Dataset: GT10-11 - cellular element quotas
Deployment: KN199-04

Element quotas of individual phytoplankton cells

Principal Investigator:

Benjamin Twining (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

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

Project:

U.S. GEOTRACES North Atlantic Transect (GA03) (U.S. GEOTRACES NAT)

Current State:

Final no updates expected

Version:

2015-02-17

Deployment Synonyms:

GA03, GT10, USGT-NAT-2010, KN199-4, GNAT, U.S. GEOTRACES NAZT Leg 1, knorr199-4/5, Section Cruise (GA03), 316N20101015

Version Date:

2015-02-17

Data URL:

https://www.bco-dmo.org/dataset-deployment/550553/data

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Description

Individual phytoplankton cells were collected on the GEOTRACES North Atlantic 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.

Download zipped images:
Chlorophyll
Light
SXRF maps
SXRF spectra

Related references:

Menden-Deuer, S. and E. J. Lessard (2000). Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton. Limnology and Oceanography 45(3): 569-579.

* Twining, B. S., S. Rauschenberg, P. L. Morton, and S. Vogt. 2015. Metal contents of phytoplankton and labile particulate material in the North Atlantic Ocean. Progress in Oceanography 137: 261-283.)

Methods & Sampling

Dataset acquisition description

SXRF samples were prepared from unfiltered water taken from GEOTRACES GO-Flo bottles at the shallowest depth and deep chlorophyll maximum. Cells were preserved with 0.25% trace-metal clean buffered glutaraldehyde and centrifuged onto C/formvar-coated Au TEM grids. 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).

Data Processing Description

Dataset Processing Description

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

Between 9 and 20 cells were analyzed from the shallowest bottle and deep chlorophyll maximum at the subset of stations. The elemental content of each cell has been corrected for elements contained in the carbon substrate. Trace element concentrations are presented as mmol/mol P. Geometric mean concentrations (+/- standard error of the mean) are presented, along with the number of cells analyzed.

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- replaced blank cells with nd
- sorted by cruise, station, grid#
- changed station 99 and 153 to cruise AT199-05 from AT199-04
- revised station 9 depths to match master events log

With the agreement of BODC and the US GEOTRACES lead PIs, BCO-DMO added standard US GEOTRACES information, such as the US GEOTRACES event number. To accomplish this, BCO-DMO compiled a 'master' dataset composed of the following parameters: station_GEOTRC, cast_GEOTRC (bottle and pump data only), event_GEOTRC, sample_GEOTRC, sample_bottle_GEOTRC (bottle data only), bottle_GEOTRC (bottle data only), depth_GEOTRC_CTD (bottle data only), depth_GEOTRC_CTD_rounded (bottle data only), BTL_ISO_DateTime_UTC (bottle data only), and GeoFish_id (GeoFish data only). 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_GT10, GT-C_Bottle_GT11, ODF_Bottle_GT10, and ODF_Bottle_GT11 datasets. Non-bottle parameters, including those from GeoFish tows, Aerosol sampling, and McLane Pumps, were taken from the Event_Log_GT10 and Event_Log_GT11 datasets. McLane pump cast numbers missing in event logs were taken from the Particulate Th-234 dataset submitted by Ken Buesseler.

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.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0928289	NSF Division of Ocean Sciences

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 synchetron 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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identification	unitless	cruise_id
station_GEOTRC	GEOTRACES station number; ranges from 1 through 12 for KN199-04 and 1 through 24 for KN204-01. Stations 7 and 9 were skipped on KN204-01. Some GeoFish stations are denoted as X_to_Y indicating the tow occurred between stations X and Y. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	station
lat	station latitude; north is positive	decimal degrees	lat
lon	station longitude; east is postive	decimal degrees	lon
cast_GEOTRC	Cast identifier; numbered consecutively within a station. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	cast
event_GEOTRC	Unique identifying number for US GEOTRACES sampling events; ranges from 2001 to 2225 for KN199-04 events and from 3001 to 3282 for KN204-01 events. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	event
depth_GEOTRC_CTD	Observation/sample depth in meters; calculated from CTD pressure. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	meters	depth
depth_GEOTRC_CTD_round	Rounded observation/sample depth in meters; calculated from CTD pressure. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	meters	depth
sample_GEOTRC	Unique identifying number for US GEOTRACES samples; ranges from 5033 to 6078 for KN199-04 and from 6112 to 8148 for KN204-01. PI-supplied values were identical to those in the intermediate US GEOTRACES master file. Originally submitted as 'GEOTRACES #'; this parameter name has been changed to conform to BCO-DMO's GEOTRACES naming conventions.	unitless	sample
sample_bottle_GEOTRC	Unique identification numbers given to samples taken from bottles; ranges from 1 to 24; often used synonymously with bottle number. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	unitless	sample
bottle_GEOTRC	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
project	GEOTRACES project: North Atlantic Zonal Transect	unitless	project
grid_type	grid type: plankton samples were mounted onto either gold (Au) or aluminum (Al) electron microscopy grids	unitless	no_bcodmo_term
grid_num	GEOTRACES bottle number followed by an internal designation for the grid	unitless	no_bcodmo_term
SXRF_run	samples were analyzed by synchrotron x-ray fluorescence (SXRF) during two analytical runs in July 2011 (2011r2) or August 2012 (2012r2).	unitless	sample
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 (Aflag); autotrophic picoplankter (Apico); or a diatom.	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_Cu	total elemental Cu 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
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-dd'T'HH:mm:ss.SS'Z'	ISO_DateTime_UTC
sta_PI	station number given by PI	unitless	sta

Database

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Dataset: GT10-11 - cellular element quotas
Deployment: KN199-04

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: GT10-11 - cellular element quotasDeployment: KN199-04

Dataset acquisition description

Dataset Processing Description

Dataset: GT10-11 - cellular element quotas
Deployment: KN199-04