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Dataset Title:  Carbonate chemistry from outdoor flumes at the UCB Gump Research Station
Moorea, French Polynesia from November of 2015 to March of 2016
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_754694)
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 {
  Flume {
    Byte _FillValue 127;
    Byte actual_range 1, 4;
    String bcodmo_name "site_descrip";
    String description "Flume number (1; 2; 3; 4)";
    String long_name "Flume";
    String units "unitless";
  }
  Treatment {
    Int16 _FillValue 32767;
    Int16 actual_range 344, 1146;
    String bcodmo_name "treatment";
    String description "pCO2 treatment (values 344; 633; 870; 1146)";
    String long_name "Treatment";
    String units "unitless";
  }
  Date {
    String bcodmo_name "date_local";
    String description "Date (HST) of measurement in ISO 8601 format yyyy-mm-dd";
    String long_name "Date";
    String source_name "Date";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  pH_24h {
    Float32 _FillValue NaN;
    Float32 actual_range 7.52, 8.16;
    String bcodmo_name "pH";
    String description "pH averaged across 24 h. Potentiometric.";
    String long_name "P H 24H";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
    String units "total hydrogen ion scale (pHT)";
  }
  pH_Day {
    Float32 _FillValue NaN;
    Float32 actual_range 7.41, 8.19;
    String bcodmo_name "pH";
    String description "pH averaged during daylight hours. Potentiometric.";
    String long_name "P H Day";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
    String units "total hydrogen ion scale (pHT)";
  }
  pH_night {
    Float32 _FillValue NaN;
    Float32 actual_range 7.57, 8.14;
    String bcodmo_name "pH";
    String description "pH averaged during nightime hours. Potentiometric.";
    String long_name "P H Night";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
    String units "total hydrogen ion scale (pHT)";
  }
  pCO2_24h {
    Float32 _FillValue NaN;
    Float32 actual_range 270.55, 1663.42;
    String bcodmo_name "pCO2";
    String description "pCO2 averaged across 24 h. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "P CO2 24h";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/";
    String units "microatmospheres (μatm)";
  }
  pCO2_Day {
    Float32 _FillValue NaN;
    Float32 actual_range 251.35, 2153.84;
    String bcodmo_name "pCO2";
    String description "pCO2 averaged during daylight hours. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "P CO2 Day";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/";
    String units "microatmospheres (μatm)";
  }
  pCO2_Night {
    Float32 _FillValue NaN;
    Float32 actual_range 289.76, 1316.88;
    String bcodmo_name "pCO2";
    String description "pCO2 averaged during nightime hours. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "P CO2 Night";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/";
    String units "microatmospheres (μatm)";
  }
  DIC_24h {
    Float32 _FillValue NaN;
    Float32 actual_range 1806.09, 2230.89;
    String bcodmo_name "DIC";
    String description "DIC averaged across 24 h. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "DIC 24h";
    String units "micromoles per kilogram (μmol kg-1)";
  }
  DIC_Day {
    Float32 _FillValue NaN;
    Float32 actual_range 1841.87, 2287.52;
    String bcodmo_name "DIC";
    String description "DIC averaged during daylight hours. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "DIC Day";
    String units "micromoles per kilogram (μmol kg-1)";
  }
  DIC_Night {
    Float32 _FillValue NaN;
    Float32 actual_range 1770.3, 2245.98;
    String bcodmo_name "DIC";
    String description "DIC averaged during nightime hours. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "DIC Night";
    String units "micromoles per kilogram (μmol kg-1)";
  }
  TA_24h {
    Float32 _FillValue NaN;
    Float32 actual_range 2053.84, 2373.75;
    String bcodmo_name "TALK";
    String description "Alkalinity averaged across 24 h. Potentiometric titration.";
    String long_name "TA 24h";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/";
    String units "micromoles per kilogram (μmol kg-1)";
  }
  TA_Day {
    Float32 _FillValue NaN;
    Float32 actual_range 2076.99, 2369.2;
    String bcodmo_name "TALK";
    String description "Alkalinity averaged during daylight hours. Potentiometric titration.";
    String long_name "TA Day";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/";
    String units "micromoles per kilogram (μmol kg-1)";
  }
  TA_Night {
    Float32 _FillValue NaN;
    Float32 actual_range 2030.7, 2379.96;
    String bcodmo_name "TALK";
    String description "Alkalinity averaged during nightime hours. Potentiometric titration.";
    String long_name "TA Night";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/";
    String units "micromoles per kilogram (μmol kg-1)";
  }
  Omega_24h {
    Float32 _FillValue NaN;
    Float32 actual_range 1.45, 4.72;
    String bcodmo_name "OM_ar";
    String description "Aragonite saturation state averaged across 24 h. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "Omega 24h";
    String units "omega aragonite (Ωa)";
  }
  Omega_Day {
    Float32 _FillValue NaN;
    Float32 actual_range 1.15, 5.07;
    String bcodmo_name "OM_ar";
    String description "Aragonite saturation state averaged during daylight hours. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "Omega Day";
    String units "omega aragonite (Ωa)";
  }
  Omega_Night {
    Float32 _FillValue NaN;
    Float32 actual_range 1.38, 4.5;
    String bcodmo_name "OM_ar";
    String description "Aragonite saturation state averaged during nightime hours. Calculated using seacarb by Lavigne and Gattuso 2013.";
    String long_name "Omega Night";
    String units "omega aragonite (Ωa)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"See Carpenter et al. (2018) for a detailed overview of the methodology of the
experiment designed to measure coral reef community metabolism responses to
ocean acidification over a 4-month period from November 13th, 2015 to March
15th, 2016 in outdoor flumes at the UCB Gump Research Station Moorea, French
Polynesia.
 
Carbonate chemistry data:  
 The pH, measured on the total hydrogen ion scale (pHT), was monitored daily
at the down-stream end of the flumes with a handheld electrode (DG 115-SC
electrode (Mettler-Toledo). Seawater carbonate chemistry and salinity were
measured weekly, both in the day (02:00) and night (20:00); salinity was
measured using a bench-top conductivity meter (Thermo Scientific, Orionstar
A212, Waltham, MA, USA). The parameters of the seawater carbonate system were
calculated from measurements of temperature, salinity, pHT, and AT, using the
R package seacarb (Lavigne and Gattuso 2013).
 
Community composition:  
 ~\\u200925% coral cover, comprised of 11% cover of massive Porites spp., 7%
Porites rus, 4% Montipora spp. and 3% Pocillopora spp. There
was\\u2009~\\u20097% cover of crustose coralline algae (CCA), with 4% Porolithon
onkodes and 3% Lithophyllum kotschyanum, and ~\\u20095% cover of small pieces
(i.e., ~\\u20091-cm diameter) of coral rubble (Fig. S2, Carpenter et al.,
2018).\"";
    String awards_0_award_nid "536317";
    String awards_0_award_number "OCE-1415268";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1415268";
    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 
"Carpenter 2018: Carbonate chemistry 
  PI: Robert Carpenter 
  Data Version 1: 2020-02-25";
    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 "2019-02-01T23:13:17Z";
    String date_modified "2020-03-06T18:22:59Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.754694.1";
    String history 
"2021-10-15T20:20:21Z (local files)
2021-10-15T20:20:21Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_754694.das";
    String infoUrl "https://www.bco-dmo.org/dataset/754694";
    String institution "BCO-DMO";
    String instruments_0_acronym "pH Sensor";
    String instruments_0_dataset_instrument_description "Handheld electrode (DG 115-SC electrode (Mettler-Toledo)).";
    String instruments_0_dataset_instrument_nid "794304";
    String instruments_0_description "General term for an instrument that measures the pH or how acidic or basic a solution is.";
    String instruments_0_instrument_name "pH Sensor";
    String instruments_0_instrument_nid "674";
    String instruments_0_supplied_name "DG 115-SC electrode";
    String instruments_1_acronym "Salinity Sensor";
    String instruments_1_dataset_instrument_description "Bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA)";
    String instruments_1_dataset_instrument_nid "794305";
    String instruments_1_description "Category of instrument that simultaneously measures electrical conductivity and temperature in the water column to provide temperature and salinity data.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/350/";
    String instruments_1_instrument_name "Salinity Sensor";
    String instruments_1_instrument_nid "710";
    String instruments_1_supplied_name "Orionstar A212";
    String keywords "24h, bco, bco-dmo, biological, carbon, carbon dioxide, chemical, co2, data, dataset, date, day, dic, DIC_24h, DIC_Day, DIC_Night, dioxide, dmo, erddap, flume, management, night, oceanography, office, omega, Omega_24h, Omega_Day, Omega_Night, pCO2_24h, pCO2_Day, pCO2_Night, pH_24h, pH_Day, pH_night, preliminary, TA_24h, TA_Day, TA_Night, time, treatment";
    String license "https://www.bco-dmo.org/dataset/754694/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/754694";
    String param_mapping "{'754694': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/754694/parameters";
    String people_0_affiliation "California State University Northridge";
    String people_0_affiliation_acronym "CSU-Northridge";
    String people_0_person_name "Robert Carpenter";
    String people_0_person_nid "51535";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "California State University Northridge";
    String people_1_affiliation_acronym "CSU-Northridge";
    String people_1_person_name "Peter J. Edmunds";
    String people_1_person_nid "51536";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "California State University Northridge";
    String people_2_affiliation_acronym "CSU-Northridge";
    String people_2_person_name "Griffin Srednick";
    String people_2_person_nid "737324";
    String people_2_role "Technician";
    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 "Amber York";
    String people_3_person_nid "643627";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "OA_Corals";
    String projects_0_acronym "OA_Corals";
    String projects_0_description 
"While coral reefs have undergone unprecedented changes in community structure in the past 50 y, they now may be exposed to their gravest threat since the Triassic. This threat is increasing atmospheric CO2, which equilibrates with seawater and causes ocean acidification (OA). In the marine environment, the resulting decline in carbonate saturation state (Omega) makes it energetically less feasible for calcifying taxa to mineralize; this is a major concern for coral reefs. It is possible that the scleractinian architects of reefs will cease to exist as a mineralized taxon within a century, and that calcifying algae will be severely impaired. While there is a rush to understand these effects and make recommendations leading to their mitigation, these efforts are influenced strongly by the notion that the impacts of pCO2 (which causes Omega to change) on calcifying taxa, and the mechanisms that drive them, are well-known. The investigators believe that many of the key processes of mineralization on reefs that are potentially affected by OA are only poorly known and that current knowledge is inadequate to support the scaling of OA effects to the community level. It is vital to measure organismal-scale calcification of key taxa, elucidate the mechanistic bases of these responses, evaluate community scale calcification, and finally, to conduct focused experiments to describe the functional relationships between these scales of mineralization.
This project is a 4-y effort focused on the effects of Ocean Acidification (OA) on coral reefs at multiple spatial and functional scales. The project focuses on the corals, calcified algae, and coral reefs of Moorea, French Polynesia, establishes baseline community-wide calcification data for the detection of OA effects on a decadal-scale, and builds on the research context and climate change focus of the Moorea Coral Reef LTER.
This project is a hypothesis-driven approach to compare the effects of OA on reef taxa and coral reefs in Moorea. The PIs will utilize microcosms to address the impacts and mechanisms of OA on biological processes, as well as the ecological processes shaping community structure. Additionally, studies of reef-wide metabolism will be used to evaluate the impacts of OA on intact reef ecosystems, to provide a context within which the experimental investigations can be scaled to the real world, and critically, to provide a much needed reference against which future changes can be gauged.
The following publications and data resulted from this project:
2016    Edmunds P.J. and 15 others.  Integrating the effects of ocean acidification across functional scales on tropical coral reefs.  Bioscience (in press Feb 2016) **not yet available**
2016    Comeau S, Carpenter RC, Lantz CA, Edmunds PJ.  Parameterization of the response of calcification to temperature and pCO2 in the coral Acropora pulchra and the alga Lithophyllum kotschyanum.  Coral Reefs (in press Feb 2016)
2016    Brown D., Edmunds P.J.  Differences in the responses of three scleractinians and the hydrocoral Millepora platyphylla to ocean acidification.  Marine Biology (in press Feb 2016) **available soon**MarBio. 2016: calcification and biomassMarBio. 2016: tank conditions
2016    Comeau, S., Carpenter, R.C., Edmunds, P.J.  Effects of pCO2 on photosynthesis and respiration of tropical scleractinian corals and calcified algae.  ICES Journal of Marine Science doi:10.1093/icesjms/fsv267
2015    Evensen NR, Edmunds PJ, Sakai K.  Effects of pCO2 on the capacity for spatial competition by the corals Montipora aequituberculata and massive Porites spp. Marine Ecology Progress Series 541: 123–134. doi: 10.3354/meps11512MEPS 2015: chemistryMEPS 2015: field surveyMEPS 2015: linear extensionDownload data for this publication (Excel file)
2015    Comeau S., Lantz C. A., Edmunds P. J., Carpenter R. C. Framework of barrier reefs threatened by ocean acidification. Global Change Biology doi: 10.1111/gcb.13023
2015    Comeau, S., Carpenter, R. C., Lantz, C. A., and Edmunds, P. J. Ocean acidification accelerates dissolution of experimental coral reef communities, Biogeosciences, 12, 365-372, doi:10.5194/bg-12-365-2015.calcification rates - flume exptcarbonate chemistry - flume expt
External data repository: http://doi.pangaea.de/10.1594/PANGAEA.847986
2014    Comeau S, Carpenter RC, Edmunds PJ.  Effects of irradiance on the response of the coral Acropora pulchra and the calcifying alga Hydrolithon reinboldii to temperature elevation and ocean acidification.  Journal of Experimental Marine Biology and Ecology (in press)
2014    Comeau S, Carpenter RC, Nojiri Y, Putnam HM, Sakai K, Edmunds PJ.  Pacific-wide contrast highlights resistance of reef calcifiers to ocean acidification.  Royal Society of London (B) 281: doi.org/10.1098/rspb.2014.1339
External data repository: http://doi.pangaea.de/10.1594/PANGAEA.832834
2014    Comeau, S., Edmunds, P. J., Lantz, C. A., & Carpenter, R. C. Water flow modulates the response of coral reef communities to ocean acidification. Scientific Reports, 4. doi:10.1038/srep06681calcification rates - flume exptcarbonate chemistry - flume expt
2014    Comeau, S., Edmunds, P. J., Spindel, N. B., & Carpenter, R. C. Fast coral reef calcifiers are more sensitive to ocean acidification in short-term laboratory incubations. Limnology and Oceanography, 59(3), 1081–1091. doi:10.4319/lo.2014.59.3.1081algae_calcificationcoral_calcification
External data repository: http://doi.pangaea.de/10.1594/PANGAEA.832584
2014    Comeau S, Edmunds PJ, Spindel NB, Carpenter RC.  Diel pCO2 oscillations modulate the response of the coral Acropora hyacinthus to ocean acidification. Marine Ecology Progress Series 453: 28-35
2013    Comeau, S, Carpenter, RC, Edmunds PJ. Response to coral reef calcification: carbonate, bicarbonate and proton flux under conditions of increasing ocean acidification. Proceedings of the Royal Society of London 280: doi.org/10.1098/rspb.2013.1153
2013    Comeau S, Carpenter RC. Edmunds PJ.  Effects of feeding and light intensity on the response of the coral Porites rus to ocean acidification.  Marine Biology 160: 1127-1134
External data repository: http://doi.pangaea.de/10.1594/PANGAEA.829815
2013    Comeau, S., Edmunds, P. J., Spindel, N. B., Carpenter, R. C. The responses of eight coral reef calcifiers to increasing partial pressure of CO2 do not exhibit a tipping point. Limnol. Oceanogr. 58, 388–398.algae_calcificationcoral_calcification
External data repository: http://doi.pangaea.de/10.1594/PANGAEA.833687
2012    Comeau, S., Carpenter, R. C., & Edmunds, P. J. Coral reef calcifiers buffer their response to ocean acidification using both bicarbonate and carbonate. Proceedings of the Royal Society B: Biological Sciences, 280(1753), 20122374. doi:10.1098/rspb.2012.2374carbonate_chemistrylight_dark_calcificationmean_calcification
External data repository: http://doi.pangaea.de/10.1594/PANGAEA.832834";
    String projects_0_end_date "2014-12";
    String projects_0_geolocation "Moorea, French Polynesia";
    String projects_0_name "The effects of ocean acidification on the organismic biology and community ecology of corals, calcified algae, and coral reefs";
    String projects_0_project_nid "2242";
    String projects_0_start_date "2011-01";
    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 "This dataset carbonate chemistry data from outdoor flumes at the UCB Gump Research Station Moorea, French Polynesia. These measurements were taken during an experiment designed to measure coral reef community metabolism responses to ocean acidification over a 4-month period from November 13th, 2015 to March 15th, 2016. These data were published in Carpenter et al. (2018).";
    String title "Carbonate chemistry from outdoor flumes at the UCB Gump Research Station Moorea, French Polynesia from November of 2015 to March of 2016";
    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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