Dataset: GP16 Cellular element quotas

Name: Element quotas of individual phytoplankton cells from GEOTRACES-EPZT cruise TN303, 2013.
Published: 2016-07-19
Keywords: Synchrotron radiation X-Ray Fluorescence, SXRF, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.643270.1

Spatial Extent: N:-10.4999 E:-77.3761 S:-16.0004 W:-151.9992

Temporal Extent: 2013-10-29 - 2013-12-16

Project:

GEOTRACES Pacific Section: Characterizing biogenic trace elements across productivity and oxygen gradients in the eastern South Pacific (South Pacific biogenic trace elements)

U.S. GEOTRACES East Pacific Zonal Transect (GP16) (U.S. GEOTRACES EPZT)

Program:

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

Principal Investigator:

Benjamin Twining (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2016-07-19

Restricted:

Release Date:

2020-08-31

Validated:

Yes

Current State:

Final no updates expected

Element quotas of individual phytoplankton cells from GEOTRACES-EPZT cruise TN303, 2013.

Abstract:

Individual phytoplankton cells were collected on the GEOTRACES East Pacific Zonal Transect cruises were analyzed for elemental content using SXRF (Synchrotron radiation X-Ray Fluorescence). Carbon was calculated from biovolume using the relationships of Menden-Deuer & Lessard (2000). Trace metal concentrations are reported.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2016-07-19	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.643270.1	2020-08-31

Description

Methods & Sampling

Samples were analyzed as described in Twining et al. (2015)

Data were processed as described in Twining et al. (2015)

Data Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- replaced blank cells with nd

Additional GEOTRACES Processing:

As was done for the GEOTRACES-NAT data, BCO-DMO added standard US GEOTRACES information, such as the US GEOTRACES event number, to each submitted dataset lacking this information. To accomplish this, BCO-DMO compiled a 'master' dataset composed of the following parameters:

cruise_id, EXPOCODE,SECT_ID, STNNBR, CASTNO, GEOTRC_EVENTNO, GEOTRC_SAMPNO, GEOTRC_INSTR, SAMPNO, GF_NO, BTLNBR, BTLNBR_FLAG_W, DATE_START_EVENT, TIME_START_EVENT, ISO_DATETIME_UTC_START_EVENT, EVENT_LAT, EVENT_LON, DEPTH_MIN, DEPTH_MAX, BTL_DATE, BTL_TIME, BTL_ISO_DATETIME_UTC, BTL_LAT, BTL_LON, ODF_CTDPRS, SMDEPTH, FMDEPTH, BTMDEPTH, CTDPRS, CTDDEPTH.

This added information will facilitate subsequent analysis and inter comparison of the datasets.

Bottle parameters in the master file were taken from the GT-C_Bottle and ODF_Bottle datasets. Non-bottle parameters, including those from GeoFish tows, Aerosol sampling, and McLane Pumps, were taken from the TN303 Event Log (version 30 Oct 2014). Where applicable, pump information was taken from the PUMP_Nuts_Sals dataset.

A standardized BCO-DMO method (called "join") was then used to merge the missing parameters to each US GEOTRACES dataset, most often by matching on sample_GEOTRC or on some unique combination of other parameters.

If the master parameters were included in the original data file and the values did not differ from the master file, the original data columns were retained and the names of the parameters were changed from the PI-submitted names to the standardized master names. If there were differences between the PI-supplied parameter values and those in the master file, both columns were retained. If the original data submission included all of the master parameters, no additional columns were added, but parameter names were modified to match the naming conventions of the master file.

See the dataset parameters documentation for a description of which parameters were supplied by the PI and which were added via the join method.

2016-07-19: Added chlrophyll .zip file in Description section.

2016-06-21: Added GP16 to dataset name.

Data Files

File
EPZT_cell_elements_joined.csv (Comma Separated Values (.csv), 56.30 KB) MD5:c7e4419440f833a003c79629729e88c4 Primary data file for dataset ID 643270

Supplemental Files

File
Cell light images filename: epzt_Light_images.zip (ZIP Archive (ZIP), 93.37 MB) MD5:44f40fececd8a415bc6efa29f4552f63 Used for cellular element quotas data
Chlorophyll images filename: epzt_Chl_images.zip (ZIP Archive (ZIP), 49.38 MB) MD5:e09ec015f330ce1f92150e1a217a341d
SXRF maps filename: epzt_SXRF_maps.zip (ZIP Archive (ZIP), 16.20 MB) MD5:79d43bc24823804c650b6737457a09e8
SXRF spectra files filename: epzt_SXRF_spectra.zip (ZIP Archive (ZIP), 5.04 MB) MD5:0ec32f0b9b2dc9cd19cb6b32de82f973

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1232814

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
TN303	GP16 GEOTRACES EPZT GEOTRACES East Pacific Zonal Transect (EPZT) GT13 325020131025	2013-10-25	R/V Thomas G. Thompson	James W. Moffett (Chief Scientist) Gregory A. Cutter (Co-Chief Scientist) Christopher R. German (Co-Chief Scientist)	data info

Instruments

GeoFish Towed near-Surface Sampler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: GeoFish Towed near-Surface Sampler

Acronym: GeoFish

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/31/

Generic Description:

The GeoFish towed sampler is a custom designed near surface (<2m) sampling system for the collection of trace metal clean seawater. It consists of a PVC encapsulated lead weighted torpedo and separate PVC depressor vane supporting the intake utilizing all PFA Teflon tubing connected to a deck mounted, air-driven, PFA Teflon dual-diaphragm pump which provides trace-metal clean seawater at up to 3.7L/min. The GeoFish is towed at up to 13kts off to the side of the vessel outside of the ship's wake to avoid possible contamination from the ship's hull. It was developed by Geoffrey Smith and Ken Bruland (University of California, Santa Cruz).

GO-FLO Bottle

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: GO-FLO Bottle

Acronym: GO-FLO

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

GO-FLO bottle cast used to collect water samples for pigment, nutrient, plankton, etc. The GO-FLO sampling bottle is specially designed to avoid sample contamination at the surface, internal spring contamination, loss of sample on deck (internal seals), and exchange of water from different depths.

Microscope - Optical

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Microscope - Optical

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

X-ray fluorescence analyzer

Supplied Name:

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 single 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
project	GEOTRACES project: Eastern Pacific Zonal Transect	unitless	project
cruise_id	cruise identification	unitless	cruise_id
STNNBR	GEOTRACES station number. GEOTRACES master file (see Processing Description). PI-supplied values were identical to those in the intermediate US GEOTRACES master file.	unitless	station
BTL_LAT	station latitude; north is positive. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	decimal degrees	lat
BTL_LON	station longitude; east is postive. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	decimal degrees	lon
GEOTRC_EVENTNO	Unique identifying number for US GEOTRACES sampling events. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	event
GEOTRC_SAMPNO	GEOTRACES sample number. Values were added from the intermediate US GEOTRACES master file (see Processing Description). PI-supplied values were identical to those in the intermediate US GEOTRACES master file.	unitless	sample
CASTNO	Cast identifier; numbered consecutively within a station. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	cast
CTDDEPTH	Observation/sample depth in meters; calculated from CTD pressure. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	meters	depth
SAMPNO	Unique identifying number for US GEOTRACES samples.	unitless	sample
BTLNBR	Alphanumeric characters identifying bottle type (e.g. NIS representing Niskin and GF representing GOFLO) and position on a CTD rosette. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	bottle
BTLNBR_FLAG_W	quality flag for bottle sample: Flag 0: good value; Flag 1: no value or unknown value; Flag 2: replacement considered good value; Flag 4: not trusted; -999: missing value	unitless	flag
ISO_DATETIME_UTC_START_EVENT	Date and time (UTC) variable recorded at start of event in ISO compliant format. Values were added from the intermediate US GEOTRACES master file (see Processing Description). This standard is based on ISO 8601:2004(E) and takes on the following form: 2009-08-30T14:05:00[.xx]Z (UTC time)	yyyy-MM-dd'T'HH:mm:ss.SS'Z'	ISO_DateTime_UTC
BTL_ISO_DATETIME_UTC	Date and time (UTC) variable recorded at the bottle sampling time in ISO compliant format. Values were added from the intermediate US GEOTRACES master file (see Processing Description). This standard is based on ISO 8601:2004(E) and takes on the following form: 2009-08-30T14:05:00[.xx]Z (UTC time)	YYYY-mm-ddTHH:MM:SS.ssZ	no_bcodmo_term
SXRF_run	samples were analyzed by synchrotron x-ray fluorescence (SXRF) during two analytical runs in March 2014 (2014-1) or August 2014 (2014-2).	unitless	sample
grid_num	GEOTRACES bottle number followed by an internal designation for the grid	unitless	no_bcodmo_term
mda_id	unique identifier given to each SXRF scan during each run	unitless	sample
cell_type	each cell was classified as either an autotrophic flagellate (Flag); autotrophic dinoflagellate (Dino); diatom; or heterotrophic ciliate.	unitless	no_bcodmo_term
cell_vol	biovolume of each cell estimated from microscope measurements of cell dimensions	um^3	volume
cell_C	cellular C content calculated from biovolume using the relationships of Menden-Deuer & Lessard (2000)	mol/cell	biomass_C
cell_Si	total elemental Si content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_P	total elemental P content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_S	total elemental S content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_Mn	total elemental Mn content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_Fe	total elemental Fe content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_Co	total elemental Co content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_Ni	total elemental Ni content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
cell_Zn	total elemental Zn content of each cell was measured with SXRF. Details provided in Twining et al. (2015).	mol/cell	trace_metal_conc
light_image_filename	light image filename	unitless	no_bcodmo_term
chl_image_filename	Chl image filename	unitless	no_bcodmo_term
SXRF_map_filename	SXRF map filename	unitless	no_bcodmo_term
SXRF_spectrum_filename	SXRF spectrum filename	unitless	no_bcodmo_term

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Dataset: GP16 Cellular element quotas