Dataset: Red Sea Gradient Physiology

Name: Coral physiology data (chlorophyll a, symbiont densities) on four collected coral species from six sites in the Red Sea from 2018 to 2020
Published: 2021-11-03
Keywords: ocean warming, Red Sea, thermal stress, coral thermotolerance, standardized acute assays, Coral Bleaching Automated Stress System (CBASS), oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.863786.1

Spatial Extent: N:29.501771 E:40.962027 S:18.985395 W:34.917925

Temporal Extent: 2018-07-31 - 2018-08-21

Project:

EAGER: Collaborative Research: Bleaching phenotypes of acute vs. chronic coral bleaching susceptibility and resilience: towards a standardized coral resilience diagnostic (EAGER-CBASS)

Principal Investigator:

Daniel J. Barshis (Old Dominion University, ODU)

Co-Principal Investigator:

Christian R. Voolstra (University of Konstanz, UK)

Scientist:

Nicolas R. Evensen (Old Dominion University, ODU)

Contact:

Nicolas R. Evensen (Old Dominion University, ODU)

BCO-DMO Data Manager:

Taylor Heyl (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

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

Version:

Version Date:

2021-11-03

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Coral physiology data (chlorophyll a, symbiont densities) on four collected coral species from six sites in the Red Sea from 2018 to 2020

Abstract:

This dataset contains measurements of coral physiology (chlorophyll a and symbiont densities) following 18-hour acute thermal stress experiments, where temperatures were ramped up to 30, 33, 36, and 39 degrees Celsius. Four coral species (Acropora hemprichii, Pocillopora verrucosa, Porites lobata, and Stylophora pistillata) were sampled from six sites along the length of the Red Sea, down to Djibouti in the Gulf of Aden.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-11-03	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.863786.1	2021-11-08

Methods & Sampling

Data are from experiments performed across multiple sites in Israel, Saudi Arabia, and Djibouti. Multiple ramets from seven genets of Acropora hemprichii, Pocillopora verrucosa, Porites lobata, and Stylophora pistillata were collected from six sites along the Red Sea and used in an 18-hour acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS).

Corals were subjected to 18-hour acute thermal profiles with four peak target temperatures (30°C, 33°C, 36°C, and 39°C). Experimental tanks were ramped up from the 30 degrees Celsius control treatment to temperature treatments reaching 33°C, 36°C, and 36.5°C in the prolonged experiment at rates of 0.5 and 1.5 degrees C per day. Each temperature treatment contained two replicate tanks (A and B).

Chlorophyll a and symbiont densities as physiological response metrics were recorded and at the end of the experiments. A MicroDisTec homogenizer 125 (Thermo Fisher Scientific), SpectraMax Paradigm Multi‐Mode Microplate Reader (Molecular Devices), and flow cytometer (BD LSRFortessa, BD Biosciences) were used.

'Chla_cm2' refers to chlorophyll a extracted from algal symbionts extracted in each ramet, normalized to the surface area of the ramet (µg per cm²). 'Sym_density' refers to symbiont densities measured in each ramet, normalized to the surface area of the ramet (cells per cm²).

Problems/Issues:
There are some missing data due to sample loss or mortality.

Data Processing Description

Data Processing:
Data were organized using Microsoft Excel and R statistical software (version 4.0.3).

Code used to analyze and plot data is available on GitHub: https://github.com/BarshisLab/Gradient-physiology.

BCO-DMO Processing:
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;
- Added a conventional header with dataset name, PI names, version date;
- Converted Collection_Date to YYYY-MM-DD format.

Originally submitted GitHub repository https://github.com/BarshisLab/Gradient-physiology was forked to https://github.com/BCODMO/Gradient-physiology/tree/v1.0 for curation purposes and tagged with release 1.0, which corresponds with this dataset submission. The code is attached to this record as a Supplemental File. Note the original repository may have continued updates.

Data Files

File
Red_Sea_Physio.csv (Comma Separated Values (.csv), 24.87 KB) MD5:e5384ff6d748c2f7d3d30809e4a6719a Primary data file for dataset ID 863786

Supplemental Files

File
Gradient-physiology-1.0.zip (ZIP Archive (ZIP), 24.45 MB) MD5:23bd53d1798c0cce2c4822f0c7543bcb Code used to analyze and plot data; associated with BCO-DMO datasets 863771, 863786, 863800. These files are also available in the following GitHub repository: https://github.com/BCODMO/Gradient-physiology/releases/tag/v1.0

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1833201

Deployments

None available yet

Instruments

Coral Bleaching Automated Stress System

Supplied Name: CBASS

Supplied Description:

Instrument Type

Generic Name: Coral Bleaching Automated Stress System

Acronym: CBASS

Generic Description:

CBASS, which stands for "Coral Bleaching Automated Stress System", are portable, field-deployable experimental tanks used to apply rapid, acute heat stress challenges. This system is described in:

Voolstra, C. R., Buitrago‐López, C., Perna, G., Cárdenas, A., Hume, B. C. C., Rädecker, N., & Barshis, D. J. (2020). Standardized short‐term acute heat stress assays resolve historical differences in coral thermotolerance across microhabitat reef sites. Global Change Biology, 26(8), 4328-4343. Portico. https://doi.org/10.1111/gcb.15148

Flow Cytometer

Supplied Name: flow cytometer (BD LSRFortessa, BD Biosciences)

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Homogenizer

Supplied Name: MicroDisTec homogenizer 125 (Thermo Fisher Scientific)

Supplied Description:

Instrument Type

Generic Name: Homogenizer

Generic Description:

A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.

plate reader

Supplied Name: SpectraMax Paradigm Multi‐Mode Microplate Reader (Molecular Devices)

Supplied Description:

Instrument Type

Generic Name: plate reader

Generic Description:

Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Collection_Date	date of collection in format YYYY-MM-DD	unitless	date
Site_Latitude	latitude North	decimal degrees	lat
Site_Longitude	longitude East (West is negative)	decimal degrees	lon
Site	sampling site	unitless	site
Temperature	Temperature of tank	degrees Celsius	temp
Species	species name	unitless	species
Genotype	genotype identifier	unitless	no_bcodmo_term
Replicate	replicate identifier (A or B)	unitless	replicate
Label	Sample identifier	unitless	sample
Sym_Density	symbiont densities measured in each ramet, normalized to the surface area of the ramet	cells per square centimeter (cells per cm2)	density
Chla_cm2	chlorophyll a extracted from algal symbionts extracted in each ramet, normalized to the surface area of the ramet	micrograms per square centimeter (µg per cm2)	chl_a

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Database

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Dataset: Red Sea Gradient Physiology