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Dataset Title:  N2O, 15N2, 15N tissue tracer in oyster aquariums (Oyster Reef N2O Emission
project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_722560)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Timepoint {
    String bcodmo_name "unknown";
    String description "Represents when the experiment began and ended ( 0 - initial, 1- final). While all aquariums started at the same time, not all ended at the same time. The reason for multiple time points (i.e., 0,0,1,1,1,1) is to accommodate the multiple samples taken during that time point. For example, Timepoint 1, Hour 5, only applies to OA1 and OA2. However, Timepoint 1, Hour 69.50 applies to the remaining aquariums ( OA3, CA1, CA2, CA3). Under the \"Timepoint\" column is \"Oyster Harvests*\", which marks the second phase of this Oyster Aquarium experiment. The data collected for that section would be Del15N digestive/ meat. \"Oyster Harvest\" is under that column since the oysters were harvested at time points indicated by the Time_Days / Hours column.";
    String long_name "Timepoint";
    String units "unitless";
  }
  Time_Days {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 17.71;
    String bcodmo_name "time_elapsed";
    String description "Time_Days gives a value that represents how much time has passed since the initial sample taken. \"Hours\" is just a conversion of the \"Time_Days\" value. An easier way to understand how much time has passed.";
    String long_name "Time Days";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "days";
  }
  Hours {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 425.0;
    String bcodmo_name "duration";
    String description "Incubation time per incubation";
    String long_name "Hours";
    String units "hours";
  }
  OA1_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.91, 1.52;
    String bcodmo_name "N";
    String description "Oyster aquarium 1 15N enrichment of dissolved N2";
    String long_name "OA1 15 N2";
    String units "permil";
  }
  OA1_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 12.04, 22.55;
    String bcodmo_name "Nitrous Oxide";
    String description "Oyster aquarium 1 Aqueous N2O concentration";
    String long_name "OA1 N2 O";
    String units "nM";
  }
  OA1_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 2.78, 4.47;
    String bcodmo_name "dissolved Oxygen";
    String description "Oyster aquarium 1 Aqueous O2 concentration";
    String long_name "OA1 O2";
    String units "mg/L";
  }
  OA1_Del15N_Digestive {
    Float32 _FillValue NaN;
    Float32 actual_range 485.01, 5617.9;
    String bcodmo_name "N";
    String description "Oyster aquarium 1 15N enrichment digestive tissue";
    String long_name "OA1 Del15 N Digestive";
    String units "permil";
  }
  OA1_Del15N_Meat {
    Float32 _FillValue NaN;
    Float32 actual_range 369.26, 2328.06;
    String bcodmo_name "N";
    String description "Oyster aquarium 1 15N enrichment other (mantle; gills) tissue";
    String long_name "OA1 Del15 N Meat";
    String units "permil";
  }
  OA2_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 1.06, 2.5;
    String bcodmo_name "N";
    String description "Oyster aquarium 2 15N enrichment of dissolved N2";
    String long_name "OA2 15 N2";
    String units "permil";
  }
  OA2_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 11.06, 19.9;
    String bcodmo_name "Nitrous Oxide";
    String description "Oyster aquarium 2 Aqueous N2O concentration";
    String long_name "OA2 N2 O";
    String units "nM";
  }
  OA2_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 2.14, 4.6;
    String bcodmo_name "dissolved Oxygen";
    String description "Oyster aquarium 2 Aqueous O2 concentration";
    String long_name "OA2 O2";
    String units "mg/L";
  }
  OA2_Del15N_Digestive {
    Float32 _FillValue NaN;
    Float32 actual_range 91.89, 3355.45;
    String bcodmo_name "N";
    String description "Oyster aquarium 2 15N enrichment digestive tissue";
    String long_name "OA2 Del15 N Digestive";
    String units "permil";
  }
  OA2_Del15N_Meat {
    Float32 _FillValue NaN;
    Float32 actual_range 104.27, 2681.23;
    String bcodmo_name "N";
    String description "Oyster aquarium 2 15N enrichment other (mantle; gills) tissue";
    String long_name "OA2 Del15 N Meat";
    String units "permil";
  }
  OA3_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.87, 38.39;
    String bcodmo_name "N";
    String description "Oyster aquarium 3 15N enrichment of dissolved N2";
    String long_name "OA3 15 N2";
    String units "permil";
  }
  OA3_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 12.3, 1474.1;
    String bcodmo_name "Nitrous Oxide";
    String description "Oyster aquarium 3 Aqueous N2O concentration";
    String long_name "OA3 N2 O";
    String units "nM";
  }
  OA3_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.16, 4.6;
    String bcodmo_name "dissolved Oxygen";
    String description "Oyster aquarium 3 Aqueous O2 concentration";
    String long_name "OA3 O2";
    String units "mg/L";
  }
  OA3_Del15N_Digestive {
    Float32 _FillValue NaN;
    Float32 actual_range 212.07, 5498.3;
    String bcodmo_name "N";
    String description "Oyster aquarium 3 15N enrichment digestive tissue";
    String long_name "OA3 Del15 N Digestive";
    String units "permil";
  }
  OA3_Del15N_Meat {
    Float32 _FillValue NaN;
    Float32 actual_range 184.07, 3847.09;
    String bcodmo_name "N";
    String description "Oyster aquarium 3 15N enrichment other (mantle; gills) tissue";
    String long_name "OA3 Del15 N Meat";
    String units "permil";
  }
  CA1_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.39, 0.57;
    String bcodmo_name "N";
    String description "Control aquarium 1 15N enrichment of dissolved N2";
    String long_name "CA1 15 N2";
    String units "permil";
  }
  CA1_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 9.52, 16.42;
    String bcodmo_name "Nitrous Oxide";
    String description "Control aquarium 1 Aqueous N2O concentration";
    String long_name "CA1 N2 O";
    String units "nM";
  }
  CA1_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 5.64, 7.08;
    String bcodmo_name "dissolved Oxygen";
    String description "Control aquarium 1 Aqueous O2 concentration";
    String long_name "CA1 O2";
    String units "mg/L";
  }
  CA2_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.4, 0.72;
    String bcodmo_name "N";
    String description "Control aquarium 2 15N enrichment of dissolved N2";
    String long_name "CA2 15 N2";
    String units "permil";
  }
  CA2_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 10.44, 27.18;
    String bcodmo_name "Nitrous Oxide";
    String description "Control aquarium 2 Aqueous N2O concentration";
    String long_name "CA2 N2 O";
    String units "nM";
  }
  CA2_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 4.48, 6.72;
    String bcodmo_name "dissolved Oxygen";
    String description "Control aquarium 2 Aqueous O2 concentration";
    String long_name "CA2 O2";
    String units "mg/L";
  }
  CA3_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.23, 0.97;
    String bcodmo_name "N";
    String description "Control aquarium 3 15N enrichment of dissolved N2";
    String long_name "CA3 15 N2";
    String units "permil";
  }
  CA3_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 11.89, 26.2;
    String bcodmo_name "Nitrous Oxide";
    String description "Control aquarium 3 Aqueous N2O concentration";
    String long_name "CA3 N2 O";
    String units "nM";
  }
  CA3_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 5.12, 6.94;
    String bcodmo_name "dissolved Oxygen";
    String description "Control aquarium 3 Aqueous O2 concentration";
    String long_name "CA3 O2";
    String units "mg/L";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Three 9.45L aquariums contained twelve 7-cm long oysters pre-exposed
to\\u00a015N labeled phytoplankton (OA1, OA2, OA3,) and three aquariums had no
oysters and served as controls (CA1, CA2, CA3). These aquariums were filled
with 0.1micron filtered seawater and a small circulation pump was added.
N2O,\\u00a015N, and oxygen were measured initially and then aquariums sealed
until oxygen had depleted to 2mgL-1. Oysters were then harvested for their
gill/mantle tissue (meat) and digestive tissue (digestive) over a period of
time.
 
Oxygen was measured insitu using an oxygen probe. Water samples for N2O
analysis were collected with a peristaltic pump through a syringe needle
directly into 12 ml exetainer that had been flushed with N2 and preserved with
KOH to a pH above 12. Approximately six ml sample was collected. N2O
concentrations in the headspace were measured on a GC-ECD.\\u00a0 Water samples
for 15N2 samples were collected with a peristaltic pump through a syringe
needle directly into 30 ml serum bottles that had been flushed with He and
preserved with KOH to a pH above 12. \\u00a0 Approximately eight ml sample was
collected. 15N2 was analyzed by GC - Isotope Ratio Mass Spectrometry (IRMS).
Oyster tissue 15N samples were collected from the aquariums from dissections.
15N was analyzed on a elemental analyzer (EA) coupled with an IRMS.";
    String awards_0_award_nid "568863";
    String awards_0_award_number "OCE-1233372";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1233372";
    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 
"Sealed Oyster Aquarium 15N Tracer, 15N2 and N2O  
 PI: Craig Tobias 
 Co-PI: Bongkuen Song, Michael Piehler, Mark Brush 
 Version: 20171231";
    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 "2018-01-05T20:22:31Z";
    String date_modified "2019-05-07T17:54:46Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.722560.1";
    String history 
"2022-10-01T14:20:33Z (local files)
2022-10-01T14:20:33Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_722560.das";
    String infoUrl "https://www.bco-dmo.org/dataset/722560";
    String institution "BCO-DMO";
    String instruments_0_acronym "IR Mass Spec";
    String instruments_0_dataset_instrument_description "15N2 was measured on a Thermo Delta V IRMS fitted with a Gas Bench II interface following separation from O2 and Ar on a mol sieve 5A column.";
    String instruments_0_dataset_instrument_nid "722569";
    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 "Thermo Delta V IRMS";
    String instruments_1_acronym "Gas Chromatograph";
    String instruments_1_dataset_instrument_description "N2O was measured on a Agilent 7890B GC with a Poropak Column.";
    String instruments_1_dataset_instrument_nid "722571";
    String instruments_1_description "Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
    String instruments_1_instrument_name "Gas Chromatograph";
    String instruments_1_instrument_nid "661";
    String instruments_1_supplied_name "Agilent 7890B GC with a Poropak Column";
    String instruments_2_acronym "Dissolved Oxygen Sensor";
    String instruments_2_dataset_instrument_description "Oxygen was measured using a Thermo Orion rugged dissolved oxygen probe.";
    String instruments_2_dataset_instrument_nid "722590";
    String instruments_2_description "An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed";
    String instruments_2_instrument_name "Dissolved Oxygen Sensor";
    String instruments_2_instrument_nid "705";
    String instruments_2_supplied_name "Thermo Orion rugged dissolved oxygen probe";
    String instruments_3_dataset_instrument_description "Oyster tissue 15N was analyzed via IRMS coupled to a Costech Elemental Analyzer.";
    String instruments_3_dataset_instrument_nid "722570";
    String instruments_3_description "Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.";
    String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
    String instruments_3_instrument_name "Elemental Analyzer";
    String instruments_3_instrument_nid "546339";
    String instruments_3_supplied_name "Costech Elemental Analyzer";
    String keywords "bco, bco-dmo, biological, ca1, CA1_15N2, CA1_N2O, CA1_O2, ca2, CA2_15N2, CA2_N2O, CA2_O2, ca3, CA3_15N2, CA3_N2O, CA3_O2, chemical, data, dataset, days, del15, digestive, dmo, erddap, hours, management, meat, O2, oa1, OA1_15N2, OA1_Del15N_Digestive, OA1_Del15N_Meat, OA1_N2O, OA1_O2, oa2, OA2_15N2, OA2_Del15N_Digestive, OA2_Del15N_Meat, OA2_N2O, OA2_O2, oa3, OA3_15N2, OA3_Del15N_Digestive, OA3_Del15N_Meat, OA3_N2O, OA3_O2, oceanography, office, oxygen, preliminary, time, Time_Days, timepoint";
    String license "https://www.bco-dmo.org/dataset/722560/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/722560";
    String param_mapping "{'722560': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/722560/parameters";
    String people_0_affiliation "University of Connecticut";
    String people_0_affiliation_acronym "UConn - Avery Point";
    String people_0_person_name "Craig Tobias";
    String people_0_person_nid "51731";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Virginia Institute of Marine Science";
    String people_1_affiliation_acronym "VIMS";
    String people_1_person_name "Mark J. Brush";
    String people_1_person_nid "568861";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "University of North Carolina at Chapel Hill";
    String people_2_affiliation_acronym "UNC-Chapel Hill-IMS";
    String people_2_person_name "Michael F. Piehler";
    String people_2_person_nid "522931";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Virginia Institute of Marine Science";
    String people_3_affiliation_acronym "VIMS";
    String people_3_person_name "Bongkeun Song";
    String people_3_person_nid "51729";
    String people_3_role "Co-Principal Investigator";
    String people_3_role_type "originator";
    String people_4_affiliation "University of Connecticut";
    String people_4_affiliation_acronym "UConn - Avery Point";
    String people_4_person_name "Craig Tobias";
    String people_4_person_nid "51731";
    String people_4_role "Contact";
    String people_4_role_type "related";
    String people_5_affiliation "Woods Hole Oceanographic Institution";
    String people_5_affiliation_acronym "WHOI BCO-DMO";
    String people_5_person_name "Mathew Biddle";
    String people_5_person_nid "708682";
    String people_5_role "BCO-DMO Data Manager";
    String people_5_role_type "related";
    String project "Oyster Reef N2O Emission";
    String projects_0_acronym "Oyster Reef N2O Emission";
    String projects_0_description 
"Extracted from the NSF award abstract:
Oyster reefs are biogeochemical hot spots and prominent estuarine habitats that provide disproportionate ecological function. Suspension-feeding eastern oysters, Crassostrea virginica, are capable of improving water quality and diminishing eutrophication by filtering nutrients and particles from the water and depositing them in the sediments. Remineralization of these deposits may enhance sedimentary denitrification that facilitates nitrogen removal in tidal estuaries. However, the scientific underpinning of oyster reef function has been challenged in various studies. In addition, recent studies of filter feeding invertebrates reported the production of nitrous oxide (N2O), a greenhouse gas, as an end product of incomplete denitrification by gut microbes. C. virginica could be another source of N2O flux from intertidal habitats. Preliminary work indicated substantial N2O production from individual oysters. The estimated N2O production from high density oyster reefs may exceed the N2O flux measured from some estuaries. With the new discovery of N2O emission and uncertainty regarding eutrophication control, the ecological value of oyster reef restoration may become equivocal.
This project will quantify N2O fluxes to understand the factors controlling N2O emission from oyster reefs. Sedimentary N processes will be examined to develop an oyster reef N model to estimate N2O emission from tidal creek estuaries relative to other N cycling processes. The PIs hypothesize that intertidal oyster reefs are a substantial source of N2O emission from estuarine ecosystems and the magnitude of emission may be linked to water quality. If substantial N2O flux from oyster reefs is validated, ecological benefits of oyster reef restoration should be reevaluated. This interdisciplinary research team includes a microbial ecologist, a biogeochemist, an ecologist and an ecosystem modeler. They will utilize stable isotope and molecular microbiological techniques to quantify oyster N2O production, elucidate microbial sources of N2O emission from oysters and sediments, and estimate seasonal variation of N2O fluxes from oyster reefs. Measurements from this study will be integrated into a coupled oyster bioenergetics-sediment biogeochemistry model to compare system level rates of N cycling on oyster reefs as a function of oyster density and water quality. Modeling results will be used to assess the relative trade-­offs of oyster restoration associated with N cycling. They expect to deliver the following end products:1) estimation of annual N2O flux from oyster reefs as an additional source of greenhouse gases from estuaries, 2) a better understanding of the environmental and microbial factors influencing N2O and N2 fluxes in tidal estuaries, 3) transformative knowledge for the effect of oyster restoration on water quality enhancement and ecosystem function, 4) direct guidance for oyster restoration projects whose goals include water quality enhancement, and 5) a modeling tool for use in research and restoration planning.";
    String projects_0_end_date "2015-08";
    String projects_0_name "Microbial Regulation of Greenhouse Gas N2O Emission from Intertidal Oyster Reefs";
    String projects_0_project_nid "527289";
    String projects_0_start_date "2012-12";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "N2O, 15N2, 15N tissue tracer in oyster aquariums";
    String title "N2O, 15N2, 15N tissue tracer in oyster aquariums (Oyster Reef N2O Emission project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

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.


 
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