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Dataset Title:  Photosynthesic parameters (calculated alpha, Pmax, Respiration, Ek and Ec) for
each P-E curve for coral Orbicella faveolata from Rosaria and Varadero reef
sites and Cartagena Bay, Colombia, 2016 and 2017
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_719161)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Source_site {
    String bcodmo_name "site";
    String description "coral collection site";
    String long_name "Source Site";
    String units "unitless";
  Tag_num {
    Byte _FillValue 127;
    Byte actual_range 2, 75;
    String bcodmo_name "sample";
    String description "coral tag number";
    String long_name "Tag Num";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  Tag_color {
    String bcodmo_name "sample";
    String description "tag color";
    String long_name "Tag Color";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  Destination_site {
    String bcodmo_name "site";
    String description "relocation site";
    String long_name "Destination Site";
    String units "unitless";
  Data_Timepoint {
    String bcodmo_name "unknown";
    String description "data collection timepoint: T1= pre-transplant (Oct. 2016); T2= 7 months post-transplant (May 2017)";
    String long_name "Data Timepoint";
    String units "unitless";
  Date_collected {
    String bcodmo_name "date";
    String description "month and year of data collection";
    String long_name "Date Collected";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  Area_cm2 {
    Float32 _FillValue NaN;
    Float32 actual_range 1.73, 22.72;
    String bcodmo_name "surface_area";
    String description "area of coral fragment";
    String long_name "Area Cm2";
    String units "centimeter^2";
  Chl_a {
    Float32 _FillValue NaN;
    Float32 actual_range 49.93, 293.38;
    String bcodmo_name "chlorophyll a";
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Chlorophyll a content per unit area";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
    String units "milligrams Chla meter^-2";
  D_675 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.76, 1.79;
    String bcodmo_name "absorbance";
    String description "Absorbance at 675 nm";
    String long_name "D 675";
    String units "unitless";
  a_star_675 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.008, 0.062;
    String bcodmo_name "absorbance";
    String description "Specific absorption coefficient of Chl a";
    String long_name "A Star 675";
    String units "meters^2 milligram Chla^-1";
  alpha {
    Float32 _FillValue NaN;
    Float32 actual_range 0.021, 0.067;
    String bcodmo_name "alpha";
    String description "Photosynthetic efficiency";
    String long_name "Alpha";
    String units "mol Oxygen mol quanta^-1";
  Ec {
    Float32 _FillValue NaN;
    Float32 actual_range 42.63, 117.45;
    String bcodmo_name "irradiance";
    String description "Compensating irradiance";
    String long_name "Ec";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/VSRW/";
    String units "micromol quanta meter^-2 second^-1";
  Ek {
    Float32 _FillValue NaN;
    Float32 actual_range 134.61, 362.11;
    String bcodmo_name "irradiance";
    String description "Saturating irradiance";
    String long_name "Ek";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/VSRW/";
    String units "micromol quanta meter^-2 second^-1";
  Rd {
    Float32 _FillValue NaN;
    Float32 actual_range -4.92, -1.74;
    String bcodmo_name "respiration";
    String description "Respiration rate (dark)";
    String long_name "RD";
    String units "micromol Oxygen meter^-2 second^-1";
  Pmax {
    Float32 _FillValue NaN;
    Float32 actual_range 3.28, 9.15;
    String bcodmo_name "Pmax";
    String description "Maximum photosynthesis";
    String long_name "Pmax";
    String units "micromol Oxygen meter^-2 second^-1";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"The Varadero Reef is located south-west of the Cartagena Bay close to the
southern strait that connects the Bay to the Caribbean Sea in Colombia
(10\\u00b018\\u201923.3\\u201dN, 75\\u00b035\\u201908.0\\u201dW). The Bay is a
receiving estuary from the Magdalena River through the Canal del Dique, a man-
made channel whose construction and operation dates back almost a century.
Three study sites with contrasting light regimes were considered in order to
evaluate the role of the light-environment perturbation associated with the
Dique channel freshwater plume on the photosynthetic performance of corals
from Varadero: 1) Varadero reef at 3.5m depth close to the Dique channel mouth
(10\\u00b018\\u201923.3\\u201dN, 75\\u00b035\\u201908.0\\u201dW), 2) Rosario reef at
12m depth as clear-control site 21 km southwest from Varadero
(10\\u00b011'12.1\\\"N, 75\\u00b044'43.0\\\"W), and 3) Cartagena Bay at 3m depth,
the closest\\u00a0 site to the Dique channel mouth and most turbid among the
three sites (10\\u00b018'5.80\\\"N, 75\\u00b034'37.10\\\"W).
The values of the photosynthetic efficiency (alpha) are expressed in umol O2
umol quanta-1, the compensating irradiance (Ec) in umol quanta m-2 s-1, the
saturating irradiance (Ek) in umol quanta m-2 s-1, the average respiration
rate (R-avg) as well as the respiration pre- and post-illumination (R0 and Rf)
are expressed in umol O2 m-2 s-1, and the net and gross maximum photosynthesis
rates (Pmax(n) and Pmax(gross)) are expressed in umoles O2 m-2 s-1.
Photosynthetic parameters of corals were obtained from PE (photosynthesis vs.
irradiance) curves conducted under laboratory conditions. A custom-made water-
jacket acrylic chamber with four independent hermetic compartments (~650 ml
each) was used to run the PE curves, maintaining a constant temperature of 28
\\u00b0C, close to natural conditions, with an external circulating water bath
(Isotemp, Fisher Scientific). During each incubation, corals were submerged on
filtered seawater (0.45 \\u00b5m) under constant agitation by magnetic
stirrers. Ten levels of irradiance between 0 and ~1400 \\u00b5mol quanta m-2
s-1 were supplied at 10-min intervals with four 26 W LED bulbs (UL PAR38, LED
Wholesalers Inc, USA). The light intensity was controlled with a custom-made
software. The LEDs were operated in continuous mode with a multifunction I/O
card (USB-6001, National Instruments Corp., USA) to avoid potential artefacts
related to the effect of different pulsating frequencies on photosynthesis.
Oxygen concentrations inside the compartments within the chamber were measured
with a 4-channel fiber optical oxygen meter system (FireSting, Pyroscience,
Germany). The photosynthetic efficiency (\\u03b1), compensating irradiance
(Ec), saturating irradiance (Ek), respiration rates (Rd), and maximum
photosynthetic rates (Pmax), were calculated from the light-limited and light-
saturated regions of the PE curves. Chlorophyll a (Chl a) content per unit of
coral surface area was determined after obtaining coral tissue slurries with
the help of an air gun connected to a scuba tank. Pigment extraction was
performed in acetone/dimethyl sulfoxide (95:5 vol/vol) after homogenizing the
slurries with a Tissue-Tearor Homogenizer (BioSpec Inc, USA). Chl a density
was estimated spectrophotometrically with a modular spectrometer (Flame-T-UV-
VIS, Ocean Optics Inc., USA). The specific absorption coefficient of Chl a
(a*Chl a) was calculated using the equation: a*Chl a = (D675/\\u03c1) \\u00b7
ln(10), where D675 is the estimated absorbance value of corals at 675 nm,
calculated from reflectance (R) measurements as [D675 = log (1/R675)], and
\\u03c1 is the pigment content per projected surface area (mg Chl a m-2).
The software Pyro Oxygen Logger was used to operate the fiber optical oxygen
meter system. The software OceanView was used to operate there modular
    String awards_0_award_nid "717027";
    String awards_0_award_number "OCE-1642311";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642311";
    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 "Michael E. Sieracki";
    String awards_0_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"Photosynthetic parameters from Orbicella faveolata coral fragments 
   For reciprocal transplant experiment of coral fragments at Varadero, Rosario and Cartagena Bay, Oct. 2016 and May 2017 
   PI: M. Medina, R. Iglesias-Prieto, T. Lopez (Penn State) 
   version date: 2020-01-16";
    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 "2017-11-13T21:21:20Z";
    String date_modified "2020-03-04T21:56:55Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.719161.3";
    String history 
"2020-08-06T10:22:13Z (local files)
2020-08-06T10:22:13Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_719161.das";
    String infoUrl "https://www.bco-dmo.org/dataset/719161";
    String institution "BCO-DMO";
    String instruments_0_acronym "Light Meter";
    String instruments_0_dataset_instrument_nid "719169";
    String instruments_0_description "Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)";
    String instruments_0_instrument_name "Light Meter";
    String instruments_0_instrument_nid "703";
    String instruments_0_supplied_name "cosine light sensor (Waltz)";
    String instruments_1_acronym "Dissolved Oxygen Sensor";
    String instruments_1_dataset_instrument_description "Used to measure oxygen evolution.";
    String instruments_1_dataset_instrument_nid "719168";
    String instruments_1_description "An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed";
    String instruments_1_instrument_name "Dissolved Oxygen Sensor";
    String instruments_1_instrument_nid "705";
    String instruments_1_supplied_name "Optical oxygen meter FireStingO2 (Pyroscience)";
    String keywords "a_star_675, alpha, area, Area_cm2, bco, bco-dmo, biological, chemical, chemistry, Chl_a, chlorophyll, cm2, collected, color, concentration, concentration_of_chlorophyll_in_sea_water, D_675, data, Data_Timepoint, dataset, date, Date_collected, destination, Destination_site, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, erddap, management, num, ocean, oceanography, oceans, office, pmax, preliminary, science, sea, seawater, site, source, Source_site, star, tag, Tag_color, Tag_num, timepoint, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/719161/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/719161";
    String param_mapping "{'719161': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/719161/parameters";
    String people_0_affiliation "Pennsylvania State University";
    String people_0_affiliation_acronym "PSU";
    String people_0_person_name "Mónica Medina";
    String people_0_person_nid "472486";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Pennsylvania State University";
    String people_1_affiliation_acronym "PSU";
    String people_1_person_name "Roberto Iglesias-Prieto";
    String people_1_person_nid "717031";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Pennsylvania State University";
    String people_2_affiliation_acronym "PSU";
    String people_2_person_name "Tomás Lopez Lodoño";
    String people_2_person_nid "732860";
    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 "Nancy Copley";
    String people_3_person_nid "50396";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Varadero Reef";
    String projects_0_acronym "Varadero Reef";
    String projects_0_description 
"NSF Award Abstract:
Coral reefs provide invaluable services to coastal communities, but coral populations worldwide are in a state of unprecedented decline. Studying resilient reefs is of primary importance for coral conservation and restoration efforts. A unique natural experiment in coral resilience to stress has been playing out in Cartagena Bay, Colombia since the Spanish conquistadors diverted the Magadalena River into the Bay in 1582. Varadero Reef at the southern mouth of the Bay has survived centuries of environmental insults and changing conditions with up to 80% coral cover. This reef provides an ideal system to test biological robustness theory. Given that Varadero is a highly perturbed system, we hypothesize that while likely more robust to perturbation than nearby pristine reefs, it will be less physiologically efficient. Some of the large star coral colonies (Orbicella faveolata) at this site have existed since before the construction of the Canal del Dique. These coral specimens contain invaluable information regarding the conditions of the Magdalena River wathershed and its construction in the XIV century. Changes in turbidity of the plume associated with the urban industrial and agricultural development of Colombia can be documented as variations in calcification rates and changes in the microstructure of the skeleton. The Colombian government has announced the approval for the construction of a shipping channel that will go right over this reef, with the goal to start dredging as early as Fall 2016 or early 2017. The RAPID funding mechanism would enable immediate collection of data and information of why this reef has survived centuries of environmental stress that can shed light on what genotype combinations of coral and its microbial constituents will fare better in similar conditions at other reef locations around the world. Coral reef conservation biology will benefit from this study by generating data for the development of stress diagnostic tools to identify resilient corals. This project will help broaden participation in science by training a diverse cohort of students to work effectively in the global arena while fostering productive collaborations with several Colombian researchers and educational institutions. Students will also gain cultural empathy and sensitivity through direct engagement with the members of society who are most directly impacted by coral reef degradation (e.g. fishermen). Student researchers from Penn State University will work alongside their Colombian counterparts to develop a series of bilingual blog posts to record the cultural and scientific aspects of this project's research expeditions. The blog postings will be submitted for wide dissemination to the Smithsonian's Ocean Portal where Penn State students have published in the past. An educational coral kit developed by the Medina Lab and extensively tested in schools in the US has been translated into Spanish and will be used in local schools in Cartagena and vicinities. All expedition data and metadata will be incorporated into the Global Coral Microbiome Project's interactive web portal, a responsive outreach tool allows researchers, students and/or teachers to access a wealth of information about every coral colony we sample and to virtually explore coral reefs around the world from any internet-enabled device.
This research will generate information to understand functional traits related to symbioses stability under different perturbation regimes. Comparative analyses of microbiome modifications generated during the reciprocal transplantation will allow us to document possible differential responses of the holobionts to acute and chronic stressors relative to corals not exposed to significant levels of perturbation. The development of local bio-optical models of coral calcification and the characterization of the coral holobiont will permit the distinction between the effects in calcification attributed to local turbidity from those that can be ;attributed to differences in host genotype and/or microbial community composition and function. The information recorded in coral skeletons can be used to reconstruct the rates of agricultural, industrial and urban development of Colombia through the last 5 centuries as changes in the turbidity of the effluent of the Magdalena River.";
    String projects_0_end_date "2018-06";
    String projects_0_geolocation "Caribbean Sea (10°18’10”N, 75°34’ 55”W)";
    String projects_0_name "RAPID: Coral robustness: lessons from an \"improbable\" reef";
    String projects_0_project_nid "717028";
    String projects_0_start_date "2016-07";
    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 contains the results of the photosynthetic parameters calculated based on the analysis of the P-E curves from coral fragment of the species Orbicella faveolata used in the transplant experiment between three sites: Varadero (10\\u00b018'23.3\\N, 75\\u00b035'08.0\\W), Rosario (10\\u00b011'12.1\\N, 75\\u00b044'43.0\\W) and Abanico (10\\u00b018'5.80\\N, 75\\u00b034'37.10\\W). The tag number/color of each fragment, the date of data collection, and the sites of origin and destination are specified.";
    String title "Photosynthesic parameters (calculated alpha, Pmax, Respiration, Ek and Ec) for each P-E curve for coral Orbicella faveolata from Rosaria and Varadero reef sites and Cartagena Bay, Colombia, 2016 and 2017";
    String version "3";
    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.

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