Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [Coastal SAR11 Physiochemical data] - Physiochemical data from samples collected along the coast of Louisiana, USA during 2018 (Collaborative Research: EAGER: Salinity-based selection between sister clades of abundant coastal bacterioplankton) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_745449) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
Site {
String bcodmo_name "site";
String description "Sampling site designation";
String long_name "Site";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 29.243342, 29.867989;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude of site";
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 -93.340714, -89.676029;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude of site";
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";
}
Date {
String bcodmo_name "date";
String description "Date of sampling; format: yyyy-mm-dd";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String time_precision "1970-01-01";
String units "unitless";
}
Time_Central {
String bcodmo_name "time";
String description "Time of sampling in the Central Time Zone, USA; format: HH:MM";
String long_name "Time Central";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
String units "unitless";
}
Offset {
String bcodmo_name "time_offset";
String description "Universal time coordinated (UTC) offset, corrected for daylight savings";
String long_name "Offset";
String units "unitless";
}
Time_UTC {
String bcodmo_name "time";
String description "Universal Time Coordinated (UTC) subtracting Central Time from the UTC offset; format: HH:MM";
String long_name "Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
String units "unitless";
}
Temp {
Float32 _FillValue NaN;
Float32 actual_range 9.38, 32.81;
String bcodmo_name "temperature";
String description "Temperature measured via YSI at the sampling site";
String long_name "Temperature";
String units "degrees Celsius";
}
Cond {
Float32 _FillValue NaN;
Float32 actual_range 0.279, 48.77;
String bcodmo_name "conductivity";
String description "Conductivity measured via YSI at the sampling site";
String long_name "Cond";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/CNDC/";
String units "ms/cm";
}
Salinity {
Float32 _FillValue NaN;
Float32 actual_range 0.12, 31.72;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "Calculated salinity based on the conductivity measurement from the YSI";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "unitless";
}
pH {
Float32 _FillValue NaN;
Float32 actual_range 7.32, 8.84;
String bcodmo_name "pH";
Float64 colorBarMaximum 9.0;
Float64 colorBarMinimum 7.0;
String description "pH of the seawater at the sampling site";
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";
}
Cell_counts {
Float32 _FillValue NaN;
Float32 actual_range 1930000.0, 1.52e+7;
String bcodmo_name "count";
String description "Number of cells passing through a 2.7 µm filter (Whatman GF/D) determined via flow cytometry";
String long_name "Cell Counts";
String units "cells/mL";
}
PO4 {
Float32 _FillValue NaN;
Float32 actual_range 0.21, 2.55;
String bcodmo_name "PO4";
String description "Concentration of phosphate in seawater from the site";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "umol/L";
}
SiOH4 {
Float32 _FillValue NaN;
Float32 actual_range 1.14, 171.83;
String bcodmo_name "SiOH_4";
String description "Concentration of silicate in seawater from the site";
String long_name "Si OH4";
String units "umol/L";
}
NO3 {
Float32 _FillValue NaN;
Float32 actual_range 0.31, 62.34;
String bcodmo_name "NO3";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Concentration of nitrate in seawater from the site";
String long_name "Mole Concentration Of Nitrate In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "umol/L";
}
NO2 {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 5.18;
String bcodmo_name "NO2";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Concentration of nitrite in seawater from the site";
String long_name "Mole Concentration Of Nitrite In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/";
String units "umol/L";
}
NH4 {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 19.23;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "Concentration of ammonium in seawater from the site";
String long_name "Mole Concentration Of Ammonium In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "umol/L";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.51707198e+9, 1.5423984e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "Date and time of sampling (UTC) formatted to ISO 8601 standard; format: yyyy-mm-ddTHH:MMZ";
String ioos_category "Time";
String long_name "ISO Date Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String source_name "ISO_DateTime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Samples were collected manually by filling an acid-washed and autoclaved 20L
carboy after three rinses. Temperature, pH, and salinity were taken using a
handheld YSI. Cell counts were obtained by filtering water through a 2.7
\\u00b5m Whatman GF/D filter, fixing with 10% formaldehyde, placing on ice, and
then counting using flow cytometry (Thrash et al., 2015, Hydrocarbon and Lipid
Microbiology Protocols). Inorganic nutrients were measured at the University
of Washington Marine Chemistry Laboratory after sequential filtration through
2.7 Whatman GF/D and 0.22 \\u00b5m Sterivex filters. Samples were initially
placed on ice in the field, and then refrigerated until shipment with ice
packs.";
String awards_0_award_nid "707004";
String awards_0_award_number "OCE-1747681";
String awards_0_data_url "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1747681";
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 awards_1_award_nid "707005";
String awards_1_award_number "OCE-1747722";
String awards_1_data_url "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1747722";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "Michael E. Sieracki";
String awards_1_program_manager_nid "50446";
String awards_2_award_nid "787323";
String awards_2_award_number "OCE-1931113";
String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1931113";
String awards_2_funder_name "NSF Division of Ocean Sciences";
String awards_2_funding_acronym "NSF OCE";
String awards_2_funding_source_nid "355";
String awards_2_program_manager "Daniel Thornhill";
String awards_2_program_manager_nid "722161";
String cdm_data_type "Other";
String comment
"Physiochemical data for coastal samples
PI: J. Cameron Thrash (USC)
Co-PI: Elizabeth B. Kujawinksi (WHOI)
Version history:
2020-02-13 - version 2 (current)
2018-08-30 - version 1";
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 "2018-08-30T19:52:45Z";
String date_modified "2020-02-14T15:37:08Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.745449.2";
Float64 Easternmost_Easting -89.676029;
Float64 geospatial_lat_max 29.867989;
Float64 geospatial_lat_min 29.243342;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -89.676029;
Float64 geospatial_lon_min -93.340714;
String geospatial_lon_units "degrees_east";
String history
"2024-12-21T17:55:39Z (local files)
2024-12-21T17:55:39Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745449.html";
String infoUrl "https://www.bco-dmo.org/dataset/745449";
String institution "BCO-DMO";
String instruments_0_acronym "Flow Cytometer";
String instruments_0_dataset_instrument_description "Used for sampling";
String instruments_0_dataset_instrument_nid "745484";
String instruments_0_description
"Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
String instruments_0_instrument_name "Flow Cytometer";
String instruments_0_instrument_nid "660";
String instruments_0_supplied_name "Millipore Guava 5HT HPL benchtop flow cytometer";
String instruments_1_dataset_instrument_description "Used for sampling";
String instruments_1_dataset_instrument_nid "745485";
String instruments_1_description "A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps";
String instruments_1_instrument_name "Pump";
String instruments_1_instrument_nid "726";
String instruments_1_supplied_name "Masterflex I/P peristaltic pump";
String instruments_2_dataset_instrument_description "YSI 556 MPS handheld meter, calibrated with salinity and pH standards immediately prior to use";
String instruments_2_dataset_instrument_nid "745486";
String instruments_2_description "An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held.";
String instruments_2_instrument_name "Multi Parameter Portable Meter";
String instruments_2_instrument_nid "489457";
String instruments_2_supplied_name "YSI 556 MPS handheld meter";
String keywords "ammonia, ammonium, bco, bco-dmo, biological, cell, Cell_counts, central, chemical, chemistry, concentration, cond, counts, data, dataset, date, density, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > pH, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Salinity/Density > Salinity, erddap, iso, latitude, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, n02, nh4, nitrate, nitrite, NO2, no3, ocean, oceanography, oceans, office, offset, oh4, phosphate, po4, practical, preliminary, reported, salinity, scale, science, sea, sea_water_ph_reported_on_total_scale, sea_water_practical_salinity, seawater, SiOH4, site, Temp, temperature, time, Time_Central, Time_UTC, total, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/745449/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/745449";
Float64 Northernmost_Northing 29.867989;
String param_mapping "{'745449': {'Lat': 'flag - latitude', 'Lon': 'flag - longitude', 'ISO_DateTime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/745449/parameters";
String people_0_affiliation "University of Southern California";
String people_0_affiliation_acronym "USC";
String people_0_person_name "J. Cameron Thrash";
String people_0_person_nid "707009";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI";
String people_1_person_name "Elizabeth Kujawinski";
String people_1_person_nid "51089";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of Southern California";
String people_2_affiliation_acronym "USC";
String people_2_person_name "J. Cameron Thrash";
String people_2_person_nid "707009";
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 "Shannon Rauch";
String people_3_person_nid "51498";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "CoastalSAR11";
String projects_0_acronym "CoastalSAR11";
String projects_0_description
"NSF award abstract:
Adaptation to new environments is a fundamental challenge for organisms, including microbes, in expanding their habitat range. It is important to investigate the cellular mechanisms underlying salinity tolerance in coastal bacterioplankton and their different responses to salinity in nature because (i) it will provide fundamental understanding for how microorganisms evolve to inhabit environments with different salinities, and (ii) alterations in coastal salinity are connected to climate change, so the way these alterations affect abundant coastal microorganisms also alters the biogeochemical cycling of, e.g., carbon. The project will examine microbial adaptations to salinity and determine how changes in salinity affect microbial metabolism using two closely related groups of abundant coastal bacterioplankton as model taxa. In addition, the research will continue and expand microbiology Course-based Undergraduate Research Experiences (mCUREs) in high-throughput cultivation and microbial characterization at the Lousiana State University. Sections of freshman biology laboratories will learn how to isolate, characterize, and molecularly identify microorganisms from local aquatic systems. mCURE sections will lead to newly isolated strains, genome sequences, and physiological data, these results will be published with the contributing students as co-authors. The relative success of mCURE sections will be assessed compared to traditional freshman biology sections. mCURE sections will offer unique opportunities for LSU students by creating excitement about research through discovery of new organisms and generating knowledge of the coastal habitats that are essential to the livelihood of the Gulf Coast.
The evolutionary transition between salt- and freshwater environments occurs rarely in microorganisms. In one of the most abundant aquatic groups, SAR11, the transition between salt- and freshwater environments has happened only once: all freshwater SAR11 belong to subclade IIIb/LD12, which has also been found to inhabit coastal environments where salinity varies widely. The first reported isolates of the SAR11 freshwater clade LD12 and a member of the sister clade IIIa from the same region are now available. These pure culture representatives provide a powerful model for experimentally investigating adaptations to new environments in microorganisms, specifically (i) the genomic pathway and regulatory distinctions that arise during the evolutionary transition from marine to freshwater environments, and (ii) the physiological mechanisms that underlie the ecological restrictions imposed on microorganisms by ionic strength in coastal and freshwater environments. Furthermore, because these organisms have distinct differences in metabolic potential, the isolates facilitate testing (iii) the effects of changing coastal salinity on microbial contributions to other biogeochemical cycles, such as that for carbon. The project will test the hypothesis that the relative ionic strength tolerances between the sister lineages (LD12, IIIa) result from fundamental differences in metabolic flexibility at a genomic and regulatory level. To do so it will assess transcriptional and metabolic responses to varied ionic strength for both taxa and measure the distribution and activity of both groups in nature to translate laboratory findings to the field. The research will provide new understanding of LD12 habitat range and insights into how the \"freshwater\" lineage evolved from a SAR11 common ancestor. The project will also more generally provide important information on microbial responses to salinity changes in coastal systems and the evolutionary paths separating freshwater and marine microorganisms.
This award is co-funded by Biological Oceanography, Division of Ocean Sciences in the Directorate for Geosciences and by Systems and Synthetic Biology, Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences.";
String projects_0_end_date "2020-12";
String projects_0_geolocation "Coastal Louisiana, northern Gulf of Mexico";
String projects_0_name "Collaborative Research: EAGER: Salinity-based selection between sister clades of abundant coastal bacterioplankton";
String projects_0_project_nid "707006";
String projects_0_start_date "2018-01";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 29.243342;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Physiochemical data from samples collected along the coast of Louisiana, USA during 2018.";
String time_coverage_end "2018-11-16T20:00:00Z";
String time_coverage_start "2018-01-27T16:53:00Z";
String title "[Coastal SAR11 Physiochemical data] - Physiochemical data from samples collected along the coast of Louisiana, USA during 2018 (Collaborative Research: EAGER: Salinity-based selection between sister clades of abundant coastal bacterioplankton)";
String version "2";
Float64 Westernmost_Easting -93.340714;
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.