Dataset: qPCR assays

Name: Results from qPCR assays to quantify the abundance and photochemical performance of symbionts relative to coral cells in three coral species collected from colonies in southeast Florida in April and October 2019 before, during, and after heat stress tests
Published: 2024-01-22
Keywords: coral bleaching, Symbiodiniaceae, qPCR, thermotolerance, symbiont shuffling, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.918220.1

Spatial Extent: N:25.6788 E:-80.0974 S:25.6773 W:-80.1005

Emerald Reef off Key Biscayne, SE Florida (USA)

Temporal Extent: 2019-05-22 - 2020-03-05

Project:

Collaborative Research: Assessing the changing symbiotic milieu on Caribbean coral reefs under climate change: magnitude, tradeoffs, interventions, and implications (Symbiont Shifts on Reefs)

Principal Investigator:

Andrew Baker (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

Co-Principal Investigator:

Ross Cunning (Shedd Aquarium)

Student:

Daisy Buzzoni (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-01-22

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Results from qPCR assays to quantify the abundance and photochemical performance of symbionts relative to coral cells in three coral species collected from colonies in southeast Florida in April and October 2019 before, during, and after heat stress tests

Abstract:

This dataset contains results from assays to quantify the abundance and photochemical performance of Breviolum, Cladocopium, and Durusdinium symbionts relative to coral cells in Montastraea cavernosa, Orbicella faveolata, and Siderastrea siderea corals collected from colonies in southeast Florida in April 2019 and in October 2019, before, during and after aquarium-based experimental heat stress tests. Bulk genomic DNA was extracted from tissue scrapings taken from 2.5cm diameter cores of corals and was used as a template for symbiont genus-specific qPCR assays. The resulting CT values were used to calculate the relative abundance of each symbiont genus within each coral core over the course of the heat stress. The photochemical efficiency of each coral core was also measured periodically throughout heat stress tests using an imaging pulse amplitude modulated (I-PAM) fluorometer. The publication based on these data is Buzzoni, et al. (2023) (DOI: 10.1007/s00338-023-02428-x).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2024-01-22	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.918220.1	2024-01-24

Methods & Sampling

Coral cores of 2.5-centimeter (cm) diameter were collected from tagged colonies of three coral species in either April 2019 or October 2019 from Emerald Reef in Southeast Florida, USA. Cores were then maintained in 300-liter (L) indoor flow-through aquaria (in the Marine Technology and Life Science Seawater complex at the University of Miami's Rosenstiel School of Marine, Atmospheric, and Earth Science) and subjected to experimental heat stress. Before, during, and following the heat stress, 2-millimeter (mm) tissue samples were collected from cores and genomic DNA was subsequently extracted from these samples as per Cunning & Baker (2016). Quantitative PCR was performed using Taqman Environmental Master Mix and symbiont genus-specific and coral species-specific primers and probes targeting the actin gene (Cunning & Baker, 2013; Cunning et al., 2015). In addition to collecting tissue samples, the photochemical efficiency of symbionts within coral cores was also assayed before, during, and after heat stress using an imaging-PAM fluorometer.

Full methodology described in Buzzoni, et al. (2023) (DOI: 10.1007/s00338-023-02428-x)

Data Processing Description

All imaging-PAM and qPCR data were analysed in RStudio V4.2.1 (R Core Team, 2022). qPCR data were filtered to exclude samples lacking two technical replicates which amplified with Ct values under 40. Ct data were used to calculate the relative abundances of symbiont genera in tissue samples (relative to all Symbiodiniaceae present and relative to coral host cells) using the stepOneR package (Cunning, 2018). Ct data were also adjusted for differences between symbiont genera and coral species in target locus copy number, DNA extraction efficiency, and probe fluorescence intensity.

The Supplemental File "Ct_corrections_table.pdf" contains correction coefficients fed into StepOneR software along with qPCR Ct data. These correct for differences in host and symbiont DNA extraction efficiency and gene copy number, and for differences in fluorescence of target-specific probes.

BCO-DMO Processing

- Imported original file "qPCR_IPAM.csv" into the BCO-DMO system.
- Flagged "NA" as a missing data identifier (missing data are empty/blank in the final CSV file).
- Converted latitude and longitude values to decimal degrees and rounded to 4 decimal places.
- Converted the date column to YYYY-MM-DD format.
- Replaced the abbreviated species name with the full genus + species name.
- Renamed fields/columns to comply with BCO-DMO naming conventions.
- Saved the final file as "918220_v1_qpcr_ipam.csv".

Data Files

File
918220_v1_qpcr_ipam.csv (Comma Separated Values (.csv), 42.06 KB) MD5:533da1834438240361b966909f9c5ecc Primary data file for dataset ID 918220, version 1

Supplemental Files

File

Ct_corrections_table.pdf

(Portable Document Format (.pdf), 344.23 KB)
MD5:7a2ac5c366f2f3ee6894890ea868a6c1

Supplemental File for dataset ID 918220. Contains correction coefficients fed into StepOneR software along with qPCR Ct data. These correct for differences in host and symbiont DNA extraction efficiency and gene copy number, and for differences in fluorescence of target-specific probes. 

BCO-DMO converted the original file "Ct corrections table.docx" from .docx format to PDF.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851305
NSF Division of Ocean Sciences	OCE-1851392

Deployments

None available yet

Instruments

Drill

Supplied Name: submersible drill

Supplied Description:

Coral cores were extracted from reef colonies using a submersible drill (Nemo Power Tools Ltd.) fitted with a diamond core drill bit (Montana Brand Tools).

Instrument Type

Generic Name: Drill

Generic Description:

A drill is a tool used for making round holes or driving fasteners. There are many types of drills: some are powered manually, and others use electricity (electric drill) or compressed air as the motive power. Drills with a percussive action (hammer drills) are mostly used in hard materials such as masonry (brick, concrete, and stone) or rock. Some types of hand-held drills are also used to drive screws and other fasteners.

Fluorometer

Supplied Name: imaging pulse amplitude modulated (PAM) fluorometer

Supplied Description:

Photochemical efficiency was calculated using measurements from an imaging pulse amplitude modulated fluorometer (MAXI Version IMAGING-PAM M-Series, Walz, Effeltrich, Germany).

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

qPCR Thermal Cycler

Supplied Name: QuantStudio3 real-time PCR system

Supplied Description:

qPCR was performed using a QuantStudio3 real-time PCR system (Applied Biosystems).

Instrument Type

Generic Name: qPCR Thermal Cycler

Acronym: qPCR

Generic Description:

An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Species	Coral host species (M. cavernosa, O. faveolata or S. siderea)	unitless	species
Treatment	Experimental heat stress treatment that core was assigned to (Bleached or Control)	unitless	treatment
Core	Unique identifier of each 2.5 cm coral core ('coral species'-'colony tag'-'core tag')	unitless	sample
Collection_Latitude	Latitude of parent collection from which cores were collected; positive values = North	decimal degrees	lat
Collection_Longitude	Longitude of parent collection from which cores were collected; negative values = West	decimal degrees	lon
Timepoint	Context of the time tissue sample or IPAM measurement was taken with respect to the experimental heat stress (Pre-bleach, Post-bleach, Recovery, or Pre-outplant)	unitless	time_point
Sym_Host	In each tissue sample, the ratio of symbiont (the sum of Breviolum, Cladocopium and Durusdinium) cells to host coral cells, calculated using the StepOneR package (see methods for details) from technical replicates of qPCR target-specific Ct values (to 9 decimal places)	unitless	ratio
Y2	Maximum quantum yield of symbionts' PSII of a coral core, as detected by I-PAM fluorometer (to 3 decimal places)	unitless	quantum yield
PropD	In each tissue sample, the ratio of Durusdinium to total symbiont (the sum of Breviolum, Cladocopium and Durusdinium) cells, calculated using the StepOneR package (see methods for details) from technical replicates of qPCR target-specific Ct values (to 9 decimal places)	unitless	ratio
Batch	Denotes whether core was collected and heat stressed in either April 2019 (1) or October 2019 (2)	unitless	sample_descrip
Date	Date tissue sample/ IPAM measurement was taken in the format YYYY-MM-DD (Eastern Standard Time) Format: %Y-%m-%d	unitless	date
Colony	Tag number of field colony from which cores were extracted (2, 3, 4, 13, 16, 18, 19, 21, 22, 23, 26, 27, 28, 34, 35, 36, 39, 41, 48, 62, 64, 65, 66, 67, 68, 71, 72, 81, 87, 100)	unitless	sample

Database

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Dataset: qPCR assays