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ERDDAP > info > bcodmo_dataset_782058

Title Sum-
Institution Dataset ID
   set  data        files  public Reconstructed genomes from North Pond, western flank of the Mid-Atlantic Ridge, from 2012-2014    ?     I   M   background (external link) RSS Subscribe 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
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 (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 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 (external link)
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 (external link)
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/ (external link)
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 (external link)
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/ (external link)
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/ (external link)
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/ (external link)
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/ (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/782058 (external link)
attribute NC_GLOBAL param_mapping String {'782058': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/782058/parameters (external link)
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 from North Pond, western flank of the Mid-Atlantic Ridge, from 2012-2014
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.

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