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Dataset Title:	[Quantitative PCR data] - Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in zooplankton project) (Microbial associations in zooplankton: significance for the marine nitrogen cycle)
Institution:	BCO-DMO (Dataset ID: bcodmo_dataset_680935)
Range:	longitude = -76.2 to -13.3°E, latitude = 24.5 to 27.8°N, time = 2011-01-28T08:25:00Z to 2011-03-09T15:10:00Z
Information:	Summary \| License \| FGDC \| ISO 19115 \| Metadata \| Background \| Subset \| Data Access Form \| Files

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  project {
    String bcodmo_name "project";
    String description "PI issued project name";
    String long_name "Project";
    String units "unitless";
  }
  date {
    String bcodmo_name "date";
    String description "Date of sampling; YYYY/mm/dd";
    String long_name "Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  time2 {
    String bcodmo_name "time";
    String description "Time of sampling; HH:MM";
    String long_name "Time";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
    String units "unitless";
  }
  station {
    Int16 _FillValue 32767;
    Int16 actual_range 1, 139;
    String bcodmo_name "station";
    String description "Station where sampling occurred";
    String long_name "Station";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 24.5, 27.8;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Latitude; N 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 -76.2, -13.3;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Longitude; E 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";
  }
  number {
    Int16 _FillValue 32767;
    Int16 actual_range 5691, 5735;
    String bcodmo_name "sample";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Sample ID number";
    String long_name "Number";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  size_fraction {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 10.0;
    String bcodmo_name "filter_size";
    Float64 colorBarMaximum 1.0;
    Float64 colorBarMinimum 0.0;
    String description "Filter size";
    String long_name "Size Fraction";
    String units "microns";
  }
  UCYN_A {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 198531.3;
    String bcodmo_name "genetic_conc";
    String description "UCYN-A gene copy concentration";
    String long_name "UCYN A";
    String units "genes per liter";
  }
  Gamma_24774A11 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 3320.6;
    String bcodmo_name "genetic_conc";
    String description "Gamma 24774A11 gene copy concentration";
    String long_name "Gamma 24774 A11";
    String units "genes per liter";
  }
  group_B {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1934.5;
    String bcodmo_name "genetic_conc";
    String description "Group B gene copy concentration";
    String long_name "Group B";
    String units "genes per liter";
  }
  Tricho {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 875890.7;
    String bcodmo_name "genetic_conc";
    String description "Tricho gene copy concentration";
    String long_name "Tricho";
    String units "genes per liter";
  }
  Het1 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 342.5;
    String bcodmo_name "genetic_conc";
    String description "Het1 gene copy concentration";
    String long_name "Het1";
    String units "genes per liter";
  }
  time {
    String _CoordinateAxisType "Time";
    Float64 actual_range 1.2962031e+9, 1.2996834e+9;
    String axis "T";
    String bcodmo_name "ISO_DateTime_UTC";
    String description "Date/Time (UTC) ISO formatted";
    String ioos_category "Time";
    String long_name "ISO Date Time UTC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
    String source_name "ISO_DateTime_UTC";
    String standard_name "time";
    String time_origin "01-JAN-1970 00:00:00";
    String time_precision "1970-01-01T00:00:00Z";
    String units "seconds since 1970-01-01T00:00:00Z";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
    String acquisition_description 
"Samples were collected from Niskin bottles, filtered, and processed for DNA
analyses. For detailed methods see Benavides et al. 2016.";
    String awards_0_award_nid "542156";
    String awards_0_award_number "OCE-1130495";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1130495";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"qPCR Data 
  Moisander and Benavidas, PIs 
  Version 2 February 2017";
    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 "2017-02-02T20:50:59Z";
    String date_modified "2019-04-04T18:19:43Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.680935.1";
    Float64 Easternmost_Easting -13.3;
    Float64 geospatial_lat_max 27.8;
    Float64 geospatial_lat_min 24.5;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -13.3;
    Float64 geospatial_lon_min -76.2;
    String geospatial_lon_units "degrees_east";
    String history 
"2024-11-14T21:46:05Z (local files)
2024-11-14T21:46:05Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_680935.das";
    String infoUrl "https://www.bco-dmo.org/dataset/680935";
    String institution "BCO-DMO";
    String instruments_0_acronym "Thermal Cycler";
    String instruments_0_dataset_instrument_description "Used to process PCR samples";
    String instruments_0_dataset_instrument_nid "680992";
    String instruments_0_description 
"General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
    String instruments_0_instrument_name "PCR Thermal Cycler";
    String instruments_0_instrument_nid "471582";
    String instruments_0_supplied_name "PCR";
    String keywords "a11, bco, bco-dmo, biological, chemical, data, dataset, date, dmo, erddap, fraction, gamma, Gamma_24774A11, group, group_B, het1, iso, latitude, longitude, management, number, oceanography, office, preliminary, project, size, size_fraction, station, time, time2, tricho, ucyn, UCYN_A";
    String license "https://www.bco-dmo.org/dataset/680935/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/680935";
    Float64 Northernmost_Northing 27.8;
    String param_mapping "{'680935': {'lat': 'master - latitude', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'master - time'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/680935/parameters";
    String people_0_affiliation "University of Massachusetts Dartmouth";
    String people_0_affiliation_acronym "UMASSD-SMAST";
    String people_0_person_name "Dr Pia Moisander";
    String people_0_person_nid "564454";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Université de Toulon";
    String people_1_person_name "Mar Benavides";
    String people_1_person_nid "680979";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Hannah Ake";
    String people_2_person_nid "650173";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Microbial associations in zooplankton";
    String projects_0_acronym "Microbial associations in zooplankton";
    String projects_0_description 
"Description from NSF award abstract:
Nitrogen (N2) fixation is a key biogeochemical process providing new N for the marine ecosystem. Current estimates of the global rates suggest that the inputs and outputs of N are not in balance, leaving an apparent deficiency in N2 fixation in the oceanic N budget. Based on recovery of N2 fixation gene fragments, however, numerous potential N2-fixing microbes are present in the euphotic layer and below, yet evidence for their contribution to N2-fixation is lacking. The goal of this study is to identify and determine the importance of potentially diazotrophic, heterotrophic prokaryotes occupying a previously unstudied niche in the upper ocean.
This project PIs hypothesize that N2 fixation in zooplankton-associated microbial communities is an important source of new N in the open ocean contributing to the oceanic N budget. In oligotrophic, N-limited open ocean waters, zooplankton are faced with the same low N availability in their diets that limits growth of primary producers and heterotrophic microbes in the open ocean. Zooplankton guts would be a particularly suitable environment for heterotrophic N2-fixers as the nitrogenase enzyme is inhibited by oxygen. In many terrestrial insects, N2 fixation by gut microbes serves as a source of N. The aim of this study is to investigate whether similar associations occur in marine zooplankton that live on N-limited phytoplankton. The PIs will investigate specific associations between copepods from N-limited and non-N limited oceanic waters with microorganisms that are potentially or actively fixing N. They will also investigate the fate of this N to study whether the new N is incorporated into the zooplankton host. The main research objectives are to determine whether:
1. diazotrophic microflora exist in copepods and what is their seasonal and spatial variability,
2. microbial communities associated with copepods are actively fixing N2,
3. diazotroph communities contribute to the N nutrition of their zooplankton hosts.
Monthly samples will be collected in the oligotrophic Sargasso Sea, in association with BATS sampling cruises. In addition, experiments and field studies will be conducted in Bermuda during the summer. For comparison to a site that is not severely N limited, and for methods development, additional studies will be carried out in coastal Gulf of Maine waters. Selected copepod species and their fecal pellets will be analyzed for the presence of nifH genes and their expression using cloning and sequencing and Reverse Transcriptase-PCR. Quantitative PCR will be employed to investigate the seasonal distributions of dominant phylotypes. Anaerobic cultivation will be used for the enrichment of the gut microflora. Zooplankton will be incubated with 15N2 to quantify microbial N2 fixation activity and its fate of N through zooplankton overall 15N content and nanoSIMS determination of 15N localization. Products of this study will include novel microbial isolates or consortia, evidence regarding taxa-specific expression of N2 fixation in these microhabitats, and a first estimate for the importance of this process for the oceanic N budget.
This project addresses fundamental issues regarding the sources of oceanic nitrogen and will test hypotheses regarding previously overlooked diazotrophic niches. As open ocean productivity is frequently N limited, characterization of new sources of N will have global impacts.";
    String projects_0_end_date "2016-08";
    String projects_0_geolocation "Sargasso Sea, Eastern and Western North Atlantic.";
    String projects_0_name "Microbial associations in zooplankton: significance for the marine nitrogen cycle";
    String projects_0_project_nid "564455";
    String projects_0_start_date "2011-09";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 24.5;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "project";
    String summary "Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in zooplankton project)";
    String time_coverage_end "2011-03-09T15:10:00Z";
    String time_coverage_start "2011-01-28T08:25:00Z";
    String title "[Quantitative PCR data] - Quantitative PCR data from samples collected on the R/V Sarmiento de Gamboa cruise in the subtropical North Atlantic Ocean between January and March 2011 (Microbial associations in zooplankton project) (Microbial associations in zooplankton: significance for the marine nitrogen cycle)";
    String version "1";
    Float64 Westernmost_Easting -76.2;
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link)

Data Access Protocol (DAP) (external link)

and its selection constraints (external link)

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.

(easy) You can get data by using the dataset's Data Access Form or Subset form. They make the URL for you.
(easy) You can make a graph or map by using the dataset's Make A Graph form. It makes the URL for you.
(not hard) You can bypass the forms and get the data or make a graph or map by generating the URL by hand or with a computer program or script.

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.