http://lod.bco-dmo.org/id/dataset/768064
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2019-05-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016
2022-07-12
publication
2022-07-12
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-07-12
publication
https://doi.org/10.26008/1912/bco-dmo.768064.2
Benjamin Twining
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Adam Martiny
University of California-Irvine
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Twining, B., Lomas, M. W., Martiny, A. (2022) Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2022-07-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.768064.2 [access date]
Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016 Dataset Description: <p>Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016.</p> Methods and Sampling: <p>Samples were collected from 5 L Teflon-coated Niskin-X bottles hung on non-metal line, and clean techniques were followed throughout (Bruland et al., 1979). Niskin-X bottles were transferred to a clean lab immediately after retrieval. At most stations a single sample was collected from 20 m. Four-depth profiles extending to 200 m were collected at 6 stations along the transect.</p>
<p>A small aliquot of unfiltered seawater was reserved from the surface-most Niskin-X bottle to collect phytoplankton cells for synchrotron X-ray fluorescence (SXRF) analysis. SXRF samples were collected following protocols described in Twining et al. (2015). Cellular metals were analyzed with the 2-ID-E microprobe beamline at the Advanced Photon Source, Argonne National Laboratory. Incident beam energy was 10 keV to enable the excitation of K<sub>α</sub> fluorescence for elements ranging in atomic number from Si (14) to Zn (30). Approximately 15 cells were analyzed at each station. Flagellated autotrophs with diameters ranging from 1.65 - 6.6 µm were analyzed using 2D raster scans with 0.5 μm pixel step sizes and detector dwell times from 10-20 sec/pixel.</p>
<p>Element quantification was performed by averaging the spectra from pixels representing the cells of interest. Spectra were also extracted from a background area close to each cell. The spectra were then fit with MAPS, a custom fitting software package (Vogt, 2003).&nbsp; Concentrations were calculated based on conversion factors obtained by running the thin-film standards NBS 1832, NBS 1833, and custom Si, P, and Fe standards made by Micromatter XRF. Cell volume was calculated based on measurements taken from bright field images of the cells and using the equations of Hillebrand et al. (1999). Cellular C was then calculated from the volumes using the equations described in Menden-Deuer and Lessard (2000).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559021 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559021
completed
Benjamin Twining
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544-0380
USA
btwining@bigelow.org
pointOfContact
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 311
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544
United States
mlomas@bigelow.org
pointOfContact
Adam Martiny
University of California-Irvine
949-824-9713
Earth System Science & Ecology and Evolutionary Biology 3208 Croul Hall
Irvine
CA
92697
USA
amartiny@uci.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Station
MDA
Grid_type
SXRF_run
Cell_type
Cell_volume
Cell_C
Cell_C_flag
Cell_Si
Cell_Si_flag
Cell_P
Cell_P_flag
Cell_S
Cell_S_flag
Cell_Mn
Cell_Mn_flag
Cell_Fe
Cell_Fe_flag
Cell_Co
Cell_Co_flag
Cell_Ni
Cell_Ni_flag
Cell_Cu
Cell_Cu_flag
Cell_Zn
Cell_Zn_flag
light_image_filename
Teflon-coated Niskin-X bottles
synchrotron X-ray fluorescence (SXRF) analysis
theme
None, User defined
station
No BCO-DMO term
biovolume
Elemental carbon (C)
Silicon
Phosphorus
Sulfur (S)
Manganese
Iron
Copper
Zinc
file_name
featureType
BCO-DMO Standard Parameters
Niskin bottle
X-ray fluorescence analyzer
instrument
BCO-DMO Standard Instruments
RR1604
service
Deployment Activity
Hydrographic line IO9, Indian Ocean
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Regional variation of phytoplankton diversity and biogeochemical functioning in the subtropical Indian Ocean
https://osprey.bco-dmo.org/project/628972
Collaborative Research: Regional variation of phytoplankton diversity and biogeochemical functioning in the subtropical Indian Ocean
<p><em>Description from NSF award abstract:</em><br />
The Indian Ocean accounts for nearly a fifth of global ocean photosynthesis and is likely a key component in global ocean nutrient and carbon cycles. However, the Indian Ocean may be the least studied major marine body on the planet. Our limited understanding suggests extensive variations in physical and chemical environmental conditions, but how this variation influences biodiversity, nutrient stress, and more broadly regional differences in the functioning of phytoplankton is unknown. To help address these gaps, the investigators will conduct a study by joining an already-funded major research cruise to this region. It will cover a northern region with some of the highest temperatures recorded in open ocean waters, an area around 10°S of predicted (but not tested in situ) iron stress, and a southern subtropical gyre with unique nitrogen to phosphorous(or N:P) ratios. The focus of this project is to quantify and synthesize the interconnectedness of environmental conditions, phytoplankton diversity and genome content, and nutrient biogeochemistry, with the goal of understanding how these may lead to unique biogeochemical regions in Indian Ocean. The research will have broader impacts on many levels. First, it will increase public awareness of the role of phytoplankton on ocean functioning, climate, and people's lives through a new partnership with the Aquarium of the Pacific (AOP), which is the fourth most-attended aquarium in the nation. Secondly, the project will train a postdoctoral scholar as well as a graduate and undergraduate students. Third, the research will dramatically increase our basic knowledge ocean biogeochemistry and in many cases will be the first measurements of their kind made in the Indian Ocean.</p>
<p>This project will address two major questions: How do environmental conditions, phytoplankton diversity, phytoplankton physiology, and biogeochemistry vary across the central Indian Ocean? Are there distinct biogeochemical regimes in the central IO? The researchers hypothesize that environmental conditions, including the relative availability of nitrogen (N) and iron (Fe), lead to three distinct phytoplankton communities and biogeochemical regimes. They will employ a series of advanced analytical tools including high sensitivity measurements of dissolved and particulate nutrients (nitrogen, phosphorus, and iron), genomics, bioassays to test for nutrient stress, and cell-sorting of specific taxa followed by measures of nutrient content and uptake. A focus of this project is to quantify and synthesize the interconnectedness of environmental conditions, phytoplankton diversity and genome content, and nutrient biogeochemistry, and how these lead to unique biogeochemical regions in Indian Ocean. This extensive set of observations can ultimately be linked to ocean models and satellite data to provide a comprehensive view of regional differences in chemistry, biodiversity and phytoplankton biogeochemical functioning in the Indian Ocean.</p>
IO Phytoplankton
largerWorkCitation
project
eng; USA
oceans
Hydrographic line IO9, Indian Ocean
87.07
95
-28.31
17
2016-03-21
2016-04-28
GO-SHIP IO9N transect: 20S 95E to 20N 95E
0
BCO-DMO catalogue of parameters from Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/768076.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/768077.rdf
Name: MDA
Units: unitless
Description: <p>unique identifier for each cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/768078.rdf
Name: Grid_type
Units: unitless
Description: <p>substrate to which cells were mounted</p>
http://lod.bco-dmo.org/id/dataset-parameter/768079.rdf
Name: SXRF_run
Units: unitless
Description: <p>analysis year and run</p>
http://lod.bco-dmo.org/id/dataset-parameter/768080.rdf
Name: Cell_type
Units: unitless
Description: <p>classification of Flag (flagellate), Dino (dinoflagellate), or Pico (picoplankton, < 2um)</p>
http://lod.bco-dmo.org/id/dataset-parameter/768081.rdf
Name: Cell_volume
Units: cubic micrometers (um^3)
Description: <p>biovolume of cell</p>
http://lod.bco-dmo.org/id/dataset-parameter/768082.rdf
Name: Cell_C
Units: mol/cell
Description: <p>cellular carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/768083.rdf
Name: Cell_C_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768084.rdf
Name: Cell_Si
Units: moles per cell (mol/cell)
Description: <p>cellular silicon</p>
http://lod.bco-dmo.org/id/dataset-parameter/768085.rdf
Name: Cell_Si_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768086.rdf
Name: Cell_P
Units: mol/cell
Description: <p>cellular phosphorus</p>
http://lod.bco-dmo.org/id/dataset-parameter/768087.rdf
Name: Cell_P_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768088.rdf
Name: Cell_S
Units: mol/cell
Description: <p>cellular sulfur</p>
http://lod.bco-dmo.org/id/dataset-parameter/768089.rdf
Name: Cell_S_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768090.rdf
Name: Cell_Mn
Units: mol/cell
Description: <p>cellular manganese</p>
http://lod.bco-dmo.org/id/dataset-parameter/768091.rdf
Name: Cell_Mn_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768092.rdf
Name: Cell_Fe
Units: mol/cell
Description: <p>cellular iron</p>
http://lod.bco-dmo.org/id/dataset-parameter/768093.rdf
Name: Cell_Fe_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768094.rdf
Name: Cell_Co
Units: mol/cell
Description: <p>cellular cobalt</p>
http://lod.bco-dmo.org/id/dataset-parameter/768095.rdf
Name: Cell_Co_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768096.rdf
Name: Cell_Ni
Units: mol/cell
Description: <p>cellular nickel</p>
http://lod.bco-dmo.org/id/dataset-parameter/768097.rdf
Name: Cell_Ni_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768098.rdf
Name: Cell_Cu
Units: mol/cell
Description: <p>cellular copper</p>
http://lod.bco-dmo.org/id/dataset-parameter/768099.rdf
Name: Cell_Cu_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768100.rdf
Name: Cell_Zn
Units: mol/cell
Description: <p>cellular zinc</p>
http://lod.bco-dmo.org/id/dataset-parameter/768101.rdf
Name: Cell_Zn_flag
Units: unitless
Description: <p>quality flag for element indicated: 1 = Good data, passed QC; 3 = Questionable or suspect data, used when a data point was oceanographically inconsistent; 4 = Bad; 6 = Below detection limit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768102.rdf
Name: light_image_filename
Units: unitless
Description: <p>Light image file name; file names here correspond to the image names in the Supplemental File "IO9N_BF_BCODMO-20220701T190351Z-001.zip"</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
13446
https://darchive.mblwhoilibrary.org/bitstream/1912/29114/1/dataset-768064_cellular-trace-elements__v2.tsv
download
13446
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/daa1c305-795d-5fb5-bd61-d087ec965943/content
download
https://doi.org/10.26008/1912/bco-dmo.768064.2
download
onLine
dataset
<p>Samples were collected from 5 L Teflon-coated Niskin-X bottles hung on non-metal line, and clean techniques were followed throughout (Bruland et al., 1979). Niskin-X bottles were transferred to a clean lab immediately after retrieval. At most stations a single sample was collected from 20 m. Four-depth profiles extending to 200 m were collected at 6 stations along the transect.</p>
<p>A small aliquot of unfiltered seawater was reserved from the surface-most Niskin-X bottle to collect phytoplankton cells for synchrotron X-ray fluorescence (SXRF) analysis. SXRF samples were collected following protocols described in Twining et al. (2015). Cellular metals were analyzed with the 2-ID-E microprobe beamline at the Advanced Photon Source, Argonne National Laboratory. Incident beam energy was 10 keV to enable the excitation of K<sub>α</sub> fluorescence for elements ranging in atomic number from Si (14) to Zn (30). Approximately 15 cells were analyzed at each station. Flagellated autotrophs with diameters ranging from 1.65 - 6.6 µm were analyzed using 2D raster scans with 0.5 μm pixel step sizes and detector dwell times from 10-20 sec/pixel.</p>
<p>Element quantification was performed by averaging the spectra from pixels representing the cells of interest. Spectra were also extracted from a background area close to each cell. The spectra were then fit with MAPS, a custom fitting software package (Vogt, 2003).&nbsp; Concentrations were calculated based on conversion factors obtained by running the thin-film standards NBS 1832, NBS 1833, and custom Si, P, and Fe standards made by Micromatter XRF. Cell volume was calculated based on measurements taken from bright field images of the cells and using the equations of Hillebrand et al. (1999). Cellular C was then calculated from the volumes using the equations described in Menden-Deuer and Lessard (2000).</p>
Specified by the Principal Investigator(s)
<p>SXRF data quality was assessed and outliers identified in two ways. First, measurements were excluded if the relative standard deviation of the element peak fit by the model was greater than 20%, indicating poor precision of the model fit.&nbsp; Second, outliers were identified by assessment of cellular log-transformed metal:biomass ratios using an ANCOVA model that included log volume, station, and cell type as effects (JMP, SAS). Ratios were removed if the Jackknife distances of the studentized residuals of this model were greater than 3. Roughly 1% of data were removed from the dataset through this process. Outliers appear as blanks with "3" flags.</p>
<p>Data quality:&nbsp;<br />
Data are flagged with the following:<br />
1 = Good data, passed QC;<br />
3 = Questionable or suspect data, used when a data point was oceanographically inconsistent;<br />
4 = Bad;<br />
6 = Below detection limit.</p>
<p>BCO-DMO Processing:&nbsp;<br />
- modified parameter names (removed units, replaced hyphens and spaces with underscores, added "_flag" to flag columns, replaced blank cells with "nd");<br />
- 2022-07-12 - removed unnecessary columns (named "SXRF_map_filename" and "SXRF_spectrum_filename") and added supplemental file of light images.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Teflon-coated Niskin-X bottles
Teflon-coated Niskin-X bottles
PI Supplied Instrument Name: Teflon-coated Niskin-X bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
synchrotron X-ray fluorescence (SXRF) analysis
synchrotron X-ray fluorescence (SXRF) analysis
PI Supplied Instrument Name: synchrotron X-ray fluorescence (SXRF) analysis Instrument Name: X-ray fluorescence analyzer Instrument Short Name:XRF analyzer 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.
Cruise: RR1604
RR1604
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel