Accessing BCO-DMO data
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| Dataset Title: | [Multi-core Arctic sediment data] - Sediment geochemical and microbial activity data collected on R/V Oden along the East Siberian Arctic Shelf from 2014 (ESAS Water Column Methane project) (The East Siberian Arctic Shelf as a Source of Atmospheric Methane: First Approach to Quantitative Assessment) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_660527) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
year {
Int16 _FillValue 32767;
Int16 actual_range 2014, 2014;
String bcodmo_name "year";
String description "Year of sampling; YYYY";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
month {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 7, 7;
String bcodmo_name "month";
String description "Month of sampling; mm";
String long_name "Month";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/";
String units "unitless";
}
collection_type {
String bcodmo_name "sampling_method";
String description "Method used to collect samples";
String long_name "Collection Type";
String units "unitless";
}
station {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 63;
String bcodmo_name "station";
String description "Station where sampling occurred";
String long_name "Station";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 74.44, 78.942;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range 125.243, 172.361;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
sample_ID {
String bcodmo_name "sample";
String description "PI issued sample ID number";
String long_name "Sample ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
sediment_depth {
Float64 _FillValue NaN;
Float64 actual_range -5.0, 52.5;
String bcodmo_name "depth_core";
String description "Depth of sediment; negative depth values represent overlying water samples";
String long_name "Sediment Depth";
String units "centimeters";
}
sed_CH4 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 53.52;
String bcodmo_name "unknown";
String description "Methane concentration in sediment";
String long_name "Sed CH4";
String units "microns (uM)";
}
AOM_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.05, 247.62;
String bcodmo_name "unknown";
String description "Anaerobic Oxidation of Methane; CH4 oxidized in sediment per day; Rates were measured at stations 13 and 23 only.";
String long_name "AOM Rate";
String units "picomole per centimeter per day (pmol/cm/day)";
}
turnover_14_CH3COO_MOG {
String bcodmo_name "unknown";
String description "14-CH3COO methanogenesis turnover; Rates were measured at stations 13 and 23 only.";
String long_name "Turnover 14 CH3 COO MOG";
String units "percent";
}
turnover_H14_CO3_MOG {
String bcodmo_name "unknown";
String description "H14-CO3 methanogenesis turnover; Rates were measured at stations 13 and 23 only.";
String long_name "Turnover H14 CO3 MOG";
String units "percent";
}
turnover_SRR {
Float32 _FillValue NaN;
Float32 actual_range 0.002, 0.127;
String bcodmo_name "unknown";
String description "Sulfate reduction methanogenesis turnover; Rates were measured at stations 13 and 23 only.";
String long_name "Turnover SRR";
String units "percent";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Acquisition methods are described in the following publication: Orcutt, B.N.
et al. 2005
Core sectioning, porewater\\u00a0collection\\u00a0and analysis
At each sampling site, sediment sub-samples were collected for porewater
analyses and at selected depths for microbial rate assays (AOM, anaerobic
oxidation of methane oxidation; methanogenesis (MOG) from bicarbonate and
acetate). Sediment was expelled from core liner using a hydraulic extruder
under anoxic conditions. The depth intervals for extrusion varied. At each
depth interval, a sub-sample was collected into a cut-off syringe for
dissolved methane concentration quantification. Another 5 mL\\u00a0sub-
sample\\u00a0was collected into pre-weighed and pre-combusted glass vial for
determination of porosity (determined by the change in weight after drying at
80 degrees celsius to a constant weight). The remaining material was used for
porewater extraction. Sample fixation and\\u00a0analyses\\u00a0for dissolved
constituents followed the methods of Joye et al. (2010).\\u00a0
Microbial Activity Measurements\\u00a0
To determine AOM and MOG rates, 8 to 12 sub-samples (5 cm3) were collected
from a core by manual insertion of a glass tube. For AOM, 100 uL of
dissolved\\u00a014CH4\\u00a0tracer (about 2,000,000 DPM as gas) was injected
into each core. Samples were incubated for 36 to 48 hours at\\u00a0in
situ\\u00a0temperature.\\u00a0 Following incubation, samples were transferred to
20 mL glass vials containing 2 mL of 2M NaOH (which served to arrest
biological activity and fix\\u00a014CO2\\u00a0as\\u00a014C-HCO3-).\\u00a0 Each
vial was sealed with a\\u00a0teflon-lined screw cap, vortexed to mix the sample
and base, and immediately frozen. Time zero samples were fixed immediately
after radiotracer injection. The specific activity of the tracer substrate
(14CH4) was determined by injecting 50 uL directly into scintillation cocktail
(Scintiverse BD) followed by liquid scintillation counting. The accumulation
of 14C product (14CO2) was determined by acid digestion following the method
of Joye et al. (2010).\\u00a0 The AOM rate was calculated using equation 1:
AOM Rate = [CH4] x alphaCH4 /t x (a-14CO2/a-14CH4)\\u00a0\\u00a0
\\u00a0\\u00a0\\u00a0 \\u00a0\\u00a0\\u00a0 \\u00a0(Eq. 1)
Here, the AOM Rate is expressed as nmol CH4 oxidized per cm3 sediment per day
(nmol\\u00a0cm-3 d-1), [CH4] is the methane concentration (uM), alphaCH4 is the
isotope fractionation factor for AOM (1.06; (ALPERIN and REEBURGH, 1988)), t
is the incubation time (d), a-14CO2 is the activity of the product pool, and
a-14CH4 is the activity of the substrate pool. If methane concentration was
not available, the turnover time of the 14CH4 tracer is presented.
Rates of bicarbonate-based-methanogenesis and acetoclastic methanogenesis were
determined by incubating samples in gas-tight, closed-tube vessels without
headspace, to prevent the loss of gaseous 14CH4 product during sample
manipulation. These sample tubes were sealed using custom-designed plungers
(black Hungate stoppers with the lip removed containing a plastic
\\u201ctail\\u201d that was run through the stopper) were inserted at the base
of the tube; the sediment was then pushed via the plunger to the top of the
tube until a small amount protruded through the tube opening. A butyl rubber
septa\\u00a0was\\u00a0then eased into the tube opening to displace sediment in
contact with the atmosphere and close the tube, which was then sealed
with\\u00a0a open-top\\u00a0screw cap.\\u00a0 The rubber materials used in these
assays were boiled in 1N NaOH for 1 hour, followed by several rinses in
boiling milliQ, to leach potentially toxic substances. \\u00a0 \\u00a0
A volume of radiotracer solution (100 uL of 14C-HCO3- tracer (~1 x
107\\u00a0dpm\\u00a0in slightly alkaline milliQ\\u00a0water) or 1,2-14C-CH3COO-
tracer (~5 x 107\\u00a0dpm\\u00a0in slightly alkaline milliQ\\u00a0water)) was
injected into each sample. Samples were incubated as described above and then
2 ml of 2N NaOH was injected through the top stopper into each sample to
terminate biological activity (time zero samples were fixed prior to tracer
injection).\\u00a0 Samples were mixed to evenly distribute NaOH through the
sample.\\u00a0 Production of 14CH4 was quantified by stripping methane from the
tubes with an air carrier, converting the 14CH4 to 14CO2 in a combustion
furnace, and subsequent trapping of the 14CO2 in NaOH as carbonate (CRAGG et
al., 1990; CRILL and MARTENS, 1986).\\u00a0\\u00a0Activity\\u00a0of 14CO2 was
measured subsequently by liquid scintillation counting.\\u00a0
The rates of Bi-MOG and Ac-MOG rates were calculated using equations 2 and 3,
respectively:
Bi-MOG Rate = [HCO3-] x alphaHCO3/t x\\u00a0 (a-14CH4/a-H14CO3-) \\u00a0 \\u00a0
(Eq. 2)
Ac-MOG Rate = [CH3COO-] x alphaCH3COO-/t\\u00a0 x\\u00a0 (a-14CH4/a-14CH314COO-)
\\u00a0 \\u00a0 (Eq. 3)
Both rates are expressed as nmol HCO3- or CH3COO-, respectively, reduced cm-3
d-1, alphaHCO3\\u00a0and alphaCH3COO- are the isotope fractionation factors for
MOG (assumed to be 1.06). [HCO3-] and [CH3COO-] are the\\u00a0pore\\u00a0water
bicarbonate (mM) and acetate (uM) concentrations, respectively, t is
incubation time (d), a-14CH4 is the activity of the product pool, and a-H14CO3
and a-14CH314COO are the activities of the substrate pools. If samples for
substrate concentration determination were not available, the substrate
turnover constant instead of the rate is presented.
For water column methane oxidation rate assays, triplicate 20 mL of live water
(in addition to one 20 mL sample which was killed with ethanol (750 uL of pure
EtOH) before tracer addition) were transferred from the CTD into serum vials.
Samples were amended with 2 x 10^6 DPM of 3H-labeled-methane tracer and
incubated for 24 to 72 hours (linearity of activity was tested and confirmed).
After incubation, samples were fixed with ethanol, as above, and a sub-sample
to determine total sample activity (3H-methane + 3H-water) was collected.
Next, the sample was purged with nitrogen to remove the 3H-methane tracer and
a sub-sample was amended with scintillation fluid and counted on a shipboard
scintillation counter to determine the activity of tracer in the product of
3H-methane oxidation, 3H-water. The methane oxidation rate was calculated as:
MOX Rate = [methane concentration in nM] x alphaCH4/t\\u00a0 x\\u00a0 (a-3H-
H2O/a-3H-CH4-) \\u00a0 \\u00a0 (Eq. 3)";
String awards_0_award_nid "651766";
String awards_0_award_number "PLR-1023444";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1023444";
String awards_0_funder_name "NSF Division of Polar Programs";
String awards_0_funding_acronym "NSF PLR";
String awards_0_funding_source_nid "490497";
String awards_0_program_manager "Henrietta N Edmonds";
String awards_0_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Arctic Sediment Data
S. Joye and V. Samarkin, PIs
Version 4 October 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 "2016-10-04T21:16:40Z";
String date_modified "2019-04-22T21:24:55Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.660527.1";
Float64 Easternmost_Easting 172.361;
Float64 geospatial_lat_max 78.942;
Float64 geospatial_lat_min 74.44;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 172.361;
Float64 geospatial_lon_min 125.243;
String geospatial_lon_units "degrees_east";
String history
"2024-12-21T03:08:57Z (local files)
2024-12-21T03:08:57Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_660527.html";
String infoUrl "https://www.bco-dmo.org/dataset/660527";
String institution "BCO-DMO";
String instruments_0_acronym "CTD";
String instruments_0_dataset_instrument_description "Used to collect water column samples";
String instruments_0_dataset_instrument_nid "660538";
String instruments_0_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.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_0_instrument_name "CTD profiler";
String instruments_0_instrument_nid "417";
String instruments_0_supplied_name "CTD";
String instruments_1_acronym "Multi Corer";
String instruments_1_dataset_instrument_description "Core used in sampling";
String instruments_1_dataset_instrument_nid "660536";
String instruments_1_description "The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/51/";
String instruments_1_instrument_name "Multi Corer";
String instruments_1_instrument_nid "532";
String instruments_1_supplied_name "Multiple core";
String instruments_2_acronym "LSC";
String instruments_2_dataset_instrument_description "Used to determine activity of tracer substrate";
String instruments_2_dataset_instrument_nid "660537";
String instruments_2_description "Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB21/";
String instruments_2_instrument_name "Liquid Scintillation Counter";
String instruments_2_instrument_nid "624";
String instruments_2_supplied_name "Liquid scintillation counter";
String keywords "aom, AOM_rate, bco, bco-dmo, biological, carbonate, ch3, ch4, chemical, co3, collection, collection_type, coo, data, dataset, depth, dmo, erddap, h14, latitude, longitude, management, mog, month, oceanography, office, preliminary, rate, sample, sample_ID, sed, sed_CH4, sediment, sediment_depth, srr, station, turnover, turnover_14_CH3COO_MOG, turnover_H14_CO3_MOG, turnover_SRR, type, year";
String license "https://www.bco-dmo.org/dataset/660527/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/660527";
Float64 Northernmost_Northing 78.942;
String param_mapping "{'660527': {'lat': 'master - latitude', 'sediment_depth': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/660527/parameters";
String people_0_affiliation "University of Georgia";
String people_0_affiliation_acronym "UGA";
String people_0_person_name "Samantha B. Joye";
String people_0_person_nid "51421";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Georgia";
String people_1_affiliation_acronym "UGA";
String people_1_person_name "Vladimir Samarkin";
String people_1_person_nid "641543";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of Georgia";
String people_2_affiliation_acronym "UGA";
String people_2_person_name "Samantha B. Joye";
String people_2_person_nid "51421";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "ESAS Water Column Methane";
String projects_0_acronym "ESAS Water Column Methane";
String projects_0_description "We propose to study methane (CH4) release over the East Siberian Arctic shelf (ESAS), the largest (~10% of the world ocean shelf area) and the shallowest shelf (mean depth";
String projects_0_end_date "2015-08";
String projects_0_geolocation "East Siberian Arctic Shelf";
String projects_0_name "The East Siberian Arctic Shelf as a Source of Atmospheric Methane: First Approach to Quantitative Assessment";
String projects_0_project_nid "651769";
String projects_0_start_date "2010-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 74.44;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "year,month,collection_type";
String summary "Sediment geochemical and microbial activity data collected on R/V Oden along the East Siberian Arctic Shelf from 2014 (ESAS Water Column Methane project)";
String title "[Multi-core Arctic sediment data] - Sediment geochemical and microbial activity data collected on R/V Oden along the East Siberian Arctic Shelf from 2014 (ESAS Water Column Methane project) (The East Siberian Arctic Shelf as a Source of Atmospheric Methane: First Approach to Quantitative Assessment)";
String version "1";
Float64 Westernmost_Easting 125.243;
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.