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Title Sum-
Institution Dataset ID
     data   graph     files  public The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the
HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008
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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 Sample processing and analyses are detailed in the publications listed below.
Briefly, 100ml of seawater was collected onto 25mm dia polycarbonate filters
(0.22um pore size), rinsed with Tris-buffered saline, flash frozen in liquid
N2, and stored at -80C until extraction. DNA was extracted using a combination
of 5min of bead beating and 15min heat lysis at 95C. Extracted DNA was used as
template of quantitative PCR reactions using primers specifically designed to
target the narB gene from the HLII and LLI clades of Prochlorococcus. Standard
curves used for quantitation of field data were derived from DNA extracted
from defined cell numbers of cultured representatives of each clade.
attribute NC_GLOBAL awards_0_award_nid String 54649
attribute NC_GLOBAL awards_0_award_number String DBI-0424599
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0424599 (external link)
attribute NC_GLOBAL awards_0_funder_name String National Science Foundation
attribute NC_GLOBAL awards_0_funding_acronym String NSF
attribute NC_GLOBAL awards_0_funding_source_nid String 350
attribute NC_GLOBAL awards_1_award_nid String 522893
attribute NC_GLOBAL awards_1_award_number String OCE-1153588
attribute NC_GLOBAL awards_1_data_url String http://nsf.gov/awardsearch/showAward?AWD_ID=1153588 (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 522915
attribute NC_GLOBAL awards_2_award_number String GBMF495
attribute NC_GLOBAL awards_2_data_url String http://www.moore.org/grants/list/GBMF495 (external link)
attribute NC_GLOBAL awards_2_funder_name String Gordon and Betty Moore Foundation
attribute NC_GLOBAL awards_2_funding_acronym String GBMF
attribute NC_GLOBAL awards_2_funding_source_nid String 361
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Two year time series Prochlorococcus with narB gene
at HOT and BATS sites
S. Chisholm, PI
P. Berube, Contact
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 2016-03-30T20:21:47Z
attribute NC_GLOBAL date_modified String 2018-11-16T20:45:44Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.641735
attribute NC_GLOBAL Easternmost_Easting double -64.1667
attribute NC_GLOBAL geospatial_lat_max double 31.6667
attribute NC_GLOBAL geospatial_lat_min double 22.75
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -64.1667
attribute NC_GLOBAL geospatial_lon_min double -158.0
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 200.0
attribute NC_GLOBAL geospatial_vertical_min double 1.0
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/641495 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String from Becton Dickinson, Franklin Lakes, NJ, USA
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 644814
attribute NC_GLOBAL instruments_0_description String Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_0_instrument_nid String 660
attribute NC_GLOBAL instruments_0_supplied_name String influx flow cytometer
attribute NC_GLOBAL keywords String abundance, altimetry, bco, bco-dmo, biological, chemical, cruiseid, data, dataset, date, day, depth, deviation, dmo, erddap, gene, laboratory, latitude, longitude, management, month, oceanography, office, preliminary, sal, satellite, sigma, sigma_0, site, standard, standard_deviation, temperature, year, yrday, yrday_gmt
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/641495/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/641495 (external link)
attribute NC_GLOBAL Northernmost_Northing double 31.6667
attribute NC_GLOBAL param_mapping String {'641495': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/641495/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Massachusetts Institute of Technology
attribute NC_GLOBAL people_0_affiliation_acronym String MIT-Dept CEE
attribute NC_GLOBAL people_0_person_name String Sallie W. Chisholm
attribute NC_GLOBAL people_0_person_nid String 50605
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 Massachusetts Institute of Technology
attribute NC_GLOBAL people_1_affiliation_acronym String MIT-Dept CEE
attribute NC_GLOBAL people_1_person_name String Paul Berube
attribute NC_GLOBAL people_1_person_nid String 522886
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 Prochloro_ecology
attribute NC_GLOBAL projects_0_acronym String Prochloro_ecology
attribute NC_GLOBAL projects_0_description String Extracted from the NSF award abstract:
First discovered in 1988, Prochlorococcus is now recognized as the most abundant photosynthetic cell in the oceans and is responsible for a significant fraction of global primary productivity. Arguably one of the best studied marine microorganisms to date, Prochlorococcus is well-developed as a model system for advancing our understanding of microbial ecology. It is comprised of a collection of genetically and physiologically distinct populations that co-exist and are differentially distributed along quantifiable gradients of light, temperature, and inorganic nutrients. Early physiological studies using cultured isolates indicated that this group of cyanobacteria was unable to assimilate nitrate, typically the most abundant inorganic nitrogen source in the open ocean. This observation was supported by the first 12 genome sequences of Prochlorococcus which all lacked the genes necessary for nitrate assimilation. The lack of these genes in Prochlorococcus was puzzling given that closely related, and co-occurring, Synechococcus cells have them, and that nitrogen availability can be a significant limiting factor for primary production in marine ecosystems. Our understanding changed in 2009 with the discovery of nitrate assimilation genes in wild Prochlorococcus genomes and the isolation of an axenic strain capable of growth on nitrate (unpublished data). This discovery has lead to the overarching questions that are the subject of this project:
- What subset of the Prochlorococcus meta-population in the wild contains nitrate assimilation genes and how do the dynamics of this sub-population vary in time and space?
- What features of the environment select for cells with this functional trait? 
- Is the phylogeny of Prochlorococcus nitrate assimilation genes better correlated with the local environment or the overall 16S-23S ITS phylogeny of Prochlorococcus?
- Do the genomes of cells that contain nitrate assimilation genes share specific features? What do they tell us about what other environmental variables influence the fitness of nitrate-assimilating cells?
- What are the physiological tradeoffs underlying the loss or gain of assimilation genes in particular strains?
These questions will be addressed using an integrative cross-scale approach to characterize nitrate assimilation by Prochlorococcus at the population, cellular, and genomic levels. Specifically, the distribution and abundance of nitrate assimilating Prochlorococcus will be measured at two contrasting open ocean time-series stations (HOT and BATS), and along a longitudinal gradient in the Atlantic (AMT). The PI will examine the regulation of nitrate assimilation, the kinetics of growth on nitrate, and the ability of Prochlorococcus to compete with Synechococcus under nitrogen limiting conditions. Further, they will use a culture independent single cell genomics approach to assess the phylogenetic diversity of nitrate assimilation genes within the genomic context of several ribotypes. These studies will advance our understanding the biogeography of functional traits in microbes, how it is shaped by selection, and the role of intra-species functional diversity in the overall population dynamics of Prochlorococcus.
attribute NC_GLOBAL projects_0_end_date String 2016-01
attribute NC_GLOBAL projects_0_geolocation String BATS station (31.7 N 64.2 W) and HOT station ALOHA (22.75 N 158 W)
attribute NC_GLOBAL projects_0_name String Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph
attribute NC_GLOBAL projects_0_project_nid String 522910
attribute NC_GLOBAL projects_0_start_date String 2012-02
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 22.75
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Two year time series of the abundance of Prochlorococcus cells containing the
nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and
Atlantic Oceans. The goal was to collect long-term, high-resolution data on
the temporal and spatial variability of Prochlorococcus narB genotypes
belonging to the HLII and LLI clades. The abundance of Prochlorococcus cells
containing narB for each of these clades was determined by quantitative PCR at
12 depths every month from October 2005 to December 2007 at two locations:
BATS location (5 nautical mile radius around 31 40'N, 64 10'W) and HOT Station
ALOHA (5 nautical mile radius around 22 45'N, 158 00' W). These field samples
are a subset of those utilized in the \Prochlorococcus HOT/BATS\ dataset

These data are reported and described in:

Berube, P. M., Coe, A., Roggensack, S. E., & Chisholm, S. W. (2015). Temporal
dynamics of Prochlorococcuscells with the potential for nitrate assimilation
in the subtropical Atlantic and Pacific oceans. Limnology and Oceanography,
61(2), 482\u2013495. doi:10.1002/lno.10226
attribute NC_GLOBAL title String The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -158.0
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable gene   String  
attribute gene bcodmo_name String unknown
attribute gene description String nitrate reductase gene (narB) in one of two clades (HLII and LLI)
attribute gene long_name String Gene
attribute gene units String text
variable site   String  
attribute site bcodmo_name String site
attribute site description String Location of the measurement at one of two sites located at the HOT and BATS sites
attribute site long_name String Site
attribute site units String text
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 22.75, 31.6667
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; north is positive
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 -158.0, -64.1667
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; east is positive
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 cruiseid   float  
attribute cruiseid _FillValue float NaN
attribute cruiseid actual_range float 174.0, 230.0
attribute cruiseid bcodmo_name String cruiseid
attribute cruiseid description String The cruise identification
attribute cruiseid long_name String Cruiseid
attribute cruiseid units String numeric
variable year   short  
attribute year _FillValue short 32767
attribute year actual_range short 2005, 2008
attribute year bcodmo_name String year
attribute year description String Year the measurement was taken in YYYY format
attribute year long_name String Year
attribute year nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/ (external link)
attribute year units String unitless
variable month   byte  
attribute month _FillValue byte 127
attribute month actual_range byte 1, 12
attribute month bcodmo_name String month_gmt
attribute month description String Month the measurement was taken
attribute month long_name String Month
attribute month units String mm
variable day   byte  
attribute day _FillValue byte 127
attribute day actual_range byte 2, 31
attribute day bcodmo_name String day
attribute day description String Day the measurement was taken
attribute day long_name String Day
attribute day nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/ (external link)
attribute day units String dd
variable date   String  
attribute date bcodmo_name String date
attribute date description String Date the sample was taken
attribute date long_name String Date
attribute date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date units String mm/dd/yy
variable yrday_gmt   int  
attribute yrday_gmt _FillValue int 2147483647
attribute yrday_gmt actual_range int 118886400, 191894400
attribute yrday_gmt bcodmo_name String yrday_gmt
attribute yrday_gmt description String The year day the sample was taken with 1 meaning January 1
attribute yrday_gmt long_name String Yrday Gmt
attribute yrday_gmt units String decimal number
variable abundance   float  
attribute abundance _FillValue float NaN
attribute abundance actual_range float 0.65, 133000.0
attribute abundance bcodmo_name String abundance
attribute abundance description String Abundance of HLII or LLI clade Prochlorococcus cells containing the narB gene
attribute abundance long_name String Abundance
attribute abundance nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute abundance units String cells/milliliter
variable temp   float  
attribute temp _FillValue float NaN
attribute temp actual_range float 15.76415, 27.9653
attribute temp bcodmo_name String temperature
attribute temp description String Temperature at the sample location
attribute temp long_name String Temperature
attribute temp nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp units String degrees centigrade
variable sal   float  
attribute sal _FillValue float NaN
attribute sal actual_range float 34.4049, 36.8736
attribute sal bcodmo_name String sal
attribute sal description String Salinity measured at the sample location
attribute sal long_name String Sal
attribute sal nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/ (external link)
attribute sal units String PSS-78
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 1.0, 200.0
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 at which the sample was taken
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 sigma_0   float  
attribute sigma_0 _FillValue float NaN
attribute sigma_0 actual_range float 22.843, 26.448
attribute sigma_0 bcodmo_name String sigma_0
attribute sigma_0 description String Potential density
attribute sigma_0 long_name String Sigma 0
attribute sigma_0 nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/SIGTPR01/ (external link)
attribute sigma_0 units String kilograms/cubic meter
variable standard_deviation   float  
attribute standard_deviation _FillValue float NaN
attribute standard_deviation actual_range float 0.118, 29500.0
attribute standard_deviation bcodmo_name String standard deviation
attribute standard_deviation colorBarMaximum double 50.0
attribute standard_deviation colorBarMinimum double 0.0
attribute standard_deviation description String Standard deviation of the abundance measurements
attribute standard_deviation long_name String Standard Deviation
attribute standard_deviation units String cells/milliliter

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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