Dataset: GN01 Element quotas of individual phytoplankton cells

Name: Element quotas of individual phytoplankton cells from samples collected on the US GEOTRACES Arctic cruise GN01 (HLY1502) on USCGC Healy in August-October 2015
Published: 2023-09-05
Keywords: iron, quota, phytoplankton, trace metals, GEOTRACES, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.904895.1

Spatial Extent: N:89.99 E:89.25 S:60.26 W:-149.43

Temporal Extent: 2015-08-12 - 2015-10-05

Project:

GEOTRACES Arctic Section: Collaborative Research: Biogeochemical cycling of particulate trace elements in the western Arctic basin (Arctic GEOTRACES bottle particles)

U.S. Arctic GEOTRACES Study (GN01) (U.S. GEOTRACES Arctic)

Program:

U.S. GEOTRACES (U.S. GEOTRACES)

Principal Investigator:

Benjamin Twining (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-09-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Element quotas of individual phytoplankton cells from samples collected on the US GEOTRACES Arctic cruise GN01 (HLY1502) on USCGC Healy in August-October 2015

Abstract:

Individual phytoplankton cells were collected on the US GEOTRACES Arctic cruise GN01 (HLY1502) on USCGC Healy in August-October 2015. The elemental (Si, P, S, Mn, Fe, Co, Ni, Cu, Zn) content of each cell was measured with synchrotron x-ray fluorescence (SXRF). Carbon was calculated from biovolume. Data can be used to assess biogenic particulate metal fraction, as well as changes in the accumulation of these elements across environmental gradients. Data are part of the larger international GEOTRACES dataset.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-09-05	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.904895.1	2023-09-05

Methods & Sampling

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 Description

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).

BCO-DMO Processing

- 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".

Data Files

File
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.

Supplemental Files

File
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.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1435862

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HLY1502	GN01 U.S. GEOTRACES Arctic 32H120150809	2015-08-09	USCGC Healy	David C. Kadko (Chief Scientist) William M. Landing (Co-Chief Scientist)	data info

Instruments

X-ray fluorescence analyzer

Supplied Name: Synchrotron X-ray Fluorescence microscope

Supplied 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.

Instrument Type

Generic Name: X-ray fluorescence analyzer

Acronym: XRF analyzer

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Run	APS run during which each cell was analyzed: 2016r1 or 2016r3 (runs 1 and 3, respectively)	unitless	exp_id
Cruise	GEOTRACES cruise the sample was collected from: Arctic (GN01, HLY02)	unitless	cruise_id
Station	Station sample was collected from	unitless	station
Lat_N	Latitude	degrees North	lat
Lon_E	Longitude	degrees East	lon
Date	Date of cast (UTC) Format: %Y-%m-%d	unitless	date
Start_time	Time of cast start (UTC) Format: %H:%M	unitless	time
ISO_DateTime_UTC	Date and time of cast start (UTC) in ISO 8601 format Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC
Depth	Depth	meters (m)	depth
DepthDescr	Descriptive depth designation: ML (mixed layer) or in ice	unitless	depth_n
ParticleSampleID	GEOTRACES sample ID for particulate trace metal sample from which phytoplankton were sampled	unitless	sample
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	sample_descrip
MDA	SXRF scan number	unitless	exp_id
UniqueCell	Unique cell ID, formatted as {RUN}_{MDA}_{ROI}	unitless	sample
GridType	Material of TEM grid used for analysis: SiN (silicon nitride) or Au (gold)	unitless	sampling_method
Volume	Cell volume	cubic microns	volume
cellC	cellular carbon contents	moles	C
cellSi	cellular silicon contents	moles	Si
cellP	cellular phosphorus	moles	P
cellS	cellular sulfur contents	moles	S
cellMn	cellular manganese contents	moles	Mn
cellFe	cellular iron contents	moles	Fe
cellCo	cellular cobalt contents	moles	Co
cellNi	cellular nickel contents	moles	Ni
cellCu	cellular copper contents	moles	Cu
cellZn	cellular zinc contents	moles	Zn
cell_image_file	filename of light microscope image of cell	unitless	file_name
spectral_file	filename of SXRF spectrum of cell	unitless	file_name
maps_file	filename of 2D heatmap of elemental contents of cell	unitless	file_name