Accessing BCO-DMO data
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| Dataset Title: | [Trace elements in CaCO3 and fluid] - Table 2. Elemental ratios and partition coefficients for CaCO3 in deepsea conditions: Mg, S, Sr, and Ba between crystallized solids and fluid. (Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_806957) |
| Information: | Summary
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Attributes {
s {
analysis {
String bcodmo_name "unknown";
String description "The type of analysis: solids; fluids; or KE (Doener-Hoskins partition coefficients between solid and fluid)";
String long_name "Analysis";
String units "unitless";
}
run {
String bcodmo_name "exp_id";
String description "experimental run identifier";
String long_name "Run";
String units "unitless";
}
press {
Int16 _FillValue 32767;
Int16 actual_range 1, 345;
String bcodmo_name "pressure";
String description "pressure";
String long_name "Press";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/";
String units "bars";
}
minerals {
String bcodmo_name "unknown";
String description "minerals identified with X-ray diffraction technique: aragonite; monoclinic carbonate (CaCO3-II)";
String long_name "Minerals";
String units "unitless";
}
Mg_Ca {
Float32 _FillValue NaN;
Float32 actual_range 8.284, 22360.0;
String bcodmo_name "unknown";
String description "magnesium to calcium ratio in carbonate crystals (solids) or in fluid at end of experiment";
String long_name "Mg Ca";
String units "millimole per mole of calcium";
}
Mg_Ca_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.414, 1118.0;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of magnesium to calcium ratio";
String long_name "Mg Ca 2sd";
String units "millimole per mole of calcium";
}
S_Ca {
Float32 _FillValue NaN;
Float32 actual_range 7.042, 11956.0;
String bcodmo_name "unknown";
String description "sulfur to calcium ratio in carbonate crystals (solids) or in fluid at end of experiment";
String long_name "S Ca";
String units "millimole per mole of calcium";
}
S_Ca_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.352, 598.0;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of sulfur to calcium ratio";
String long_name "S Ca 2sd";
String units "micromole per mole of calcium";
}
Sr_Ca {
Float32 _FillValue NaN;
Float32 actual_range 8.17, 16.676;
String bcodmo_name "unknown";
String description "strontium to calcium ratio in carbonate crystals (solids) or in fluid at end of experiment";
String long_name "Sr Ca";
String units "millimole per mole of calcium";
}
Sr_Ca_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.408, 0.834;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of strontium to calcium ratio";
String long_name "Sr Ca 2sd";
String units "millimole per mole of calcium";
}
Ba_Ca {
Float32 _FillValue NaN;
Float32 actual_range 3.73, 27.7;
String bcodmo_name "unknown";
String description "barium to calcium ratio in carbonate crystals (solids) or in fluid at end of experiment";
String long_name "Ba Ca";
String units "millimole per mole of calcium";
}
Ba_Ca_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.187, 1.4;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of barium to calcium ratio";
String long_name "Ba Ca 2sd";
String units "micromole per mole of calcium";
}
KMg {
Float32 _FillValue NaN;
Float32 actual_range 0.848, 3.37;
String bcodmo_name "unknown";
String description "Doener-Hoskins partition coefficients of magnesium multiplied by 1000";
String long_name "KMG";
String units "unitless";
}
KMg_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.0167, 0.129;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of Doener-Hoskins partition coefficients of magnesium multiplied by 1000";
String long_name "KMG 2SD";
String units "unitless";
}
KS {
Float32 _FillValue NaN;
Float32 actual_range 1.31, 3.85;
String bcodmo_name "unknown";
String description "Doener-Hoskins partition coefficients of sulfur multiplied by 1000";
String long_name "KS";
String units "unitless";
}
KS_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.169, 0.406;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of Doener-Hoskins partition coefficients of sulfur multiplied by 1000";
String long_name "KS 2SD";
String units "unitless";
}
KSr {
Float32 _FillValue NaN;
Float32 actual_range 0.769, 1.197;
String bcodmo_name "unknown";
String description "Doener-Hoskins partition coefficients of strontium";
String long_name "KSR";
String units "unitless";
}
KSr_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.048, 0.1;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of Doener-Hoskins partition coefficients of strontium";
String long_name "KSR 2SD";
String units "unitless";
}
KBa {
Float32 _FillValue NaN;
Float32 actual_range 1.12, 2.23;
String bcodmo_name "unknown";
String description "Doener-Hoskins partition coefficients of barium";
String long_name "KBa";
String units "unitless";
}
Kba_2sd {
Float32 _FillValue NaN;
Float32 actual_range 0.127, 0.591;
String bcodmo_name "unknown";
String description "two standard deviations from the mean of Doener-Hoskins partition coefficients of barium";
String long_name "Kba 2sd";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"X-ray diffraction (XRD)
Powdered samples were examined for mineral presence using a Rigaku Ultima III
X-ray Diffraction (XRD) System at the Institute of Imaging and Analytical
Technologies (i2AT) at Mississippi State University. These analyses were
conducted at 40 kV and 40 mA.
Elemental analysis of experimental aragonite crystals and experimental fluids
with ICP-MS
Crystals were dissolved and solutions were analyzed by ICP-MS. Experimental
fluids were also analyzed with ICP-MS, as well. Analyses were conducted on an
Agilent 7900 quadrupole ICP-MS equipped with a glass nebulizer at the
University of Rochester (Rochester, NY). Prior to analysis, fluid samples were
diluted with 2% trace metal grade HNO3 (Fisher) in the volume proportion of
1:100. Aragonite crystals were dissolved in HNO3 in the mass proportion of
1:1000. Experimental fluid samples were analyzed using a 5-point calibration
curve (one blank and four standards). Seawater standards were prepared by
diluting a seawater certificate reference material (CRM-SW; High-Purity
Standards) to a final concentration of ~300, 200, 150, and 80 ppm.
Experimental crystals were analyzed using a 5-point calibration curve (one
blank and four standards). Calcium carbonate standards were prepared by
dissolving and diluting the original MACS-3 powder to a final concentration of
~111, 55, 27, and 11 ppm. Because S concentration was not reported in the
certificate of analysis provided by the USGS, we added a small amount of
sulfur single element standard (Inorganic Ventures) to a final concentration
of ~1.5, 0.75, 0.375, and 0.150 ppm, in each MACS-3 standard we prepared.
Samples, blanks, and standards were also spiked with 2 ppb indium, which was
used as the internal standard to check for possible instrumental drift during
each analytical session.
The instrument was tuned at the beginning of each analytical session (two
analytical sessions in two consecutive days). 24Mg, 34S, 43Ca, 88Sr, 138Ba,
and 238U were analyzed.\\u00a0 Integration times were the following: 0.3 s for
24Mg; 0.12 s for 43Ca, 88Sr, and 138Ba; 0.99 s for 238U. The calibration curve
was run before analyzing each set of samples. For each element analyzed, the
correlation among standards was 0.9923 or better. Elements were identified
using three peaks. Each analysis included three replicates, with 100
sweeps/replicate. The carrier gas (argon) flow was set at 1.15 L/min. In
addition, we used helium flow of 4.2 milliliters per minute in the collision
reaction cell in the ICP-MS to minimize oxide interference. At the end of each
tuning, oxides and doubly-charged ion interferences were below 0.8% and 1.4%,
respectively. Data were computed automatically during the run using the
Agilent Mass Hunter 4.1 workstation software v. C.01.01.
Results
XRD spectra identified the presence of aragonite and monohydrocalcite (Table
2). Only aragonite crystallized at intermediate pressure (110 bars).
Calculations of fluid carbonate chemistry were conducted with a CO2SYS
spreadsheet (Lewis and Wallace, 1998) \\u00a0and presented in Table 1. There,
measured pH and total alkalinity (TA) were used to calculate the concentration
of CO32-, which together with Ca2+ is necessary to calculate fluid saturation
states with respect to aragonite (Omega-Ar). Precipitation started at
saturation state, which exceeds that of artificial seawater (ASW) by the
factor of ~25. Over the course of the experiments, Omega-Ar decreased back to
2, i.e. Omega-Ar value of ASW prior to the addition of Na2CO3. Table 2
contains E/Ca of experimental products (solids and liquids) as well as the
Doener-Hoskins apparent partition coefficients between solid and fluid (KE).
Fluid composition changed during individual experiments, and therefore, values
of KE were calculated using the Doener-Hoskins relationship:
\\u00a0\\u00a0\\u00a0\\u00a0\\u00a0\\u00a0\\u00a0KE= log(1+ mE^aragonite /mE^fluid) /
log(1+ mCa^aragonite /mCa^fluid)\\u00a0 \\u00a0 (1)
where m^aragonite is the total number of moles of element (i.e., Mg, S, Sr,
Ba, or U) or Ca in the final precipitate, and m^fluid is the total number of
moles of element or Ca in the final fluid (Doerner and Hoskins, 1925).
Software products used:
XRD: Jade and Microsoft Excel
ICP-MS: Agilent Mass Hunter 4.1 workstation software v. C.01.01 and
Microsoft Excel";
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
"Trace elements in CaCO3 and fluid
Table 2. Elemental ratios and partition coefficients for CaCO3 in deepsea conditions (Mg, S, Sr, and Ba between crystallized solids and fluid)
PI: R. Gabitov (Miss. State)
version date: 2020-03-25
(*) - KE Doener-Hoskins values cannot be used for aragonite-fluid partitioning because other carbonate minerals precipitated in those runs.
Runs: ASW = Artificial SeaWater (Instant Ocean); other fluid samples are from the end of experiments;
LP = low pressure run; RPI = runs performed at Rensselaer Polytechnic Institute
Minerals: Ar = aragonite; MHC = monohydrocalcite; CaCO3-II = monoclinic calcium carbonate.";
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 "2020-03-25T19:25:25Z";
String date_modified "2020-04-09T12:58:47Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.806957.1";
String history
"2024-11-23T16:45:17Z (local files)
2024-11-23T16:45:17Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_806957.html";
String infoUrl "https://www.bco-dmo.org/dataset/806957";
String institution "BCO-DMO";
String instruments_0_acronym "unknown";
String instruments_0_dataset_instrument_description "Custom designed pressure chamber used to simulate the high-pressure conditions at the seafloor for this set of experiments (designed at Rensselaer Polytech Institute, Department of Earth and Environmental Sciences).";
String instruments_0_dataset_instrument_nid "806964";
String instruments_0_description "No relevant match in BCO-DMO instrument vocabulary.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/999/";
String instruments_0_instrument_name "unknown";
String instruments_0_instrument_nid "575";
String instruments_0_supplied_name "high-pressure apparatus";
String instruments_1_acronym "XRD";
String instruments_1_dataset_instrument_description "Located at at Mississippi State University";
String instruments_1_dataset_instrument_nid "806976";
String instruments_1_description "Instruments that identify crystalline solids by measuring the characteristic spaces between layers of atoms or molecules in a crystal.";
String instruments_1_instrument_name "X-ray diffractometer";
String instruments_1_instrument_nid "625931";
String instruments_1_supplied_name "Rigaku Ultima III X-ray Diffraction (XRD) System at the Institute of Imaging and Analytical Technologies (i2AT)";
String instruments_2_acronym "ICP-OES";
String instruments_2_dataset_instrument_nid "806975";
String instruments_2_description "Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.";
String instruments_2_instrument_name "Inductively Coupled Plasma Optical Emission Spectrometer";
String instruments_2_instrument_nid "639924";
String instruments_2_supplied_name "Agilent 7900 quadrupole ICP-MS equipped with a glass nebulizer at the University of Rochester (Rochester, NY)";
String keywords "2sd, analysis, Ba_Ca, Ba_Ca_2sd, bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, kba, Kba_2sd, kmg, KMg_2sd, KS_2sd, ksr, KSr_2sd, management, Mg_Ca, Mg_Ca_2sd, minerals, oceanography, office, preliminary, press, run, S_Ca, S_Ca_2sd, Sr_Ca, Sr_Ca_2sd";
String license "https://www.bco-dmo.org/dataset/806957/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/806957";
String param_mapping "{'806957': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/806957/parameters";
String people_0_affiliation "Mississippi State University";
String people_0_affiliation_acronym "MSU";
String people_0_person_name "Rinat Gabitov";
String people_0_person_nid "743432";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Rochester";
String people_1_person_name "Chiara Borrelli";
String people_1_person_nid "743434";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Rensselaer Polytechnic Institute";
String people_2_affiliation_acronym "RPI";
String people_2_person_name "Karyn Rogers";
String people_2_person_nid "661573";
String people_2_role "Co-Principal Investigator";
String people_2_role_type "originator";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Nancy Copley";
String people_3_person_nid "50396";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Deep Sea Geochem CaCO3";
String projects_0_acronym "Deep Sea Geochem CaCO3";
String projects_0_description "Biologically-mediated CaCO3 precipitation widely occurs in aquatic systems and is often directly linked to the metabolic activity of microorganisms, which could significantly affect the local environment. An example is oxidation of methane and reduction of sulfate mediated by a consortium of Bacteria and Archaea. In order to investigate geochemistry of CaCO3precipitated abiotically and under microbial activity experimental work was initiated. The abiotic experiments were performed at different temperatures and pressures (nitrogen and nitrogen-methane mixture). Further geochemical analyses will allow evaluating of the effect of total pressure and methane partial pressure on the geochemistry of CaCO3. Sulfate reducing bacterial (Desulfovibrio salexigens) was successfully cultured and precipitation experiments on microbially mediated CaCO3 are in progress. This work is relevant to C-DEBI Research Theme I (Activity in the Deep Subseafloor Biosphere: function & rates of global biogeochemical processes) because carbonate growth rate is linked to microbial activity and the rate of methane oxidation.";
String projects_0_end_date "2014-09";
String projects_0_name "Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study";
String projects_0_project_nid "743426";
String projects_0_project_website "https://www.darkenergybiosphere.org/award/biologically-induced-methane-oxidation-and-precipitation-of-carbonate-minerals-an-experimental-study/";
String projects_0_start_date "2014-05";
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 "Trace elements in CaCO3 and fluid. Table 2. Elemental ratios and partition coefficients for CaCO3 in deepsea conditions: Mg, S, Sr, and Ba between crystallized solids and fluid.";
String title "[Trace elements in CaCO3 and fluid] - Table 2. Elemental ratios and partition coefficients for CaCO3 in deepsea conditions: Mg, S, Sr, and Ba between crystallized solids and fluid. (Biologically induced methane oxidation and precipitation of carbonate minerals: An experimental study)";
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.