http://lod.bco-dmo.org/id/dataset/882086
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
2022-10-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microsatellite and chloroplast 23S genotypes of Breviolum sp. symbionts within Orbicella faveolata adults from reefs in the Florida Keys from 2009-2011 (SymBioSys project)
2022-10-10
publication
2022-10-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-05-24
publication
https://doi.org/10.26008/1912/bco-dmo.882086.1
Mary Alice Coffroth
State University of New York at Buffalo
principalInvestigator
Margaret W. Miller
NOAA Southeast Fisheries Science Center
principalInvestigator
David Sheets
Canisius College
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: Coffroth, M. A., Miller, M. W., Sheets, D. (2023) Microsatellite and chloroplast 23S genotypes of Breviolum sp. symbionts within Orbicella faveolata adults from reefs in the Florida Keys from 2009-2011 (SymBioSys project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-10-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.882086.1 [access date]
Methods and Sampling: <p><strong>Sampling and Analytical Methodology</strong></p>
<p>Tissue samples were collected from the top, middle and bottom portions of adult Orbicella faveolata colonies using the syringe method as described in Correa et al. (2009) and DNA extracted following Coffroth et al. (1992).&nbsp;</p>
<p>Genotypes of the algal symbionts within the genus Breviolum were characterized using three polymorphic microsatellite loci, B7Sym34, B7Sym36 and CA6.38, which were adapted for use with O. faveolata (Thornhill et al. 2009).</p>
<p>Cp-23S genotypes of the algal symbionts within the genus Breviolum were characterized following the protocol of Santos et al. (2003).</p>
<p><strong>Locations in the Florida Keys (Table of reef abbreviations)</strong></p>
<table border="1" cellpadding="1" cellspacing="1">
<tbody>
<tr>
<td>Reef</td>
<td>Abbreviation</td>
</tr>
<tr>
<td>Alligator</td>
<td>AR</td>
</tr>
<tr>
<td>Coral Garden</td>
<td>CG</td>
</tr>
<tr>
<td>Cheeca Rocks</td>
<td>CR</td>
</tr>
<tr>
<td>East Turtle</td>
<td>ET</td>
</tr>
<tr>
<td>Grecian Rocks</td>
<td>GR</td>
</tr>
<tr>
<td>Looe Key</td>
<td>LK</td>
</tr>
<tr>
<td>Sand Island</td>
<td>SI</td>
</tr>
<tr>
<td>Tennessee</td>
<td>TR</td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0926822 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0926822
completed
Mary Alice Coffroth
State University of New York at Buffalo
716-645-4871
Department of Geology 126 Cooke Hall
Buffalo
NY
14260
USA
Coffroth@buffalo.edu
pointOfContact
Margaret W. Miller
NOAA Southeast Fisheries Science Center
SECORE International, Inc.
Miami
Florida
33145
USA
margaret.w.miller@noaa.gov
pointOfContact
David Sheets
Canisius College
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Year
Site
Latitude_decimal_degrees
Longitude_decimal_degrees
B7Sym34
B7Sym36
Colony_Number
Location_in_colony
Depth_m
CA_6_38
Assigned_Genotype
CP_type
theme
None, User defined
sample identification
year
site
latitude
longitude
sample description
site description
depth
featureType
BCO-DMO Standard Parameters
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.
Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective
https://osprey.bco-dmo.org/project/472478
Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective
<p>PROJECT SUMMARY:<br />
The symbiosis between corals (Cnidaria:Hexacorallia:Scleractinia) and photosynthetic dinoflagellate symbionts (Alveolata: Dinophycea: Symbiodinium) provides the foundation and structure of the coral reef ecosystem, as well as significant contributions to global carbon and biogeochemical cycles. Given the importance of this symbiosis to the coral-algal holobiont and the reef ecosystem, understanding the mechanisms governing the establishment and long term maintenance of this symbiosis is essential. The overall aim of this project is to identify the mechanisms and selective processes that lead to the final assemblage of symbionts harbored by adult hosts. This question will be approached from two perspectives, ecologic and genomic, with the specific aims of determining (1) if different Symbiodinium strains differentially affect fitness of corals as the adult settles into a mature symbiosis (2) if competition among symbionts or environmental conditions contribute to the final host-symbiont pairing and (3) how host/symbiont transcriptomes varying as the symbiont community within a host is winnowed to the final assemblage found in the adult host. Traits that directly affect coral fitness (i.e. growth, survivorship, energy production) will be measured under different environmental conditions over the ontogeny of coral recruits that are experimentally infected with different types of Symbiodinium. Concurrently, high throughput gene expression profiling will be used to follow changes in gene expression between host and symbiont. Together, these data will be used to validate or falsify the hypotheses that the final symbiont assemblage found in the adult host is determined by (a) host selection (b) competition among symbionts and/or (c) environmental condition.</p>
<p>This study pools the expertise of two labs that have focused on these aspects of the symbiosis. The Coffroth lab pioneered the studies on early ontogeny of the symbiosis and symbiont diversity and will continue to take the lead in the ecological studies. The Medina lab is at the forefront in the development and utilization of genomic technology to study transcriptomic changes during the establishment and breakdown of the symbiosis. Furthermore, the Medina lab has the coral microarrays to be used in this study and in 2009 will also have oligo arrays for two Symbiodinium species based on 454 EST data. Although several groups have initial studies of the host transcriptome, none have combined an approach that examines the host and the symbiont in a single experiment. This will be a powerful approach as it will allow the investigators to track complementary changes in gene expression between host and symbiont and relate those to turnover in the symbiont community as the final symbiont complement is established.</p>
<p>The data resulting form the study will bridge an important gap in our understanding of the establishment and maintenance of coral-Symbiodinium symbiosis. Understanding the mechanism(s) regulating the establishment of the symbiosis will broaden our knowledge and help to predict the response of this symbiosis to future climate conditions. As in the past, the genomic tools (arrays, ESTs) will be made readily available to researchers via array distribution at cost, microarray analysis training, or sequence data, providing valuable resources to continue exploring these systems.</p>
<p>In conjunction the Aquarium of Niagara, Coffroth will develop educational and outreach programs to train and disseminate information on coral reefs to local area teachers and the general public. The Medina lab will continue to produce science and environment podcasts in multiple languages (English, Spanish and Hmong) with undergraduate students at UC Merced and will continue to collaborate with the California Academy of Sciences (CAS) in their coral reef outreach efforts. Additionally, this work will result in the training and mentoring of a postdoctoral fellow, at least one graduate student and at least 2 undergraduates. Through this project these students will have the opportunity to participate in research in both a lab and field setting, learning a range of ecological, molecular and algal culturing techniques. The extensive culture collection housed at the University at Buffalo is an important resource that is available to researchers worldwide which the proposed funding will help to maintain. Our EST annotations are publicly available through our EST database (<a href="http://montastraea.psu.edu/SymBioSys/" target="_blank">http://montastraea.psu.edu/SymBioSys/</a>).</p>
SymBioSys
largerWorkCitation
project
eng; USA
oceans
-81.4094
-80.2833
24.5449
25.1167
2009-01-01
2011-12-31
Florida Keys, Bahamas, Panama, Mexico
0
BCO-DMO catalogue of parameters from Microsatellite and chloroplast 23S genotypes of Breviolum sp. symbionts within Orbicella faveolata adults from reefs in the Florida Keys from 2009-2011 (SymBioSys 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/891350.rdf
Name: Sample_ID
Units: unitless
Description: <p>Identification of tissue sample collected from adult Orbicella faveolata colonies.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891351.rdf
Name: Year
Units: unitless
Description: <p>Year in which sample was collected.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891352.rdf
Name: Site
Units: unitless
Description: <p>Reef where sample was collected� see abbreviation key above.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891353.rdf
Name: Latitude_decimal_degrees
Units: decimal degrees
Description: <p>Latitude of reef where samples were taken in decimal degrees. A positive value indicates a Northern coordinate value.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891354.rdf
Name: Longitude_decimal_degrees
Units: decimal degrees
Description: <p>Longitude of reef where samples were taken in decimal degrees. A negative value indicatres a Western coordinate value.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891355.rdf
Name: B7Sym34
Units: basepair
Description: <p>Fragment size of the B7Sym34 microsatellite allele. NA indicates "No Amp - did not amplify after multiple attempts", and ND indicates "Not Determined - because one or more loci did not amplify.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891356.rdf
Name: B7Sym36
Units: basepair
Description: <p>Fragment size of the B7Sym36 microsatellite allele. NA indicates "No Amp - did not amplify after multiple attempts", and ND indicates "Not Determined - because one or more loci did not amplify.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891357.rdf
Name: Colony_Number
Units: unitless
Description: <p>Identification number for colony.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891358.rdf
Name: Location_in_colony
Units: unitless
Description: <p>Location within the colony where the sample as taken; T: Top, M: Middle, B: Bottom.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891359.rdf
Name: Depth_m
Units: meters (m)
Description: <p>Depth where sample was taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891360.rdf
Name: CA_6_38
Units: basepair
Description: <p>Fragment size of the CA6.38 microsatellite allele. NA indicates "No Amp - did not amplify after multiple attempts", and ND indicates "Not Determined - because one or more loci did not amplify.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891361.rdf
Name: Assigned_Genotype
Units: unitless
Description: <p>Genotype assigned based on the combination of microsatellite alleles at the three loci. Numbering is arbitrary.</p>
http://lod.bco-dmo.org/id/dataset-parameter/891362.rdf
Name: CP_type
Units: unitless
Description: <p>Fragment size of the hypervariable region of domain B of chloroplast large subunit rDNA (cp23S) allele.</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
43526
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a0c87437-1e7f-46f4-b7b8-70d9c5a53015/content
download
https://doi.org/10.26008/1912/bco-dmo.882086.1
download
onLine
dataset
<p><strong>Sampling and Analytical Methodology</strong></p>
<p>Tissue samples were collected from the top, middle and bottom portions of adult Orbicella faveolata colonies using the syringe method as described in Correa et al. (2009) and DNA extracted following Coffroth et al. (1992).&nbsp;</p>
<p>Genotypes of the algal symbionts within the genus Breviolum were characterized using three polymorphic microsatellite loci, B7Sym34, B7Sym36 and CA6.38, which were adapted for use with O. faveolata (Thornhill et al. 2009).</p>
<p>Cp-23S genotypes of the algal symbionts within the genus Breviolum were characterized following the protocol of Santos et al. (2003).</p>
<p><strong>Locations in the Florida Keys (Table of reef abbreviations)</strong></p>
<table border="1" cellpadding="1" cellspacing="1">
<tbody>
<tr>
<td>Reef</td>
<td>Abbreviation</td>
</tr>
<tr>
<td>Alligator</td>
<td>AR</td>
</tr>
<tr>
<td>Coral Garden</td>
<td>CG</td>
</tr>
<tr>
<td>Cheeca Rocks</td>
<td>CR</td>
</tr>
<tr>
<td>East Turtle</td>
<td>ET</td>
</tr>
<tr>
<td>Grecian Rocks</td>
<td>GR</td>
</tr>
<tr>
<td>Looe Key</td>
<td>LK</td>
</tr>
<tr>
<td>Sand Island</td>
<td>SI</td>
</tr>
<tr>
<td>Tennessee</td>
<td>TR</td>
</tr>
</tbody>
</table>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Processing Notes from Researcher:&nbsp;</strong></p>
<ul>
<li>For parameters B7Sym34, B7Sym36, CA6.38 (CA_6_38), Assigned_Genotype, and CP_type, NA indicates "no amp - did not amplify after multiple attempts," and ND indicates "not determined because one or more loci did not amplify."</li>
</ul>
<p><strong>BCO-DMO Processing Notes:&nbsp;</strong></p>
<ul>
<li>Special characters and spaces replaced by underscores ("_") in parameter names</li>
<li>Longitude and latitude are split into separate columns and converted to decimal degrees</li>
<li>Separate data tables related to&nbsp;<em>Orbicella faveolata&nbsp;</em>adults merged into one data table&nbsp;</li>
</ul>
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