Contributors | Affiliation | Role |
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Twining, Benjamin | Bigelow Laboratory for Ocean Sciences | Principal Investigator |
Rauch, Shannon | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Single-cell SXRF samples were collected from the surface mixed layer using the GEOTRACES rosette. Whole water samples were preserved with 0.25% trace-metal clean buffered glutaraldehyde (Twining et al., 2003) and centrifuged onto Au or SiN TEM windows. Grids were briefly rinsed with a drop of ultrapure water and dried in a Class-100 cabinet. SXRF analysis was performed using the 2-ID-E beamline at the Advanced Photon source (Argonne National Laboratory) following the protocols of Twining et al. (2011). Each cell was raster scanned with a focused 10 keV x-ray beam with a diameter of approximately 0.5 micrometers (µm).
Data Processing:
Fluorescence spectra from the pixels covering the cell were averaged to calculate whole-cell quotas, and a fluorescence spectrum from a neighboring empty section of the grid was subtracted. Cellular elemental fluorescence intensities were fit with a modified-Gaussian model using custom software and peak areas converted to areal element concentrations using NBS-certified standard reference materials (Núnez-Milland et al., 2010; Twining et al., 2011). Spatial regions of interest (ROI) representing the whole cell (including any adsorbed elements, if present) were prepared for each cell and used to calculate element quotas. Cellular C quotas were calculated from cell biovolume using the equations of Menden-Deuer and Lessard (2000). Cell biovolume was calculated for each cell from measurements of cell diameter, length, and height using digital image processing software Image J. Shape and volume equations were taken from Hillebrand et al. (1999).
- imported original file named "Arctic SXRF.csv" into the BCO-DMO system;
- removed "NA" as a missing data value (missing data is blank/empty in the final CSV file);
- replaced spaces with underscores in column names to comply with BCO-DMO naming conventions;
- changed Date format to YYYY-mm-dd;
- added the date-time field in ISO 8601 format;
- named the final file "904895_v1_gn01_phytoplankton_element_quotas.csv".
File |
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904895_v1_gn01_phytoplankton_element_quotas.csv (Comma Separated Values (.csv), 72.74 KB) MD5:e33cd35ebb35ccc4f8cfad27f6f6fbff Primary data file for dataset ID 904895, version 1. |
File |
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maps.zip (ZIP Archive (ZIP), 26.90 MB) MD5:62c5e0264eb99a930054df7f1fd98c96 Supplemental file for dataset 904895, version 1. Contains 2D heatmaps of elemental contents of cells (in .jpg format). Files in this folder correspond to file names in the "maps_file" column of the primary data file. |
spectra_gifs.zip (ZIP Archive (ZIP), 4.96 MB) MD5:4a1ff7c795e5d17da723c4983b1b326c Supplemental file for dataset 904895, version 1. Contains SXRF spectra of cells (in .gif format). Files in this folder correspond to file names in the "spectral_file" column of the primary data file. |
vlm.zip (ZIP Archive (ZIP), 30.97 MB) MD5:2f0f29945c0366a33a26d8aaf1433f09 Supplemental file for dataset 904895, version 1. Contains light microscope images of cells (in .jpg format). Files in this folder correspond to file names in the "cell_image_file" column of the primary data file. |
Parameter | Description | Units |
Run | APS run during which each cell was analyzed: 2016r1 or 2016r3 (runs 1 and 3, respectively) | unitless |
Cruise | GEOTRACES cruise the sample was collected from: Arctic (GN01, HLY02) | unitless |
Station | Station sample was collected from | unitless |
Lat_N | Latitude | degrees North |
Lon_E | Longitude | degrees East |
Date | Date of cast (UTC) | unitless |
Start_time | Time of cast start (UTC) | unitless |
ISO_DateTime_UTC | Date and time of cast start (UTC) in ISO 8601 format | unitless |
Depth | Depth | meters (m) |
DepthDescr | Descriptive depth designation: ML (mixed layer) or in ice | unitless |
ParticleSampleID | GEOTRACES sample ID for particulate trace metal sample from which phytoplankton were sampled | unitless |
CellType | Taxonomic classification of cell: Chaet = chaetoceros, centric = centric diatom, Cosco = coscinodiscus, Dino = dinoflagellage, flag = flagellate, Melosira, Oval diatom, pennate = pennate diatom, Silicaflag = silicaflagellate | unitless |
MDA | SXRF scan number | unitless |
UniqueCell | Unique cell ID, formatted as {RUN}_{MDA}_{ROI} | unitless |
GridType | Material of TEM grid used for analysis: SiN (silicon nitride) or Au (gold) | unitless |
Volume | Cell volume | cubic microns |
cellC | cellular carbon contents | moles |
cellSi | cellular silicon contents | moles |
cellP | cellular phosphorus | moles |
cellS | cellular sulfur contents | moles |
cellMn | cellular manganese contents | moles |
cellFe | cellular iron contents | moles |
cellCo | cellular cobalt contents | moles |
cellNi | cellular nickel contents | moles |
cellCu | cellular copper contents | moles |
cellZn | cellular zinc contents | moles |
cell_image_file | filename of light microscope image of cell | unitless |
spectral_file | filename of SXRF spectrum of cell | unitless |
maps_file | filename of 2D heatmap of elemental contents of cell | unitless |
Dataset-specific Instrument Name | Synchrotron X-ray Fluorescence microscope |
Generic Instrument Name | X-ray fluorescence analyzer |
Dataset-specific Description | SXRF analysis was performed on the 2-ID-E beamline at the Advanced Photon source (Argonne National Laboratory). The synchrotron consists of a storage ring which produces high energy electromagnetic radiation. X-rays diverted to the 2-ID-E beamline are used for x-ray fluorescence mapping of biological samples. X-rays were tuned to an energy of 10 keV to enable the excition of K-alpha fluorescence for the elements reported. The beam is focused using Fresnel zoneplates to achieve high spatial resolution; for our application a focused spot size of 0.5um was used. A multi-element germanium energy dispersive detector is used to record the X-ray fluorescence spectrum. |
Generic Instrument Description | Instruments that identify and quantify the elemental constituents of a sample from the spectrum of electromagnetic radiation emitted by the atoms in the sample when excited by X-ray radiation. |
Website | |
Platform | USCGC Healy |
Report | |
Start Date | 2015-08-09 |
End Date | 2015-10-12 |
Description | Arctic transect encompassing Bering and Chukchi Shelves and the Canadian, Makarov and Amundsen sub-basins of the Arctic Ocean. The transect started in the Bering Sea (60°N) and traveled northward across the Bering Shelf, through the Bering Strait and across the Chukchi shelf, then traversing along 170-180°W across the Alpha-Mendeleev and Lomonosov Ridges to the North Pole (Amundsen basin, 90°N), and then back southward along ~150°W to terminate on the Chukchi Shelf (72°N).
Additional cruise information is available in the GO-SHIP Cruise Report (PDF) and from the Rolling Deck to Repository (R2R): https://www.rvdata.us/search/cruise/HLY1502 |
Description from NSF award abstract:
In pursuit of its goal "to identify processes and quantify fluxes that control the distributions of key trace elements and isotopes in the ocean, and to establish the sensitivity of these distributions to changing environmental conditions", in 2015 the International GEOTRACES Program will embark on several years of research in the Arctic Ocean. In a region where climate warming and general environmental change are occurring at amazing speed, research such as this is important for understanding the current state of Arctic Ocean geochemistry and for developing predictive capability as the regional ecosystem continues to warm and influence global oceanic and climatic conditions. The three investigators funded on this award, will manage a large team of U.S.scientists who will compete through the regular NSF proposal process to contribute their own unique expertise in marine trace metal, isotopic, and carbon cycle geochemistry to the U.S. effort. The three managers will be responsible for arranging and overseeing at-sea technical services such as hydrographic measurements, nutrient analyses, and around-the-clock management of on-deck sampling activites upon which all participants depend, and for organizing all pre- and post-cruise technical support and scientific meetings. The management team will also lead educational outreach activities for the general public in Nome and Barrow, Alaska, to explain the significance of the study to these communities and to learn from residents' insights on observed changes in the marine system. The project itself will provide for the support and training of a number of pre-doctoral students and post-doctoral researchers. Inasmuch as the Arctic Ocean is an epicenter of global climate change, findings of this study are expected to advance present capability to forecast changes in regional and globlal ecosystem and climate system functioning.
As the United States' contribution to the International GEOTRACES Arctic Ocean initiative, this project will be part of an ongoing multi-national effort to further scientific knowledge about trace elements and isotopes in the world ocean. This U.S. expedition will focus on the western Arctic Ocean in the boreal summer of 2015. The scientific team will consist of the management team funded through this award plus a team of scientists from U.S. academic institutions who will have successfully competed for and received NSF funds for specific science projects in time to participate in the final stages of cruise planning. The cruise track segments will include the Bering Strait, Chukchi shelf, and the deep Canada Basin. Several stations will be designated as so-called super stations for intense study of atmospheric aerosols, sea ice, and sediment chemistry as well as water-column processes. In total, the set of coordinated international expeditions will involve the deployment of ice-capable research ships from 6 nations (US, Canada, Germany, Sweden, UK, and Russia) across different parts of the Arctic Ocean, and application of state-of-the-art methods to unravel the complex dynamics of trace metals and isotopes that are important as oceanographic and biogeochemical tracers in the sea.
NSF Award Abstract:
As part of this project, two investigators will participate in the 2015 U.S. GEOTRACES Arctic expedition to determine the trace element composition of different suspended particles in the water column of the Arctic Ocean to identify the sources and scavenging capabilities of these particles. In common with other multinational initiatives in the International GEOTRACES Program, the goals of the U.S. Arctic expedition are to identify processes and quantify fluxes that control the distributions of key trace elements and isotopes in the ocean, and to establish the sensitivity of these distributions to changing environmental conditions. Some trace elements are essential to life, others are known biological toxins, and still others are important because they can be used as tracers of a variety of physical, chemical, and biological processes in the sea. This team of trace element scientists will focus on the measurement of particulate trace elements, which will enable scientists to better estimate the sources of particulate metals to the Arctic Ocean and to better understand their contribution to biological processes. This project will also provide educational opportunities for undergraduate students, K-12 teachers, and the general public.
Particulate trace element distributions, sources, sinks and cycling are predicted to be controlled by physical, biological, anthropogenic and geochemical processes in the Arctic. Furthermore, many trace elements are required nutrients for marine phytoplankton, playing a key role in oceanic primary productivity. However, few integrated oceanographic studies have been conducted to specifically investigate these relationships in this region, despite the changing conditions and global significance of the Arctic. This project will significantly advance understanding of the complete geochemical cycles of a number of trace elements in the Arctic Ocean basin by measuring the concentrations of particulate trace elements in bulk particles collected through the water column and in sediments, as well as in phytoplankton from the upper water column. These measurements will enable scientists to constrain the inputs of particulate elements from rivers, shelves and ice, and to assess the removal of dissolved trace elements via passive scavenging and biological uptake.
GEOTRACES is a SCOR sponsored program; and funding for program infrastructure development is provided by the U.S. National Science Foundation.
GEOTRACES gained momentum following a special symposium, S02: Biogeochemical cycling of trace elements and isotopes in the ocean and applications to constrain contemporary marine processes (GEOSECS II), at a 2003 Goldschmidt meeting convened in Japan. The GEOSECS II acronym referred to the Geochemical Ocean Section Studies To determine full water column distributions of selected trace elements and isotopes, including their concentration, chemical speciation, and physical form, along a sufficient number of sections in each ocean basin to establish the principal relationships between these distributions and with more traditional hydrographic parameters;
* To evaluate the sources, sinks, and internal cycling of these species and thereby characterize more completely the physical, chemical and biological processes regulating their distributions, and the sensitivity of these processes to global change; and
* To understand the processes that control the concentrations of geochemical species used for proxies of the past environment, both in the water column and in the substrates that reflect the water column.
GEOTRACES will be global in scope, consisting of ocean sections complemented by regional process studies. Sections and process studies will combine fieldwork, laboratory experiments and modelling. Beyond realizing the scientific objectives identified above, a natural outcome of this work will be to build a community of marine scientists who understand the processes regulating trace element cycles sufficiently well to exploit this knowledge reliably in future interdisciplinary studies.
Expand "Projects" below for information about and data resulting from individual US GEOTRACES research projects.
Funding Source | Award |
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NSF Division of Ocean Sciences (NSF OCE) |