Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_756997) |
| Range: | longitude = 166.666 to 166.666°E, latitude = -77.8 to -77.8°N, time = 2016-11-03 to 2016-11-15 |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Data Access Form
| Files
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Zoom:
![[The graph you specified. Please be patient.]](https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_756997.png?longitude,latitude,Sediment_Depth_cm&time%3E=2016-11-09&time%3C=2016-11-16&.draw=markers&.marker=5%7C5&.color=0x000000&.colorBar=%7C%7C%7C%7C%7C&.bgColor=0xffccccff)
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Attributes {
s {
accession {
String bcodmo_name "accession number";
String description "NCBI accession number for the archive";
String long_name "Accession";
String units "unitless";
}
sample_name {
String bcodmo_name "sample";
String description "reference file name used in NCBI";
String long_name "Sample Name";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
organism {
String bcodmo_name "sample_descrip";
String description "type of organism analyzed: all are marine sediment whose microbial community has been extracted";
String long_name "Organism";
String units "unitless";
}
host {
String bcodmo_name "sample_type";
String description "host type: these are environmental samples rather than from individual organisms";
String long_name "Host";
String units "unitless";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.4781312e+9, 1.479168e+9;
String axis "T";
String bcodmo_name "date";
String description "Date sample was collected formatted as yyyy-mm-dd";
String ioos_category "Time";
String long_name "Collection Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "collection_date";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01";
String units "seconds since 1970-01-01T00:00:00Z";
}
geo_loc_name {
String bcodmo_name "site_descrip";
String description "location sampled";
String long_name "Geo Loc Name";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range -77.8, -77.8;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "latitude; north is positive";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range 166.666, 166.666;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude; east is positive";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
Replicate {
String bcodmo_name "replicate";
String description "Individual identifier for the core";
String long_name "Replicate";
String units "unitless";
}
Sediment_Depth_cm {
Float64 _FillValue NaN;
String bcodmo_name "depth_core";
String description "depth range from which microbial community was analyzed";
String long_name "Sediment Depth Cm";
String units "centimeters";
}
Habitat {
String bcodmo_name "site_descrip";
String description "Whether the sample was from an area of active methane seepage or sampled as a control for this habitat.";
String long_name "Habitat";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Sediment cores were collected from the Cinder Cones site including a methane
seep habitat and vertically sectioned into cm intervals with the exterior of
the cores discarded to avoid vertical smearing.\\u00a0 Sediments\\u00a0were
placed in whirlpack bags and kept at -80 until DNA was extracted.
Between 0.25 and 0.5 grams of frozen sediment had DNA extracted using the
MoBio (now Qiagen) PowerSoil kits. Primers and amplification procedures follow
the Earth Microbiome Project Protocol ([http://www.earthmicrobiome.org
/protocols-and-standards/16s/](\\\\\"http://www.earthmicrobiome.org/protocols-
and-standards/16s/\\\\\")) using the updated primers in Apprill et al (2015)
following Caporaso et al. (2011).\\u00a0 In short, triplicate PCRs were run
using the 515FB and the 806RB primers that copy the V4 region if the 16s rRNA
gene. These primers were barcoded allowing later in silico separation of
pooled samples.\\u00a0 Controls and all samples were run on a gel to check for
contamination.\\u00a0 DNA was cleaned up using the MoBio UltraClean PCR Clean-
Up Kit, samples were pooled into equal molar concentrations and submitted for
sequencing.
Data were de-multiplexed and primers trimmed. No other data manipulation has
been performed.";
String awards_0_award_nid "709614";
String awards_0_award_number "OPP-1642570";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642570";
String awards_0_funder_name "NSF Office of Polar Programs (formerly NSF PLR)";
String awards_0_funding_acronym "NSF OPP";
String awards_0_funding_source_nid "713360";
String awards_0_program_manager "Christian Fritsen";
String awards_0_program_manager_nid "683959";
String cdm_data_type "Other";
String comment
"Microbial community composition of the Cinder Cones Cold Seep
16s V4 region community composition of Methane seep in the Ross Sea Region, Antarctica, Nov. 2016
PI: A. Thurber (OSU)
version date: 2019-02-25
See also 16S amplicon, NCBI, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720";
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 "2019-02-27T13:55:54Z";
String date_modified "2019-03-20T13:15:48Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.756997.1";
Float64 Easternmost_Easting 166.666;
Float64 geospatial_lat_max -77.8;
Float64 geospatial_lat_min -77.8;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 166.666;
Float64 geospatial_lon_min 166.666;
String geospatial_lon_units "degrees_east";
String history
"2024-04-23T10:10:04Z (local files)
2024-04-23T10:10:04Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_756997.das";
String infoUrl "https://www.bco-dmo.org/dataset/756997";
String institution "BCO-DMO";
String instruments_0_acronym "Automated Sequencer";
String instruments_0_dataset_instrument_nid "757053";
String instruments_0_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_0_instrument_name "Automated DNA Sequencer";
String instruments_0_instrument_nid "649";
String instruments_1_acronym "Thermal Cycler";
String instruments_1_dataset_instrument_nid "757052";
String instruments_1_description
"General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
String instruments_1_instrument_name "PCR Thermal Cycler";
String instruments_1_instrument_nid "471582";
String keywords "accession, bco, bco-dmo, biological, chemical, collection, data, dataset, date, depth, dmo, erddap, geo, geo_loc_name, habitat, host, latitude, loc, longitude, management, name, oceanography, office, organism, preliminary, replicate, sample, sample_name, sediment, Sediment_Depth_cm, time";
String license "https://www.bco-dmo.org/dataset/756997/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/756997";
Float64 Northernmost_Northing -77.8;
String param_mapping "{'756997': {'collection_date': 'flag - time', 'lat': 'master - latitude', 'Sediment_Depth_cm': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/756997/parameters";
String people_0_affiliation "Oregon State University";
String people_0_affiliation_acronym "OSU-CEOAS";
String people_0_person_name "Andrew Thurber";
String people_0_person_nid "709617";
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 "Nancy Copley";
String people_1_person_nid "50396";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Cinder Cone Seep";
String projects_0_acronym "Cinder Cone Seep";
String projects_0_description
"NSF abstract:
Methane is a potent greenhouse gas that is naturally emitted into the oceans by geologic seeps and microbial production. Based on studies of persistent deep-sea seeps at mid- and northern latitudes, researchers have learned that bacteria and archaea can create a \"sediment filter\" that oxidizes methane prior to its release. Antarctica is thought to contain large reservoirs of organic carbon buried beneath its ice which could a quantity of methane equivalent to all of the permafrost in the Arctic and yet we know almost nothing about the methane oxidizing microbes in this region. How these microbial communities develop and potentially respond to fluctuations in methane levels is an under-explored avenue of research. A bacterial mat was recently discovered at 78 degrees south, suggesting the possible presence of a methane seep, and associated microbial communities. This project will explore this environment in detail to assess the levels and origin of methane, and the nature of the microbial ecosystem present.
An expansive bacterial mat appeared and/or was discovered at 78 degrees south in 2011. This site, near McMurdo Station Antarctica, has been visited since the mid-1960s, but this mat was not observed until 2011. The finding of this site provides an unusual opportunity to study an Antarctic marine benthic habitat with active methane cycling and to examine the dynamics of recruitment and community succession of seep fauna including bacteria, archaea, protists and metazoans. This project will collect the necessary baseline data to facilitate further studies of Antarctic methane cycling. The concentration and source of methane will be determined at this site and at potentially analogous sites in McMurdo Sound. In addition to biogeochemical characterization of the sites, molecular analysis of the microbial community will quantify the time scales on which bacteria and archaea respond to methane input and provide information on rates of community development and succession in the Southern Ocean. Project activities will facilitate the training of at least one graduate student and results will be shared at both local and international levels. A female graduate student will be mentored as part of this project and data collected will form part of her dissertation. Lectures will be given in K-12 classrooms in Oregon to excite students about polar science. National and international audiences will be reached through blogs and presentations at a scientific conference. The PI's previous blogs have been used by K-12 classrooms as part of their lesson plans and followed in over 65 countries.";
String projects_0_end_date "2018-07";
String projects_0_geolocation "Ross Sea, Antarctica (78 S, 166 E)";
String projects_0_name "EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat";
String projects_0_project_nid "709615";
String projects_0_start_date "2016-08";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing -77.8;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "organism,host,geo_loc_name,latitude,longitude";
String summary "This dataset includes microbial community composition from 16s V4 region amplicon sequencing on 151 marine sediment community samples collected from the Cinder Cones Cold Seep site [-77.8, 166.666] in the Ross Sea region, Antarctica in November 2016. Data are uploaded to the NCBI Sequence Read Archive under submission SUB2655615 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720] with a subset of the data from that archive originating from this project.";
String time_coverage_end "2016-11-15";
String time_coverage_start "2016-11-03";
String title "Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016";
String version "1";
Float64 Westernmost_Easting 166.666;
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.