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 Seawater (~180 L) was collected from the stable hydrothermal vent plume\nissuing from the black smoker chimney Inferno (CTD17, 1 450 m). Whole water\nwas transferred to clean 50 L polystyrene reservoirs and concentrated to ~230\nml with a Pellicon 2 tangential flow filtration system equipped with a 30 kDa\nBiomax Polyethersulfone cassette (Millipore Corporation, Billerica, MA) as\ndescribed previously (Morris et al 2010). Cells were collected and\nconcentrated in approximately 2 hours. Concentrated cells were flash frozen in\nliquid nitrogen and stored at -80 \\u00baC until further processing at the\nUniversity of Washington.Cell counts before and after filtration (6.9 x 1010\nand 2.9 x 1010, respectively) indicate that we recovered 42% of the cells\npresent in 180 L of hydrothermal vent plume water. Cells in the concentrated\nsample were divided into replicate samples (Av1 and Av2, ~115 ml each) and\nharvested by centrifuging at 4\\u00b0C for 60 min (17,000 x g). The supernatant\nwas discarded and cell pellets were rinsed with 100 uL of 20 mM Tris buffer pH\n7.4 and stored -80\\u00b0C.\n \nCells were lysed using a titanium sonicating micro-probe (20 sec, 10\nrepetitions) in a 6M urea and 50 \\u03bcM ammonium bicarbonate solution.\nDisulfide bonds were reduced with dithiothreitol and alkylated with iodo-\nacetic acid. After additions of ammonium bicarbonate and methanol, 2 \\u03bcg\nof sequence grade trypsin (Promega, Madison, WI) were added to each sample.\nEnzymatic digestions were incubated for 12 h at 37 oC. Resulting peptides were\ndesalted using a macro-spin C18 column (NestGroup) following the manufacturers\nguidelines prior to analysis by mass spectrometry (MS).\n \nPeptide concentrations from Axial volcano hydrothermal vent plume proteome\nreplicates Av1 and Av2 were measured using the Thermo Scientific Nanodrop\n2000/2000c, which measures the peptide bond absorbance at wavelength of 205\nnm. Approximately 1 \\u03bcg of peptide digest was used for each injection into\nthe mass spectrometer. Each sample consisted of a complex mixture of peptides\nthat were introduced into the mass spectrometer by reverse-phase\nchromatography using a brand new 15 cm long, 75 \\u03bcm i.d. fused silica\ncapillary column packed with C18 particles (Magic C18AQ, 100 \\u00c5, 5\n\\u03bcm; Michrom, Bioresources, Inc., CA) fitted with a 2 cm long, 100 \\u03bcm\ni.d. pre-column (Magic C18AQ, 200 \\u00c5, 5\\u03bcm; Michrom). Peptides were\nfirst trapped on the pre-column (5% ACN; 4 ml min-1; 7 min). Chromatographic\nseparations were performed using an acidified (formic acid, 0.1% v/v) water-\nacetonitrile gradient (5-35% acetonitrile in 60 min) with a total run-time of\n95 minutes.\n \nMass spectrometry was performed on replicates Av1 and Av2 independently using\nthe Thermo Fisher (San Jose, Ca) linear ion trap \\u2013Orbitrap (LTQ-OT)\nhybrid tandem mass spectrometer. Peptides were analyzed using the data-\nindependent Precursor Acquisition Independent from Ion Count (PAcIFIC) method\n(Panchaud et al 2009). Rather than requiring the mass spectrometer to select\nions for fragmentation based on MS1 data, the PAcIFIC method systematically\nfragments ions at all m/z channels (Panchaud et al 2011). Each method file\nincludes the full 95 minute linear HPLC gradient of 5-35% ACN over 60 minutes\n(see above) and covers a 21.5 m/z range using 14 contiguous, unique channels\nthat span 2.5 m/z in the mass spectrometer. This results in a total of 45\nmethod files per PAcIFIC analytical cycle to cover a full m/z range of\n400-1400.
attribute NC_GLOBAL awards_0_award_nid String 529021
attribute NC_GLOBAL awards_0_award_number String OCE-1232840
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1232840 (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 Inferno Plume Proteins \n    replicate Av1 \n      (Supplementary Table 3) \n    only protein probability > .9 reported \n     location and depth added by DMO \n    R.Morris, PI
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 2015-11-25T16:24:25Z
attribute NC_GLOBAL date_modified String 2017-11-12T19:58:17Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.643630
attribute NC_GLOBAL Easternmost_Easting double -130.0138
attribute NC_GLOBAL geospatial_lat_max double 45.934
attribute NC_GLOBAL geospatial_lat_min double 45.934
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -130.0138
attribute NC_GLOBAL geospatial_lon_min double -130.0138
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 1450.0
attribute NC_GLOBAL geospatial_vertical_min double 1450.0
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/627835 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String CTD SBE 9
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Seabird 9plus CTD with temperature and conductivity sensors.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 637597
attribute NC_GLOBAL instruments_0_description String The Sea-Bird SBE 9 is a type of CTD instrument package.  The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911.  The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used.  more information from Sea-Bird Electronics
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 Sea-Bird 9
attribute NC_GLOBAL instruments_0_instrument_nid String 488
attribute NC_GLOBAL instruments_0_supplied_name String CTD Seabird 9 plus
attribute NC_GLOBAL instruments_1_acronym String Mass Spec
attribute NC_GLOBAL instruments_1_dataset_instrument_description String \"The hybrid Fourier Transform (FT) mass spectrometer(MS) combines a linear ion trap\nMS and the Orbitrap mass analyzer. Ions generated by API\nare collected in the LTQ XL followed by axial ejection to the\nC-shaped storage trap which is used to store and collisionally\ncool ions before injection into the orbital trap. The ions\ntransferred from the C-Trap are captured in the orbital trap\nby rapidly increasing the electric field and the detection of\nthe image current from coherent ion packets takes place\nafter the voltages have stabilized. Signals from each of the\norbital trap outer electrodes are amplified and transformed\ninto a frequency spectrum by fast Fourier transformation\nwhich is finally converted into a mass spectrum.\" (From Fisher Scientific)
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 627987
attribute NC_GLOBAL instruments_1_description String General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB16/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Mass Spectrometer
attribute NC_GLOBAL instruments_1_instrument_nid String 685
attribute NC_GLOBAL instruments_1_supplied_name String Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer
attribute NC_GLOBAL instruments_2_acronym String Spectrophotometer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Measured peptide bond absorbance at wavelength 205nm
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 637598
attribute NC_GLOBAL instruments_2_description String An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB20/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Spectrophotometer
attribute NC_GLOBAL instruments_2_instrument_nid String 707
attribute NC_GLOBAL instruments_2_supplied_name String Thermo Scientific Nanodrop 2000/2000c Spectrophotometer
attribute NC_GLOBAL keywords String annotation, bco, bco-dmo, biological, category, chemical, consensus, consensus_annotation, data, dataset, depth, dmo, entry, erddap, fasta, indep, indep_spectra_tot, kegg, KEGG_category, latitude, link, longitude, management, ncbi, NCBI_FASTA_link, num, num_unique_peptide, oceanography, office, peptide, peptide_seq, preliminary, probability, protein, protein_probability, seq, spectra, tot, unique
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/627835/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/627835 (external link)
attribute NC_GLOBAL Northernmost_Northing double 45.934
attribute NC_GLOBAL param_mapping String {'627835': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/627835/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Washington
attribute NC_GLOBAL people_0_affiliation_acronym String UW
attribute NC_GLOBAL people_0_person_name String Robert Morris
attribute NC_GLOBAL people_0_person_nid String 51295
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 University of Washington
attribute NC_GLOBAL people_1_affiliation_acronym String UW
attribute NC_GLOBAL people_1_person_name String Robert Morris
attribute NC_GLOBAL people_1_person_nid String 51295
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 Ms Dicky Allison
attribute NC_GLOBAL people_2_person_nid String 50382
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 Sulfur Oxidizers
attribute NC_GLOBAL projects_0_acronym String Sulfur Oxidizers
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nThe ocean serves an immense reservoir of carbon, nitrogen, phosphorus, sulfur, and other elements required for all life. The active and diverse microbial populations that inhabit the oceans are responsible for mediating nutrient transformations that maintain the chemistry of seawater. A recent study identified a ubiquitous group of marine bacteria from the Arctic96BD-19 gamma-proteobacterial sulfur oxidizer (GSO) lineage that is closely related to known sulfur oxidizing species that fix inorganic carbon and oxidize sulfide in low-oxygen waters. The potential for GSOs to use reduced forms of sulfur in oxygenated waters suggests that they are a keystone species that link the marine carbon and sulfur cycles. The only known isolates from the Arctic96BD-19 lineage of GSOs are now in culture, allowing fundamental questions about their roles in carbon and sulfur cycling to be investigated. Preliminary data suggest that they use energy from the oxidation of sulfur to assimilate carbon. This project seek to address the overarching hypothesis that sulfur transformations provide the Arctic96BD- 19 lineage of GSOs with energy for organic and inorganic carbon cycling throughout the water column.\nThree specific hypotheses will be tested.\n1. Arctic96BD-19 cells assimilate either organic carbon or fixes inorganic carbon, depending on environmental conditions.\n2. Arctic96BD-19 cells oxidize thiosulfate via formation of a tetrathionate intermediate, or using the branched thiosulfate oxidation pathway.\n3. Arctic96BD-19 cells are ubiquitous sulfur oxidizers that assimilate organic and inorganic carbon through the Pacific Northwest.\nA combination of laboratory growth studies of the investigator's pure cultures and comparative genomic analyses will be used. The genomic data will be used to determine whether the Arctic96BD-19 cultures possess the genetic potential to oxidize reduced sulfur to sulfate (based on possession of known core and ancillary sulfur oxidation genes), which potential oxidation pathways are used, and whether they can fix inorganic carbon. These data will help guide the physiology studies by determining the most likely forms of inorganic and organic compounds that can be utilized.\nMarine bacteria are critical players in global nutrient cycles, but many of their individual and community functions in the ecosystem are not well understood. Future oceanographers will need to use cultivation-dependent and cultivation-independent methods to identify metabolic process that shape microbial communities and impact biogeochemical cycles. Student education, scientific advancement, and public awareness are all important components of this project.
attribute NC_GLOBAL projects_0_end_date String 2015-09
attribute NC_GLOBAL projects_0_geolocation String North Pacific Ocean
attribute NC_GLOBAL projects_0_name String Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
attribute NC_GLOBAL projects_0_project_nid String 529022
attribute NC_GLOBAL projects_0_project_website String http://morrislab.ocean.washington.edu/ (external link)
attribute NC_GLOBAL projects_0_start_date String 2012-10
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 45.934
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String latitude,longitude,depth
attribute NC_GLOBAL summary String Proteins identified in the Inferno hydrothermal vent plume meta-proteome\n(replicate Av1).\\u00a0 Only proteins identified by peptides with a protein\nprobability >0.9 are listed.\\u00a0\n \nThese data are reported as Supplementary Table 3 and discussed in [Mattes et\nal., 2013](\\\\http://dmoserv3.bco-\ndmo.org/data_docs/SulfurOxidizers/Mattes_2013_PlumeProt.pdf\\\\).\n(doi:10.1038/ismej.2013.113)\n \nThe FASTA information in the data was expanded to include the metadata when\nthose FASTA headers were linked to GenBank.\\u00a0\n \nProteins that were identified in biological replicate Av2 that were not\nidentified in biological replicate Av1. (GSO: Gamma Sulfur Oxidizer)\n \n  \n \\u00a0\n \n\\u00a0\n \n\\u00a0\n \n\\u00a0\n \n\\u00a0\n \n\\Although fewer proteins were identified in Av2, nearly all (94%) of the\nproteins identified in Av2 were also identified in Av1.\\u00a0 Differences in\nthe total number of proteins identified in replicate samples may result from\ndifferences in the amount of biomass obtained during sample processing.\\\n \nDMO notes:  \n Put multiple FASTA entries on separate lines  \n Split out one number in FASTA header for linking  \n Left it sorted by Total Independent Spectra column  \n Added linkage column  \n Removed commas in 'consensus annotation' column (signals database to put in\nnew column)  \n Reordered columns to put KEGG last -- much longer than any other column
attribute NC_GLOBAL title String [Inferno vent plume proteins-Av1] - Proteins identified from the black smoker chimney Inferno hydrothermal vent plume meta-proteome - replicate Av1 - on the Axial seamount off the coast of Washington in 2011. (Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -130.0138
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable entry String
attribute entry bcodmo_name String sample
attribute entry description String data entry number; each entry number is a unit and all columns of information with the same entry number should be considered together
attribute entry long_name String Entry
attribute entry nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute entry units String number
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 45.934, 45.934
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String latitude of sample collection
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
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 -130.0138, -130.0138
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 sample collection; 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 1450.0, 1450.0
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 of sample collection
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 NCBI_FASTA_link String
attribute NCBI_FASTA_link bcodmo_name String external_link
attribute NCBI_FASTA_link description String FASTA header with embedded NCBI reference number; link is to protein page in that database; several entries with multiple links separated by commas had to be put on separate lines to enable multiple links
attribute NCBI_FASTA_link long_name String NCBI FASTA Link
attribute NCBI_FASTA_link units String link
variable protein_probability float
attribute protein_probability _FillValue float NaN
attribute protein_probability actual_range float 0.9052, 1.0
attribute protein_probability bcodmo_name String unknown
attribute protein_probability description String the probability that the protein identified from the peptide sequences is correct. Only proteins identified by peptides with a protein probability of >0.9 are listed
attribute protein_probability long_name String Protein Probability
attribute protein_probability units String decimal number
variable num_unique_peptide byte
attribute num_unique_peptide _FillValue byte 127
attribute num_unique_peptide actual_range byte 1, 20
attribute num_unique_peptide bcodmo_name String unknown
attribute num_unique_peptide description String the number of unique peptide sequences identified; unique peptide is defined as a peptide -- irrespective of its length -- that exists only in one protein of a proteome of interest. The peptide sequences themselves are in the peptide sequence column
attribute num_unique_peptide long_name String Num Unique Peptide
attribute num_unique_peptide units String number
variable indep_spectra_tot short
attribute indep_spectra_tot _FillValue short 32767
attribute indep_spectra_tot actual_range short 1, 218
attribute indep_spectra_tot bcodmo_name String unknown
attribute indep_spectra_tot description String number of identifying peaks from the tandem mass spectrometer
attribute indep_spectra_tot long_name String Indep Spectra Tot
attribute indep_spectra_tot units String number
variable peptide_seq String
attribute peptide_seq bcodmo_name String unknown
attribute peptide_seq description String amino acids identified in the peptide; A=Alanine; G=Glycine; etc
attribute peptide_seq long_name String Peptide Seq
attribute peptide_seq units String text
variable consensus_annotation String
attribute consensus_annotation bcodmo_name String unknown
attribute consensus_annotation description String describing protein X in terms of topic Y; these dominant active bacterial groups are determined by consensus annotation of identified proteins
attribute consensus_annotation long_name String Consensus Annotation
attribute consensus_annotation units String text
variable KEGG_category String
attribute KEGG_category bcodmo_name String unknown
attribute KEGG_category description String Kyoto Encyclopedia of Genes and Genomes; used to identify dominant functional classifications like metabolism or genetic information processing
attribute KEGG_category long_name String KEGG Category
attribute KEGG_category units String text

 
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