Accessing BCO-DMO data
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| Dataset Title: | [EN556 seawater measurements and initial conditions] - Measurements of nutrients, bacterial cell concentration and bacterial production from RV/ Endeavor EN556, June 2015 (Patterns of activities project) (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_717577) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
cruise_id {
String bcodmo_name "cruise_id";
String description "cruise identifier";
String long_name "Cruise Id";
String units "unitless";
}
station {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 8;
String bcodmo_name "station";
String description "station number";
String long_name "Station";
String units "unitless";
}
cast {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 14;
String bcodmo_name "cast";
String description "cast number";
String long_name "Cast";
String units "unitless";
}
depth_id {
String bcodmo_name "depth_comment";
String description "depth description: sequence of depths sampled with 1 is surface and higher numbers at greater depths";
String long_name "Depth";
String standard_name "depth";
String units "unitless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 1.0, 4574.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "actual depth at which water collected";
String ioos_category "Location";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
lat_degdecmin {
String bcodmo_name "latitude";
String description "latitude formatted as degrees.decimal_minutes";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees and decimal minutes";
}
lon_degdecmin_W {
String bcodmo_name "longitude";
String description "longitude formatted as degrees.decimal_minutes";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees and decimal minutes";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 37.6018, 40.7072;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "latitude; north is positive";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String source_name "lat_dec";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -71.028, -68.4037;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude; north is positive";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "lon_dec";
String standard_name "longitude";
String units "degrees_east";
}
temp {
Float32 _FillValue NaN;
Float32 actual_range 2.16, 18.7;
String bcodmo_name "temperature";
String description "water temperature as determined by CTD";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees Celsius";
}
salinity {
Float32 _FillValue NaN;
Float32 actual_range 34.879, 36.392;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "salinity as determined by CTD";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "per mil";
}
timepoint {
String bcodmo_name "time_point";
String description "sampling time point (0; 1; 2; etc.) post-incubation";
String long_name "Timepoint";
String units "unitless";
}
time_elapsed_hr {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 0;
String bcodmo_name "time_elapsed";
String description "hours elapsed to reach a specific timepoint";
String long_name "Time Elapsed Hr";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "hours";
}
NO2_NO3_uM {
Float32 _FillValue NaN;
Float32 actual_range 0.04, 19.59;
String bcodmo_name "NO3_NO2";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "nitrite plus nitrate concentration";
String long_name "Mole Concentration Of Nitrate In Sea Water";
String units "micromolar";
}
NH4_uM {
Float32 _FillValue NaN;
Float32 actual_range 0.24, 1.99;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "ammonium concentration";
String long_name "Mole Concentration Of Ammonium In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "micromolar";
}
PO4_uM {
Float32 _FillValue NaN;
Float32 actual_range 0.27, 1.39;
String bcodmo_name "PO4";
String description "phosphate concentration";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "micromolar";
}
DOC_uM {
Float32 _FillValue NaN;
Float32 actual_range 34.48, 137.14;
String bcodmo_name "DOC";
String description "dissolved organic carbon concentration";
String long_name "DOC U M";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromolar";
}
cells_per_mL {
Int32 _FillValue 2147483647;
Int32 actual_range 4043, 378165;
String bcodmo_name "cell_concentration";
String description "prokaryotic cell counts per mL seawater";
String long_name "Cells Per M L";
String units "cells/milliliter";
}
Leu_3H_rep_1 {
Float32 _FillValue NaN;
Float32 actual_range 0.28, 92.22;
String bcodmo_name "leuc_incorp";
String description "replicate 1 of leucine incorporation rate (bacterial protein production)";
String long_name "Leu 3 H Rep 1";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/UPLERIP4/";
String units "pico mol leucine/hour";
}
Leu_3H_rep_2 {
Float32 _FillValue NaN;
Float32 actual_range 0.22, 46.16;
String bcodmo_name "leuc_incorp";
String description "replicate 2 of leucine incorporation rate (bacterial protein production)";
String long_name "Leu 3 H Rep 2";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/UPLERIP4/";
String units "pico mol leucine/hour";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Seawater was transferred to a 20 L carboy that were rinsed three times with
water from the sampling depth and then filled with seawater from three Niskin
bottles, using silicone tubing that had been acid washed then rinsed with
distilled water prior to use. From each carboy, water was dispensed into
smaller glass containers that were cleaned and pre-rinsed three times with
water from the carboy prior to dispensing. This water was used to measure cell
counts, bacterial productivity, and the activities of polysaccharide
hydrolases, peptidases, and glucosidases. A separate glass Duran bottle was
filled with seawater from the carboy and sterilized in an autoclave for 20-30
minutes to serve as a killed control for microbial activity measurements.
Bacterial cells were counted by flow cytometry following the procedure
described in Gasol and Del Giorgio [2000]. Water samples (2 mL) were fixed
with 0.1% glutaraldehyde (final concentration) for 10 min at room temperature
in the dark, and stored frozen at -80\\u00b0C. Prior to analysis, thawed
samples were pipetted through a cell strainer (Flowmi, 70 m porosity) and
stained with SYBR Green I for 15 min on ice in the dark. Counts were performed
on a FACSCalibur flow cytometer (Becton-Dickson) using fluorescent
microspheres (Molecular Probes) of 1 \\u00b5m in diameter as internal size
standard. Cells were enumerated according to their green fluorescence and
right angle scatter using\\u00a0the FloJo 7.6.1\\u00a0software.
Samples were analyzed for nutrients and DOC content modified after Grasshoff
and Kremling [1999]. Clean and acid washed syringes, tubing, and filter
holders were used for each sampling. Duplicate DOC samples were filtered using
the same 60 cc syringe through combusted glass fiber filters (Whatman
1825-025) secured within a polycarbonate filter holder into two combusted 20
mL scintillation vials and acidified using 100 \\u03bcL of 50% phosphoric acid
then immediately frozen at -20\\u00b0C.\\u00a0 DOC samples were analyzed by
high-temperature catalytic oxidation (HTCO) using a Shimadzu Total Organic
Carbon analyzer (TOC-8000A/5050A).
Following DOC sampling, nutrient samples were analyzed for colorimetric
determination of ammonia, nitrate, nitrite, and soluble reactive phosphorous
[Grasshoff and Kremling, 1999]. Samples were syringe filtered using a 60 cc
syringe through 0.2 \\u03bcm syringe filters (Sartorius Minisart 17823) into 50
mL Falcon tubes and immediately frozen at -20\\u00b0C aboard ship. A 15 mL
subsample was sent to the LSU-College of the Coast & Environment, Wetland,
Biogeochemistry, Analytical Services (WBAS) facility for analysis.\\u00a0
Bacterial protein production was measured from 3H-leucine incorporation by
heterotrophic bacteria using the cold trichloroacetic acid (TCA) and
microcentrifuge extraction method [as in Kirchman, 2001]. All work was
performed aboard ship. In brief, triplicate live samples of 1.5 mL seawater as
well as one 100% (w/v) TCA-killed control were incubated with 23 \\u03bcL of
L-[3,4,5-3H(N)]-Leucine (PerkinElmer, NET460250UC) for between 4 and 24 hours
in the dark at as close to in situ temperature as possible. Live samples were
then killed with 89 \\u03bcL of 100% (w/v) TCA and centrifuged (10,000 rpm at
4\\u00b0C for 10 min) to pelletize cell material.\\u00a0 The supernatant liquid
was removed and 1 mL of 5% (w/v) TCA solution was added, followed by vortex
mixing and centrifugation. Supernatant removal, mixing, and centrifugation
were repeated using 1 mL of 80% ethanol solution.\\u00a0 Finally, the
supernatant liquid was removed and each sample was dried overnight.\\u00a0
After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher
SX23-5) was added and incorporated radioactivity was measured using an LSA
scintillation counter (PerkinElmer Tri-Carb 2910TR). Leucine incorporation
rate was calculated from the incorporated radioactivity, compared to 1 mL of
scintillation cocktail spiked with 23 \\u03bcL of L-[3,4,5-3H(N)]-Leucine
radioactivity, divided by incubation time.";
String awards_0_award_nid "712358";
String awards_0_award_number "OCE-1332881";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332881";
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 "Henrietta N Edmonds";
String awards_0_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Bulk water experiment: nutrients, bacterial cell counts and productivity
EN556, Apr/May 2015
C. Arnosti (UNC)
version: 2017-10-27";
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 "Final and no updates";
String date_created "2017-10-24T19:36:42Z";
String date_modified "2020-05-13T16:58:40Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.717577.1";
Float64 Easternmost_Easting -68.4037;
Float64 geospatial_lat_max 40.7072;
Float64 geospatial_lat_min 37.6018;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -68.4037;
Float64 geospatial_lon_min -71.028;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 4574.0;
Float64 geospatial_vertical_min 1.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-31T01:27:17Z (local files)
2024-12-31T01:27:17Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_717577.html";
String infoUrl "https://www.bco-dmo.org/dataset/717577";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_description "Used to collect water for large volume mesocosm experiments";
String instruments_0_dataset_instrument_nid "717583";
String instruments_0_description "A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/";
String instruments_0_instrument_name "Niskin bottle";
String instruments_0_instrument_nid "413";
String instruments_0_supplied_name "20 liter Niskin bottles";
String instruments_1_acronym "LSC";
String instruments_1_dataset_instrument_description "Used to measure incorporated radioactive 3H-leucine";
String instruments_1_dataset_instrument_nid "717586";
String instruments_1_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_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB21/";
String instruments_1_instrument_name "Liquid Scintillation Counter";
String instruments_1_instrument_nid "624";
String instruments_1_supplied_name "LSA scintillation counter, PerkinElmer Tri-Carb 2910TR";
String instruments_2_acronym "TOC analyzer";
String instruments_2_dataset_instrument_description "Used to measure dissolved organic carbon concentration in the samples.";
String instruments_2_dataset_instrument_nid "717587";
String instruments_2_description "A unit that accurately determines the carbon concentrations of organic compounds typically by detecting and measuring its combustion product (CO2). See description document at: http://bcodata.whoi.edu/LaurentianGreatLakes_Chemistry/bs116.pdf";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB04/";
String instruments_2_instrument_name "Total Organic Carbon Analyzer";
String instruments_2_instrument_nid "652";
String instruments_2_supplied_name "Shimadzu Total Organic Carbon analyzer (TOC-8000A/5050A)";
String instruments_3_dataset_instrument_nid "717585";
String instruments_3_description "A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.";
String instruments_3_instrument_name "Shipboard Incubator";
String instruments_3_instrument_nid "629001";
String instruments_4_dataset_instrument_description "Used to concentrate cell material.";
String instruments_4_dataset_instrument_nid "717584";
String instruments_4_description "A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.";
String instruments_4_instrument_name "Centrifuge";
String instruments_4_instrument_nid "629890";
String keywords "ammonia, ammonium, bco, bco-dmo, biological, cast, cells, cells_per_mL, chemical, chemistry, commerce, concentration, cruise, cruise_id, data, dataset, density, department, depth, depth_id, depth_m, dmo, doc, DOC_uM, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Salinity/Density > Salinity, elapsed, erddap, lat_degdecmin, latitude, leu, Leu_3H_rep_1, Leu_3H_rep_2, lon_degdecmin_W, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, n02, nh4, NH4_uM, nitrate, NO2_NO3_uM, no3, ocean, oceanography, oceans, office, per, phosphate, po4, PO4_uM, practical, preliminary, rep, salinity, science, sea, sea_water_practical_salinity, seawater, station, temperature, time, time_elapsed_hr, timepoint, u, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/717577/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/717577";
Float64 Northernmost_Northing 40.7072;
String param_mapping "{'717577': {'lat_dec': 'flag - latitude', 'depth_m': 'master - depth', 'lon_dec': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/717577/parameters";
String people_0_affiliation "University of North Carolina at Chapel Hill";
String people_0_affiliation_acronym "UNC-Chapel Hill";
String people_0_person_name "Carol Arnosti";
String people_0_person_nid "661940";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Nancy Copley";
String people_1_person_nid "50396";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Patterns of activities";
String projects_0_acronym "Patterns of activities";
String projects_0_description
"NSF Award Abstract:
Heterotrophic microbial communities are key players in the marine carbon cycle, transforming and respiring organic carbon, regenerating nutrients, and acting as the final filter in sediments through which organic matter passes before long-term burial. Microbially-driven carbon cycling in the ocean profoundly affects the global carbon cycle, but key factors determining rates and locations of organic matter remineralization are unclear. In this study, researchers from the University of North Carolina at Chapel Hill will investigate the ability of pelagic microbial communities to initiate the remineralization of polysaccharides and proteins, which together constitute a major pool of organic matter in the ocean. Results from this study will be predictive on a large scale regarding the nature of the microbial response to organic matter input, and will provide a mechanistic framework for interpreting organic matter reactivity in the ocean.
Broader Impacts: This study will provide scientific training for undergraduate and graduate students from underrepresented groups. The project will also involve German colleagues, thus strengthening international scientific collaboration.";
String projects_0_end_date "2017-07";
String projects_0_geolocation "Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland";
String projects_0_name "Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?";
String projects_0_project_nid "712359";
String projects_0_start_date "2013-08";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 37.6018;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "cruise_id,timepoint,time_elapsed_hr";
String summary "Nutrients, bacterial cell counts, and bacterial protein production as measured by 3H-leucine incorporation from the 'bulk water experiments'. Water was collected on EN556. See Niskin Bottle and Cast List EN556 to link specific casts and bottles to each experiment: https://www.bco-dmo.org/dataset/717427.";
String title "[EN556 seawater measurements and initial conditions] - Measurements of nutrients, bacterial cell concentration and bacterial production from RV/Endeavor EN556, June 2015 (Patterns of activities project) (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?)";
String version "1";
Float64 Westernmost_Easting -71.028;
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.