Accessing BCO-DMO data
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| Dataset Title: | [Prochlorococcus_narB] - 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 (Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_641495) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
gene {
String bcodmo_name "unknown";
String description "nitrate reductase gene (narB) in one of two clades (HLII and LLI)";
String long_name "Gene";
String units "text";
}
site {
String bcodmo_name "site";
String description "Location of the measurement at one of two sites located at the HOT and BATS sites";
String long_name "Site";
String units "text";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 22.75, 31.6667;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude; north is positive";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -158.0, -64.1667;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude; east is positive";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
cruiseid {
Float32 _FillValue NaN;
Float32 actual_range 174.0, 230.0;
String bcodmo_name "cruiseid";
String description "The cruise identification";
String long_name "Cruiseid";
String units "numeric";
}
year {
Int16 _FillValue 32767;
Int16 actual_range 2005, 2008;
String bcodmo_name "year";
String description "Year the measurement was taken in YYYY format";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
month {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 12;
String bcodmo_name "month_gmt";
String description "Month the measurement was taken";
String long_name "Month";
String units "mm";
}
day {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 2, 31;
String bcodmo_name "day";
String description "Day the measurement was taken";
String long_name "Day";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/";
String units "dd";
}
date {
String bcodmo_name "date";
String description "Date the sample was taken";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "mm/dd/yy";
}
yrday_gmt {
Int32 _FillValue 2147483647;
Int32 actual_range 118886400, 191894400;
String bcodmo_name "yrday_gmt";
String description "The year day the sample was taken with 1 meaning January 1";
String long_name "Yrday Gmt";
String units "decimal number";
}
abundance {
Float32 _FillValue NaN;
Float32 actual_range 0.65, 133000.0;
String bcodmo_name "abundance";
String description "Abundance of HLII or LLI clade Prochlorococcus cells containing the narB gene";
String long_name "Abundance";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells/milliliter";
}
temp {
Float32 _FillValue NaN;
Float32 actual_range 15.76415, 27.9653;
String bcodmo_name "temperature";
String description "Temperature at the sample location";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees centigrade";
}
sal {
Float32 _FillValue NaN;
Float32 actual_range 34.4049, 36.8736;
String bcodmo_name "sal";
String description "Salinity measured at the sample location";
String long_name "Sal";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "PSS-78";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 1.0, 200.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth at which the sample was taken";
String ioos_category "Location";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
sigma_0 {
Float32 _FillValue NaN;
Float32 actual_range 22.843, 26.448;
String bcodmo_name "sigma_0";
String description "Potential density";
String long_name "Sigma 0";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SIGTPR01/";
String units "kilograms/cubic meter";
}
standard_deviation {
Float32 _FillValue NaN;
Float32 actual_range 0.118, 29500.0;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of the abundance measurements";
String long_name "Standard Deviation";
String units "cells/milliliter";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"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.";
String awards_0_award_nid "54649";
String awards_0_award_number "DBI-0424599";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0424599";
String awards_0_funder_name "National Science Foundation";
String awards_0_funding_acronym "NSF";
String awards_0_funding_source_nid "350";
String awards_1_award_nid "522893";
String awards_1_award_number "OCE-1153588";
String awards_1_data_url "http://nsf.gov/awardsearch/showAward?AWD_ID=1153588";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "David L. Garrison";
String awards_1_program_manager_nid "50534";
String awards_2_award_nid "522915";
String awards_2_award_number "GBMF495";
String awards_2_data_url "http://www.moore.org/grants/list/GBMF495";
String awards_2_funder_name "Gordon and Betty Moore Foundation";
String awards_2_funding_acronym "GBMF";
String awards_2_funding_source_nid "361";
String cdm_data_type "Other";
String comment
"Two year time series Prochlorococcus with narB gene
at HOT and BATS sites
S. Chisholm, PI
P. Berube, Contact";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2016-03-30T20:21:47Z";
String date_modified "2018-11-16T20:45:44Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.641735";
Float64 Easternmost_Easting -64.1667;
Float64 geospatial_lat_max 31.6667;
Float64 geospatial_lat_min 22.75;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -64.1667;
Float64 geospatial_lon_min -158.0;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 200.0;
Float64 geospatial_vertical_min 1.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-23T17:01:35Z (local files)
2024-11-23T17:01:35Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_641495.html";
String infoUrl "https://www.bco-dmo.org/dataset/641495";
String institution "BCO-DMO";
String instruments_0_acronym "Flow Cytometer";
String instruments_0_dataset_instrument_description "from Becton Dickinson, Franklin Lakes, NJ, USA";
String instruments_0_dataset_instrument_nid "644814";
String instruments_0_description
"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)";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
String instruments_0_instrument_name "Flow Cytometer";
String instruments_0_instrument_nid "660";
String instruments_0_supplied_name "influx flow cytometer";
String keywords "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";
String license "https://www.bco-dmo.org/dataset/641495/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/641495";
Float64 Northernmost_Northing 31.6667;
String param_mapping "{'641495': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/641495/parameters";
String people_0_affiliation "Massachusetts Institute of Technology";
String people_0_affiliation_acronym "MIT-Dept CEE";
String people_0_person_name "Sallie W. Chisholm";
String people_0_person_nid "50605";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Massachusetts Institute of Technology";
String people_1_affiliation_acronym "MIT-Dept CEE";
String people_1_person_name "Paul Berube";
String people_1_person_nid "522886";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Ms Dicky Allison";
String people_2_person_nid "50382";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Prochloro_ecology";
String projects_0_acronym "Prochloro_ecology";
String projects_0_description
"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.";
String projects_0_end_date "2016-01";
String projects_0_geolocation "BATS station (31.7 N 64.2 W) and HOT station ALOHA (22.75 N 158 W)";
String projects_0_name "Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph";
String projects_0_project_nid "522910";
String projects_0_start_date "2012-02";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 22.75;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary
"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
([https://www.bco-dmo.org/dataset/3381](\\\\http://www.bco-
dmo.org/dataset/3381\\\\)).
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";
String title "[Prochlorococcus_narB] - 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 (Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph)";
String version "1";
Float64 Westernmost_Easting -158.0;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.