Transcriptomics of thermal stress response in corals
Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals
Recommendation: posted 26 August 2019, validated 04 September 2019
Jacob, S. (2019) Transcriptomics of thermal stress response in corals. Peer Community in Ecology, 100028. 10.24072/pci.ecology.100028
Climate change presents a challenge to many life forms and the resulting loss of biodiversity will critically depend on the ability of organisms to timely respond to a changing environment. Shifts in ecological parameters have repeatedly been attributed to global warming, with the effectiveness of these responses varying among species [1, 2]. Organisms do not only have to face a global increase in mean temperatures, but a complex interplay with another crucial but largely understudied aspect of climate change: thermal fluctuations. Understanding the mechanisms underlying adaptation to thermal fluctuations is thus a timely and critical challenge.
Coral reefs are among the most threaten ecosystems in the context of current global changes . Brener-Raffalli and colleagues  provided a very complete study digging into the physiological, symbiont-based and transcriptomic mechanisms underlying response of corals to temperature changes. They used an experimental approach, following the heat stress response of coral colonies from different species of the genus Pocillopora. While the symbiont community composition did not significantly change facing exposure to warmer temperatures, the authors provided evidence for transcriptomic changes especially linked to stress response genes that may underlie plastic responses to heat stress.
The authors furthermore investigated the thermal stress response of corals originating from two sites differing in their natural thermal regimes, and found that they differ in the extent and nature of plastic response, including the expression of gene regulation factors and the basal expression level of some genes. These two sites also differ in a variety of aspects, including the focal coral species, which precludes from concluding about the role of thermal regime adaptation into the differences observed. However, these results still highlight a very interesting and important direction deserving further investigation , and point out the importance of variability in thermal stress response among localities  that might potentially mediate global warming consequences on coral reefs.
 Parmesan, C., & Yohe, G. (2003). A globally coherent fingerprint of climate change impacts across natural systems. Nature, 421(6918), 37–42. doi: 10.1038/nature01286
 Menzel, A., Sparks, T. H., Estrella, N., Koch, E., Aasa, A., Ahas, R., … Zust, A. (2006). European phenological response to climate change matches the warming pattern. Global Change Biology, 12(10), 1969–1976. doi: 10.1111/j.1365-2486.2006.01193.x
 Bellwood, D. R., Hughes, T. P., Folke, C., & Nyström, M. (2004). Confronting the coral reef crisis. Nature, 429(6994), 827–833. doi: 10.1038/nature02691
 Brener-Raffalli, K., Vidal-Dupiol, J., Adjeroud, M., Rey, O., Romans, P., Bonhomme, F., Pratlong, M., Haguenauer, A., Pillot, R., Feuillassier, L., Claereboudt, M., Magalon, H., Gélin, P., Pontarotti, P., Aurelle, D., Mitta, G. and Toulza, E. (2019). Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals. BioRxiv, 398602, ver 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/398602
 Kenkel, Carly D., and Matz, M. V. (2017). Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nature Ecology and Evolution, 1(1), 0014. doi: 10.1038/s41559-016-0014
 Kenkel, C. D., Meyer, E., and Matz, M. V. (2013). Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Molecular Ecology, 22(16), 4322–4334. doi: 10.1111/mec.12390
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/398602
Version of the preprint: 2
Author's Reply, 20 Aug 2019
Decision by Staffan Jacob, posted 17 May 2019
Dear Eve Toulza,
following the submissions of your revisions, the two reviewers and myself agree to acknowledge helpful clarifications of several aspects of your manuscript. The reviewers still pointed out a number issues that should be dealt with, especially regarding the introduced concepts on the link between plasticity and adaptation and the way analyses were performed. I thus invite you to carefully use the reviewers’ comments to revise your manuscript.
All the best, Staffan.
Additional requirements of the managing board:
As indicated in the 'How does it work?’ section and in the code of conduct, please make sure that:
-Data are available to readers, either in the text or through an open data repository such as Zenodo (free), Dryad (to pay) or some other institutional repository. Data must be reusable, thus metadata or accompanying text must carefully describe the data.
-Details on quantitative analyses (e.g., data treatment and statistical scripts in R, bioinformatic pipeline scripts, etc.) and details concerning simulations (scripts, codes) are available to readers in the text, as appendices, or through an open data repository, such as Zenodo, Dryad or some other institutional repository. The scripts or codes must be carefully described so that they can be reused.
-Details on experimental procedures are available to readers in the text or as appendices.
-Authors have no financial conflict of interest relating to the article. The article must contain a "Conflict of interest disclosure" paragraph before the reference section containing this sentence: "The authors of this preprint declare that they have no financial conflict of interest with the content of this article." If appropriate, this disclosure may be completed by a sentence indicating that some of the authors are PCI recommenders: “XXX is one of the PCI XXX recommenders.”
Reviewed by Mar Sobral, 16 Apr 2019
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/398602
Version of the preprint: 1
Author's Reply, 08 Apr 2019
Decision by Staffan Jacob, posted 26 Oct 2018
two reviewers have read your manuscript entitled "Gene expression plasticity and frontloading promote thermotolerance in Pocilloporid corals" and provided detailed and constructive reviews. As you will see, they both appreciated the topic, the experimental approach used and the impressive diversity of measures performed. However, they also raised a number of important concerns and requests, from the theory concepts to clarification of experimental design and important changes into the way analyses were performed. The authors should also modify throughout the manuscript the statements made about the link between thermal sensitivity and the traits quantified to make clear that the study consist in contrasting two populations (and even species), that differ in thermal regime but certainly not only. I need to make clear that, although your manuscript potentially represent an interesting contribution to the literature, that the conclusions hold on a comparison between two populations/species is a critical specificity of this study that should be outlined and made clear throughout the manuscript.
I encourage the authors to consider these detailed reviews to carefully revise their manuscript. Please keep in mind that the correct integration of the reviewers' requests is compulsory for the acceptance of this manuscript, but that I am uncertain at this step whether all these serious objections can be adequately addressed.
Thank you for submitting your work to PCI Ecology. I look forward to see the revised version of your manuscript soon.