ERDDAP > info > bcodmo_dataset_782058

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			files	public	[reconstructed genomes] - Reconstructed genomes from North Pond, western flank of the Mid- Atlantic Ridge, from 2012-2014 (Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling)		I   M	background			BCO-DMO	bcodmo_dataset_782058

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
attribute	NC_GLOBAL	acquisition_description	String	Ribosomal rRNA identification and relative abundance From the high-quality paired-end Illumina sequencing reads, 16S rRNA gene fragments were identified using Meta-RNA (Huang et al., 2009; v.H3; -e 1e-10). Putative rRNA fragments and associated mate pairs from each sample were processed through EMIRGE (Miller et al., 2011, 2013); emirge_amplicon.py; -l 113 -i 163 -s 33 -a 32 \u2014phred33) to generate full-length sequences using the SILVA (Quast et al., 2012) SSURef111 reference database ([https://github.com/csmiller/EMIRGE](\\"https://github.com/csmiller/EMIRGE\\")). Reconstructed 16S rRNA genes were assigned taxonomy using mothur (v1.34.4) by first aligning the sequences to the SILVA SSURef123 database (align.seqs; flip=T), removing sequences that failed to align, if necessary (remove.seqs), and classifying the sequences (classify.seqs; cutoff=80, iters=1000).
attribute	NC_GLOBAL	awards_0_award_nid	String	554913
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1061934
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1061934
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	awards_1_award_nid	String	554917
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1061827
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1061827
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	50534
attribute	NC_GLOBAL	awards_2_award_nid	String	554921
attribute	NC_GLOBAL	awards_2_award_number	String	OCE-1062006
attribute	NC_GLOBAL	awards_2_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1062006
attribute	NC_GLOBAL	awards_2_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_2_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_2_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_2_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_2_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Reconstructed genomes from North Pond, western flank of the Mid-Atlantic Ridge PI: Julie Huber Version: 2019-11-19
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	2019-11-19T19:00:07Z
attribute	NC_GLOBAL	date_modified	String	2019-12-02T21:10:06Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.782058.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/782058
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	CTD
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Deep bottom water was sampled in 2012 and 2014 via a CTD at 100 m above the seafloor and filtered in the same manner as the crustal fluids onto Sterivex filters.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	782068
attribute	NC_GLOBAL	instruments_0_description	String	The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/130/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	CTD profiler
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	417
attribute	NC_GLOBAL	instruments_0_supplied_name	String	CTD
attribute	NC_GLOBAL	instruments_1_acronym	String	AOO
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Fluid systems were flushed and allowed to equilibrate before sampling, and dissolved oxygen concentrations were measured during pumping using an Aanderaa sensor (Meyer et al., 2016).
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	782069
attribute	NC_GLOBAL	instruments_1_description	String	Aanderaa Oxygen Optodes are instrument for monitoring oxygen in the environment. For instrument information see the Aanderaa Oxygen Optodes Product Brochure.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/351/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Aanderaa Oxygen Optodes
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	563
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Aanderaa sensor
attribute	NC_GLOBAL	instruments_2_acronym	String	Automatic titrator
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Fluids also were analyzed for dissolved silicon and nitrate using automated colorimetric analysis and pH was measured with an electrode before a potentiometric titration for the determination of alkalinity (Wheat et al., 2017).
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	782072
attribute	NC_GLOBAL	instruments_2_description	String	Instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached.
attribute	NC_GLOBAL	instruments_2_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB12/
attribute	NC_GLOBAL	instruments_2_instrument_name	String	Automatic titrator
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	682
attribute	NC_GLOBAL	instruments_2_supplied_name	String	automated colorimetric analysis
attribute	NC_GLOBAL	instruments_3_dataset_instrument_description	String	Total microbial biomass in fluids was enumerated with DAPI (4′,6′-diamidino-2-phenylindole; Sigma-Aldrich, St Louis, MO, USA) and epifluorescent microscopy (Porter and Feig, 1980).
attribute	NC_GLOBAL	instruments_3_dataset_instrument_nid	String	782071
attribute	NC_GLOBAL	instruments_3_description	String	Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.
attribute	NC_GLOBAL	instruments_3_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB06/
attribute	NC_GLOBAL	instruments_3_instrument_name	String	Microscope-Fluorescence
attribute	NC_GLOBAL	instruments_3_instrument_nid	String	695
attribute	NC_GLOBAL	instruments_3_supplied_name	String	epifluorescent microscopy
attribute	NC_GLOBAL	instruments_4_acronym	String	GeoMICROBE
attribute	NC_GLOBAL	instruments_4_dataset_instrument_description	String	After sampling in 2012, a battery-powered GeoMICROBE sled was left at each CORK for time series autonomous sampling of the fluid delivery lines (Cowen et al., 2012).
attribute	NC_GLOBAL	instruments_4_dataset_instrument_nid	String	782070
attribute	NC_GLOBAL	instruments_4_description	String	Integrated Ocean Drilling Program borehole CORK (Circulation Obviation Retrofit Kit) observatories provide long-term access to hydrothermal fluids circulating within the basaltic crust (basement), providing invaluable opportunities to study the deep biosphere. We describe the design and application parameters of the GeoMICROBE instrumented sled, an autonomous sensor and fluid sampling system. The GeoMICROBE system couples with CORK fluid delivery lines to draw large volumes of fluids from crustal aquifers to the seafloor. These fluids pass a series of in-line sensors and an in situ filtration and collection system. GeoMICROBE’s major components include a primary valve manifold system, a positive displacement primary pump, sensors (e.g., fluid flow rate, temperature, dissolved O2, electrochemistry-voltammetry analyzer), a 48-port in situ filtration and fluid collection system, computerized controller, seven 24 V-40 A batteries and wet-mateable (ODI) communications with submersibles. This constantly evolving system has been successfully connected to IODP Hole 1301A on the eastern flank of the Juan de Fuca Ridge.  Reference: Cowen, J.P., Copson, D., Jolly, J., Hsieh, C.-C., Matsumoto, R., Glazer, B.T. et al. (2012) Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere., Deep-Sea Research I, 61: 43-56 doi:10.1016/j.dsr.2011.11.004
attribute	NC_GLOBAL	instruments_4_instrument_name	String	GeoMICROBE
attribute	NC_GLOBAL	instruments_4_instrument_nid	String	565376
attribute	NC_GLOBAL	instruments_4_supplied_name	String	GeoMICROBE sled
attribute	NC_GLOBAL	keywords	String	assembly, bco, bco-dmo, bio, biological, bioproject, bioproject_id, BioSample, chemical, data, dataset, dmo, erddap, isolate, level, management, oceanography, office, preliminary, sample, taxonomy, wgs
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/782058/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/782058
attribute	NC_GLOBAL	param_mapping	String	{'782058': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/782058/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Marine Biological Laboratory
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	MBL
attribute	NC_GLOBAL	people_0_person_name	String	Julie Huber
attribute	NC_GLOBAL	people_0_person_nid	String	51266
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	Harvard University
attribute	NC_GLOBAL	people_1_person_name	String	Peter Girguis
attribute	NC_GLOBAL	people_1_person_nid	String	544586
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	University of Hawaii at Manoa
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	SOEST
attribute	NC_GLOBAL	people_2_person_name	String	Brian Glazer
attribute	NC_GLOBAL	people_2_person_nid	String	554919
attribute	NC_GLOBAL	people_2_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_2_role_type	String	originator
attribute	NC_GLOBAL	project	String	North Pond Microbes
attribute	NC_GLOBAL	projects_0_acronym	String	North Pond Microbes
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: Current estimates suggest that the volume of ocean crust capable of sustaining life is comparable in magnitude to that of the oceans. To date, there is little understanding of the composition or functional capacity of microbial communities in the sub-seafloor, or their influence on the chemistry of the oceans and subsequent consequences for global biogeochemical cycles. This project focuses on understanding the relationship between microbial communities and fluid chemistry in young crustal fluids that are responsible for the transport of energy, nutrients, and organisms in the crust. Specifically, the PIs will couple microbial activity measurements, including autotrophic carbon, nitrogen and sulfur metabolisms as well as mineral oxide reduction, with quantitative assessments of functional gene expression and geochemical transformations in basement fluids. Through a comprehensive suite of in situ and shipboard analyses, this research will yield cross-disciplinary advances in our understanding of the microbial ecology and geochemistry of the sub-seafloor biosphere. The focus of the effort is at North Pond, an isolated sediment pond located on ridge flank oceanic crust 7-8 million years old on the western side of the Mid-Atlantic Ridge. North Pond is currently the target for drilling on IODP expedition 336, during which it will be instrumented with three sub-seafloor basement observatories. The project will leverage this opportunity for targeted and distinct sampling at North Pond on two German-US research cruises to accomplish three main objectives: 1. to determine if different basement fluid horizons across North Pond host distinct microbial communities and chemical milieus and the degree to which they change over a two-year post-drilling period. 2. to quantify the extent of autotrophic metabolism via microbially-mediated transformations in carbon, nitrogen, and sulfur species in basement fluids at North Pond. 3. to determine the extent of suspended particulate mineral oxides in basement fluids at North Pond and to characterize their role as oxidants for fluid-hosted microbial communities. Specific outcomes include quantitative assessments of microbial activity and gene expression as well as geochemical transformations. The program builds on the integrative research goals for North Pond and will provide important data for guiding the development of that and future deep biosphere research programs. Results will increase understanding of microbial life and chemistry in young oceanic crust as well as provide new insights into controls on the distribution and activity of marine microbial communities throughout the worlds oceans. There are no data about microbial communities in ubiquitous cold, oceanic crust, the emphasis of the proposed work. This is an interdisciplinary project at the interface of microbial ecology, chemistry, and deep-sea oceanography with direct links to international and national research and educational organizations.
attribute	NC_GLOBAL	projects_0_end_date	String	2015-05
attribute	NC_GLOBAL	projects_0_geolocation	String	North Pond, mid-Atlantic Ridge
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling
attribute	NC_GLOBAL	projects_0_project_nid	String	554914
attribute	NC_GLOBAL	projects_0_start_date	String	2011-06
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	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	bioproject_id
attribute	NC_GLOBAL	summary	String	Reconstructed genomes from North Pond
attribute	NC_GLOBAL	title	String	[reconstructed genomes] - Reconstructed genomes from North Pond, western flank of the Mid-Atlantic Ridge, from 2012-2014 (Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	bioproject_id		String
attribute	bioproject_id	bcodmo_name	String	accession number
attribute	bioproject_id	description	String	NIH bioproject term
attribute	bioproject_id	long_name	String	Bioproject Id
attribute	bioproject_id	units	String	unitless
variable	Assembly		String
attribute	Assembly	bcodmo_name	String	unknown
attribute	Assembly	description	String	GenBank assembly accession
attribute	Assembly	long_name	String	Assembly
attribute	Assembly	units	String	unitless
variable	Level		String
attribute	Level	bcodmo_name	String	unknown
attribute	Level	description	String	contig or scaffold
attribute	Level	long_name	String	Level
attribute	Level	units	String	unitless
variable	WGS		String
attribute	WGS	bcodmo_name	String	unknown
attribute	WGS	description	String	Whole Genome Shotgun Submission
attribute	WGS	long_name	String	WGS
attribute	WGS	units	String	unitless
variable	BioSample		String
attribute	BioSample	bcodmo_name	String	accession number
attribute	BioSample	description	String	BioSample accession numbers
attribute	BioSample	long_name	String	Bio Sample
attribute	BioSample	units	String	unitless
variable	Isolate		String
attribute	Isolate	bcodmo_name	String	unknown
attribute	Isolate	description	String	Genome designation (eg. NORP is NORthPond)
attribute	Isolate	long_name	String	Isolate
attribute	Isolate	units	String	unitless
variable	Taxonomy		String
attribute	Taxonomy	bcodmo_name	String	taxon
attribute	Taxonomy	description	String	Sepcies assigned with mothur for reconstructed 16SrRNA genes
attribute	Taxonomy	long_name	String	Taxonomy
attribute	Taxonomy	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.