Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [MRP sediments with pretreatment] - Molybdate reactive phosphorus concentrations in NMR pretreatment extracts from sediment samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011 (Potential phosphorus uptake mechanisms of the deep sedimentary biosphere) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_816527) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
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Attributes {
s {
Extract {
String bcodmo_name "sample_descrip";
String description "Extraction solution";
String long_name "Extract";
String units "unitless";
}
Step {
String bcodmo_name "sample_descrip";
String description "Step in the sequential extraction scheme (1–4)";
String long_name "Step";
String units "unitless";
}
Dilution {
String bcodmo_name "treatment";
String description "Sample dilution or \"None\"";
String long_name "Dilution";
String units "unitless";
}
Date {
String bcodmo_name "date";
String description "Date the samples were analyzed in ISO 8601 format yyyy-mm-dd";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "Date";
String time_precision "1970-01-01";
String units "unitless";
}
Sample_ID {
String bcodmo_name "sample";
String description "Unique sample identifier";
String long_name "Sample ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Analyte_Name {
String bcodmo_name "sample_descrip";
String description "Element analyzed";
String long_name "Analyte Name";
String units "unitless";
}
Peak_Concentration {
Float32 _FillValue NaN;
Float32 actual_range 0.029, 10.3;
String bcodmo_name "PO4";
String description "Phosphate concentration (uncorrected)";
String long_name "Peak Concentration";
String units "micromolar (uM)";
}
Peak_Area {
Float32 _FillValue NaN;
Float32 actual_range -0.018, 1.55;
String bcodmo_name "unknown";
String description "Peak area";
String long_name "Peak Area";
String units "volts";
}
Peak_Height {
Float32 _FillValue NaN;
Float32 actual_range -0.007, 0.546;
String bcodmo_name "unknown";
String description "Peak height";
String long_name "Peak Height";
String units "volts";
}
Blank_corrected {
Float32 _FillValue NaN;
Float32 actual_range 0.123, 2.761;
String bcodmo_name "sample_descrip";
String description "Concentration adjusted after blank";
String long_name "Blank Corrected";
String units "unitless";
}
Actual_PO4 {
Float32 _FillValue NaN;
Float32 actual_range 1.23, 57.4;
String bcodmo_name "PO4";
String description "Concentration corrected for dilution";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "micromolar (uM)";
}
P_extracted {
Float32 _FillValue NaN;
Float32 actual_range 0.277, 12.915;
String bcodmo_name "PO4";
String description "Amount of phosphorus extracted";
String long_name "P Extracted";
String units "micromoles (umol)";
}
Sed_mass {
Float32 _FillValue NaN;
Float32 actual_range 1.5, 1.506;
String bcodmo_name "mass_dry";
String description "Dried sediment mass";
String long_name "Sed Mass";
String units "grams (g)";
}
PO4 {
Float32 _FillValue NaN;
Float32 actual_range 0.184, 8.583;
String bcodmo_name "PO4";
String description "Micromoles of phosphorus per gram of sediment (ground dry weight)";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "micromoles per gram (umol/g)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Location:\\u00a0North Atlantic, western flank of the mid-Atlantic
Ridge\\u00a022.75589 N 46.08125 W
Methodology:
Prior to the extraction, we freeze-dried, ground and sieved sediment samples
to less than 125 \\u03bcm (Ruttenberg 1992). For a given sample, we weighed
four sample replicates (2 g) and placed each in 250 mL HDPE bottles. Sodium
dithionite (F.W. 147.12 g/mol; 7.4 g) was added to each sample split, followed
by 200 mL of citrate-bicarbonate solution (pH 7.6). This step produces
effervescence, so the solution should be added slowly to the sample. We shook
samples for 8 h and then centrifuged them at 3,700 rpm for 15 min. We filtered
the supernatants with a 0.4 \\u03bcm polycarbonate filter. We took 20 mL
aliquots from the filtrate for each sample split for MRP and total P analyses,
and kept them refrigerated until analysis within 24 h. We added 200 mL of
ultrapure water to the solid residue for each sample split as a wash step
after the above reductive step, shook samples for 2 h, and then centrifuged
them at 3,700 rpm for 15 min. We filtered the supernatants with 0.4 \\u03bcm
polycarbonate filters and set aside 20 mL of filtrate from each sample split
for MRP and total P analyses. We then extracted the solid sample residues in
200 mL of sodium acetate buffer (pH 4.0) for 6 h. At the end of this
extraction step, we centrifuged the bottles at 3,700 rpm for 15 min, filtered
the supernatants with 0.4 \\u03bcm polycarbonate filters and took a 20 mL
aliquot of filtrate from each sample split for MRP and total P analyses. We
added 200 mL of ultrapure water to the solid residue for each sample split as
a wash step, shook samples for 2 h, and then centrifuged them at 3,700 rpm for
15 min.\\u00a0 We filtered the supernatants with 0.4 \\u03bcm polycarbonate
filters and set aside 20 mL of filtrate from each sample split for MRP and
total P analyses. We repeated the water rinse step, and collected aliquots for
MRP and total P analyses as in the previous steps. The concentrations of\\u00a0
MRP were determined as described below.
The MRP concentrations were measured on a QuikChem 8000 automated ion
analyzer. Standards were prepared with the same solutions used for the
extraction step to minimize matrix effects on P measurements. Sediment
extracts and standards (0 \\u2013 30 \\u03bcM PO4) were diluted ten-fold to
prevent matrix interference with color development. The detection limit for P
on this instrument is 0.2 \\u03bcM. We derived MUP concentrations by
subtracting MRP from total P concentrations, which are included in a different
spreadsheet.";
String awards_0_award_nid "554980";
String awards_0_award_number "OCE-0939564";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564";
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
"Iodp336 mrp sed pre
PI: Adina Paytan
Data Version 1: 2020-06-23";
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 dataset_current_state "Preliminary and in progress";
String date_created "2020-06-23T17:56:03Z";
String date_modified "2020-06-30T18:11:00Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.816527.1";
String history
"2024-11-15T01:25:32Z (local files)
2024-11-15T01:25:32Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_816527.html";
String infoUrl "https://www.bco-dmo.org/dataset/816527";
String institution "BCO-DMO";
String instruments_0_acronym "FIA";
String instruments_0_dataset_instrument_nid "816548";
String instruments_0_description "An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB36/";
String instruments_0_instrument_name "Flow Injection Analyzer";
String instruments_0_instrument_nid "657";
String instruments_0_supplied_name "QuikChem 8000 automated ion analyzer";
String keywords "Actual_PO4, analyte, Analyte_Name, area, bco, bco-dmo, biological, blank, Blank_corrected, chemical, chemistry, concentration, corrected, data, dataset, date, dilution, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Phosphate, erddap, extract, extracted, height, management, mass, mass_concentration_of_phosphate_in_sea_water, name, ocean, oceanography, oceans, office, P_extracted, peak, Peak_Area, Peak_Concentration, Peak_Height, phosphate, po4, preliminary, sample, Sample_ID, science, sea, seawater, sed, Sed_mass, step, time, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/816527/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/816527";
String param_mapping "{'816527': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/816527/parameters";
String people_0_affiliation "University of California-Santa Cruz";
String people_0_affiliation_acronym "UC Santa Cruz";
String people_0_person_name "Adina Paytan";
String people_0_person_nid "50821";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Santa Cruz";
String people_1_affiliation_acronym "UC Santa Cruz";
String people_1_person_name "Dr Delphine Defforey";
String people_1_person_nid "664058";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Amber D. York";
String people_2_person_nid "643627";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Deep sea sediments";
String projects_0_acronym "Deep sea sediments";
String projects_0_description
"The goal of this project is to explore potential microbial P uptake mechanisms in marine sediments beneath the North Atlantic Gyre and their effects on the relative distribution of organic P compounds as a function of burial depth and changing redox conditions. We use a combination of metagenomic analyses and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) to investigate (1) the presence of microbial functional genes pertaining to P uptake and metabolism and (2) the possible P substrates for the deep biosphere in these oligotrophic sediments.
NSF C-DEBI Award #156246 to Dr. Adina Paytan
NSF C-DEBI Award #157598 to Dr. Delphine Defforey";
String projects_0_end_date "2015-04";
String projects_0_geolocation "Mid-Atlantic Ridge flank";
String projects_0_name "Potential phosphorus uptake mechanisms of the deep sedimentary biosphere";
String projects_0_project_nid "664073";
String projects_0_start_date "2015-03";
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 subsetVariables "Analyte_Name";
String summary "Molybdate reactive phosphorus concentrations in nuclear magnetic resonance (NMR) pretreatment extracts from sediment samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011. Samples were analyzed in 2016.";
String title "[MRP sediments with pretreatment] - Molybdate reactive phosphorus concentrations in NMR pretreatment extracts from sediment samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011 (Potential phosphorus uptake mechanisms of the deep sedimentary biosphere)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.5";
}
}
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.