ; Iron ; Light ; Nitrogen ; Nitrogen fixation ; Oxygen ; Photosynthesis ; Temperature
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-10-21
    Description: Presented at 2022 OCB Summer Workshop, Woods Hole, MA, 20 - 23, June 2022
    Description: An unparalleled data catalog of well-documented, interoperable oceanographic data and information, openly accessible to all end-users through an intuitive web-based interface for the purposes of advancing marine research, education, and policy. Conference Website: https://web.whoi.edu/ocb-workshop/
    Description: NSF #1924618
    Keywords: Data management
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 5
    Publication Date: 2022-10-21
    Description: Presented at Ocean Sciences, San Diego, 16-21, February 2020
    Description: BCO-DMO curates earth science data where models become increasingly important. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of chemical and biological properties within the ocean ecosystem. We feel the time is at hand for the scientific community to begin a concerted and holistic approach to the curation of code and software.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 6
    Publication Date: 2022-10-21
    Description: Presented at Ocean Sciences, San Diego, 16-21, February 2020
    Description: Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 7
    Publication Date: 2022-10-21
    Description: Presented at Fall AGU (ESIP Data Helpdesk), New Orleans, 11-17, December 2021
    Description: BCO-DMO curates a database of research-ready data spanning the full range of marine ecosystem related measurements including in-situ and remotely sensed observations, experimental and model results, and synthesis products. We work closely with investigators to publish data and information from research projects supported by the National Science Foundation (NSF), as well as those supported by state, private, and other funding sources. BCO-DMO supports all phases of the data life cycle and ensures open access of well-curated project data and information. We employ F.A.I.R. Principles that comprise a set of values intended to guide data producers and publishers in establishing good data management practices that will enable effective reuse.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 8
    Publication Date: 2022-10-31
    Description: Dataset: Trichodesmium field metaproteomes - sequence fasta
    Description: FASTA file of sequences in Trichodesmium field metaproteomes analyzed by 2D LC-MS/MS mapped to a Trichodesmium metagenome (IMG ID 2821474806) plus cyanoGEBA species genomes (Shih et al, 2013). Samples were collected in North Atlantic surface waters, at station BATS (Bermuda Atlantic Time-series Study), and station ALOHA (A Long-Term Oligotrophic Habitat Assessment) between 2000 and 2018. Related datasets: Trichodesmium field metaproteomes - peptide spectral counts: https://www.bco-dmo.org/dataset/787168 Trichodesmium field metaproteomes - protein spectral counts: https://www.bco-dmo.org/dataset/787147 Trichodesmium sample provenance: https://www.bco-dmo.org/dataset/787093 - Sample provenance file, which includes sample locations, filter sizes For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/787181
    Description: Gordon and Betty Moore Foundation (GBMF) GBMF3934, Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) GBMF3782, NSF Division of Ocean Sciences (NSF OCE) OCE-1657766, NSF Division of Ocean Sciences (NSF OCE) OCE-1850719
    Keywords: Trichodesmium ; Metaproteomics
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 9
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: Pacific Nitrite Oxidoreductase
    Description: Nitrite Oxidoreductase targeted metaproteomics from R/V Kilo Moana cruise KM1128 and R/V Falkor cruise FK160115 in the Central Pacific Ocean in 2011 and 2016. NxrA and NxrB peptide concentrations in fmol/L. Peptide names are using the GEOTRACES naming convention (PEP for peptide, full tryptic peptide amino acid sequence, Protein name, Sampling device (=Pump)). Quality flags follow each peptide column and use the GEOTRACES convention of 1 for good, 6 for below detection limit. These data were published in Saito et al., 2020 as Supplementary Table 1. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/806510
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1031271, Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) GBMF3782, NSF Division of Ocean Sciences (NSF OCE) OCE-1657766, NSF Division of Ocean Sciences (NSF OCE) OCE-1736599, NSF Division of Ocean Sciences (NSF OCE) OCE-1850719, NSF Division of Ocean Sciences (NSF OCE) OCE-1924554
    Keywords: Nitrite ; Nitrogen ; Enzyme ; Iron ; ProteOMZ ; Metzyme
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 10
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: Ruergeria pomeroyi DSS-3 replete proteome
    Description: This dataset represents the global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3 (collected in triplicate). This dataset is an initial examination of the proteome allocation of this heterotrophic bacteria and will contribute to C-CoMP's efforts that are focused on understanding the physiology of model marine bacteria. A total of 2341 proteins were identified in DSS-3. The Moran laboratory at University of Georgia grew and prepared the cultures and the Saito laboratory at Woods Hole Oceanographic Institution conducted the proteomics analyses. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/875600
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-2019589
    Keywords: Proteomics ; Marine bacteria ; Physiology ; Metabolites ; Biogeochemistry
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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