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Title Sum-
Institution Dataset ID
   set  data   graph     files  public 16S rRNA gene (from RNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough,
Japan from September to October 2010
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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. RNA was
extracted using a phenol chloroform protocol. The RNA extract was DNAse
treated using the Invitrogen\u2122 Ambion\u2122 Turbo DNA-free Kit and
purified using the Qiagen\u00ae RNeasy Mini Kit. A cDNA library was made using
the Qiagen \u00ae QuantiTec Reverse Transcription Kit. Polymerase chain
reactions used the KAPABiosystems\u00ae KAPA2G Robust HotStart ReadyMix PCR
Kit for 32 cycles.

Sequencing of the product was performed on the Illumina\u00ae MiSeq 2500.
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 RNA)
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 2019-11-06T21:03:22Z
attribute NC_GLOBAL date_modified String 2019-11-22T18:50:06Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.781114.1
attribute NC_GLOBAL Easternmost_Easting double 126.911944
attribute NC_GLOBAL geospatial_lat_max double 27.791667
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 126.911944
attribute NC_GLOBAL geospatial_lon_min double 126.900556
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/781114 (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 781193
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_0_supplied_name String Illumina MiSeq 2500
attribute NC_GLOBAL instruments_1_acronym String APC
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 782754
attribute NC_GLOBAL instruments_1_description String The JOIDES Resolution's Advanced Piston Corer (APC) is used in soft ooze and sediments. The APC is a hydraulically actuated piston corer designed to recover relatively undisturbed samples from very soft to firm sediments.

More information is available from IODP (PDF).
attribute NC_GLOBAL instruments_1_instrument_name String Advanced Piston Corer
attribute NC_GLOBAL instruments_1_instrument_nid String 628015
attribute NC_GLOBAL instruments_1_supplied_name String hydraulic piston coring system (HPCS)
attribute NC_GLOBAL keywords String acid, amplified, bco, bco-dmo, biological, bottom, Bottom_Depth, chemical, cruise, Cruise_ID, data, dataset, depth, dmo, erddap, estimated, Estimated_Temp, illumina, Illumina_dataset, latitude, longitude, management, name, notes, nucleic, Nucleic_Acid_amplified, oceanography, office, preliminary, primer, Primer_Set_16S_rRNA, rna, sample, Sample_Name, sediment, Sediment_type, set, temperature, top, Top_Depth, type, water, Water_depth
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/781114/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/781114 (external link)
attribute NC_GLOBAL Northernmost_Northing double 27.791667
attribute NC_GLOBAL param_mapping String {'781114': {'Latitude': 'flag - latitude', 'Longitude': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/781114/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 subsetVariables String Notes
attribute NC_GLOBAL summary String RNA extractions were attempted from sediments at Sites C0014 and C0017 to selectively investigate the active microbial populations at these sites. This study was conducted to supplement the gene-based and metagenomic studies. However, the results from sequenced reverse transcribe 16S rRNA demonstrate the sensitivity of extraction and amplification to external nucleic acids and attest to the challenges in working with low biomass environmental samples. Inconsistencies between primersets and replicates make conclusions about the results of this RNA study extremely tenuous.
attribute NC_GLOBAL title String 16S rRNA gene (from RNA) 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 126.900556
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 Sample_Name   String  
attribute Sample_Name bcodmo_name String sample
attribute Sample_Name description String Sample name
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 latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 27.790278, 27.791667
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 126.900556, 126.911944
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 1059.0, 1229.5
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, 63.72
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, 63.633
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 5.0, 25.0
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 Nucleic_Acid_amplified   String  
attribute Nucleic_Acid_amplified bcodmo_name String sample_descrip
attribute Nucleic_Acid_amplified description String Type of nucleic acid amplified
attribute Nucleic_Acid_amplified long_name String Nucleic Acid Amplified
attribute Nucleic_Acid_amplified units String unitless
variable Primer_Set_16S_rRNA   String  
attribute Primer_Set_16S_rRNA bcodmo_name String sample_descrip
attribute Primer_Set_16S_rRNA description String 16S rRNA primer set
attribute Primer_Set_16S_rRNA long_name String Primer Set 16 S R RNA
attribute Primer_Set_16S_rRNA units String unitless
variable Illumina_dataset   String  
attribute Illumina_dataset bcodmo_name String sample_descrip
attribute Illumina_dataset description String Illumina dataset ID
attribute Illumina_dataset long_name String Illumina Dataset
attribute Illumina_dataset units String unitless
variable Notes   double  
attribute Notes _FillValue double NaN
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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