Metabolic profiling of Mytilus coruscus mantle in response of shell repairing under acute acidification

Xiaojun Fan; Ying Wang; Changsheng Tang; Xiaolin Zhang; Jianyu He; Isabella Buttino; Xiaojun Yan; Zhi Liao

doi:10.1371/journal.pone.0293565

Peer Review History

Original SubmissionJuly 17, 2023
7 Sep 2023 Decision Letter - Hugh Cowley, Editor PONE-D-23-22159Metabolic profiling of Mytilus coruscus mantle in response of shell repairing under acute acidificationPLOS ONE Dear Dr. Liao, 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 note that we have only been able to secure a single reviewer to assess your manuscript. We are issuing a decision on your manuscript at this point to prevent further delays in the evaluation of your manuscript. Please be aware that the editor who handles your revised manuscript might find it necessary to invite additional reviewers to assess this work once the revised manuscript is submitted. However, we will aim to proceed on the basis of this single review if possible. The reviewer has raised a number of concerns for your attention, particularly regarding details of the methodology, additional data and clarity regarding comparisons performed as part of this study. Please ensure that you address each of the reviewer's comments when revising your manuscript. We note that the reviewer has recommended that you cite specific previously published works. As always, we recommend that you please review and evaluate the requested works to determine whether they are relevant and should be cited. It is not a requirement to cite these works. We appreciate your attention to this request. Please submit your revised manuscript by Oct 22 2023 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, Hugh Cowley Staff Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (http://learn.aje.com/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services. If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free. Upon resubmission, please provide the following: The name of the colleague or the details of the professional service that edited your manuscript A copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a supporting information file) A clean copy of the edited manuscript (uploaded as the new manuscript file) 3. Thank you for stating the following financial disclosure: “This study was supported by the National Natural Science Foundation of China (Grant Nos. 32271580, 42020104009, and 32200083). Zhejiang Provincial Natural Science Foundation (Grant Nos. LQ23D060002 and LTGS23C010001).” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “ This research was supported by the National Natural Science Foundation of China (Grant Nos. 32271580, 42020104009, and 32200083). Zhejiang Provincial Natural Science Foundation (Grant Nos. LQ23D060002 and LTGS23C010001).” We note that you have provided funding information that is currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “This study was supported by the National Natural Science Foundation of China (Grant Nos. 32271580, 42020104009, and 32200083). Zhejiang Provincial Natural Science Foundation (Grant Nos. LQ23D060002 and LTGS23C010001).” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 6. We are unable to open your Supporting Information file [Supporting information.rar]. Please kindly revise as necessary and re-upload. [Note: HTML markup is below. Please do not edit.] 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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 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: Yes ****** 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 ****** 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 entitled “Metabolic profiling of Mytilus coruscus mantle in response of shell repairing under acute acidification” presents reasonable experimental design and data analysis process, and reports results of the physiological impact of shell damage and ocean acidification conditions on Mytilus coruscus. Overall, the authors' findings provide some interesting data for explaining the possible molecular responses of the mussel mantle to the low pH and shell damage, and thusly make it worthy of publication. Some specific comments were provided below. The authors are welcome to follow my suggestions for improving the manuscript. Introduction: Introduction is generally elucidative. The cited references are exhaustive and updated, and provide an adequate background regarding the topic of the research. In a picky way, the following recently published article or book might be appropriate citations to further strengthen the background of this study. https://doi.org/10.1016/j.aquatox.2020.105740 https://doi.org/10.1016/C2019-0-04274-4 Materials and Methods: The experimental design needs to be more detailed. - How was the experimental system calibrated to ensure that the reported pH values (8.1 and 7.4) were precise? - Additionally, could the authors please provide some type of environmental/ecological justification for the low pH value used? - The authors stated that there are four groups of mussels used in this study. Was there pH treatment-level replication? - were drilled/undrilled mussels that were reared in low pH all in the same low pH tank? - How many individuals for each group, and in each tank? Results: - The standard curve of FAA analysis used for qualitative and quantitative analysis of free amino acids and other nitrogenous compounds should be provided as supplementary file. - Also in the section of FAA analysis, the authors used “μg/g wet tissue” as the unit of free amino acids content in Table 1, and “μg/g dry tissue” in other place. Which one is correct? Discussion: - The authors should clearly specify which comparisons were performed and base the interpretation of results on those specific comparisons. This will help avoid any misinterpretation of the findings. For example, in Line 415, “The SDMs in various comparisons…”, and Line 445, “The up-regulation of GSSG under the acute acidification…”. In addition, the following articles might be decent for authors to further strengthen their discussion. https://doi.org/10.1021/acs.est.1c06735 https://doi.org/10.1016/j.scitotenv.2022.156442 https://doi.org/10.1016/j.chemosphere.2019.125415 Other minor errors: Some typo errors should be corrected. Such as: - In the section of Enzymatic assay, “described in the section 2.1”, where is the section 2.1? - In Line 386, “no mark changes” should be “no marked changes”; - In Discussion, paragraph six, “overserved” should be “observed”; in the next paragraph, “as one of negative effect for…” should be “as one of negative effects on…”, etc. ****** 6. 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 #1: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] 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. https://doi.org/10.1371/journal.pone.0293565.r001
Revision 1
28 Sep 2023 Author Response We express our gratitude to the reviewers and editors for their valuable comments. We are glad that the reviewers give us the opportunity to upload a revised version of our manuscripts. Below there are our responds to the reviewer´s comments. Review Comments to the Author Reviewer #1: The manuscript entitled “Metabolic profiling of Mytilus coruscus mantle in response of shell repairing under acute acidification” presents reasonable experimental design and data analysis process, and reports results of the physiological impact of shell damage and ocean acidification conditions on Mytilus coruscus. Overall, the authors' findings provide some interesting data for explaining the possible molecular responses of the mussel mantle to the low pH and shell damage, and thusly make it worthy of publication. Some specific comments were provided below. The authors are welcome to follow my suggestions for improving the manuscript. Introduction: Introduction is generally elucidative. The cited references are exhaustive and updated, and provide an adequate background regarding the topic of the research. In a picky way, the following recently published article or book might be appropriate citations to further strengthen the background of this study. https://doi.org/10.1016/j.aquatox.2020.105740 https://doi.org/10.1016/C2019-0-04274-4 Response: thanks for reviewer’s comments. We checked the references and one of them was added in Introduction as reference 21. Materials and Methods: The experimental design needs to be more detailed. - How was the experimental system calibrated to ensure that the reported pH values (8.1 and 7.4) were precise? - Additionally, could the authors please provide some type of environmental/ecological justification for the low pH value used? - The authors stated that there are four groups of mussels used in this study. Was there pH treatment-level replication? - were drilled/undrilled mussels that were reared in low pH all in the same low pH tank? - How many individuals for each group, and in each tank? Response: thanks for reviewer’s suggestions. We rewrote the section and the detail information was added accordingly. - In this study, the pH value was monitored using a pH meter, and adjusted using a CO2 pump to ensure the precise of pH value. - The two pH levels used in this study were selected based on the average pH value at the local mussel farm and the estuarine habitat where M. coruscus lives in a highly ﬂuctuating pH environments due to river run oﬀ [doi: 10.1016/j.scitotenv.2020.142838.]. The low pH 7.2-7.6 had been observed previously in this area [doi: 10.1007/s11356-022-21122-z.], and pH 7.4 representing coastal acidification had been used for other estuarine species, such as oyster, in previous studies [doi: 10.1111/mec.16751.]. - Furthermore, three pH treatment-level replications were used for the mussels in this study. For each pH treatment-level replication, the mussels with intact-shell and damaged-shell were mixed and raised in the same tank. Six tanks were prepared for the mussels and 30 mussel individuals, including 15 intact-shell and 15 damaged-shell mussels were raised in each tank. A total of 180 mussels were used for our experiment, and 45 individuals for each group. Results: - The standard curve of FAA analysis used for qualitative and quantitative analysis of free amino acids and other nitrogenous compounds should be provided as supplementary file. - Also in the section of FAA analysis, the authors used “μg/g wet tissue” as the unit of free amino acids content in Table 1, and “μg/g dry tissue” in other place. Which one is correct? Response: thanks for reviewer’s suggestions. - The standard curve of FAA analysis was added in the revised manuscript as S5 Fig according to the reviewer’s suggestion. - We used μg/g of dry tissue as unit of the FAA analysis result, and the “μg/g wet tissue” is a mistake and we corrected accordingly. Discussion: - The authors should clearly specify which comparisons were performed and base the interpretation of results on those specific comparisons. This will help avoid any misinterpretation of the findings. For example, in Line 415, “The SDMs in various comparisons…”, and Line 445, “The up-regulation of GSSG under the acute acidification…”. In addition, the following articles might be decent for authors to further strengthen their discussion. https://doi.org/10.1021/acs.est.1c06735 https://doi.org/10.1016/j.scitotenv.2022.156442 https://doi.org/10.1016/j.chemosphere.2019.125415 Response: thanks for reviewer’s suggestions. We revised some ambiguous descriptions in Discussion, and one of the suggested references was added. Other minor errors: Some typo errors should be corrected. Such as: - In the section of Enzymatic assay, “described in the section 2.1”, where is the section 2.1? - In Line 386, “no mark changes” should be “no marked changes”; - In Discussion, paragraph six, “overserved” should be “observed”; in the next paragraph, “as one of negative effect for…” should be “as one of negative effects on…”, etc. Response: thanks for reviewer’s suggestions. The errors were corrected and the English of this manuscript was re-edited by Editage (www.editage.com). Journal requirements: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response: thanks for Editor’s suggestions. We checked and revised our manuscript to meet the PLOS ONE's style requirements 2. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (http://learn.aje.com/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services. If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free. Upon resubmission, please provide the following: The name of the colleague or the details of the professional service that edited your manuscript A copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a supporting information file) A clean copy of the edited manuscript (uploaded as the new manuscript file) Response: thanks for Editor’s suggestions. The manuscript was polished by Editage (www.editage.com), and the language usage, spelling, and grammar were revised thoroughly. The Editing Certificate was attached below. 3. Thank you for stating the following financial disclosure: “This study was supported by the National Natural Science Foundation of China (Grant Nos. 32271580, 42020104009, and 32200083). Zhejiang Provincial Natural Science Foundation (Grant Nos. LQ23D060002 and LTGS23C010001).” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Response: the role the funders took in this study was stated in the section of Founding, 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “ This research was supported by the National Natural Science Foundation of China (Grant Nos. 32271580, 42020104009, and 32200083). Zhejiang Provincial Natural Science Foundation (Grant Nos. LQ23D060002 and LTGS23C010001).” We note that you have provided funding information that is currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “This study was supported by the National Natural Science Foundation of China (Grant Nos. 32271580, 42020104009, and 32200083). Zhejiang Provincial Natural Science Foundation (Grant Nos. LQ23D060002 and LTGS23C010001).” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Response: the founding information in Acknowledgments Section was deleted. 5. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. Response: thanks for Editor’s suggestion. We accept that we will provide the relevant accession numbers or DOIs necessary to access our data if our manuscript be accepted for publication. 6. We are unable to open your Supporting Information file [Supporting information.rar]. Please kindly revise as necessary and re-upload. Response: we are sorry for that. We previously compressed our Supporting Information file using RAR format, and we will provide the Supporting Information files using ZIP format. Attachments Attachment Submitted filename: Responses to reviwers.docx https://doi.org/10.1371/journal.pone.0293565.r002
16 Oct 2023 Decision Letter - Amitava Mukherjee, Editor Metabolic profiling of Mytilus coruscus mantle in response of shell repairing under acute acidification PONE-D-23-22159R1 Dear Dr. Liao, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Amitava Mukherjee, ME, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): 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 #1: All comments have been addressed ******** 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 #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 #1: 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 #1: 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 #1: All my questions have been successfully addressed by authors and I believe the MS can be accepted now. ****** 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 #1: No ******** https://doi.org/10.1371/journal.pone.0293565.r003
Formally Accepted
19 Oct 2023 Acceptance Letter - Amitava Mukherjee, Editor PONE-D-23-22159R1 Metabolic profiling of Mytilus coruscus mantle in response of shell repairing under acute acidification Dear Dr. Liao: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Professor Dr. Amitava Mukherjee Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0293565.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .