Dataset: Cellular element quotas: Si in Synechococcus cells

Name: Element quotas of individual Synechococcus cells collected during Bermuda Atlantic Time-series Study (BATS) cruises aboard the R/V Atlantic Explorer between dates 2012-07-11 and 2013-10-13 (Si_in_Syn project)
Published: 2016-05-06
Keywords: SXRF, Synchrotron radiation X-Ray Fluorescence, Synechococcus, cellular element quotas, BATS, silica cycling, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.651474

Spatial Extent: N:31.6691 E:-64.1614 S:21.6699 W:-65.6664

Temporal Extent: 2012-07-11 - 2013-10-13

Project:

Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle (Si_in_Syn)

Principal Investigator:

Benjamin Twining (Bigelow Laboratory for Ocean Sciences)

Contact:

Daniel C. Ohnemus (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Ms Dicky Allison (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Final

Version Date:

2016-05-06

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Element quotas of individual Synechococcus cells collected during Bermuda Atlantic Time-series Study (BATS) cruises aboard the R/V Atlantic Explorer between dates 2012-07-11 and 2013-10-13 (Si_in_Syn project)

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2016-05-06	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.651474	2016-07-08

Description

Field work at the Bermuda Atlantic Time Series (BATS) site was done to assess the contribution of Synechococcus and diatoms to total biogenic silica in surface waters. The data include information about the elemental content (Silicon, Phosphorus, and Sulfur) of Synechococcus cells as measured by synchrotron-based x-ray fluorescence (SBXF) microscopy. Derived mole ratios (Si:P, and Si:S) are also provided.

References:

Twining, B. S., Rauschenberg, S., Morton, P. L., & Vogt, S. (2015). Metal contents of phytoplankton and labile particulate material in the North Atlantic Ocean. Progress in Oceanography, 137, 261–283. doi:10.1016/j.pocean.2015.07.001
https://www.researchgate.net/publication/282626294_Metal_contents_of_phytoplankton_and_labile_particulate_material_in_the_North_Atlantic_Ocean

DMO notes:

Changed formatting of lat/lon to 4 decimal places from 5.
Elemental content values rounded to two decimal places from 15.

Methods & Sampling

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

Bottle samples were collected during BATS cruises from surface level and the deep chlorophyll max (DCM) using a CTD. The SXRF runs were done with a Beamline 2-ID-E during three analytical runs in December 2012, April 2013, and December 2013.

Data Processing Description

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

Data Files

File
si_in_syn.csv (Comma Separated Values (.csv), 10.09 KB) MD5:17a346bf35a2e5ceec900487e12c4bf6 Primary data file for dataset ID 644840

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1131046
NSF Division of Ocean Sciences	OCE-1131139
NSF Division of Ocean Sciences	OCE-1335012

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AE1218	BATS 283	2012-07-11	R/V Atlantic Explorer	James Sadler (Chief Scientist)	data info
AE1228	BATS 286	2012-10-18	R/V Atlantic Explorer	Rodney J. Johnson (Chief Scientist)	data info
AE1322	BVAL 048 BATS BV48	2013-09-28	R/V Atlantic Explorer	Rodney J. Johnson (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name: CTD

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

X-ray fluorescence analyzer

Supplied Name: Synchrotron X-ray Fluorescence Microprobe

Supplied Description:

Abbreviation: SXRF

For this dataset the model used was: Beamline:2-ID-D

The instrument quantifies and maps elements (e.g. Si, Mn, Fe, Ni, S, P) in single cells.

Used in the following paper to look at trace elements in aquatic protists:

B. Twining, S. Baines, N. Fisher, J. Maser, S. Vogt, C. Jacobsen, A. Tovar-Sanchez, S. Sanudo-Wilhelmy; “Quantifying Trace Elements in Individual Aquatic Protist Cells with a Synchrotron X-ray Fluorescence Microprobe”, Analytical Chemistry 2003, 75, 3806-3816. DOI: 10.1021/ac034227z

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
BATS_bottle_ID	unique identified given to each bottle sample collected on BATS cruises	text	bottle
cruise_id	cruise on which sample was collected	text	cruise_id
cast	CTD cast on which whole seawater was collected	text	cast
depth_nom	nominal depth; Surface or DCM (deep cholorophyll max)	text	depth_n
depth	bottle target trip depth in meters	meters	depth
lat	latitude	decimal degrees	lat
lon	longitude; west is negative	decimal degrees	lon
SXRF_run	SXRF run identifier	text	sample
mda_id	SXRF scan id within the run	text	sample
cell_Si	total silicon content within each Synechococcus cell measured with SXRF	mol/cell	trace_metal_conc
cell_P	total phosphorus content within each Synechococcus cell measured with SXRF	mol/cell	trace_element_conc
cell_S	total sulfur content within each Synechococcus cell measured with SXRF	mol/cell	trace_element_conc
cell_Si_to_P	derived mole ratio of silicon to phosphorous for each Synechococcus cell with determinable silicon and phosphorus content	dimensionless	mole_ratio
cell_Si_to_S	derived mole ratio of silicon to sulfur for each Synechococcus cell with determinable silicon and sulfur content	dimensionless	mole_ratio

Database

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Dataset: Cellular element quotas: Si in Synechococcus cells