http://lod.bco-dmo.org/id/dataset/709909
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
2017-07-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS project)
2017-07-26
publication
2017-07-26
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-03-20
publication
https://doi.org/10.1575/1912/bco-dmo.709909.1
Dr Mauricio Rodriguez-Lanetty
Florida International University
principalInvestigator
Dr Diego Lirman
University of Miami Rosenstiel School of Marine and Atmospheric Science
principalInvestigator
Dr Laurie Richardson
Florida International 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: Rodriguez-Lanetty, M., Lirman, D., Richardson, L. (2017) Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-07-26 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.709909.1 [access date]
Symbiodinium community composition for individual A. cervicornis. Dataset Description: <p>Symbiodinium community composition for individual A. cervicornis. Sampled from&nbsp;Biscayne Bay Coral Nursery near Elliot Key, Florida.</p>
<p><strong>Associated Publications:</strong></p>
<p>Seibeck et al., 2006: Monitoring coral bleaching using a colour reference card</p> Methods and Sampling: <p>At indicated dates, individual corals were visually assessed for bleaching. Bleaching was noted for those corals paling or entirely lacking in pigmentation.&nbsp; A reference color card (Seibeck et al., 2006) was used as a pigmentation reference. The normal level of pigmentation was C3 or darker (not bleached). Colors lighter than C3 were considered bleached. Using bone cutters, a small sub-apical piece was broken off of each coral. On the boat, samples were transferred to CHAOS buffer (listed below) and extracted for DNA:</p>
<p><strong>Chaos Buffer:</strong></p>
<p>4.5M Guanidinium thiocyanate<br />
2% N-lauroylsarcosine (sarcosyl)<br />
50mM EDTA<br />
25mM Tris-HCl, pH 7.5<br />
0.2% antifoam A (Sigma)<br />
0.1M b-mercaptoethanol (BME)</p>
<p><strong>Binding buffer (BB):</strong></p>
<p>6 M GuSCN 1 , (Guanidine Thiocyanate)<br />
20 mM EDTA pH 8.0<br />
10 mM Tris-HCl pH 7.5<br />
4% Triton X-100</p>
<p><strong>Protein wash buffer (PWB):</strong></p>
<p>70 mL of ethanol (96%) was thoroughly mixed with 26 mL of BB (stable at 20 deg&nbsp;C for1 week).</p>
<p><strong>Wash buffer (WB):</strong></p>
<p>ethanol (60%),<br />
50 mM NaCl<br />
10 mM Tris-HCl pH 7.4<br />
0.5 mM EDTA pH 8.0 (stored at -20 deg&nbsp;C)</p>
<p>-Allow coral fragments to sit covered in CHAOS buffer in 1.5 - 2.0 mL tube for days- weeks.<br />
-Pipet the Supernatant mixture into a silica spin column placed in a 2 ml collection tube. Centrifuge at 6000 x g (8000 rpm) for 1 min. Discard flow-through. Repeat as needed to load entire sample.<br />
-Add 700 ul PWB to column, and centrifuge for 1 min at 6000 x g (8000 rpm). Discard flow-through.<br />
-Repeat 2x (3 washes total).<br />
-Add 700 ul WB to column and centrifuge for 1 min at 20,000 x g (14,000 rpm). Discard flow-through.<br />
-Repeat wash and centrifuge for 3 min at 20,000 x g (14,000 rpm) to dry the DNeasy membrane.<br />
-Discard flow-through and collection tube.<br />
-Place the spin column in a clean 1.5 ml or 2 ml microcentrifuge tube, and pipet 100 ul 0.1x TE directly onto the spin column.<br />
-Incubate at room temperature for 1 min, and then centrifuge for 1 min at 6000 x g (8000 rpm) to elute.<br />
(May repeat with another 100 ul of 0.1x TE).</p>
<p>Purified DNA was sent to MR DNA in stillwater Texas for Illumina sequencing of the cp-23S gene for Symbiodinium typing.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1503483 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1503483
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1503430 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1503430
completed
Dr Mauricio Rodriguez-Lanetty
Florida International University
305-348-4922
Florida International University / Department of Biological Sciences 11200 SW 8th Street
Miami
FL
33199
United States
rodmauri@fiu.edu
pointOfContact
Dr Diego Lirman
University of Miami Rosenstiel School of Marine and Atmospheric Science
FL
USA
dlirman@rsmas.miami.edu
pointOfContact
Dr Laurie Richardson
Florida International University
richardl@fiu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
genet_clonalPopulation_ID
ramet_individualColony_ID
visit
bleaching
disease
mortality
theme
None, User defined
sample identification
month of year
sample description
featureType
BCO-DMO Standard Parameters
Coral_Bleaching_FRRP
service
Deployment Activity
Florida Reef Tract
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.
RAPID: A hyper-thermal anomaly in the Florida Reef Tract: An opportunity to explore the mechanisms underpinning patterns of coral bleaching and disease
https://osprey.bco-dmo.org/project/637743
RAPID: A hyper-thermal anomaly in the Florida Reef Tract: An opportunity to explore the mechanisms underpinning patterns of coral bleaching and disease
<p><em>Description from NSF award abstract:</em><br />
Coral reefs are among the most biologically diverse and economically important ecosystems on the planet. However, coral reefs are in a state of global decline due to effects of climate change, disease outbreaks, and other stressors. Mass coral bleaching events, a breakdown of the association between corals and their symbiotic algae, are predicted to become more frequent and severe in response to climate change, and it is expected that subsequent disease outbreaks will become more common. Beginning in August 2014, nearly all coral species in the Florida Reef Tract have undergone severe bleaching, in some cases followed by coral mortality and/or disease outbreaks. This widespread, thermal-induced event presents a unique time-sensitive opportunity to explore the mechanisms underpinning the patterns of coral bleaching, disease, and recovery. The mechanisms linking patterns of bleaching, disease, mortality, and recovery remain relatively unexplored. This research will explore the influences that genotype combinations of host polyps, their algal symbionts, and associated bacterial have on bleaching/disease likelihood and recovery/mortality predisposition of coral specimens. By providing a mechanistic understanding of the processes that underlie coral bleaching and subsequent recovery this research will contribute to measures in support of preserving this invaluable natural resource. The study will further involve students from diverse backgrounds as well as provide project internship opportunities for high school students. A web based radio blog will disseminate project results and other relevant developments to the broad audiences</p>
<p>Mass coral bleaching events are predicted to become more frequent and severe in response to climate change, and it is expected that subsequent disease outbreaks will become more common. The lack of a baseline genetic datasets for coral holobionts prior to previous natural bleaching events has hindered our understanding of recovery patterns and physiological tolerance to thermal stress, also known as coral bleaching. An extensive pre-thermal stress baseline of genotypic identity of coral hosts, Symbiodinium, and associated bacterial community offers a unique opportunity to analyze changes associated with current bleaching event along the Florida coastline and to document holobiont compositions most and least resistant/resilient to bleaching and disease. Repeated sampling of the same coral colonies will allow the investigators to compare holobiont composition before, during and after bleaching of both healthy and diseased individuals. This bleaching event is a time-sensitive natural experiment to examine the dynamics of microbes (Symbiodinium and bacteria) associated with affected colonies, including their potential influence on disease susceptibility and resistance of reef corals. This effort would constitute the first time that high throughput sequencing of coral, Symbiodinium endosymbiont, and the coral-associated bacterial community genotypes are together used to explain patterns of disease, recovery, and mortality following natural bleaching. This study will likely change the way investigators study emerging wasting diseases of keystone species that define marine benthic communities.</p>
EMUCoReS
largerWorkCitation
project
eng; USA
oceans
Florida Reef Tract
-90.109
-90.109
25.488
25.488
2014-09-05
2015-10-13
Florida Reef Tract (24.868358, -80.643495)
0
BCO-DMO catalogue of parameters from Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS 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/709923.rdf
Name: genet_clonalPopulation_ID
Units: unitless
Description: <p>Azexual clone identifier; A through X</p>
http://lod.bco-dmo.org/id/dataset-parameter/709924.rdf
Name: ramet_individualColony_ID
Units: unitless
Description: <p>Individual coral ID within each genet; 1 through 10</p>
http://lod.bco-dmo.org/id/dataset-parameter/709925.rdf
Name: visit
Units: unitless
Description: <p>Month sampled: September 14; March 15; October 15</p>
http://lod.bco-dmo.org/id/dataset-parameter/709926.rdf
Name: bleaching
Units: unitless
Description: <p>Presence or absence of bleaching categorically binned as bleaching, or healthy</p>
http://lod.bco-dmo.org/id/dataset-parameter/709927.rdf
Name: disease
Units: unitless
Description: <p>Presence or absence of disease categorically binned as: no disease; white band disease; or rapid tissue loss</p>
http://lod.bco-dmo.org/id/dataset-parameter/709928.rdf
Name: mortality
Units: unitless
Description: <p>Relative partial mortality categorically binned as; no mortality; partial mortality; mostly dead; or dead</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
47168
https://darchive.mblwhoilibrary.org/bitstream/1912/23897/1/dataset-709909_symbiodinium-community-composition__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.709909.1
download
onLine
dataset
<p>At indicated dates, individual corals were visually assessed for bleaching. Bleaching was noted for those corals paling or entirely lacking in pigmentation.&nbsp; A reference color card (Seibeck et al., 2006) was used as a pigmentation reference. The normal level of pigmentation was C3 or darker (not bleached). Colors lighter than C3 were considered bleached. Using bone cutters, a small sub-apical piece was broken off of each coral. On the boat, samples were transferred to CHAOS buffer (listed below) and extracted for DNA:</p>
<p><strong>Chaos Buffer:</strong></p>
<p>4.5M Guanidinium thiocyanate<br />
2% N-lauroylsarcosine (sarcosyl)<br />
50mM EDTA<br />
25mM Tris-HCl, pH 7.5<br />
0.2% antifoam A (Sigma)<br />
0.1M b-mercaptoethanol (BME)</p>
<p><strong>Binding buffer (BB):</strong></p>
<p>6 M GuSCN 1 , (Guanidine Thiocyanate)<br />
20 mM EDTA pH 8.0<br />
10 mM Tris-HCl pH 7.5<br />
4% Triton X-100</p>
<p><strong>Protein wash buffer (PWB):</strong></p>
<p>70 mL of ethanol (96%) was thoroughly mixed with 26 mL of BB (stable at 20 deg&nbsp;C for1 week).</p>
<p><strong>Wash buffer (WB):</strong></p>
<p>ethanol (60%),<br />
50 mM NaCl<br />
10 mM Tris-HCl pH 7.4<br />
0.5 mM EDTA pH 8.0 (stored at -20 deg&nbsp;C)</p>
<p>-Allow coral fragments to sit covered in CHAOS buffer in 1.5 - 2.0 mL tube for days- weeks.<br />
-Pipet the Supernatant mixture into a silica spin column placed in a 2 ml collection tube. Centrifuge at 6000 x g (8000 rpm) for 1 min. Discard flow-through. Repeat as needed to load entire sample.<br />
-Add 700 ul PWB to column, and centrifuge for 1 min at 6000 x g (8000 rpm). Discard flow-through.<br />
-Repeat 2x (3 washes total).<br />
-Add 700 ul WB to column and centrifuge for 1 min at 20,000 x g (14,000 rpm). Discard flow-through.<br />
-Repeat wash and centrifuge for 3 min at 20,000 x g (14,000 rpm) to dry the DNeasy membrane.<br />
-Discard flow-through and collection tube.<br />
-Place the spin column in a clean 1.5 ml or 2 ml microcentrifuge tube, and pipet 100 ul 0.1x TE directly onto the spin column.<br />
-Incubate at room temperature for 1 min, and then centrifuge for 1 min at 6000 x g (8000 rpm) to elute.<br />
(May repeat with another 100 ul of 0.1x TE).</p>
<p>Purified DNA was sent to MR DNA in stillwater Texas for Illumina sequencing of the cp-23S gene for Symbiodinium typing.</p>
Specified by the Principal Investigator(s)
<p>Data was processed with MR DNA's proprietary pipeline.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- filled all blank cells with 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
Deployment: Coral_Bleaching_FRRP
Coral_Bleaching_FRRP
shoreside Florida_Coral_Reefs
shoreside Florida_Coral_Reefs
shoreside
Coral_Bleaching_FRRP
Dr Mauricio Rodriguez-Lanetty
Florida International University
shoreside Florida_Coral_Reefs
shoreside Florida_Coral_Reefs
shoreside