Dataset: Cellular Trace Elements
Deployment: RR1604

Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016

Principal Investigator:

Benjamin Twining (Bigelow Laboratory for Ocean Sciences)

Co-Principal Investigator:

Michael W. Lomas (Bigelow Laboratory for Ocean Sciences)

Adam Martiny (University of California-Irvine, UC Irvine)

BCO-DMO Data Manager:

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

Project:

Collaborative Research: Regional variation of phytoplankton diversity and biogeochemical functioning in the subtropical Indian Ocean (IO Phytoplankton)

Current State:

Final no updates expected

Deployment Synonyms:

GO-SHIP IO9

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/768067/data

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Description

Cellular trace elements collected on cruise RR1604 (GO-SHIP transect IO9N) in the Eastern Indian Ocean from March to April 2016.

Methods & Sampling

Dataset acquisition description

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.

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 Kα 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.

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). 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).

Data Processing Description

Dataset Processing Description

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. 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.

Data quality:
Data are flagged with the following:
1 = Good data, passed QC;
3 = Questionable or suspect data, used when a data point was oceanographically inconsistent;
4 = Bad;
6 = Below detection limit.

BCO-DMO Processing:
- modified parameter names (removed units, replaced hyphens and spaces with underscores, added "_flag" to flag columns, replaced blank cells with "nd");
- 2022-07-12 - removed unnecessary columns (named "SXRF_map_filename" and "SXRF_spectrum_filename") and added supplemental file of light images.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1559021	NSF Division of Ocean Sciences

Instruments

Niskin bottle

Supplied Name: Teflon-coated Niskin-X bottles

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

X-ray fluorescence analyzer

Supplied Name: synchrotron X-ray fluorescence (SXRF) analysis

Supplied Description:

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Station	Station number	unitless	station
MDA	unique identifier for each cell	unitless	no_bcodmo_term
Grid_type	substrate to which cells were mounted	unitless	no_bcodmo_term
SXRF_run	analysis year and run	unitless	no_bcodmo_term
Cell_type	classification of Flag (flagellate), Dino (dinoflagellate), or Pico (picoplankton, < 2um)	unitless	no_bcodmo_term
Cell_volume	biovolume of cell	cubic micrometers (um^3)	biovolume
Cell_C	cellular carbon	mol/cell	C
Cell_C_flag	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.	unitless	C
Cell_Si	cellular silicon	moles per cell (mol/cell)	Si
Cell_Si_flag	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.	unitless	Si
Cell_P	cellular phosphorus	mol/cell	P
Cell_P_flag	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.	unitless	P
Cell_S	cellular sulfur	mol/cell	S
Cell_S_flag	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.	unitless	S
Cell_Mn	cellular manganese	mol/cell	Mn
Cell_Mn_flag	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.	unitless	Mn
Cell_Fe	cellular iron	mol/cell	Fe
Cell_Fe_flag	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.	unitless	Fe
Cell_Co	cellular cobalt	mol/cell	no_bcodmo_term
Cell_Co_flag	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.	unitless	no_bcodmo_term
Cell_Ni	cellular nickel	mol/cell	no_bcodmo_term
Cell_Ni_flag	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.	unitless	no_bcodmo_term
Cell_Cu	cellular copper	mol/cell	Cu
Cell_Cu_flag	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.	unitless	Cu
Cell_Zn	cellular zinc	mol/cell	Zn
Cell_Zn_flag	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.	unitless	Zn
light_image_filename	Light image file name; file names here correspond to the image names in the Supplemental File "IO9N_BF_BCODMO-20220701T190351Z-001.zip"	unitless	file_name

Database

Contribute Data

Dataset: Cellular Trace Elements
Deployment: RR1604

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Cellular Trace ElementsDeployment: RR1604

Dataset acquisition description

Dataset Processing Description

Dataset: Cellular Trace Elements
Deployment: RR1604