Dataset: Cellular element quotas: Si in Synechococcus cells
Deployment: AE1218

element quotas of individual Synechococcus cells

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)

Project:

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

Current State:

Final with updates expected

Version:

working on final

Deployment Synonyms:

BATS 283

Version Date:

2016-05-13

Data URL:

https://www.bco-dmo.org/dataset-deployment/645482/data

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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

Dataset acquisition description

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

Dataset Processing Description

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

More information about this dataset deployment

Funding

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

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

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

Contribute Data

Dataset: Cellular element quotas: Si in Synechococcus cells
Deployment: AE1218

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Cellular element quotas: Si in Synechococcus cellsDeployment: AE1218

Dataset acquisition description

Dataset Processing Description

Dataset: Cellular element quotas: Si in Synechococcus cells
Deployment: AE1218