Accessing BCO-DMO data
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| Dataset Title: | [Amino acid d13C values of diatoms and bacteria] - Amino acid d13C values of diatoms, bacteria, and core M772-003-2 samples from the R/V Meteor (M77) in the Peruvian ocean margin from November to December 2008. (The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_715160) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
sample_description {
String bcodmo_name "sample_descrip";
String description "Type of sample";
String long_name "Sample Description";
String units "unitless";
}
ID {
String bcodmo_name "sample";
String description "Sample ID";
String long_name "ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Ala {
Float32 _FillValue NaN;
Float32 actual_range -22.6, -1.3;
String bcodmo_name "amino_conc";
String description "Alanine d13C value";
String long_name "Ala";
String units "per mil";
}
Ala_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.5;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Ala St Dev";
String units "per mil";
}
Asx {
Float32 _FillValue NaN;
Float32 actual_range -24.4, -4.2;
String bcodmo_name "amino_conc";
String description "Aspartic Acid + Asparagine d13C value";
String long_name "Asx";
String units "per mil";
}
Asx_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.0;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Asx St Dev";
String units "per mil";
}
Glx {
Float32 _FillValue NaN;
Float32 actual_range -24.1, -7.4;
String bcodmo_name "amino_conc";
String description "Glutamic Acid + Glutamine d13C value";
String long_name "GLX";
String units "per mil";
}
Glx_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.3;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Glx St Dev";
String units "per mil";
}
Gly {
Float32 _FillValue NaN;
Float32 actual_range -25.3, -5.5;
String bcodmo_name "amino_conc";
String description "Glycine d13C value";
String long_name "GLY";
String units "per mil";
}
Gly_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.6;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Gly St Dev";
String units "per mil";
}
His {
Float32 _FillValue NaN;
Float32 actual_range -22.2, -7.8;
String bcodmo_name "amino_conc";
String description "Histodine d13C value";
String long_name "His";
String units "per mil";
}
His_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.9;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "His St Dev";
String units "per mil";
}
Ile {
Float32 _FillValue NaN;
Float32 actual_range -24.0, -9.7;
String bcodmo_name "amino_conc";
String description "Isoleucine d13C value";
String long_name "Ile";
String units "per mil";
}
Ile_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.3;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Ile St Dev";
String units "per mil";
}
Leu {
Float32 _FillValue NaN;
Float32 actual_range -31.6, -12.8;
String bcodmo_name "amino_conc";
String description "Leucine d13C value";
String long_name "Leu";
String units "per mil";
}
Leu_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.9;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Leu St Dev";
String units "per mil";
}
Lys {
Float32 _FillValue NaN;
Float32 actual_range -24.8, -6.2;
String bcodmo_name "amino_conc";
String description "Lysine d13C value";
String long_name "LYS";
String units "per mil";
}
Lys_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.1;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Lys St Dev";
String units "per mil";
}
Met {
Float32 _FillValue NaN;
Float32 actual_range -31.6, -8.2;
String bcodmo_name "amino_conc";
String description "Methoinine d13C value";
String long_name "Met";
String units "per mil";
}
Met_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 0.9;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Met St Dev";
String units "per mil";
}
Phe {
Float32 _FillValue NaN;
Float32 actual_range -29.3, -16.0;
String bcodmo_name "amino_conc";
String description "Phenylalanine d13C value";
String long_name "Phe";
String units "per mil";
}
Phe_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.7;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Phe St Dev";
String units "per mil";
}
Thr {
Float32 _FillValue NaN;
Float32 actual_range -17.9, -2.0;
String bcodmo_name "amino_conc";
String description "Threonine d13C value";
String long_name "THR";
String units "per mil";
}
Thr_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 1.6;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Thr St Dev";
String units "per mil";
}
Tyr {
Float32 _FillValue NaN;
Float32 actual_range -27.7, -14.4;
String bcodmo_name "amino_conc";
String description "Tyrosine d13C value";
String long_name "TYR";
String units "per mil";
}
Tyr_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.6;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Tyr St Dev";
String units "per mil";
}
Val {
Float32 _FillValue NaN;
Float32 actual_range -29.1, -13.6;
String bcodmo_name "amino_conc";
String description "Valine d13C value";
String long_name "Val";
String units "per mil";
}
Val_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.7;
String bcodmo_name "amino_conc";
String description "Standard deviation";
String long_name "Val St Dev";
String units "per mil";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Culturing
The marine diatom Thalassiosira weiss\\ufb02ogii Grunow (strain CCMP 1010) was
cultured in sterile filtered natural North Sea water (Schleswig-Holstein,
Germany) or Baltic Sea water (Schleswig-Holstein, Germany). The medium was
enriched with f/4 concentrations of macro- and micronutrients (nitrate,
phosphate, silicic acid, trace metal mixture, vitamin mixture (Guillard and
Ryther, 1962). All experiments were performed in sterile 2.1 L Schott Duran
glass bottles. These bottles were made of borosilicate glass (filters UV
radiation <310 nm) except for the quartz glass bottles (pure silica without UV
radiation filter) used in the UV experiment. The cultures were either
incubated in climate chambers with 400 \\u2013700 nm radiation or 10 cm below
water level at low tide in Kiel Fjord in May 2011. Water temperature and light
irradiance data were obtained from the weather station maintained by the
GEOMAR institute in Kiel, Germany. Growth conditions for the various
treatments, i.e. salinity, pH, temperature and irradiance are given in Table
1. pH values (reported on free scale) were measured \\u00a0with separate glass
and reference electrodes (Metrohm) and calculated with equation 3 from DOE
2007 chapter 6b (Dickson et al., 2007) as described in (Bach et al., 2012).
Cultures were inoculated with densities of 20 cells ml-1. \\u00a0Cell densities
and equivalent spherical diameters were determined with a Coulter Counter
(Beckman Coulter) at the beginning and the end of the experiment,
respectively. When incubations ended, cells were filtered on 47 mm diameter, 5
um mesh size Nucleopore Track-Etch Membrane filters (Whatman) and frozen at
-18 deg C immediately after filtration.
Sediment sampling
Sediment samples were retrieved from a 14.97 m core, station M772-003-2,
collected November 26, 2008 by the Meteor cruise M77 at 271 m water depth
within the main upwelling area off Peru (15 deg 06.21\\u00b4S, 75 deg
41.28\\u00b4W). The Peruvian ocean margin is characterized by a high particle
flux and a well-defined oxygen minimum zone. At the time of sampling, the O2
concentration at the seafloor was measured to 1.1 uM, the salinity to 34.9 psu
and the temperature to 12.2 \\u00a0deg C.
Prior to analysis, sediment samples were pre-treated with an acid-alkali-acid
cleaning with HCl and NaOH (Grootes et al., 2004).) \\u00a0 \\u00a0 \\u00a0
\\u00a0
Analyses
Both diatom and sediment samples were freeze dried prior to isotopic analysis.
To prepare aliquots for derivatization of amino acids, we used 3-4 mg of
diatoms and 100-150 mg of sediments. The samples were transferred to Pyrex
culture tubes (13 x 100 mm), flushed with N2 gas, sealed, and hydrolysed in 1
ml 6N HCl at 110 \\u00a0deg C for 20 h. After hydrolysis, lipophilic compounds
were removed by vortexing with 2 ml n-hexane/DCM (6:5, v/v) for 30 sec. The
aqueous phase was subsequently transferred through disposable glass pipettes
lined with glass wool into 4 ml dram vials. Samples were evaporated to dryness
under a stream of N2 gas for 30 min at 110 deg C before being stored at 18 deg
C until required for analysis. The derivatisation procedure was modified from
Corr et al. (2007) as described by Larsen et al. (2013). In short, the dried
samples were methylated with acidified methanol and subsequently acetylated
with a mixture of acetic anhydride, triethylamine, and acetone, forming
N-acetyl methyl ester derivatives. As a precautionary measure to reduce the
oxidation of amino acids, we flushed and sealed reaction vials with N2 gas
prior to methylation and acetylation. Another modification from Corr et al.
(2007) was that icebaths were substituted with solid aluminum blocks at room
temperature. We used known d13C values of pure amino acids prepared and
analyzed under the same conditions as the samples to calculate correction
factors specific to each amino acid to account for carbon addition and
fractionation during derivatization. The derivatised AAs were dissolved in 250
ul ethyl acetate and stored at 18 deg C until required for analysis.
Amino acid d13C values were obtained from Leibniz-Laboratory for Radiometric
Dating and Stable Isotope Research in Kiel. We injected the AA derivatives
into a PTV injector held at 250 deg C for 4 min. before GC separation on an
Agilent 6890N GC. Diatom samples were separated on an Rtx-200 column (60m x
0.32mm x 0.25um, Fig. S1) and sediment samples on a Thermo Trace GOLD TG-200MS
GC column (60m x 0.32mm x 0.25um). For both GC columns, the oven temperature
of the GC was started at 50 deg C and heated at 15 deg C min-1 to 140 deg C,
followed by 3 deg C min-1 to 152 deg C and held for 4 min, then 10 deg C min-1
to 245 deg C and held for 10 min, and finally 5 deg C min-1 to 290 deg C and
held for 5 min. The GC was interfaced with a MAT 253 isotope ratio mass
spectrometer (IRMS) via a GC-III combustion (C) interface (Thermo-Finnigan
Corporation). We obtained consistently good chromatography for alanine (Ala),
valine (Val), leucine (Leu), isoleucine (Ile), asparagine/aspartate (Asx),
threonine (Thr), methionine (Met), glutamine/glutamate (Glx), phenylalanine
(Phe), tyrosine (Tyr), lysine (Lys), and arginine (Arg) with the exception
that Asx and Thr partially coeluted with the Rtx-200 column. Serine (Ser) and
proline (Pro) coeluted on both columns. The average reproducibility for the
norleucine internal standard was \\u00b1 0.4\\u2030 (n = 3 for each sample), and
the reproducibility of amino acid standards ranged from \\u00b1 0.1\\u2030 for
Phe to \\u00b1 0.6\\u2030 for Thr (n = 3).
Amino acid composition of the diatom samples was determined with the
derivative samples used for d13CAA analysis. The amino acids were separated on
an Rxi-35SIL MS column (30m x 0.32mm x 0.25um) with an Agilent 6890 N GC with
a flame ionization detector. With this column we obtained good chromatography
for Ala, Asx, Glx, Gly, Ser, Tyr, Arg, Ile, Leu, Lys, Met, Phe, Thr, and Val.
For quantification, we used internal references consisting of pure amino acids
(Alfa Aesar, Karlsruhe, Germany). The composition of the amino acids are shown
in Table 3 according to the following biosynthetic families: \\u00a0Pyruvate
(Ala, Leu, Val), Oxaloacetate (Asx, Ile, Lys, Met, Thr), \\u03b1-ketoglutarate
(Arg, Glx), 3-phosphoglycerate (Gly, Ser), and Shikimate (Phe, Tyr).
Bulk 13C, %C, 15N and %N values of the diatom samples were determined at the
UC Davis Stable Isotope Facility using a PDZ Europa ANCA-GSL elemental
analyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer
(Sercon Ltd., Cheshire, UK). The dry weight of the samples ranged between 1.5
and 2.5 mg. During analysis, samples were interspersed with several replicates
of at least three different laboratory standards. These laboratory standards,
which were selected to be compositionally similar to the samples being
analyzed, had previously calibrated against NIST Standard Reference Materials
(IAEA-N1, IAEA-N2, IAEA-N3, USGS-40, and USGS-41). A sample\\u2019s preliminary
isotope ratio was measured relative to reference gases analyzed with each
sample. These preliminary values were finalized by correcting the values for
the entire batch based on the known values of the included laboratory
standards. The long term standard deviation is 0.2\\u2030 for 13C and 0.3\\u2030
for 15N.";
String awards_0_award_nid "704683";
String awards_0_award_number "OCE-1131816";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1131816";
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 "Candace O. Major";
String awards_0_program_manager_nid "51690";
String cdm_data_type "Other";
String comment
"Amino Acids
M. McCarthy, PI
Version 14 September 2017";
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 "2017-09-15T21:46:59Z";
String date_modified "2019-06-11T17:34:58Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.715160.1";
String history
"2024-12-21T16:23:07Z (local files)
2024-12-21T16:23:07Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_715160.html";
String infoUrl "https://www.bco-dmo.org/dataset/715160";
String institution "BCO-DMO";
String instruments_0_acronym "IR Mass Spec";
String instruments_0_dataset_instrument_description "Used with PDZ Europa ANCA-GSL elemental analyzer";
String instruments_0_dataset_instrument_nid "715168";
String instruments_0_description "The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_0_instrument_name "Isotope-ratio Mass Spectrometer";
String instruments_0_instrument_nid "469";
String instruments_0_supplied_name "PDZ Europa 20-20 isotope ratio mass spectrometer";
String instruments_1_acronym "IR Mass Spec";
String instruments_1_dataset_instrument_description "Used with Thermo Trace GOLD GC";
String instruments_1_dataset_instrument_nid "715465";
String instruments_1_description "The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_1_instrument_name "Isotope-ratio Mass Spectrometer";
String instruments_1_instrument_nid "469";
String instruments_1_supplied_name "MAT 253 isotope ratio mass spectrometer (IRMS)";
String instruments_2_acronym "Gas Chromatograph";
String instruments_2_dataset_instrument_description "Used with MAT 253 isotope ratio mass spectrometer (IRMS) via a GC-III combustion (C) interface (Thermo-Finnigan Corporation)";
String instruments_2_dataset_instrument_nid "715167";
String instruments_2_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_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
String instruments_2_instrument_name "Gas Chromatograph";
String instruments_2_instrument_nid "661";
String instruments_2_supplied_name "Thermo Trace GOLD GC";
String instruments_3_dataset_instrument_description "Interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK)";
String instruments_3_dataset_instrument_nid "715166";
String instruments_3_description "Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.";
String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
String instruments_3_instrument_name "Elemental Analyzer";
String instruments_3_instrument_nid "546339";
String instruments_3_supplied_name "PDZ Europa ANCA-GSL elemental analyzer";
String keywords "ala, Ala_st_dev, asx, Asx_st_dev, bco, bco-dmo, biological, chemical, data, dataset, description, dev, dmo, erddap, glx, Glx_st_dev, gly, Gly_st_dev, his, His_st_dev, ile, Ile_st_dev, leu, Leu_st_dev, lys, Lys_st_dev, management, met, Met_st_dev, oceanography, office, phe, Phe_st_dev, preliminary, sample, sample_description, thr, Thr_st_dev, tyr, Tyr_st_dev, val, Val_st_dev";
String license "https://www.bco-dmo.org/dataset/715160/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/715160";
String param_mapping "{'715160': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/715160/parameters";
String people_0_affiliation "University of California-Santa Cruz";
String people_0_affiliation_acronym "UC Santa Cruz";
String people_0_person_name "Matthew D. McCarthy";
String people_0_person_nid "557245";
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 "Amino Acid Sediment 15N";
String projects_0_acronym "Amino Acid Sediment 15N";
String projects_0_description
"The bioavailability of nutrients plays a crucial role in oceanic biological productivity, the carbon cycle, and climate change. The global ocean inventory of nitrogen (N) is determined by the balance of N-fixation (sources) and denitrification (sinks). In this three-year project, a researcher from the University of California, Santa Cruz, will focus on developing compound-specific N isotope (d15N) analysis of amino acids as a new tool for understanding N source and transformation of organic matter in paleo-reservoirs. The offsets in the isotopic ratios of individual amino acid groups may yield information about trophic transfer, heterotrophic microbial reworking, and autotrophic versus heterotrophic sources. By measuring and comparing the bulk and amino acid d15N in size-fractioned samples from plankton tows, sediments traps, and multi-cores in oxic and suboxic depositional environments, the researcher will: (1) Provide a proxy of the d15N of average exported photoautotrophic organic matter; and (2) Provide a new level of detail into sedimentary organic N degradation and preservation.
Broader impacts:
This project will improve understanding of the fundamental underpinnings and behaviors of d15N amino acid patterns and how they behave in contrasting sedimentary environments, while also developing a potential paleoceanographic proxy. Funding will support a graduate student and undergraduate research at the institution. The researcher will also conduct community outreach in the form of a workshop/tutorial on the proxy development.";
String projects_0_end_date "2016-09";
String projects_0_geolocation "California Margin , Santa Barbara Basin , CA current system, Eastern Tropical Pacific";
String projects_0_name "The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records";
String projects_0_project_nid "704684";
String projects_0_start_date "2011-10";
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 "Amino acid d13C values of diatoms, bacteria, and core M772-003-2 samples from the R/V Meteor (M77) in the Peruvian ocean margin from November to December 2008.";
String title "[Amino acid d13C values of diatoms and bacteria] - Amino acid d13C values of diatoms, bacteria, and core M772-003-2 samples from the R/V Meteor (M77) in the Peruvian ocean margin from November to December 2008. (The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records)";
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.