Accessing BCO-DMO data
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| Dataset Title: | [Seeded microcosm experiments: all data] - Nutrients, microbiology, trace metals, and environmental conditions from seeded microcosm experiments (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_682298) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
year {
Int16 _FillValue 32767;
Int16 actual_range 2014, 2015;
String bcodmo_name "year";
String description "year of measurement";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "year";
}
expt {
String bcodmo_name "exp_id";
String description "experiment identifier";
String long_name "Expt";
String units "unitless";
}
treatment {
String bcodmo_name "treatment";
String description
"experimental treatments:
For 2014:
control acidified water;
dust= dust leachate from Whatman41 filters used to collect dust aerosols from Barbados (added to provide +1 nM Fe); FeCl = FeCl3 (added to provide +1 nM Fe)
For 2015:
control acidified water;
2nMFe: 2 nM Fe provided by FeCl3
20nMFe: 20 nM Fe provided by FeCl3
control_leachate: control leachate (leached from Whatman41 blank filter);
dust_barbados: dust leachate from Whatman41 filters used to collect dust aerosols from Barbados (added to provide +2 nM Fe);
Fe: FeCl3 (added to provide +1 nM Fe);
NO3: HNO3 added to provide +0.2 uM N;
PO4: K2HPO4 added to provide +0.01 uM P;
C: Pyruvate added to provide +10 uM C;
FeCNP: mix of FeCl3 (+2 nM Fe), pyruvate (+10 uM C), HNO3 (+0.2 uM), and K2HPO4 (+0.01 uM)";
String long_name "Treatment";
String units "unitless";
}
light_dark {
String bcodmo_name "treatment";
String description "whether experiment took place in the light or dark";
String long_name "Light Dark";
String units "unitless";
}
vessel {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 42;
String bcodmo_name "sample";
String description "sample vessel identifier";
String long_name "Vessel";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
replicate {
String bcodmo_name "replicate";
String description "replicate identifier";
String long_name "Replicate";
String units "unitless";
}
time_elapsed_hr {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 94;
String bcodmo_name "time_elapsed";
String description "time since start of experiment";
String long_name "Time Elapsed Hr";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "hours";
}
sample {
String bcodmo_name "sample";
String description "sample identifier: 'year_treatment_light or dark_vessel number_replicate_time";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Vibrio {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 2800.0;
String bcodmo_name "unknown";
String description "Vibrio concentration: determined by spread plating on TCBS agar and countng ager 18-24 incubation at 30 C. Limit of detection was 3.3 CFU/ml (determined using 100 ul spread volume in triplicate). The data uses a value of 0.0 for below detection limit.";
String long_name "Vibrio";
String units "colony forming units/milliliter (CFU/ml)";
}
Chl_a {
Float32 _FillValue NaN;
Float32 actual_range 0.03, 0.59;
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-acidificaton). Data went through internal lab QAQC process. BDL= 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 "microgram/liter (ug/L)";
}
DOC {
Float32 _FillValue NaN;
Float32 actual_range 61.0, 339.7;
String bcodmo_name "DOC";
String description "Dissolved organic carbon concentration: determined using oxidatve high temperature combuston-infrared analysis. MDL is 11.16 micro mol/L.";
String long_name "DOC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromol/liter C (umol/L)";
}
DON {
Float32 _FillValue NaN;
Float32 actual_range 1.4, 26.1;
String bcodmo_name "Dissolved Organic Nitrogen";
String description "Dissolved organic nitrogen concentration: determined the same as DOC samples but the sample is converted to nitrogen monoxide and measured by a chemoluminescence gas analyzer. The analyte sampled is TDN and the inorganic values are subtracted to get DON. MDL is 5.38 micro mol/L.";
String long_name "DON";
String units "micromol/liter N (umol/L)";
}
NH4 {
String bcodmo_name "Ammonium";
String description "Ammonium concentration: determined by the automated phenate method 4500-NH3G. 20th Edition Std. Meth. MDL is 0.3 micro gram/L.";
String long_name "NH4";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "micromol/liter N (umol/L)";
}
NO3 {
String bcodmo_name "NO3";
String description "Nitrate concentration: determined by the automated cadmium reducton method 4500-NO3- F. 20th Edition Std. Method. MDL is 0.3 micro gram/L.";
String long_name "NO3";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "micromol/liter N (umol/L)";
}
NO2 {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 0.14;
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.";
String long_name "Mole Concentration Of Nitrite In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/";
String units "micromol/liter N (umol/L)";
}
Orthophosphate {
String bcodmo_name "PO4";
String description "Orthophosphate concentration: determined by the automated ascorbic acid reducton method 4500-P F. 20th Edition Std. Meth. MDL is 0.2 micro gram/ L.";
String long_name "Orthophosphate";
String units "micromol/liter P (umol/L)";
}
SiO4 {
String bcodmo_name "SiO4";
String description "Silicate concentration: determined by the automated molybdate-reactve silica method 4500-SiO2 E. 20th Edition Std. Meth. MDL is 0.3 micro gram/L.";
String long_name "Si O4";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SLCAAAZX/";
String units "micromol/liter Si (umol/L)";
}
dFe {
Float32 _FillValue NaN;
Float32 actual_range 0.71, 6.38;
String bcodmo_name "Fe";
String description "dissolved iron concentration: determined in the 0.2 um filtered fracton using ICP-MSas described in Milne et al. 2010. Analytca Chimera Acta 665: 200-207";
String long_name "D Fe";
String units "nanoMolar (nM)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Samples were collected offshore from Alligator Reef (2014) and Looe Key Reef
(2015). The experimental treatments included additions of dust and iron in
2014 with a control of acidified water. In 2015, treatments included additions
of dust from Barbados, iron, nitrates, phosphates, and carbon with controls of
acidified water and leachate.
Nutrients data went through internal lab QAQC process. BDL means below
detection limit. \\u00a0The 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
Nutrients, microbiology, trace metals, and environmental conditions
PI's: E. Lipp (UGA), W. Landing (FSU) E. Ottesen (UGA), M. Wetz (TAMU)
version: 2016-11-01
BDL = below detection limit";
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 "2017-02-15T15:51:25Z";
String date_modified "2020-05-18T19:24:17Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.682298.1";
String history
"2024-11-23T16:49:35Z (local files)
2024-11-23T16:49:35Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_682298.html";
String infoUrl "https://www.bco-dmo.org/dataset/682298";
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 "682308";
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 "682307";
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 "ammonium, bco, bco-dmo, biological, chemical, chemistry, Chl_a, chlorophyll, commerce, concentration, concentration_of_chlorophyll_in_sea_water, dark, data, dataset, department, dFe, dmo, doc, don, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, elapsed, erddap, expt, light, light_dark, management, mole, mole_concentration_of_nitrite_in_sea_water, nh4, nitrate, nitrite, NO2, no3, ocean, oceanography, oceans, office, orthophosphate, preliminary, replicate, sample, science, sea, seawater, SiO4, time, time_elapsed_hr, treatment, vessel, vibrio, water, year";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/682298/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/682298";
String param_mapping "{'682298': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/682298/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)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Nutrients, microbiology, trace metals, and environmental conditions from seeded microcosm experiments.";
String title "[Seeded microcosm experiments: all data] - Nutrients, microbiology, trace metals, and environmental conditions from seeded microcosm experiments (Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters)";
String version "1";
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.