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Title Sum-
Institution Dataset ID
     data   graph     files  public 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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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String 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
attribute NC_GLOBAL awards_0_award_nid String 717027
attribute NC_GLOBAL awards_0_award_number String OCE-1642311
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642311 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String 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
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2017-11-13T21:21:20Z
attribute NC_GLOBAL date_modified String 2020-03-04T21:56:55Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.719161.3
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/719161 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Light Meter
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 719169
attribute NC_GLOBAL instruments_0_description String 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)
attribute NC_GLOBAL instruments_0_instrument_name String Light Meter
attribute NC_GLOBAL instruments_0_instrument_nid String 703
attribute NC_GLOBAL instruments_0_supplied_name String cosine light sensor (Waltz)
attribute NC_GLOBAL instruments_1_acronym String Dissolved Oxygen Sensor
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used to measure oxygen evolution.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 719168
attribute NC_GLOBAL instruments_1_description String An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
attribute NC_GLOBAL instruments_1_instrument_name String Dissolved Oxygen Sensor
attribute NC_GLOBAL instruments_1_instrument_nid String 705
attribute NC_GLOBAL instruments_1_supplied_name String Optical oxygen meter FireStingO2 (Pyroscience)
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/719161/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/719161 (external link)
attribute NC_GLOBAL param_mapping String {'719161': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/719161/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Pennsylvania State University
attribute NC_GLOBAL people_0_affiliation_acronym String PSU
attribute NC_GLOBAL people_0_person_name String Mónica Medina
attribute NC_GLOBAL people_0_person_nid String 472486
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Pennsylvania State University
attribute NC_GLOBAL people_1_affiliation_acronym String PSU
attribute NC_GLOBAL people_1_person_name String Roberto Iglesias-Prieto
attribute NC_GLOBAL people_1_person_nid String 717031
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Pennsylvania State University
attribute NC_GLOBAL people_2_affiliation_acronym String PSU
attribute NC_GLOBAL people_2_person_name String Tomás Lopez Lodoño
attribute NC_GLOBAL people_2_person_nid String 732860
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Nancy Copley
attribute NC_GLOBAL people_3_person_nid String 50396
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Varadero Reef
attribute NC_GLOBAL projects_0_acronym String Varadero Reef
attribute NC_GLOBAL projects_0_description String 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.
attribute NC_GLOBAL projects_0_end_date String 2018-06
attribute NC_GLOBAL projects_0_geolocation String Caribbean Sea (10°18’10”N, 75°34’ 55”W)
attribute NC_GLOBAL projects_0_name String RAPID: Coral robustness: lessons from an "improbable" reef
attribute NC_GLOBAL projects_0_project_nid String 717028
attribute NC_GLOBAL projects_0_start_date String 2016-07
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String 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.
attribute NC_GLOBAL title String 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
attribute NC_GLOBAL version String 3
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Source_site   String  
attribute Source_site bcodmo_name String site
attribute Source_site description String coral collection site
attribute Source_site long_name String Source Site
attribute Source_site units String unitless
variable Tag_num   byte  
attribute Tag_num _FillValue byte 127
attribute Tag_num actual_range byte 2, 75
attribute Tag_num bcodmo_name String sample
attribute Tag_num description String coral tag number
attribute Tag_num long_name String Tag Num
attribute Tag_num nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Tag_num units String unitless
variable Tag_color   String  
attribute Tag_color bcodmo_name String sample
attribute Tag_color description String tag color
attribute Tag_color long_name String Tag Color
attribute Tag_color nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Tag_color units String unitless
variable Destination_site   String  
attribute Destination_site bcodmo_name String site
attribute Destination_site description String relocation site
attribute Destination_site long_name String Destination Site
attribute Destination_site units String unitless
variable Data_Timepoint   String  
attribute Data_Timepoint bcodmo_name String unknown
attribute Data_Timepoint description String data collection timepoint: T1= pre-transplant (Oct. 2016); T2= 7 months post-transplant (May 2017)
attribute Data_Timepoint long_name String Data Timepoint
attribute Data_Timepoint units String unitless
variable Date_collected   String  
attribute Date_collected bcodmo_name String date
attribute Date_collected description String month and year of data collection
attribute Date_collected long_name String Date Collected
attribute Date_collected nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute Date_collected units String unitless
variable Area_cm2   float  
attribute Area_cm2 _FillValue float NaN
attribute Area_cm2 actual_range float 1.73, 22.72
attribute Area_cm2 bcodmo_name String surface_area
attribute Area_cm2 description String area of coral fragment
attribute Area_cm2 long_name String Area Cm2
attribute Area_cm2 units String centimeter^2
variable Chl_a   float  
attribute Chl_a _FillValue float NaN
attribute Chl_a actual_range float 49.93, 293.38
attribute Chl_a bcodmo_name String chlorophyll a
attribute Chl_a colorBarMaximum double 30.0
attribute Chl_a colorBarMinimum double 0.03
attribute Chl_a colorBarScale String Log
attribute Chl_a description String Chlorophyll a content per unit area
attribute Chl_a long_name String Concentration Of Chlorophyll In Sea Water
attribute Chl_a nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/ (external link)
attribute Chl_a units String milligrams Chla meter^-2
variable D_675   float  
attribute D_675 _FillValue float NaN
attribute D_675 actual_range float 0.76, 1.79
attribute D_675 bcodmo_name String absorbance
attribute D_675 description String Absorbance at 675 nm
attribute D_675 long_name String D 675
attribute D_675 units String unitless
variable a_star_675   float  
attribute a_star_675 _FillValue float NaN
attribute a_star_675 actual_range float 0.008, 0.062
attribute a_star_675 bcodmo_name String absorbance
attribute a_star_675 description String Specific absorption coefficient of Chl a
attribute a_star_675 long_name String A Star 675
attribute a_star_675 units String meters^2 milligram Chla^-1
variable alpha   float  
attribute alpha _FillValue float NaN
attribute alpha actual_range float 0.021, 0.067
attribute alpha bcodmo_name String alpha
attribute alpha description String Photosynthetic efficiency
attribute alpha long_name String Alpha
attribute alpha units String mol Oxygen mol quanta^-1
variable Ec   float  
attribute Ec _FillValue float NaN
attribute Ec actual_range float 42.63, 117.45
attribute Ec bcodmo_name String irradiance
attribute Ec description String Compensating irradiance
attribute Ec long_name String Ec
attribute Ec nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/VSRW/ (external link)
attribute Ec units String micromol quanta meter^-2 second^-1
variable Ek   float  
attribute Ek _FillValue float NaN
attribute Ek actual_range float 134.61, 362.11
attribute Ek bcodmo_name String irradiance
attribute Ek description String Saturating irradiance
attribute Ek long_name String Ek
attribute Ek nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/VSRW/ (external link)
attribute Ek units String micromol quanta meter^-2 second^-1
variable Rd   float  
attribute Rd _FillValue float NaN
attribute Rd actual_range float -4.92, -1.74
attribute Rd bcodmo_name String respiration
attribute Rd description String Respiration rate (dark)
attribute Rd long_name String RD
attribute Rd units String micromol Oxygen meter^-2 second^-1
variable Pmax   float  
attribute Pmax _FillValue float NaN
attribute Pmax actual_range float 3.28, 9.15
attribute Pmax bcodmo_name String Pmax
attribute Pmax description String Maximum photosynthesis
attribute Pmax long_name String Pmax
attribute Pmax units String micromol Oxygen meter^-2 second^-1

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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