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
2016-05-06
publication
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2016-07-08
publication
http://dx.doi.org/10.1575/1912/bco-dmo.651474
Dr Benjamin Twining
Bigelow Laboratory for Ocean Sciences
principalInvestigator
documentDigital
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., et al. Metal contents of phytoplankton and labile particulate material in the North Atlantic Ocean. Prog. Oceanogr. (2015)<br />http://dx.doi.org/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> Acquisition Description: <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 Ocean Sciences (NSF OCE) Award Number: OCE-1131139 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1131139
Funding provided by NSF Ocean Sciences (NSF OCE) Award Number: OCE-1335012 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1135012
Funding provided by NSF Ocean Sciences (NSF OCE) Award Number: OCE-1131046 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1131046
completed
Dr Benjamin Twining
Bigelow Laboratory for Ocean Sciences
207-315-2567
Bigelow Laboratory for Ocean Sciences PO Box 380
East Boothbay
ME
04544-0380
USA
btwining@bigelow.org
pointOfContact
asNeeded
Dataset Version: Final
bottle
cruise_id
cast
depth_n
depth
latitude
longitude
sample
sample
trace_metal_conc
trace_metal_conc
trace_metal_conc
mole_ratio
mole_ratio
CTD
Synchrotron X-ray Fluorescence Microprobe
theme
None, User defined
bottle
cruise id
cast
depth nominal
depth
latitude
longitude
sample identification
trace metal concentration
mole_ratio
featureType
BCO-DMO Standard Parameters
CTD profiler
unknown
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
http://www.bco-dmo.org/project/544555
Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
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.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.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.
Si_in_Syn
largerWorkCitation
project
eng; USA
oceans
Bermuda
-65.6664
-64.1614
21.6699
31.6691
2012-07-11
2013-10-13
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
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: unique identified given to each bottle sample collected on BATS cruises
http://lod.bco-dmo.org/id/dataset-parameter/644980.rdf
Name: cruise_id
Units: text
Description: cruise on which sample was collected
http://lod.bco-dmo.org/id/dataset-parameter/644981.rdf
Name: cast
Units: text
Description: CTD cast on which whole seawater was collected
http://lod.bco-dmo.org/id/dataset-parameter/644982.rdf
Name: depth_nom
Units: text
Description: nominal depth; Surface or DCM (deep cholorophyll max)
http://lod.bco-dmo.org/id/dataset-parameter/644983.rdf
Name: depth
Units: meters
Description: bottle target trip depth in meters
http://lod.bco-dmo.org/id/dataset-parameter/644984.rdf
Name: lat
Units: decimal degrees
Description: latitude
http://lod.bco-dmo.org/id/dataset-parameter/644985.rdf
Name: lon
Units: decimal degrees
Description: longitude; west is negative
http://lod.bco-dmo.org/id/dataset-parameter/644986.rdf
Name: SXRF_run
Units: text
Description: SXRF run identifier
http://lod.bco-dmo.org/id/dataset-parameter/644987.rdf
Name: mda_id
Units: text
Description: SXRF scan id within the run
http://lod.bco-dmo.org/id/dataset-parameter/644988.rdf
Name: cell_Si
Units: mol/cell
Description: total silicon content within each Synechococcus cell measured with SXRF
http://lod.bco-dmo.org/id/dataset-parameter/644989.rdf
Name: cell_P
Units: mol/cell
Description: total phosphorus content within each Synechococcus cell measured with SXRF
http://lod.bco-dmo.org/id/dataset-parameter/644990.rdf
Name: cell_S
Units: mol/cell
Description: total sulfur content within each Synechococcus cell measured with SXRF
http://lod.bco-dmo.org/id/dataset-parameter/644991.rdf
Name: cell_Si_to_P
Units: dimensionless
Description: derived mole ratio of silicon to phosphorous for each Synechococcus cell with determinable silicon and phosphorus content
http://lod.bco-dmo.org/id/dataset-parameter/644992.rdf
Name: cell_Si_to_S
Units: dimensionless
Description: derived mole ratio of silicon to sulfur for each Synechococcus cell with determinable silicon and sulfur content
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
http://vocab.nerc.ac.uk/collection/P09/current/DEPH/
Name: DEPTH BELOW SEA SURFACE
Description: The distance of a sensor or sampling point below the sea surface.
http://vocab.nerc.ac.uk/collection/P09/current/LATX/
Name: LATITUDE
Description: The angular distance north or south from the equator, measured along the meridian of the point of interest.
http://vocab.nerc.ac.uk/collection/P09/current/LONX/
Name: LONGITUDE
Description: The angular distance east or west east or west of Greenwich to the point of interest.
http://vocab.nerc.ac.uk/collection/P02/current/ACYC/
Name: Reference numbers
Description: Data record, event, sample or measurement reference numbers
http://vocab.nerc.ac.uk/collection/P02/current/ACYC/
Name: Reference numbers
Description: Data record, event, sample or measurement reference numbers
http://vocab.nerc.ac.uk/collection/P03/current/C035/
Name: Metal and metalloid concentrations
Description: Parameters pertaining to metal and trace metalloid (i.e. excluding Si) concentrations in any material.
http://vocab.nerc.ac.uk/collection/P03/current/C035/
Name: Metal and metalloid concentrations
Description: Parameters pertaining to metal and trace metalloid (i.e. excluding Si) concentrations in any material.
http://vocab.nerc.ac.uk/collection/P03/current/C035/
Name: Metal and metalloid concentrations
Description: Parameters pertaining to metal and trace metalloid (i.e. excluding Si) concentrations in any material.
Parameters for this dataset
physicalMeasurement
BATS_bottle_ID
bottle
PI-supplied Description: unique identified given to each bottle sample collected on BATS cruises; General Description: water bottle number, generally assigned to a position on a CTD rosette, identifies all samples drawn from a given bottle
http://lod.bco-dmo.org/id/dataset-parameter/644979.rdf
text
cruise_id
cruise id
PI-supplied Description: cruise on which sample was collected; General Description: cruise designation; name
http://lod.bco-dmo.org/id/dataset-parameter/644980.rdf
text
cast
cast
PI-supplied Description: CTD cast on which whole seawater was collected; General Description: cast or profile number
http://lod.bco-dmo.org/id/dataset-parameter/644981.rdf
text
depth_nom
depth nominal
PI-supplied Description: nominal depth; Surface or DCM (deep cholorophyll max); General Description: depth; nominal
http://lod.bco-dmo.org/id/dataset-parameter/644982.rdf
text
depth
depth
PI-supplied Description: bottle target trip depth in meters; General Description: observation/sample depth, in meters; best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable NERC Description: The distance of a sensor or sampling point below the sea surface.
http://lod.bco-dmo.org/id/dataset-parameter/644983.rdf
meters
lat
latitude
PI-supplied Description: latitude; General Description: latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes NERC Description: The angular distance north or south from the equator, measured along the meridian of the point of interest.
http://lod.bco-dmo.org/id/dataset-parameter/644984.rdf
decimal degrees
lon
longitude
PI-supplied Description: longitude; west is negative; General Description: longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes NERC Description: The angular distance east or west east or west of Greenwich to the point of interest.
http://lod.bco-dmo.org/id/dataset-parameter/644985.rdf
decimal degrees
SXRF_run
sample identification
PI-supplied Description: SXRF run identifier; General Description: unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent NERC Description: Data record, event, sample or measurement reference numbers
http://lod.bco-dmo.org/id/dataset-parameter/644986.rdf
text
mda_id
sample identification
PI-supplied Description: SXRF scan id within the run; General Description: unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent NERC Description: Data record, event, sample or measurement reference numbers
http://lod.bco-dmo.org/id/dataset-parameter/644987.rdf
text
cell_Si
trace metal concentration
PI-supplied Description: total silicon content within each Synechococcus cell measured with SXRF; General Description: Concentration of a trace metal in seawater. Refer to dataset for element name and units. NERC Description: Parameters pertaining to metal and trace metalloid (i.e. excluding Si) concentrations in any material.
http://lod.bco-dmo.org/id/dataset-parameter/644988.rdf
mol/cell
cell_P
trace metal concentration
PI-supplied Description: total phosphorus content within each Synechococcus cell measured with SXRF; General Description: Concentration of a trace metal in seawater. Refer to dataset for element name and units. NERC Description: Parameters pertaining to metal and trace metalloid (i.e. excluding Si) concentrations in any material.
http://lod.bco-dmo.org/id/dataset-parameter/644989.rdf
mol/cell
cell_S
trace metal concentration
PI-supplied Description: total sulfur content within each Synechococcus cell measured with SXRF; General Description: Concentration of a trace metal in seawater. Refer to dataset for element name and units. NERC Description: Parameters pertaining to metal and trace metalloid (i.e. excluding Si) concentrations in any material.
http://lod.bco-dmo.org/id/dataset-parameter/644990.rdf
mol/cell
cell_Si_to_P
mole_ratio
PI-supplied Description: derived mole ratio of silicon to phosphorous for each Synechococcus cell with determinable silicon and phosphorus content; General Description: Also known as "mole_fraction." The amount of one quantity in moles divided by the another quantity in moles.This is dimensionless because the units cancel themselves in this ratio.
http://lod.bco-dmo.org/id/dataset-parameter/644991.rdf
dimensionless
cell_Si_to_S
mole_ratio
PI-supplied Description: derived mole ratio of silicon to sulfur for each Synechococcus cell with determinable silicon and sulfur content; General Description: Also known as "mole_fraction." The amount of one quantity in moles divided by the another quantity in moles.This is dimensionless because the units cancel themselves in this ratio.
http://lod.bco-dmo.org/id/dataset-parameter/644992.rdf
dimensionless
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://dx.doi.org/10.1575/1912/bco-dmo.651474
download
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>
<p>Data were processed as described in Twining et al. (2015).</p>
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:CTD 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 and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the 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 instrument designation is used when specific make and model are not known. 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: SXRFFor this dataset the model used was: Beamline:2-ID-DThe 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: unknown Instrument Short Name:unknown Instrument Description: The correct value is not known to and not computable by the creator of this information. However a correct value probably exists. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
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
Dr Rodney 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
Dr Rodney Johnson
Bermuda Institute of Ocean Sciences