Dataset: Final Physiology

Name: Physiological metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress
Published: 2021-08-11
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.858150.1

Spatial Extent: N:22.275795 E:39.113112 S:22.275795 W:39.113112

Temporal Extent: 2019-07-29 - 2019-08-11

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:

Mark E. Warner (University of Delaware)

Scientist:

Nicolas R. Evensen (Old Dominion University, ODU)

BCO-DMO Data Manager:

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

Version:

Version Date:

2021-08-11

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Physiological metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress

Abstract:

This dataset includes physiological response metrics recorded at the end of experiments conducted to examine two coral species' responses to thermal stress. Species examined were Acropora hemprichii and Porites lobata. Experiments were performed in Thuwal, Saudi Arabia in July-August 2019.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-08-11	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.858150.1	2021-08-11

Methods & Sampling

Multiple ramets of five genets of Acropora hemprichii and five genets of Porites lobata were collected from two sites (protected and exposed) used in two experiments: an 18 h acute thermal stress assay using the Coral Bleaching Automated Stress System (CBASS) and a two-week prolonged heating experiment using the indoor aquarium system at the King Abdullah University of Science and Technology (KAUST) Coastal and Marine Resources laboratory. Physiological responses of the coral host and associated endosymbionts were measured during (Fv/Fm, and phosynthesis and respiration) and at the end of the experiments (Final: symbiont densities, host protein, and chlorophyll a concentrations per cell and per cm2). Experimental tanks were ramped up from the 32°C control treatment to temperature treatments reaching 35°C, 36.5°C, and 38°C over 3h in the CBASS, and temperature treatments reaching 33.5°C, 35°C, and 36.5°C in the prolonged experiment at rates of 0.5 and 1.5°C per day. Each temperature treatment contained two replicate tanks (A and B).

Corals were subjected to short-term (7h) acute thermal profiles with four peak target temperatures (32°C, 35°C, 36.5°C, and 38°C), versus more prolonged heat exposures lasting 7 to 15 days, where temperatures were raised 0.5 and 1.5°C per day to four target temperatures (32°C, 33.5°C, 35°C, and 36.5°C). Physiological response metrics were recorded during and at the end of the experiments.

This dataset includes the final physiological metrics from both experiments.

Problem report:
Missing data were samples that were not measured or that are missing due to sample mortality.

Data Processing Description

Data Processing:
Data were organised using R statistical software (version 4.0.3).

BCO-DMO Processing:
- renamed fields to comply with BCO-DMO naming conventions.

The originally submitted GitHub repository https://github.com/BarshisLab/Heating-Duration-vs-Intensity-vs-RampRate was forked to https://github.com/BCODMO/Heating-Duration-vs-Intensity-vs-RampRate and tagged with release 1.0, which corresponds with this dataset submission. The original repository may have continued updates.

Data Files

File
final_physio.csv (Comma Separated Values (.csv), 32.69 KB) MD5:746f3ead8adf0bc6f2fbd79922a0f22f Primary data file for dataset ID 858150

Supplemental Files

File
Heating-Duration-vs-Intensity-vs-RampRate-1.0.zip (ZIP Archive (ZIP), 9.89 MB) MD5:a762f0b8e1419f74653bf7da72a16296 Code used to analyze and plot data; associated with BCO-DMO datasets 858112, 858150, and 858180. These files are also available in the following GitHub repository: https://github.com/BCODMO/Heating-Duration-vs-Intensity-vs-RampRate/releases/tag/1.0

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1833201
NSF Division of Ocean Sciences	OCE-1833215

Deployments

None available yet

Instruments

3D scanner

Supplied Name: 3D scanner (HDI 120, LMI Technologies Inc.)

Supplied Description:

Instrument Type

Generic Name: 3D scanner

Generic Description:

A 3D scan captures digital information about the shape of an object with equipment that uses a laser or light to measure the distance between the scanner and the object.

Aquarium

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Aquarium

Generic Description:

Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept

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)

Fluorometer

Supplied Name: Pulse amplitude-modulated (PAM) fluorometer (MINI-PAM, WALZ)

Supplied Description:

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.

Homogenizer

Supplied Name: handheld homogenizer (Diax 900, Heidolph Instruments)

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.

Oxygen Sensor

Supplied Name: fiberoptic oxygen probes (FireSting O2, Pyroscience)

Supplied Description:

Instrument Type

Generic Name: Oxygen Sensor

Acronym: Dissolved Oxygen Sensor

Generic Description:

An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed

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
Species	species: Acropora or Porites	unitless	species
Experiment	experiment: CBASS = Coral Bleaching Automated Stress System; Prolonged = two-week prolonged heating experiment at the King Abdullah University of Science and Technology (KAUST)	unitless	exp_type
Ramp	method of ramping up temperature	unitless	treatment
Temperature	temperature	degrees Celsius	temp
Treatment	treatment	unitless	treatment
Tank	tank ID	unitless	tank
Site	description of coral collection site: exposed or protected	unitless	site_descrip
Genotype	genotype	unitless	species
Replicate	replicate: each temperature treatment contained two replicate tanks (A and B)	unitless	replicate
Sym_density	symbiont densities measured in each ramet, normalised to the surface area of the ramet	cells per square centimeter (cells per cm2)	density
Pro	animal protein concentrations extracted from each ramet, normalised to the surface area of the ramet	milligrams per square centimeter (mg per cm2)	proteins
Chla_cell	chlorophyll a extracted from algal symbionts extracted in each ramet, normalised to number of symbiont cells in each ramet	picograms per (pg per cell)	chl_a
Chla	chlorophyll a extracted from algal symbionts extracted in each ramet, normalised to the surface area of the ramet	micrograms per square centimeter (ug per cm2)	chl_a

Status message

Database

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Dataset: Final Physiology