Accessing BCO-DMO data
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| Dataset Title: | [bacterial_production] - Bacterial production in microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project) (En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_3872) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
exp_id {
String bcodmo_name "exp_id";
String description "Name of the experiment. DICE = Dauphin Island Cubitainer Experiment.";
String long_name "Exp Id";
String units "text";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 30.05068, 30.05068;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude of the sample collection site. North = 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 -87.99513, -87.99513;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude of the sample collection. West = Negative.";
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";
}
site_desc {
String bcodmo_name "site_descrip";
String description "Description of the sample collection site.";
String long_name "Site Desc";
String units "text";
}
microcosm {
String bcodmo_name "sample";
String description
"Identifier for the microcosm experiment.
C1 and C2 were control microcosms containing Gulf of Mexico seawater.
E1 and E2 were experimental microcosms containing Gulf of Mexico seawater amended with inorganic N and P.";
String long_name "Microcosm";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "text";
}
microcosm_type {
String bcodmo_name "sample_descrip";
String description "Type of microcosm. Experimental or Control.";
String long_name "Microcosm Type";
String units "text";
}
exp_day {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 6;
String bcodmo_name "unknown";
String description "Sequential day of the experiment. Day 0 = start of the experiment.";
String long_name "Exp Day";
String units "integer";
}
mean {
Int32 _FillValue 2147483647;
Int32 actual_range 12761, 286110;
String bcodmo_name "unknown";
String description "Calculated average of triplicates (including the blank).";
String long_name "Mean";
String units "dpm";
}
mean_minus_blank {
Int32 _FillValue 2147483647;
Int32 actual_range 10457, 284639;
String bcodmo_name "unknown";
String description "Average corrected for the blank.";
String long_name "Mean Minus Blank";
String units "dpm";
}
stdev {
Int16 _FillValue 32767;
Int16 actual_range 59, 11389;
String bcodmo_name "unknown";
String description "Standard deviation of the mean.";
String long_name "Stdev";
String units "dpm";
}
coeff_var {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.13;
String bcodmo_name "unknown";
String description "Coefficient of variation of the mean.";
String long_name "Coeff Var";
String units "%";
}
inc_time {
Float32 _FillValue NaN;
Float32 actual_range 0.97, 1.04;
String bcodmo_name "unknown";
String description "Incubation time.";
String long_name "Inc Time";
String units "hours";
}
leu_inc_per_h {
Float32 _FillValue NaN;
Float32 actual_range 0.0278, 1.2127;
String bcodmo_name "unknown";
String description "Measure of bacterial production in nanomoles of radiolabeled leucine incorporated per hour of incubation.";
String long_name "Leu Inc Per H";
String units "nM Leu per hour";
}
leu_inc_per_d {
Float32 _FillValue NaN;
Float32 actual_range 0.666, 29.104;
String bcodmo_name "unknown";
String description "Measure of bacterial production in nanomoles of radiolabeled leucine incorporated per day of incubation.";
String long_name "Leu Inc Per D";
String units "nM Leu per day";
}
stdev_calc {
Float32 _FillValue NaN;
Float32 actual_range 0.013, 0.997;
String bcodmo_name "unknown";
String description "Estimated variation about the mean based on % CV in specific activity measurements.";
String long_name "Stdev Calc";
String units "nM Leu per day";
}
bact_prod {
Float32 _FillValue NaN;
Float32 actual_range 172.1, 7518.6;
String bcodmo_name "unknown";
String description "Measure of bacterial Carbon production in nanomoles of carbon substrate converted to bacterial biomass each day.";
String long_name "Bact Prod";
String units "nM Carbon per day";
}
bact_prod_err {
Float32 _FillValue NaN;
Float32 actual_range 3.46, 257.48;
String bcodmo_name "unknown";
String description "Estimated variation about the mean of bacterial production based on % CV in specific activity measurements.";
String long_name "Bact Prod Err";
String units "nM Carbon per day";
}
bact_C_demand {
Float32 _FillValue NaN;
Float32 actual_range 1147.6, 50124.0;
String bcodmo_name "unknown";
String description "Nanomoles of carbon substrate needed by bacteria each day, including bacterial production and bacterial respiration. This assumes a bacterial growth efficiency of 15%.";
String long_name "Bact C Demand";
String units "nM Carbon per day";
}
bact_C_demand_err {
Float32 _FillValue NaN;
Float32 actual_range 23.05, 1716.56;
String bcodmo_name "unknown";
String description "Estimated variation about the mean of bacterial carbon demand based on % CV in specific activity measurements.";
String long_name "Bact C Demand Err";
String units "nM Carbon per day";
}
bact_S_prod {
Float32 _FillValue NaN;
Float32 actual_range 0.69, 30.32;
String bcodmo_name "unknown";
String description "Nanomoles of sulfur substrate needed by bacteria each day. This assumes a C:S ratio of 248 in bacterial biomass.";
String long_name "Bact S Prod";
String units "nM Sulfur per day";
}
replicate {
String bcodmo_name "replicate";
String description
"Replicate identifier.
a, b, and c are replicate samples from the same treatment.
blank is a killed control, with formaldehyde added prior to addition of isotope.";
String long_name "Replicate";
String units "unitless";
}
dpm {
Float32 _FillValue NaN;
Float32 actual_range 171.41, 295274.0;
String bcodmo_name "unknown";
String description "Disintegrations per minute (dpm) measured per replicate.";
String long_name "DPM";
String units "dpm";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"See Howard et al. (2010), Rinta-Kanto et al. (2011), and Vila-Coast et al.
(2010) for detailed methods, summarized below:
\\\"In October 2006, seawater was collected from surface waters (<1 m deep) in
the Gulf of Mexico off the coast of Dauphin Island, AL (lat: 30 03.041N; lon:
87 59.708W). Water was filtered through a 200-um mesh into six 20-liter
polyethylene Cubitainers with minimal headspace.
Three microcosms were amended with 10 um sodium nitrate (NaNO3) and 0.6 um
potassium phosphate (K2HPO4) to serve as the experimental microcosms. Three
microcosms were left untreated to serve as the control. The Cubitainers were
maintained at 27 degrees C on a 12-hour light/dark cycle for the duration of
the experiment.
Chemical and activity measurements were collected from the microcosms at the
beginning of the experiment (Day 0) and every day for the duration of the
experiment at the same time. Bacterial production was measured by 3H-leucine
incorporation into trichloroacetic acid (TCA) -insoluble material. Incubations
were carried out in triplicate in the dark at in situ temperature with
additions of 20 nM of 3H-leucine for 4 hours, starting immediately after water
collection. One TCA-killed sample was used as a control. Samples were
processed by the microcentrifugation method. Bacterial sulfur requirements
were estimated through conversion of bacterial heterotrophic production
assuming a bacterial C/S molar ratio of 248.\\\"";
String awards_0_award_nid "55114";
String awards_0_award_number "OCE-0724017";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0724017";
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
"Bacterial production in microcosm experiments
PI: Mary Ann Moran (UGA); Co-PIs: Ronald Kiene (DISL) and William Whitman (UGA)
Version: 19 Nov 2012
Notes: Volume (l) = 0.0015; Final Leucine Conc = 20 nM; C:S ratio = 248;
Specific activity = 117 Ci/mmol; bacterial growth efficiency = 15%.
\t dpm = disintegrations per minute
Started using diluted stock at start of exp_day = T3 (specific activity = 29.25)";
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 "2013-02-04T18:45:39Z";
String date_modified "2019-11-01T15:22:29Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.3872.1";
Float64 Easternmost_Easting -87.99513;
Float64 geospatial_lat_max 30.05068;
Float64 geospatial_lat_min 30.05068;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -87.99513;
Float64 geospatial_lon_min -87.99513;
String geospatial_lon_units "degrees_east";
String history
"2024-11-08T05:56:59Z (local files)
2024-11-08T05:56:59Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_3872.html";
String infoUrl "https://www.bco-dmo.org/dataset/3872";
String institution "BCO-DMO";
String instruments_0_acronym "bucket";
String instruments_0_dataset_instrument_description "Water was collected in the field using a clean bucket.";
String instruments_0_dataset_instrument_nid "6088";
String instruments_0_description "A bucket used to collect surface sea water samples.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0536/";
String instruments_0_instrument_name "bucket";
String instruments_0_instrument_nid "569";
String instruments_0_supplied_name "bucket";
String keywords "bact, bact_C_demand, bact_C_demand_err, bact_prod, bact_prod_err, bact_S_prod, bco, bco-dmo, biological, blank, calc, chemical, coeff, coeff_var, data, dataset, day, demand, desc, deviation, dmo, dpm, erddap, error, exp, exp_day, exp_id, inc, inc_time, latitude, leu, leu_inc_per_d, leu_inc_per_h, longitude, management, mean, mean_minus_blank, microcosm, microcosm_type, minus, oceanography, office, per, preliminary, prod, replicate, site, site_desc, standard, standard deviation, stdev, stdev_calc, time, type";
String license "https://www.bco-dmo.org/dataset/3872/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/3872";
Float64 Northernmost_Northing 30.05068;
String param_mapping "{'3872': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/3872/parameters";
String people_0_affiliation "University of Georgia";
String people_0_affiliation_acronym "UGA";
String people_0_person_name "Mary Ann Moran";
String people_0_person_nid "51592";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Dauphin Island Sea Lab";
String people_1_affiliation_acronym "DISL";
String people_1_person_name "Ronald Kiene";
String people_1_person_nid "51594";
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 "William Whitman";
String people_2_person_nid "51593";
String people_2_role "Co-Principal Investigator";
String people_2_role_type "originator";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Shannon Rauch";
String people_3_person_nid "51498";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "En-Gen DMSP Cycling";
String projects_0_acronym "En-Gen DMSP Cycling";
String projects_0_description
"The recent discovery of key genes that mediate competing pathways at a critical juncture in the marine sulfur cycle has allowed biogeochemists to make rapid advances in understanding where and when sulfur transformations occur in the ocean, and most importantly, what factors regulate them. This project describes an environmental functional genomics project that will rapidly increase our knowledge of the role that bacterioplankton play in dimethylsulfoniopropionate (DMSP) cycling in ocean surface waters, focusing particularly on biological controls of volatile sulfur exchange across the ocean/atmosphere boundary.
The investigators have asked three critical hypotheses to explain the regulation of bacterial DMSP degradation: that involve investigations on the energy constraints of DMSP cycling, the role that DMSP concentration in the oceans plays, and the sulfur requirements for bacterial growth. These research areas serve as the focus for hypothesis-driven laboratory and field studies using functional genomics approaches that will track patterns in gene expression in relation to sulfur metabolism. The hypotheses will be tested with:
1) chemostat systems with a model marine bacterium Silicibacter pomeroyi;
2) microcosm experiments with Gulf of Mexico seawater; and
3) field studies at various sites in the Gulf of Mexico. Marine bacterioplankton play a key role in regulating the flux of DMSP-derived sulfur to the atmosphere, a process of great importance for global climate regulation and marine productivity.
The investigators will also be involved in graduate and undergraduate student education, and two post-doctoral associates will be trained to address multidisciplinary challenges in environmental microbiology. High school biology students in Athens, GA will participate in marine microbial biology research that includes bacterial diversity and discovery studies in coastal Georgia, follow-up training in molecular tools and bioinformatics in their own classroom, and summer internships at the University of Georgia and Dauphin Island Sea Laboratory.
(The description above is from the NSF Award Abstract).";
String projects_0_end_date "2012-09";
String projects_0_geolocation "Sapelo Island, GA, USA, 31.4° N Lat, 81.3° W Lon / Dauphin Island, AL, USA, 30.3 ° N Lat, 88.1° W Lon";
String projects_0_name "En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean";
String projects_0_project_nid "2244";
String projects_0_start_date "2007-10";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 30.05068;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "exp_id,latitude,longitude,site_desc";
String summary "Bacterial production measurements from control and experimental microcosms from the Dauphin Island Cubitainer Experiment (DICE).";
String title "[bacterial_production] - Bacterial production in microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project) (En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean)";
String version "1";
Float64 Westernmost_Easting -87.99513;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
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.