BCO-DMO ERDDAP
Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > tabledap > Data Access Form ?

Dataset Title:  Denitrification and DNRA data from Little Lagoon, Alabama collected from 2012-
2013
  RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_723966)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 Year (unitless) ?          1    2
 Value_Description (unitless) ?              
 Date (unitless) ?              
 East (umol N m-2 hr-1; umol N m-2 d-1; mmol NH4+ m-2 d-1) ?          -55.13    5072.2
 East_SE (umol N m-2 hr-1; umol N m-2 d-1; mmol NH4+ m-2 d-1) ?          0.0    1260.2
 Mouth (umol N m-2 hr-1; umol N m-2 d-1; mmol NH4+ m-2 d-1) ?          -52.28    2549.4
 Mouth_SE (umol N m-2 hr-1; umol N m-2 d-1; mmol NH4+ m-2 d-1) ?          0.0    458.2
 West (umol N m-2 hr-1; umol N m-2 d-1; mmol NH4+ m-2 d-1) ?          -77.78    5678.0
 West_SE (umol N m-2 hr-1; umol N m-2 d-1; mmol NH4+ m-2 d-1) ?          0.0    1181.1
 
Server-side Functions ?
 distinct() ?
? (" ")

File type: (more info)

(Documentation / Bypass this form ? )
 
(Please be patient. It may take a while to get the data.)


 

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Year {
    Byte _FillValue 127;
    Byte actual_range 1, 2;
    String description "Year ID that samples were taken";
    String ioos_category "Time";
    String long_name "Year";
    String units "unitless";
  }
  Value_Description {
    String description "Description of the measurment taken; description includes relevant units for each sample taken; Descriptions include: DIN:DIP = ratio of dissolved inorganic nitrogen to dissolved inorganic phosphate; Denitrification = Denitrification; p14 ambient denitrification = ambient denitrification rates; DNRA = dissimilatory nitrate reduction to ammonium; D15 denitrification = denitrification from added heavy labeled isotope.";
    String ioos_category "Unknown";
    String long_name "Value Description";
    String units "unitless";
  }
  Date {
    String description "Month and day that samples were taken; MMM-DD";
    String ioos_category "Time";
    String long_name "Date";
    String units "unitless";
  }
  East {
    Float32 _FillValue NaN;
    Float32 actual_range -55.13, 5072.2;
    String description "Denitrification and DNRA values collected at the East site; location of site is 30.253347, -87.724729";
    String ioos_category "Unknown";
    String long_name "East";
    String units "umol N m-2 hr-1;  umol N m-2 d-1;  mmol NH4+ m-2 d-1";
  }
  East_SE {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1260.2;
    String description "Standard error of denitrification and DNRA values collected at the East site";
    String ioos_category "Unknown";
    String long_name "East SE";
    String units "umol N m-2 hr-1;  umol N m-2 d-1;  mmol NH4+ m-2 d-1";
  }
  Mouth {
    Float32 _FillValue NaN;
    Float32 actual_range -52.28, 2549.4;
    String description "Denitrification and DNRA values collected at the Mouth site; location of site is 30.243683, -87.738407";
    String ioos_category "Unknown";
    String long_name "Mouth";
    String units "umol N m-2 hr-1;  umol N m-2 d-1;  mmol NH4+ m-2 d-1";
  }
  Mouth_SE {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 458.2;
    String description "Standard error of denitrification and DNRA values collected at the Mouth site";
    String ioos_category "Unknown";
    String long_name "Mouth SE";
    String units "umol N m-2 hr-1;  umol N m-2 d-1;  mmol NH4+ m-2 d-1";
  }
  West {
    Float32 _FillValue NaN;
    Float32 actual_range -77.78, 5678.0;
    String description "Denitrification and DNRA values collected at the West site; location of site is 30.247181, -87.767856";
    String ioos_category "Unknown";
    String long_name "West";
    String units "umol N m-2 hr-1;  umol N m-2 d-1;  mmol NH4+ m-2 d-1";
  }
  West_SE {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1181.1;
    String description "Standard error of denitrification and DNRA values collected at the West site";
    String ioos_category "Unknown";
    String long_name "West SE";
    String units "umol N m-2 hr-1;  umol N m-2 d-1;  mmol NH4+ m-2 d-1";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Little Lagoon is a shallow coastal lagoon that is tidally connected to the
Gulf of Mexico but has no riverine inputs. The water in the lagoon is
replenished solely from precipitation and groundwater inputs primarily on the
East end (Su et al. 2012). Because of the rapid development in Baldwin County,
a large amount of NO3- enters the Little Lagoon system through SGD (Murgulet &
Tick 2008). In this region, there can be rapid changes in the depth to
groundwater (Fig. 4.1 inset) and episodic SGD inputs to the lagoon (Su et
al.2013). Within the lagoon, three sites were selected (East, Mouth, and West)
to represent the gradient that exists across the lagoon from the input of
groundwater. Sites were sampled on a near-monthly basis from February 2012 to
February 2013.
 
DNRA\\u00a0  
 Approximately 1 L of outflow water was collected from the inflow water and
each core forDNRA analysis. Appropriate sample volume was determined after NH4
+ nutrient analysis and expected atom % enrichment. \\u03b415N-NH4 + was
measured in samples, constructed blanks, and standards that bracketed the NH4
+ concentration of the samples following a modified ammonium diffusion
procedure (Holmes et al. 1998) that collects NH4 + dissolved in water by
converting NH4 + to NH3 under basic conditions and then traps the NH3 on an
acidified glass fiber filter. Non diffused standards were prepared according
to Stark and Hart (1996) to account for blank corrections. After 15N analysis
on a Europa Scientific SL-2020 system (Stable Isotope Lab, Utah State
University), DNRA was calculated from the production rate of 15NH4 + (p15NH4
+) during the incubation according to Christensen et. al (2000): (7) where is
the production of 15N-NH4 + and D14 and D15 are the denitrification rates of
14N-NO3 - and 15N-NO3 -, respectively. This assumes that DNRA takes place in
the same sediment layers as denitrification and that the 15N labeling of NO3 -
being reduced to NH4 + equals the 15N labeling of NO3 - being reduced to N2
(Christensen et al. 2000).
 
Denitrification and anammox from slurry assays
 
Volumetric rates of denitrification, anammox, and the relative contribution of
anammox to gross N2 production were determined from sediment slurry
incubations. Slurry rates for depth-integrated sediments (0-50 mm) were
prepared in Exetainers (Thamdrup & Dalsgaard 2002) with artificial seawater
(ASW) (70.2g NaCl, 3.0g KCl, 49.4 g MgSO4*7H2O, 5.8g CaCl2*2H2O L-1)
constructed at a salinity of 52 and diluted with deionized water to match the
salinity of each site. After dilution, homogenized sediment from 0 to 50 mm
was added to the ASW and the incubation bottle was sparged with N2 and amended
with 100 \\u03bcmol L-1 Na15NO3 - (99 atom %). Sediment slurry was dispensed to
12 ml Exetainers, yielding approximately 1 ml of sediment and 11 ml ASW with
no headspace. For each site, 12 vials total were incubated with three vials
stopped at time points 0 to 36 h. Incubations were stopped by adding 250
\\u03bcL of ZnCl2 and resealing the vials without headspace. Denitrification
and anammox rates in slurries were calculated according to equations 5 and 6
described below.\\u00a0
 
Excess 29N2 and 30N2 concentrations for intact core and slurry incubations
were calculated from dissolved 29N2:28N2 and 30N2:28N2 measured using a MIMS.
Rates of excess 29N2 (p29) and 30N2 (p30) production were calculated from the
flux calculation described above. Rates of ambient 14N2 production (p14) in
core incubations with 15NO3 - tracer addition were determined as (Nielsen
1992, Risgaard-Petersen et al. 2003):\\u00a0
 
(1) p14 = 2 x r14 \\u00b1 [p29 + p30 \\u00b1 (1 - r16)]
 
The 14N:15N ratio of NO3 - undergoing reduction to N2 (r14) was determined as
follows:\\u00a0
 
(2) r14 = [R29 x (1 - ra) - ra] x (2 - ra) ^-1
 
where R29 was the ratio of p29 to p30 determined for the cores and ra was the
relative contribution of anammox to gross N2 production determined in vial
slurry incubations. Gross denitrification and anammox rates within intact
sediment cores with 15NO3 - tracer addition were calculated as follows:\\u00a0
 
(3) denitrification = p14 \\u00b1 (1 - ra)
 
(4) anammox = p14 \\u00b1 ra
 
Denitrification stimulated by the added 15N-NO3 - (D15) was calculated from
the classical IPT (Nielsen 1992) and these amended rates are a measure of the
denitrification capacity under field conditions when NO3 - is not
limiting.\\u00a0
 
Rates of denitrification and anammox in vial slurry incubations with 15NO3 -
amendments were calculated from the equations of Thamdrup and Dalsgaard
(2002): (5) (6) where FN was the fraction of 15N in NO3 -. For months when
anammox slurry incubations were not performed (August and November 2012), p14
is calculated as D14 from the IPT (Nielsen 1992). Potential denitrification
and anammox rates were converted to an areal basis using the wet weight of the
sediment in the slurry. All rates and fluxes pertaining to N species in this
study were normalized to one atom N.
 
Additional methodology can be found in:
 
Bernard, Rebecca & Mortazavi, Behzad & A. Kleinhuizen, Alice. (2015).
Dissimilatory nitrate reduction to ammonium (DNRA) seasonally dominates
NO3\\u2212 reduction pathways in an anthropogenically impacted sub-tropical
coastal lagoon. Biogeochemistry. 125.
47-64.\\u00a0[10.1007/s10533-015-0111-6](\\\\\"https://link.springer.com/article/10.1007%2Fs10533-015-0111-6\\\\\").\\u00a0";
    String awards_0_award_nid "497637";
    String awards_0_award_number "OCE-0962008";
    String awards_0_data_url "http://nsf.gov/awardsearch/showAward?AWD_ID=0962008";
    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 "Dr David  L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Denitrification and DNRA 
  B. Mortazavi and W. Burnett, PIs 
  Version 16 January 2018";
    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 2.2d  13 Jun 2019";
    String date_created "2018-01-17T20:11:39Z";
    String date_modified "2019-03-15T18:07:13Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.723966.1";
    String history 
"2019-08-18T23:24:11Z (local files)
2019-08-18T23:24:11Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_723966.html";
    String infoUrl "https://www.bco-dmo.org/dataset/723966";
    String institution "BCO-DMO";
    String instruments_0_acronym "IR Mass Spec";
    String instruments_0_dataset_instrument_description "Used for 15N analysis";
    String instruments_0_dataset_instrument_nid "724410";
    String instruments_0_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_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
    String instruments_0_instrument_name "Isotope-ratio Mass Spectrometer";
    String instruments_0_instrument_nid "469";
    String instruments_0_supplied_name "Europa Scientific SL-2020 system";
    String instruments_1_dataset_instrument_description "Used to filter sediment";
    String instruments_1_dataset_instrument_nid "724409";
    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 "Multichannel proportioning pump";
    String instruments_2_acronym "MIMS";
    String instruments_2_dataset_instrument_description "Used to measure dissolved gas";
    String instruments_2_dataset_instrument_nid "724407";
    String instruments_2_description "Membrane-introduction mass spectrometry (MIMS) is a method of introducing analytes into the mass spectrometer's vacuum chamber via a semipermeable membrane.";
    String instruments_2_instrument_name "Membrane Inlet Mass Spectrometer";
    String instruments_2_instrument_nid "661606";
    String instruments_2_supplied_name "MIMS";
    String instruments_3_acronym "CFA";
    String instruments_3_dataset_instrument_description "Used to measure continuous flow rate";
    String instruments_3_dataset_instrument_nid "724408";
    String instruments_3_description "A sample is injected into a flowing carrier solution passing rapidly through small-bore tubing.�";
    String instruments_3_instrument_name "Continuous Flow Analyzer";
    String instruments_3_instrument_nid "661968";
    String instruments_3_supplied_name "Continuous Flow Analyzer";
    String keywords "bco, bco-dmo, biological, chemical, data, dataset, date, description, dmo, east, East_SE, erddap, management, mouth, Mouth_SE, oceanography, office, preliminary, time, value, Value_Description, west, West_SE, year";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/723966";
    String param_mapping "{'723966': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/723966/parameters";
    String people_0_affiliation "National Science Foundation";
    String people_0_affiliation_acronym "NSF-DEB";
    String people_0_person_name "Dr Behzad Mortazavi";
    String people_0_person_nid "491316";
    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 "Dr William C. Burnett";
    String people_1_person_nid "491315";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "National Science Foundation";
    String people_2_affiliation_acronym "NSF-DEB";
    String people_2_person_name "Dr Behzad Mortazavi";
    String people_2_person_nid "491316";
    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 "Hannah Ake";
    String people_3_person_nid "650173";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Groundwater Discharge, Benthic Coupling and Microalgal Community Structure in a Shallow Coastal Lagoon";
    String projects_0_acronym "LittleLagoonGroundwater";
    String projects_0_description 
"�
This project�investigated the link between submarine groundwater discharge (SGD) and microalgal dynamics in Little Lagoon, Alabama. �In contrast to most near-shore environments, it is fully accessible; has no riverine inputs; and is large enough to display ecological diversity (c. 14x 0.75 km) yet small enough to be comprehensively sampled on appropriate temporal and spatial scales. The PIs have previously demonstrated that the lagoon is a hot-spot for toxic blooms of the diatom Pseudo-nitzchia spp. that are correlated with discharge from the surficial aquifer. This project�assessed variability in SGD, the dependence of benthic nutrient fluxes on microphytobenthos (MPB) abundance and productivity, and the response of the phytoplankton to nutrient enrichment and dilution. The work integrated multiple temporal and spatial scales and demonstrated both the relative importance of SGD vs. benthic recycling as a source of nutrients, and the role of SGD in structuring the microalgal community. (paraphrased from Award abstract)";
    String projects_0_end_date "2014-08";
    String projects_0_geolocation "southern Alabama, east of Mobile";
    String projects_0_name "Groundwater Discharge, Benthic Coupling and Microalgal Community Structure in a Shallow Coastal Lagoon";
    String projects_0_project_nid "491318";
    String projects_0_start_date "2010-03";
    String publisher_name "Hannah Ake";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "Denitrification and DNRA data from Little Lagoon, Alabama collected from 2012-2013";
    String title "Denitrification and DNRA data from Little Lagoon, Alabama collected from 2012-2013";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5-beta";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
ERDDAP, Version 1.82
Disclaimers | Privacy Policy | Contact