Accessing BCO-DMO data
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| Dataset Title: | [M. jannaschii high/low H2: isotopes and fractionation factors] - Carbon isotopic compositions and fractionation factors of M. jannaschii in high and low hydrogen (H2) environments (Bioenergetic influences upon carbon flow in alkaliphilic sulfate-reducing microbial populations with relevance to the subsurface biosphere at the Lost City Hydrothermal Field) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_812240) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
Experiment {
String bcodmo_name "treatment";
String description "Experiment description: either high (abundant) or low (limited) hydrogen";
String long_name "Experiment";
String units "unitless";
}
Culture_ID {
String bcodmo_name "sample";
String description "culture identifier";
String long_name "Culture ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
d13C_ppt_Ala {
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of alanine";
String long_name "D13 C Ppt Ala";
String units "parts per thousand (ppt)";
}
d13C_ppt_Gly {
Float32 _FillValue NaN;
Float32 actual_range -62.3, -51.8;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of glycine";
String long_name "D13 C PPT GLY";
String units "parts per thousand (ppt)";
}
d13C_ppt_Thr {
Float32 _FillValue NaN;
Float32 actual_range -58.8, -40.5;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of threonine";
String long_name "D13 C PPT THR";
String units "parts per thousand (ppt)";
}
d13C_ppt_Ser {
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of serine";
String long_name "D13 C Ppt Ser";
String units "parts per thousand (ppt)";
}
d13C_ppt_Val {
Float32 _FillValue NaN;
Float32 actual_range -68.1, -57.1;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of valine";
String long_name "D13 C Ppt Val";
String units "parts per thousand (ppt)";
}
d13C_ppt_Leu {
Float32 _FillValue NaN;
Float32 actual_range -71.4, -58.9;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of leucine";
String long_name "D13 C Ppt Leu";
String units "parts per thousand (ppt)";
}
d13C_ppt_Iso {
Float32 _FillValue NaN;
Float32 actual_range -68.5, -57.5;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of isoleucine";
String long_name "D13 C Ppt Iso";
String units "parts per thousand (ppt)";
}
d13C_ppt_Pro {
Float32 _FillValue NaN;
Float32 actual_range -58.8, -51.8;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of proline";
String long_name "D13 C Ppt Pro";
String units "parts per thousand (ppt)";
}
d13C_ppt_Glu {
Float32 _FillValue NaN;
Float32 actual_range -51.4, -41.5;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of glu";
String long_name "D13 C Ppt Glu";
String units "parts per thousand (ppt)";
}
d13C_ppt_Phe {
Float32 _FillValue NaN;
Float32 actual_range -59.7, -50.4;
String bcodmo_name "amino_conc";
String description "13C isotopic ratio of phenylalanine";
String long_name "D13 C Ppt Phe";
String units "parts per thousand (ppt)";
}
Weighted_Avg_d13C_THAA_ppt {
Float32 _FillValue NaN;
Float32 actual_range -65.1, -54.2;
String bcodmo_name "amino_conc";
String description "Weighted isotopic ratio of each amino acid as a toal";
String long_name "Weighted Avg D13 C THAA Ppt";
String units "parts per thousand (ppt)";
}
d13C_ppt_Sq_3 {
String bcodmo_name "lipids_biota";
String description "13C isotopic ratio of squalenoid with three double bonds";
String long_name "D13 C PPT SQ 3";
String units "parts per thousand (ppt)";
}
d13C_ppt_Sq_4 {
Float32 _FillValue NaN;
Float32 actual_range -72.8, -57.6;
String bcodmo_name "lipids_biota";
String description "13C isotopic ratio of squalenoid with four double bonds";
String long_name "D13 C PPT SQ 4";
String units "parts per thousand (ppt)";
}
d13C_ppt_Sq_5 {
Float32 _FillValue NaN;
Float32 actual_range -69.7, -56.7;
String bcodmo_name "lipids_biota";
String description "13C isotopic ratio of squalenoid with five double bonds";
String long_name "D13 C PPT SQ 5";
String units "parts per thousand (ppt)";
}
d13C_ppt_Sq_6 {
String bcodmo_name "lipids_biota";
String description "13C isotopic ratio of squalene";
String long_name "D13 C PPT SQ 6";
String units "parts per thousand (ppt)";
}
Weighted_Avg_ppt_d13C_Sq {
Float32 _FillValue NaN;
Float32 actual_range -71.0, -57.0;
String bcodmo_name "lipids_biota";
String description "weighted average of the isotopic composition of squalenoids";
String long_name "Weighted Avg Ppt D13 C Sq";
String units "parts per thousand (ppt)";
}
DIC_mM_To {
Float32 _FillValue NaN;
Float32 actual_range 3.7, 4.4;
String bcodmo_name "DIC";
String description "Concentration of dissolved inorganic carbon at the start of the experiment";
String long_name "DIC M M To";
String units "milliMolar (mM)";
}
DIC_mM_Tf {
Float32 _FillValue NaN;
Float32 actual_range 3.1, 4.5;
String bcodmo_name "DIC";
String description "Concentration of dissolved inorganic carbon at the end of the experiment";
String long_name "DIC M M Tf";
String units "milliMolar (mM)";
}
TFAA_uM_To {
Float32 _FillValue NaN;
Float32 actual_range 0.3, 1.7;
String bcodmo_name "amino_conc";
String description "Concentration of total free amino acids at the start of the experiment";
String long_name "TFAA U M To";
String units "microMolar (uM)";
}
TFAA_uM_Tf {
Float32 _FillValue NaN;
Float32 actual_range 3.7, 10.0;
String bcodmo_name "amino_conc";
String description "Concentration of total free amino acids at the end of the experiment";
String long_name "TFAA U M Tf";
String units "microMolar (uM)";
}
THAA_uM_To {
Float32 _FillValue NaN;
Float32 actual_range 2.1, 11.0;
String bcodmo_name "amino_conc";
String description "Concentration of total hydrolizable amino acids at the start of the experiment";
String long_name "THAA U M To";
String units "microMolar (uM)";
}
THAA_uM_Tf {
Float32 _FillValue NaN;
Float32 actual_range 16.4, 50.9;
String bcodmo_name "amino_conc";
String description "Concentration of total hydrolizable amino acids at the end of the experiment";
String long_name "THAA U M Tf";
String units "microMolar (uM)";
}
Fractionation_factor_ppt_eCO2_CH4 {
Float32 _FillValue NaN;
Float32 actual_range 28.5, 45.9;
String bcodmo_name "unknown";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Fractionation factor between CO2-and methane";
String long_name "Fractionation Factor Ppt E CO2 CH4";
String units "parts per thousand (ppt)";
}
Fractionation_factor_ppt_eCO2_B {
Float32 _FillValue NaN;
Float32 actual_range 22.4, 27.1;
String bcodmo_name "unknown";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Fractionation factor between CO2-and biomass";
String long_name "Fractionation Factor Ppt E CO2 B";
String units "parts per thousand (ppt)";
}
Fractionation_factor_ppt_eCO2_AA {
Float32 _FillValue NaN;
Float32 actual_range 27.5, 35.0;
String bcodmo_name "unknown";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Fractionation factor between CO2-and amino acids";
String long_name "Fractionation Factor Ppt E CO2 AA";
String units "parts per thousand (ppt)";
}
Fractionation_factor_ppt_eCO2_squalenoids {
String bcodmo_name "unknown";
String description "Fractionation factor between CO2-and squalenoids";
String long_name "Fractionation Factor Ppt E CO2 Squalenoids";
String units "parts per thousand (ppt)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Isolation and isotopic analysis of squalenoids:
Cell pellets were freeze-dried overnight, ground with a clean spatula, and
extracted three times by sonication in a centrifuge tube filled with 50 mL of
3:1 dichloromethane:methanol (DCM:MeOH). All glassware was combusted overnight
at 500\\u00b0C to remove organics prior to use. After sonication, the extracts
were spun in a centrifuge at 125 g for 15 min and the supernatant was decanted
to a separate vial. All extracts were combined and the solvent was evaporated
to dryness in a rotary evaporator.\\u00a0 A maximum of 2 mL of 9:1 DCM:MeOH was
added to dissolve the total extract that was then passed over Na2SO4 to remove
water. The water-free extract was then separated into different fractions over
SepraTM NH2 bulk-packing (P/N 1001711653 572122 \\u2013 U) silica column by
eluting with solvents of increasing polarity (F1 = 5 mL of hexane, F2 = 6 mL
of 3:1 hexane:DCM, F3 = 7 mL of 9:1 DCM:acetone, F4 = 8 mL of 4% formic acid
in DCM). The apolar fraction (F1) was dried under N2, then re-dissolved in 50
\\u00b5L of hexane for identification.
The lipids in the apolar fraction were identified and quantified using an
Agilent Technologies 5975 inert XL Mass Selective Detector after separation on
an Agilent J&W GC HP-5MS UI capillary column (30 m \\u00d7 0.25 mm i.d., 0.25
\\u00b5m film thickness, P/N 19091S \\u2013 433UIE) using He as the carrier gas.
Samples were injected in pulse splitless mode. The GC oven was from an initial
temperature of 70\\u00b0C, then heated to 150\\u00b0C at 15\\u00b0C per min, then
to 300\\u00b0C at 5\\u00b0C per min. Peaks were quantified by comparison to a
5-point standard curve of a C7-C30 alkane series (P/N 49451 \\u2013 U, Sigma
Aldrich). The isotopic composition of biomarkers in the apolar fraction was
determined on a Thermo Scientific Gas Chromatograph-IsolinkII-Isotope Ratio
Mass Spectrometer (GC-IsolinkII-IRMS) equipped with an Agilent DB-5 fused
silica column (30 m \\u00d7 0.25 mm i.d., 0.25 \\u00b5m film thickness) with He
as the carrier gas.
Isolation, characterization, and isotopic analysis of amino acids:
Pelleted cells were hydrolyzed with 6 M HCl (Ultrapure grade) with 1% of 11
mM ascorbic acid under N2 at 110\\u00b0C for 20 h (Henrichs, 1991). After
cooling, hydrolyzed amino acids were spiked with internal standard norvaline
and derivatized with acidified isopropanol and acetyl chloride for 1 h at
110\\u00b0C (Silfer et al., 1991). The samples then reacted at 110\\u00b0C for 1
h on a hot plate. They were then esterified with trifluoroacetic anhydride
(TFAA) for 10 min at 110\\u00b0C for 10 min. The resulting derivatives were
dissolved in dichloromethane. The isotopic signatures of derivatized amino
acids were determined by GC-IsolinkII-IRMS";
String awards_0_award_nid "554980";
String awards_0_award_number "OCE-0939564";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564";
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
"M. jannaschii high/low H2: isotopes and fractionation factors
PI: S. Lang (USC-Columbia)
version date: 20200-5-25";
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 "2020-05-20T21:48:29Z";
String date_modified "2020-07-09T13:22:31Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.812240.1";
String history
"2024-12-30T17:17:12Z (local files)
2024-12-30T17:17:12Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_812240.html";
String infoUrl "https://www.bco-dmo.org/dataset/812240";
String institution "BCO-DMO";
String instruments_0_acronym "IR Mass Spec";
String instruments_0_dataset_instrument_description "For measuring isotopic composition of dissolved inorganic carbon.";
String instruments_0_dataset_instrument_nid "812251";
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 "Thermo Scientific GasBench- Delta V Isotope Radio Mass Spectrometer";
String instruments_1_dataset_instrument_description "For or identification and abundance of carbon isotopes. Agilent Technologies 5975 inert XL Mass Selective Detector after separation on an Agilent J&W GC HP-5MS UI capillary column (30 m × 0.25 mm i.d., 0.25 µm film thickness, P/N 19091S – 433UIE)";
String instruments_1_dataset_instrument_nid "812249";
String instruments_1_description "Instruments 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 by a mass spectrometer.";
String instruments_1_instrument_name "Gas Chromatograph Mass Spectrometer";
String instruments_1_instrument_nid "812252";
String instruments_1_supplied_name "Gas Chromatograph Mass Spectrometer";
String instruments_2_dataset_instrument_description "For measuring isotopic composition of biomarkers, including amino acid and lipids: Thermo Scientific Trace 1310 Gas Chromatograph-IsolinkII-Delta V Isotope Ratio Mass Spectrometer equipped with an Agilent DB-5 fused silica column (30 m × 0.25 mm i.d., 0.25 µm film thickness) and a Gerstel CIS – 6 inlet.";
String instruments_2_dataset_instrument_nid "812250";
String instruments_2_description "Instruments 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 by a mass spectrometer.";
String instruments_2_instrument_name "Gas Chromatograph Mass Spectrometer";
String instruments_2_instrument_nid "812252";
String instruments_2_supplied_name "Thermo Scientific Trace 1310 Gas Chromatograph-IsolinkII-Delta V Isotope Ratio Mass Spectrometer";
String keywords "ala, average, bco, bco-dmo, biological, carbon, carbon dioxide, ch4, chemical, co2, culture, Culture_ID, d13, d13C_ppt_Ala, d13C_ppt_Glu, d13C_ppt_Gly, d13C_ppt_Iso, d13C_ppt_Leu, d13C_ppt_Phe, d13C_ppt_Pro, d13C_ppt_Ser, d13C_ppt_Sq_3, d13C_ppt_Sq_4, d13C_ppt_Sq_5, d13C_ppt_Sq_6, d13C_ppt_Thr, d13C_ppt_Val, data, dataset, dic, DIC_mM_Tf, DIC_mM_To, dioxide, dmo, erddap, experiment, factor, fractionation, Fractionation_factor_ppt_eCO2_AA, Fractionation_factor_ppt_eCO2_B, Fractionation_factor_ppt_eCO2_CH4, Fractionation_factor_ppt_eCO2_squalenoids, glu, gly, iso, leu, management, oceanography, office, phe, ppt, preliminary, pro, ser, squalenoids, tfaa, TFAA_uM_Tf, TFAA_uM_To, thaa, THAA_uM_Tf, THAA_uM_To, thr, u, val, weighted, Weighted_Avg_d13C_THAA_ppt, Weighted_Avg_ppt_d13C_Sq";
String license "https://www.bco-dmo.org/dataset/812240/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/812240";
String param_mapping "{'812240': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/812240/parameters";
String people_0_affiliation "University of South Carolina at Columbia";
String people_0_person_name "Susan Q. Lang";
String people_0_person_nid "658607";
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 "Carbon flow through SRB";
String projects_0_acronym "Carbon flow through SRB";
String projects_0_description
"Project description from C-DEBI:
The microbial biosphere in serpentinizing subseafloor rocks is globally significant. Tantalizing evidence from studies of the Lost City Hydrothermal Field and continental ophiolites indicates that hydrogendriven microbial metabolisms prevails under the highly reducing, high pH conditions that characterize these environments. Interest in these processes is evident from an upcoming cruise to the Atlantis Massif in Fall 2015 to obtain drill cores in the vicinity of the Lost City Hydrothermal Field (IODP Expedition #357; both PIs were proponents of the IODP proposal and have applied as shipboard scientists). The PIs and colleagues have made headway over the last decade in identifying the key organisms and metabolisms present at the LCHF, and in constraining the sources and fates of carbon compounds. The linkages between geology and biology remain enigmatic, however, because of the precipitation of inorganic carbon at high pHs and overlapping biogenic and abiogenic carbon sources. We propose here to investigate the influence of free energy availability by sulfate reduction in resource utilization and carbon flow by model alkaliphilic prokaryotes. The laboratory approach using a model system will inform shipboard experiments with fresh samples from the AM, and the potential characterization of new organisms from serpentinizing terrains.
This project was funded by a C-DEBI Research Grant";
String projects_0_end_date "2016-03";
String projects_0_geolocation "Atlantis Massif, 30 8'N, 42 8'W";
String projects_0_name "Bioenergetic influences upon carbon flow in alkaliphilic sulfate-reducing microbial populations with relevance to the subsurface biosphere at the Lost City Hydrothermal Field";
String projects_0_project_nid "661802";
String projects_0_start_date "2015-04";
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 "Carbon isotopic compositions and fractionation factors of amino acids and squalenoid lipids in Methanocaldococcus jannaschii in high and low hydrogen (H2) environments.";
String title "[M. jannaschii high/low H2: isotopes and fractionation factors] - Carbon isotopic compositions and fractionation factors of M. jannaschii in high and low hydrogen (H2) environments (Bioenergetic influences upon carbon flow in alkaliphilic sulfate-reducing microbial populations with relevance to the subsurface biosphere at the Lost City Hydrothermal Field)";
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.