http://lod.bco-dmo.org/id/dataset/719130
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-11-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Photosynthesis-Irradiance curve (P-E) raw data for coral Orbicella faveolata from Varadero and Rosario reef sites, Colombia, Oct. 2016 and May 2017 (Varadero Reef project)
2018-03-05
publication
2018-03-05
revision
BCO-DMO Linked Data URI
2018-03-05
creation
http://lod.bco-dmo.org/id/dataset/719130
Mónica Medina
Pennsylvania State University
principalInvestigator
Roberto Iglesias-Prieto
Pennsylvania State University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Medina, M., Iglesias-Prieto, R. (2018) Photosynthesis-Irradiance curve (P-E) raw data for coral Orbicella faveolata from Varadero and Rosario reef sites, Colombia, Oct. 2016 and May 2017 (Varadero Reef project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2018-03-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/719130 [access date]
Photosynthesis-Irradiance curve Dataset Description: <p>This dataset contains the raw data from the Photosynthesis-Irradiance (P-E) curves for each coral Orbicella faveolata from Varadero and Rosario Reef sites.</p>
<p><strong>Related Reference:</strong><br />
Pizarro V, Rodríguez SC, López-Victoria M, Zapata FA, Zea S, Galindo-Martínez CT, Iglesias-Prieto R, Pollock J, Medina M. (2017) Unraveling the structure and composition of Varadero Reef, an improbable and imperiled coral reef in the Colombian Caribbean. PeerJ 5:e4119 <a href="https://doi.org/10.7717/peerj.4119" target="_blank">https://doi.org/10.7717/peerj.4119</a></p> Methods and Sampling: <p>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. 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. The depth of the particular transplant site in Varadero is 3.5m, while in Abanico, a nearby site with low coral cover, and Rosario, a site inside a marine protected area located south-west with relatively high coral cover, is 3m and 12m.</p>
<p>The P-E curves were constructed by measuring the consumption/evolution of oxygen by each coral fragment used in the transplant experiment after exposing them to different levels of increasing light intensity. A high precision fiber-optical sensor connected to a PC-based oxygen meter was used to measure the oxygen concentration at each light level in hermetic water-jacked chambers with filtered seawater (0.45µm) and controlled magnetic stirrers producing agitation. The temperature was maintained at 28°C. Dark respiration was calculated by averaging the oxygen consumption rate at the beginning (pre-illumination) and at the end (post-illumination) of each incubation. Photosynthetic descriptors were calculated from the P-E curves based on Iglesias-Prieto and Trench (1994) and Osinga et al. (2012).</p>
<p>The software Pyro Oxygen Logger (PyroScience GmbH, Germany) was used to manage the oximeter and data operations during incubations.</p>
<p><strong>Methodology Reference:</strong><br />
- Iglesias-Prieto, R. &amp; R.K. Trench. 1994. Acclimation and adaptation to irradiance in symbiotic dinoflagellates. I. Responses of the photosynthetic unit to changes in photon flux density. Mar Ecol Prog Ser 113: 163-175. Stable URL: http://www.jstor.org/stable/24849586.<br />
- Osinga, R., R. Iglesias-Prieto and S. Enríquez. 2012. Measuring photosynthesis in symbiotic invertebrates: a review of methodologies, rates and processes. 220-256. In: Najafpour, M.N. (Ed.) Applied Photosynthesis. InTech. 422 p. Full text url: http://library.wur.nl/WebQuery/wurpubs/fulltext/245530</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1642311 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1642311
completed
Mónica Medina
Pennsylvania State University
814-321-5684
326 Mueller
University Park
PA
16802
USA
momedinamunoz@gmail.com
pointOfContact
Roberto Iglesias-Prieto
Pennsylvania State University
814-777-0438
325 Mueller Lab
University Park
PA
16802
USA
rzi3@psu.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Species
Parent_Colony_id
Parent_tag_color
Fragment_id
Fragment_tag_color
Date_collected
Transplanted_from
Transplanted_to
Chamber_channel
Light_Level
Light_integ
Slope_O2_prod
Rate_O2_prod
cosine light sensor (Waltz)
Optical oxygen meter FireStingO2 (Pyroscience)
theme
None, User defined
species scientific name (binomial)
sample identification
tagid
date
site
No BCO-DMO term
irradiance
photosynthetic rate
featureType
BCO-DMO Standard Parameters
Light Meter
Oxygen Sensor
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
RAPID: Coral robustness: lessons from an "improbable" reef
https://osprey.bco-dmo.org/project/717028
RAPID: Coral robustness: lessons from an "improbable" reef
<p><em>NSF Award Abstract:</em><br />
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.</p>
<p>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.</p>
Varadero Reef
largerWorkCitation
project
eng; USA
biota
oceans
-75.5819
-75.5819
10.3028
10.3028
2016-10-01
2017-05-01
Caribbean Sea (10°18’10”N, 75°34’ 55”W)
0
BCO-DMO catalogue of parameters from Photosynthesis-Irradiance curve (P-E) raw data for coral Orbicella faveolata from Varadero and Rosario reef sites, Colombia, Oct. 2016 and May 2017 (Varadero Reef project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/729533.rdf
Name: Species
Units: unitless
Description: <p>taxonomic species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/729534.rdf
Name: Parent_Colony_id
Units: unitless
Description: <p>parent colony number</p>
http://lod.bco-dmo.org/id/dataset-parameter/729535.rdf
Name: Parent_tag_color
Units: unitless
Description: <p>parent colony tag color</p>
http://lod.bco-dmo.org/id/dataset-parameter/729536.rdf
Name: Fragment_id
Units: unitless
Description: <p>fragment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/729537.rdf
Name: Fragment_tag_color
Units: unitless
Description: <p>fragment tag color</p>
http://lod.bco-dmo.org/id/dataset-parameter/729538.rdf
Name: Date_collected
Units: unitless
Description: <p>date collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/729539.rdf
Name: Transplanted_from
Units: unitless
Description: <p>location coral fragment was transplanted from</p>
http://lod.bco-dmo.org/id/dataset-parameter/729540.rdf
Name: Transplanted_to
Units: unitless
Description: <p>location coral fragment was transplanted to</p>
http://lod.bco-dmo.org/id/dataset-parameter/729541.rdf
Name: Chamber_channel
Units: unitless
Description: <p>sample chamber identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/729542.rdf
Name: Light_Level
Units: unitless
Description: <p>light level</p>
http://lod.bco-dmo.org/id/dataset-parameter/729543.rdf
Name: Light_integ
Units: micromol quanta/meter^2/second
Description: <p>light intensity</p>
http://lod.bco-dmo.org/id/dataset-parameter/729544.rdf
Name: Slope_O2_prod
Units: micromol O2/centimeter^2/hour
Description: <p>rate of oxygen production curve</p>
http://lod.bco-dmo.org/id/dataset-parameter/729545.rdf
Name: Rate_O2_prod
Units: micromol O2/centimeter^2/hour
Description: <p>rate of oxygen production was normalized per surface area</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
72879
https://datadocs.bco-dmo.org/file/6YYMlXJTPqJPXn/PE_raw_all_v2.csv
PE_raw_all_v2.csv
Primary data file for dataset ID 719130
download
https://osprey.bco-dmo.org/dataset/719130/data/download
download
onLine
dataset
<p>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. 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. The depth of the particular transplant site in Varadero is 3.5m, while in Abanico, a nearby site with low coral cover, and Rosario, a site inside a marine protected area located south-west with relatively high coral cover, is 3m and 12m.</p>
<p>The P-E curves were constructed by measuring the consumption/evolution of oxygen by each coral fragment used in the transplant experiment after exposing them to different levels of increasing light intensity. A high precision fiber-optical sensor connected to a PC-based oxygen meter was used to measure the oxygen concentration at each light level in hermetic water-jacked chambers with filtered seawater (0.45µm) and controlled magnetic stirrers producing agitation. The temperature was maintained at 28°C. Dark respiration was calculated by averaging the oxygen consumption rate at the beginning (pre-illumination) and at the end (post-illumination) of each incubation. Photosynthetic descriptors were calculated from the P-E curves based on Iglesias-Prieto and Trench (1994) and Osinga et al. (2012).</p>
<p>The software Pyro Oxygen Logger (PyroScience GmbH, Germany) was used to manage the oximeter and data operations during incubations.</p>
<p><strong>Methodology Reference:</strong><br />
- Iglesias-Prieto, R. &amp; R.K. Trench. 1994. Acclimation and adaptation to irradiance in symbiotic dinoflagellates. I. Responses of the photosynthetic unit to changes in photon flux density. Mar Ecol Prog Ser 113: 163-175. Stable URL: http://www.jstor.org/stable/24849586.<br />
- Osinga, R., R. Iglesias-Prieto and S. Enríquez. 2012. Measuring photosynthesis in symbiotic invertebrates: a review of methodologies, rates and processes. 220-256. In: Najafpour, M.N. (Ed.) Applied Photosynthesis. InTech. 422 p. Full text url: http://library.wur.nl/WebQuery/wurpubs/fulltext/245530</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- blank values were replaced with no data value 'nd'</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
cosine light sensor (Waltz)
cosine light sensor (Waltz)
PI Supplied Instrument Name: cosine light sensor (Waltz) Instrument Name: Light Meter Instrument Short Name:Light Meter Instrument 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)
Optical oxygen meter FireStingO2 (Pyroscience)
Optical oxygen meter FireStingO2 (Pyroscience)
PI Supplied Instrument Name: Optical oxygen meter FireStingO2 (Pyroscience) PI Supplied Instrument Description:Used to measure oxygen evolution. Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed