the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Implementing a coral reef CaCO3 production module in the iLOVECLIM climate model
Nathaelle Bouttes
Lester Kwiatkowski
Manon Berger
Victor Brovkin
Guy Munhoven
Abstract. Coral reef development is intricately linked to both climate and the concentration of atmospheric CO2, specifically through temperature and carbonate chemistry in the upper ocean. In turn, the calcification of corals modifies the concentration of dissolved inorganic carbon and total alkalinity in the ocean, impacting air-sea gas exchange, atmospheric CO2 concentration, and ultimately the climate. This retroaction between atmospheric conditions and coral biogeochemistry can only be accounted for with a coupled coral-carbon-climate model. Here we present the implementation of a coral reef calcification module into an Earth System model. Simulated coral reef production of the calcium carbonate mineral aragonite depends on photosynthetically active radiation, nutrient concentrations, salinity, temperature and the aragonite saturation state. An ensemble of 210 parameter perturbation simulations was performed to identify carbonate production parameter values that optimise the simulated distribution of coral reefs and associated carbonate production. The tuned model simulates the presence of coral reefs and regional-to-global carbonate production values in good agreement with data-based estimates. The model enables assessment of past and future coral-climate coupling on seasonal to millennial timescales, highlighting how climatic trends and variability may affect reef development and the resulting climate-carbon feedback.
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Nathaelle Bouttes et al.
Status: open (until 25 Oct 2023)
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CC1: 'Quick comment on PAR data', Jean-Pierre Gattuso, 21 Jul 2023
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I will read this paper with great interest. You may want to consider using PAR at the bottom (with KD PAR rather than K490). A global dataset with 4.6 km resolution at the equator is available here:
- Gattuso J.-P., Gentili B., Antoine D. & Doxaran D., 2020. Global distribution of photosynthetically available radiation on the seafloor. Earth System Science Data 12:1697-1709. http://dx.doi.org/10.5194/essd-12-1697-2020
- Gentili, B.; Gattuso, J.-P. (2020): Photosynthetically available radiation (PAR) on the seafloor calculated from 21 years of ocean colour satellite data. PANGAEA, https://doi.org/10.1594/PANGAEA.910898
I doubt that using phytoplankton biomass and productivity, which are notoriously very low in coral reef areas, would provide better estimates of the light attenuation coefficient at such large spatial scale than using satelitte data. Note that the preferred unit for PAR is μmol photons m-2 s-1 (μmol m-2 s-1) and that EGU journals use negative exponents in units: μmol l-1 rather than μmol/l.
Citation: https://doi.org/10.5194/egusphere-2023-1162-CC1 -
CEC1: 'Comment on egusphere-2023-1162', Juan Antonio Añel, 03 Aug 2023
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Dear authors,
Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".https://www.geoscientific-model-development.net/policies/code_and_data_policy.htmlYour submission contains several flaws that must be addressed, specifically:- As the handling topical editor mentioned, the title must contain the version number and the name of the code that you have developed (iCORAL). Also, in the manuscript, you must clarify the iLOVECLIM version you use for your work.- You need to provide a repository for the iLOVECLIM version you use for your work. It is not enough to provide the iCoral module code, as it is only possible to test it with the remainder of the model.- The "Data Availability" section states that the data will be available in Zenodo. We do not admit this. Our policy is clear and requests that all the assets for a submitted manuscript must be available and public at submission time.I note that your manuscript should not have been accepted in Discussions, given this lack of compliance with our policy. Therefore, the current situation with your manuscript is irregular. In this way, if you do not fix this problem, we will have to reject your manuscript for publication in our journal.Therefore, please, provide the details (link and DOI) about versions and code and the input and output data used in your work, public in one of the appropriate repositories. You must do it by replying to this comment with the relevant information as soon as possible, as it should be available before the Discussions stage.Juan A. AñelGeosci. Model Dev. Executive EditorCitation: https://doi.org/10.5194/egusphere-2023-1162-CEC1 -
AC1: 'Reply on CEC1', Nathaelle Bouttes, 24 Aug 2023
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Dear editor,
We are sorry we did not comply with the policies. We have modified the manuscript accordingly.
Following the instructions, we have:
- added the name of the module with its version number (iCORAL version 1.0) in the title, which is now: “Implementing the iCORAL (version 1.0) coral reef CaCO3 production module in the iLOVECLIM climate model”.
We have also added the version numbers in the next, as well as the version number of iLOVECLIM (version 1.1.6). - provided a repository for the iLOVECLIM code for the reviewers by email
- made available the outputs from the model simulations used in the figures on zenodo (doi: 5281/zenodo.8279283), the data can be accessed at: https://doi.org/10.5281/zenodo.8279283
Nathaelle Bouttes
Citation: https://doi.org/10.5194/egusphere-2023-1162-AC1 - added the name of the module with its version number (iCORAL version 1.0) in the title, which is now: “Implementing the iCORAL (version 1.0) coral reef CaCO3 production module in the iLOVECLIM climate model”.
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CC2: 'Reply on CEC1', Didier Roche, 28 Aug 2023
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Dear Juan Anel,
Being responsible for the iLOVECLIM special issue, I would like to comment on your latest position on the availability of the code of iLOVECLIM in the current manuscript namely that "the problem with your manuscript continues to be that you are not publishing all the code necessary to reproduce your manuscript. That is, you should publish the code of iLOVECLIM."
To my knowledge, the current policy of GMD is what is defined in the Editorial v1.2 ( https://gmd.copernicus.org/articles/12/2215/2019/ ).
On the iLOVECLIM side, the present manuscript relies on the different versions that have been published according to that policy, with the caveat that we do not hold the Licensing on all the pieces of the iLOVECLIM code and that therefore we are unable to provide the code on an open source basis. I have been working on the topic and still hope to do so in the future, but it is not the case at present.
This has been reflected in subsequent publications of the iLOVECLIM Special Issue, for example Quiquet et al., 2018:Code availability. The iLOVECLIM source code is based on the
LOVECLIM model version 1.2 whose code is accessible at http://
www.elic.ucl.ac.be/modx/elic/index.php?id=289 (UCL, 2018). The
developments on the iLOVECLIM source code are hosted at http:
//forge.ipsl.jussieu.fr/ludus (IPSL, 2018), but are not publicly avail-
able due to copyright restrictions. Access can be granted on demand
by request to D. M. Roche (didier.roche@lsce.ipsl.fr) to those who
conduct research in collaboration with the iLOVECLIM user group.
For this work we used the model at revision 706This approach is at present compliant with the Editorial v1.2 of the GMD journal that states :
" All manuscripts must at a minimum provide confidential access to the code and data developed in the manuscript for the editor and reviewers in order to enable peer review (see Appendix A1)."
"In the case where the new code and data described in the paper are not restricted but are part of a larger code and data structure that has other restricted elements, it is still possible to satisfy the GMD requirements by making the new parts of the code and data available. As the result is usually not a coherent model which can be expected to compile, authors sometimes prefer to upload these code fragments to the supplement rather than to a repository. Authors may have to remove restricted elements from their model code base, but in the meantime this remains an acceptable if somewhat unsatisfactory solution."
The latest changes proposed by Bouttes et al. in the comment above do match those two definitiions unless I am mistaken, since the complete code has been made available to the reviewers under the cover of the managing editor.
Coule you then please highlight where the issue stills stands for this manuscript (if at all)?
Best wishes,
Didier ROCHE
Citation: https://doi.org/10.5194/egusphere-2023-1162-CC2 -
CEC2: 'Reply on CC2', Juan Antonio Añel, 28 Aug 2023
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Dear Didier, dear authors,
Many thanks for the explanation provided regarding the iLOVECLIM model.
I find especially relevant the explanation that you can not share parts of the model because their licenses do not permit it, and that you do not own the copyright. I understand that this is the meaning of "hold the licensing". This is reasonable, and acceptable according to our policy. Also, it is great to know that you are working to solve the situation.
My only concern now is that the links that you provide for the code, are simple web servers, and although they seem to have been working since 2018, and continue to work, they are not the kind of repository that we trust as listed in the policy. It would be desirable that you make copies of them in Zenodo private repositories, which, additionally, will provide a DOI. In this way, you would continue to have the distribution of the code under control, and we can be sure that it is properly stored and will not be lost in future. This is not mentioned in our policy, but we have been asking for it since some time ago to authors, as a best practice.
Otherwise, with your explanation, I agree that your manuscript is now compliant with the policy, and the issue is solved with the information that you have provided.
Regards,
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2023-1162-CEC2
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CEC2: 'Reply on CC2', Juan Antonio Añel, 28 Aug 2023
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AC1: 'Reply on CEC1', Nathaelle Bouttes, 24 Aug 2023
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CC3: 'Comment on egusphere-2023-1162', David Archer, 20 Sep 2023
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The goal of this work, to create a coastal CaCO3 coral module for a long-term climate / carbon cycle code, is extremely useful and strategic. There is no doubt that corals must have had a strong impact on the carbon cycle evolution through time. The model construction and validation are thorough and thoughtful, and the presentation is clear and polished. The actual scientific fruits of this work will come in future simulations of the interactions of the corals with the rest of the climate system; the current paper is more of a model description and tuning relative to present-day data. Which is necessary and fine. I'm not coming up with many suggestions for improvement, but rather an endorsement of publication as is, as far as I am concerned.
Citation: https://doi.org/10.5194/egusphere-2023-1162-CC3
Nathaelle Bouttes et al.
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