Accessing BCO-DMO data
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| Dataset Title: | Microbial enzyme activities: glucosidase and peptidase activities of bulk seawater samples from the RV\\Sonne cruise SO248 in the South and North Pacific, along 180 W, May, 2016 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_743224) |
| 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, 1.46461812e+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, 58.9;
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 -179.0, 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 20.0, 4000.0;
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:
L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)
AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA
AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA
QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA
FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA";
String long_name "Substrate";
String units "unitless";
}
timepoint {
Byte _FillValue 127;
Byte actual_range 1, 4;
String bcodmo_name "time_point";
String description "sampling point post-incubation";
String long_name "Timepoint";
String units "unitless";
}
time_elapsed_hr {
Float32 _FillValue NaN;
Float32 actual_range 11.1, 74.8;
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 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 848.319433;
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 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 959.721043;
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)";
}
rep3_rate {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 824.866787;
String bcodmo_name "unknown";
String description "replicate 3 hydrolysis rate";
String long_name "Rep3 Rate";
String units "nanomoles/liter/hour (nmol L-1 h-1)";
}
average {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 790.116399;
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 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 519.337604;
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)";
}
}
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.
Two substrates, -glucose and -glucose linked to a 4-methylumbelliferyl (MUF)
fluorophore, were used to measure glucosidase activities. Five substrates
linked to a 7-amido-4-methyl coumarin (MCA) fluorophore, one amino acid \\u2013
leucine \\u2013 and four oligopeptides \\u2013 the chymotrypsin substrates
alanine-alanine-phenylalanine (AAF) and alanine-alanine-proline-phenylalanine
(AAPF), and the trypsin substrates glutamine-alanine-arginine (QAR) and
phenylalanine-serine-arginine (FSR) \\u2013 were used to measure exo- and endo-
acting peptidase activities, respectively. Hydrolysis rates of the substrates
were measured as an increase in fluorescence as the fluorophore was hydrolyzed
from the substrate over time [as in Hoppe, 1993; Obayashi and Suzuki, 2005].
Incubations with the seven low molecular weight substrates were set up in a
96-well plate. For each substrate, triplicate wells were filled with a total
volume of 200 L seawater for experimental incubations; triplicate wells were
filled with 200 L autoclaved seawater for killed control incubations.
Substrate was added at saturating concentrations. A saturation curve was
determined with surface water from each station to determine saturating
concentrations of substrate. The saturating concentration was identified as
the lowest tested concentration of substrate at which additional substrate did
not yield higher rates of hydrolysis. Fluorescence was measured over 24-48
hours incubation time with a plate reader (TECAN spectrafluor plus; 360 nm
excitation, 460 emission), with timepoints taken every 4-6 hours. Hydrolysis
rates were calculated from the rate of increase of fluorescence in the
incubation over time relative to a set of standards of known concentration of
fluorophore. Scripts to calculate hydrolysis rates and produce the figures
shown here are available in the associated Github repository [Hoarfrost,
2017].
L = substrate to measure leucine aminopeptidase (L-leucine-7-amido-4 MCA)
AAF = substrate to measure chymotrypsin activity: ala-ala-phe-MCA
AAPF = substrate to measure chymotrypsin activity: N-succinyl-ala-ala-pro-
phe-MCA
QAR = substrate to measure trypsin activity: Boc-gln-ala-arg-MCA\\u00a0\\u00a0
FSR = substrate to measure trypsin activity: N-t-boc-phe-ser-arg-MCA\\u00a0";
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: Bulk MCAMUF
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 "2018-08-06T14:30:10Z";
String date_modified "2020-04-27T19:01:47Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.743224.1";
Float64 Easternmost_Easting 180.0;
Float64 geospatial_lat_max 58.9;
Float64 geospatial_lat_min -30.0008;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 180.0;
Float64 geospatial_lon_min -179.0;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 4000.0;
Float64 geospatial_vertical_min 20.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-04-16T18:13:35Z (local files)
2024-04-16T18:13:35Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_743224.html";
String infoUrl "https://www.bco-dmo.org/dataset/743224";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_nid "743230";
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 "743231";
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 "743232";
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 keywords "average, bco, bco-dmo, biological, cast, cast_no, chemical, data, dataset, date, depth, depth_m, depth_no, dev, dmo, elapsed, erddap, iso, latitude, longitude, management, oceanography, office, preliminary, profiler, rate, rep1, rep1_rate, rep2, rep2_rate, rep3, rep3_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/743224/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/743224";
Float64 Northernmost_Northing 58.9;
String param_mapping "{'743224': {'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/743224/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 summary "This dataset includes MCAMUF (glucosidase and peptidase) hydrolysis rates to measure microbial enzyme activities in bulk (not filter-fractionated) seawater. Samples were collected on RV/Sonne cruise SO248 in May 2016. Links to archived CTD data are also provided.";
String time_coverage_end "2016-05-30T14:22Z";
String time_coverage_start "2016-05-02T16:51Z";
String title "Microbial enzyme activities: glucosidase and peptidase activities of bulk seawater samples from the RV\\\\Sonne cruise SO248 in the South and North Pacific, along 180 W, May, 2016";
String version "1";
Float64 Westernmost_Easting -179.0;
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.