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

ERDDAP > tabledap > Data Access Form ?

Dataset Title:  Calcification and linear extension rates for Oculina arbuscula corals grown
under different pCO2 levels; from the Cohen lab at WHOI in Woods Hole, MA (OA
Nutrition and Coral Calcification project)
Subscribe RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_490464)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Files | Make a graph
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   or a List of Values ?
   Maximum ?
 omega_Arg (dimensionless) ?          0.77    2.6
 species (dimensionless) ?      
   - +  ?
 sample (dimensionless) ?          "A01"    "D17"
 buoyant_wt_init (milligrams (mg)) ?          1180    3964
 buoyant_wt_final (milligrams (mg)) ?          1329    4340
 calcification_rate (percent (%)) ?          0.8    13.9
 linear_ext (micrometers (um)) ?          119    1550
Server-side Functions ?
 distinct() ?
? ("Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.")

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 {
  omega_Arg {
    Float32 _FillValue NaN;
    Float32 actual_range 0.77, 2.6;
    String bcodmo_name "OM_ar";
    String description "Saturation state with respect to aragonite.";
    String long_name "Omega Arg";
    String units "dimensionless";
  species {
    String bcodmo_name "species";
    String description "Name of the coral species.";
    String long_name "Species";
    String units "dimensionless";
  sample {
    String bcodmo_name "sample";
    String description "Unique sample indentifier.";
    String long_name "Sample";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "dimensionless";
  buoyant_wt_init {
    Int16 _FillValue 32767;
    Int16 actual_range 1180, 3964;
    String bcodmo_name "weight";
    String description "Initial buoyant weight of the coral; measured at the beginning of the experiment.";
    String long_name "Buoyant Wt Init";
    String units "milligrams (mg)";
  buoyant_wt_final {
    Int16 _FillValue 32767;
    Int16 actual_range 1329, 4340;
    String bcodmo_name "weight";
    String description "Final buoyant weight of the coral; measured at the end of the experiment.";
    String long_name "Buoyant Wt Final";
    String units "milligrams (mg)";
  calcification_rate {
    Float32 _FillValue NaN;
    Float32 actual_range 0.8, 13.9;
    String bcodmo_name "unknown";
    String description "Calcification rate measured as the percent change in buoyant weight over the course of the experiment (60 days).";
    String long_name "Calcification Rate";
    String units "percent (%)";
  linear_ext {
    Int16 _FillValue 32767;
    Int16 actual_range 119, 1550;
    String bcodmo_name "unknown";
    String description "Linear extension of the coral skeleton; distance from the 137Ba/138Ba spike to the outer edge of the coral skeleton. Measured on 4 specimens randomly selected from each of the treatments.";
    String long_name "Linear Ext";
    String units "micrometers (um)";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Methodology as described in Ries et al. (2010):  
 Zooxanthellate colonies of Oculina arbuscula were collected offshore of
Bogue Banks North Carolina in August 2007. After collection, the organisms
were transported to the Marine Calcification Laboratory at Woods Hole
Oceanographic Institution. After acclimation to the laboratory conditions,
fragments of each colony were harvested and mounted on acrylic slides.
Specimens were then transferred to the experimental seawaters for additional
acclimation for 14 days prior to the start of the experiment.
The O. arbuscula specimens were reared for 60 days from Sept. to Nov. 2007 in
four 38-liter glass aquaria filled with filtered seawater. The experimental
seawaters were bubbled continuously with air-CO2 mixtures of 409, 606, 903, or
2856 ppm pCO2. Temperature was maintained at 25 +/- 1 degrees Celsius. Aquaria
were illuminated 10 hours per day. Seventy-five percent seawater changes were
made every 14 days. Coral fragments were fed Artemia sp. every other day. The
experimental air-CO2 gas mixtures were formulated using Aalborg mass flow
controllers, yielding average seawater saturation states of 2.6, 2.3, 1.6, and
0.8 with respect to aragonite. Salinity, temperature, and pH of the seawaters,
and pCO2 of the mixed gases were measured weekly. Total alkalinity was
measured every 2 weeks. DIC, bicarbonate ion concentration, dissolved CO2,
aragonite saturation state, and pCO2 were calculated from the measured
parameters. Refer to Table 1 of [Ries et al. (2010)
](\\\\\"https://dx.doi.org/10.1007/s00338-010-0632-3\\\\\")for more detail on the
measured and calculated carbonate chemistry parameters, including mean, range,
and standard deviation.
A buoyant weighing method was used to estimate the corals' calcification
rates. Calcification rates were calculated as the percent change in buoyant
weight between the beginning and end of the experiment.
Each aquarium was dosed with 137BaCO3 for 14 days at the beginning of the
experiment. After 14 days, the 137Ba-enriched seawaters were replaced with
seawaters of natural Ba isotopic composition. This temporary increase in the
concentration of Barium-137 in the experimental seawaters resulted in a five-
fold spike in the ratio of Ba-137 to Ba-138 in the coral skeletons accreted
during the first 14 days of the experiment. This spike provided the baseline
from which linear extension of the coral skeletons could be measured. Four
coral specimens were randomly selected from each of the treatments and
sectioned parallel to the growth axis. 137Ba/138Ba ratios were measured using
laser ablation-inductively coupled plasma-mass spectrometry. To determine
linear extension, the time elapsed from the detection of the 137Ba/138Ba spike
and the outer edge of the coral skeleton was converted to distance by
multiplying the elapsed time by the scan rate of the laser.";
    String awards_0_award_nid "54896";
    String awards_0_award_number "OCE-1041106";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1041106";
    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 
"Coral (<i>Oculina arbuscula</i>) OA experiment 
 Lead PI: Anne Cohen (WHOI) 
 Co-PI: Dan McCorkle (WHOI) 
 Contact: Justin Ries (Northeastern Univ.) 
 Version: 06 Feb 2014";
    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 "2014-02-06T16:12:34Z";
    String date_modified "2019-11-21T17:47:32Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.490464.1";
    String history 
"2024-07-12T16:55:49Z (local files)
2024-07-12T16:55:49Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_490464.html";
    String infoUrl "https://www.bco-dmo.org/dataset/490464";
    String institution "BCO-DMO";
    String instruments_0_acronym "ICP Mass Spec";
    String instruments_0_dataset_instrument_description "The ratio of 137Ba to138Ba was measured using laser ablation inductively coupled plasma-mass spectrometry (Thermo-Finnegan Element2 LA-ICP-MS; beam diameter = 5 lm; scan speed = 6 lm/sec; intensity = 35%; frequency 8 Hz).";
    String instruments_0_dataset_instrument_nid "490480";
    String instruments_0_description "An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB15/";
    String instruments_0_instrument_name "Inductively Coupled Plasma Mass Spectrometer";
    String instruments_0_instrument_nid "530";
    String instruments_0_supplied_name "ICP Mass Spec";
    String instruments_1_acronym "salinometer";
    String instruments_1_dataset_instrument_description "Salinity was determined using an Autosal conductivity meter in the WHOI Hydrographic Laboratory and/or using a refractometer.";
    String instruments_1_dataset_instrument_nid "490476";
    String instruments_1_description "The salinometer is an instrument for measuring the salinity of a water sample.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB30/";
    String instruments_1_instrument_name "Autosal salinometer";
    String instruments_1_instrument_nid "576";
    String instruments_1_supplied_name "Autosal conductivity meter";
    String instruments_2_acronym "Water Temp Sensor";
    String instruments_2_dataset_instrument_description "Temperature was measured with a partial-immersion mercury-glass thermometer (precision = +/- 0.3%, accuracy = +/- 0.4%).";
    String instruments_2_dataset_instrument_nid "490475";
    String instruments_2_description "General term for an instrument that measures the temperature of the water with which it is in contact (thermometer).";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/134/";
    String instruments_2_instrument_name "Water Temperature Sensor";
    String instruments_2_instrument_nid "647";
    String instruments_2_supplied_name "Mercury-glass thermometer";
    String instruments_3_acronym "Refractometer";
    String instruments_3_dataset_instrument_description "Salinity was determined using an Autosal conductivity meter in the WHOI Hydrographic Laboratory and/or using a refractometer calibrated with simultaneous measurements of conductivity (precision = +/- 0.3%; accuracy = +/- 0.4%).";
    String instruments_3_dataset_instrument_nid "490477";
    String instruments_3_description 
"A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.

In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.";
    String instruments_3_instrument_name "Refractometer";
    String instruments_3_instrument_nid "679";
    String instruments_3_supplied_name "Refractometer";
    String instruments_4_acronym "Benchtop pH Meter";
    String instruments_4_dataset_instrument_description "Seawater pH was determined weekly using an Orion pH electrode/meter (precision = +/- 0.005; accuracy = +/- 0.02).";
    String instruments_4_dataset_instrument_nid "490478";
    String instruments_4_description 
"An instrument consisting of an electronic voltmeter and pH-responsive electrode that gives a direct conversion of voltage differences to differences of pH at the measurement temperature.  (McGraw-Hill Dictionary of Scientific and Technical Terms) 
This instrument does not map to the NERC instrument vocabulary term for 'pH Sensor' which measures values in the water column.  Benchtop models are typically employed for stationary lab applications.";
    String instruments_4_instrument_name "Benchtop pH Meter";
    String instruments_4_instrument_nid "681";
    String instruments_4_supplied_name "pH Meter";
    String instruments_5_acronym "Aquarium";
    String instruments_5_dataset_instrument_description "Specimens of O. arbuscula were reared in each of four 38-liter glass aquaria (76 specimens in total) filled with 0.2 um-filtered seawater.";
    String instruments_5_dataset_instrument_nid "490472";
    String instruments_5_description "Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept";
    String instruments_5_instrument_name "Aquarium";
    String instruments_5_instrument_nid "711";
    String instruments_5_supplied_name "Aquarium";
    String instruments_6_acronym "MFC";
    String instruments_6_dataset_instrument_description "The experimental air-CO2 gases were formulated using Aalborg mass flow controllers. See more information from Aalborg.";
    String instruments_6_dataset_instrument_nid "490473";
    String instruments_6_description "Mass Flow Controller (MFC) - A device used to measure and control the flow of fluids and gases";
    String instruments_6_instrument_name "Mass Flow Controller";
    String instruments_6_instrument_nid "712";
    String instruments_6_supplied_name "MFC";
    String instruments_7_acronym "Scale";
    String instruments_7_dataset_instrument_description "Buoyant weights were determined using an aluminum wire hanging from a Cole Parmer bottom-loading scale.";
    String instruments_7_dataset_instrument_nid "490479";
    String instruments_7_description "An instrument used to measure weight or mass.";
    String instruments_7_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB13/";
    String instruments_7_instrument_name "Scale";
    String instruments_7_instrument_nid "714";
    String instruments_7_supplied_name "Scale";
    String instruments_8_acronym "Gas Analyzer";
    String instruments_8_dataset_instrument_description "Mixed gas pCO2 was measured with a Qubit S151 infrared analyzer (calibrated using certified air-CO2 gas standards; precision = +/- 2.0%; accuracy = +/- 1.8%). More information from the manufacturer: Q-S151 CO2 Analyzer";
    String instruments_8_dataset_instrument_nid "490474";
    String instruments_8_description "Gas Analyzers - Instruments for determining the qualitative and quantitative composition of gas mixtures.";
    String instruments_8_instrument_name "Gas Analyzer";
    String instruments_8_instrument_nid "720";
    String instruments_8_supplied_name "Qubit S151 infrared analyzer";
    String keywords "arg, bco, bco-dmo, biological, buoyant, buoyant_wt_final, buoyant_wt_init, calcification, calcification_rate, chemical, data, dataset, dmo, erddap, ext, final, init, linear, linear_ext, management, oceanography, office, omega, omega_Arg, preliminary, rate, sample, species";
    String license "https://www.bco-dmo.org/dataset/490464/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/490464";
    String param_mapping "{'490464': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/490464/parameters";
    String people_0_affiliation "Woods Hole Oceanographic Institution";
    String people_0_affiliation_acronym "WHOI";
    String people_0_person_name "Anne L Cohen";
    String people_0_person_nid "51428";
    String people_0_role "Lead Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI";
    String people_1_person_name "Daniel C McCorkle";
    String people_1_person_nid "51429";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Northeastern University";
    String people_2_affiliation_acronym "NEU";
    String people_2_person_name "Justin B. Ries";
    String people_2_person_nid "51345";
    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 "Shannon Rauch";
    String people_3_person_nid "51498";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "OA Nutrition and Coral Calcification";
    String projects_0_acronym "OA Nutrition and Coral Calcification";
    String projects_0_description 
"The project description is a modification of the original NSF award abstract.
This research project is part of the larger NSF funded CRI-OA collaborative research initiative and was funded as an Ocean Acidification-Category 1, 2010 award. Over the course of this century, all tropical coral reef ecosystems, whether fringing heavily populated coastlines or lining remote islands and atolls, face unprecedented threat from ocean acidification caused by rising levels of atmospheric CO2. In many laboratory experiments conducted to date, calcium carbonate production (calcification) by scleractinian (stony) corals showed an inverse correlation to seawater saturation state OMEGAar), whether OMEGAar was manipulated by acid or CO2 addition. Based on these data, it is predicted that coral calcification rates could decline by up to 80% of modern values by the end of this century. A growing body of new experimental data however, suggests that the coral calcification response to ocean acidification may be less straightforward and a lot more variable than previously recognized. In at least 10 recent experiments including our own, 8 different tropical and temperate species reared under nutritionally-replete but significantly elevated CO2 conditions (780-1200 ppm, OMEAGar ~1.5-2), continued to calcify at rates comparable to conspecifics reared under ambient CO2. These experimental results are consistent with initial field data collected on reefs in the eastern Pacific and southern Oman, where corals today live and accrete their skeletons under conditions equivalent to 2X and 3X pre-industrial CO2. On these high CO2, high nutrient reefs (where nitrate concentrations typically exceed 2.5 micro-molar), coral growth rates rival, and sometimes even exceed, those of conspecifics in low CO2, oligotrophic reef environments.
The investigators propose that a coral's energetic status, tightly coupled to the availability of inorganic nutrients and/or food, is a key factor in the calcification response to CO2-induced ocean acidification. Their hypothesis, if confirmed by the proposed laboratory investigations, implies that predicted changes in coastal and open ocean nutrient concentrations over the course of this century, driven by both climate impacts on ocean stratification and by increased human activity in coastal regions, could play a critical role in exacerbating and in some areas, modulating the coral reef response to ocean acidification. This research program builds on the investigators initial results and observations. The planned laboratory experiments will test the hypothesis that: (1) The coral calcification response to ocean acidification is linked to the energetic status of the coral host. The relative contribution of symbiont photosynthesis and heterotrophic feeding to a coral's energetic status varies amongst species. Enhancing the energetic status of corals reared under high CO2, either by stimulating photosynthesis with inorganic nutrients or by direct heterotrophic feeding of the host lowers the sensitivity of calcification to decreased seawater OMEGAar; (2) A species-specific threshold CO2 level exists over which enhanced energetic status can no longer compensate for decreased OMEGAar of the external seawater. Similarly, we will test the hypothesis that a nutrient threshold exists over which nutrients become detrimental for calcification even under high CO2 conditions; and (3) Temperature-induced reduction of algal symbionts is one stressor that can reduce the energetic reserve of the coral host and exacerbate the calcification response to ocean acidification.
The investigator's initial findings highlight the critical importance of energetic status in the coral calcification response to ocean acidification. Verification of these findings in the laboratory, and identification of nutrient and CO2 thresholds for a range of species will have immediate, direct impact on predictions of reef resilience in a high CO2 world. The research project brings together a diverse group of expertise in coral biogeochemistry, chemical oceanography, molecular biology and coral reproductive ecology to focus on a problem that has enormous societal, economic and conservation relevance.";
    String projects_0_end_date "2013-09";
    String projects_0_geolocation "global; experimental";
    String projects_0_name "An Investigation of the Role of Nutrition in the Coral Calcification Response to Ocean Acidification";
    String projects_0_project_nid "2183";
    String projects_0_start_date "2010-10";
    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 subsetVariables "species";
    String summary 
"Data from experiments examining the effect of CO2-induced ocean acidification
on the scleractinian coral Oculina arbuscula.
For more information on the experimental methods and results, see Ries et al.,
These data have also been deposited to PANGAEA where additional carbonate
system variables were calculated as described by Nisumaa et al. (2010). See:
    String title "Calcification and linear extension rates for Oculina arbuscula corals grown under different pCO2 levels; from the Cohen lab at WHOI in Woods Hole, MA (OA Nutrition and Coral Calcification 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
For example,
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 2.02
Disclaimers | Privacy Policy | Contact