Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [HADES-K bacterial biomarker phospholipid fatty acid (PLFA)] - Sample log for HADESK bacterial biomarker phospholipid fatty acid content from sediment cores collected on R/V Thomas G. Thompson cruise TN309, May 2014 (Controls on Hadal Megafaunal Community Structure: a Systematic Examination of Pressure, Food Supply, and Topography) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_763873) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
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Attributes {
s {
sample {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 81;
String bcodmo_name "sample";
String description "sample identifier";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
cruise_id {
String bcodmo_name "cruise_id";
String description "cruise identifier";
String long_name "Cruise Id";
String units "unitless";
}
dive {
String bcodmo_name "dive_id";
String description "dive identifier";
String long_name "Dive";
String units "unitless";
}
site {
String bcodmo_name "site";
String description "site name";
String long_name "Site";
String units "unitless";
}
date_utc {
String bcodmo_name "date_utc";
String description "sample collection date in UTC";
String long_name "Date Utc";
String source_name "date_utc";
String time_precision "1970-01-01";
String units "unitless";
}
station {
String bcodmo_name "station";
String description "station identifier";
String long_name "Station";
String units "unitless";
}
core {
String bcodmo_name "core_id";
String description "core identifier";
String long_name "Core";
String units "unitless";
}
NiWa_id {
String bcodmo_name "sample";
String description "National Institute for Water and Atmosphere identifier";
String long_name "Ni Wa Id";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
horizon_core_cm {
String bcodmo_name "depth_core";
String description "depth horizon in core";
String long_name "Horizon Core Cm";
String units "centimeters";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Push cores (6.35 cm diameter) of sediment were collected in situ using the
manipulator arm of the Hybrid Remotely Operated Vehicle Nereus on the margin
of the Kermadec Trench (6013m) and along the main trench axis (7137 to 9177m)
at roughly 1000m increments.
Cores were sectioned at 1cm intervals and sieved for the meiofaunal fraction.
Upon retrieval of sediment cores, the 0-1, 1-2, 2-3, 3-5, 5-10 cm depth
horizons were sectioned and stored frozen (-80 \\u00b0C) until analysis.
Benthic bacterial biomass were calculated from sediment concentrations of the
bacterial biomarker phospholipid fatty acids (PLFAs) i14:0, i15:0, ai15:0,
i16:0. In brief, PLFAs were extracted and purified from known quantities of
freeze-dried sediment samples and subsequently derivatized to yield fatty acid
methyl esters (FAMEs). FAMEs were quantified using GC-FID (Agilent
Technologies 6890N). Bacterial biomass was calculated using the well-
established PLFA:C conversion factor of 0.056 gC PLFA/gC biomass.
Attempts were made to obtain 3 replicate cores at each depth horizon (every
1000 meters from 6000m to 10,000m.\\u00a0 For logistical reasons with vehicle
performance (and loss at 10,000), all of the replicates were not able to be
collected.";
String awards_0_award_nid "536451";
String awards_0_award_number "OCE-1131620";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1131620";
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
"Sediment sample log from push cores used for PLFA (phospholipid fatty acid) and OM (Organic Matter) analyses
collected at the Kermadec Trench on R/V Thomas G. Thompson cruise TN309, May 2014
PI: T. Shank (WHOI)
version: 2019-03-28
'n.u.' indicates deeper sections in the core that were not used for the analysis";
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 "2019-03-28T13:17:19Z";
String date_modified "2019-06-17T17:28:04Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.763873.1";
String history
"2024-11-08T06:19:40Z (local files)
2024-11-08T06:19:40Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_763873.html";
String infoUrl "https://www.bco-dmo.org/dataset/763873";
String institution "BCO-DMO";
String instruments_0_acronym "HROV Nereus";
String instruments_0_dataset_instrument_nid "763881";
String instruments_0_description
"Nereus is an efficient, multi-purpose “hybrid” vehicle that can explore and operate in the crushing pressures of the greatest ocean depths. An unmanned vehicle, Nereus operates in two complementary modes. It can swim freely as an autonomous underwater vehicle (AUV) to survey large areas of the depths, map the seafloor, and give scientists a broad overview. When Nereus locates something interesting, the vehicle’s support team can bring the vehicle back on board the ship and transforms it into a remotely operated vehicle (ROV) tethered to the ship via a micro-thin, fiber-optic cable. Through this tether, Nereus can transmit high-quality, real-time video images and receive commands from skilled pilots on the ship to collect samples or conduct experiments with a manipulator arm.
Technical specifications:
\tWeight on land: 2,800 kg
\tPayload capacity: 25 kg
\tMaximum speed: 3 knots
\tBatteries: rechargable lithium ion, 15 kilowatt hours in two pressure housings
\tThrusters: 2 fore and aft, 2 vertical, 1 lateral (ROV mode) 2 fore and aft, 1 vertical (AUV mode)
\tLights: variable output LED array, strobes
\tManipulator arm: Kraft TeleRobotics 7-function hydraulic manipulator
\tSonar: scanning sonar, forward look and profile, 675 KHz
\tSensors: magnetometer, CTD (to measure conductivity, temperature, and depth)
Nereus supports a variety of science operations: Push coring, measuring heat flow, geotechnical and geochemical sensing, rock sampling and drilling, biological sampling, water sampling, high resolution acoustic bathymetry, and optical still and video imagery.
More information is available from the operator site at URL.";
String instruments_0_instrument_name "HROV Nereus";
String instruments_0_instrument_nid "706";
String instruments_1_dataset_instrument_nid "763892";
String instruments_1_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_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
String instruments_1_instrument_name "Elemental Analyzer";
String instruments_1_instrument_nid "546339";
String instruments_1_supplied_name "Fisons NA 1500 elemental analyzer";
String instruments_2_dataset_instrument_description "Push cores were borrowed from the National Deep Submergence Facility to be able to standardize results. The push cores were 6.35cm diameter).";
String instruments_2_dataset_instrument_nid "763882";
String instruments_2_description
"Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/";
String instruments_2_instrument_name "Push Corer";
String instruments_2_instrument_nid "628287";
String keywords "bco, bco-dmo, biological, chemical, core, cruise, cruise_id, data, dataset, date, dive, dmo, erddap, horizon, horizon_core_cm, management, NiWa_id, oceanography, office, preliminary, sample, site, station, time";
String license "https://www.bco-dmo.org/dataset/763873/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/763873";
String param_mapping "{'763873': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/763873/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Timothy M. Shank";
String people_0_person_nid "536454";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Hawaii at Manoa";
String people_1_affiliation_acronym "SOEST";
String people_1_person_name "Jeffrey C. Drazen";
String people_1_person_nid "491313";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Whitman College";
String people_2_person_name "Paul Yancey";
String people_2_person_nid "536477";
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 "HADES";
String projects_0_acronym "HADES";
String projects_0_description
"Extracted from the NSF award abstract:
Severe technical challenges associated with the extremes of hydrostatic pressure have prevented major advances in hadal ecological studies, and relegated hadal systems to among the most poorly investigated habitats on Earth. Through this project, Hadal Ecosystems Studies (HADES) program, PIs will determine the composition and distribution of hadal species, the role of hadal pressures (piezolyte concentrations, enzyme function under pressure), food supply (distribution of POC with the abundance and biomass of trench organisms, and metabolic rates/energetic demand), and depth/topography (genetic divergence and spatial connectivity of populations) have on impacting deep-ocean community structure. This project will examine these factors using the world's first full-ocean depth hybrid remotely operated vehicle (HROV) in conjunction with the only full-ocean depth imaging lander (Hadal-Lander). This project will provide the first seafloor data and samples in one of the world's best, yet little known trenches- the Kermadec Trench (SW Pacific Ocean). Megafaunal community structure and the relationship between POC and benthic bacterial biomass will be examined as a function of depth and location by systematic high-definition imaging and sediment/faunal sampling transects from abyssal to full trench depths both along and perpendicular to the trench axis. Population genetic approaches will provide levels of genetic divergence and evolutionarily independent lineages to assess the role of depth and topography in trenches and their adjacent abyssal plain in promoting the formation of species. Physiological constraints will be investigated by examining in-situ respiration of selected fauna and tissue concentrations of such protein stabilizers as trimethylamine oxide (TMAO), and the structural adaptations of macromolecules.
Image of NEREUS Deployment Sites. [click on the image to view a larger version]";
String projects_0_end_date "2015-08";
String projects_0_geolocation "Kermadec Trench adjacent to New Zealand: approximately 37 12.75 S and 178 51.43 E to 31 51.29 S and 176 49.07 W";
String projects_0_name "Controls on Hadal Megafaunal Community Structure: a Systematic Examination of Pressure, Food Supply, and Topography";
String projects_0_project_nid "536452";
String projects_0_project_website "https://www.whoi.edu/hades/";
String projects_0_start_date "2011-09";
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 subsetVariables "cruise_id";
String summary "This dataset contains the sample log for HADESK bacterial biomarker phospholipid fatty acid (PLFA) content from sediment push cores. The same samples were also used for the organic matter (OM) analysis. Samples were taken in the Kermadec Trench in the Southwest Pacific, 4000 to ~10,000m from the RV/ Thomas G. Thompson during cruise TN309, May 2014.";
String title "[HADES-K bacterial biomarker phospholipid fatty acid (PLFA)] - Sample log for HADESK bacterial biomarker phospholipid fatty acid content from sediment cores collected on R/V Thomas G. Thompson cruise TN309, May 2014 (Controls on Hadal Megafaunal Community Structure: a Systematic Examination of Pressure, Food Supply, and Topography)";
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.