http://lod.bco-dmo.org/id/dataset/642860
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
2016-04-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Acropora cervicornis coral disease exposure experiment conducted on Summerland Key, FL from August to September of 2015 (Resilient Acerv project)
2016-04-11
publication
2016-04-11
revision
BCO-DMO Linked Data URI
2016-04-11
creation
http://lod.bco-dmo.org/id/dataset/642860
Erinn M. Muller
Mote Marine Laboratory
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: Muller, E. M. (2016) Acropora cervicornis coral disease exposure experiment conducted on Summerland Key, FL from August to September of 2015 (Resilient Acerv project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 11 April 2016) Version Date 2016-04-11 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/642860 [access date]
Acropora cervicornis coral disease exposure experiment Dataset Description: <p>Summer 2015 disease susceptibility tests</p> Methods and Sampling: <p><strong>Sampling and Analytical Methodology: </strong><br />
Three&nbsp;trials were conducted to test the disease susceptibility of 15 different genotypes of Acropora cervicornis in August 2015.&nbsp;Approximately 10&nbsp;replicates of each genotype were collected from the Mote offshore coral nursery. Replicates consisted of approximately 5cm branch tips collected from different individuals of the same genotype. Fragments were attached to glass microscope slides using super glue and allowed to acclimate in outdoor raceways for 2 days prior to treatment. One replicate of each genotype was placed within a single five gallon glass tank, holding approximately&nbsp;10&nbsp;liters&nbsp;of water. A total of ten tanks were used, five for the disease homogenate applications, and five for healthy homogenate applications. Temperature within the raceways were kept at ~28.5C;&nbsp;pH (8.0), and salinity (34ppt) were measured daily and remained constant throughout the trials.</p>
<p>After the acclimation period, fragments of diseased corals were collected from a natural reef located at 24'31.640N, 81'29.938W (Permit: FKNMS 2015-84). Fragments showing active signs of tissue loss were snipped off of the donor colony, placed in plastic containers and brought back to the boat for transport to Mote TRL. Upon return to the lab, the diseased corals were airbrushed with filtered sterilized seawater and collected in 50 ml falcon tubes. Tissue adjacent to the disease edge, up to 4 cm away was removed through this method and collected to create a disease homogenate. Healthy homogenates were created from nursery coral fragments. Approximately 10, 5 cm long fragments were airbrushed and collected for the healthy homogenate applications for each trial. Each tank, holding 10 L of water, were treated with either 100 ml of disease homogenate or 100 ml of healthy homogenate.</p>
<p>For the next 8 days the presence of tissue loss was identified from each individual replicate. Photographs of each coral were taken daily. The rate of tissue loss was calculated (cm/day) from each replicate using ImageJ software.</p>
<p>An imaging pulse amplitude fluorometer was used after the 2 day acclimation period to quantify the photochemical efficiency of each replicate coral. The photochemical yield was quantified and a light reaction curve was applied.</p>
<p>Snips, approximately 2 cm in size, were taken from two random replicates within each genotype for Symbiodinium sequencing. Preliminary analyses indicate that all genotypes contain only A3 clade symbiodinium, but they may harbor different genotypes of the symbiont. These samples were flash frozed at -80C and stored until processing. DNA was isolated and extracted from 2 - 3 polyps worth of tissue using the Qiagen DNAeasy DNA isolation kit. Samples will be sent to Dr. Iliana Baums at Penn State University for microsatellite analysis and identification of possible variations in symbiont genotypes within coral genets.</p>
<p>In September of 2015, when corals were visibly bleached from anomalous high water temperatures, a fourth trial was conducted using the same methods described above to test the difference in susceptibility during a thermal stress event. Diseased fragments were collected from the same location as the original trial.</p>
<p>Changes from original proposal: Ideally, all 48 genotypes would have been tested during the summer of 2015. However, even in August 2015 (prior to peak bleaching), several coral genotypes were suffering from thermal stress already. Only the 15 genotypes collected and used for experimentation did not visually appear to be initally stressed during August. Collaborator and nursery manager, Erich Bartels, did not encourage the collection of the other genotypes as they were already thermally stressed; however, Erich agreed to provide the same 15 genotypes in September 2015 even though they were visibly bleached for the sake of a novel research experiment.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1452538 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1452538
completed
Erinn M. Muller
Mote Marine Laboratory
941-388-4441 x 310
1600 Ken Thompson Parkway
Sarasota
FL
34241
USA
emuller@mote.org
pointOfContact
asNeeded
Dataset Version: 11 April 2016
Unknown
Site
Latitude
Longitude
Trial
Tank
Date_Collected
Date_Innoculated
Treatment
Genotype
Color
Initial_disease_signs
Complete_mortality
Fv2Fm_at_innoculation
Fv2Fm_after_innoculation
Second_Fv2Fm_data_after_innoculation
Glass tanks
Qiagen DNAeasy DNA isolation kit
Imaging pulse amplitude fluorometer
theme
None, User defined
site
latitude
longitude
experiment id
tank
date
treatment
No BCO-DMO term
Fv to Fm ratio
featureType
BCO-DMO Standard Parameters
Aquarium
Automated DNA Sequencer
Fluorometer
instrument
BCO-DMO Standard Instruments
MOTE_Muller_SummerlandKey-Summer2015
service
Deployment Activity
Florida Keys, Summerland Key, FL 24.563595°, -81.278572°
place
Locations
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.
CAREER: Applying phenotypic variability to identify resilient Acropora cervicornis genotypes in the Florida Keys
https://osprey.bco-dmo.org/project/642850
CAREER: Applying phenotypic variability to identify resilient Acropora cervicornis genotypes in the Florida Keys
<p><em>NSF Award Abstract:</em><br />
Caribbean staghorn coral was one of the most common corals within reefs of the Florida Keys several decades ago. Over the last 40 years disease, bleaching, overfishing and habitat degradation caused a 95% reduction of the population. Staghorn coral is now listed as threatened under the U.S. Endangered Species Act of 1973. Within the past few years, millions of dollars have been invested for the purpose of restoring the population of staghorn coral within Florida and the U.S. Virgin Islands. Significant effort has been placed on maintaining and propagating corals of known genotypes within coral nurseries for the purpose of outplanting. However, little is known about the individual genotypes that are currently being outplanted from nurseries onto coral reefs. Are the genotypes being used for outplanting resilient enough to survive the three major stressors affecting the population in the Florida Keys: disease, high water temperatures, and ocean acidification? The research within the present study will be the first step in answering this critically important question. The funded project will additionally develop a research-based afterschool program with K-12 students in the Florida Keys and U.S. Virgin Islands that emphasizes an inquiry-based curriculum, STEM research activities, and peer-to-peer mentoring. The information from the present study will help scientists predict the likelihood of species persistence within the lower Florida Keys under future climate-change and ocean-acidification scenarios. Results of this research will also help guide restoration efforts throughout Florida and the Caribbean, and lead to more informative, science-based restoration activities.</p>
<p><em>Acropora cervicornis</em> dominated shallow-water reefs within the Florida Keys for at least the last half a million years, but the population has recently declined due to multiple stressors. Understanding the current population level of resilience to three major threats - disease outbreaks, high water temperatures, and ocean acidification conditions - is critical for the preservation of this threatened species. Results from the present study will answer the primary research question: will representative genotypes from the lower Florida Keys provide enough phenotypic variation for this threatened species to survive in the future? The present proposal will couple controlled laboratory challenge experiments with field data and modeling applications, and collaborate with local educators to fulfill five objectives: 1) identify <em>A. cervicornis</em> genotypes resistant to disease, 2) identify <em>A. cervicornis</em> genotypes resilient to high water temperature and ocean acidification conditions, 3) quantify how high water temperature and ocean acidification conditions impact disease dynamics on <em>A. cervicornis</em>; 4) determine tradeoffs in life-history traits because of resilience factors; and 5) apply a trait-based model, which will predict genotypic structure of a population under different environmental scenarios.</p>
Resilient Acerv
largerWorkCitation
project
eng; USA
oceans
Florida Keys, Summerland Key, FL 24.563595°, -81.278572°
2016-04-11
Florida Keys, Summerland Key, FL 24.563595°, -81.278572°
0
BCO-DMO catalogue of parameters from Acropora cervicornis coral disease exposure experiment conducted on Summerland Key, FL from August to September of 2015 (Resilient Acerv 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/642869.rdf
Name: Site
Units: text
Description: <p>Sampling/Work Site</p>
http://lod.bco-dmo.org/id/dataset-parameter/642870.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude (South is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/642871.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude (West is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/642872.rdf
Name: Trial
Units: dimensionless
Description: <p>Trial: characterizes the order of the experimental exposure</p>
http://lod.bco-dmo.org/id/dataset-parameter/642873.rdf
Name: Tank
Units: dimensionless
Description: <p>Tank: denotes the exact aquaria that held the fragment</p>
http://lod.bco-dmo.org/id/dataset-parameter/642874.rdf
Name: Date_Collected
Units: YYYYMMDD
Description: <p>Date Collected: date that the fragment was collected from the coral nursery</p>
http://lod.bco-dmo.org/id/dataset-parameter/642875.rdf
Name: Date_Innoculated
Units: YYYYMMDD
Description: <p>Date Inoculated: date that the disease or healthy homogenate was applied to the tanks</p>
http://lod.bco-dmo.org/id/dataset-parameter/642876.rdf
Name: Treatment
Units: text
Description: <p>Treatment: identifies whether the tank was either treated with the disease homogenate (E); or the healthy homogenate (C)</p>
http://lod.bco-dmo.org/id/dataset-parameter/642877.rdf
Name: Genotype
Units: integer
Description: <p>Genotype: identifying number of the distinct genotype of the coral fragment</p>
http://lod.bco-dmo.org/id/dataset-parameter/642878.rdf
Name: Color
Units: text
Description: <p>Color - Color represents a certain genotype of coral, which is also denoted within the genotype number as well.</p>
http://lod.bco-dmo.org/id/dataset-parameter/642879.rdf
Name: Initial_disease_signs
Units: M/DD/YYYY HH:MM (AM/PM)
Description: <p>Initial disease signs: the date that first disease associated mortality was observed</p>
http://lod.bco-dmo.org/id/dataset-parameter/642880.rdf
Name: Complete_mortality
Units: M/DD/YYYY HH:MM (AM/PM)
Description: <p>Complete mortality: the date that the entire fragment was dead</p>
http://lod.bco-dmo.org/id/dataset-parameter/642881.rdf
Name: Fv2Fm_at_innoculation
Units: dimensionless
Description: <p>Fv/Fm at inoculation: photochemical efficiency on the day of inoculation (prior to exposure)</p>
http://lod.bco-dmo.org/id/dataset-parameter/642882.rdf
Name: Fv2Fm_after_innoculation
Units: dimensionless
Description: <p>Fv/Fm after inoculation: photochemical efficiency 3 days after inoculation occurred</p>
http://lod.bco-dmo.org/id/dataset-parameter/642883.rdf
Name: Second_Fv2Fm_data_after_innoculation
Units: dimensionless
Description: <p>Second Fv/Fm after inoculation: a repeat measurement of photochemical efficiency 3 days after inolculation occurred</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
https://osprey.bco-dmo.org/dataset/642860/data/download
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology: </strong><br />
Three&nbsp;trials were conducted to test the disease susceptibility of 15 different genotypes of Acropora cervicornis in August 2015.&nbsp;Approximately 10&nbsp;replicates of each genotype were collected from the Mote offshore coral nursery. Replicates consisted of approximately 5cm branch tips collected from different individuals of the same genotype. Fragments were attached to glass microscope slides using super glue and allowed to acclimate in outdoor raceways for 2 days prior to treatment. One replicate of each genotype was placed within a single five gallon glass tank, holding approximately&nbsp;10&nbsp;liters&nbsp;of water. A total of ten tanks were used, five for the disease homogenate applications, and five for healthy homogenate applications. Temperature within the raceways were kept at ~28.5C;&nbsp;pH (8.0), and salinity (34ppt) were measured daily and remained constant throughout the trials.</p>
<p>After the acclimation period, fragments of diseased corals were collected from a natural reef located at 24'31.640N, 81'29.938W (Permit: FKNMS 2015-84). Fragments showing active signs of tissue loss were snipped off of the donor colony, placed in plastic containers and brought back to the boat for transport to Mote TRL. Upon return to the lab, the diseased corals were airbrushed with filtered sterilized seawater and collected in 50 ml falcon tubes. Tissue adjacent to the disease edge, up to 4 cm away was removed through this method and collected to create a disease homogenate. Healthy homogenates were created from nursery coral fragments. Approximately 10, 5 cm long fragments were airbrushed and collected for the healthy homogenate applications for each trial. Each tank, holding 10 L of water, were treated with either 100 ml of disease homogenate or 100 ml of healthy homogenate.</p>
<p>For the next 8 days the presence of tissue loss was identified from each individual replicate. Photographs of each coral were taken daily. The rate of tissue loss was calculated (cm/day) from each replicate using ImageJ software.</p>
<p>An imaging pulse amplitude fluorometer was used after the 2 day acclimation period to quantify the photochemical efficiency of each replicate coral. The photochemical yield was quantified and a light reaction curve was applied.</p>
<p>Snips, approximately 2 cm in size, were taken from two random replicates within each genotype for Symbiodinium sequencing. Preliminary analyses indicate that all genotypes contain only A3 clade symbiodinium, but they may harbor different genotypes of the symbiont. These samples were flash frozed at -80C and stored until processing. DNA was isolated and extracted from 2 - 3 polyps worth of tissue using the Qiagen DNAeasy DNA isolation kit. Samples will be sent to Dr. Iliana Baums at Penn State University for microsatellite analysis and identification of possible variations in symbiont genotypes within coral genets.</p>
<p>In September of 2015, when corals were visibly bleached from anomalous high water temperatures, a fourth trial was conducted using the same methods described above to test the difference in susceptibility during a thermal stress event. Diseased fragments were collected from the same location as the original trial.</p>
<p>Changes from original proposal: Ideally, all 48 genotypes would have been tested during the summer of 2015. However, even in August 2015 (prior to peak bleaching), several coral genotypes were suffering from thermal stress already. Only the 15 genotypes collected and used for experimentation did not visually appear to be initally stressed during August. Collaborator and nursery manager, Erich Bartels, did not encourage the collection of the other genotypes as they were already thermally stressed; however, Erich agreed to provide the same 15 genotypes in September 2015 even though they were visibly bleached for the sake of a novel research experiment.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing: </strong><br />
Statistical analyses:</p>
<p>To&nbsp;determine variations in disease susceptibility we compared&nbsp;fragments exposed to disease homogenates and those exposed to healthy homogenates&nbsp;using a relative risk analysis. The relative risk of exposed (disease homogenates) individuals was compared with the relative risk of non-exposed (healthy homogenate) individuals. The relative risk, or risk ratio, is the number of individuals with disease after exposure to the risk divided by the number of individuals with disease that have not been exposed to the risk:</p>
<p>Relative risk (RR) = &nbsp;Risk in exposed/Risk in non-exposed&nbsp;,</p>
<p>where the <em>risk in exposed </em>individuals was calculated as the prevalence (diseased/total population) of&nbsp;exposed corals and the <em>risk in non-exposed</em> individuals was calculated as the prevalence of disease in&nbsp;non-exposed corals. When RR=1 then there is no association between the risk and disease occurrence. However when RR&gt;1 then there is a positive association and when RR&lt;1 there is a negative association. The relative risk was calculated using a Bayesian approach and estimated using a binomial likelihood distribution and a uniform-Beta prior distribution. To obtain an estimate of relative risk, Markov Chain Monte Carlo simulations were used with Gibbs sampling in OpenBUGS (MRC Biostatistics Unit, Cambridge, UK). Ninety-five percent credible intervals were calculated for each estimate of relative risk. The relative risk was calculated for each&nbsp;genotype. Credible intervals that did not include a value of one were considered significant, with a credible interval above one signifying a higher risk of disease because of damage. A credible interval below one signified a higher risk of disease from the lack of damage. Furthermore, the range of the 95% credible intervals provided a general measure of the confidence in each relative-risk estimate, with a large range signifying low confidence in the estimate.</p>
<p>An additional relative risk analysis was conducted where the disease exposed individuals of the non-thermally stressed corals were compared with the disease exposed individuals of the thermally stressed corals. Here, thermal stress was considered the 'exposure' in the relative risk analysis.</p>
<p><strong>BCO-DMO Processing Notes</strong><br />
- Generated from original file "Disease susceptibility Summer 2015_data submitted.xlsx" contributed by Erinn Muller<br />
- Parameter names edited to conform to BCO-DMO naming convention found at <a href="http://usjgofs.whoi.edu/naming-guidelines.html" target="_blank">Choosing Parameter Name</a><br />
- Site, Latitude and Longitude added to data to enable mapping<br />
- "nd" (no data) inserted into blank cells<br />
- "NA" and "n/a" replaced with "nd" (no data)<br />
- "Date_Collected" and "Date_Inoculated" values reformatted to YYYYMMDD</p>
<p>&nbsp;</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
Glass tanks
Glass tanks
PI Supplied Instrument Name: Glass tanks PI Supplied Instrument Description:One replicate of each genotype was placed within a single five gallon glass tank, holding approximately 10 liters of water. A total of ten tanks were used, five for the disease homogenate applications, and five for healthy homogenate applications.
Each tank, holding 10 L of water, were treated with either 100 ml of disease homogenate or 100 ml of healthy homogenate. Instrument Name: Aquarium Instrument Short Name:Aquarium Instrument Description: Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept
Qiagen DNAeasy DNA isolation kit
Qiagen DNAeasy DNA isolation kit
PI Supplied Instrument Name: Qiagen DNAeasy DNA isolation kit PI Supplied Instrument Description:Snips, approximately 2 cm in size, were taken from two random replicates within each genotype for Symbiodinium sequencing. Preliminary analyses indicate that all genotypes contain only A3 clade symbiodinium, but they may harbor different genotypes of the symbiont. These samples were flash frozed at -80C and stored until processing. DNA was isolated and extracted from 2 - 3 polyps worth of tissue using the Qiagen DNAeasy DNA isolation kit. Samples will be sent to Dr. Iliana Baums at Penn State University for microsatellite analysis and identification of possible variations in symbiont genotypes within coral genets. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Imaging pulse amplitude fluorometer
Imaging pulse amplitude fluorometer
PI Supplied Instrument Name: Imaging pulse amplitude fluorometer PI Supplied Instrument Description:An imaging pulse amplitude fluorometer was used after the 2 day acclimation period to quantify the photochemical efficiency of each replicate coral. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Deployment: MOTE_Muller_SummerlandKey-Summer2015
MOTE_Muller_SummerlandKey-Summer2015
Mote Offshore Coral Nursery
island
MOTE_Muller_SummerlandKey-Summer2015
Erinn M. Muller
Mote Marine Laboratory
Mote Offshore Coral Nursery
island