ERDDAP > info > bcodmo_dataset_756997

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	[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)		F   I   M	background			BCO-DMO	bcodmo_dataset_756997

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,.odvTxt
attribute	NC_GLOBAL	acquisition_description	String	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.
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
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 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
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	2019-02-27T13:55:54Z
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
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. (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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/756997
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
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: 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.
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/
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/
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/
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/
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

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.