PONE-D-22-09910Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativaPLOS ONE

Dear Dr. Song,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Please submit your revised manuscript by Jul 30 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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Shanxi Province Key Research and Development Program Key Project analysis”

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript written by Song et al. PONE-D-22-09910 `Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativa` investigates the effects of CO2 enrichment on physiology, growth and transcripts of Lactuca sativa. Here, authors investigate the CO2 effects inside a greenhouse, under controlled conditions. In the context of current climate changes, CO2 studies are crucial for a better understanding of future food security and productivity. The manuscript is well-written, clear, and experiments were conducted with adequate methods. However, much more details are necessary in the methods section. Therefore, the manuscript can be accepted after major revisions. A list with my suggestions can be found bellow:

Title

Title is clear and informative.

Abstract

In general, abstract is well-written and concise. I listed a few recommendations bellow:

Page 2. in `… attention from all walks of life…`the expression walks of life seems strange here, maybe authors can rewrite this sentence in a more scientific approach.

Regarding the sentence ` The rational utilization of CO2 by plants is an effective way to promote carbon neutrality`. How is possible that lettuce cultivation will promote carbon neutrality? Carbon neutrality achievement by plants is only possible when large carbon flux is occurring, such as CO2 flux in forest and other ecosystems. This information seems out of context here. In addition, authors need to decide what will be focus of the manuscript: (1) anthropogenic increase of atmospheric CO2 or (2) CO2 fertilization techniques in controlled environments to increase lettuce production. In the situation 1, authors need to put into account that productivity of plants in the future will also occur under elevated temperatures conditions and different rainfall patterns, therefore, the results obtained here cannot be extrapolated to future conditions since both, temperature and drought can negate or fully mitigate the benefits of a CO2 increase. In the situation 2, authors can focus only in CO2 fertilization under controlled conditions for a higher lettuce production, without taking into account the future increases in temperature, since plants are growing under controlled conditions (controlled temperature, CO2, etc). It seems that situation 2 is the more adequate approach for this manuscript and all sentences related to climate change and atmospheric CO2 increased by human activity are not necessary and should be removed.

Along the manuscript authors used sentences such as `… effect of CO2 on lettuce…`. Authors are not testing the effects of CO2 on plants, but the effects of ELEVATED CO2 on plants. In phrases such as this one, it is important to include this information.

Introduction

In general, introduction is well-written and concise. However, the introduction needs a hypothesis. Which plant responses authors expected according to the literature? In the discussion section, authors should clarify if the hypothesis was corroborated or not.

Material and methods

S1 Fig. Please, insert a subtitle in the supplementary figure.

Why authors decided to initiate the CO2 enrichment only after one week of transplanting? Is there any reason for this?

Please, change `release time` for `CO2 fumigation period `

Why CO2 was not fumigated in rainy or snowy days? How many rainy/snowy days occurred during the experiment? Please, include both information in the manuscript.

Please, describe in more details what `traditional management practices` means. I imagine that each lettuce color has a different management strategy. In addition, in different countries `traditional management practices` for lettuce cultivation will have different meanings.

Which gas exchange parameters were measured? How light curves (light intensity steps) were conducted to obtain LSP and LCP parameters?

Please, include the statistical methods used to analyze the data in the entire manuscript in the material and methods section. This information is crucial for data interpretation. Did authors used ANOVA? Student t tests?

Results

Within each table we have lowercase and uppercase letters presumably indicating statistical differences between average values. However, we can`t find the meaning of these letters in the subtitle or methods section. Please, include this information in all subtitles.

Page 10. The following sentence `The comprehensive analysis showed that the application of CO2 improved the light energy utilization rate to different extents and caused the plants to accumulate more photosynthetic products, which may partially explain the acceleration of leaf growth under CO2 enrichment of lettuce.` should be placed in the discussion section.

Page 11. Again, sentences such as `Elevated CO2 in the environment will lead to changes in the content of various metabolites in plants, which will further affect their nutritional quality [16].` should be placed in other sections of the manuscript such as introduction or discussion.

All subtitles can be improved with more details. In the current form, subtitles are too simple.

Discussion

It was a great idea to split the discussion in sub-sections. In general, discussion section is ok. However, especially in the subsection of photosynthesis, the discussion is too simple. Much more mechanistic discussion is possible using your data.

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Reviewer #1: No

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PONE-D-22-09910R1Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativaPLOS ONE

Dear Dr. Song,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Nov 03 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Mohammad Irfan, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

In particular, I agree with reviewer #3 who has valid concerns. 

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: All comments have been addressed

Reviewer #3: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

Reviewer #3: Partly

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

Reviewer #3: No

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

Reviewer #3: No

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: The paper describes about “Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativa”

Authors have revised but still new references are missing

Yr 2022- nil

Yr 2021~1

So, include relevant references to update discussion

Reviewer #3: The manuscript titled “Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativa” investigated the effects of elevated CO2 on three varieties of lettuce. The author found that elevated CO2 promoted the photosynthesis of lettuce, as well as the growth and quality of lettuce. The authors also performed RNA-seq for the three varieties of lettuce under elevated CO2 and identified responsive genes (and their associated pathways) shared by all three varieties. Overall, the manuscript easy to follow. However, it is very descriptive and lacks necessary experimental details. Please see detailed comments below.

Selected major comments are listed below:

1. Experiment details about CO2 application, what is the concentration of ambient CO2 and what is the concentration of elevated CO2, was the CO2 concentration monitored throughout the experiment?

2. Please clarify how the statistical significance was obtained, was the comparison between elevated CO2 and ambient CO2 done for each variable (from plant growth, photosynthesis, lettuce quality) and each variety or there are different grouping?

3. Line 115-116 and 118-119: “One leaf per plant was chosen for conducting the light curve” and “Three healthy leaves were selected for each measurement”. Please provide details for how these leaf were selected, were they consistent between different plants?

4. Line 133-136: It seems that there is only one replicate used for RNA-seq from S6, S16, S24 varieties. Please clarify this in the methods.

5. Line 140-147: Please provide additional information for 1) how the RNA-seq data was pre-processed; 2) how the RNA-seq reads were mapped (tool and genome used); 3) how DEGs were identified (which tool was used); 4) whether DEGs were identified for each lettuce variety separately or all together; and 5) how functional enrichment was performed for both KEGG and GO (what tools were used). Reference Sun et al. doesn’t provide these details.

6. Line 177: 1) Please clarify how leaf width, plant height and width were defined in the current study; 2) Please reformat Table 1 to have a clear separation between S6, S16 and S24 groups.

7. The authors mentioned multiple RNA-seq studies from line 64-74 about the effect of elevated CO2 in different species. Did the authors compare the results from current study to the results from these previous studies to see if there are any genes/pathways being differentially regulated by elevated CO2 regardless of species or these species might have very distinct response to the elevated CO2?

Selected minor comments:

1. Please provide figures with higher resolution.

2. Line 198: Please justify why there are uppercase and lowercase significance letters. Do they represent different grouping?

3. Data used in the current study doesn’t seem to be accessible accession number PRJNA859388 (http://www.ncbi.nlm.nih.gov/bioproject/859388).

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Reviewer #2: Yes: Dr. Saurabh Yadav,

Reviewer #3: No

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PONE-D-22-09910R2Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativaPLOS ONE

Dear Dr. Song,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Specifically, please address the comment raised by the reviewer with proper justification regarding the biological replicates. 

Please submit your revised manuscript by Dec 04 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Mohammad Irfan, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: The authors addressed most of the initial comments. However, the use of only one replicate for RNA-seq is lower than the minimum requirement of three replicates, which will dramatically reduce the statistical power of detecting DEGs. One way the authors could consider is to use S6, S16, S24 varieties as biological replicates to investigate the effect of elevated CO2.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #3: No

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While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Comparative physiological and transcriptomic analyses reveal the mechanisms of CO2 enrichment in promoting the growth and quality in Lactuca sativa

PONE-D-22-09910R3

Dear Dr. Song,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Mohammad Irfan, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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