Accessing BCO-DMO data
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| Dataset Title: | [Metal quotas of Line P diatoms in added Zn and Co incubation studies] - Metal quotas of NE Pacific and Altantic diatom isolates measured via ICP-MS after growth in zinc and cobalt media amendments in experiments with cultures collected from R/V Thomas G. Thompson cruise TN280, along Line P in the NE Pacific, in May of 2012 (US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_807299) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
Culture {
String bcodmo_name "sample_descrip";
String description "Culture name (e.g. Thalassiosira UNC12032)";
String long_name "Culture";
String units "unitless";
}
Added_Zn {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 100;
String bcodmo_name "trace_metal_conc";
String description "Total amount of added zinc (Zn) to incubation.";
String long_name "Added Zn";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
Added_Co {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 100;
String bcodmo_name "trace_metal_conc";
String description "Total amount of added cobalt (Co) to incubation.";
String long_name "Added Co";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
Total_Zn {
Float32 _FillValue NaN;
Float32 actual_range 1.9, 100.9;
String bcodmo_name "trace_metal_conc";
String description "Total zinc (Zn). Added Zn and background media Zn.";
String long_name "Total Zn";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
Total_Co {
Float32 _FillValue NaN;
Float32 actual_range 1.1, 100.1;
String bcodmo_name "trace_metal_conc";
String description "Total cobalt (Co). Added Co and background media Co.";
String long_name "Total Co";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
log_Zn2plus {
Float32 _FillValue NaN;
Float32 actual_range -12.7, -10.99;
String bcodmo_name "trace_metal_conc";
String description "Log of calculated free Zn2+ ion concentration in media. [Zn2+]";
String long_name "Log Zn2plus";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "moles per liter (mol/L)";
}
log_Co2plus {
Float32 _FillValue NaN;
Float32 actual_range -12.59, -10.63;
String bcodmo_name "trace_metal_conc";
String description "Log of calculated free Co2+ ion concentration in media. [Co2+]";
String long_name "Log Co2plus";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "moles per liter (mol/L)";
}
CO_to_P_avg {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.44;
String bcodmo_name "unknown";
String description "Average ratio of cobalt (Co) in millimoles to phosphorous (P) in moles. Co (mmol):P(mol) quota.";
String long_name "CO To P Avg";
String units "dimensionless";
}
ZN_to_P_avg {
String bcodmo_name "unknown";
String description "Average ratio of zinc (Zn) in millimoles to phosphorous (P) in moles. Zn (mmol):P(mol) quota.";
String long_name "ZN To P Avg";
String units "dimensionless";
}
CD_to_P_avg {
String bcodmo_name "unknown";
String description "Average ratio of cadmium (Cd) in micromoles to phosphorous (P) in moles. Cd (umol):P(mol) quota.";
String long_name "CD To P Avg";
String units "dimensionless";
}
MN_to_P_avg {
Float32 _FillValue NaN;
Float32 actual_range 0.12, 4.51;
String bcodmo_name "unknown";
String description "Average ratio of manganese (Mn) in millmoles to phosphorous (P) in moles. Mn (mmol):P(mol) quota.";
String long_name "MN To P Avg";
String units "dimensionless";
}
FE_to_P_avg {
Float32 _FillValue NaN;
Float32 actual_range 2.21, 17.17;
String bcodmo_name "unknown";
String description "Average ratio of iron (Fe) in millmoles to phosphorous (P) in moles. Fe (mmol):P(mol) quota.";
String long_name "FE To P Avg";
String units "dimensionless";
}
NI_to_P_avg {
String bcodmo_name "unknown";
String description "Average ratio of nickel (Ni) in millmoles to phosphorous (P) in moles. Ni (mmol):P(mol) quota.";
String long_name "NI To P Avg";
String units "dimensionless";
}
CU_to_P_avg {
Float32 _FillValue NaN;
Float32 actual_range 0.062, 1.62;
String bcodmo_name "unknown";
String description "Average ratio of copper (Cu) in millmoles to phosphorous (P) in moles. Cu (mmol):P(mol) quota.";
String long_name "CU To P Avg";
String units "dimensionless";
}
MO_to_P_avg {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 0.04;
String bcodmo_name "unknown";
String description "Average ratio of molybdenum (Mo) in millmoles to phosphorous (P) in moles. Mo (mmol):P(mol) quota.";
String long_name "MO To P Avg";
String units "dimensionless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Location: Cultures collected from Northeast Pacific Line P Transect 48.8167 N
128.667 W
Metal quotas
Cellular metal quotas were measured by inductively coupled plasma mass
spectrometry (ICP-MS). Biomass from replicate 25 mL matrix cultures of P.
tricornutum CCMP632, P. delicatissima UNC1205, and Thalassiosira UNC1203 were
pooled upon entering stationary phase and were centrifuged at 11,000 RPM
(14,610 x g) for 40 minutes at 4\\u00b0C. The cell pellet was resuspended in ~1
mL media and transferred to an acid-cleaned microcentrifuge tube. Cultures
were centrifuged again for 30 min at 14,100 RPM (13,336 x g) at 4\\u00b0C
before the supernatant was discarded. The remaining cell pellet was acidified
in 800 L of 5% nitric acid (Optima) containing 1 ppb indium for at least seven
days. Solids were removed by centrifugation. No attempt was made to remove
extracellular metals by washing cells with additional metal chelators in order
to minimize processing blanks. Quota determinations therefore include
contributions from both intracellular and extracellular pools. Process blank
digestions containing acid but no cells were performed in parallel. Digests
were diluted by a factor of 9 with 5% nitric acid 1 ppb indium solution before
being analyzed in duplicate on a Thermo ICAP-Q plasma mass spectrometer
calibrated to a multi-element standard curve (Spex Certiprep) over a range of
1 \\u2013 20 ppb. Samples were analyzed in KED mode after an 85s sample uptake
window and element mass windows were scanned 3 times during measurements. The
1 ppb indium internal standard was used to correct for variation in sample
delivery and plasma suppression between samples. Process blanks were
subtracted from measured concentrations. Phosphorus concentrations were also
measured by ICP-MS simultaneously and were calibrated to a standard curve
ranging from 100 \\u2013 3,200 ppb using a 1 ppm certified P stock (Alfa Aesar
Specpure). The seawater media base used for all growth experiments was
similarly analyzed via ICP-MS using a 1:10 dilution of media base into 5%
nitric acid 1 ppb indium and analyzed as above to determine background media
concentrations of total Zn and Co (0.9 nmol L-1 and 0.1 nmol L-1,
respectively).
Missing data identifiers in this dataset include:
* \"nd\" indicating no data
* Below Detection
* \"contam\" indicating the sample was contaminated
Isolation sources and locations
* Pseudonitzschia delicatissima UNC1205 and Thalassiosira UNC1203 were
isolated from
station P8 of the Line P transect, 48.817\\uf0b0N 128.666\\uf0b0W
* Phaeodactylum tricornutum CCMP632 was ordered from Bigelow, the strains
original
location of isolation was 54\\uf0b0N 4\\uf0b0W
* Thalassiosira pseudonana CCMP1335 was also from Bigelow, original location
of
isolation was 40.756\\u00b0 N 72.82\\u00b0 W";
String awards_0_award_nid "646122";
String awards_0_award_number "GBMF3782";
String awards_0_data_url "https://www.moore.org/grant-detail?grantId=GBMF3782";
String awards_0_funder_name "Gordon and Betty Moore Foundation: Marine Microbiology Initiative";
String awards_0_funding_acronym "MMI";
String awards_0_funding_source_nid "385";
String awards_1_award_nid "785825";
String awards_1_award_number "OCE-1736599";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1736599";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "Henrietta N Edmonds";
String awards_1_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Line P Metal quotas
PI: Mak Saito
Data Version 1: 2020-03-31";
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 "2020-03-31T20:11:49Z";
String date_modified "2020-04-10T14:55:44Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.807299.1";
String history
"2024-11-23T17:04:10Z (local files)
2024-11-23T17:04:10Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_807299.html";
String infoUrl "https://www.bco-dmo.org/dataset/807299";
String institution "BCO-DMO";
String instruments_0_acronym "Mass Spec";
String instruments_0_dataset_instrument_nid "807325";
String instruments_0_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_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_0_instrument_name "Mass Spectrometer";
String instruments_0_instrument_nid "685";
String instruments_0_supplied_name "Thermo ICAP-Q plasma mass spectrometer";
String keywords "added, Added_Co, Added_Zn, average, bco, bco-dmo, biological, CD_to_P_avg, chemical, co2plus, CO_to_P_avg, CU_to_P_avg, culture, data, dataset, dmo, erddap, FE_to_P_avg, log, log_Co2plus, log_Zn2plus, management, MN_to_P_avg, MO_to_P_avg, NI_to_P_avg, oceanography, office, preliminary, total, Total_Co, Total_Zn, zn2plus, ZN_to_P_avg";
String license "https://www.bco-dmo.org/dataset/807299/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/807299";
String param_mapping "{'807299': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/807299/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Mak A. Saito";
String people_0_person_nid "50985";
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 "Amber York";
String people_1_person_nid "643627";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "PMT Cobalt and Metalloenzymes,MM Saito";
String projects_0_acronym "PMT Cobalt and Metalloenzymes";
String projects_0_description
"NSF abstract:
Cobalt is important for many forms of marine life, yet it is one of the scarcest nutrients in the sea. Cobalt's oceanic abundance and distribution, along with other scarce nutrients, can influence the growth of microscopic plants (phytoplankton). This in turn can influence carbon cycles in the ocean and atmosphere. Therefore, knowledge of the controls on cobalt's abundance and chemical forms in seawater is a valuable component of our ability to understand the ocean's influence on global carbon cycling. Within phytoplankton and other marine microbes, metals such as cobalt, iron, nickel, and copper are used as critical components of enzymes responsible for key cellular reactions. Since these enzymes require metals to work, they are named metalloenzymes. Participating in a Pacific Ocean cruise from Alaska to Tahiti, this project will study the oceanic distributions of dissolved cobalt and the cellular content of a group of metalloenzymes known to influence biogeochemical cycles. The project will provide scientific impact by creating new knowledge about oceanic micronutrients in regions of economic interest with regard to fisheries and deep-sea mining. Measurement of proteins in the North Pacific will provide data of broad biological and chemical interest and will be made available through a new NSF-funded \"EarthCube Ocean Protein Portal\" data base. Educational impact will stem from participation of a graduate student and two young technicians, as well as the PI's development of a high school chemistry curriculum for use in two local high schools, thus allowing teachers to include real oceanic and environmental data at their first introduction to chemistry.
Cobalt has a complex biogeochemical cycle. Both its inorganic and organic forms are used by biology in the upper ocean and it is removed from solution by being scavenged in the intermediate and deep ocean. This scavenging removal results in cobalt having the smallest oceanic inventory of any biologically utilized element. Recent studies, however, have found that large dissolved cobalt plumes occur in major oxygen minimum zones due to a combination of less scavenging and additions from sedimentary and remineralization fluxes. The GP15 US GEOTRACES Pacific Meridional Transect (PMT) provides an opportunity to examine the influence of oxygen depletion on cobalt chemistry. Moreover, the study of the protein component of microbial communities using new proteomic techniques will provide evidence of how different major microorganisms respond to the chemical environment (e.g. through transporter production for specific nutrients and micronutrients) as well as the biochemical basis for metal requirements related to the use of specific metalloenzymes. Specifically, the PMT provides an opportunity to confirm that the Pacific oxygen minimum zones contain a large amount of cobalt and to test the hypotheses that simultaneous zinc scarcity could induce wide-scale biochemical substitution of cobalt for zinc in the North Pacific Ocean.";
String projects_0_end_date "2019-10";
String projects_0_geolocation "Laboratory Study and Cultures from Northeast Pacific Line P Transect 48.8167 N 128.667 W";
String projects_0_name "US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean";
String projects_0_project_nid "785826";
String projects_0_start_date "2017-11";
String projects_1_acronym "MM Saito";
String projects_1_description "In support of obtaining deeper knowledge of major biogeochemically relevant proteins to inform a mechanistic understanding of global marine biogeochemical cycles.";
String projects_1_end_date "2019-12";
String projects_1_name "Marine Microbial Investigator Award: Investigator Mak Saito";
String projects_1_project_nid "786672";
String projects_1_start_date "2013-05";
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 "Metal quotas of two NE Pacific Line P diatom isolates and one Atlantic diatom isolate measured via ICP-MS after growth in zinc and cobalt media amendments. Experiments with cultures collected from the GeoMICS expedition on the R/V Thomas G. Thompson (cruise TN280), along Line P in the NE Pacific, in May of 2012.";
String title "[Metal quotas of Line P diatoms in added Zn and Co incubation studies] - Metal quotas of NE Pacific and Altantic diatom isolates measured via ICP-MS after growth in zinc and cobalt media amendments in experiments with cultures collected from R/V Thomas G. Thompson cruise TN280, along Line P in the NE Pacific, in May of 2012 (US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean)";
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.