http://lod.bco-dmo.org/id/dataset/644840
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-05-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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)
2016-05-06
publication
2016-05-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2016-07-08
publication
https://doi.org/10.1575/1912/bco-dmo.651474
Benjamin Twining
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Twining, B. (2016) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version Final) Version Date 2016-05-06 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.651474 [access date]
element quotas of individual Synechococcus cells Dataset Description: <p>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.&nbsp; Derived mole ratios (Si:P, and Si:S) are also provided.</p>
<h3><strong>References:</strong></h3>
<p>Twining, B. S., Rauschenberg, S., Morton, P. L., &amp; 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<br />
<a href="https://www.researchgate.net/publication/282626294_Metal_contents_of_phytoplankton_and_labile_particulate_material_in_the_North_Atlantic_Ocean">https://www.researchgate.net/publication/282626294_Metal_contents_of_phytoplankton_and_labile_particulate_material_in_the_North_Atlantic_Ocean</a></p>
<h3><strong>DMO notes:</strong></h3>
<ul>
<li>Changed formatting of lat/lon to 4 decimal places from 5.</li>
<li>Elemental content values rounded to two decimal places from 15.</li>
</ul> Methods and Sampling: <p>Samples were analyzed as described in Twining et al. (2015).</p>
<p>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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1131139 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1131139
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1335012 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1135012
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1131046 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1131046
completed
Benjamin Twining
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544-0380
USA
btwining@bigelow.org
pointOfContact
asNeeded
Dataset Version: Final
Unknown
BATS_bottle_ID
cruise_id
cast
depth_nom
depth
lat
lon
SXRF_run
mda_id
cell_Si
cell_P
cell_S
cell_Si_to_P
cell_Si_to_S
CTD
Synchrotron X-ray Fluorescence Microprobe
theme
None, User defined
bottle
Cruise identfier
cast
depth nominal
depth
latitude
longitude
sample identification
trace metal concentration
trace element concentration
mole_ratio
featureType
BCO-DMO Standard Parameters
CTD - profiler
X-ray fluorescence analyzer
instrument
BCO-DMO Standard Instruments
AE1218
AE1228
AE1322
service
Deployment Activity
Bermuda
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
https://osprey.bco-dmo.org/project/544555
Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
<p><em>Extracted from the NSF award abstract:</em></p>
<p>INTELECTUAL MERIT: The investigators will follow-up on their discovery of significant accumulation of silicon by marine picocyanobacteria of the genus Synechococcus to assess the contribution of these organisms to the cycling of biogenic silica in the ocean. Oceanographers have long assumed that diatoms are the dominant marine organisms controlling the cycling of silica in the ocean. Recently, however, single-cell analyses of picocyanobacterial cells from field samples surprisingly revealed the presence of substantial amounts of silicon within Synechococcus. The contribution of Synechococcus to biogenic silica often rivaled that of living diatoms in the two systems examined. Moreover, size fractionation of biogenic silica indicates that up to 25% of biogenic silica can exist in the picoplanktonic size fraction. Given that picocyanobacteria dominate phytoplankton biomass and primary production over much of the world's ocean, these findings raise significant questions about the factors controlling the marine silica cycle globally, as well as the proper interpretation of biogenic silica measurements, Si:N ratios in particulate matter, and ratios of silicate and nitrate depletion. It also suggests that picocyanobacterial populations may be subject to previously unknown constraints on their productivity.</p>
<p>The project will have both laboratory and field components. Because cellular Si varies substantially among the field-collected samples and laboratory strains so far analyzed, the laboratory component will document variability in Si uptake and cellular Si concentrations, while determining what role physiological and phylogenetic factors play in this variability. The investigators will use strains of Synechococcus for which there are already genome sequences. Laboratory experiments will 1) use 32Si radiotracer uptake experiments to assess the degree of variability in Si content and Si uptake kinetics among strains of Synechococcus acclimated to different levels of silicate, 2) characterize the intracellular distribution and chemistry of silicon within cells using fractionation techniques, density centrifugation, electron microscopy and x-ray absorption spectroscopy, and 3) use bioinformatic analyses of published genomes to determine whether uptake of Si can be predicted based on phylogenetic relationships, to identify candidate genes involved in cyanobacterial Si metabolism, and to develop probes for community structure that can be related to cellular Si content. Field work at the Bermuda Atlantic Time Series (BATS) site will assess the contribution of Synechococcus and diatoms to total biogenic silica in surface waters at times of the year when the former are typically dominant. Field measurements will include size fractionation of biogenic silica biomass and Si uptake, and synchrotron-based x-ray fluorescence microscopy, and the phylogenetic composition of the Synechococcus assemblage.</p>
<p>BROADER IMPACTS: This project has the potential to drive a major paradigm shift in our understanding of the marine silicon cycle. In addition, one PhD student will be trained at Stony Brook. Each PI will provide research experience to a number of undergraduates working on original research projects for credit, as a part of an REU program or as the basis for undergraduate theses. Stony Brook research programs for undergraduates are supported with summer research money from the Undergraduate Research and Creative Activities (URECA) program, and draw on its very diverse student body. The investigators will also engage promising high school level students through several residential programs that the PIs have been a part of in the past. These include the BLOOM program at Bigelow and the Simons Summer Research Fellowship Program at Stony Brook. The PI has continuing relationship with a regional high school (Brentwood) with a high proportion of underrepresented minorities. PI Twining is involved in the Café Scientifique program at Bigelow. Baines will engage in similar outreach through the Center for Science and Mathematics Education (CESAME) sponsored Open Science Nights. Finally, PI Baines will cooperate with CESAMEs teacher education programs, with the aim of incorporating biological oceanography into K-12 curricula. PIs Krause and Brzezinski will incorporate aspects of phytoplankton ecology into UCSB's Oceans to Classroom Program that brings marine research at UCSB to life for over 18,000 K-12 students each year.</p>
Si_in_Syn
largerWorkCitation
project
eng; USA
oceans
Bermuda
-65.6664
-64.1614
21.6699
31.6691
2012-07-11
2013-10-13
Samples collected in western North Atlantic Ocean between Puerto Rico, Bermuda, and Gulf of Maine.
0
BCO-DMO catalogue of parameters from 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)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/644979.rdf
Name: BATS_bottle_ID
Units: text
Description: <p>unique identified given to each bottle sample collected on BATS cruises</p>
http://lod.bco-dmo.org/id/dataset-parameter/644980.rdf
Name: cruise_id
Units: text
Description: <p>cruise on which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/644981.rdf
Name: cast
Units: text
Description: <p>CTD cast on which whole seawater was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/644982.rdf
Name: depth_nom
Units: text
Description: <p>nominal depth; Surface or DCM (deep cholorophyll max)</p>
http://lod.bco-dmo.org/id/dataset-parameter/644983.rdf
Name: depth
Units: meters
Description: <p>bottle target trip depth in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/644984.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/644985.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/644986.rdf
Name: SXRF_run
Units: text
Description: <p>SXRF run identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/644987.rdf
Name: mda_id
Units: text
Description: <p>SXRF scan id within the run</p>
http://lod.bco-dmo.org/id/dataset-parameter/644988.rdf
Name: cell_Si
Units: mol/cell
Description: <p>total silicon content within each Synechococcus cell measured with SXRF</p>
http://lod.bco-dmo.org/id/dataset-parameter/644989.rdf
Name: cell_P
Units: mol/cell
Description: <p>total phosphorus content within each Synechococcus cell measured with SXRF</p>
http://lod.bco-dmo.org/id/dataset-parameter/644990.rdf
Name: cell_S
Units: mol/cell
Description: <p>total sulfur content within each Synechococcus cell measured with SXRF</p>
http://lod.bco-dmo.org/id/dataset-parameter/644991.rdf
Name: cell_Si_to_P
Units: dimensionless
Description: <p>derived mole ratio of silicon to phosphorous for each Synechococcus cell with determinable silicon and phosphorus content</p>
http://lod.bco-dmo.org/id/dataset-parameter/644992.rdf
Name: cell_Si_to_S
Units: dimensionless
Description: <p>derived mole ratio of silicon to sulfur for each Synechococcus cell with determinable silicon and sulfur content</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://doi.org/10.1575/1912/bco-dmo.651474
download
onLine
dataset
<p>Samples were analyzed as described in Twining et al. (2015).</p>
<p>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.</p>
Specified by the Principal Investigator(s)
<p>Data were processed as described in Twining et al. (2015).</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
CTD
CTD
PI Supplied Instrument Name: CTD Instrument Name: CTD - profiler Instrument Short Name: Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Synchrotron X-ray Fluorescence Microprobe
Synchrotron X-ray Fluorescence Microprobe
PI Supplied Instrument Name: Synchrotron X-ray Fluorescence Microprobe PI Supplied Instrument 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 Name: X-ray fluorescence analyzer Instrument Short Name:XRF analyzer Instrument 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.
Cruise: AE1218
AE1218
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1218
James Sadler
Bermuda Institute of Ocean Sciences
Cruise: AE1228
AE1228
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1228
Rodney J. Johnson
Bermuda Institute of Ocean Sciences
Cruise: AE1322
AE1322
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1322
Rodney J. Johnson
Bermuda Institute of Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel