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,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Rock material was crushed while still frozen in a Progressive Exploration Jaw\nCrusher (Model 150) whose surfaces were sterilized with 70% ethanol and RNase\nAWAY (Thermo Fisher Scientific, USA) inside a laminar flow hood. Powdered rock\nmaterial was returned to the -80\\u00b0C freezer until extraction.\n \nDNA was extracted from 20, 30, or 40 grams of powdered rock material,\ndepending on the quantity of rock available. A DNeasy PowerMax Soil Kit\n(Qiagen, USA) was used following the manufacturer\\u2019s protocol modified to\nincluded three freeze/thaw treatments prior to the addition of Soil Kit\nsolution C1. Each treatment consisted of 1 minute in liquid nitrogen followed\nby 5 minutes at 65 \\u00b0C. DNA extracts were concentrated by isopropanol\nprecipitation overnight at 4\\u00b0C.\n \nThe low biomass in our samples required whole genome amplification (WGA) prior\nto PCR amplification of marker genes. Genomic DNA was amplified by Multiple\nDisplacement Amplification (MDA) using the REPLI-g Single Cell Kit (Qiagen) as\ndirected. MDA bias was minimized by splitting each WGA sample into triplicate\n16 \\u03bcL reactions after 1 hr of amplification and then resuming\namplification for the manufacturer-specified 7 hrs (8 hrs total).\n \nDNA was also recovered from samples of drilling mud and drilling fluid\n(surface water collected during the coring process) for negative controls, as\nwell as two \\u201ckit control\\u201d samples, in which no sample was added, to\naccount for any contaminants originating from either the DNeasy PowerMax Soil\nKit or the REPLI-g Single Cell Kit.\n \nBacterial SSU rRNA gene fragments were PCR amplified from MDA samples and\nsequenced at Georgia Genomics and Bioinformatics Core (Univ. of Georgia). The\nprimers used were: Bac515-Y and Bac926R. Dual-indexed libraries were prepared\nwith (HT) iTruS (Kappa Biosystems) chemistry and sequencing was performed on\nan Illumina MiSeq 2 x 300 bp system with all samples combined equally on a\nsingle flow cell.\n \nRaw sequence reads were processed through Trim Galore\n[[http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/]](\\\\\"http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\\]\\\\\"),\nFLASH (ccb.jhu.edu/software/FLASH/) and FASTX Toolkit\n[[http://hannonlab.cshl.edu/fastx_toolkit/]](\\\\\"http://hannonlab.cshl.edu/fastx_toolkit/\\]\\\\\")\nfor trimming and removal of low quality/short reads.\n \nQuality filtering included requiring a minimum average quality of 25 and\nrejection of paired reads less than 250 nucleotides.\n \nOperational Taxonomic Unit (OTU) clusters were constructed at 99% similarity\nwith the script pick_otus.py within the Quantitative Insights Into Microbial\nEcology (QIIME) v.1.9.1 software and \\u2018uclust\\u2019. Any OTU that matched\nan OTU in one of our control samples (drilling fluids, drilling mud,\nextraction and WGA controls) was removed (using filter_otus_from_otu_table.py)\nalong with any sequences of land plants and human pathogens that may have\nsurvived the control filtering due to clustering at 99%\n(filter_taxa_from_otu_table.py). As an additional quality control measure,\ngenera that are commonly identified as PCR contaminants were removed.\nUnclassified OTUs were queried using BLAST against the GenBank nr database and\nfurther information about these OTUs is provided in the Supplementary\nDiscussion text under the section \\u201cTaxonomic diversity information from\niTAGs.\\u201d OTUs that could not be assigned to Bacteria or Archaea were\nremoved from further analysis. For downstream analyses, any OTUs not\nrepresenting more than 0.01% of relative abundance of sequences overall were\nremoved as those are unlikely to contribute significantly to in situ\ncommunities. The OTU data table was transformed to a presence/absence table\nand the Jaccard method was used to generate a distance matrix using the\ndist.binary() function in the R package ade4.
attribute NC_GLOBAL awards_0_award_nid String 709555
attribute NC_GLOBAL awards_0_award_number String OCE-1658031
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1658031 (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 cdm_data_type String Other
attribute NC_GLOBAL comment String Supplementary Table 4C: iTAG \n  PI: Virginia Edgcomb  \n  Data Version 1: 2020-05-28
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 dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2020-05-28T12:54:12Z
attribute NC_GLOBAL date_modified String 2020-07-09T16:05:24Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.813173.1
attribute NC_GLOBAL Easternmost_Easting double 57.278183
attribute NC_GLOBAL geospatial_lat_max double -32.70567
attribute NC_GLOBAL geospatial_lat_min double -32.70567
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double 57.278183
attribute NC_GLOBAL geospatial_lon_min double 57.278183
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 747.7
attribute NC_GLOBAL geospatial_vertical_min double 10.7
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/813173 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String DNA sequencing performed using the Illumina MiSeq 2 x 300 bp platform (Univ. of Georgia)
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 813183
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_0_supplied_name String Illumina MiSeq 2 x 300 bp platform
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, contmnt, data, dataset, depth, dmo, erddap, iTAG_OTU, iTAG_Paired_Contmnt_Rem, iTAG_Paired_QC, iTAG_Raw, latitude, longitude, management, metatr, Metatr_Paired_Contmnt_Rem, Metatr_Paired_QC, Metatr_Raw, Metatr_Reads_Remaining, oceanography, office, otu, paired, preliminary, raw, reads, rem, remaining, sample, Sample_ID, tag
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/813173/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/813173 (external link)
attribute NC_GLOBAL Northernmost_Northing double -32.70567
attribute NC_GLOBAL param_mapping String {'813173': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/813173/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_0_affiliation_acronym String WHOI
attribute NC_GLOBAL people_0_person_name String Virginia P. Edgcomb
attribute NC_GLOBAL people_0_person_nid String 51284
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
attribute NC_GLOBAL people_1_person_name String Virginia P. Edgcomb
attribute NC_GLOBAL people_1_person_nid String 51284
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
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 Karen Soenen
attribute NC_GLOBAL people_2_person_nid String 748773
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 Subseafloor Lower Crust Microbiology
attribute NC_GLOBAL projects_0_acronym String Subseafloor Lower Crust Microbiology
attribute NC_GLOBAL projects_0_description String NSF abstract:\nThe lower ocean crust has remained largely unexplored and represents one of the last frontiers for biological exploration on Earth. Preliminary data indicate an active subsurface biosphere in samples of the lower oceanic crust collected from Atlantis Bank in the SW Indian Ocean as deep as 790 m below the seafloor. Even if life exists in only a fraction of the habitable volume where temperatures permit and fluid flow can deliver carbon and energy sources, an active lower oceanic crust biosphere would have implications for deep carbon budgets and yield insights into microbiota that may have existed on early Earth. This is all of great interest to other research disciplines, educators, and students alike. A K-12 education program will capitalize on groundwork laid by outreach collaborator, A. Martinez, a 7th grade teacher in Eagle Pass, TX, who sailed as outreach expert on Drilling Expedition 360. Martinez works at a Title 1 school with ~98% Hispanic and ~2% Native American students and a high number of English Language Learners and migrants. Annual school visits occur during which the project investigators present hands on-activities introducing students to microbiology, and talks on marine microbiology, the project, and how to pursue science related careers. In addition, monthly Skype meetings with students and PIs update them on project progress. Students travel to the University of Texas Marine Science Institute annually, where they get a campus tour and a 3-hour cruise on the R/V Katy, during which they learn about and help with different oceanographic sampling approaches. The project partially supports two graduate students, a Woods Hole undergraduate summer student, the participation of multiple Texas A+M undergraduate students, and 3 principal investigators at two institutions, including one early career researcher who has not previously received NSF support of his own.\nGiven the dearth of knowledge of the lower oceanic crust, this project is poised to transform our understanding of life in this vast environment. The project assesses metabolic functions within all three domains of life in this crustal biosphere, with a focus on nutrient cycling and evaluation of connections to other deep marine microbial habitats. The lower ocean crust represents a potentially vast biosphere whose microbial constituents and the biogeochemical cycles they mediate are likely linked to deep ocean processes through faulting and subsurface fluid flow. Atlantis Bank represents a tectonic window that exposes lower oceanic crust directly at the seafloor. This enables seafloor drilling and research on an environment that can transform our understanding of connections between the deep subseafloor biosphere and the rest of the ocean. Preliminary analysis of recovered rocks from Expedition 360 suggests the interaction of seawater with the lower oceanic crust creates varied geochemical conditions capable of supporting diverse microbial life by providing nutrients and chemical energy. This project is the first interdisciplinary investigation of the microbiology of all 3 domains of life in basement samples that combines diversity and \"meta-omics\" analyses, analysis of nutrient addition experiments, high-throughput culturing and physiological analyses of isolates, including evaluation of their ability to utilize specific carbon sources, Raman spectroscopy, and lipid biomarker analyses. Comparative genomics are used to compare genes and pathways relevant to carbon cycling in these samples to data from published studies of other deep-sea environments. The collected samples present a rare and time-sensitive opportunity to gain detailed insights into microbial life, available carbon and energy sources for this life, and of dispersal of microbiota and connections in biogeochemical processes between the lower oceanic crust and the overlying aphotic water column.\nAbout the study area:\nThe International Ocean Discovery Program (IODP) Expedition 360 explored the lower crust at Atlantis Bank, a 12 Ma oceanic core complex on the ultraslow-spreading SW Indian Ridge. This oceanic core complex represents a tectonic window that exposes lower oceanic crust and mantle directly at the seafloor, and the expedition provided an unprecedented opportunity to access this habitat in the Indian Ocean.
attribute NC_GLOBAL projects_0_end_date String 2020-01
attribute NC_GLOBAL projects_0_geolocation String SW Indian Ridge, Indian Ocean
attribute NC_GLOBAL projects_0_name String Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches
attribute NC_GLOBAL projects_0_project_nid String 709556
attribute NC_GLOBAL projects_0_start_date String 2017-02
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 -32.70567
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String latitude,longitude
attribute NC_GLOBAL summary String Supplementary Table 4C: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data. Samples  taken on board of the R/V JOIDES Resolution between November 30, 2015 and January 30, 2016
attribute NC_GLOBAL title String [IODP360 - iTAG and metatranscriptome data] - Supplementary Table 4C: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data. (Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double 57.278183
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable Sample_ID String
attribute Sample_ID bcodmo_name String sample
attribute Sample_ID description String Sample ID
attribute Sample_ID long_name String Sample ID
attribute Sample_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Sample_ID units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double -32.70567, -32.70567
attribute latitude axis String Y
attribute latitude bcodmo_name String unknown
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude of sample, south is negative
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
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 57.278183, 57.278183
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 of samples, west is negative
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/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable depth double
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 10.7, 747.7
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String Depth - meters below seafloor (mbsf)
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable iTAG_Raw int
attribute iTAG_Raw _FillValue int 2147483647
attribute iTAG_Raw actual_range int 29227, 810682
attribute iTAG_Raw bcodmo_name String unknown
attribute iTAG_Raw description String iTAG data - Raw reads
attribute iTAG_Raw long_name String I TAG Raw
attribute iTAG_Raw units String number of reads
variable iTAG_Paired_QC int
attribute iTAG_Paired_QC _FillValue int 2147483647
attribute iTAG_Paired_QC actual_range int 19196, 599653
attribute iTAG_Paired_QC bcodmo_name String unknown
attribute iTAG_Paired_QC colorBarMaximum double 150.0
attribute iTAG_Paired_QC colorBarMinimum double 0.0
attribute iTAG_Paired_QC description String iTAG data - paired reads after QC
attribute iTAG_Paired_QC long_name String I TAG Paired QC
attribute iTAG_Paired_QC units String number of reads
variable iTAG_Paired_Contmnt_Rem int
attribute iTAG_Paired_Contmnt_Rem _FillValue int 2147483647
attribute iTAG_Paired_Contmnt_Rem actual_range int 38, 39021
attribute iTAG_Paired_Contmnt_Rem bcodmo_name String unknown
attribute iTAG_Paired_Contmnt_Rem description String iTAG data - Paired reads surviving  removal of potential contaminants matching sequences in control samples or known contaminants.
attribute iTAG_Paired_Contmnt_Rem long_name String I TAG Paired Contmnt Rem
attribute iTAG_Paired_Contmnt_Rem units String number of reads
variable iTAG_OTU byte
attribute iTAG_OTU _FillValue byte 127
attribute iTAG_OTU actual_range byte 8, 97
attribute iTAG_OTU bcodmo_name String unknown
attribute iTAG_OTU description String iTAG data - Number of OTUs at 99% identity
attribute iTAG_OTU long_name String I TAG OTU
attribute iTAG_OTU units String number of OTUs
variable Metatr_Raw int
attribute Metatr_Raw _FillValue int 2147483647
attribute Metatr_Raw actual_range int 13032452, 63348900
attribute Metatr_Raw bcodmo_name String unknown
attribute Metatr_Raw description String Metatranscriptome data - Raw reads from sequencing
attribute Metatr_Raw long_name String Metatr Raw
attribute Metatr_Raw units String number of reads
variable Metatr_Paired_QC int
attribute Metatr_Paired_QC _FillValue int 2147483647
attribute Metatr_Paired_QC actual_range int 5807873, 29212385
attribute Metatr_Paired_QC bcodmo_name String unknown
attribute Metatr_Paired_QC colorBarMaximum double 150.0
attribute Metatr_Paired_QC colorBarMinimum double 0.0
attribute Metatr_Paired_QC description String Metatranscriptome data - Paired reads after QC
attribute Metatr_Paired_QC long_name String Metatr Paired QC
attribute Metatr_Paired_QC units String number of reads
variable Metatr_Paired_Contmnt_Rem int
attribute Metatr_Paired_Contmnt_Rem _FillValue int 2147483647
attribute Metatr_Paired_Contmnt_Rem actual_range int 1724455, 16336790
attribute Metatr_Paired_Contmnt_Rem bcodmo_name String unknown
attribute Metatr_Paired_Contmnt_Rem description String Metatranscriptome data - Paired reads surviving  removal of potential contaminants matching sequences in control samples or known contaminants.
attribute Metatr_Paired_Contmnt_Rem long_name String Metatr Paired Contmnt Rem
attribute Metatr_Paired_Contmnt_Rem units String number of reads
variable Metatr_Reads_Remaining float
attribute Metatr_Reads_Remaining _FillValue float NaN
attribute Metatr_Reads_Remaining actual_range float 0.2344, 0.6815
attribute Metatr_Reads_Remaining bcodmo_name String unknown
attribute Metatr_Reads_Remaining description String Metatranscriptome data - Percent  of original paired reads remaining
attribute Metatr_Reads_Remaining long_name String Metatr Reads Remaining
attribute Metatr_Reads_Remaining units String percentage (%)

 
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