Accessing BCO-DMO data
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| Dataset Title: | [Pleurochrysis carterae light-dark calcification] - Light-dark calcification rates of Pleurochrysis carterae analyzed at Bigelow Laboratory in 2013 (OA Copes Coccoliths project) (Effects of ocean acidification on Emiliania huxleyi and Calanus finmarchicus; insights into the oceanic alkalinity and biological carbon pumps) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_664013) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
pCO2_treatment {
Int16 _FillValue 32767;
Int16 actual_range 280, 750;
String bcodmo_name "treatment";
String description "The independent variable - one of three pCO2 levels (280 ppm, 380 ppm, or 750 ppm) These treatment levels are nominal values as they represent the target pCO2 for each treatment.";
String long_name "P CO2 Treatment";
String units "parts per million (ppm)";
}
sample {
String bcodmo_name "sample";
String description
"For each pCO2 treatment there are three types of samples;
After de-lithing: These samples were taken immediately after the coccolithophores were acidified to dissolve their coccoliths and then neutralized to return the culture pH to the original pH. These samples were taken before the 24 h incubation period and therefore do not have a Light or Dark treatment.
Replicate: These represent the three replicates for each light condition and each CO2 treatment. These samples were taken after the cells incubated in either light or dark conditions for 24 h.
Blank: These samples were killed by the addition of formalin but were allowed to incubate in either light or dark conditions for 24 h.";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
light_conditions {
String bcodmo_name "PAR";
String description "This identifies whether the sample was incubated for 24 h in light (470 umol photons/m-2/s PAR) or dark (0 umol photons/m-2/s PAR) conditions.";
String long_name "Light Conditions";
String units "unitless";
}
attached {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 33.0;
String bcodmo_name "cell_concentration";
String description "This is the number of attached coccoliths observed per cell. This number represents an average of counts from at least 15 cells per replicate or sample.";
String long_name "Attached";
String units "coccoliths per cell";
}
attached_blankCorrected {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 32.8;
String bcodmo_name "cell_concentration";
String description "This is the number of attached coccoliths observed per cell with the number of coccoliths observed per cell from the blank samples subtracted to account for any coccoliths that might have remained after cells were de-lithed.";
String long_name "Attached Blank Corrected";
String units "coccoliths per cell";
}
mean_attached_blankCorrected {
Float32 _FillValue NaN;
Float32 actual_range 0.21, 30.72;
String bcodmo_name "mean";
String description "The average value for each set of three replicates.";
String long_name "Mean Attached Blank Corrected";
String units "coccoliths per cell";
}
stdev_attached_blankCorrected {
Float32 _FillValue NaN;
Float32 actual_range 0.37, 2.75;
String bcodmo_name "standard deviation";
String description "The standard deviation for each set of three replicates.";
String long_name "Stdev Attached Blank Corrected";
String units "coccoliths per cell";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Cultures:\\u00a0Pleurochrysis carterae\\u00a0cultures were maintained in
exponential growth phase under axenic conditions in semi-continuous batch
culture using L1-Si media prepared on 0.2 um-filtered, UV-sterilized,
autoclaved seawater.\\u00a0 Cultures were acclimated to one of
three\\u00a0pCO2\\u00a0treatments for > 9 generations before experiments were
performed.\\u00a0 Cultures were maintained in an incubator at 16.5 +/- 0.5 deg
C and 470 umol photons/m-2/s\\u00a0PAR.
pCO2: Carbonate chemistry was manipulated by bubbling cultures and prepared
media with 500 mL/min\\u00a0with 0.2 um-filtered 280, 380, or 750
ppm\\u00a0pCO2\\u00a0air.\\u00a0 The\\u00a0pCO2\\u00a0levels of the treatment air
were established using two mass flow controllers (Aalborg, Orangeburg, NY,
USA) for each treatment to precisely mix in-house compressed air and pure
CO2\\u00a0(Maine Oxy, Auburn, ME, USA).\\u00a0 The in-house compressed air was
stripped of CO2\\u00a0to less than 10 ppm CO2\\u00a0using a Puregas VCD
CO2\\u00a0Adsorber (Puregas, LLC, Broomfield, CO, USA).\\u00a0
The\\u00a0pCO2\\u00a0of the gas mixtures was stable to +/- 8
ppm.\\u00a0\\u00a0pCO2\\u00a0values of the cultures may be different than the
target levels due to biological activity.
Dissolution of existing coccoliths:\\u00a0 Coccoliths were dissolved by 1.75 M
HCl to drop the pH to 5.5 for 2 min.\\u00a0 Following the dissolution (de-
lithing), 1.75 M NaOH was added to bring the pH back to the respective
starting pH.\\u00a0 Dissolution of coccoliths was immediately confirmed by
looking at the cells under cross-polarized light microscopy to verify the
absence of birefringence indicative of CaCO3.\\u00a0 Dissolution was further
confirmed by filtering the acidified/neutralized sample onto a 0.4 um
polycarbonate filter.\\u00a0 Filters were mounted on stubs, sputter-coated with
gold using a Denton Desk IV sputter coater (Denton Vacuum, Moorestown, NJ,
USA), and imaged on a Zeiss Supra25 field emission scanning electron
microscope (Carl Zeiss Microscopy, LLC, Thornwood, NY, USA).\\u00a0 At least 15
cells per sample were imaged and the number of coccoliths/cell\\u00a0was
manually counted to determine the number of coccoliths that remained after the
acidification/neutralization dissolution step.
24 h incubation in either light or dark conditions:\\u00a0 To determine the
number of coccoliths formed (as a proxy for calcification rate) in 24 h in
either light or dark conditions, for each\\u00a0pCO2\\u00a0level, 15 mL of de-
lithed culture were added to 8 scintillation vials.\\u00a0 Three vials were
\\u2018light\\u2019 replicates, three vials were \\u2018dark\\u2019 replicates,
and two vials were poisoned with buffered formalin to serve as a
\\u2018light\\u2019 blank and a \\u2018dark\\u2019 blank.\\u00a0 Dark replicate and
blank vials were covered in black aluminum foil and all vials were incubated
together for 24 h in an incubator set at 16.5 +/- 0.5 deg C and 470 umol
photons/m-2/s\\u00a0PAR on a 14-10 h light-dark cycle.\\u00a0The experiment was
timed to start when the lights in the incubator turned on in the morning, thus
the \\u2018light\\u2019 replicates were exposed to light for 14 of 24 h.\\u00a0
Determination of attached coccoliths:\\u00a0\\u00a0Coccolith formation was
assessed by counting the number of coccoliths formed during the incubation
period.\\u00a0 After the 24 h incubation period, each replicate and blank vial
was filtered onto a 0.4 um polycarbonate filters.\\u00a0 Filters were mounted
on stubs, sputter-coated with gold using a Denton Desk IV sputter coater
(Denton Vacuum, Moorestown, NJ, USA), and imaged on a Zeiss Supra25 field
emission SEM (Carl Zeiss Microscopy, LLC, Thornwood, NY, USA).\\u00a0 At least
15 cells per replicate were imaged and the number of coccoliths/cell\\u00a0was
manually counted.\\u00a0 The counted coccoliths represented calcification
during the 24 h incubation period and the average number of coccoliths per
cell for each replicate and blank is reported.";
String awards_0_award_nid "514411";
String awards_0_award_number "OCE-1220068";
String awards_0_data_url "http://nsf.gov/awardsearch/showAward?AWD_ID=1220068";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Light-Dark Calcification
W. Balch and D. Fields, PIs
Version 4 November 2016";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2016-11-04T21:25:51Z";
String date_modified "2019-04-18T15:55:03Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.664013.1";
String history
"2024-12-03T17:22:55Z (local files)
2024-12-03T17:22:55Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_664013.html";
String infoUrl "https://www.bco-dmo.org/dataset/664013";
String institution "BCO-DMO";
String instruments_0_acronym "in-situ incubator";
String instruments_0_dataset_instrument_description "Dark replicate and blank vials were covered in black aluminum foil and all vials were incubated together for 24 h in an incubator set at 16.5 +/- 0.5 deg C and 470 umol photons/m-2/s PAR on a 14-10 h light-dark cycle.";
String instruments_0_dataset_instrument_nid "664040";
String instruments_0_description "A device on shipboard or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/82/";
String instruments_0_instrument_name "In-situ incubator";
String instruments_0_instrument_nid "494";
String instruments_0_supplied_name "Incubator";
String instruments_1_acronym "pH Sensor";
String instruments_1_dataset_instrument_description "Orion ROSS electrode was connected to an Orion Star A211 Benchtop pH meter (ThermoFisher Scientific, Waltham, MA, USA)";
String instruments_1_dataset_instrument_nid "664025";
String instruments_1_description "General term for an instrument that measures the pH or how acidic or basic a solution is.";
String instruments_1_instrument_name "pH Sensor";
String instruments_1_instrument_nid "674";
String instruments_1_supplied_name "Orion ROSS electrode";
String instruments_2_dataset_instrument_description "Carl Zeiss Microscopy, LLC, Thornwood, NY, USA";
String instruments_2_dataset_instrument_nid "664039";
String instruments_2_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB07/";
String instruments_2_instrument_name "Microscope-Electron";
String instruments_2_instrument_nid "709";
String instruments_2_supplied_name "Zeiss Supra25 field emission SEM";
String instruments_3_acronym "MFC";
String instruments_3_dataset_instrument_description "Indicate and control set flow rates of gases. Manufactured in Orangeburg, NY USA.";
String instruments_3_dataset_instrument_nid "664022";
String instruments_3_description "Mass Flow Controller (MFC) - A device used to measure and control the flow of fluids and gases";
String instruments_3_instrument_name "Mass Flow Controller";
String instruments_3_instrument_nid "712";
String instruments_3_supplied_name "Aalborg Mass Flow Controller";
String instruments_4_acronym "CO2 Adsorber";
String instruments_4_dataset_instrument_description "Instrument stripped compressed air of CO2";
String instruments_4_dataset_instrument_nid "664023";
String instruments_4_description "CO2 Adsorber - an instrument designed to remove CO2 and moisture from compressed air.";
String instruments_4_instrument_name "CO2 Adsorber";
String instruments_4_instrument_nid "651526";
String instruments_4_supplied_name "Puregas VCD CO2 Adsorber";
String instruments_5_acronym "Sputter Coater";
String instruments_5_dataset_instrument_description "Filters were mounted on stubs, sputter-coated with gold using a Denton Desk IV sputter coater (Denton Vacuum, Moorestown, NJ, USA).";
String instruments_5_dataset_instrument_nid "664042";
String instruments_5_description "Sputter coating is the standard method for preparing non-conducting or poorly conducting specimens prior to observation in a scanning electron microscope (SEM)";
String instruments_5_instrument_name "Sputter Coater";
String instruments_5_instrument_nid "664041";
String instruments_5_supplied_name "Denton Desk IV sputter coater";
String keywords "attached, attached_blankCorrected, bco, bco-dmo, biological, blank, carbon, carbon dioxide, chemical, co2, conditions, corrected, data, dataset, deviation, dioxide, dmo, erddap, light, light_conditions, management, mean, mean_attached_blankCorrected, oceanography, office, pCO2_treatment, preliminary, sample, standard, standard deviation, stdev, stdev_attached_blankCorrected, treatment";
String license "https://www.bco-dmo.org/dataset/664013/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/664013";
String param_mapping "{'664013': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/664013/parameters";
String people_0_affiliation "Bigelow Laboratory for Ocean Sciences";
String people_0_person_name "William M. Balch";
String people_0_person_nid "50650";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Bigelow Laboratory for Ocean Sciences";
String people_1_person_name "David Fields";
String people_1_person_nid "51141";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Bigelow Laboratory for Ocean Sciences";
String people_2_person_name "William M. Balch";
String people_2_person_nid "50650";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Bigelow Laboratory for Ocean Sciences";
String people_3_person_name "Meredith White";
String people_3_person_nid "514420";
String people_3_role "Contact";
String people_3_role_type "related";
String people_4_affiliation "Woods Hole Oceanographic Institution";
String people_4_affiliation_acronym "WHOI BCO-DMO";
String people_4_person_name "Hannah Ake";
String people_4_person_nid "650173";
String people_4_role "BCO-DMO Data Manager";
String people_4_role_type "related";
String project "OA_Copes_Coccoliths";
String projects_0_acronym "OA_Copes_Coccoliths";
String projects_0_description
"(Extracted from the NSF award abstract)
Ocean acidification is one of the most pressing marine science issues of our time, with potential biological impacts spanning all marine phyla and potential societal impacts affecting man's relationship to the sea. Rising levels of atmospheric pCO2 are increasing the acidity of the world oceans. It is generally held that average surface ocean pH has already declined by 0.1 pH units relative to the pre-industrial level (Orr et al., 2005), and is projected to decrease 0.3 to 0.46 units by the end of this century, depending on CO2 emission scenarios (Caldeira and Wickett, 2005). The overall goal of this research is to parameterize how changes in pCO2 levels could alter the biological and alkalinity pumps of the world ocean. Specifically, the direct and indirect effects of ocean acidification will be examined within a simple, controlled predator/prey system containing a single prey phytoplankton species (the coccolithophore, Emiliania huxleyi) and a single predator (the oceanic metazoan grazer, Calanus finmarchicus). The experiments are designed to elucidate both direct effects (i.e. effects of ocean acidification on the individual organisms only) and interactive effects (i.e. effects on the combined predator/prey system). Interactive experiments with phytoplankton prey and zooplankton predator are a critical starting point for predicting the overall impact of ocean acidification in marine ecosystems. To meet these goals, a state-of-the-art facility will be constructed with growth chambers that are calibrated and have highly-controlled pH and alkalinity levels. The strength of this approach lies in meticulous calibration and redundant measurements that will be made to ensure that conditions within the chambers are well described and tightly monitored for DIC levels. Growth and calcification rates in coccolithophores and the developmental rates, morphological and behavioral effects on copepods will be measured. The PIC and POC in the algae and the excreted fecal pellets will be monitored for changes in the PIC/POC ratio, a key parameter for modeling feedback mechanisms for rising pCO2 levels. In addition, 14C experiments are planned to measure calcification rates in coccolithophores and dissolution rates as a result of grazing. These key experiments will verify closure in the mass balance of PIC, allowing the determination of actual dissolution rates of PIC within the guts of copepod grazers.";
String projects_0_end_date "2015-07";
String projects_0_geolocation "Laboratory experiments; East Boothbay, Maine";
String projects_0_name "Effects of ocean acidification on Emiliania huxleyi and Calanus finmarchicus; insights into the oceanic alkalinity and biological carbon pumps";
String projects_0_project_nid "514415";
String projects_0_start_date "2012-08";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Light-dark calcification rates of Pleurochrysis carterae analyzed at Bigelow Laboratory in 2013 (OA Copes Coccoliths project)";
String title "[Pleurochrysis carterae light-dark calcification] - Light-dark calcification rates of Pleurochrysis carterae analyzed at Bigelow Laboratory in 2013 (OA Copes Coccoliths project) (Effects of ocean acidification on Emiliania huxleyi and Calanus finmarchicus; insights into the oceanic alkalinity and biological carbon pumps)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.