http://lod.bco-dmo.org/id/dataset/719349
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
2017-11-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
DEPRECATED: Optical properties of Orbicella faveoalta fragments (chl-a, Symbiodinium density, absorbance, and absorbance efficiency) from Rosaria and Varadero reef sites, Colombia, 2016 and 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/719349
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) DEPRECATED: Optical properties of Orbicella faveoalta fragments (chl-a, Symbiodinium density, absorbance, and absorbance efficiency) from Rosaria and Varadero reef sites, Colombia, 2016 and 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/719349 [access date]
DEPRECATED: Optical properties 2016 & 2017 Dataset Description: <p>DEPRECATED: This dataset has been resubmitted and combined with data originally in dataset&nbsp;<a href="https://www.bco-dmo.org/dataset/719161">https://www.bco-dmo.org/dataset/719161</a>.&nbsp;Please see <a href="https://www.bco-dmo.org/dataset/719161">https://www.bco-dmo.org/dataset/719161</a> for updated data.</p>
<p>This dataset contains the chlorophyll-a concentration, Symbiodinium density, absorbance, and absorbance efficiency of pigments extracted from coral Orbicella faveolata&nbsp;fragments collected at Rosaria and Varadero reef sites, Colombia, October 2016 and May 2017.</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 at Rosario, a site inside a marine protected area located south-west with relatively high coral cover, is 3m and 12m.</p>
<p>These are results of the preliminary analysis of the optical descriptors calculated from the raw data for each coral fragment:&nbsp;<br />
- The average (AVG) and standard deviation (SD) of Chlorophyll a density (mg Chl a m-2),<br />
- Estimated absorbance at 675 nm (D 675nm),<br />
- The specific absorption coefficient per unit of pigment (aChl a*, m2 mg Chla -1) and per symbiont (aSymb*, m2 cell-1),<br />
- Symbiodinium density (cell-cm2), and pigment content per symbiont (Ci) (pg Chl a cell-1).<br />
- Coral fragments area (cm2) was calculated using the aluminum foil technique (Marsh 1970).<br />
- Chlorophyll a concentration (mg Chl a cm-2)<br />
- The specific absorption coefficient (a*)</p>
<p>Chlorophyll a concentration was estimated spectrophotometrically after extraction from symbiont cells in acetone/dimethyl sulfoxide (95:5, Vol:Vol; Iglesias-Prieto et al. 1992), using the equations of Jeffrey and Humphrey (1975). Cell numbers were estimated from preserved samples (40 μml Lugol’s iodine) by direct count using a hemocytometer. Coral tissue area was estimated with the aluminum foil technique (Marsh, 1970). Reflectance (R) spectra of coral samples were measured between 400 and 750 nm (5 scans to average per measurement, boxcar width of 1.65 nm). Reflectance is expressed as the ratio of the radiance measured from the coral tissue surface, relative to the radiance obtained from the reference standard, a bleached O. faveolata skeleton. Absorbance (D) spectra were calculated as D=log (1/R), assuming that transmission through the skeleton is negligible. Optical determinations were estimated following Shibata (1969) and Enríquez et al. (2005).</p>
<p>The spectroscopy analyses were performed with a Flame mini-spectrophotometer (Ocean Optics Inc, Florida, USA). Cell counting was performed using a phase hemocytometer (Hausser Scientific, Horsham, USA) .</p>
<p>OceanView 1.6.7 was the software used for processing the tasks of the Flame spectrophotometer.</p>
<p><strong>Methodology References:</strong></p>
<p>- Iglesias-Prieto, R., Matta, J.L., Robins, W.A. and R.K. Trench. 1992. Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture. Proc Natl Acad Sci U S A. 89:10302-10305. Full text pdf: http://www.pnas.org/content/89/21/10302.full.pdf.<br />
- Jeffrey, S.W. and G.F. Humphrey. 1975. New spectrophotometric equations for determining chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem. Physiol. Pflanzen 167: 191-194. DOI:10.1016/S0015-3796(17)30778-3<br />
- Marsh, J. A. 1970. Primary productivity of reef-building calcareous red algae. Ecology 51: 255–265. DOI: 10.2307/1933661.<br />
- Shibata, K. 1969. Pigments and a UV-absorbing substance in corals and a blue-green alga living in the Great Barrier Reef. Plant Cell Physiol. 10: 325–335. DOI: 10.1093/oxfordjournals.pcp.a074411<br />
- Enríquez, S., E.R. Méndez and R. Iglesias-Prieto. 2005. Multiple scattering on coral skeletons enhances light absorption by symbiotic algae. Limnol. Oceanogr., 50(4), 2005, 1025–1032. DOI: 10.4319/lo.2005.50.4.1025</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
onGoing
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
Area_cm2
AVG_Chl_a
SD_Chl_a
absorbance_D_675nm
absorp_coeff_pigm_unit
Symb_density
pigment_Symb_Ci
absorp_coeff_aSymb
phase hemocytometer (Hausser Scientific, Horsham, USA)
mini spectrophotometer (Ocean Optics USB4000)
theme
None, User defined
species scientific name (binomial)
sample identification
tagid
date
site
surface_area
chlorophyll a
absorption coefficient
cell_concentration
pigment concentration
featureType
BCO-DMO Standard Parameters
Hemocytometer
Spectrophotometer
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 DEPRECATED: Optical properties of Orbicella faveoalta fragments (chl-a, Symbiodinium density, absorbance, and absorbance efficiency) from Rosaria and Varadero reef sites, Colombia, 2016 and 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/729464.rdf
Name: Species
Units: unitless
Description: <p>taxonomic species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/729465.rdf
Name: Parent_Colony_id
Units: unitless
Description: <p>parent colony number</p>
http://lod.bco-dmo.org/id/dataset-parameter/729466.rdf
Name: Parent_tag_color
Units: unitless
Description: <p>parent colony tag color</p>
http://lod.bco-dmo.org/id/dataset-parameter/729467.rdf
Name: Fragment_id
Units: unitless
Description: <p>fragment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/729468.rdf
Name: Fragment_tag_color
Units: unitless
Description: <p>fragment tag color</p>
http://lod.bco-dmo.org/id/dataset-parameter/729469.rdf
Name: Date_collected
Units: unitless
Description: <p>date collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/729470.rdf
Name: Transplanted_from
Units: unitless
Description: <p>location coral fragment was transplanted from</p>
http://lod.bco-dmo.org/id/dataset-parameter/729471.rdf
Name: Transplanted_to
Units: unitless
Description: <p>location coral fragment was transplanted to</p>
http://lod.bco-dmo.org/id/dataset-parameter/729472.rdf
Name: Area_cm2
Units: centimeters^2
Description: <p>area of coral fragment</p>
http://lod.bco-dmo.org/id/dataset-parameter/729473.rdf
Name: AVG_Chl_a
Units: milligrams Chla/meter^2
Description: <p>average chlorophyll-a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/729474.rdf
Name: SD_Chl_a
Units: milligrams Chla/meter^2
Description: <p>standard deviation of chlorophyll-a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/729475.rdf
Name: absorbance_D_675nm
Units: unitless
Description: <p>estimated absorbance at 675 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/729476.rdf
Name: absorp_coeff_pigm_unit
Units: meters^2/mg Chla
Description: <p>the specific absorption coefficient (a*) per unit of pigment</p>
http://lod.bco-dmo.org/id/dataset-parameter/729477.rdf
Name: Symb_density
Units: cells/centimeter^2
Description: <p>Symbiodinium density</p>
http://lod.bco-dmo.org/id/dataset-parameter/729478.rdf
Name: pigment_Symb_Ci
Units: pigment Chl-a/cell
Description: <p>pigment content per symbiont (Ci)</p>
http://lod.bco-dmo.org/id/dataset-parameter/729479.rdf
Name: absorp_coeff_aSymb
Units: meters^2/cell
Description: <p>the specific absorption coefficient per symbiont (absorption of symbiont * m2 cell-1)</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
9436
https://datadocs.bco-dmo.org/file/KAAGN1DTZ4vGkP/optical_compiled_all_v2.csv
optical_compiled_all_v2.csv
Primary data file for dataset ID 719349
download
https://osprey.bco-dmo.org/dataset/719349/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 at Rosario, a site inside a marine protected area located south-west with relatively high coral cover, is 3m and 12m.</p>
<p>These are results of the preliminary analysis of the optical descriptors calculated from the raw data for each coral fragment:&nbsp;<br />
- The average (AVG) and standard deviation (SD) of Chlorophyll a density (mg Chl a m-2),<br />
- Estimated absorbance at 675 nm (D 675nm),<br />
- The specific absorption coefficient per unit of pigment (aChl a*, m2 mg Chla -1) and per symbiont (aSymb*, m2 cell-1),<br />
- Symbiodinium density (cell-cm2), and pigment content per symbiont (Ci) (pg Chl a cell-1).<br />
- Coral fragments area (cm2) was calculated using the aluminum foil technique (Marsh 1970).<br />
- Chlorophyll a concentration (mg Chl a cm-2)<br />
- The specific absorption coefficient (a*)</p>
<p>Chlorophyll a concentration was estimated spectrophotometrically after extraction from symbiont cells in acetone/dimethyl sulfoxide (95:5, Vol:Vol; Iglesias-Prieto et al. 1992), using the equations of Jeffrey and Humphrey (1975). Cell numbers were estimated from preserved samples (40 μml Lugol’s iodine) by direct count using a hemocytometer. Coral tissue area was estimated with the aluminum foil technique (Marsh, 1970). Reflectance (R) spectra of coral samples were measured between 400 and 750 nm (5 scans to average per measurement, boxcar width of 1.65 nm). Reflectance is expressed as the ratio of the radiance measured from the coral tissue surface, relative to the radiance obtained from the reference standard, a bleached O. faveolata skeleton. Absorbance (D) spectra were calculated as D=log (1/R), assuming that transmission through the skeleton is negligible. Optical determinations were estimated following Shibata (1969) and Enríquez et al. (2005).</p>
<p>The spectroscopy analyses were performed with a Flame mini-spectrophotometer (Ocean Optics Inc, Florida, USA). Cell counting was performed using a phase hemocytometer (Hausser Scientific, Horsham, USA) .</p>
<p>OceanView 1.6.7 was the software used for processing the tasks of the Flame spectrophotometer.</p>
<p><strong>Methodology References:</strong></p>
<p>- Iglesias-Prieto, R., Matta, J.L., Robins, W.A. and R.K. Trench. 1992. Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture. Proc Natl Acad Sci U S A. 89:10302-10305. Full text pdf: http://www.pnas.org/content/89/21/10302.full.pdf.<br />
- Jeffrey, S.W. and G.F. Humphrey. 1975. New spectrophotometric equations for determining chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem. Physiol. Pflanzen 167: 191-194. DOI:10.1016/S0015-3796(17)30778-3<br />
- Marsh, J. A. 1970. Primary productivity of reef-building calcareous red algae. Ecology 51: 255–265. DOI: 10.2307/1933661.<br />
- Shibata, K. 1969. Pigments and a UV-absorbing substance in corals and a blue-green alga living in the Great Barrier Reef. Plant Cell Physiol. 10: 325–335. DOI: 10.1093/oxfordjournals.pcp.a074411<br />
- Enríquez, S., E.R. Méndez and R. Iglesias-Prieto. 2005. Multiple scattering on coral skeletons enhances light absorption by symbiotic algae. Limnol. Oceanogr., 50(4), 2005, 1025–1032. DOI: 10.4319/lo.2005.50.4.1025</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'<br />
- corrected spelling of Orbicella faveoalta to Orbicella faveolata</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
phase hemocytometer (Hausser Scientific, Horsham, USA)
phase hemocytometer (Hausser Scientific, Horsham, USA)
PI Supplied Instrument Name: phase hemocytometer (Hausser Scientific, Horsham, USA) PI Supplied Instrument Description:Used for cell counting Instrument Name: Hemocytometer Instrument Short Name:Hemocytometer Instrument Description: A hemocytometer is a small glass chamber, resembling a thick microscope slide, used for determining the number of cells per unit volume of a suspension. Originally used for performing blood cell counts, a hemocytometer can be used to count a variety of cell types in the laboratory. Also spelled as "haemocytometer". Description from:
http://hlsweb.dmu.ac.uk/ahs/elearning/RITA/Haem1/Haem1.html.
mini spectrophotometer (Ocean Optics USB4000)
mini spectrophotometer (Ocean Optics USB4000)
PI Supplied Instrument Name: mini spectrophotometer (Ocean Optics USB4000) Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/