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     data   graph     files  public 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)
   ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_644840

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String 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.
attribute NC_GLOBAL awards_0_award_nid String 544554
attribute NC_GLOBAL awards_0_award_number String OCE-1131139
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1131139 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Dr David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL awards_1_award_nid String 544560
attribute NC_GLOBAL awards_1_award_number String OCE-1335012
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1135012 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String Dr David L. Garrison
attribute NC_GLOBAL awards_1_program_manager_nid String 50534
attribute NC_GLOBAL awards_2_award_nid String 544561
attribute NC_GLOBAL awards_2_award_number String OCE-1131046
attribute NC_GLOBAL awards_2_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1131046 (external link)
attribute NC_GLOBAL awards_2_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_2_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_2_funding_source_nid String 355
attribute NC_GLOBAL awards_2_program_manager String Dr David L. Garrison
attribute NC_GLOBAL awards_2_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Cellular element quotas: Si in Synechococcus
P.I. Ben Twining
version 6 May 2016
N.B. bd = below detection
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.2d 13 Jun 2019
attribute NC_GLOBAL date_created String 2016-05-06T20:13:35Z
attribute NC_GLOBAL date_modified String 2018-11-16T20:49:08Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.651474
attribute NC_GLOBAL Easternmost_Easting double -64.1614
attribute NC_GLOBAL geospatial_lat_max double 31.6691
attribute NC_GLOBAL geospatial_lat_min double 21.6699
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -64.1614
attribute NC_GLOBAL geospatial_lon_min double -65.6664
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 88.0
attribute NC_GLOBAL geospatial_vertical_min double 1.0
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/644840 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String CTD
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 644996
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/130/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String CTD profiler
attribute NC_GLOBAL instruments_0_instrument_nid String 417
attribute NC_GLOBAL instruments_0_supplied_name String CTD
attribute NC_GLOBAL instruments_1_acronym String XRF analyzer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String 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
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 647671
attribute NC_GLOBAL instruments_1_description String 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.
attribute NC_GLOBAL instruments_1_instrument_name String X-ray fluorescence analyzer
attribute NC_GLOBAL instruments_1_instrument_nid String 648910
attribute NC_GLOBAL instruments_1_supplied_name String Synchrotron X-ray Fluorescence Microprobe
attribute NC_GLOBAL keywords String bats, BATS_bottle_ID, bco, bco-dmo, biological, bottle, cast, cell, cell_P, cell_S, cell_Si, cell_Si_to_P, cell_Si_to_S, chemical, chemistry, concentration, cruise, cruise_id, data, dataset, depth, depth_nom, dissolved, dissolved nutrients, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Silicate, erddap, identifier, latitude, longitude, management, mass, mass_concentration_of_silicate_in_sea_water, mda, mda_id, nutrients, ocean, oceanography, oceans, office, preliminary, run, science, sea, seawater, silicate, sxrf, time, water
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/644840 (external link)
attribute NC_GLOBAL Northernmost_Northing double 31.6691
attribute NC_GLOBAL param_mapping String {'644840': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/644840/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Bigelow Laboratory for Ocean Sciences
attribute NC_GLOBAL people_0_person_name String Benjamin Twining
attribute NC_GLOBAL people_0_person_nid String 51087
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Bigelow Laboratory for Ocean Sciences
attribute NC_GLOBAL people_1_person_name String Daniel Ohnemus
attribute NC_GLOBAL people_1_person_nid String 640096
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Ms Dicky Allison
attribute NC_GLOBAL people_2_person_nid String 50382
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Amber York
attribute NC_GLOBAL people_3_person_nid String 643627
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
attribute NC_GLOBAL projects_0_acronym String Si_in_Syn
attribute NC_GLOBAL projects_0_description String Extracted from the NSF award abstract:
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 Caf� 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.
attribute NC_GLOBAL projects_0_end_date String 2015-12
attribute NC_GLOBAL projects_0_geolocation String Samples collected in western North Atlantic Ocean between Puerto Rico, Bermuda, and Gulf of Maine.
attribute NC_GLOBAL projects_0_name String Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle
attribute NC_GLOBAL projects_0_project_nid String 544555
attribute NC_GLOBAL projects_0_start_date String 2012-01
attribute NC_GLOBAL publisher_name String Ms Dicky Allison, Amber York
attribute NC_GLOBAL publisher_role String BCO-DMO Data Manager(s)
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 21.6699
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v29
attribute NC_GLOBAL summary String 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.\u00a0 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\u2013283.
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](\\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.
attribute NC_GLOBAL title String 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)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -65.6664
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5-beta
variable cruise_id   String  
attribute cruise_id description String cruise on which sample was collected
attribute cruise_id ioos_category String Identifier
attribute cruise_id long_name String Cruise Id
attribute cruise_id units String text
variable BATS_bottle_ID   int  
attribute BATS_bottle_ID _FillValue int 2147483647
attribute BATS_bottle_ID actual_range int 102830102, 500481408
attribute BATS_bottle_ID description String unique identified given to each bottle sample collected on BATS cruises
attribute BATS_bottle_ID ioos_category String Identifier
attribute BATS_bottle_ID long_name String BATS Bottle ID
attribute BATS_bottle_ID units String text
variable cast   String  
attribute cast description String CTD cast on which whole seawater was collected
attribute cast ioos_category String Unknown
attribute cast long_name String Cast
attribute cast units String text
variable depth_nom   String  
attribute depth_nom colorBarMaximum double 8000.0
attribute depth_nom colorBarMinimum double -8000.0
attribute depth_nom colorBarPalette String TopographyDepth
attribute depth_nom description String nominal depth; Surface or DCM (deep cholorophyll max)
attribute depth_nom ioos_category String Location
attribute depth_nom long_name String Depth
attribute depth_nom standard_name String depth
attribute depth_nom units String text
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 1.0, 88.0
attribute depth axis String Z
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String bottle target trip depth in meters
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 21.6699, 31.6691
attribute latitude axis String Y
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String latitude
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -65.6664, -64.1614
attribute longitude axis String X
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String longitude; west is negative
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable SXRF_run   String  
attribute SXRF_run description String SXRF run identifier
attribute SXRF_run ioos_category String Unknown
attribute SXRF_run long_name String SXRF Run
attribute SXRF_run source_name String SXRF_run
attribute SXRF_run units String text
variable mda_id   short  
attribute mda_id _FillValue short 32767
attribute mda_id actual_range short 91, 444
attribute mda_id description String SXRF scan id within the run
attribute mda_id ioos_category String Identifier
attribute mda_id long_name String Mda Id
attribute mda_id units String text
variable cell_Si   String  
attribute cell_Si description String total silicon content within each Synechococcus cell measured with SXRF
attribute cell_Si ioos_category String Dissolved Nutrients
attribute cell_Si long_name String Mass Concentration Of Silicate In Sea Water
attribute cell_Si units String mol/cell
variable cell_P   String  
attribute cell_P description String total phosphorus content within each Synechococcus cell measured with SXRF
attribute cell_P ioos_category String Unknown
attribute cell_P long_name String Cell P
attribute cell_P units String mol/cell
variable cell_S   String  
attribute cell_S description String total sulfur content within each Synechococcus cell measured with SXRF
attribute cell_S ioos_category String Unknown
attribute cell_S long_name String Cell S
attribute cell_S units String mol/cell
variable cell_Si_to_P   float  
attribute cell_Si_to_P _FillValue float NaN
attribute cell_Si_to_P actual_range float 0.05, 90.39
attribute cell_Si_to_P description String derived mole ratio of silicon to phosphorous for each Synechococcus cell with determinable silicon and phosphorus content
attribute cell_Si_to_P ioos_category String Dissolved Nutrients
attribute cell_Si_to_P long_name String Mass Concentration Of Silicate In Sea Water
attribute cell_Si_to_P units String dimensionless
variable cell_Si_to_S   float  
attribute cell_Si_to_S _FillValue float NaN
attribute cell_Si_to_S actual_range float 0.05, 34.12
attribute cell_Si_to_S description String derived mole ratio of silicon to sulfur for each Synechococcus cell with determinable silicon and sulfur content
attribute cell_Si_to_S ioos_category String Dissolved Nutrients
attribute cell_Si_to_S long_name String Mass Concentration Of Silicate In Sea Water
attribute cell_Si_to_S units String dimensionless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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