Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | CSIA 15N AA data from phytoplankton, microzooplankton, and Calanus pacificus.
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_744468) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Files
|
Attributes {
s {
Experiment {
Byte _FillValue 127;
Byte actual_range 3, 6;
String bcodmo_name "exp_id";
String description "Experiment number";
String long_name "Experiment";
String units "unitless";
}
Organism {
String bcodmo_name "species";
String description "Species name or Particulate organic matter (POM)";
String long_name "Organism";
String units "unitless";
}
stage {
String bcodmo_name "exp_type";
String description "Refers to the experimental stage";
String long_name "Stage";
String units "unitless";
}
bulk_d15N {
String bcodmo_name "d15N";
String description "15N of bulk material";
String long_name "Bulk D15 N";
String units "per mil";
}
Ala_d15N {
String bcodmo_name "d15N";
String description "15N of AA Alanine";
String long_name "Ala D15 N";
String units "per mil";
}
Asp_d15N {
String bcodmo_name "d15N";
String description "15N of AA Aspartic acid";
String long_name "Asp D15 N";
String units "per mil";
}
Glu_d15N {
String bcodmo_name "d15N";
String description "15N of AA Glutamic acid";
String long_name "Glu D15 N";
String units "per mil";
}
IsoL_d15N {
String bcodmo_name "d15N";
String description "15N of AA IsoLeucine";
String long_name "Iso L D15 N";
String units "per mil";
}
Leu_d15N {
String bcodmo_name "d15N";
String description "15N of AA Leucine";
String long_name "Leu D15 N";
String units "per mil";
}
Pro_d15N {
String bcodmo_name "d15N";
String description "15N of AA Proline";
String long_name "Pro D15 N";
String units "per mil";
}
Val_d15N {
String bcodmo_name "d15N";
String description "15N of AA Valine";
String long_name "Val D15 N";
String units "per mil";
}
Gly_d15N {
String bcodmo_name "d15N";
String description "15N of AA Glycine";
String long_name "GLY D15 N";
String units "per mil";
}
Lys_d15N {
String bcodmo_name "d15N";
String description "15N of AA Lysine";
String long_name "LYS D15 N";
String units "per mil";
}
Phe_d15N {
String bcodmo_name "d15N";
String description "15N of AA Phenylalanine";
String long_name "Phe D15 N";
String units "per mil";
}
Ser_d15N {
String bcodmo_name "d15N";
String description "15N of AA Serine";
String long_name "Ser D15 N";
String units "per mil";
}
Thr_d15N {
String bcodmo_name "d15N";
String description "15N of AA Treonine";
String long_name "THR D15 N";
String units "per mil";
}
Note_Organism {
String bcodmo_name "comment";
String description "Each note corresponds to the cell in this row in the Organism column";
String long_name "Note Organism";
String units "unitless";
}
Note_bulk_d15N {
String bcodmo_name "comment";
String description "Each note corresponds to the cell in this row in the bulk d15N column";
String long_name "Note Bulk D15 N";
String units "unitless";
}
Note_Gly_d15N {
String bcodmo_name "comment";
String description "Each note corresponds to the cell in this row in the Gly d15N column";
String long_name "Note Gly D15 N";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Hydrolysis, derivatization and analyses of samples for CSIA \\u2013\\u00a0 For
Exps. 3-4, samples (1-2 mg dry weight) for CSIA-AA were added to 1 ml 6 N
HPLC-grade HCl, then flushed with N2, capped with a Teflon-lined cap, and
hydrolyzed at 150\\u00b0C for 70 min.\\u00a0 The resulting hydrolysate was
evaporated to dryness under N2 at 55\\u00b0C, redissolved in 1 ml 0.01 N HCl,
purified by filtration (0.45-\\u03bcm hydrophilic filter), washed with 1 ml of
0.01 N HCl, and further purified using cation-exchange chromatography with a
5-cm resin column (Dowex 50WX8-400) in a glass Pasteur pipette.\\u00a0 AAs were
eluted with 4 ml of 2 N NH4OH and evaporated to dryness under a stream of N2
at 80\\u00b0C, then reacidified with 0.5 ml of 0.2 N HCl, flushed with N2,
heated to 110\\u00b0C for 5 min and evaporated to dryness under N2 at
55\\u00b0C.\\u00a0 Hydrolyzed samples were esterified with 2 ml of 4:1
isopropanol:acetyl chloride, flushed with N2 and heated to 110\\u00b0C for 60
min.\\u00a0 After drying at 60\\u00b0C under N2, the samples were acylated by
adding 1 ml of 3:1 methylene chloride:trifluoracetic anhydride (TFAA) and
heated to 100\\u00b0C for 15 min.\\u00a0 The derivatized AAs were further
purified by solvent extraction following (Ueda et al. 1989).\\u00a0 The
acylated AA esters were evaporated at room temperature under N2 and
redissolved in 3 ml of 1:2 chloroform:P-buffer (KH2PO4 + Na2HPO4 in Milli-Q
water, pH 7).\\u00a0 Vigorous shaking ensured that the derivitized AAs were
partitioned into chloroform while contaminants remained in the P-buffer.\\u00a0
The solvents were separated by centrifugation (10 min at 600 g), the
chloroform was transferred to a clean vial, and the solvent extraction process
repeated.\\u00a0 Finally, to ensure derivatization, the acylation step was
repeated.\\u00a0 Samples were stored at \\u201320\\u00b0C in 3:1 methylene
chloride:TFAA for up to 2 weeks until analysis.\\u00a0 AA derivatives were then
analyzed by isotope monitoring gas chromatography-mass spectrometry.\\u00a0 We
used a Delta V Plus mass spectrometer interfaced with a Trace GC gas
chromatograph through a GC-C III combustion furnace (980\\u00b0C), reduction
furnace (650\\u00b0C), and liquid nitrogen cold trap.\\u00a0 Internal reference
compounds (aminoadipic acid and norleucine) of known nitrogen isotopic
composition were co-injected with samples and used to normalize the measured
\\u03b415N values of unknown AAs, and a suite of eight AAs with known isotopic
composition was analyzed every 3 injections for additional quality
control.\\u00a0 At least three injections per sample were analyzed.\\u00a0 For
Exps. 5 and 6, CSIA-AA samples were hydrolyzed in 6N HCl at 110\\u00b0C for 20
h.\\u00a0 The hydrolysate was evaporated to dryness at temperature under a
continuous stream of N2 gas, then esterified with 4:1 isotopropanol:acetyl
chloride at 110\\u00b0C for 60 min, acylated in a 1:1 solution of methylene
chloride:trifluoracetic anhydride (DCM:TFAA) for 10 min at 110\\u00b0C.\\u00a0
Samples were stored at -20\\u00b0C in 1:1 DCM:TFAA for up to 3 months before
isotope analysis using a Delta V Plus mass spectrometer (Thermo Scientific)
interfaced through a Conflo IV to a GC 1310 gas chromatograph coupled to a GC
Isolink combustion-reduction furnace (1000\\u00b0C) and liquid nitrogen cold
trap.\\u00a0 All samples were injected (splitless injector) onto a forte BPx5
capillary column (60 m x 0.32 mm x 1.0-\\u03bcm film thickness) at an injector
temperature of 250\\u00b0C with a constant helium flow rate of 1.4 ml
min\\u20131.\\u00a0 The column was initially held at 50\\u00b0C for 2 min and
then increased to 125 \\u00b0C at a rate of 15\\u00b0C min-1.\\u00a0 Once at
125\\u00b0C, the temperature was increased at a rate of 3\\u00b0C min-1 to
160\\u00b0C and then to 190\\u00b0C at a rate of 4\\u00b0C min-1.\\u00a0 The final
temperature of 300\\u00b0C was reached by ramping to 275\\u00b0C at 6\\u00b0C
min-1 and then 15\\u00b0C min-1 afterward.\\u00a0 Samples were analyzed in
triplicate and normalized to the known \\u03b415N values of a suite of 14 AAs
analyzed before and after each set of 3 samples.";
String awards_0_award_nid "556513";
String awards_0_award_number "OCE-1260055";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1260055";
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 "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Zooplankton/phytoplankton CSIA-AA
Michael Landry, PI
Version 23 August 2018";
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 "2018-08-22T18:54:54Z";
String date_modified "2019-06-10T16:29:39Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.744468.1";
String history
"2024-04-25T12:30:03Z (local files)
2024-04-25T12:30:03Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_744468.html";
String infoUrl "https://www.bco-dmo.org/dataset/744468";
String institution "BCO-DMO";
String instruments_0_acronym "Gas Chromatograph";
String instruments_0_dataset_instrument_description "Used with mass spectrometer";
String instruments_0_dataset_instrument_nid "744477";
String instruments_0_description "Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
String instruments_0_instrument_name "Gas Chromatograph";
String instruments_0_instrument_nid "661";
String instruments_0_supplied_name "Trace GC gas chromatograph, GC 1310 gas chromatograph";
String instruments_1_acronym "Gas Chromatograph";
String instruments_1_dataset_instrument_description "Coupled to a GC Isolink combustion-reduction furnace (1000 deg C) and liquid nitrogen cold trap.";
String instruments_1_dataset_instrument_nid "744547";
String instruments_1_description "Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
String instruments_1_instrument_name "Gas Chromatograph";
String instruments_1_instrument_nid "661";
String instruments_1_supplied_name "GC 1310";
String instruments_2_acronym "Mass Spec";
String instruments_2_dataset_instrument_description "Used for sampling";
String instruments_2_dataset_instrument_nid "744476";
String instruments_2_description "General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_2_instrument_name "Mass Spectrometer";
String instruments_2_instrument_nid "685";
String instruments_2_supplied_name "Delta V Plus";
String keywords "ala, Ala_d15N, asp, Asp_d15N, bco, bco-dmo, biological, bulk, bulk_d15N, chemical, d15, data, dataset, dmo, erddap, experiment, glu, Glu_d15N, gly, Gly_d15N, iso, IsoL_d15N, leu, Leu_d15N, lys, Lys_d15N, management, note, Note_bulk_d15N, Note_Gly_d15N, Note_Organism, oceanography, office, organism, phe, Phe_d15N, preliminary, pro, Pro_d15N, ser, Ser_d15N, stage, thr, Thr_d15N, val, Val_d15N";
String license "https://www.bco-dmo.org/dataset/744468/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/744468";
String param_mapping "{'744468': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/744468/parameters";
String people_0_affiliation "University of California-San Diego";
String people_0_affiliation_acronym "UCSD-SIO";
String people_0_person_name "Michael R. Landry";
String people_0_person_nid "50545";
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 "Hannah Ake";
String people_1_person_nid "650173";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "CSIA-AA Mesozooplankton TP";
String projects_0_acronym "CSIA-AA Mesozooplankton TP";
String projects_0_description
"Description from NSF award abstract:
Energy dissipation and elemental cycling by protistan consumers in lower trophic levels of ocean food webs are of sufficient magnitude, based on global mean measures of the amount of primary production consumed, to strongly alter the efficiencies of material transfers to higher-level consumers and to export. We presently know very little about these microbial food web steps, how they vary regionally or temporally, or how they might be altered by climate change. Compound Specific Isotope Analysis of Amino Acids (CSIA-AA) offers an approach for advancing our understanding of microbial food web structure and trophic fluxes based on the trophic positions (TP) of mesozooplankton as temporal integrators of the fluxes from direct feeding on phytoplankton and indirect transfers via protistan microzooplankton. Preliminary laboratory experiments to test this idea have demonstrated that the standard application of the method, using labeled phenylalanine as the representative source AA for the primary producer baseline and labeled glutamic acid as the indicator AA for trophic enrichment, does not produce a measureable trophic-step signal for protistan grazers. However, the results have also shown that an alternative high-turnover AA, alanine, strongly enriches in protistan as well as metazoan consumers, and leads to substantially higher TP estimates of mesozooplankton in field-collected specimens than that based on labeled glutamic acid.
This research project will test the hypothesis that labeled alanine provides a quantifiable and consistent index of trophic enrichment for protistan steps in marine food webs. The research will involve three major elements. First, controlled laboratory experiments will be conducted with chemostat systems to compare 15N enrichments of alanine to other AAs for a representative suite of ciliate and flagellate grazers feeding on phytoplankton, and to evaluate the two-step enrichment from phytoplankton via a protistan grazer to a suspension-feeding copepod. Second, field-collected mesozooplankton from four distinct ecological regions of the Pacific Ocean will be analyzed by CSIA-AA to test the transfer of alanine enrichment through a metazoan trophic step (comparing suspension feeding species to primary carnivores) and to assess how the TP index differs with trophic structure over a broad range of ecological conditions. Last, CSIA-AA assessments of TP for size-structured zooplankton will be integrated into inverse models of nitrogen flows in the four regions (equatorial Pacific, subtropical North Pacific, California Current and Costa Rica Dome) as a major constraint for resolving and comparing fluxes through the microbial food web over the range of ecological conditions. A properly calibrated CSIA-AA assessment of mesozooplankton trophic position will provide a new and valuable approach for regional intercomparisons of lower-level food web structure, for assessing temporal and spatial trends in climate change, for ocean ecosystem model validation, and for better understanding of lower food-web energetic constraints on ocean fisheries.";
String projects_0_end_date "2018-03";
String projects_0_geolocation "California Current, eastern Pacific Ocean";
String projects_0_name "Resolving the trophic connection between protistan grazers and mesozooplankton in marine food webs using amino acid-specific stable isotope analyses";
String projects_0_project_nid "556514";
String projects_0_start_date "2013-04";
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 summary "CSIA 15N AA data from phytoplankton, microzooplankton, and Calanus pacificus.";
String title "CSIA 15N AA data from phytoplankton, microzooplankton, and Calanus pacificus.";
String version "1";
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.