the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Quantifying the role of ozone-caused damage to vegetation in the Earth system: A new parameterization scheme for photosynthetic and stomatal responses
Abstract. Surface ozone (O3) is the primary air pollutant threatening global vegetation. It typically reduces photosynthetic rate and stomatal conductance, leading to changes in carbon, water, and energy cycles, vegetation structure and composition, and climate. Several parameterization schemes have been developed to integrate the photosynthetic and stomatal responses to O3 exposure in regional and global process-based models to simulate time- and space-varying O3 plant damage and its cascading dynamic influence. However, these schemes are calibrated based on limited observations and often fail to reproduce the response relationships in observations, impeding accurate assessments of the role of O3 plant damage in the Earth system. This study proposes a new parameterization scheme to utilize the extensive observations from O3 fumigation experiments to inform large-scale modeling. It is built on 4210 paired data points of photosynthetic and stomatal responses compiled from peer-reviewed literature, over six times larger than those employed in earlier schemes. Functions of phytotoxic O3 dose (POD) are found to accurately reproduce the statistically significant linear or nonlinear relationships observed between POD and either relative leaf photosynthetic rate or relative stomatal conductance for needleleaf trees, broadleaf trees, shrubs, grasses, and crops. These eliminate the practice in earlier schemes of setting response functions as constants and applying the response function from one vegetation type to another. It outperforms the old scheme in the Community Land Model (CLM) which skillfully reproduces the observed response for crop photosynthetic rate only. The nonlinear response functions we developed depict decreasing plant sensitivity with increases in POD, enabling models to implicitly capture the variability in plant ozone tolerance and the shift among plant species for both intra- and inter-PFT within a vegetation type observed in the real world. Then, the new scheme is incorporated into the Community Earth System Model version 2.2 (CESM2.2), specifically its land component CLM5, to quantify the global impacts of present-day O3 plant damage by comparing the simulations with and without O3 plant damage. Results show that O3 exposure reduces the global leaf photosynthetic rate by 8.5 % and stomatal conductance by 7.4 %, around half the estimates using the old scheme. Furthermore, the new scheme improves global GPP simulations, decreasing RMSE by 11.1 % relative to simulations without O3 plant damage and by 11.7 % compared against the old scheme. These results underscore the importance of including O3 plant damage in large-scale process-based models and the effectiveness of the new scheme in global assessing and projecting the role of O3 plant damage in the Earth system.
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CEC1: 'Comment on gmd-2024-6 - No compliance with GMD's policy', Juan Antonio Añel, 11 May 2024
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.htmlYou have not published the code used in your manuscript previously to submit it to our journal. Actually, your manuscript does not even contain a "Code and Data Policy" which is mandatory for all the manuscripts submitted to our journal.
Therefore, you must reply to this comment as soon as possible, with the information on the permanent repository where you have published all the code and data used and produced in your work, including DOI and link.
Also, you must include in a potentially reviewed version of your manuscript the 'Code and Data Availability' section, with the DOI of the code, and another DOI for the dataset if necessary. Note that with the code you must include a license. If you do not include a license, the code continues to be your property and can not be used by others, despite any statement on being free to use. Therefore, when uploading the model's code to the repository, you could want to choose a free software/open-source (FLOSS) license.
In this way, if you do not fix this problem quickly, we will reject your manuscript for publication in our journal. I should note that, given this lack of compliance with our policy, your manuscript should not have been accepted in Discussions. Therefore, the current situation with your manuscript is irregular.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/gmd-2024-6-CEC1 -
AC1: 'Reply on CEC1', Fang Li, 13 May 2024
Dear Editor Prof. Añel,
Thanks for your detailed guidance on adhering to the GMD Code and Data Policy. We appreciate your effort in helping us meet the journal's requirements.
In response to your comments, we have now published the code (with its license) and the data used in our study in a permanent repository. Accordingly, we have revised our "Code and Data Availability" section from "The code and data will be available on Zenodo after manuscript acceptance." to:
"The new parameterization scheme for modeling ozone-caused damage to vegetation in process-based models is available at https://zenodo.org/records/11183913 (Li, 2024). The code and default input data for CESM2.2 can be downloaded from GitHub - ESCOMP/CESM at https://github.com/ESCOMP/CESM/tree/release-cesm2.2.2 and the CESM documentation at https://escomp.github.io/CESM/versions/cesm2.2/html/downloading_cesm.html#downloading-input-data. The ozone concentration input data, as well as observations and simulations used in this study, are available at https://zenodo.org/records/11185196 (Li, 2024)."
We hope this addresses the concerns raised. Regarding submitting the revised manuscript, I am unsure whether to upload it now or wait for further revisions based on the reviewers' comments. When I replied to your comment, the system advised, 'Attention: please do NOT submit your revised manuscript here as supplement.' Could you please advise on the best course of action?
Best regards,
Fang Li
Citation: https://doi.org/10.5194/gmd-2024-6-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 18 May 2024
Dear authors,
Unfortunately, your proposed solution does not comply with our policy. For some of your assets you use Git repositories, which are not valid. Please, store all the assets in a repository that we can accept according to our policy, and with a DOI.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/gmd-2024-6-CEC2 -
AC2: 'Reply on CEC2', Fang Li, 19 May 2024
Dear Editor,
Thanks for your feedback.
Based on your comment, we have updated our "Code and Data Availability" section from "The code and data will be available on Zenodo after manuscript acceptance." to:
"The code (including its license) for the new parameterization scheme for modeling ozone-caused damage to vegetation in process-based models is accessible at https://zenodo.org/records/11183913 (Li, 2024). The input data for ozone concentration, along with the observations and simulations utilized in this study, are available at https://zenodo.org/records/11185196 (Li, 2024)."
The Git repositories you referred to are for the default code of the Earth system model CESM2.2, developed by NCAR and publicly available. We have now excluded the description from the "Code and Data Availability" section, and have instead included the website for CESM2.2 code, input data, and Quickstart guide in section 2.3.1 (Model platform) as follows: "For our study, we adopt the latest version of CESM2.2 (https://www.cesm.ucar.edu/models/cesm2), which incorporates CLM5 as its land component (Lawrence et al., 2019)."
Please let me know if any further adjustments are required.
Best regards,
Fang Li on behalf of all coauthors
Citation: https://doi.org/10.5194/gmd-2024-6-AC2 -
CEC3: 'Reply on AC2', Juan Antonio Añel, 20 May 2024
Dear authors,
Unfortunately, again, your proposed solution does not comply with our policy. You must include a permanent repository for CESM2, clearly indicating the version you have used. Neither the NCAR webpage nor the Git repository linked on it, are acceptable. Therefore, you must store the complete code of the CESM model you have used in one of the repositories acceptable according to our policy and reply to this comment with its link and DOI. Also, you must include such information in any new manuscript version. For some CESM versions, it could be that such a repository already exists, for example, for CESM2.1.1 (https://zenodo.org/records/3895315) or CESM2.1.0. You only need to reply here with the version number you used and the appropriate link instead of creating a new repository.
Regards,
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/gmd-2024-6-CEC3 -
AC3: 'Reply on CEC3', Fang Li, 21 May 2024
Dear Editor,
Thanks for your guidance. Following your suggestions, we have updated our 'Code and Data Availability' section as follows:
"The code (including its license) for the new parameterization scheme for modeling ozone-caused damage to vegetation in process-based models is accessible at https://zenodo.org/records/11183913 (Li, 2024). The input data for ozone concentration, along with the observations and simulations utilized in this study, are available at https://zenodo.org/records/11185196 (Li, 2024). The code of Earth system model CESM2.2.0 is archived at https://zenodo.org/records/11229776 (CESM Team, 2024).".
Best regards,
Fang Li, on behalf of all co-authors
Citation: https://doi.org/10.5194/gmd-2024-6-AC3
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AC3: 'Reply on CEC3', Fang Li, 21 May 2024
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CEC3: 'Reply on AC2', Juan Antonio Añel, 20 May 2024
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AC2: 'Reply on CEC2', Fang Li, 19 May 2024
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CEC2: 'Reply on AC1', Juan Antonio Añel, 18 May 2024
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AC1: 'Reply on CEC1', Fang Li, 13 May 2024
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RC1: 'Comment on gmd-2024-6', Anonymous Referee #1, 14 May 2024
The mechanism of ozone stress on plant physiology, especially on photosynthesis, is well realized. However, the ozone stress scheme in land surface models is at the very beginning stage, introducing large uncertainties in GPP estimation. The authors compiled over 4000 paired data from peer-reviewed literature and proposed new response functions to reproduce statistically significant relationships between the relative reduction of physiological variables and accumulated phytotoxic O3 dose (POD). I believe this work potentially pushes the development of the ozone stress scheme in land surface models one big step further for the following reasons: 1) The new data samples are more comprehensive including almost all plant functional types of CLM5, and the new scheme is more reasonable than the previous schemes. The previous schemes only found skill response functions for crops, or estimated the photosynthetic response function based on yield/biomass response observations with the implicit assumption that all the processes and variables from photosynthesis to biomass were correctly modeled which is obviously not true; 2) the ozone-stress-induced global GPP reduction is predicted to be a more reasonable and moderate number of 13%. The original one is 28%, which almost indicates the original model without ozone stress is completely wrong in global GPP estimation, even the number more or less matches the observation-based dataset (e.g., FLUXCOM). While this work is publishable, I have a few minor comments that could enhance the quality of the manuscript, particularly regarding how the empirical relationships are derived from 4000 paired data. Please see my detailed comments below.
Figures 3 and 4: I acknowledge that these data are sourced from diverse literature and encompass a variety of environmental conditions and locations. Consequently, expecting a clear linear relationship might be unrealistic. Nonetheless, given the big unexplained variation, there may be potential to improve the fitting. I wonder if incorporating environmental factors or applying region-specific fitting functions could better capture the photosynthetic response. I recommend that the authors discuss potential strategies to account for the remaining variation in the data.
Line 63-67: The sentence is too long. Consider separating it into two sentences.
Line 87: “physical” I would say “biophysical”.
Line 115-116: Better put the version number of CLM and CESM and mention whether the current implementation is on the same or different versions of CLM and CESM. So, the reader will know whether or not L15 is comparable with this ozone stress scheme.
Line 166-167: “only data categorized as high and medium confidence defined by Lombardozzi et al., (2013)” Need generally mention the confidence level is defined based on what standard in Lombardozzi et al., (2013).
Line 169-171: “if the data are previously or more completely reported in another article” do you mean the data is repeatedly reported?
Line 290-291:”2000Clm50Sp” and “2000Clm45Sp” Better use a simple description rather than the CESM configuration abbreviation, which will be more friendly for those who don’t use CESM.
Line 306: 1.9o should be 1.875o .
Line 311: Missed one atmospheric forcing “Downward longwave radiation”
Line 313-314: “have no interannual variability” mislead. MODIS data, of course, have interannual variability. Maybe you just want to say “you use a prescribed climatology of vegetation distribution and structure, which is based on present-day MODIS satellite observation”
Line 319: “28.9655/47.9982” I'm not sure if we really need such high precision.
Line 340-341: “there is no need to use a function from one vegetation type for another” reads obscure. “no need” assumes readers know the original scheme derives the function from observation of another vegetation type. But I guess most of them don’t unless reading further. I suggest a direct introduction like “Each vegetation type owns its individual function based on observation.”
Line 481-486: I am wondering how are these modeled relative responses compared to the literature? More discussion will be helpful.
Line 631: “decouple”. How the results show the decouple? Maybe need more specific discussion. Also, I was expecting a photosynthetic rate versus stomata conductance scatter plot to show the decoupling.
Citation: https://doi.org/10.5194/gmd-2024-6-RC1 -
AC4: 'Reply on RC1', Fang Li, 14 Jun 2024
Dear reviewer:
We appreciate your recognition of the potential impact of our work on modeling ozone-caused damage to vegetation in land surface models, especially the positive feedback on the comprehensiveness of our new data samples and the reasonableness of the new scheme.
Our point-by-point response is provided in the supplement, and the manuscript has also been revised accordingly.
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AC4: 'Reply on RC1', Fang Li, 14 Jun 2024
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RC2: 'Comment on gmd-2024-6', Ye Liu, 14 May 2024
The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2024-6/gmd-2024-6-RC2-supplement.pdf
- AC5: 'Reply on RC2', Fang Li, 14 Jun 2024
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