Dataset: Cultures isolated from A. bipinnata 2008-2016

Name: 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)
Published: 2018-02-16
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.728215.1

Spatial Extent: N:25.1326 E:-80.26195 S:24.54955 W:-81.75458

Temporal Extent: 2008 - 2016

Project:

RUI: Collaborative Research: Genetic variation as a driver of host and symbiont response to increased temperature on coral reefs (Host Symbiont Temp Response)

Principal Investigator:

Mary Alice Coffroth (State University of New York at Buffalo, SUNY Buffalo)

Co-Principal Investigator:

Casey terHorst (California State University Northridge, CSUN)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-02-16

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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)

Abstract:

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.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2018-02-16	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.728215.1	2019-10-02

Description

Symbiodinium cultures isolated from adult colonies of the octocoral Antillogorgia bipinnata in 2008, 2013 and 2016, grown at either 26 or 30 degrees C.

Cultures initially isolated from Antillogorgia bipinnata colonies collected in the lower keys in the vicinity of Looe Key (24 32.973'N 81 22.849'W) in 2008, the middle keys near Tennessee Reef (24 45.150'N 81 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). Culture have been maintained in the Coffroth lab, University at Buffalo.

Methods & Sampling

Symbionts were isolated from adult colonies of Antillogorgia bipinnata 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. The mesh was washed with 1 ml FSW several times for a final volume between 3 and 10 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. This step was repeated again and then the pellet was resuspended in 1.0 ml of F/2 (Gulliard and Ryther 1962). Cultures were started by using 20-50 µl of the resuspended pellets to inoculate 30ml of F/2 and incubated at the appropriate temperature.

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). 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 (https://blast.ncbi.nlm.nih.gov/Blast.cgi).

Data Processing Description

BCO-DMO processing:

added conventional header with dataset name, PI name, version date
modified parameter names to conform with BCO-DMO naming conventions
converted latitude and longitude format from degrees, decimal minutes, hemisphere (DD MM.MMH) to decimal degrees (DD.DDDD).
Adjusted the Incubation_Temperature values to remove the additional units from the values. (eg. 16_C converted to 16).

Data Files

File
Symbiodinium_cultures.csv (Comma Separated Values (.csv), 16.53 KB) MD5:b3066810e9d143d2992069105f53b7eb Primary data file for dataset ID 728215

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1559286

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Coffroth_2008-16		2008-01-01	SUNY-Buffalo	Mary Alice Coffroth (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: LI-COR 4200 NEN® Global IR2 DNA

Supplied 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 Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Automated DNA Sequencer

Supplied Name: 3730XL DNA Analyzer

Supplied 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 Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

Centrifuge

Supplied Name: Beckman J6-HC centrifuge

Supplied 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 Type

Generic Name: Centrifuge

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Culture_ID	Identification of sample; culture name (08-0689.4; 08-0689.6; 08-0690.1; 13-117; 13-143; etc.)	unitless	sample
Incubation_Temperature	Temperature at which the culture is maintained	degree Celsius (C)	temp_inc
Host	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)	unitless	species
Putative_Species	Putative species based on sequence analysis of B7 SYM15 flanking region (LaJeunesse et al 2012; Parkinson et al 2015)	unitless	species
Location	Location where adult colony was collected	unitless	site_descrip
Latitude	Latitude of sample location; positive north.	decimal degrees	lat
longitude	Longitude of sample location; positive east	decimal degrees	lon
State_Country	State/Country where adult colony was collected	unitless	region
Ocean	Ocean where adult colony was collected	unitless	region
Host_stage	Developmental stage of host	unitless	stage
Axenic	Whether or not the culture is axenic	unitless	no_bcodmo_term
Isolated_by	Researcher who isolated the culture	unitless	person
Year_isolated	The year in which the culture was isolated in four digit year format	years	year
Clade	Clade designation	unitless	taxon
cp_type	Fragment length of the hypervariable region of Domain V of symbiont 23S rDNA (Santos et al 2003) as base pairs	unitless	no_bcodmo_term