http://lod.bco-dmo.org/id/dataset/700149
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
2017-05-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, 2015-2016 (EMUCoReS project)
2017-05-17
publication
2017-05-17
revision
BCO-DMO Linked Data URI
2017-05-17
creation
http://lod.bco-dmo.org/id/dataset/700149
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., Richardson, L., Lirman, D. (2017) Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, 2015-2016 (EMUCoReS project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-05-17 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/700149 [access date]
Dendrogyra cylindrus 23S Illumina 2015-16 - relative abundance Dataset Description: <p>This dataset includes the relative abundance of <em>Dendrogyra </em><em>cylindrus</em> which were analyzed for 23S on an Illumina platform from three sites in the Florida Reef Tract, one each in the upper, middle and lower Keys in 2015-2016.</p> Methods and Sampling: <p><em>Dendrogyra </em><em>cylindrus</em> tissue sampling: syringe micro-sampling method (described in Kemp et al. 2008); samples filtered with Swinnex filter holder (13mm) with 3.0µm glass fiber filter; filter preserved in 95% ETOH.</p>
<p><strong>DNA extraction</strong>: DNeasy Plant Mini kit (Qiagen) with modifications:<br />
5 min bead beating – acid-washed glass beads<br />
20µl Proteinase K - incubate 1 hr at 56°C</p>
<p><strong>amplicon sequencing:</strong> partial chloroplast large subunit 23S rDNA Domain V gene hyper-variable region (Santos et al 2003)</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
onGoing
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
Unknown
OTU_id
species
sample_785_thru_1292
Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com)
theme
None, User defined
sample identification
taxon
relative abundance
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
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
biota
oceans
Florida Reef Tract
-81.75
-80.4
24.47
25
2015-04-01
2016-04-30
Florida Reef Tract (24.868358, -80.643495)
0
BCO-DMO catalogue of parameters from Symbiodinium species and relative abundance in Dendrogyra cylindrus from 3 regions of the Florida Reef Tract, 2015-2016 (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/700160.rdf
Name: OTU_id
Units: unitless
Description: <p>operational taxonomic unit identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/700161.rdf
Name: species
Units: unitless
Description: <p>Symbiodinium species identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/700162.rdf
Name: sample_785_thru_1292
Units: percent
Description: <p>relative abundance of OTU</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
121536
https://datadocs.bco-dmo.org/file/wnnxzmkho6EWr/abund_Dcyl_Symb_2015_16.csv
abund_Dcyl_Symb_2015_16.csv
Primary data file for dataset ID 700149
download
https://osprey.bco-dmo.org/dataset/700149/data/download
download
onLine
dataset
<p><em>Dendrogyra </em><em>cylindrus</em> tissue sampling: syringe micro-sampling method (described in Kemp et al. 2008); samples filtered with Swinnex filter holder (13mm) with 3.0µm glass fiber filter; filter preserved in 95% ETOH.</p>
<p><strong>DNA extraction</strong>: DNeasy Plant Mini kit (Qiagen) with modifications:<br />
5 min bead beating – acid-washed glass beads<br />
20µl Proteinase K - incubate 1 hr at 56°C</p>
<p><strong>amplicon sequencing:</strong> partial chloroplast large subunit 23S rDNA Domain V gene hyper-variable region (Santos et al 2003)</p>
Specified by the Principal Investigator(s)
<p>MR DNA analysis pipeline: MR DNA, Shallowater, TX, USA<br />
Mothur software v1.37.2 (Schloss e t al. 2009) Operational taxonomic units (OTUs) generated, 0.03 similarity cutoff<br />
&nbsp;</p>
<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</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
Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com)
Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com)
PI Supplied Instrument Name: Illumina Mi-Seq - MR.DNA Next Generation Sequencing, Shallowater, Texas (www.mrdnalab.com) 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.
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