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| Dataset Title: | [DON_Oxidation] - Dissolved Organic Nitrogen oxidation collected on cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017 (Collaborative Research: Direct Oxidation of Organic Nitrogen by Marine Ammonia Oxidizing Organisms) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_767048) |
| Information: | Summary
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Attributes {
s {
Cruise_ID {
String bcodmo_name "cruise_id";
String description "R2R catalog identifier for this cruise";
String long_name "Cruise ID";
String units "unitless";
}
Sta {
String bcodmo_name "station";
String description "Station Identifier. Marsh Landing is on the Duplin River a tidal channel adjacent to Sapelo Island GA.";
String long_name "Sta";
String units "unitless";
}
Region {
String bcodmo_name "unknown";
String description "Arbitratry assignment of stations to zones in the study area identified by location and water properties: I = Inshore; M = midshelf; S = Shelf-break; O = Oceanic";
String long_name "Region";
String units "unitless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 0.2, 500.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth sampled 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";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -81.36, -78.77;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "degrees longitude with positive values eastward";
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";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 30.32, 31.99;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "degrees latitude with positive values northward";
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";
}
latitude2 {
String bcodmo_name "latitude";
String description "Latitude in degrees and decimal minutes N";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees and decimal minutes N";
}
longitude2 {
String bcodmo_name "longitude";
String description "Longitude in degrees and decimal minutes W";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees and decimal minutes W";
}
Date {
String bcodmo_name "date";
String description "Sampling date: MM/DD/YYYY";
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 "unitless";
}
ISO_Date {
String bcodmo_name "date";
String description "Date following the ISO convention of YYYY-MM-DD";
String long_name "ISO Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String time_precision "1970-01-01";
String units "unitless";
}
Bacterial_16S_rRNA {
Float32 _FillValue NaN;
Float32 actual_range 3.36e+7, 9.4800003e+10;
String bcodmo_name "unknown";
String description "Concentration of genes for Bacteria 16S rRNA determined by qPCR (see qPCR parameter table) in units of copies L-1; Blank Cells = no data; either not sampled or the sample was lost; BLD = Below Limit of Detection. See qPCR parameter table. qPCR data are from single biological replicates; means of triplicate qPCR reactions. Limit of detection is given as copies per mL of template DNA; the limit thus varies by sample depending on volume filtered; extract volume and template volume per per reaction. The limits given are from this sample set assuming the minimum detectable concentration in the template used and 1 uL of template per reaction. They are thus conservative as some reactions were run with 10 uL of template.";
String long_name "Bacterial 16 S R RNA";
String units "copies per liter filtered";
}
Thaumarchaeal_16S_rRNA {
String bcodmo_name "unknown";
String description "Concentration of genes for Marine Group 1 Archaea (Thaumarchaeota) 16S rRNA determined by qPCR (see qPCR parameter table) in units of copies L-1 Blank Cells = no data either not sampled or the sample was lost; BLD = Below Limit of Detection. See qPCR parameter table. qPCR data are from single biological replicates; means of triplicate qPCR reactions. Limit of detection is given as copies per mL of template DNA; the limit thus varies by sample depending on volume filtered extract volume and template volume per per reaction. The limits given are from this sample set assuming the minimum detectable concentration in the template used and 1 uL of template per reaction. They are thus conservative as some reactions were run with 10 uL of template.";
String long_name "Thaumarchaeal 16 S R RNA";
String units "copies per liter filtered";
}
WCA_amoA {
String bcodmo_name "unknown";
String description "Concentration of genes for Archaeal ammonia monooxygenase subunit A from the Water Column A clade; determined by qPCR (see qPCR parameter table) in units of copies L-1; Blank Cells = no data; either not sampled or the sample was lost; BLD = Below Limit of Detection. See qPCR parameter table. qPCR data are from single biological replicates; means of triplicate qPCR reactions. Limit of detection is given as copies per mL of template DNA; the limit thus varies by sample depending on volume filtered; extract volume and template volume per per reaction. The limits given are from this sample set assuming the minimum detectable concentration in the template used and 1 uL of template per reaction. They are thus conservative as some reactions were run with 10 uL of template.";
String long_name "WCA Amo A";
String units "copies per liter filtered";
}
WCB_amoA {
String bcodmo_name "unknown";
String description "Concentration of genes for Archaeal ammonia monooxygenase subunit A from the Water Column A clade; determined by qPCR (see qPCR parameter table) in units of copies L-1; \"Blank Cells = no data either not sampled or the sample was lost; BLD = Below Limit of Detection. See qPCR parameter table. qPCR data are from single biological replicates means of triplicate qPCR reactions. Limit of detection is given as copies per mL of template DNA; the limit thus varies by sample depending on volume filtered extract volume and template volume per per reaction. The limits given are from this sample set assuming the minimum detectable concentration in the template used and 1 uL of template per reaction. They are thus conservative as some reactions were run with 10 uL of template.";
String long_name "WCB Amo A";
String units "copies per liter filtered";
}
Nitrospina_16S_rRNA {
String bcodmo_name "unknown";
String description "Concentration of genes for Nitrospina 16S rRNA determined by qPCR (see qPCR parameter table) in units of copies L-1; Blank Cells = no data; either not sampled or the sample was lost; BLD = Below Limit of Detection. See qPCR parameter table. qPCR data are from single biological replicates; means of triplicate qPCR reactions. Limit of detection is given as copies per mL of template DNA; the limit thus varies by sample depending on volume filtered; extract volume and template volume per per reaction. The limits given are from this sample set assuming the minimum detectable concentration in the template used and 1 uL of template per reaction. They are thus conservative as some reactions were run with 10 uL of template.";
String long_name "Nitrospina 16 S R RNA";
String units "copies per liter filtered";
}
N15_added {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 10, 50;
String bcodmo_name "unknown";
String description "Final concentration of uniformly 15N labeled test substrates";
String long_name "N15 Added";
String units "nanomoles per liter";
}
Ammonia_Oxidation {
String bcodmo_name "unknown";
String description "Ammonia oxidation rate determined from conversion of 15N-labeled ammonium to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "Ammonia Oxidation";
String units "nanomoles per liter per day";
}
Ammonia_Oxidation_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.12, 48.28;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Deviation of ammonia oxidation rate determined from conversion of 15N-labeled ammonium to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "Ammonia Oxidation Sd";
String units "nanomoles per liter per day";
}
N15_ox_from_PUT {
String bcodmo_name "unknown";
String description "Oxidation rate of 15N from putrescine (1;4 diamino butane) determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From PUT";
String units "nanomoles per liter per day";
}
N15_ox_from_PUT_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 8.09;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Deviation of oxidation rate of 15N from putrescine (1;4 diamino butane) determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From PUT Sd";
String units "nanomoles per liter per day";
}
N15_ox_from_GLU {
String bcodmo_name "unknown";
String description "Oxidation rate of 15N from L-glutamate determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From GLU";
String units "nanomoles per liter per day";
}
N15_ox_from_GLU_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 2.63;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "deviation of oxidation rate of 15N from L-glutamate determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From GLU Sd";
String units "nanomoles per liter per day";
}
N15_ox_from_UREA {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 62.53;
String bcodmo_name "unknown";
String description "Oxidation rate of 15N from urea determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From UREA";
String units "nanomoles per liter per day";
}
N15_ox_from_UREA_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 39.41;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Deviation of oxidation rate of 15N from urea determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From UREA Sd";
String units "nanomoles per liter per day";
}
N15_ox_from_DAE {
Float32 _FillValue NaN;
Float32 actual_range -0.02, 8.68;
String bcodmo_name "unknown";
String description "Oxidation rate of 15N from 1;2 diamino ethane determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From DAE";
String units "nanomoles per liter per day";
}
N15_ox_from_DAE_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 2.43;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Deviation of oxidation rate of 15N from 1;2 diamino ethane determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From DAE Sd";
String units "nanomoles per liter per day";
}
N15_ox_from_DAP {
Float32 _FillValue NaN;
Float32 actual_range -0.01, 53.63;
String bcodmo_name "unknown";
String description "Oxidation rate of 15N from 1;3 diamino propane determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From DAP";
String units "nanomoles per liter per day";
}
N15_ox_from_DAP_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 2.99;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Deviation of oxidation rate of 15N from 1;3 diamino propane determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation; our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From DAP Sd";
String units "nanomoles per liter per day";
}
N15_ox_from_ARG {
Float32 _FillValue NaN;
Float32 actual_range 0.07, 75.04;
String bcodmo_name "unknown";
String description "Oxidation rate of 15N from L-arginine determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From ARG";
String units "nanomoles per liter per day";
}
N15_ox_from_ARG_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.11, 13.58;
String bcodmo_name "unknown";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Deviation of oxidation rate of 15N from L-arginine determined from conversion of the 15N label to 15N-labeled nitrite plus nitrate; BLD = Below Limit of Detection. 15N data are mean ± S.E.M. of duplicate biological replicates (see Damashek et al. 2018 for details) . Based on a propagation of error calculation our conservative estimate of the precision of 15N measurements ±4‰ for samples at natural abundance and ±5.2‰ for samples artificially enriched with carrier 15N. Our limit of detection was similar to that reported by Santoro et al. (2013) and Beman et al. (2011).";
String long_name "N15 Ox From ARG Sd";
String units "nanomoles per liter per day";
}
Nitrate {
String bcodmo_name "NO3";
String description "Concentration of nitrate determined by cadmium reduction to nitrite followed by subtraction nitrite already present in the sample; Samples run on an autoanalyzer by Francis Wilkerson's lab at San Francisco State University";
String long_name "Nitrate";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "micromoles per liter";
}
Nitrite {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 5.12;
String bcodmo_name "NO2";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Concentration of nitrite determined by autoanalyzer; Samples run on an autoanalyzer by Francis Wilkerson's lab at San Francisco State University";
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 per liter";
}
Ammonium {
Float32 _FillValue NaN;
Float32 actual_range 0.03, 1.35;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "Concentration of ammonium determined by autoanalyzer; Samples run on an autoanalyzer by Francis Wilkerson's lab at San Francisco State University";
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 per liter";
}
Urea {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.18;
String bcodmo_name "Urea";
String description "Concentration of urea determined by the carboxythiazole method; Samples run in Hollibaugh lab at UGA";
String long_name "Urea";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/UREAAAZX/";
String units "micromoles per liter";
}
Silicate {
Float32 _FillValue NaN;
Float32 actual_range 0.7, 77.73;
String bcodmo_name "SiOH_4";
String description "Concentration of silicate determined by autoanalyzer; Samples run on an autoanalyzer by Francis Wilkerson's lab at San Francisco State University";
String long_name "Mass Concentration Of Silicate In Sea Water";
String units "micromoles per liter";
}
Phosphate {
Float32 _FillValue NaN;
Float32 actual_range 0.024, 1.853;
String bcodmo_name "unknown";
String description "Concentration of phosphate determined by autoanalyzer; Samples run on an autoanalyzer by Francis Wilkerson's lab at San Francisco State University";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "micromoles per liter";
}
Temperature {
Float32 _FillValue NaN;
Float32 actual_range 7.82, 31.3;
String bcodmo_name "temperature";
String description "Water temperature in centigrade degrees at the depth sampled measured by the environmental sensing package on the samplling rosette";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees centigrade";
}
Salinity {
Float32 _FillValue NaN;
Float32 actual_range 22.1, 36.86;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "Salinity at the depth sampled derived from temperature and conductivity measured by the environmental sensing package on the samplling rosette";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "PSU";
}
Diss_Oxygen {
Float32 _FillValue NaN;
Float32 actual_range 3.63, 6.38;
String bcodmo_name "dissolved Oxygen";
String description "Dissolved oxygen concentration at the depth sampled measured by the environmental sensing package on the samplling rosette";
String long_name "Diss Oxygen";
String units "milliliters per liter";
}
Relative_Fluor {
Float32 _FillValue NaN;
Float32 actual_range 0.46, 16.44;
String bcodmo_name "fluorescence";
String description "Relative Fluorescence measured by the fluorometer on the Niskin rosette sampler converted to mg Chl a L-1 using a regression equation based on extracted chlorophyll data: Chl a = 1.7869RF - 2.2541; R² = 0.83";
String long_name "Relative Fluor";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
String units "relative fluorescence";
}
Atten_Coeff {
Float32 _FillValue NaN;
Float32 actual_range 0.01, 1.47;
String bcodmo_name "beam_cp";
String description "PAR attenuation coefficient kz in m-1 calculated as the slope of log(PAR) vs depth";
String long_name "Atten Coeff";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ATTNZZ01/";
String units "per meter";
}
comment {
String bcodmo_name "comment";
String description "identifier for the comment. comment value a signifies Environmental data, bacterial 16S, thaumarchaeal 16S, AOB amoA, ammonia oxidation, and urea oxidation data were reported previously in Liu et al. (2015) or Tolar et al. (2017);";
String long_name "Comment";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Nutrient analysis
\\u00a0
Nutrient samples were filtered through 0.22 \\u03bcm pore size
Durapore\\u00a0GVWP filters (Millipore Sigma) and frozen at \\u221220_C
immediately\\u00a0after collection, then stored at \\u221280_C until
analysis.\\u00a0Dissolved nitrate (NO3\\u00a0\\u2212), nitrite (NO2\\u00a0\\u2212),
phosphate (PO4\\u00a03\\u2212), and\\u00a0silicate (SiO4\\u00a04\\u2212) were
measured using a Bran and Luebbe AA3\\u00a0autoanalyzer as described previously
(Wilkerson et al. 2015).\\u00a0Ammonium and urea were measured manually using
the\\u00a0phenolhypochlorite method (Sol\\u00f3rzano 1969) and the
diacetylmonoxime\\u00a0method (Rahmatullah and Boyde 1980; Mulvenna\\u00a0and
Savidge 1992), respectively.\\u00a0
Oxidation rate measurements\\u00a0
We used 15N-labeled substrates (98\\u201399% 15N, Cambridge\\u00a0Isotope
Laboratories) to measure the oxidation of N supplied\\u00a0as NH4+, urea,
1,2-diaminoethane (DAE), 1,3-diaminopropane\\u00a0(DAP), 1,4-diaminobutane
(putrescine, PUT), L-glutamic acid\\u00a0(GLU), and L-arginine (ARG). 15N
oxidation from NH4+, urea,\\u00a0PUT, and GLU were measured extensively,
whereas 15N oxidation\\u00a0from DAE, DAP, and ARG was only measured at a
subset\\u00a0of stations (Supporting Information Table S1). GLU and
ARG\\u00a0were included as a control for remineralization, as their
central\\u00a0roles in microbial metabolism leads to rapid catabolism
and\\u00a0NH4\\u00a0+ regeneration (Hollibaugh 1978; Goldman et al.
1987).\\u00a0PUT was used in routine assessments of the oxidation
of\\u00a0polyamine-N because it is one of the most consistently
detected\\u00a0polyamines in seawater (Nishibori et al. 2001a, 2003; Lu\\u00a0et
al. 2014; Liu et al. 2015). Although spermine and spermidine\\u00a0are also
common in seawater, 15N-labeled stocks of these polyamines\\u00a0were not
commercially available. We measured the oxidation\\u00a0of N from DAE and DAP
to investigate the effect of\\u00a0aliphatic chain length (which affects pKa)
on oxidation rate.\\u00a0
Duplicate seawater samples contained in 1-liter polycarbonate\\u00a0or 250 mL
high density polyethylene (HDPE) bottles\\u00a0wrapped with aluminum foil (to
exclude light) were\\u00a0amended with 10\\u201350 nM 15N-labeled substrate.
Marsh\\u00a0Landing samples were then placed in an incubator held at\\u00a0in
situ temperature in the dark. Samples taken at the Skidaway\\u00a0dock were
placed in a mesh bag and immersed at the\\u00a0sea surface at the sampling
site. Samples collected at sea\\u00a0were incubated in a tank of flowing
surface seawater or in an\\u00a0incubator held at 18 C in the dark. Incubation
bottles were sampled\\u00a0for 15N analysis immediately after substrate
addition and\\u00a0again after a period of ~ 24 h. 15N samples were subsampled
into\\u00a050 mL polypropylene centrifuge tubes, frozen at \\u221220_C,
and\\u00a0stored at \\u221280_C until analysis. The 15N/14N ratios of the
NO3\\u00a0\\u2212\\u00a0plus NO2\\u00a0\\u2212 (NOX) pools (\\u03b415NNOx) in the
samples were measured\\u00a0using the bacterial denitrifier method to convert
NOX to nitrous\\u00a0oxide (N2O; Sigman et al. 2001). The \\u03b415N values of
the N2O\\u00a0produced were measured using a Finnigan MAT-252
isotope\\u00a0ratio mass spectrometer coupled with a modified GasBench II
interface (Casciotti et al. 2002; Beman et al. 2011; McIlvin\\u00a0and
Casciotti 2011). Oxidation rates were calculated using an\\u00a0endpoint model
(Beman et al. 2011; Damashek et al. 2016).\\u00a0Since the substrates used were
uniformly labeled with 15N, the\\u00a0amount of the N added as the 15N spike
(in \\u03bcM) was multiplied\\u00a0by the number of moles of 15N per mole of
substrate, which\\u00a0assumes that all of the N atoms have equal probability
of being\\u00a0oxidized. This is likely true for urea, DAE, DAP, and PUT,
which\\u00a0are symmetrical molecules, but not likely to be true for
ARG,\\u00a0which contains 4 N atoms (one in the \\u03b1-amino position
and\\u00a0three in the guanidine structure of its R-group). Abiotic
oxidation\\u00a0of organic N was assessed by measuring 15NOX
production\\u00a0following 15N amendment and incubation of 0.22 \\u03bcm
filtered\\u00a0seawater (as described above), and potential metabolism
of\\u00a0DON by the denitrifying bacteria used to convert NOX to N2O\\u00a0was
checked by adding 15N-labeled substrates into the bacterial\\u00a0cultures
prior to mass spectrometry.\\u00a0
We were unable to measure the in situ concentrations of\\u00a0the individual
components of DON used in oxidation experiments,\\u00a0other than urea. Based
on previous measurements\\u00a0made in the SAB (Lu et al. 2014; Liu et al.
2015), we assumed\\u00a0concentrations of 1 nM and 0.25 nM for DAE, DAP and
PUT,\\u00a0and 10 nM and 5 nM for GLU and ARG, at inshore and\\u00a0mid-shelf
/shelf-break/oceanic stations, respectively. Rates of\\u00a0polyamine and amino
acid oxidation reported below should\\u00a0therefore be considered potential
rates, as amendments as low\\u00a0as 10\\u201350 nM are likely to increase
substrate concentrations\\u00a0substantially above in situ. Initial substrate
15N activity was\\u00a0calculated using isotope mass balance using the known
concentration\\u00a0and 15N activity of the labeled substrates added\\u00a0and
assuming the concentrations described above and natural\\u00a0abundance 15N
activity (i.e., 0.3663 atom% 15N).\\u00a0";
String awards_0_award_nid "757586";
String awards_0_award_number "OCE-1537995";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1537995";
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 "Henrietta N Edmonds";
String awards_0_program_manager_nid "51517";
String awards_1_award_nid "757590";
String awards_1_award_number "OCE-1538677";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538677";
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 "Henrietta N Edmonds";
String awards_1_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"DON Oxidation data collected on cruise SAV 17-16
PI: James T. Hollibaugh
Version: 2019-05-08
comment value a = Environmental data, bacterial 16S, thaumarchaeal 16S, AOB amoA, ammonia oxidation, and urea oxidation data were reported previously in Liu et al. (2015) or Tolar et al. (2017);";
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 "2019-05-08T14:21:19Z";
String date_modified "2019-06-21T18:12:18Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.767048.1";
Float64 Easternmost_Easting -78.77;
Float64 geospatial_lat_max 31.99;
Float64 geospatial_lat_min 30.32;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -78.77;
Float64 geospatial_lon_min -81.36;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 500.0;
Float64 geospatial_vertical_min 0.2;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-22T15:33:53Z (local files)
2024-12-22T15:33:53Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_767048.html";
String infoUrl "https://www.bco-dmo.org/dataset/767048";
String institution "BCO-DMO";
String instruments_0_acronym "CTD SBE 25";
String instruments_0_dataset_instrument_description "Water from multiple depths was collected using 12-liter Niskin bottles mounted on a rosette equipped with a Sea-Bird SBE25 CTD. Profiles of salinity, temperature, dissolved oxygen, fluorescence, and photosynthetically active radiation (PAR) were collected using the CTD system as described previously (Liu et al. 2018).";
String instruments_0_dataset_instrument_nid "767193";
String instruments_0_description "The Sea-Bird SBE 25 SEALOGGER CTD is battery powered and is typically used to record data in memory, eliminating the need for a large vessel, electrical sea cable, and on-board computer. All SBE 25s can also operate in real-time, transmitting data via an opto-isolated RS-232 serial port. Temperature and conductivity are measured by the SBE 3F Temperature sensor and SBE 4 Conductivity sensor (same as those used on the premium SBE 9plus CTD). The SBE 25 also includes the SBE 5P (plastic) or 5T (titanium) Submersible Pump and TC Duct. The pump-controlled, TC-ducted flow configuration significantly reduces salinity spiking caused by ship heave, and in calm waters allows slower descent rates for improved resolution of water column features. Pressure is measured by the modular SBE 29 Temperature Compensated Strain-Gauge Pressure sensor (available in eight depth ranges to suit the operating depth requirement). The SBE 25's modular design makes it easy to configure in the field for a wide range of auxiliary sensors, including optional dissolved oxygen (SBE 43), pH (SBE 18 or SBE 27), fluorescence, transmissivity, PAR, and optical backscatter sensors. More information from Sea-Bird Electronics: http:www.seabird.com.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0040/";
String instruments_0_instrument_name "CTD Sea-Bird 25";
String instruments_0_instrument_nid "421";
String instruments_0_supplied_name "Sea-Bird SBE25 CTD";
String instruments_1_acronym "IR Mass Spec";
String instruments_1_dataset_instrument_description "The δ15N values of the N2O produced were measured using a Finnigan MAT-252 isotope ratio mass spectrometer coupled with a modified GasBench II interface";
String instruments_1_dataset_instrument_nid "767195";
String instruments_1_description "The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_1_instrument_name "Isotope-ratio Mass Spectrometer";
String instruments_1_instrument_nid "469";
String instruments_1_supplied_name "Finnigan MAT-252 isotope ratio mass spectrometer";
String instruments_2_acronym "Bran Luebbe AA3 AutoAnalyzer";
String instruments_2_dataset_instrument_description "Dissolved nitrate (NO3 −), nitrite (NO2 −), phosphate (PO4 3−), and silicate (SiO4 4−) were measured using a Bran and Luebbe AA3 autoanalyzer as described previously (Wilkerson et al. 2015).";
String instruments_2_dataset_instrument_nid "767194";
String instruments_2_description
"Bran Luebbe AA3 AutoAnalyzer
See the description from the manufacturer.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB04/";
String instruments_2_instrument_name "Bran Luebbe AA3 AutoAnalyzer";
String instruments_2_instrument_nid "700";
String instruments_2_supplied_name "Bran and Luebbe AA3 autoanalyzer";
String instruments_3_acronym "qPCR";
String instruments_3_dataset_instrument_description "All reactions (25 μL total volume) were run in triplicate on a C1000 Touch Thermal Cycler equipped with a CFX96 Real-Time System (Bio- Rad), using either the iTaq Universal Green SYBR Mix (Bio-Rad) or the Platinum qPCR SuperMix-UDG (Thermo Fisher).";
String instruments_3_dataset_instrument_nid "767196";
String instruments_3_description "An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).";
String instruments_3_instrument_name "qPCR Thermal Cycler";
String instruments_3_instrument_nid "707569";
String instruments_3_supplied_name "C1000 Touch Thermal Cycler";
String keywords "added, ammonia, Ammonia_Oxidation, Ammonia_Oxidation_sd, ammonium, amo, arg, atten, Atten_Coeff, bacterial, Bacterial_16S_rRNA, bco, bco-dmo, biological, chemical, chemistry, coeff, comment, concentration, cruise, Cruise_ID, dae, dap, data, dataset, date, density, depth, diss, Diss_Oxygen, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, Earth Science > Oceans > Salinity/Density > Salinity, erddap, fluor, glu, iso, ISO_Date, latitude, latitude2, longitude, longitude2, management, mass, mass_concentration_of_phosphate_in_sea_water, mass_concentration_of_silicate_in_sea_water, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrite_in_sea_water, n02, n15, N15_added, N15_ox_from_ARG, N15_ox_from_ARG_sd, N15_ox_from_DAE, N15_ox_from_DAE_sd, N15_ox_from_DAP, N15_ox_from_DAP_sd, N15_ox_from_GLU, N15_ox_from_GLU_sd, N15_ox_from_PUT, N15_ox_from_PUT_sd, N15_ox_from_UREA, N15_ox_from_UREA_sd, nh4, nitrate, nitrite, nitrospina, Nitrospina_16S_rRNA, no3, O2, ocean, oceanography, oceans, office, oxidation, oxygen, phosphate, po4, practical, preliminary, put, region, relative, Relative_Fluor, rna, salinity, science, sea, sea_water_practical_salinity, seawater, silicate, sta, temperature, thaumarchaeal, Thaumarchaeal_16S_rRNA, time, urea, water, wca, WCA_amoA, wcb, WCB_amoA";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/767048/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/767048";
Float64 Northernmost_Northing 31.99;
String param_mapping "{'767048': {'lat': 'flag - latitude', 'depth': 'flag - depth', 'lon': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/767048/parameters";
String people_0_affiliation "University of Georgia";
String people_0_affiliation_acronym "UGA";
String people_0_person_name "Dr James T. Hollibaugh";
String people_0_person_nid "662307";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Hawaii";
String people_1_person_name "Brian N. Popp";
String people_1_person_nid "51093";
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 "Mathew Biddle";
String people_2_person_nid "708682";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "DON Oxidation";
String projects_0_acronym "DON Oxidation";
String projects_0_description
"NSF Abstract:
Nitrogen is an essential nutrient for phytoplankton that often limits primary production in the ocean, and its availability therefore plays a key role in global ocean productivity. The amounts and form in which nitrogen exist are controlled by microorganisms. One microorganism-mediated process is known as nitrification, which oxidizes ammonia or ammonium to nitrite and nitrite to nitrate, nitrate being the bioavailable form of nitrogen. While this is the well-accepted process of nitrification, preliminary results strongly suggest that a nitrogen-containing compound know as polyamine nitrogen may be directly converted by some microorganisms to nitrate. However, the importance of this process for global biogeochemical nitrogen cycling is unknown. The goal of this study is to evaluate the biogeochemical significance of direct oxidation of polyamine nitrogen, as a model organic nitrogen compound, to nitrification compared to canonical nitrification of ammonia. The project will result in training a postdoctoral researcher and provide opportunities for undergraduates to gain hands-on experience with research on microbial geochemistry and coastal ecosystem processes. Project personnel will also work with the Georgia Coastal Ecosystems Long-Term Ecological Research program to engage a K-12 science teacher in the project.
Ammonia oxidation is a key step in the process of converting fixed nitrogen to dinitrogen gas and thus is central to the global nitrogen cycle and to removing excess fixed nitrogen from coastal waters with high concentrations of nutrients. Recent research has shown that Thaumarchaeota play a major role in ammonia oxidation in the ocean. Experiments with enrichment cultures and coastal water samples where ammonia oxidizing archaea are the dominant ammonia oxidizers, show that some forms of organic nitrogen may be oxidized directly to nitrogen oxides without first being regenerated as ammonium. Of the substrates tested, polyamine and particularly putrescine nitrogen appear to be oxidized directly to nitrogen oxides, while amino acid and urea nitrogen is first regenerated as ammonium and then oxidized. The investigators will examine this process in detail over three years using enrichment cultures and experiments conducted with coastal bacterioplankton. Specifically, they will aim to better understand 1) the consequences of this novel process to ocean geochemistry, 2) the fate of the carbon present in polyamines, 3) what organisms are responsible for the direct oxidation, and 4) the chemical characteristics of the organic nitrogen compounds accessible to direct oxidation.";
String projects_0_end_date "2018-11";
String projects_0_geolocation "Coastal waters and the South Atlantic Bight continental shelf from Savannah GA out to the shelf break (SAV 17-16, UNOLS STR _104733, Marsden Grid 117, Navy Ops NA06), coastal waters around Sapelo Island, Georgia USA";
String projects_0_name "Collaborative Research: Direct Oxidation of Organic Nitrogen by Marine Ammonia Oxidizing Organisms";
String projects_0_project_nid "757587";
String projects_0_start_date "2015-12";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 30.32;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "This dataset contains the results of analyses related to ammonia oxidation rates, including oxidation rates of 15N supplied as ammonia, urea, 1,2 diamino ethane, 1,3 diamino propane, 1,4 diamino butane (putrescine), arginine and glutamate. Ancillary data including nutrient concentrations and the abundance of ammonia- and nitrite-oxidizing microorganisms are also reported. The samples analyzed to produce the dataset were collected off the coast of Georgia, USA. Most data were collected on one cruise in August 2017, incidental data from 2011, 2013 and 2016 are also reported.";
String title "[DON_Oxidation] - Dissolved Organic Nitrogen oxidation collected on cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017 (Collaborative Research: Direct Oxidation of Organic Nitrogen by Marine Ammonia Oxidizing Organisms)";
String version "1";
Float64 Westernmost_Easting -81.36;
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.