BCO-DMO ERDDAP
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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\nprofiling\n \nTo summarize crustal bacterial and archaeal taxa for this review, we\nsynthesized publicly-available sequence datasets of the 16S rRNA gene in\nenvironmental DNA extracted from seafloor and subseafloor basalts generated\nusing 454, Illumina and Ion Torrent amplicon platforms. These include seafloor\nbasalts from the Dorado Outcrop (Lee et al., 2015) and the L\\u014d'ihi\nSeamount (Jacobsen Meyers et al., 2014) in the Pacific Ocean and subseafloor\nbasalts from North Pond on the western flank of the Mid-Atlantic Ridge\n(J\\u00f8rgensen & Zhao, 2016) and the Juan de Fuca Ridge flank in the\nnortheastern Pacific Ocean (LaBont\\u00e9 et al., 2017). Datasets from rock\ncolonization experiments conducted in the subseafloor at the Juan de Fuca\nRidge flank site (Smith et al., 2016; Ram\\u00edrez et al., 2019) were also\nincluded, as well as microbial community surveys of the subseafloor crustal\nfluids from the anoxic Juan de Fuca site (Jungbluth et al., 2016) and the oxic\nNorth Pond site (Tully et al., 2017; Meyer et al., 2016). For comparison, we\nincluded select reference datasets from oxic (Reese et al., 2018; Zinke et\nal., 2018) and anoxic sediment (LaBont\\u00e9 et al., 2017) and the overlying\nbottom seawater (Lee et al., 2015) from these same study sites.\n \nRaw sequence data from the reviewed studies were downloaded from the NCBI\nShort Read Archive. Sequencing reads generated using Illumina and Ion Torrent\nplatforms were quality filtered and processed to unique Amplicon Sequence\nVariants (ASVs) using DADA2 (Callahan et al, 2016), with taxonomy determined\nby the na\\u00efve Bayesian classifier in DADA2 using a training set from the\nSILVA v132 database (Quast et al., 2013; Yilmaz et al., 2014; Gl\\u00f6ckner et\nal., 2017). For the 454 GS-FLX sequence datasets, operational taxonomic units\n(OTUs) constructed with 97% or greater sequence similarity in the original\nanalyses were reprocessed in mothur V.1.37.6 (Schloss et al., 2009) against\nthe same SILVA database. All short read datasets were merged and summarized to\nthe relative abundance at phylum resolution (or to class level for\nProteobacteria phyla) using Phyloseq v1.24.0 (McMurdie & Holmes, 2013).\nFigures were produced using ggplot2 R package version 2.2.1 (Wickham, 2016) in\nRStudio (RStudio Team, 2017). Taxonomic grouping in each sample separated taxa\ninto common (>5% abundance in at least one sample) versus rare (never more\nthan 5% in any sample). Supplemental Figure S1 shows the breakdown of\nGammaproteobacteria families in the samples presented in Figure 4 of the main\ntext, and Supplemental Figure S2 highlights the abundance of rare taxa (never\n>5% abundance in any sample). The Bray-Curtis distances between samples was\ncalculated using the same dataset described above, summarized to relative\nabundance at the Family taxonomic level using Phyloseq and the Vegan package\n(Oksanen et al., 2018). A Non-Metric Multidimensional Scaling (NMDS)\nordination was produced from this distance matrix. It should be noted that\ncommon rules for beta diversity comparisons, such as common library\npreparation/sequencing protocols and library-size normalization, were not\nperformed in this analysis due to the diversity of the datasets being\nconsidered and the resulting NMDS ordination having high-stress (>20%).\nTherefore, the results should be viewed as broadly qualitative and not\nquantitative.\n \nAll data processing steps and markdown files are available via github:\n[https://github.com/orcuttlab/ocean-crust-\nmicro](\\\\\"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 (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 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 \n  PI: Beth Orcutt (Bigelow) \n  Co-PI: Timothy D'Angelo (Bigelow) \n  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/ (external link)
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 (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/789136 (external link)
attribute NC_GLOBAL param_mapping String {'789136': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/789136/parameters (external link)
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:\nThe 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.\nThis 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 [Ocean Crust Microbiome Amplicon Metadata] - Synthesis of publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor samples from the Dorado outcrop, Lō'ihi Seamount, North Pond, and Juan de Fuca Ridge flank (Microbial activity in the crustal deep biosphere)
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/ (external link)
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/ (external link)
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

 
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