Accessing BCO-DMO data
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| Dataset Title: | [Field collections: all data] - Nutrient concentrations, microbiology (Vibrio abundance), trace metals, and environmental conditions from collection sites in the Florida Keys National Marine Sanctuary, 2014-2016 (Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_663707) |
| Information: | Summary
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Attributes {
s {
sample {
String bcodmo_name "sample";
String description "sample identifier";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
date {
String bcodmo_name "date";
String description "sampling date formatted as yyyy-mm-dd";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "date";
String time_precision "1970-01-01";
String units "year-month-day";
}
time_start_local {
String bcodmo_name "time_start_local";
String description "local start time formatted as HH:MM";
String long_name "Time Start Local";
String units "hours:minutes";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 28.0, 317.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "depth";
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";
}
location {
String bcodmo_name "site";
String description "sample collection location";
String long_name "Location";
String units "unitless";
}
station_notes {
String bcodmo_name "comment";
String description "comments pertaining to the station";
String long_name "Station Notes";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 24.54322, 24.74287;
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 -81.41115, -80.68487;
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";
}
temp {
Float32 _FillValue NaN;
Float32 actual_range 25.0, 29.0;
String bcodmo_name "temperature";
String description "temperature";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees Celsius";
}
sal {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 35, 36;
String bcodmo_name "sal";
String description "salinity";
String long_name "Sal";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "Practical Salinity Units (PSU)";
}
pH {
Float32 _FillValue NaN;
Float32 actual_range 7.86, 8.01;
String bcodmo_name "pH";
Float64 colorBarMaximum 9.0;
Float64 colorBarMinimum 7.0;
String description "pH: The measure of the acidity or basicity of an aqueous solution";
String long_name "Sea Water Ph Reported On Total Scale";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
String units "unitless; pH scale";
}
Vibrio {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1250.0;
String bcodmo_name "unknown";
String description "Vibrio colony concentration. CFU/ml determined by spread on TCBS agar in triplicate for each experimental replicate and counting green and yellow colonies after 18 - 24 incubation at 30 C. limit of detection was 3.3 CFU/ml (determined using 100 ul spread volume in triplicate); 0.0 = below detection limit.";
String long_name "Vibrio";
String units "colony forming units/milliliter (CFU/ml)";
}
Chl_a {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 1.04;
String bcodmo_name "chlorophyll a";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "Chlorophyll-a concentration determined by acetone freeze thaw using EPA method 445.0 (non-acidification); bdl for below detection limit.";
String long_name "Concentration Of Chlorophyll In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
String units "micrograms/liter (ug/ml)";
}
DOC {
Float32 _FillValue NaN;
Float32 actual_range 58.4, 181.2;
String bcodmo_name "DOC";
String description "Dissolved organic carbon concentration: determined using oxidative high temperature combustion-infrared analysis. MDL is 11.16 micromol/L.";
String long_name "DOC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromoles/liter (ug/ml)";
}
TDN {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 14.6;
String bcodmo_name "Total Dissolved Nitrogren";
String description "Total dissolved nitrogen concentration determined using oxidative high temperature combustion-infrared analysis.";
String long_name "TDN";
String units "micromoles/liter (ug/ml)";
}
DON {
Float32 _FillValue NaN;
Float32 actual_range 1.4, 12.8;
String bcodmo_name "Dissolved Organic Nitrogen";
String description "Dissolved organic nitrogen concentration; MDL is 5.38 micromol/L (determined using 9 samples on two different runs and correct student-T value). bdl = below detection limit.";
String long_name "DON";
String units "micromoles/liter (ug/ml)";
}
NH4 {
Float32 _FillValue NaN;
Float32 actual_range 0.6, 7.95;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "Ammonium concentration determined by the automated phenate method 4500-NH3G. (20th Edition Std. Meth.); MDL is 0.3 micro gram/L (determined using 9 samples on two different runs and correct student-T value). bdl = below detection limit.";
String long_name "Mole Concentration Of Ammonium In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "micromoles/liter (ug/ml)";
}
NO3 {
String bcodmo_name "NO3";
String description "Nitrate concentration determined by the automated cadmium reduction method 4500-NO3- F (20th Edition Std. Meth.); MDL is 0.3 micro gram/L (determined using 9 samples on two different runs and correct student-T value). bdl = below detection limit.";
String long_name "NO3";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "micromoles/liter (ug/ml)";
}
NO2 {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 0.2;
String bcodmo_name "NO2";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Nitrite concentration determined as with Nitrate without running the sample through a cadmium column (20th Edition Std. Meth.); MDL is 0.1 micro gram/L (determined using 9 samples on two different runs and correct student-T value). bdl = below detection limit.";
String long_name "Mole Concentration Of Nitrite In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/";
String units "micromoles/liter (ug/ml)";
}
Orthophosphate {
String bcodmo_name "PO4";
String description "Orthophosphate concentration determined by the automated ascorbic acid reduction method 4500-P F. (20th Edition Std. Meth.); MDL is 0.2 micro gram/L (determined using 9 samples on two different runs and correct student-T value). bdl = below detection limit.";
String long_name "Orthophosphate";
String units "micromoles/liter (ug/ml)";
}
SiO4 {
String bcodmo_name "SiO4";
String description "Silicate concentration determined by the automated molybdate-reactive silica method 4500-SiO2 E. (20th Edition Std. Meth.); MDL is 0.3 micro gram/L (determined using 9 samples on two different runs and correct student-T value). bdl = below detection limit.";
String long_name "Si O4";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SLCAAAZX/";
String units "micromoles/liter (ug/ml)";
}
dFe {
Float32 _FillValue NaN;
Float32 actual_range 0.71, 5.662;
String bcodmo_name "Fe";
String description "dissolved iron concentration determined in the 0.2 um filtered fraction using ICP-MSas described in Milne et al. 2010. Analytica Chimera Acta 665: 200-207";
String long_name "D Fe";
String units "nanomoles/liter (ug/ml)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Samples were collected offshore from Alligator Reef (2014) and Looe Key Reef
(2015-2016). Measurements included temperature, salinity, pH, abundance of
Vibrio, chlorophyll-a, DOC, TDN, DON, NH4, NO3, NO2, Orthophosphate ,SiO4, and
dFe.
Dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were
determined using the filtrate of water samples that were passed through
precombusted 25 mm GF/F filters and stored frozen (-20C) until analysis.\\u00a0
Samples were subsequently analyzed using the High Temperature Catalytic
Oxidation method on a Shimadzu TOC-Vs analyzer with nitrogen module.\\u00a0
Standard curves were run twice daily using a DIW blank and five concentrations
of either acid potassium phthalate solution or potassium nitrate for DOC and
TDN, respectively.\\u00a0 Three to five subsamples were taken from each
standard and water sample and injected in sequence.\\u00a0 Reagent grade
glucosamine was used as a laboratory check standard and inserted throughout
each run, as were Certified Reference Material Program (CRMP) deep-water
standards of known DOC/TDN concentration.\\u00a0
Nutrients data went through internal lab QAQC process. BDL means below
detection limit. The method detection limit (MDL) was determined using 9
samples on two different runs and correct student-T value.";
String awards_0_award_nid "553932";
String awards_0_award_number "OCE-1357423";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1357423";
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 "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Seeded microcosm experiments: collection data
Nutrient concentrations, microbiology (Vibrio abundance), trace metals, and environmental conditions
PI's: E. Lipp (UGA), W. Landing (FSU) E. Ottesen (UGA), M. Wetz (TAMU)
version: 2018-05-03 [added 2016 data]
replaces version: 2016-11-01";
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 with updates expected";
String date_created "2016-11-01T20:39:57Z";
String date_modified "2020-06-03T14:11:32Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.663707.1";
Float64 Easternmost_Easting -80.68487;
Float64 geospatial_lat_max 24.74287;
Float64 geospatial_lat_min 24.54322;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -80.68487;
Float64 geospatial_lon_min -81.41115;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 317.0;
Float64 geospatial_vertical_min 28.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T08:49:03Z (local files)
2024-11-21T08:49:03Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_663707.html";
String infoUrl "https://www.bco-dmo.org/dataset/663707";
String institution "BCO-DMO";
String instruments_0_acronym "Gas Analyzer";
String instruments_0_dataset_instrument_description "To measure dissolved organic nitrogen";
String instruments_0_dataset_instrument_nid "663737";
String instruments_0_description "Gas Analyzers - Instruments for determining the qualitative and quantitative composition of gas mixtures.";
String instruments_0_instrument_name "Gas Analyzer";
String instruments_0_instrument_nid "720";
String instruments_0_supplied_name "chemoluminescence gas analyzer";
String instruments_1_dataset_instrument_description "To measure colony counts";
String instruments_1_dataset_instrument_nid "663736";
String instruments_1_description "Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: https://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.";
String instruments_1_instrument_name "plate reader";
String instruments_1_instrument_nid "528693";
String keywords "altimetry, ammonia, ammonium, bco, bco-dmo, biological, chemical, chemistry, Chl_a, chlorophyll, commerce, concentration, concentration_of_chlorophyll_in_sea_water, data, dataset, date, department, depth, dFe, dmo, doc, don, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > pH, erddap, laboratory, latitude, local, longitude, management, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrite_in_sea_water, nh4, nitrate, nitrite, NO2, no3, notes, ocean, oceanography, oceans, office, orthophosphate, preliminary, reported, sal, sample, satellite, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, SiO4, start, station, station_notes, tdn, temperature, time, time_start_local, total, vibrio, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/663707/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/663707";
Float64 Northernmost_Northing 24.74287;
String param_mapping "{'663707': {'lat': 'master - latitude', 'depth': 'master - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/663707/parameters";
String people_0_affiliation "University of Georgia";
String people_0_affiliation_acronym "UGA";
String people_0_person_name "Erin K. Lipp";
String people_0_person_nid "553935";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Florida State University";
String people_1_affiliation_acronym "FSU - EOAS";
String people_1_person_name "William M. Landing";
String people_1_person_nid "51302";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of Georgia";
String people_2_affiliation_acronym "UGA";
String people_2_person_name "Elizabeth Ottesen";
String people_2_person_nid "553937";
String people_2_role "Co-Principal Investigator";
String people_2_role_type "originator";
String people_3_affiliation "Texas A&M University";
String people_3_affiliation_acronym "TAMU";
String people_3_person_name "Michael Wetz";
String people_3_person_nid "553945";
String people_3_role "Co-Principal Investigator";
String people_3_role_type "originator";
String people_4_affiliation "Woods Hole Oceanographic Institution";
String people_4_affiliation_acronym "WHOI BCO-DMO";
String people_4_person_name "Nancy Copley";
String people_4_person_nid "50396";
String people_4_role "BCO-DMO Data Manager";
String people_4_role_type "related";
String project "Vibrio-dust deposition";
String projects_0_acronym "Vibrio-dust deposition";
String projects_0_description
"Description from NSF award abstract:
Dust and mineral aerosols are a significant source of micro and macronutrients to oligotrophic ocean surface waters. Evidence is growing that heterotrophic microbes may play key roles in processing deposited minerals and nutrients. Yet it is not known which components of dust stimulate the heterotrophic bacteria, which cellular mechanisms are responsible for the utilization of those components and how the activity of these bacteria affect the availability and utilization of dust-derived minerals and nutrients by marine autotrophs. Knowledge of these factors is key to understanding how dust deposition impacts carbon cycles and for predicting the response of tropical oceans to future changes in the frequency and intensity of dust deposition events. The objective of this project is to examine the specific effects of aeolian dust on heterotrophic microbes in a tropical marine system under controlled conditions. The central hypothesis is that in oligotrophic tropical systems numerically minor opportunistic bacteria are the first responders to influx of dust constituents and respond primarily by rapidly accessing soluble trace metals and limiting nutrients that are deposited with Saharan dust. The project will focus on two specific aims: 1) Quantify changes in community structure, composition and transcriptional activity among marine microbial populations upon exposure to dust, and 2) Identify key components in Saharan dust aerosols that stimulate or repress growth and/or activity in Vibrio, a model opportunistic marine heterotrophic group. The study will use a series of controlled experiments designed to identify and quantify heterotrophic microbial response to dust deposition events using both natural communities and model bacteria (Vibrio) through metagenomics, transcriptomics and atmospheric and marine biogeochemical techniques. This innovative approach will identify the most critical (reactive) components leached from dust aerosols on the microbial community as well as elucidate potential mechanisms of response.
There is great interest in the biological response to dust aerosols given its potentially large influence on biogeochemical cycling, but there has been relatively little work that has addressed the mechanisms of response (especially among the heterotrophic microbial fraction) or identified the relative importance of specific constituents of dust aerosols. A detailed framework for microbial response (focusing on opportunistic heterotrophs) will facilitate efforts to link autotrophic and heterotrophic processing. This contribution is significant because it will provide one of the first end-to-end (chemistry to physiology to ecology) mechanistic pathways for marine biological response to desert dust aerosols.";
String projects_0_end_date "2017-03";
String projects_0_geolocation "Florida Keys, FL, USA";
String projects_0_name "Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters";
String projects_0_project_nid "553933";
String projects_0_start_date "2014-04";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 24.54322;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Nutrient concentrations, microbiology (Vibrio abundance), trace metals, and environmental conditions from collection sites in the Florida Keys National Marine Sanctuary, 2014-2016.";
String title "[Field collections: all data] - Nutrient concentrations, microbiology (Vibrio abundance), trace metals, and environmental conditions from collection sites in the Florida Keys National Marine Sanctuary, 2014-2016 (Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters)";
String version "1";
Float64 Westernmost_Easting -81.41115;
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.