Dataset: Symbiont type in recovering corals
Deployment: Coffroth_2010

symbiont type in recovering Porites divaricata corals

Principal Investigator:

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

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective (SymBioSys)

Current State:

Final no updates expected

Version:

2015-01-15

Version Date:

2015-01-15

Data URL:

https://www.bco-dmo.org/dataset-deployment/546157/data

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Description

Data on symbiont type in recovering corals (Porites divaracata) by treatment following inoculation with a specific symbiont type following heat-induced bleaching.

Related Reference:

Coffroth MA, Poland DM, Petrou EL, Brazeau DA, Holmberg JC (2010) Environmental Symbiont Acquisition May Not Be the Solution to Warming Seas for Reef-Building Corals. PLoS ONE 5(10): e13258. doi:10.1371/journal.pone.0013258. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013258

Methods & Sampling

Dataset acquisition description

All cultures were obtained from the BURR Culture Collection and used to inoculate bleached colonies of Porites divaricata. Collections were made in the vicinity of Long Key, FL, oceanside (N24^o 49.791’ W80^o 45.743’) and experimentation was performed at the Keys Marine Laboratory, Long Key, FL

Coral colonies were sampled a total of 4 times throughout the experiment. Symbionts present in the tissue samples were characterized based on sequence variation in the symbiont chloroplast 23S rDNA following the protocols of Santos et al. 2003, Mar.Biotech. 5:130-140

Reference:
- Santos SR, Gutiérrez-Rodríguez C, Coffroth MA (2003) Phylogenetic identification of symbiotic dinoflagellates via length heteroplasmy in domain V of chloroplast large subunit (cp23S)-rDNA sequences. Mar Biotech 5: 130-140 for technique to characterize symbionts based on of chloroplast large subunit (cp23S)-rDNA

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

- original file: Coffroth et al 2010_ Data Summary_cp-type.xlsx
- added conventional header with dataset name, PI name, version date, reference information
- changed parameter names to be BCO-DMO compatible
- combined 7 tables and reformated data to flat file
- removed or replaced spaces with underscores
- replaced > with gt_ and < with lt_
- changed 'no amp' to 'no_amplification'

Revisions:
2015-01-29: small formatting changes to strong and weak bp columns
2015-01-15: originally submitted data

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0424996	NSF Division of Ocean Sciences
OCE-0926822	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

LI-COR 4200 NENH Global IR2 DNA sequencing system (LI-COR Biosciences, Lincoln, NE,USA)

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.

Spectrophotometer

Supplied Description:

Nano-Drop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE)

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Thermal Cycler

Supplied Description:

Stratagene Mx3005P QPCR System (Stratagene, La Jolla, CA.)

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
lab	laboratory identification; for mapping puposes	unitless	laboratory
lat	latitude of lab; north is positive	decimal degrees	lat
lon	londitude of lab; east is positive	decimal degrees	lon
genotype	23S chloroplast genotype	unitless	no_bcodmo_term
treatment_inoculant	infection treatment of Porites: Symbiodinium types A188; B211; B224 and D206 (letter=clade code; number=base pair size of the particular cp23S-rDNA domain V allele)	unitless	treatment
sample_id	specimen identification: Pd=Porites divaricata	unitless	sample
date	sampling date	yyyy-mm-dd	date
description	whether sampling was pre- or post-bleaching	unitless	no_bcodmo_term
strong_base_pairs	sequence variation of strong base pairs of symbiont chloroplast 23S rDNA	unitless	no_bcodmo_term
weak_base_pairs	sequence variation of weak base pairs of symbiont chloroplast 23S rDNA	unitless	no_bcodmo_term
comments	comments	unitless	comment

Database

Contribute Data

Dataset: Symbiont type in recovering corals
Deployment: Coffroth_2010

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Symbiont type in recovering coralsDeployment: Coffroth_2010

Dataset acquisition description

Dataset Processing Description

Dataset: Symbiont type in recovering corals
Deployment: Coffroth_2010