Accessing BCO-DMO data
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| Dataset Title: | [EN584 LV polysaccharide hydrolysis rates] - Measurements of polysaccharide hydrolase activities in large volume mesocosm incubations RV/Endeavor EN584, July 2016 (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_717495) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
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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 12, 16;
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, 5;
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 2.5, 5050.0;
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";
}
treatment {
String bcodmo_name "treatment";
String description "LV experiments treatments: amended or not with Thalassiosira";
String long_name "Treatment";
String units "unitless";
}
meso_no {
String bcodmo_name "sample";
String description "Large volume experiment mesocosm number";
String long_name "Meso No";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
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 time point (0; 1; 2; etc.) post-incubation";
String long_name "Timepoint";
String units "unitless";
}
time_elapsed_hr {
Int16 _FillValue 32767;
Int16 actual_range 0, 720;
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";
}
rep1_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 53.087;
String bcodmo_name "unknown";
String description "replicate 1 hydrolysis rate";
String long_name "Rep1 Rate";
String units "nanomol monosaccharide/liter/hour";
}
rep2_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 50.359;
String bcodmo_name "unknown";
String description "replicate 2 hydrolysis rate";
String long_name "Rep2 Rate";
String units "nanomol monosaccharide/liter/hour";
}
rep3_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 47.827;
String bcodmo_name "unknown";
String description "replicate 3 hydrolysis rate";
String long_name "Rep3 Rate";
String units "nanomol monosaccharide/liter/hour";
}
average {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 50.122;
String bcodmo_name "unknown";
String description "average of the 3 hydrolysis rates";
String long_name "Average";
String units "nanomol monosaccharide/liter/hour";
}
std_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 13.424;
String bcodmo_name "unknown";
String description "standard deviation of the 3 hydrolysis rates";
String long_name "Std Dev";
String units "nanomol monosaccharide/liter/hour";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"For mesocosm (large volume) incubation experiments (referred to as
\\u201cLV\\u201d incubations), a 30L Niskin bottle rosette was used to collect
the water. Separate casts were used to collect surface water, bottom water,
and water from the depth at which oxygen showed a minimum, according to the
CTD. From each depth, 20L seawater from single Niskin bottles was dispensed
using cleaned silicon tubing into a single carboy. Prior to filling, carboys
were rinsed 3x with water from the same Niskin bottle used to fill the carboy.
Four carboys were filled at each depth. Triplicate 20L carboys were amended
with ca. 500 mg (exact mass was recorded for each addition) of HMW
Thalassiosira; unamended single carboys were used for controls. All mesocosms
were incubated in the dark at near in-situ temperatures. Mesocosms were sub-
sampled at the start of incubation (0 days), and then after 2 d, 7d, and 16d
for the following assays: bacterial production using 3H-Leucine, dissolved
organic carbon (DOC), nutrients, bacterial cell counts,\\u00a0peptidase and
glucosidase activity measurements. At the 16d subsampling timepoint,
polysaccharide hydrolase activity measurements were initiated, using
fluorescently labeled polysaccharides (Arnosti 2003). These polysaccharide
incubations were sampled at time points of 0, 2, 5, 10, 17, and 30 days (with
the zero-time sample being at the 16-day timepoint of the mesocosm
experiment).
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].";
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
"Large volume experiment: polysaccharide hydrolysis rates
EN584, July 2016
C. Arnosti (UNC)
version: 2017-10-20";
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 "2017-10-24T12:36:04Z";
String date_modified "2020-05-13T14:36:23Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.717495.1";
Float64 geospatial_vertical_max 5050.0;
Float64 geospatial_vertical_min 2.5;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T09:11:59Z (local files)
2024-11-21T09:11:59Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_717495.html";
String infoUrl "https://www.bco-dmo.org/dataset/717495";
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 "717501";
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 "30 liter Niskin bottles";
String instruments_1_acronym "Fluorometer";
String instruments_1_dataset_instrument_nid "718103";
String instruments_1_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_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
String instruments_1_instrument_name "Fluorometer";
String instruments_1_instrument_nid "484";
String instruments_2_acronym "GPC";
String instruments_2_dataset_instrument_nid "719747";
String instruments_2_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_2_instrument_name "Gel Permeation Chromatograph";
String instruments_2_instrument_nid "669469";
String keywords "average, bco, bco-dmo, biological, cast, chemical, cruise, cruise_id, data, dataset, depth, depth_id, depth_m, dev, dmo, elapsed, erddap, management, meso, meso_no, oceanography, office, preliminary, profiler, rate, rep1, rep1_rate, rep2, rep2_rate, rep3, rep3_rate, salinity, salinity-temperature-depth, station, std, std_dev, substrate, temperature, time, time_elapsed_hr, timepoint, treatment";
String license "https://www.bco-dmo.org/dataset/717495/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/717495";
String param_mapping "{'717495': {'depth_m': 'master - depth'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/717495/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)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "cruise_id";
String summary "Measurements of polysaccharide hydrolase activities in large volume mesocosm incubations RV/Endeavor EN584, July 2016. See Niskin Bottle and Cast List EN584 to link specific casts and bottles to each experiment: https://www.bco-dmo.org/dataset/717427.";
String title "[EN584 LV polysaccharide hydrolysis rates] - Measurements of polysaccharide hydrolase activities in large volume mesocosm incubations RV/Endeavor EN584, July 2016 (Patterns of activities project) (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?)";
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.