Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [MO - biogeochemical and microbial field surveys] - Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013 (Ocean Microbial Observatory project) (Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_543314) |
| Information: | Summary
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| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
cruise_id {
String bcodmo_name "cruise_id";
String description "UNOLS cruise identification";
String long_name "Cruise Id";
String units "unitless";
}
cruise_id2 {
String bcodmo_name "cruise_id";
String description "alternate cruise id";
String long_name "Cruise Id2";
String units "unitless";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.2453393e+9, 1.372104e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "date and time at start of cast [UTC], formatted as yyyymmddThh:mm";
String ioos_category "Time";
String long_name "ISO Date Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String units "seconds since 1970-01-01T00:00:00Z";
}
station {
String bcodmo_name "station";
String description "station label. HS = Hydrostation \"S\"";
String long_name "Station";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 31.66381, 32.1829;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude at start of cast; 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 -64.51155, -64.16473;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude at start of cast; 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";
}
cast_type {
String bcodmo_name "cast_type";
String description "cast type; B for bottle";
String long_name "Cast Type";
String units "unitless";
}
cast {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 9;
String bcodmo_name "cast";
String description "unique Identified Code for each cast";
String long_name "Cast";
String units "unitless";
}
sample {
String bcodmo_name "sample";
String description "rosette bottle number";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
depth_n {
Int16 _FillValue 32767;
Int16 actual_range 0, 2600;
String bcodmo_name "depth_n";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Bottle target depth";
String long_name "Depth";
String standard_name "depth";
String units "meters";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range -999.0, 2601.1;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "CTD Depth in meters";
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";
}
DOC {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 74.2;
String bcodmo_name "DOC";
String description "Dissolved organic carbon concentration by HTCO. Glass fiber filtrate type GF/F (Whatman). Methodological reference is Carlson et al. 2010 DSRII";
String long_name "DOC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromoles per liter";
}
DOC_stdev {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 3.8;
String bcodmo_name "standard deviation";
String description "standard deviation for DOC";
String long_name "DOC Stdev";
String units "umol/L";
}
POC {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 5.87;
String bcodmo_name "POC";
String description "Particulate organic carbon measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman).";
String long_name "Particulate Organic Carbon";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGCAP1/";
String units "umol/L";
}
bact_abund {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 14.58;
String bcodmo_name "bact_abundance";
String description "Bacterioplankton abundance by microscopy. Methodological reference: Porter, K.G. and Y.S. Feig (1980)";
String long_name "Bact Abund";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/BNTX";
String units "10^8 cells/liter";
}
bact_abund_stdev {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 2.01;
String bcodmo_name "standard deviation";
String description "standard deviation for bacterioplankton abundance";
String long_name "Bact Abund Stdev";
String units "10^8 cells/liter";
}
leuc_incorp {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 23.572;
String bcodmo_name "leuc_incorp";
String description "Heterotrophic bacterial production by 3H Leu uptake. Methodological reference: Smith DC, Azam F (1992)";
String long_name "Leuc Incorp";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/UPLERIP4/";
String units "picomoles per liter per hour";
}
leu_sd {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 2.67;
String bcodmo_name "leuc_sd";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "standard deviation for leucine incorporation";
String long_name "Leu Sd";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SDLERIP4/";
String units "picomoles per liter per hour";
}
thy_incorp {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 1.865;
String bcodmo_name "thy_incorp";
String description "heterotrophic bacterial production by 3H Thymidine uptake";
String long_name "Thy Incorp";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/UPTHRIP4/";
String units "picomoles per liter per hour";
}
thy_sd {
Float32 _FillValue NaN;
Float32 actual_range -999.0, 0.34;
String bcodmo_name "thy_sd";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "standard deviation of heterotrophic bacterial production by 3H Thymidine uptake";
String long_name "THY SD";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SDTHRIP4/";
String units "picomoles per liter per hour";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Methods\\u00a0References:
- Dissolved organic carbon method reference:\\u00a0Carlson,\\u00a0et al.
(2010).
- Particulate organic carbon methodological references, calibrations,
precision and accuracy detailed at the UCSB MSI Analytical Lab Website:
[http://www.msi.ucsb.edu/services/analytical-
lab](\\\\\"http://www.msi.ucsb.edu/services/analytical-lab\\\\\")
- Bacterioplankton Abundance methodological reference:\\u00a0Porter, K.G. and
Y.S. Feig (1980)
- Bacterial Production method reference:\\u00a0Smith, D.C. and F. Azam
(1992).";
String awards_0_award_nid "514363";
String awards_0_award_number "OCE-0802004";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0802004";
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
"Biogeochemical and microbial field surveys
C. Carlson (UC-SB)
version date: 2020-05-04";
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 dataset_current_state "Final and no updates";
String date_created "2014-12-19T20:28:26Z";
String date_modified "2020-05-11T19:08:52Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.543314.1";
Float64 Easternmost_Easting -64.16473;
Float64 geospatial_lat_max 32.1829;
Float64 geospatial_lat_min 31.66381;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -64.16473;
Float64 geospatial_lon_min -64.51155;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 2601.1;
Float64 geospatial_vertical_min -999.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-03T17:42:21Z (local files)
2024-12-03T17:42:21Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_543314.html";
String infoUrl "https://www.bco-dmo.org/dataset/543314";
String institution "BCO-DMO";
String instruments_0_acronym "Shimadzu TOC-V";
String instruments_0_dataset_instrument_description "Shimadzu TOC-V, used to measure DOC";
String instruments_0_dataset_instrument_nid "551058";
String instruments_0_description "A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.";
String instruments_0_instrument_external_identifier "http://onto.nerc.ac.uk/CAST/124";
String instruments_0_instrument_name "Shimadzu TOC-V Analyzer";
String instruments_0_instrument_nid "603";
String instruments_0_supplied_name "Shimadzu TOC-V";
String instruments_1_acronym "CHN_EA";
String instruments_1_dataset_instrument_description "CE440 Elemental Analyzer from Control Equipment Corp. (now Exeter Analytical) - for POC measurements";
String instruments_1_dataset_instrument_nid "554362";
String instruments_1_description "A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.";
String instruments_1_instrument_name "CHN Elemental Analyzer";
String instruments_1_instrument_nid "625";
String instruments_1_supplied_name "CHN Elemental Analyzer";
String instruments_2_dataset_instrument_description "for measuring bacterioplankton abundance";
String instruments_2_dataset_instrument_nid "551057";
String instruments_2_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_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
String instruments_2_instrument_name "Microscope-Fluorescence";
String instruments_2_instrument_nid "695";
String keywords "abund, bact, bact_abund, bact_abund_stdev, bco, bco-dmo, biological, carbon, cast, cast_type, chemical, commerce, cruise, cruise_id, cruise_id2, data, dataset, date, department, depth, depth_n, deviation, dmo, doc, DOC_stdev, erddap, id2, incorp, iso, ISO_DateTime_UTC, latitude, leu, leu_sd, leuc, leuc_incorp, longitude, management, oceanography, office, organic, particulate, POC, preliminary, sample, standard, standard deviation, station, stdev, thy, thy_incorp, thy_sd, time, type";
String license "https://www.bco-dmo.org/dataset/543314/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/543314";
Float64 Northernmost_Northing 32.1829;
String param_mapping "{'543314': {'lat': 'master - latitude', 'depth': 'master - depth', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/543314/parameters";
String people_0_affiliation "University of California-Santa Barbara";
String people_0_affiliation_acronym "UCSB";
String people_0_person_name "Craig Carlson";
String people_0_person_nid "50575";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Oregon State University";
String people_1_affiliation_acronym "OSU";
String people_1_person_name "Dr Stephen Giovannoni";
String people_1_person_nid "514364";
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 "Nancy Copley";
String people_2_person_nid "50396";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Ocean Microbial Observatory";
String projects_0_acronym "Ocean Microbial Observatory";
String projects_0_description
"(Adapted from the NSF award abstract)
The premise of this project is that stratified bacterioplankton clades engage in specialized biogeochemical activities that can be identified by integrated oceanographic and microbiological approaches. Specifically, the objective of this project is to assess if the mesopelagic microbial community rely on diagenetically altered organic matter and subcellular fragments that are produced by microbial processes in the euphotic zone and delivered into the upper mesopelagic by sinking or mixing. In past efforts this microbial observatory had greater success cultivating members of the euphotic zone microbial community, and revealed an unanticipated growth requirement for reduced sulfur compounds in alphaproteobacteria of the SAR11 clade. Genomic information showed that intense competition for substrates imposes trade-offs on bacterioplankton - there are regions of N dimensional nutrient space where specialists win. We postulate that specific growth requirements may explain some the regular spatial and temporal patterns that have been observed in upper mesopelagic bacterioplankton communities, and the difficulties of culturing some of these organisms.
The specific objectives of this project are: 1) to produce 13C and 15N labeled subcellular (e.g., soluble, cell wall, and membrane) and DOM fractions from photosynthetic plankton cultures and use stable isotope probing to identify specific clades in the surface and upper mesopelagic microbial community that assimilate fractions of varying composition and lability. 2) to use fluorescence in situ hybridization approaches to monitor temporal and spatial variability of specific microbial populations identified from the SIP and HTC experiments. To increase resolution we will use CARD-FISH protocols. 3) to measure the proteomes of bacterioplankton communities to identify highly translated genes in the surface layer and upper mesopelagic, and community responses to seasonal nutrient limitation. 4) and, to cultivate these organisms via high throughput culturing (HTC) by pursuing the hypothesis that they require specific nutrient factors and/or diagenetically altered organic substrates. Complete genome sequences from key organisms will be sought and used as queries to study patterns of natural variation in genes and populations that have been associated with biogeochemically important functions.";
String projects_0_end_date "2014-07";
String projects_0_geolocation "Bermuda Atlantic Time-Series study site";
String projects_0_name "Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory";
String projects_0_project_nid "514365";
String projects_0_project_website "http://www.bios.edu/research/projects/oceanic-microbial-observatory/";
String projects_0_start_date "2008-08";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 31.66381;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "cast_type";
String summary "Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013. This dataset includes water samples collected from 2009-2013 at the Bermuda Hydrostation that were analyzed for DOC, POC, bacterial abundance, leucine, and thymidine incorporation.";
String time_coverage_end "2013-06-24T20:00:00Z";
String time_coverage_start "2009-06-18T15:35:00Z";
String title "[MO - biogeochemical and microbial field surveys] - Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013 (Ocean Microbial Observatory project) (Transitions in the Surface Layer and the Role of Vertically Stratified Microbial Communities in the Carbon Cycle - An Oceanic Microbial Observatory)";
String version "1";
Float64 Westernmost_Easting -64.51155;
String xml_source "osprey2erddap.update_xml() v1.5";
}
}
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.