ERDDAP > info > bcodmo_dataset_789136

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data			files	public	Synthesis of publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor samples from the Dorado outcrop, L\u014d'ihi Seamount, North Pond, and Juan de Fuca Ridge flank		I   M	background			BCO-DMO	bcodmo_dataset_789136

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	Analysis of publicly available 16S rRNA gene sequence datasets for taxonomic profiling To summarize crustal bacterial and archaeal taxa for this review, we synthesized publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor basalts generated using 454, Illumina and Ion Torrent amplicon platforms. These include seafloor basalts from the Dorado Outcrop (Lee et al., 2015) and the L\u014d'ihi Seamount (Jacobsen Meyers et al., 2014) in the Pacific Ocean and subseafloor basalts from North Pond on the western flank of the Mid-Atlantic Ridge (J\u00f8rgensen & Zhao, 2016) and the Juan de Fuca Ridge flank in the northeastern Pacific Ocean (LaBont\u00e9 et al., 2017). Datasets from rock colonization experiments conducted in the subseafloor at the Juan de Fuca Ridge flank site (Smith et al., 2016; Ram\u00edrez et al., 2019) were also included, as well as microbial community surveys of the subseafloor crustal fluids from the anoxic Juan de Fuca site (Jungbluth et al., 2016) and the oxic North Pond site (Tully et al., 2017; Meyer et al., 2016). For comparison, we included select reference datasets from oxic (Reese et al., 2018; Zinke et al., 2018) and anoxic sediment (LaBont\u00e9 et al., 2017) and the overlying bottom seawater (Lee et al., 2015) from these same study sites. Raw sequence data from the reviewed studies were downloaded from the NCBI Short Read Archive. Sequencing reads generated using Illumina and Ion Torrent platforms were quality filtered and processed to unique Amplicon Sequence Variants (ASVs) using DADA2 (Callahan et al, 2016), with taxonomy determined by the na\u00efve Bayesian classifier in DADA2 using a training set from the SILVA v132 database (Quast et al., 2013; Yilmaz et al., 2014; Gl\u00f6ckner et al., 2017). For the 454 GS-FLX sequence datasets, operational taxonomic units (OTUs) constructed with 97% or greater sequence similarity in the original analyses were reprocessed in mothur V.1.37.6 (Schloss et al., 2009) against the same SILVA database. All short read datasets were merged and summarized to the relative abundance at phylum resolution (or to class level for Proteobacteria phyla) using Phyloseq v1.24.0 (McMurdie & Holmes, 2013). Figures were produced using ggplot2 R package version 2.2.1 (Wickham, 2016) in RStudio (RStudio Team, 2017). Taxonomic grouping in each sample separated taxa into common (>5% abundance in at least one sample) versus rare (never more than 5% in any sample). Supplemental Figure S1 shows the breakdown of Gammaproteobacteria families in the samples presented in Figure 4 of the main text, and Supplemental Figure S2 highlights the abundance of rare taxa (never >5% abundance in any sample). The Bray-Curtis distances between samples was calculated using the same dataset described above, summarized to relative abundance at the Family taxonomic level using Phyloseq and the Vegan package (Oksanen et al., 2018). A Non-Metric Multidimensional Scaling (NMDS) ordination was produced from this distance matrix. It should be noted that common rules for beta diversity comparisons, such as common library preparation/sequencing protocols and library-size normalization, were not performed in this analysis due to the diversity of the datasets being considered and the resulting NMDS ordination having high-stress (>20%). Therefore, the results should be viewed as broadly qualitative and not quantitative. All data processing steps and markdown files are available via github: [https://github.com/orcuttlab/ocean-crust- micro](\\"https://github.com/orcuttlab/ocean-crust-micro\\")
attribute	NC_GLOBAL	awards_0_award_nid	String	700323
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1737017
attribute	NC_GLOBAL	awards_0_data_url	String	https://www.nsf.gov/awardsearch/showAward?AWD_ID=1737017
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	Michael E. Sieracki
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50446
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Metadata for sequence datasets used in ocean crust microbiome survey PI: Beth Orcutt (Bigelow) Co-PI: Timothy D'Angelo (Bigelow) Version date: 04-Feb-2020
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	2020-02-04T18:08:53Z
attribute	NC_GLOBAL	date_modified	String	2020-02-05T16:01:31Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.789136.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/789136
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, data, dataset, depth, depth2, dmo, dnaextraction, doi, erddap, library, Location, management, name, nickname, oceanography, office, order, plot, Plot_Order, preliminary, primers, region16, region16S, run, sample, Sample_Name, Sample_Type, sequencer, Sequencer_Type, sra, SRA_LibraryName, SRA_Run, SRA_Study, study, Study_Nickname, Temp, temperature, type
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/789136/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/789136
attribute	NC_GLOBAL	param_mapping	String	{'789136': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/789136/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Bigelow Laboratory for Ocean Sciences
attribute	NC_GLOBAL	people_0_person_name	String	Beth N. Orcutt
attribute	NC_GLOBAL	people_0_person_nid	String	565799
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	Bigelow Laboratory for Ocean Sciences
attribute	NC_GLOBAL	people_1_person_name	String	Timothy D'Angelo
attribute	NC_GLOBAL	people_1_person_nid	String	756164
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	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	Slow Life in Crust
attribute	NC_GLOBAL	projects_0_acronym	String	Slow Life in Crust
attribute	NC_GLOBAL	projects_0_description	String	NSF Award Abstract: The marine deep biosphere is the habitat for life existing under the sea floor. The zone has remarkably low energy sources creating a paradox of how life can persist there. Resolving this energy paradox is a grand challenge in deep biosphere research. The Juan de Fuca Ridge flank off the coast of Washington, USA, is an accessible, low energy environment making it an attractive location for addressing this challenge. A series of experiments will be conducted on the seafloor at the Juan de Fuca Ridge flank, using established subseafloor observatories that access the crustal deep biosphere, to provide the first direct in situ measurement of microbial activity in the crustal subsurface. This project will provide essential information about the ability of life to survive under conditions that we are not able to replicate in the laboratory, but that are increasingly important for understanding microbial community interaction in the environment. This information can then be used in models of global microbial activity for estimating the impact of this biosphere on elemental cycling, transforming our understanding of microbial processes within this vast subseafloor habitat. To communicate these discoveries to the public, the project will include a ship-to-shore outreach program during the cruise. In addition public lectures will be presented, and an interactive display of deep-sea video footage will be set up for the annual public Open House at the Bigelow Laboratory for Ocean Sciences in Maine. Diverse undergraduate students and a postdoctoral researcher will be recruited to participate in the research and public outreach activities. This project proposes to leverage existing subsurface infrastructure on the eastern flank of the Juan de Fuca Ridge with advances in single-cell based molecular and geochemical approaches to make fundamental new discoveries about the activity of life in the deep crustal biosphere. During a two-week research cruise, the research team will incubate crustal fluids in situ and in the laboratory with labeled substrates for tracking single-cell activity, coupled with radioisotope tracer activity and potentiostat measurements, with the objective of determining in situ and potential rates of activity and cellular physiology. The research will also identify which metabolisms active microorganisms utilize under in situ and laboratory conditions, the rates of these processes, and the microorganisms involved. The results are expected to provide explicit hypothesis testing of microbial activity and in situ microbial growth rates from the crustal deep biosphere to transform understanding of microbial activity in the crustal deep biosphere and generate critical information about the ability of life to survive under low energy conditions.
attribute	NC_GLOBAL	projects_0_geolocation	String	Juan de Fuca Ridge flank CORKs, 47N/127W
attribute	NC_GLOBAL	projects_0_name	String	Microbial activity in the crustal deep biosphere
attribute	NC_GLOBAL	projects_0_project_nid	String	700324
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	summary	String	To summarize crustal bacterial and archaeal taxa for this review, we synthesized publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor basalts generated using 454, Illumina and Ion Torrent amplicon platforms. These include seafloor basalts from the Dorado Outcrop and the L\u014d'ihi Seamount in the Pacific Ocean and subseafloor basalts from North Pond on the western flank of the Mid-Atlantic Ridge and the Juan de Fuca Ridge flank in the northeastern Pacific Ocean. Datasets from rock colonization experiments conducted in the subseafloor at the Juan de Fuca Ridge flank site were also included, as well as microbial community surveys of the subseafloor crustal fluids from the anoxic Juan de Fuca site and the oxic North Pond site.
attribute	NC_GLOBAL	title	String	Synthesis of publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor samples from the Dorado outcrop, L\u014d'ihi Seamount, North Pond, and Juan de Fuca Ridge flank
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	Plot_Order		String
attribute	Plot_Order	bcodmo_name	String	sample
attribute	Plot_Order	description	String	Numerical order on the "Sample" Axis of invididual samples in Figure 4 of the main text. Values: integers from 1 to 120 for samples included in plot; none, samples from blank DNA extractions used for comparison; not-in-plot_used-in-NMDS, additional sediment comparison samples not included in plots but used in NMDS analysis
attribute	Plot_Order	long_name	String	Plot Order
attribute	Plot_Order	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Plot_Order	units	String	unitless
variable	Sample_Name		String
attribute	Sample_Name	bcodmo_name	String	sample
attribute	Sample_Name	description	String	Unique name of the sample used in the plot
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	SRA_Run		String
attribute	SRA_Run	bcodmo_name	String	accession number
attribute	SRA_Run	description	String	Unique Seqence Read Archive (SRA) Accession Number to download fastq-formatted file of sequence data for the Sample_Name from the NCBI Archive
attribute	SRA_Run	long_name	String	SRA Run
attribute	SRA_Run	units	String	unitless
variable	SRA_LibraryName		String
attribute	SRA_LibraryName	bcodmo_name	String	sample_descrip
attribute	SRA_LibraryName	description	String	The unique library name given to the Sample_Name by the authors as listed on the NCBI archive
attribute	SRA_LibraryName	long_name	String	SRA Library Name
attribute	SRA_LibraryName	units	String	unitless
variable	Study_Nickname		String
attribute	Study_Nickname	bcodmo_name	String	reference_paper
attribute	Study_Nickname	description	String	Short hand code referencing the first author and location of a given study
attribute	Study_Nickname	long_name	String	Study Nickname
attribute	Study_Nickname	units	String	unitless
variable	Sample_Type		String
attribute	Sample_Type	bcodmo_name	String	sample_descrip
attribute	Sample_Type	description	String	Environmental type that the sample was collected from. Values: Basalt, Seafloor or subseafloor basalt core samle; FLOCS, mineral colonization experiment from an in situ sytem; Fluids, subsurface crustal fluids collected from a subseafloor observatory; Sediment, sediment core samples; SW, bottom seawater near field sites; blank, DNA extraction blank
attribute	Sample_Type	long_name	String	Sample Type
attribute	Sample_Type	units	String	unitless
variable	Temp		String
attribute	Temp	bcodmo_name	String	sample_descrip
attribute	Temp	description	String	Description of the temperature of the sampling environment. Values: cool, 10 degrees C; na, not applicable
attribute	Temp	long_name	String	Temperature
attribute	Temp	units	String	unitless
variable	Location		String
attribute	Location	bcodmo_name	String	site
attribute	Location	description	String	Descriptive name of field site where Sample_Name originated. Values: NorthPond; Dorado; Loihi; JuanDeFuca
attribute	Location	long_name	String	Location
attribute	Location	units	String	unitless
variable	depth2		String
attribute	depth2	bcodmo_name	String	sample_descrip
attribute	depth2	description	String	Descriptive category of the relative position of the Sample_Name in the environment. Values: seafloor, collected from the seafloor; subsurface, below the seafloor; none, not applicable
attribute	depth2	long_name	String	Depth
attribute	depth2	standard_name	String	depth
attribute	depth2	units	String	unitless
variable	Sequencer_Type		String
attribute	Sequencer_Type	bcodmo_name	String	instrument
attribute	Sequencer_Type	description	String	Sequencing platform used to sequence extracted DNA from the Sample_Name. Values: IonTorrent; Illumina; 454
attribute	Sequencer_Type	long_name	String	Sequencer Type
attribute	Sequencer_Type	units	String	unitless
variable	region16S		String
attribute	region16S	bcodmo_name	String	sample_descrip
attribute	region16S	description	String	Variable region(s) of the 16S rRNA gene that was sequenced from the extracted DNA from the Sample_Name, as desxcribed in the primary literature. Values: V4; V6; V4-V6; V1-V3
attribute	region16S	long_name	String	Region16 S
attribute	region16S	units	String	unitless
variable	Primers		String
attribute	Primers	bcodmo_name	String	sampling_method
attribute	Primers	description	String	Primer set used to amplify the 16S rRNA variable region(s) from the DNA prior to sequencing of the Sample_Name, as described in the primary literature. Values: 519F-805R; 515F-806R; 967F-1046R; 518F-1064R; 28F-388R; 27F-518R
attribute	Primers	long_name	String	Primers
attribute	Primers	units	String	unitless
variable	DNAextraction		String
attribute	DNAextraction	bcodmo_name	String	sampling_method
attribute	DNAextraction	description	String	Short-hand name for protocol used for extracting DNA from the sample, as described in the primary literature. Values: MPBiomedicalsFastDNA; CTABPhenolChloroform; TCEPPhenolChloroform; MoBioPowerSoil; EnzymePhenolChloroform; SDSPhenolChloroform
attribute	DNAextraction	long_name	String	DNAextraction
attribute	DNAextraction	units	String	unitless
variable	DOI		String
attribute	DOI	bcodmo_name	String	reference_paper
attribute	DOI	description	String	Digital Object Identitfyer information for publications that describe the original study for the data used here
attribute	DOI	long_name	String	DOI
attribute	DOI	units	String	unitless
variable	SRA_Study		String
attribute	SRA_Study	bcodmo_name	String	accession number
attribute	SRA_Study	description	String	Sequence Read Archive Identifier number for finding original datafiles on the NCBI Archive
attribute	SRA_Study	long_name	String	SRA Study
attribute	SRA_Study	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.