Accessing BCO-DMO data
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| Dataset Title: | [SO248: GF FLA hydrolysis rates] - Microbial enzyme activities: polysaccharide hydrolase activities of gravity filtered seawater samples from the RV\Sonne cruise SO248 in the South and North Pacific, along 180 W, May, 2016 (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_743274) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
station_no {
String bcodmo_name "station";
String description "refers to station number for cruise";
String long_name "Station No";
String units "unitless";
}
cast_no {
String bcodmo_name "cast";
String description "cast number (refers to cast of CTD/Niskin bottles on cruise)";
String long_name "Cast No";
String units "unitless";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.46220786e+9, 1.46455818e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "date and time in ISO format (yyyy-mm-ddTHH:MM:SS";
String ioos_category "Time";
String long_name "ISO Date Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String source_name "ISO_DateTime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range -30.0008, 56.9999;
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 standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -176.4753, 180.0;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude; east is postivie";
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";
}
depth_no {
String bcodmo_name "unknown";
String description "sequence of depths sampled (1 is surface; 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 60.0, 1000.0;
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";
}
substrate {
String bcodmo_name "unknown";
String description "substrates for measurement of enzymatic activities. ara:arabinogalactan; chn:chondroitin sulfate; fuc:fucoidan; lam:laminarin ; pul:pullulan; xyl:xylan";
String long_name "Substrate";
String units "unitless";
}
timepoint {
String bcodmo_name "time_point";
String description "sampling point post-incubation";
String long_name "Timepoint";
String units "unitless";
}
time_elapsed_hr {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 627.4166667;
String bcodmo_name "time_elapsed";
String description "incubation time";
String long_name "Time Elapsed Hr";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "hours";
}
rep1_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.342319;
String bcodmo_name "unknown";
String description "replicate 1 hydrolysis rate";
String long_name "Rep1 Rate";
String units "nanomoles/liter/hour (nmol L-1 h-1)";
}
rep2_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.35826;
String bcodmo_name "unknown";
String description "replicate 2 hydrolysis rate";
String long_name "Rep2 Rate";
String units "nanomoles/liter/hour (nmol L-1 h-1)";
}
average {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.348874;
String bcodmo_name "unknown";
String description "average of hydrolysis rates";
String long_name "Average";
String units "nanomoles/liter/hour (nmol L-1 h-1)";
}
std_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.145735;
String bcodmo_name "unknown";
String description "std deviation of hydrolysis rates";
String long_name "Std Dev";
String units "nanomoles/liter/hour (nmol L-1 h-1)";
}
filter_um {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 3, 3;
String bcodmo_name "filter_size";
String description "filter pore size used for gravity filtration";
String long_name "Filter Um";
String units "micrometers";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Water was collected via Niskin bottles mounted on a rosette, equipped with a
CTD.
Experiments on (operationally defined) particles were carried out by gravity-
filtering water through 3 um pore size filters.\\u00a0 1/12th sections of the 3
um pore-size filters were submerged in 15 mL artificial seawater; enzyme
activities were measured as described below.
The potential of the seawater microbial community associated with large
particles (> 3 micrometer pore size filter) to hydrolyze six high-molecular-
weight polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan,
laminarin, pullulan, and xylan) was investigated in surface and bottom water.
For each substrate, three\\u00a0 15 mL falcon tubes were filled with autoclaved
artificial seawater and one 15 mL falcon tube was filled with autoclaved
seawater and a blank filter piece to serve as a killed control. Substrate was
added at 3.5 uM monomer-equivalent concentrations, except for fucoidan, which
was added at 5 uM concentrations (a higher concentration was necessary for
sufficient fluorescence signal). Two 15 mL falcon tubes \\u2013 one with
seawater and one with autoclaved seawater \\u2013 with no added substrate
served as blank controls. Incubations were stored in the dark at as close to
in situ temperature as possible. Subsamples of the incubations were collected
at time zero, and at six subsequent timepoints. At each timepoint, 2 mL of
seawater was collected from the 50 mL falcon tube using a sterile syringe,
filtered through a 0.2 um pore size syringe filter, and stored frozen until
processing.
The hydrolysis of high molecular weight substrate to lower molecular weight
hydrolysis products was measured using gel permeation chromatography with
fluorescence detection, after the method of Arnosti [1996, 2003]. In short,
the subsample was injected onto a series of columns consisting of a 21 cm
column of G50 and a 19 cm column of G75 Sephadex gel. The fluorescence of the
column effluent was measured at excitation and emission wavelengths of 490 and
530 nm, respectively. Hydrolysis rates were calculated from the change in
molecular weight distribution of the substrate over time, as described in
detail in Arnosti [2003].
ara = arabinogalactan
chn = chondroitin sulfate
fuc = fucoidan
lam = laminarin\\u00a0
pul = pullulan
xyl = xylan";
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
"Microbial Activities: GF FLA
RV/Sonne So248, South and North Pacific, along 180 W
P.I.: C. Arnosti (UNC-CH)
version: 2018-07-31
NOTE: Date/time and location data from CTD cast data (https://doi.pangaea.de/10.1594/PANGAEA.864673) were joined to original dataset";
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 "2018-08-06T16:35:36Z";
String date_modified "2020-04-27T18:12:06Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.743274.1";
Float64 Easternmost_Easting 180.0;
Float64 geospatial_lat_max 56.9999;
Float64 geospatial_lat_min -30.0008;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 180.0;
Float64 geospatial_lon_min -176.4753;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 1000.0;
Float64 geospatial_vertical_min 60.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T12:17:43Z (local files)
2024-11-21T12:17:43Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_743274.html";
String infoUrl "https://www.bco-dmo.org/dataset/743274";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_nid "743280";
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_1_acronym "CTD";
String instruments_1_dataset_instrument_nid "743281";
String instruments_1_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_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_1_instrument_name "CTD profiler";
String instruments_1_instrument_nid "417";
String instruments_2_acronym "Fluorometer";
String instruments_2_dataset_instrument_nid "743282";
String instruments_2_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
String instruments_2_instrument_name "Fluorometer";
String instruments_2_instrument_nid "484";
String instruments_3_acronym "GPC";
String instruments_3_dataset_instrument_nid "743283";
String instruments_3_description "Instruments that separate components in aqueous or organic solution based on molecular size generally for molecular weight determination. Gel permeation chromatography (GPC) is a type of size exclusion chromatography (SEC), that separates analytes on the basis of size.";
String instruments_3_instrument_name "Gel Permeation Chromatograph";
String instruments_3_instrument_nid "669469";
String keywords "average, bco, bco-dmo, biological, cast, cast_no, chemical, data, dataset, date, depth, depth_m, depth_no, dev, dmo, elapsed, erddap, filter, filter_um, iso, latitude, longitude, management, oceanography, office, preliminary, profiler, rate, rep1, rep1_rate, rep2, rep2_rate, salinity, salinity-temperature-depth, station, station_no, std, std_dev, substrate, temperature, time, time_elapsed_hr, timepoint";
String license "https://www.bco-dmo.org/dataset/743274/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/743274";
Float64 Northernmost_Northing 56.9999;
String param_mapping "{'743274': {'Latitude': 'flag - latitude', 'depth_m': 'flag - depth', 'Longitude': 'flag - longitude', 'ISO_DateTime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/743274/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 -30.0008;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "filter_um";
String summary "This dataset includes polysaccharide hydrolysis rates measured on particles collected from gravity-filtered seawater. Gravity filtered samples were collected on RV/Sonne cruise SO248 in May 2016. Links to archived CTD data are also provided.";
String time_coverage_end "2016-05-29T21:43Z";
String time_coverage_start "2016-05-02T16:51Z";
String title "[SO248: GF FLA hydrolysis rates] - Microbial enzyme activities: polysaccharide hydrolase activities of gravity filtered seawater samples from the RV\\Sonne cruise SO248 in the South and North Pacific, along 180 W, May, 2016 (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?)";
String version "1";
Float64 Westernmost_Easting -176.4753;
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.