BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt
attribute NC_GLOBAL acquisition_description String Sediment cores were collected from the Cinder Cones site including a methane\nseep habitat and vertically sectioned into cm intervals with the exterior of\nthe cores discarded to avoid vertical smearing.\\u00a0 Sediments\\u00a0were\nplaced in whirlpack bags and kept at -80 until DNA was extracted.\n \nBetween 0.25 and 0.5 grams of frozen sediment had DNA extracted using the\nMoBio (now Qiagen) PowerSoil kits. Primers and amplification procedures follow\nthe Earth Microbiome Project Protocol ([http://www.earthmicrobiome.org\n/protocols-and-standards/16s/](\\\\\"http://www.earthmicrobiome.org/protocols-\nand-standards/16s/\\\\\")) using the updated primers in Apprill et al (2015)\nfollowing Caporaso et al. (2011).\\u00a0 In short, triplicate PCRs were run\nusing the 515FB and the 806RB primers that copy the V4 region if the 16s rRNA\ngene. These primers were barcoded allowing later in silico separation of\npooled samples.\\u00a0 Controls and all samples were run on a gel to check for\ncontamination.\\u00a0 DNA was cleaned up using the MoBio UltraClean PCR Clean-\nUp Kit, samples were pooled into equal molar concentrations and submitted for\nsequencing.\n \nData were de-multiplexed and primers trimmed. No other data manipulation has\nbeen performed.
attribute NC_GLOBAL awards_0_award_nid String 709614
attribute NC_GLOBAL awards_0_award_number String OPP-1642570
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642570 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Office of Polar Programs (formerly NSF PLR)
attribute NC_GLOBAL awards_0_funding_acronym String NSF OPP
attribute NC_GLOBAL awards_0_funding_source_nid String 713360
attribute NC_GLOBAL awards_0_program_manager String Christian Fritsen
attribute NC_GLOBAL awards_0_program_manager_nid String 683959
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Microbial community composition of the Cinder Cones Cold Seep \n     16s V4 region community composition of Methane seep in the Ross Sea Region, Antarctica, Nov. 2016 \n   PI: A. Thurber (OSU) \n   version date: 2019-02-25 \n  \n   See also 16S amplicon, NCBI, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2019-02-27T13:55:54Z
attribute NC_GLOBAL date_modified String 2019-03-20T13:15:48Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.756997.1
attribute NC_GLOBAL Easternmost_Easting double 166.666
attribute NC_GLOBAL geospatial_lat_max double -77.8
attribute NC_GLOBAL geospatial_lat_min double -77.8
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double 166.666
attribute NC_GLOBAL geospatial_lon_min double 166.666
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/756997 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 757053
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_1_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 757052
attribute NC_GLOBAL instruments_1_description String 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.\n\n(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute NC_GLOBAL instruments_1_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_1_instrument_nid String 471582
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/756997/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/756997 (external link)
attribute NC_GLOBAL Northernmost_Northing double -77.8
attribute NC_GLOBAL param_mapping String {'756997': {'collection_date': 'flag - time', 'lat': 'master - latitude', 'Sediment_Depth_cm': 'flag - depth', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/756997/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Oregon State University
attribute NC_GLOBAL people_0_affiliation_acronym String OSU-CEOAS
attribute NC_GLOBAL people_0_person_name String Andrew Thurber
attribute NC_GLOBAL people_0_person_nid String 709617
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Cinder Cone Seep
attribute NC_GLOBAL projects_0_acronym String Cinder Cone Seep
attribute NC_GLOBAL projects_0_description String NSF abstract:\nMethane 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.\nAn 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.
attribute NC_GLOBAL projects_0_end_date String 2018-07
attribute NC_GLOBAL projects_0_geolocation String Ross Sea, Antarctica (78 S, 166 E)
attribute NC_GLOBAL projects_0_name String EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat
attribute NC_GLOBAL projects_0_project_nid String 709615
attribute NC_GLOBAL projects_0_start_date String 2016-08
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double -77.8
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String organism,host,geo_loc_name,latitude,longitude
attribute NC_GLOBAL summary String 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.
attribute NC_GLOBAL time_coverage_end String 2016-11-15
attribute NC_GLOBAL time_coverage_start String 2016-11-03
attribute NC_GLOBAL title String [Microbial community composition of the Cinder Cones Cold Seep] - Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016 (EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double 166.666
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable accession String
attribute accession bcodmo_name String accession number
attribute accession description String NCBI accession number for the archive
attribute accession long_name String Accession
attribute accession units String unitless
variable sample_name String
attribute sample_name bcodmo_name String sample
attribute sample_name description String reference file name used in NCBI
attribute sample_name long_name String Sample Name
attribute sample_name nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_name units String unitless
variable organism String
attribute organism bcodmo_name String sample_descrip
attribute organism description String type of organism analyzed: all are marine sediment whose microbial community has been extracted
attribute organism long_name String Organism
attribute organism units String unitless
variable host String
attribute host bcodmo_name String sample_type
attribute host description String host type: these are environmental samples rather than from individual organisms
attribute host long_name String Host
attribute host units String unitless
variable time double
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.4781312E9, 1.479168E9
attribute time axis String T
attribute time bcodmo_name String date
attribute time description String Date sample was collected formatted as yyyy-mm-dd
attribute time ioos_category String Time
attribute time long_name String Collection Date
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute time source_name String collection_date
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01
attribute time units String seconds since 1970-01-01T00:00:00Z
variable geo_loc_name String
attribute geo_loc_name bcodmo_name String site_descrip
attribute geo_loc_name description String location sampled
attribute geo_loc_name long_name String Geo Loc Name
attribute geo_loc_name units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double -77.8, -77.8
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String latitude; north is positive
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude double
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double 166.666, 166.666
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String longitude; east is positive
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable Replicate String
attribute Replicate bcodmo_name String replicate
attribute Replicate description String Individual identifier for the core
attribute Replicate long_name String Replicate
attribute Replicate units String unitless
variable Sediment_Depth_cm double
attribute Sediment_Depth_cm _FillValue double NaN
attribute Sediment_Depth_cm bcodmo_name String depth_core
attribute Sediment_Depth_cm description String depth range from which microbial community was analyzed
attribute Sediment_Depth_cm long_name String Sediment Depth Cm
attribute Sediment_Depth_cm units String centimeters
variable Habitat String
attribute Habitat bcodmo_name String site_descrip
attribute Habitat description String Whether the sample was from an area of active methane seepage or sampled as a control for this habitat.
attribute Habitat long_name String Habitat
attribute Habitat units String unitless

 
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