http://lod.bco-dmo.org/id/dataset/728215
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
2018-02-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response project)
2018-02-16
publication
2018-02-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-10-02
publication
https://doi.org/10.1575/1912/bco-dmo.728215.1
Mary Alice Coffroth
State University of New York at Buffalo
principalInvestigator
Casey terHorst
California State University Northridge
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., terHorst, C. (2018) Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-02-16 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.728215.1 [access date]
Symbiodinium cultures isolated from adult colonies of the octocoral Antillogorgia bipinnata in 2008, 2013 and 2016, grown at either 26 or 30 degrees C Dataset Description: <p><em>Symbiodinium </em>cultures isolated from adult colonies of the octocoral <em>Antillogorgia bipinnata</em> in 2008, 2013 and 2016, grown at either 26 or 30 degrees C.</p>
<p>Cultures initially isolated from <em>Antillogorgia bipinnata </em>colonies collected in the lower keys in the vicinity of Looe Key (24&nbsp;32.973'N 81&nbsp;22.849'W) in 2008, the middle keys near Tennessee Reef (24&nbsp;45.150'N&nbsp; 81&nbsp;45.275'W) in 2013 and the upper keys at Pickles Reef (24 59.016'N 80 24.832'W) and Elbow Reef (25 07.956'N 80 15.810'W and 25 07.925'N 80 15.717'W).&nbsp; Culture have been maintained in the Coffroth lab, University at Buffalo.</p> Methods and Sampling: <p>Symbionts were isolated from adult colonies of <em>Antillogorgia bipinnata</em> following the protocol outline in Santos et al 2001. Briefly, a small piece (1-2 cm) of the branch was ground in a glass tissue homogenizer with 2 ml of filtered seawater (FSW) and poured through a series of meshes (250 µm on top, then 120 µm, then 70 µm mesh) into a 15 ml tube.&nbsp; The mesh was washed with 1 ml FSW several times for a final volume between 3 and 10&nbsp;ml. This slurry was spun for 5 min at 500-800 rpm on a Beckman J6-HC centrifuge to pellet symbiont cells, the supernatant removed and resuspended in 10 ml of FSW.&nbsp; This step was repeated again and then the pellet was resuspended in 1.0 ml of F/2 (Gulliard and Ryther 1962).&nbsp; Cultures were started by using 20-50 µl of the resuspended pellets to inoculate 30ml of F/2 and incubated at the appropriate temperature.&nbsp; &nbsp; &nbsp;</p>
<p>Clade identity and Cp-type were determined following the protocols outline in Santos et al (2003). Briefly, DNA was amplified using the primers HYPERUP and HYPERDN on and MJ96 or BioRad thermocyclers. PCR products were visualized and scored using size standards on a LI-COR 4200 NEN® Global IR2 DNA sequencing system as specified in Santos et al (2003). Putative species identity was based on sequence analysis of B7SYM15 flanking region (LaJeunesse et al. 2012, Parkinson et al. 2015).&nbsp; Briefly, the B7SYM15 flanking region was amplified and directly sequenced in 5’ and 3’ directions on a 3730XL DNA Analyzer (High Throughput Genomics Center, University of Washington). Sequences were compared to known species within the GenBank database using BLAST- Basic Local Alignment Search Tool (<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a>).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559286 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559286
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
Casey terHorst
California State University Northridge
818-677-3352
Department of Biology 18111 Nordhoff Street
Northridge
CA
91330-8303
USA
casey.terhorst@csun.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Culture_ID
Incubation_Temperature
Host
Putative_Species
Location
Latitude
longitude
State_Country
Ocean
Host_stage
Axenic
Isolated_by
Year_isolated
Clade
cp_type
LI-COR 4200 NEN® Global IR2 DNA
3730XL DNA Analyzer
Beckman J6-HC centrifuge
theme
None, User defined
sample identification
incubation temperature
species scientific name (binomial)
site description
latitude
longitude
region
stage
No BCO-DMO term
person name
year
taxon
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Centrifuge
instrument
BCO-DMO Standard Instruments
Coffroth_2008-16
service
Deployment Activity
SUNY - Buffalo lab
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.
RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs
https://osprey.bco-dmo.org/project/632538
RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs
<p><em>Description from NSF award abstract:</em><br />
On coral reefs, mutualisms with single celled algae (Symbiodinium) and reef species literally and figuratively form the foundation of reef ecosystems. Coral reefs are among the most threatened ecosystems under a changing climate and are rapidly declining due to increasing levels of environmental stress, namely increased temperatures. Climate change is resulting in even warmer ocean temperatures that threaten associations between Symbiodinium and their hosts. In this project the investigators examine the genetic diversity of Symbiodinium and the potential for this important species to evolve in response to temperature. The project will also address whether the ecological and evolutionary dynamics of the Symbiodinium population affect the performance of their host. If so, this suggests that the evolution of microscopic organisms with short generation times could confer adaptation to longer-lived host species on ecologically and economically vital coral reefs. Given that diversity is already being lost on many reefs, considering how evolutionary changes in Symbiodinium will affect reef species is crucial for predicting the responses of reefs to future climate change. This project provides training for two graduate students and several undergraduates at a Hispanic-serving institution. This work includes outreach to the students and the general public through the Aquarium of Niagara, local K-12 schools, and web-based education modules.</p>
<p>The effects of evolution on contemporary ecological processes are at the forefront of research in evolutionary ecology. This project will answer the call for experiments elucidating the effects of genetic variation in Symbiodinium performance and the effect on the response of the holobiont (host and symbiont) to increased temperature. These experiments examine the effects of temperature through both ecological and evolutionary mechanisms and will determine the relative importance of adaptation and acclimatization in replicated experimental populations. The investigators will examine how genetic variation within a species (Symbiodinium antillogorgium) affects symbiont performance in culture and in the host and how this affects the response of the holobiont to increased temperature. Further, the project examines whether holobiont response to increased temperature associated with climate change depends on particular GxG host-symbiont combinations. Moreover, the investigators will examine the effects of symbiont history on mutualist hosts, which have been largely ignored in eco-evolutionary studies. These experiments provide a first step in predicting whether invertebrate hosts on coral reefs will respond to global change via adaptation of their symbionts.</p>
Host Symbiont Temp Response
largerWorkCitation
project
eng; USA
oceans
SUNY - Buffalo lab
-81.75458
-80.26195
24.54955
25.1326
2008-01-01
2016-12-31
Florida Keys, Caribbean
0
BCO-DMO catalogue of parameters from Symbiodinium cultures isolated from the octocoral Antillogorgia bipinnata in the Florida Keys and processed at Coffroth lab at the University at Buffalo in 2008, 2013 and 2016 (Host Symbiont Temp Response 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/728495.rdf
Name: Culture_ID
Units: unitless
Description: <p>Identification of sample; culture name (08-0689.4; 08-0689.6; 08-0690.1; 13-117; 13-143; etc.)</p>
http://lod.bco-dmo.org/id/dataset-parameter/728496.rdf
Name: Incubation_Temperature
Units: degree Celsius (C)
Description: <p>Temperature at which the culture is maintained</p>
http://lod.bco-dmo.org/id/dataset-parameter/728497.rdf
Name: Host
Units: unitless
Description: <p>Octocoral from which the symbiont was isolated. Note - In the vast majority of cases; the culture is NOT representative of the host symbiont population (Santos et al 2001)</p>
http://lod.bco-dmo.org/id/dataset-parameter/728498.rdf
Name: Putative_Species
Units: unitless
Description: <p>Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/728499.rdf
Name: Location
Units: unitless
Description: <p>Location where adult colony was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/728500.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample location; positive north.</p>
http://lod.bco-dmo.org/id/dataset-parameter/728501.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of sample location; positive east</p>
http://lod.bco-dmo.org/id/dataset-parameter/728502.rdf
Name: State_Country
Units: unitless
Description: <p>State/Country where adult colony was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/728503.rdf
Name: Ocean
Units: unitless
Description: <p>Ocean where adult colony was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/728504.rdf
Name: Host_stage
Units: unitless
Description: <p>Developmental stage of host</p>
http://lod.bco-dmo.org/id/dataset-parameter/728505.rdf
Name: Axenic
Units: unitless
Description: <p>Whether or not the culture is axenic</p>
http://lod.bco-dmo.org/id/dataset-parameter/728506.rdf
Name: Isolated_by
Units: unitless
Description: <p>Researcher who isolated the culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/728507.rdf
Name: Year_isolated
Units: years
Description: <p>The year in which the culture was isolated in four digit year format</p>
http://lod.bco-dmo.org/id/dataset-parameter/728508.rdf
Name: Clade
Units: unitless
Description: <p>Clade designation</p>
http://lod.bco-dmo.org/id/dataset-parameter/728509.rdf
Name: cp_type
Units: unitless
Description: <p>Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003) as base pairs</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
17165
https://darchive.mblwhoilibrary.org/bitstream/1912/24646/1/dataset-728215_cultures-isolated-bipinnata-2008-2016__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.728215.1
download
onLine
dataset
<p>Symbionts were isolated from adult colonies of <em>Antillogorgia bipinnata</em> following the protocol outline in Santos et al 2001. Briefly, a small piece (1-2 cm) of the branch was ground in a glass tissue homogenizer with 2 ml of filtered seawater (FSW) and poured through a series of meshes (250 µm on top, then 120 µm, then 70 µm mesh) into a 15 ml tube.&nbsp; The mesh was washed with 1 ml FSW several times for a final volume between 3 and 10&nbsp;ml. This slurry was spun for 5 min at 500-800 rpm on a Beckman J6-HC centrifuge to pellet symbiont cells, the supernatant removed and resuspended in 10 ml of FSW.&nbsp; This step was repeated again and then the pellet was resuspended in 1.0 ml of F/2 (Gulliard and Ryther 1962).&nbsp; Cultures were started by using 20-50 µl of the resuspended pellets to inoculate 30ml of F/2 and incubated at the appropriate temperature.&nbsp; &nbsp; &nbsp;</p>
<p>Clade identity and Cp-type were determined following the protocols outline in Santos et al (2003). Briefly, DNA was amplified using the primers HYPERUP and HYPERDN on and MJ96 or BioRad thermocyclers. PCR products were visualized and scored using size standards on a LI-COR 4200 NEN® Global IR2 DNA sequencing system as specified in Santos et al (2003). Putative species identity was based on sequence analysis of B7SYM15 flanking region (LaJeunesse et al. 2012, Parkinson et al. 2015).&nbsp; Briefly, the B7SYM15 flanking region was amplified and directly sequenced in 5’ and 3’ directions on a 3730XL DNA Analyzer (High Throughput Genomics Center, University of Washington). Sequences were compared to known species within the GenBank database using BLAST- Basic Local Alignment Search Tool (<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a>).&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO processing:</strong></p>
<ul>
<li>added conventional header with dataset name, PI name, version date</li>
<li>modified parameter names to conform with BCO-DMO naming conventions</li>
<li>converted latitude and longitude format from degrees, decimal&nbsp;minutes, hemisphere (DD MM.MMH) to decimal degrees (DD.DDDD).</li>
<li>Adjusted the Incubation_Temperature values to remove the additional units from the values. (eg. 16_C converted to 16).</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
LI-COR 4200 NEN® Global IR2 DNA
LI-COR 4200 NEN® Global IR2 DNA
PI Supplied Instrument Name: LI-COR 4200 NEN® Global IR2 DNA PI Supplied Instrument Description:DNA was amplified using the primers HYPERUP and HYPERDN on and MJ96 thermocycler and PCR products were visualized and scored using size standards on the LI-COR 4200 NEN® Global IR2 DNA sequencing system as specified in Santos et al (2003). 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.
3730XL DNA Analyzer
3730XL DNA Analyzer
PI Supplied Instrument Name: 3730XL DNA Analyzer PI Supplied Instrument Description:The B7SYM15 flanking region was amplified and directly sequenced in 5’ and 3’ directions on a 3730XL DNA Analyzer (High Throughput Genomics Center, University of Washington). 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.
Beckman J6-HC centrifuge
Beckman J6-HC centrifuge
PI Supplied Instrument Name: Beckman J6-HC centrifuge PI Supplied Instrument Description:This slurry was spun for 5 min at 500-800 rpm on a Beckman J6-HC centrifuge to pellet symbiont cells, the supernatant removed and responded in 10 ml of FSW. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Deployment: Coffroth_2008-16
Coffroth_2008-16
SUNY-Buffalo
laboratory
Coffroth_2008-16
Mary Alice Coffroth
State University of New York at Buffalo
SUNY-Buffalo
laboratory