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     data   graph     files  public 16S rRNA gene (from DNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough,
Japan from September to October 2010
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_780926

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Sampling of cores was done in accordance with IODP protocols.

All C0014 samples were cored on 16 September 2010 via via HPCS (hydraulic
piston coring system).
All C0015 samples were cored on 18 September 2010 via HPCS.
All C0017 samples were cored on 27 September 2010 via HPCS.

Core sections were kept frozen (-80\u00b0C) until DNA extractions. A
MoBio\u00ae Power Soil kit was used to extract environmental DNA. See
publication below for sequencing and analysis methodologies.
attribute NC_GLOBAL awards_0_award_nid String 554980
attribute NC_GLOBAL awards_0_award_number String OCE-0939564
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String 16S rRNA gene (from DNA)
PI: Christopher House (PSU)
Version date: 05 November 2019
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 2019-11-05T21:19:38Z
attribute NC_GLOBAL date_modified String 2019-11-22T18:37:16Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.780926.1
attribute NC_GLOBAL Easternmost_Easting double 126.900833
attribute NC_GLOBAL geospatial_lat_max double 27.794444
attribute NC_GLOBAL geospatial_lat_min double 27.790278
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double 126.900833
attribute NC_GLOBAL geospatial_lon_min double 126.891667
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/780926 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Piston Corer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 782753
attribute NC_GLOBAL instruments_0_description String The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/51/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Piston Corer
attribute NC_GLOBAL instruments_0_instrument_nid String 519
attribute NC_GLOBAL instruments_0_supplied_name String hydraulic piston coring system (HPCS)
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, biological, bottom, Bottom_Depth, chemical, cruise, Cruise_ID, data, dataset, depth, dmo, erddap, estimated, Estimated_Temp, iodp, IODP_Sample_Number, latitude, longitude, management, mgrast, MGRAST_Accession_ID, notes, number, oceanography, office, preliminary, sample, sediment, Sediment_type, temperature, top, Top_Depth, type, water, Water_depth
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/780926/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/780926 (external link)
attribute NC_GLOBAL Northernmost_Northing double 27.794444
attribute NC_GLOBAL param_mapping String {'780926': {'Latitude': 'master - latitude', 'Longitude': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/780926/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Pennsylvania State University
attribute NC_GLOBAL people_0_affiliation_acronym String PSU
attribute NC_GLOBAL people_0_person_name String Christopher House
attribute NC_GLOBAL people_0_person_nid String 714235
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 Pennsylvania State University
attribute NC_GLOBAL people_1_affiliation_acronym String PSU
attribute NC_GLOBAL people_1_person_name String Leah Brandt
attribute NC_GLOBAL people_1_person_nid String 782699
attribute NC_GLOBAL people_1_role String Scientist
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Shannon Rauch
attribute NC_GLOBAL people_2_person_nid String 51498
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Subvent_Biosphere_Sediments
attribute NC_GLOBAL projects_0_acronym String Subvent_Biosphere_Sediments
attribute NC_GLOBAL projects_0_description String The Iheya North Hydrothermal Field in the Okinawa Backarc Basin represents an ideal environment in which to investigate the biotic temperature fringe of microbial life at depth because of its subsurface hydrothermal activity within its continental margin-type sediment profile. Geographically, the Okinawa Backarc Basin is situated along a continental margin, which is a sediment profile type commonly sampled and studied across the seafloor (e.g. Peru Margin, Costa Rica Margin, Cascadia Margin). The hydrothermal network within the subsurface here supplies an additional temperature obstacle to microbial life existing in the sediments. In particular, the sediment profile at Site C0014 exhibits a transition from hemipelagic ooze with pumiceous volcaniclastic sediments and low temperature (4�C) to a hydrothermally altered sequence of clays within the top ~10 mbsf of sediment. Temperature measurements indicate a gradient of approximately 3�C/m, which is roughly an order of magnitude greater than continental margin sites (e.g. Cascadia Margin, IODP 311 and Costa Rica Margin, IODP 344), but is more gradual than intense, centimeter-scale gradients from other hot, surface sediments. We have focused on the application of culture-independent, molecular methods to understand taxonomic and functional characteristics through this hydrothermal gradient. Confidence in DNA recovery suggests a microbial biosphere extent of approximately 15 mbsf (55�C).
Results from both 16S rRNA gene surveys and metagenomics analyses suggest a temperature-dependent stratigraphy of taxonomic and functional adaptations between the shallowest and deepest sample horizons. Cosmopolitan marine subsurface bacterial and archaeal taxa are present throughout the top 10 mbsf, whereas, hyperthermophilic heterotrophic as well as thermophilic anaerobic methanotrophic archaea appear in varying local abundances in deeper, hydrothermal clay horizons. "An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments" encompasses datasets funded through C-DEBI to investigate the microbial communities in IODP 331 Iheya North Hydrothermal Field sediments. Site C0014 at this field site is 500 m away from the active vent and experiences a 3C/m temperature gradient with depth. In the research grant "Investigating the active microbial populations in near hydrothermal vent sediments" and the Research Exchange grant "Learning new RNA extraction techniques", we used an RNA-based approach to explore the active microbial community. Upon analysis, the RNA dataset does not appear to reflect the same information as the phylogenetic signals coming from both the 16S rRNA gene as well as the metagenomes. The data indicate significant background noise from the RNA extraction process rather than from an indigenous representation of the subsurface biosphere.
The graduate fellowship "An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field" provided an opportunity to bring together metagenomic, 16S rRNA gene amplicon (DNA), and 16S rRNA amplicon datasets from IODP 331 Iheya North Hydrothermal Field sediments to understand the biogeography of this subvent biosphere.
For more information, refer to the following C-DEBI grants/projects.
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field:https://www.darkenergybiosphere.org/award/an-in-depth-analysis-of-the-subvent-biosphere-within-the-okinawa-backarc-basin-iheya-north-hydrothermal-field/
Investigating the active microbial populations in near hydrothermal vent sediments:�https://www.darkenergybiosphere.org/award/investigating-the-active-microbial-populations-in-near-hydrothermal-vent-sediments/
Learn new RNA extraction techniques:�https://www.darkenergybiosphere.org/award/learn-new-rna-extraction-techniques/
attribute NC_GLOBAL projects_0_end_date String 2016-05
attribute NC_GLOBAL projects_0_geolocation String Iheya North Hydrothermal Field, Pacific Ocean
attribute NC_GLOBAL projects_0_name String An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments
attribute NC_GLOBAL projects_0_project_nid String 714230
attribute NC_GLOBAL projects_0_start_date String 2014-06
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 27.790278
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String The purpose of this dataset was to investigate taxonomic changes via the 16S rRNA gene from extractable DNA across 45 meters of recovered core. The temperature gradient in this section of the dynamic Iheya North Hydrothermal system was estimated to be ~3C/m. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay.
attribute NC_GLOBAL title String 16S rRNA gene (from DNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double 126.891667
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Cruise_ID   String  
attribute Cruise_ID bcodmo_name String cruise_id
attribute Cruise_ID description String Cruise ID number
attribute Cruise_ID long_name String Cruise ID
attribute Cruise_ID units String unitless
variable IODP_Sample_Number   String  
attribute IODP_Sample_Number bcodmo_name String sample
attribute IODP_Sample_Number description String IODP sample number
attribute IODP_Sample_Number long_name String IODP Sample Number
attribute IODP_Sample_Number nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute IODP_Sample_Number units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 27.790278, 27.794444
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; positive values = North
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 126.891667, 126.900833
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; positive values = East
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 Water_depth   float  
attribute Water_depth _FillValue float NaN
attribute Water_depth actual_range float 886.0, 1060.0
attribute Water_depth bcodmo_name String depth_w
attribute Water_depth description String Water depth
attribute Water_depth long_name String Water Depth
attribute Water_depth units String meters
variable Top_Depth   float  
attribute Top_Depth _FillValue float NaN
attribute Top_Depth actual_range float 0.23, 44.51
attribute Top_Depth bcodmo_name String depth_bsf
attribute Top_Depth description String Top depth
attribute Top_Depth long_name String Top Depth
attribute Top_Depth units String meters below seafloor
variable Bottom_Depth   float  
attribute Bottom_Depth _FillValue float NaN
attribute Bottom_Depth actual_range float 0.38, 44.66
attribute Bottom_Depth bcodmo_name String depth_bsf
attribute Bottom_Depth description String Bottom depth
attribute Bottom_Depth long_name String Bottom Depth
attribute Bottom_Depth units String meters below seafloor
variable Sediment_type   String  
attribute Sediment_type bcodmo_name String sample_descrip
attribute Sediment_type description String Sediment type
attribute Sediment_type long_name String Sediment Type
attribute Sediment_type units String unitless
variable Estimated_Temp   float  
attribute Estimated_Temp _FillValue float NaN
attribute Estimated_Temp actual_range float 5.26, 151.38
attribute Estimated_Temp bcodmo_name String temperature
attribute Estimated_Temp description String Estimated temperature; based on 3 degrees C/m
attribute Estimated_Temp long_name String Estimated Temp
attribute Estimated_Temp nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute Estimated_Temp units String degrees Celsius
variable MGRAST_Accession_ID   String  
attribute MGRAST_Accession_ID bcodmo_name String accession number
attribute MGRAST_Accession_ID description String MG-RAST accession ID number
attribute MGRAST_Accession_ID long_name String MGRAST Accession ID
attribute MGRAST_Accession_ID units String unitless
variable Notes   String  
attribute Notes bcodmo_name String comment
attribute Notes description String Notes
attribute Notes long_name String Notes
attribute Notes units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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