Accessing BCO-DMO data
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| Dataset Title: | [Mariana Back-arc Macrofauna 2014] - Macrofauna collected on colonization panels at Snail Vent Field on the Mariana Back-arc in 2014 (RAPID: Larval Abundance, Behavior and Dispersal at Deep-sea Hydrothermal Vents in the Southern Mariana Trough) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_783880) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
occurrenceID {
String bcodmo_name "sample";
String description "A globally unique, persistent identifier for the occurrence.";
String long_name "Occurrence ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "none";
}
kingdom {
String bcodmo_name "kingdom";
String description "The full scientific name of the kingdom in which the taxon is classified.";
String long_name "Kingdom";
String units "none";
}
phylum {
String bcodmo_name "phylum";
String description "The full scientific name of the phylum in which the taxon is classified.";
String long_name "Phylum";
String units "none";
}
scientificName {
String bcodmo_name "species";
String description "The full scientific name to the lowest taxonomic rank that can be determined.";
String long_name "Scientific Name";
String units "none";
}
scientificNameID {
String bcodmo_name "taxon_code";
String description "WoRMS identifier for the nomenclatural (not taxonomic) details of a scientific name.";
String long_name "Scientific Name ID";
String units "none";
}
taxonRank {
String bcodmo_name "taxon";
String description "The taxonomic rank of the most specific name in the scientificName.";
String long_name "Taxon Rank";
String units "none";
}
identificationRemarks {
String bcodmo_name "comment";
String description "Comments/notes about the identification.";
String long_name "Identification Remarks";
String units "none";
}
identificationQualifier {
String bcodmo_name "q_flag";
String description "A controlled value to express the determiner's doubts about the Identification.";
String long_name "Identification Qualifier";
String units "none";
}
occurrenceStatus {
String bcodmo_name "sample_descrip";
String description "A statement about the presence or absence of a Taxon at a Location.";
String long_name "Occurrence Status";
String units "none";
}
basisOfRecord {
String bcodmo_name "instrument";
String description "The specific nature of the data record, using the standard label of one of the Darwin Core classes.";
String long_name "Basis Of Record";
String units "none";
}
eventDate {
String bcodmo_name "date";
String description "The date-time during which an Event occurred. For occurrences, this is the date-time when the event was recorded.";
String long_name "Event Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "eventDate";
String time_precision "1970-01-01";
String units "none";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range 143.619, 143.619;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "The geographic longitude (in decimal degrees) of the geographic center of a Location.";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "decimalLongitude";
String standard_name "longitude";
String units "degrees_east";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 12.9531, 12.9531;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "The geographic latitude (in decimal degrees) of the geographic center of a Location.";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String source_name "decimalLatitude";
String standard_name "latitude";
String units "degrees_north";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 2848.0, 2848.0;
String axis "Z";
String bcodmo_name "depth";
String description "Depth below the local surface in meters.";
String ioos_category "Location";
String long_name "Maximum Depth In Meters";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
minimumDepthInMeters {
Int16 _FillValue 32767;
Int16 actual_range 2848, 2848;
String bcodmo_name "depth";
String description "Depth below the local surface in meters.";
String long_name "Minimum Depth In Meters";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String units "meters";
}
waterBody {
String bcodmo_name "site";
String description "The name from the Getty Thesaurus of Geographic Names of the water body in which the Location occurs.";
String long_name "Water Body";
String units "none";
}
locality {
String bcodmo_name "site";
String description "The specific description of the place.";
String long_name "Locality";
String units "none";
}
countryCode {
String bcodmo_name "site";
String description "The ISO-3166 standard code for the country in which the Location occurs.";
String long_name "Country Code";
String units "none";
}
identifiedBy {
String bcodmo_name "recorder";
String description "A list (concatenated and separated with space vertical bar space ( | )) of names of people who assigned the Taxon to the subject.";
String long_name "Identified By";
String units "none";
}
associatedMedia {
String bcodmo_name "file_name";
String description "File name of media associated with the Occurrence. See \"Data Files\" section of metadata for .zip file of images.";
String fileAccessBaseUrl "https://datadocs.bco-dmo.org/docs/Mariana_Back-arc_Vents/data_docs/783880/";
String long_name "Associated Media";
String units "none";
}
total_sorted {
Int16 _FillValue 32767;
Int16 actual_range 1, 650;
String bcodmo_name "count";
String description "The total number of specimens of this taxon that have been sorted and morphologically identified; as specimens from some colonization panels have yet to be sorted and identified, this is not an absolute count";
String long_name "Total Sorted";
String units "individuals";
}
associatedSequences {
String bcodmo_name "sequence";
String description "Genetic sequence information associated with the Occurrence. We provide a full URL path; the sequence identifier at the end of the URL, starting with SNLBE, is persistent";
String long_name "Associated Sequences";
String units "none";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Deployment of Colonization Substrate
Two sets of three colonization \\\"sandwiches\\\" were deployed at Snail Vent, a
hydrothermal vent in the Mariana Back-arc, during cruise YK10-11 in 2010.
\\\"Sandwiches\\\" consisted of six Lexan plastic settlement plates, each
measuring 0.7cm by 10cm by 10cm, separated from each other by 1cm spacers. The
sandwich sets were placed near the base of a hydrothermal vent by the
submersible Shinkai 6500. For additional deployment metadata, please refer to:
[https://www.marine-geo.org/tools/search/entry.php?id=YK10-11](\\\\\"http://www
.marine-geo.org/tools/search/entry.php?id=YK10-11\\\\\"), in particular the
Bottom:Deployed Event Marker-Sandwiches and
Sampler:Biology:ColonizationSubstrate. We want to thank Chief Scientist
Shigeaki Kojima for this sample deployment.
Recovery of Colonization Substrate
The sandwiches were left for approximately 4 years, and recovered by the ROV
Jason II in 2014 on cruise RR1413. Only one set of colonization sandwiches was
retrieved, as the other set was buried and could not be recovered. The maximum
temperature observed at the sandwiches during recovery was 17.36 deg C.
Sandwiches were initially placed into a biobox onboard the ROV, then
transferred to another biobox on an elevator for recovery. During this
transfer, as well as during the recovery of the elevator at the surface, some
specimens may have been lost.
Shipboard Sample Processing
Sandwiches were removed from the biobox into individual bags and the
elevator biobox washings were siphoned into a jar. The bags and jar were
filled with ammonium sulfate solution buffered with EDTA and sodium citrate.
We want to thank Shawn Arellano for this sample recovery and shipboard sample
processing.
Laboratory Sorting and Morphological Identification
Samples remained in the ammonium sulfate solution for 1 to 1.5 years.
Samples were rinsed with TE buffer prior to placement in 95% ethanol. The
sandwiches were manually disassembled, and each entire plate- inclusive of
both sides and edges- was examined for all attached macrofauna under a
dissecting microscope at 25x. Washings were passed over a 63 micron sieve, and
also examined at 25x.
Macrofauna, including foraminifera, were sorted to lowest taxonomic level,
tallied, and placed into separate vials. Ciliates were tallied, but not
usually retained; some were placed into sorted vials. Morphological
identification was limited due to the degradation of the sample. We consulted
with international experts to identify many of the morphotypes. All
morphotypes, except the ciliates, were photographed. Potentially, ciliates
could be identified through metabarcoding of the sorted vials. All photographs
were by Mary Toner, with the exception of barnacles by Hiromi Watanabe.
This dataset is complete for one of the three \\\"sandwiches\\\", and for the
biobox washings.
Genetic Barcoding
A subset of eight individuals, representing eight morphotypes, was prepared
for the Canadian Centre for DNA Barcoding. We used sterile techniques to
provide snips of larger specimens. The five submitted in 2017 used the CCDB
regular protocol for extraction, amplification, (with two primer sets,
C_LepFoIF/C_LepFOIR and ZplankF1/ZplankR1) and sequencing for the Cytochrome
Oxidase Subunit 1 - 5 prime region (COI). The three submitted in 2018 used the
CCDB protocol for Next Generation Sequencing for COI. Results may be viewed in
the Barcode of Life Data System (BOLD) Public Data Portal using the project
search SNLBE. We also consulted with international experts on genetic
sequences.
Problem Report
One set of colonization \\\"sandwiches\\\" could not be recovered, as it was
buried by a partial collapse of surrounding rock.
Some specimens may have been lost during a transfer of samples between
bioboxes at the seafloor, as well as upon recovery at the surface. As such,
our counts cannot be used for quantitative analysis of hydrothermal
macrofauna.";
String awards_0_award_nid "557458";
String awards_0_award_number "OCE-1155756";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1155756";
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 awards_1_award_nid "767732";
String awards_1_award_number "OCE-1028862";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1028862";
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 "David L. Garrison";
String awards_1_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Macrofauna collected on colonization panels
at Snail Vent Field on the Mariana Back-arc in 2014
PI: Stace Beaulieu (WHOI)
Co-PIs: Mary Toner & Susan Mills (WHOI)
Version history:
2020-02-11 (current) - changed \"no photo\" in associatedMedia column to \"nd\"
2019-12-10 (v1) - origial file served";
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 "2019-12-10T18:02:51Z";
String date_modified "2020-02-11T15:41:41Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.783880.2";
Float64 Easternmost_Easting 143.619;
Float64 geospatial_lat_max 12.9531;
Float64 geospatial_lat_min 12.9531;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 143.619;
Float64 geospatial_lon_min 143.619;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 2848.0;
Float64 geospatial_vertical_min 2848.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-23T17:13:13Z (local files)
2024-11-23T17:13:13Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_783880.html";
String infoUrl "https://www.bco-dmo.org/dataset/783880";
String institution "BCO-DMO";
String instruments_0_acronym "ROV Jason";
String instruments_0_dataset_instrument_nid "783944";
String instruments_0_description "The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on \"elevator\" platforms that float heavier loads to the surface. More information is available from the operator site at URL.";
String instruments_0_instrument_name "ROV Jason";
String instruments_0_instrument_nid "638";
String instruments_1_dataset_instrument_nid "783946";
String instruments_1_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
String instruments_1_instrument_name "Microscope-Optical";
String instruments_1_instrument_nid "708";
String instruments_1_supplied_name "dissecting microscope";
String keywords "associated, associatedMedia, associatedSequences, basis, basisOfRecord, bco, bco-dmo, biological, body, chemical, code, country, countryCode, data, dataset, date, depth, dmo, erddap, event, identification, identificationQualifier, identificationRemarks, identified, identifiedBy, kingdom, latitude, locality, longitude, management, maximum, maximumDepthInMeters, media, meters, minimum, minimumDepthInMeters, name, occurrence, occurrenceID, occurrenceStatus, oceanography, office, phylum, preliminary, qualifier, rank, record, remarks, scientific, scientificName, scientificNameID, sequences, sorted, status, taxon, taxonRank, time, total, total_sorted, water, waterBody";
String license "https://www.bco-dmo.org/dataset/783880/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/783880";
Float64 Northernmost_Northing 12.9531;
String param_mapping "{'783880': {'decimalLongitude': 'flag - longitude', 'decimalLatitude': 'flag - latitude', 'maximumDepthInMeters': 'flag - depth'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/783880/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Stace Beaulieu";
String people_0_person_nid "665150";
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";
String people_1_person_name "Susan Mills";
String people_1_person_nid "783891";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI";
String people_2_person_name "Mary Toner";
String people_2_person_nid "783888";
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 "Shannon Rauch";
String people_3_person_nid "51498";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Mariana Back-arc Vents";
String projects_0_acronym "Mariana Back-arc Vents";
String projects_0_description
"NSF Award Abstract:
Summary: Since the discovery of deep-sea hydrothermal vents over thirty years ago, scientists have been perplexed by the question: How are these vent sites colonized and, more specifically, How are the faunal populations established and maintained at these very discrete and often ephemeral habitats. For animals that are sessile or have limited mobility as adults, dispersal to these habitats occurs early in the life cycle, as planktonic larvae in the water column. Due to the difficulties in sampling deep-sea larvae, including low abundances (dilute concentrations), we have very few quantitative estimates of larval dispersal between or larval supply to hydrothermal vents. We also have little to no knowledge of the behavior of vent larvae. The PIs will use large-volume plankton pumps to collect larvae near vents in the southern Mariana Trough in a collaborative effort to quantify larval abundance, behavior, and dispersal in this little-studied region. The collaboration combines the PI's strengths in the collection and morphological identification of larvae and quantifying and modeling dispersal between deep-sea vents, and those of Japanese partners in rearing larvae of hydrothermal vent fauna, molecular genetic identification of larvae, and population genetics of vent fauna.
Intellectual merit: The southern Mariana Trough is a very interesting region in which to study dispersal of vent-endemic fauna, due to the proximity of vents in the back-arc spreading center to vents along the Mariana Arc. These two tectonic settings create different habitat conditions and support vent communities with different species composition. Vent sites the PIs will visit, in the axis and just off-axis of the back-arc spreading center are as close as 25 km to vents on the arc, yet 600 km south of the other known vents in the back-arc. In addition to the new information on larval abundance, diversity, behavior, and dispersal that will be gained for this little-studied region of the world's ridge system, this project has direct relevance to the integration and synthesis goals of the U.S. Ridge 2000 Program. The PI's lab group has conducted previous work at the Ridge 2000 East Pacific Rise (EPR) Integrated Studies Site (ISS). They will be making a direct comparison of the larval abundance and diversity at the EPR ISS to this very different setting along the global 'baseball seam' of oceanic spreading centers. No other such comparison has been possible due to the lack of sampling effort for larvae with large-volume pumps. Also, they are proposing the first experiments with live vent larvae (to the best of our knowledge - with the exception of brachyuran megalopae at 1 atm) to estimate swimming and sinking rates that are important for adding behavioral information to models of larval dispersal.
Broader Impacts: The project involves reciprocal training and cultural exchange - the PIs will learn field and laboratory research techniques from the Japanese PIs, and they will learn from the U.S. PIs. The project will also benefit the career development of a junior researcher (Beaulieu). The proposed activity broadens the participation of both U.S. and Japanese women scientists in sea-going, oceanographic research. The PIs will broadcast the cruise activities in a web log posted by the international InterRidge Program Office, and they anticipate at least three scientific publications will emerge. New species will be added to the online photographic identification guide for vent larvae and included in the second edition of the printed guide.
Additional cruise data and information are available from MGDS: https://www.marine-geo.org/tools/search/entry.php?id=YK10-11";
String projects_0_end_date "2012-04";
String projects_0_geolocation "Southern Mariana Trough";
String projects_0_name "RAPID: Larval Abundance, Behavior and Dispersal at Deep-sea Hydrothermal Vents in the Southern Mariana Trough";
String projects_0_project_nid "767733";
String projects_0_start_date "2010-05";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 12.9531;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "kingdom,occurrenceStatus,basisOfRecord,longitude,latitude,minimumDepthInMeters,waterBody,locality,countryCode";
String summary "This dataset indicates organisms, identified to varying levels of taxonomic granularity, present on colonization surfaces deployed at deep-sea vents in the West Pacific.";
String title "[Mariana Back-arc Macrofauna 2014] - Macrofauna collected on colonization panels at Snail Vent Field on the Mariana Back-arc in 2014 (RAPID: Larval Abundance, Behavior and Dispersal at Deep-sea Hydrothermal Vents in the Southern Mariana Trough)";
String version "2";
Float64 Westernmost_Easting 143.619;
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.