ERDDAP > info > bcodmo_dataset_781114

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	[16S rRNA gene from RNA] - 16S rRNA gene (from RNA) from samples collected on cruise Chikyu- 331 in the Okinawa Trough, Japan from September to October 2010 (An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments)		F   I   M	background			BCO-DMO	bcodmo_dataset_781114

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
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/781114
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
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] - 16S rRNA gene (from RNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010 (An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments)
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/
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/
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/
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/
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.