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Title Sum-
Institution Dataset ID
   set  data   graph     files  public Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample
Processor deployment in Monterey Bay, CA in 2016.
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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,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String The Environmental Sample Processor (ESP) filtered seawater sequentially
through 5.0 um and 0.2 um pore size polyvinylidene fluoride filters. Seawater
was evacuated from filters and followed twice with a 2 minute incubation with
1 ml of RNAlater\u2122. RNAlater was evacuated, and filters were stored in the
ESP until they were transferred to -80 C upon instrument recovery.\u00a0

Grab samples for sequencing while the ESP was not deployed were taken using
Niskin bottles that collected seawater at the same depth and location of the
ESP. Water was transferred to a low-density polyethylene cubitainer and
maintained at ambient temperature until return to lab within 30 min. Seawater
was filtered as above with vacuum filtration and preserved immediately in
liquid nitrogen and transferred to -80 C.

Single-cell sequencing: Seawater was transferred directly from the Niskin
bottle to a 50 ml Falcon tube and placed on ice until brought back to lab.
Each sampling day, 3 x 1 ml of seawater was preserved in cryovials using 100
ul of glyTe (5 ml glycerol, 3 ml Milli-Q H2O, 1 ml 100 x TE pH 8.0, 0.2 um
filter sterilized after mixing the above, and stored in -20 C freezer).
Preserved samples were then placed in a -80 C freezer. Samples were processed
and sequenced at JGI
attribute NC_GLOBAL awards_0_award_nid String 541254
attribute NC_GLOBAL awards_0_award_number String OCE-1342694
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1342694 (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 Metagenomic, metatranscriptomic, and single cell sequencing data from the Fall 2016 ESP deployment in Monterey Bay, CA
PI: Mary Ann Moran
Version: 2020-03-10
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 2019-01-22T20:12:37Z
attribute NC_GLOBAL date_modified String 2020-04-01T17:17:54Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.753343.2
attribute NC_GLOBAL Easternmost_Easting double -121.901
attribute NC_GLOBAL geospatial_lat_max double 36.835
attribute NC_GLOBAL geospatial_lat_min double 36.835
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -121.901
attribute NC_GLOBAL geospatial_lon_min double -121.901
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/753343 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL keywords String accession, analysis, Analysis_Project_Name, assembly, Assembly_Method, bases, bco, bco-dmo, bio, biological, biome, chemical, collection, Collection_Date, contigs, data, dataset, date, dmo, env, env_biome, env_feature, env_material, erddap, feature, filtered, geo, geo_loc_name, gold, GOLD_Project_ID, instrument, jgi, JGI_Contigs_Link, JGI_Project_ID, JGI_Sample_ID, JGI_Sequencing_Project_ID, JGI_Sequencing_Project_Name, latitude, Latitude_and_Longitude, link, loc, longitude, management, material, method, mode, name, ncbi, NCBI_BioProject_Accession, NCBI_BioSample_Accession, NCBI_Project_ID, NCBI_SRA_Accession_ID, oceanography, office, preliminary, project, run, sample, Sample_Name, sea, seawater, sequencing, Sequencing_Run_Mode, sra, total, Total_Bases, type, volume, Volume_Seawater_Filtered, water
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/753343/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/753343 (external link)
attribute NC_GLOBAL Northernmost_Northing double 36.835
attribute NC_GLOBAL param_mapping String {'753343': {'lat': 'flag - latitude', 'lon': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/753343/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Georgia
attribute NC_GLOBAL people_0_affiliation_acronym String UGA
attribute NC_GLOBAL people_0_person_name String Mary Ann Moran
attribute NC_GLOBAL people_0_person_nid String 51592
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 Georgia
attribute NC_GLOBAL people_1_affiliation_acronym String UGA
attribute NC_GLOBAL people_1_person_name String Brent Nowinski
attribute NC_GLOBAL people_1_person_nid String 662396
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 Mathew Biddle
attribute NC_GLOBAL people_2_person_nid String 708682
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 OceanSulfurFluxBact
attribute NC_GLOBAL projects_0_acronym String OceanSulfurFluxBact
attribute NC_GLOBAL projects_0_description String Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling.
The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation.
This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.
attribute NC_GLOBAL projects_0_end_date String 2018-12
attribute NC_GLOBAL projects_0_name String Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
attribute NC_GLOBAL projects_0_project_nid String 541255
attribute NC_GLOBAL projects_0_start_date String 2014-01
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 36.835
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String latitude,longitude
attribute NC_GLOBAL summary String These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.
attribute NC_GLOBAL title String Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016.
attribute NC_GLOBAL version String 2
attribute NC_GLOBAL Westernmost_Easting double -121.901
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable GOLD_Project_ID   String  
attribute GOLD_Project_ID bcodmo_name String accession number
attribute GOLD_Project_ID description String Accession number at DOE JGI IMG database: https://img.jgi.doe.gov
attribute GOLD_Project_ID long_name String GOLD Project ID
attribute GOLD_Project_ID units String unitless
variable Analysis_Project_Name   String  
attribute Analysis_Project_Name bcodmo_name String project
attribute Analysis_Project_Name description String Name of sequencing project
attribute Analysis_Project_Name long_name String Analysis Project Name
attribute Analysis_Project_Name units String unitless
variable Type   String  
attribute Type bcodmo_name String sample_descrip
attribute Type description String Material type sequenced
attribute Type long_name String Type
attribute Type units String unitless
variable Assembly_Method   String  
attribute Assembly_Method bcodmo_name String sampling_method
attribute Assembly_Method description String assembly method
attribute Assembly_Method long_name String Assembly Method
attribute Assembly_Method units String unitless
variable Collection_Date   String  
attribute Collection_Date bcodmo_name String date
attribute Collection_Date description String collection date of samples
attribute Collection_Date long_name String Collection Date
attribute Collection_Date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute Collection_Date units String unitless
variable Instrument   String  
attribute Instrument bcodmo_name String instrument
attribute Instrument description String instrument
attribute Instrument long_name String Instrument
attribute Instrument units String unitless
variable JGI_Contigs_Link   String  
attribute JGI_Contigs_Link bcodmo_name String unknown
attribute JGI_Contigs_Link description String JGI Contigs Link
attribute JGI_Contigs_Link long_name String JGI Contigs Link
attribute JGI_Contigs_Link units String unitless
variable JGI_Project_ID   int  
attribute JGI_Project_ID _FillValue int 2147483647
attribute JGI_Project_ID actual_range int 1174504, 1190880
attribute JGI_Project_ID bcodmo_name String unknown
attribute JGI_Project_ID description String JGI Project ID
attribute JGI_Project_ID long_name String JGI Project ID
attribute JGI_Project_ID units String unitless
variable JGI_Sample_ID   int  
attribute JGI_Sample_ID _FillValue int 2147483647
attribute JGI_Sample_ID actual_range int 166736, 178378
attribute JGI_Sample_ID bcodmo_name String sample
attribute JGI_Sample_ID description String JGI Sample ID
attribute JGI_Sample_ID long_name String JGI Sample ID
attribute JGI_Sample_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute JGI_Sample_ID units String unitless
variable JGI_Sequencing_Project_ID   int  
attribute JGI_Sequencing_Project_ID _FillValue int 2147483647
attribute JGI_Sequencing_Project_ID actual_range int 1174680, 1190883
attribute JGI_Sequencing_Project_ID bcodmo_name String unknown
attribute JGI_Sequencing_Project_ID description String JGI Sequencing Project ID
attribute JGI_Sequencing_Project_ID long_name String JGI Sequencing Project ID
attribute JGI_Sequencing_Project_ID units String unitless
variable JGI_Sequencing_Project_Name   String  
attribute JGI_Sequencing_Project_Name bcodmo_name String unknown
attribute JGI_Sequencing_Project_Name description String JGI Sequencing Project Name
attribute JGI_Sequencing_Project_Name long_name String JGI Sequencing Project Name
attribute JGI_Sequencing_Project_Name units String unitless
variable Latitude_and_Longitude   String  
attribute Latitude_and_Longitude bcodmo_name String unknown
attribute Latitude_and_Longitude description String Latitude and Longitude
attribute Latitude_and_Longitude long_name String Longitude
attribute Latitude_and_Longitude standard_name String longitude
attribute Latitude_and_Longitude units String unitless
variable NCBI_BioProject_Accession   String  
attribute NCBI_BioProject_Accession bcodmo_name String unknown
attribute NCBI_BioProject_Accession description String NCBI BioProject Accession
attribute NCBI_BioProject_Accession long_name String NCBI Bio Project Accession
attribute NCBI_BioProject_Accession units String unitless
variable NCBI_BioSample_Accession   String  
attribute NCBI_BioSample_Accession bcodmo_name String unknown
attribute NCBI_BioSample_Accession description String NCBI BioSample Accession
attribute NCBI_BioSample_Accession long_name String NCBI Bio Sample Accession
attribute NCBI_BioSample_Accession units String unitless
variable NCBI_Project_ID   int  
attribute NCBI_Project_ID _FillValue int 2147483647
attribute NCBI_Project_ID actual_range int 467720, 511331
attribute NCBI_Project_ID bcodmo_name String unknown
attribute NCBI_Project_ID description String NCBI Project ID
attribute NCBI_Project_ID long_name String NCBI Project ID
attribute NCBI_Project_ID units String unitless
variable NCBI_SRA_Accession_ID   String  
attribute NCBI_SRA_Accession_ID bcodmo_name String unknown
attribute NCBI_SRA_Accession_ID description String NCBI SRA Accession ID
attribute NCBI_SRA_Accession_ID long_name String NCBI SRA Accession ID
attribute NCBI_SRA_Accession_ID units String unitless
variable Sample_Name   String  
attribute Sample_Name bcodmo_name String sample
attribute Sample_Name description String sample name
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 Sequencing_Run_Mode   String  
attribute Sequencing_Run_Mode bcodmo_name String unknown
attribute Sequencing_Run_Mode description String sequencing run mode
attribute Sequencing_Run_Mode long_name String Sequencing Run Mode
attribute Sequencing_Run_Mode units String unitless
variable Total_Bases   String  
attribute Total_Bases bcodmo_name String unknown
attribute Total_Bases description String total bases
attribute Total_Bases long_name String Total Bases
attribute Total_Bases units String unitless
variable Volume_Seawater_Filtered   float  
attribute Volume_Seawater_Filtered _FillValue float NaN
attribute Volume_Seawater_Filtered actual_range float 73.5, 1000.0
attribute Volume_Seawater_Filtered bcodmo_name String vol_filt
attribute Volume_Seawater_Filtered description String Volume Seawater Filtered
attribute Volume_Seawater_Filtered long_name String Volume Seawater Filtered
attribute Volume_Seawater_Filtered units String milliliters (mL)
variable env_biome   String  
attribute env_biome bcodmo_name String unknown
attribute env_biome description String environmental biome
attribute env_biome long_name String Env Biome
attribute env_biome units String unitless
variable env_feature   String  
attribute env_feature bcodmo_name String unknown
attribute env_feature description String environmental feature
attribute env_feature long_name String Env Feature
attribute env_feature units String unitless
variable env_material   String  
attribute env_material bcodmo_name String unknown
attribute env_material description String environmental material
attribute env_material long_name String Env Material
attribute env_material units String unitless
variable geo_loc_name   String  
attribute geo_loc_name bcodmo_name String unknown
attribute geo_loc_name description String location name
attribute geo_loc_name long_name String Geo Loc Name
attribute geo_loc_name units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 36.835, 36.835
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 with positive values indicating North
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 -121.901, -121.901
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 with negative values indicating West
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

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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