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Dataset Title:  Closed Oyster Mesocosm 15N Tracer (Oyster Reef N2O Emission project)   RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_722517)
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 {
  Incubation {
    String description "First Closed Incubation or Second Closed Incubation";
    String ioos_category "Unknown";
    String long_name "Incubation";
    String units "unitless";
  }
  Time_Hours {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 48.0;
    String description "Incubation time per incubation";
    String ioos_category "Time";
    String long_name "Time Hours";
    String units "hours";
  }
  O1_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.5, 19.7;
    String description "Oyster mecosm 1 15N enrichment of dissolved N2";
    String ioos_category "Unknown";
    String long_name "O1 15 N2";
    String units "permil (/mL)";
  }
  O1_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 15.4, 59.3;
    String description "Oyster mecosm 1 Aqueous N2O concentration";
    String ioos_category "Unknown";
    String long_name "O1 N2 O";
    String units "nanomole (nM)";
  }
  O1_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 1.3, 6.5;
    String description "Oyster mecosm 1 dissolved oxygen";
    String ioos_category "Dissolved O2";
    String long_name "O1 O2";
    String units "mgL-1";
  }
  O1_Sed_15N {
    Float32 _FillValue NaN;
    Float32 actual_range 8.6, 1300.0;
    String description "Oyster mecosm 1 15N enrichment sediment (0-3 cm)";
    String ioos_category "Statistics";
    String long_name "O1 Sed 15 N";
    String units "permil (/mL)";
  }
  O2_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.7, 48.7;
    String description "Oyster mecosm 2 15N enrichment of dissolved N2";
    String ioos_category "Dissolved O2";
    String long_name "O2 15 N2";
    String units "permil (/mL)";
  }
  O2_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 16.1, 128.1;
    String description "Oyster mecosm 2 Aqueous N2O concentration";
    String ioos_category "Dissolved O2";
    String long_name "O2 N2 O";
    String units "nanomole (nM)";
  }
  O2_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 1.2, 6.6;
    String description "Oyster mecosm 2 dissolved oxygen";
    String ioos_category "Dissolved O2";
    String long_name "O2 O2";
    String units "mgL-1";
  }
  O2_Sed_15N {
    Float32 _FillValue NaN;
    Float32 actual_range 8.6, 350.0;
    String description "Oyster mecosm 2 15N enrichment sediment (0-3 cm)";
    String ioos_category "Dissolved O2";
    String long_name "O2 Sed 15 N";
    String units "permil (/mL)";
  }
  O3_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 8.7;
    String description "Oyster mecosm 3 15N enrichment of dissolved N2";
    String ioos_category "Unknown";
    String long_name "O3 15 N2";
    String units "permil (/mL)";
  }
  O3_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 12.1, 43.9;
    String description "Oyster mecosm 3 Aqueous N2O concentration";
    String ioos_category "Unknown";
    String long_name "O3 N2 O";
    String units "nanomole (nM)";
  }
  O3_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 2.9, 6.1;
    String description "Oyster mecosm 3 dissolved oxygen";
    String ioos_category "Dissolved O2";
    String long_name "O3 O2";
    String units "mgL-1";
  }
  O3_Sed_15N {
    Float32 _FillValue NaN;
    Float32 actual_range 8.6, 320.0;
    String description "Oyster mecosm 3 15N enrichment sediment (0-3 cm)";
    String ioos_category "Statistics";
    String long_name "O3 Sed 15 N";
    String units "permil (/mL)";
  }
  C1_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.4, 43.2;
    String description "Control mecosm 1 15N enrichment of dissolved N2";
    String ioos_category "Unknown";
    String long_name "C1 15 N2";
    String units "permil (/mL)";
  }
  C1_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 13.0, 72.8;
    String description "Control mecosm 1 Aqueous N2O concentration";
    String ioos_category "Unknown";
    String long_name "C1 N2 O";
    String units "nanomole (nM)";
  }
  C1_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.8, 6.5;
    String description "Control mecosm 1 dissolved oxygen";
    String ioos_category "Dissolved O2";
    String long_name "C1 O2";
    String units "mgL-1";
  }
  C1_Sed_15N {
    Float32 _FillValue NaN;
    Float32 actual_range 8.6, 220.0;
    String description "Control mecosm 1 15N enrichment sediment (0-3 cm)";
    String ioos_category "Statistics";
    String long_name "C1 Sed 15 N";
    String units "permil (/mL)";
  }
  C2_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.8, 17.8;
    String description "Control mecosm 2 15N enrichment of dissolved N2";
    String ioos_category "Unknown";
    String long_name "C2 15 N2";
    String units "permil (/mL)";
  }
  C2_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 13.5, 36.7;
    String description "Control mecosm 2 Aqueous N2O concentration";
    String ioos_category "Unknown";
    String long_name "C2 N2 O";
    String units "nanomole (nM)";
  }
  C2_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 3.1, 6.8;
    String description "Control mecosm 2 dissolved oxygen";
    String ioos_category "Dissolved O2";
    String long_name "C2 O2";
    String units "mgL-1";
  }
  C2_Sed_15N {
    Float32 _FillValue NaN;
    Float32 actual_range 8.6, 500.0;
    String description "Control mecosm 2 15N enrichment sediment (0-3 cm)";
    String ioos_category "Statistics";
    String long_name "C2 Sed 15 N";
    String units "permil (/mL)";
  }
  C3_15N2 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.9, 43.1;
    String description "Control mecosm 3 15N enrichment of dissolved N2";
    String ioos_category "Unknown";
    String long_name "C3 15 N2";
    String units "permil (/mL)";
  }
  C3_N2O {
    Float32 _FillValue NaN;
    Float32 actual_range 13.0, 71.4;
    String description "Control mecosm 3 Aqueous N2O concentration";
    String ioos_category "Unknown";
    String long_name "C3 N2 O";
    String units "nanomole (nM)";
  }
  C3_O2 {
    Float32 _FillValue NaN;
    Float32 actual_range 1.1, 6.7;
    String description "Control mecosm 3 dissolved oxygen";
    String ioos_category "Dissolved O2";
    String long_name "C3 O2";
    String units "mgL-1";
  }
  C3_Sed_15N {
    Float32 _FillValue NaN;
    Float32 actual_range 8.6, 850.0;
    String description "Control mecosm 3 15N enrichment sediment (0-3 cm)";
    String ioos_category "Statistics";
    String long_name "C3 Sed 15 N";
    String units "permil (/mL)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"15N labeled phytoplankton was continuously pumped for three days into 30.5 cm
diameter mesocosms\\u00a0 containing\\u00a0 10 cm of sediment and 20 liters of
overlying water. \\u00a0 Three mesocosms contained twelve 7-cm long oysters
(O1, O2, O2) and three mesocosms had no oysters and served as controls
(C1,C2,C3). Mesoscosms were flow through with a 0.3 day residence time and
open to the atmosphere. After phytoplankton feeding period, oysters were
removed and mesocosms allowed to flush for 3 days.\\u00a0 Tank feed water was
then stopped and mesocosms sealed. Time series N2O,\\u00a015N2\\u00a0, and
sediment\\u00a015N were measured during the period when the mesocom was sealed
until the dissolved oxygen reached 2 mgL-1.\\u00a0 Then the mesocosms were
reopened and the feed water restarted. This first incubation ID is CS1.\\u00a0
The mesocosms functioned in flow through mode for several days (rest period)
and then the incubation / measurement procedure was repeated.\\u00a0 This
second incubation period ID is CS2.\\u00a0 After CS2, the mesocosms were
reopened and put into flow through.\\u00a0 In total there were 5 closed system
incubation periods.\\u00a0 The following \\u2018rest periods\\u2019 (hours) were
established between CS1-2, 2-3, 3-4, 4-5: 49 hours, 90 hours, 110.5 hours,
138.5 hours.
 
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). Sediment 15N samples were collected from the mesocoms
using a 2cm diameter core.\\u00a0 The top 3 cm was retained for analysis.";
    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 "Dr David  L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"N2O, 15N2, 15N Sediment tracer in oyster mesocosms 
 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.pl v1.0";
    String date_created "2018-01-05T19:42:34Z";
    String date_modified "2019-05-07T17:53:19Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.722517.1";
    String history 
"2019-06-17T08:32:22Z (local files)
2019-06-17T08:32:22Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_722517.das";
    String infoUrl "https://www.bco-dmo.org/dataset/722517";
    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 "722526";
    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 "722528";
    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_dataset_instrument_description "Sediment�15N Phyto sample� was analyzed on the IRMS coupled to a Costech Elemental Analyzer.";
    String instruments_2_dataset_instrument_nid "722527";
    String instruments_2_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_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
    String instruments_2_instrument_name "Elemental Analyzer";
    String instruments_2_instrument_nid "546339";
    String instruments_2_supplied_name "Costech Elemental Analyzer";
    String keywords "bco, bco-dmo, biological, C1_15N2, C1_N2O, C1_O2, C1_Sed_15N, C2_15N2, C2_N2O, C2_O2, C2_Sed_15N, C3_15N2, C3_N2O, C3_O2, C3_Sed_15N, chemical, data, dataset, dissolved, dissolved o2, dmo, erddap, hours, incubation, management, O1_15N2, O1_N2O, O1_O2, O1_Sed_15N, O2, O2_15N2, O2_N2O, O2_O2, O2_Sed_15N, O3_15N2, O3_N2O, O3_O2, O3_Sed_15N, oceanography, office, oxygen, preliminary, sed, statistics, time, Time_Hours";
    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/722517";
    String param_mapping "{'722517': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/722517/parameters";
    String people_0_affiliation "University of Connecticut";
    String people_0_affiliation_acronym "UConn - Avery Point";
    String people_0_person_name "Dr 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 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 "Dr 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 "Dr 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 "Microbial Regulation of Greenhouse Gas N2O Emission from Intertidal Oyster Reefs";
    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 "Mathew Biddle";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "Closed Oyster Mesocosm 15N Tracer";
    String title "Closed Oyster Mesocosm 15N Tracer (Oyster Reef N2O Emission project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.0-alpha";
  }
}

 

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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