Accessing BCO-DMO data
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| Dataset Title: | [L. pertusa calcification records from pH experiments] - Calcification rates from pH experiments on Lophelia pertusa specimens collected from the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_659379) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
location {
String bcodmo_name "site";
String description "Location where specimen was collected; Tisler Reef or the Gulf of Mexico";
String long_name "Location";
String units "unitless";
}
pH_treatment {
Float32 _FillValue NaN;
Float32 actual_range 7.6, 8.1;
String bcodmo_name "treatment";
String description "Level of pH treatment";
String long_name "P H Treatment";
String units "unitless";
}
tank {
String bcodmo_name "tank";
String description "Tank number";
String long_name "Tank";
String units "unitless";
}
fragment_num {
String bcodmo_name "sample";
String description "Fragment ID number";
String long_name "Fragment Num";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
polyps_num {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 3, 15;
String bcodmo_name "count";
String description "Number of polyps on fragment";
String long_name "Polyps Num";
String units "count";
}
starting_DW {
Float32 _FillValue NaN;
Float32 actual_range 7.08, 79.74;
String bcodmo_name "dry_wgt";
String description "Starting dry weight";
String long_name "Starting DW";
String units "grams";
}
AFDM {
Float32 _FillValue NaN;
Float32 actual_range 0.25, 3.29;
String bcodmo_name "dry_wgt";
String description "Ash free dry mass";
String long_name "AFDM";
String units "grams";
}
day {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 14;
String bcodmo_name "day";
String description "Day of measurement; 0 or 14";
String long_name "Day";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/";
String units "day";
}
ttl_alkalinity_change {
Float32 _FillValue NaN;
Float32 actual_range 113.5, 1052.0;
String bcodmo_name "TALK";
String description "Total alkalinity change";
String long_name "Ttl Alkalinity Change";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/";
String units "Unknown";
}
net_calcification {
Float32 _FillValue NaN;
Float32 actual_range -0.0149, 0.087;
String bcodmo_name "growth";
String description "Percent growth of coral colony per day";
String long_name "Net Calcification";
String units "percent per day (%/d -1)";
}
bouyant_weight {
Float32 _FillValue NaN;
Float32 actual_range 5.73, 50.87;
String bcodmo_name "weight";
String description "Bouyant weight of sample";
String long_name "Bouyant Weight";
String units "grams";
}
dry_weight {
Float32 _FillValue NaN;
Float32 actual_range 9.02, 79.85;
String bcodmo_name "dry_wgt";
String description "Dry weight of sample";
String long_name "Dry Weight";
String units "grams";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Acquisition Description for Tisler\\u00a0Reef Data:
Net calcification was measured using the total alkalinity anomaly (Smith & Key
1975; Ohde & Hossain 2004). Corals were individually placed in closed glass
chambers (220 ml) in a water bath that maintained temperature to +/-0.2
degrees C during all trials. To avoid hypoxia or the severe reductions of pH
during incubations, ambient air was continuously bubbled into the chambers at
a slow rate (1-2 bubbles s-1). This also provided adequate circulation within
the chamber. A 60 ml water sample was collected by syringe before and after
the incubation period, and measured for total alkalinity in duplicate. The
respiration rate of each colony was measured as oxygen consumption in
a\\u00a0400 ml closed acrylic chamber during hour-long incubations. Dissolved
oxygen concentrations were measured in\\u00a0umol\\u00a0L-1\\u00a0using a
Strathkelvin 782 dual oxygen meter and SI130\\u00a0microcathode\\u00a0electrode.
The feeding rate of each colony was measured as the capture rate of
adult\\u00a0Artemia salina\\u00a0during a one-hour period in 0.8 L incubation
chambers containing a starting prey density of 125\\u00a0Artemia\\u00a0L-1.
Acquisition Description for Gulf of Mexico Data:
The buoyant weight of each colony was obtained at the start and end of the
two-week experimental period by weighing fragments submerged in seawater and
attached by a hook to an analytical balance (Denver
Instrument,\\u00a0precision\\u00a0of 0.1 mg). The respiration rate of each
colony was measured as oxygen consumption in an 800 ml closed acrylic chamber
during hour-long incubations. Dissolved oxygen concentrations were measured
in\\u00a0umol\\u00a0L-1\\u00a0using a Strathkelvin 782 dual oxygen meter and
SI130\\u00a0microcathode\\u00a0electrode. The feeding rate of each colony was
measured as the capture rate of adult\\u00a0Artemia salina\\u00a0during a one-
hour period in 0.8 L incubation chambers containing a starting prey density of
125\\u00a0Artemia\\u00a0L-1.";
String awards_0_award_nid "54992";
String awards_0_award_number "OCE-1220478";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1220478";
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
"Physiology - Calcification
E. Cordes & R. Kulalthinal, PIs
Version 16 September 2016";
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 "2016-09-20T21:06:24Z";
String date_modified "2019-05-10T17:09:03Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.659379.1";
String history
"2024-12-21T11:53:22Z (local files)
2024-12-21T11:53:22Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_659379.html";
String infoUrl "https://www.bco-dmo.org/dataset/659379";
String institution "BCO-DMO";
String instruments_0_acronym "O2 microsensor";
String instruments_0_dataset_instrument_description "Measured dissolved oxygen concentrations";
String instruments_0_dataset_instrument_nid "659388";
String instruments_0_description "A miniaturized Clark-type dissolved oxygen instrument, including glass micro-sensors with minute tips (diameters ranging from 1 to 800 um). A gold or platinum sensing cathode is polarized against an internal reference and, driven by external partial pressure, oxygen from the environment penetrates through the sensor tip membrane and is reduced at the sensing cathode surface. A picoammeter converts the resulting reduction current to a signal. The size of the signal generated by the electrode is proportional to the flux of oxygen molecules to the cathode.The sensor also includes a polarized guard cathode, which scavenges oxygen in the electrolyte, thus minimizing zero-current and pre-polarization time.With the addition of a meter and a sample chamber, the respiration of a small specimen can be measured. Example: Strathkelvin Inst. http://www.strathkelvin.com";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/351/";
String instruments_0_instrument_name "Oxygen Microelectrode Sensor";
String instruments_0_instrument_nid "701";
String instruments_0_supplied_name "SI130 microcathode electrode";
String instruments_1_acronym "Dissolved Oxygen Sensor";
String instruments_1_dataset_instrument_description "Measured dissolved oxygen concentrations";
String instruments_1_dataset_instrument_nid "659389";
String instruments_1_description "An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed";
String instruments_1_instrument_name "Dissolved Oxygen Sensor";
String instruments_1_instrument_nid "705";
String instruments_1_supplied_name "Strathkelvin 782 dual oxygen meter";
String instruments_2_acronym "Scale";
String instruments_2_dataset_instrument_description "Used to weigh specimens";
String instruments_2_dataset_instrument_nid "659597";
String instruments_2_description "An instrument used to measure weight or mass.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB13/";
String instruments_2_instrument_name "Scale";
String instruments_2_instrument_nid "714";
String instruments_2_supplied_name "Scale";
String keywords "afdm, alkalinity, bco, bco-dmo, biological, bouyant, bouyant_weight, calcification, change, chemical, data, dataset, day, dmo, dry, dry_weight, erddap, fragment, fragment_num, management, net, net_calcification, num, oceanography, office, pH_treatment, polyps, polyps_num, preliminary, starting, starting_DW, tank, treatment, ttl, ttl_alkalinity_change, weight";
String license "https://www.bco-dmo.org/dataset/659379/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/659379";
String param_mapping "{'659379': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/659379/parameters";
String people_0_affiliation "Temple University";
String people_0_affiliation_acronym "Temple";
String people_0_person_name "Erik E Cordes";
String people_0_person_nid "51539";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Temple University";
String people_1_affiliation_acronym "Temple";
String people_1_person_name "Dr Robert J. Kulathinal";
String people_1_person_nid "51540";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Temple University";
String people_2_affiliation_acronym "Temple";
String people_2_person_name "Erik E Cordes";
String people_2_person_nid "51539";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Lophelia OA";
String projects_0_acronym "Lophelia OA";
String projects_0_description
"The Gulf of Mexico deep water ecosystems are threatened by the persistent threat of ocean acidification. Deep-water corals will be among the first to feel the effects of this process, in particular the deep-water scleractinians that form their skeleton from aragonite. The continued shoaling of the aragonite saturation horizon (the depth below which aragonite is undersaturated) will place many of the known, and as yet undiscovered, deep-water corals at risk in the very near future. The most common deep-water framework-forming scleractinian in the world's oceans is Lophelia pertusa. This coral is most abundant in the North Atlantic, where aragonite saturation states are relatively high, but it also creates extensive reef structures between 300 and 600 m depth in the Gulf of Mexico where aragonite saturation states were previously unknown. Preliminary data indicate that pH at this depth range is between 7.85 and 8.03, and the aragonite saturation state is typically between 1.28 and 1.69. These are the first measurements of aragonite saturation state for the deep Gulf of Mexico, and are among the lowest Aragonite saturation state yet recorded for framework-forming corals in any body of water, at any depth.
This project will examine the effects of ocean acidification on L. pertusa, combining laboratory experiments, rigorous oceanographic measurements, the latest genome and transcriptome sequencing platforms, and quantitative PCR and enzyme assays to examine changes in coral gene expression and enzyme activity related to differences in carbonate chemistry. Short-term and long-term laboratory experiments will be performed at Aragonite saturation state of 1.45 and 0.75 and the organismal (e.g., survivorship and calcification rate) and genetic (e.g., transcript abundance) responses of the coral will be monitored. Genomic DNA and RNA will be extracted, total mRNA purified, and comprehensive and quantitative profiles of the transcriptome generated using a combination of 454 and Illumina sequencing technologies. Key genes in the calcification pathways as well as other differentially expressed genes will be targeted for specific qPCR assays to verify the Illumina sequencing results. On a research cruise, L. pertusa will be sampled (preserved at depth) along a natural gradient in carbonate chemistry, and included in the Illumina sequencing and qPCR assays. Water samples will be obtained by submersible-deployed niskin bottles adjacent to the coral collections as well as CTD casts of the water column overlying the sites. Water samples will be analyzed for pH, alkalinity, nitrates and soluble reactive phosphorus. These will be used in combination with historical data in a model to hindcast Aragonite saturation state.
This project will provide new physiological and genetic data on an ecologically-significant and anthropogenically-threatened deepwater coral in the Gulf of Mexico. An experimental system, already developed by the PIs, offers controlled conditions to test the effect of Aragonite saturation state on calcification rates in scleractinians and, subsequently, to identify candidate genes and pathways involved in the response to reduced pH and Aragonite saturation state. Both long-term and population sampling experiments will provide additional transcriptomic data and specifically investigate the expression of the candidate genes. These results will contribute to our understanding of the means by which scleractinians may acclimate and acclimatize to low pH, alkalinity, and Aragonite saturation state. Furthermore, the investigators will continue a time series of oceanographic measurements of the carbonate system in the Gulf of Mexico, which will allow the inclusion of this significant body of water in models of past and future ocean acidification scenarios.";
String projects_0_end_date "2015-08";
String projects_0_geolocation "Northern Gulf of Mexico";
String projects_0_name "Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico";
String projects_0_project_nid "2224";
String projects_0_start_date "2012-09";
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 "Calcification rates from pH experiments on Lophelia pertusa specimens collected from the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project)";
String title "[L. pertusa calcification records from pH experiments] - Calcification rates from pH experiments on Lophelia pertusa specimens collected from the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico)";
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.