Accessing BCO-DMO data
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Dataset Title:  Cell abundance of xenic and axenic marine Prochlorococcus and Synechococcus
cultures from laboratory experiments conducted in 2016 and 2017
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_774628)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   Maximum ?
 Culture (unitless) ?          "Axenic_Prochloroco..."    "Xenic_Synechococcu..."
 Days (count (days)) ?          1    19
 Cell_Abundance_rep1 (cells per mL) ?          408070.74    1.828156904E8
 Cell_Abundance_rep2 (cells per mL) ?          599863.98    1.836318319E8
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File type: (more info)

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(Please be patient. It may take a while to get the data.)


The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Culture {
    String bcodmo_name "sample_descrip";
    String description "Culture name";
    String long_name "Culture";
    String units "unitless";
  Days {
    Byte _FillValue 127;
    Byte actual_range 1, 19;
    String bcodmo_name "time_elapsed";
    String description "Days since experiment start";
    String long_name "Days";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "count (days)";
  Cell_Abundance_rep1 {
    Float64 _FillValue NaN;
    Float64 actual_range 408070.74, 1.828156904e+8;
    String bcodmo_name "abundance";
    String description "Cell abundance as determined using epifluorescence microscopy for replicate 1.";
    String long_name "Cell Abundance Rep1";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
    String units "cells per mL";
  Cell_Abundance_rep2 {
    Float64 _FillValue NaN;
    Float64 actual_range 599863.98, 1.836318319e+8;
    String bcodmo_name "abundance";
    String description "Cell abundance as determined using epifluorescence microscopy for replicate 2.";
    String long_name "Cell Abundance Rep2";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
    String units "cells per mL";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
Duplicate cultures of Synechococcus WH8102 (axenic), Synechococcus WH7805
(xenic) and Prochlorococcus marinus MED4 (xenic and axenic) were sampled every
other day for 17-19 days for the quantification of single cells, suspended
aggregates (aggregates ca. 5-60 \\u03bcm), and TEP. Single cell abundance was
determined using epifluorescence microscopy.";
    String awards_0_award_nid "710238";
    String awards_0_award_number "OCE-1658527";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1658527";
    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 
"Picocyanobacteria TEP: Cell Abundance 
  PI: Susanne Neuer 
  Data Version 1: 2019-08-13";
    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 "2019-08-06T20:50:57Z";
    String date_modified "2019-12-24T16:30:52Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.774628.1";
    String history 
"2024-04-18T04:35:44Z (local files)
2024-04-18T04:35:44Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_774628.html";
    String infoUrl "https://www.bco-dmo.org/dataset/774628";
    String institution "BCO-DMO";
    String instruments_0_dataset_instrument_description "AxioScope.A1, Carl Zeiss, Germany";
    String instruments_0_dataset_instrument_nid "779231";
    String instruments_0_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
    String instruments_0_instrument_name "Microscope-Fluorescence";
    String instruments_0_instrument_nid "695";
    String instruments_0_supplied_name "AxioScope.A1";
    String keywords "abundance, bco, bco-dmo, biological, cell, Cell_Abundance_rep1, Cell_Abundance_rep2, chemical, culture, data, dataset, days, dmo, erddap, management, oceanography, office, preliminary, rep1, rep2";
    String license "https://www.bco-dmo.org/dataset/774628/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/774628";
    String param_mapping "{'774628': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/774628/parameters";
    String people_0_affiliation "Arizona State University";
    String people_0_affiliation_acronym "ASU";
    String people_0_person_name "Susanne Neuer";
    String people_0_person_nid "51336";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Arizona State University";
    String people_1_affiliation_acronym "ASU";
    String people_1_person_name "Bianca N. Cruz";
    String people_1_person_nid "774775";
    String people_1_role "Student";
    String people_1_role_type "related";
    String people_2_affiliation "Arizona State University";
    String people_2_affiliation_acronym "ASU";
    String people_2_person_name "Susanne Neuer";
    String people_2_person_nid "51336";
    String people_2_role "Contact";
    String people_2_role_type "related";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Amber York";
    String people_3_person_nid "643627";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Marine Plankton Aggregation";
    String projects_0_acronym "Marine Plankton Aggregation";
    String projects_0_description 
"NSF abstract:
Marine phytoplankton are microscopic algae that live in the sunlit zone of the ocean. They play an important role in the uptake of carbon dioxide from the atmosphere through photosynthesis, similar to what plants do on land, and are the basis of the marine food web. However, instead of storing this organic carbon in leaf tissue and roots, marine phytoplankton are grazed by planktonic animals, or die and subsequently sink out of the sunlit zone in the form of aggregates, also called \"Marine Snow\". These particles not only export the organic carbon contained in their cells to the deep ocean, but also serve as food for animals and bacteria that live in the deep. A considerable portion of these phytoplankton are extremely small, among the tiniest of all organisms known. These extremely small cells have not been thought to play an important role in the formation and sinking of marine snow; however, recent findings challenge this view. This project will investigate how the smallest of these phytoplankton contribute to the rain of sinking particles from the sunlit surface to the deep ocean. This research is important because, in some of the largest expanses of the open oceans, these minute cells dominate the phytoplankton community, and larger plankton organisms are very sparse. The project, through a combination of work in the laboratory and at a field station, will shed light on how these tiny phytoplankton cells make aggregates, which ultimately enable them to sink as \"Marine Snow\". The project also provides unique opportunities for undergraduate students at Arizona State University, a land-locked public university, to gain experience in working with marine research. The project will serve to educate one PhD student, one MS student in an accelerated BS-MS program, and 8-10 undergraduate students/semester in a unique, inquiry based learning effort termed Microbial EducatioN Training and OutReach (MENTOR). The undergraduate students will also participate in Arizona State University (ASU)'s School of Life Sciences, Undergraduate Research Program (SOLUR), which seeks to increase the participation of minorities in science. They will also contribute towards developing web and classroom materials, based on this project, which will then be distributed through a partnership with the award-winning ASU-sponsored Ask A Biologist K-12 web site.
The oceanic \"biological carbon pump\", the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon and its subsequent export to deep water, functions as a significant driver of atmospheric carbon uptake by the oceans. The traditional view of the biological carbon pump in the ocean is that of sinking of large aggregates (marine snow) or fecal pellets, which are made up of large, mineral ballasted cells of phytoplankton. However, recent evidence, stemming from in situ investigations of particulate matter, trap studies and modelling studies, have shown that micron-sized phytoplankton such as picocyanobacteria as well as picoeukaryotes can contribute significantly to the sinking of particulate matter. The specific mechanisms behind the sinking of these micrometer sized cells remain elusive as the cells are too small to sink on their own, and mesozooplankton is likely unable to ingest single cells. Intriguingly, recent research by the investigators has shown that the ubiquitous picocyanobacteria Synechococcus are able to form aggregates and sink at velocities comparable to those of marine snow. They found that the matrix of the Synechococcus aggregates was made of Transparent Exopolymeric Particles (TEP), and that TEP production was enhanced under nutrient limited culture conditions. Interaction with clays and presence of heterotrophic bacteria also enhanced aggregation and sinking velocity. This study aims to further investigate aggregation of other common picoplankton in the laboratory and aggregation occurring in natural settings at an oligotrophic open ocean site, the Bermuda Atlantic Time-series Site (BATS). Ultimately, this project will increase and refine our understanding of the role of the smallest phytoplankton in aggregation and sinking - information vital to understanding carbon cycling processes in the oceans.";
    String projects_0_end_date "2020-02";
    String projects_0_geolocation "Bermuda Atlantic Time-Series station";
    String projects_0_name "Aggregation of Marine Picoplankton";
    String projects_0_project_nid "710239";
    String projects_0_start_date "2017-03";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Cell abundance of xenic and axenic marine Prochlorococcus and Synechococcus cultures from laboratory experiments conducted in 2016 and 2017.";
    String title "Cell abundance of xenic and axenic marine Prochlorococcus and Synechococcus cultures from laboratory experiments conducted in 2016 and 2017";
    String version "1";
    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.

Tabledap request URLs must be in the form
For example,
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.

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