Optimizing type, date, and dose of compost fertilization of organic cotton under climate change in Mali: A modeling study

Ginette Dembélé; Romain Loison; Amadou Traoré; Sidiki Gabriel Dembélé; Fagaye Sissoko

doi:10.1371/journal.pone.0308736

Peer Review History

Original SubmissionOctober 19, 2023
22 Mar 2024 Decision Letter - Sudeshna Bhattacharjya, Editor PONE-D-23-33999Optimizing type, date and dose of compost fertilization of organic cotton under climate change in Mali: A modeling studyPLOS ONE Dear Dr. Loison, 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 May 06 2024 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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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. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 4. Thank you for stating the following financial disclosure: AgrECo CML1430 whose financing agreement has been signed between AFD and the Government of Mali 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. [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 Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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 is very well written and experimental methods as well as the model optimization are well executed. Very minor rectifications are required which are highlighted in the comment section. The study should be published with having those rectification incorporated. Reviewer #2: Composting is an effective and sustainable technique in organic farming because it helps to reduce nutrient loss through leaching and reduces the need for synthetic fertilizers. It acts as a natural storehouse of both micronutrients like zinc, iron, copper, and manganese, and macronutrients such as nitrogen, phosphorus, potassium, calcium, and magnesium etc. The specific nutrients present depend on the type and composition of the organic material being composted. Additionally, composting provides a reliable method for improving the physical, chemical, and biological qualities of soil in agricultural contexts. Furthermore, applying compost leads to higher crop yields, mainly because it enhances soil fertility and provides essential micronutrients and macronutrients. Numerous studies have highlighted the beneficial effects of compost on the growth and physical characteristics of cotton plants. Thus, before accepting needs to be modify as per the comments given below: Some of the study reported that Cotton is C3 and CO2 enrichment enhances yield (Sankaranarayanan et al., 2010) thus specifying the date application of compost enhanced the yield of cotton crop need to be more discussed. In Introduction, importance of the study needs to be highlighted with more recent references so that study can be justified. Write the importance of this study in global context. Why DSSATCSM-CROPGRO-Cotton model was used, need more justification as well as include R2 value in both the RCPs. Is this model considered mineralization of compost in soil for prediction? Whether different sources of composts (elemental composition) were analyzed or not? In this study, date of sowing of cotton is July 01, 2021, Generally, application of compost 2-3 week before sowing is recommended, but in this study application in mid-May emphasized therefore proper discussion is required indicating to show why application of this model is important rather than going for general recommendation ****** 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 Reviewer #2: Yes: Rahul Mishra, ICAR-Indian Institute of Soil Science, Bhopal, M.P. India ******** [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. Attachments Attachment Submitted filename: Review sheet_PlosONE.docx Attachment Submitted filename: Review report.docx https://doi.org/10.1371/journal.pone.0308736.r001
Revision 1
22 Apr 2024 Author Response The authors are grateful to the reviewers for their comments, which have helped improve the manuscript. In the revised manuscript with track changes, revisions related to reviewer #1's comments are highlighted in yellow, and those of reviewer #2 are highlighted in blue. Reviewer #1: C1. Line no 64-78: In this paragraph, authors should highlight the urgency or potential lacunas that this study addresses. The title highlights the type, date and dose of organic input, in that direction, authors should highlight that how these factors are currently affecting the seed yield of cotton in Mali with references. The gaps and objectives of this study has to come in this section. R1. Thank you. The introduction has been augmented to present better the gap in knowledge and the study's objective. C2. L32-33. Key words are lengthy. Try to reduce it and give those key words that best describe the article R2. We modified the keywords, making them shorter and ensuring they describe the content of the article. C3. L85. Check the journal guidelines. It should be Fig 1 not Figure 1 R3. Thank you. All references to figures have been updated to comply with the journal guidelines. C4. L87. Check the figure caption style and follow journal guideline R4. Thank you. All figure captions have been updated to comply with the journal guidelines. C5. L186. Check the journal guidelines. It should be Fig 2 not Figure 2 R5. Thank you. All references to figures have been updated to comply with the journal guidelines. C6. L190. Check the figure caption style and follow journal guideline R6. Thank you. All figure captions have been updated to comply with the journal guidelines. C7. L214. Check the abbreviation and use same abbreviation uniformly throughout the manuscript R7. We replaced NMRSE by nRMSE C8. L235. Interchange the minimum and maximum words according to the data R8. We interchanged the min and max to correspond to what they refer to in the text. C9. L242. Check the solar radiation data, use point instead of comma R9. We replaced the comma by point. C10. L254. Check the journal guidelines. It should be Fig 3 not Figure 3 R10. Thank you. All references to figures have been updated to comply with the journal guidelines. C11. L258. Use past tense. R11. We used past tense (had instead of has). C12. L268. Check the figure caption style and follow journal guideline. R12. Thank you. All figure captions have been updated to comply with the journal guidelines. C13. L274. See the citation format. R13. Thank you, all references to figures have been updated to comply with the journal guidelines. C14. L282. Modify figure citation according to the journal guideline R14. Thank you. All references to figures have been updated to comply with the journal guidelines. C15. L296. Figure caption. R15. Thank you. All figure captions have been updated to comply with the journal guidelines. Reviewer #2: C16. Some of the study reported that Cotton is C3 and CO2 enrichment enhances yield (Sankaranarayanan et al., 2010) thus specifying the date application of compost enhanced the yield of cotton crop need to be more discussed. R16. Thank you for your comment. We indeed used the suggested review paper in our introduction to highlight the importance of organic manure like compost in increasing soil organic content in cotton systems under climate change to reduce the impact of climate change. C17. In introduction, importance of the study needs to be highlighted with more recent references so that study can be justified. Write the importance of this study in global context. R17. Thank you very much; please kindly see the response to comment C1 in yellow in the introduction. Some recent publications have been added (2 from 2022, 1 from 2023). We rewrote the end of the introduction to highlight better the importance of this study in the global context. C18. Why DSSAT CSM-CROPGRO-Cotton model was used, need more justification as well as include R2 value in both the RCPs. Is this model considered mineralization of compost in soil for prediction? R18. Thank you for your comment. We justified the choice of model and described it better. The details are highlighted in blue in the M&M section 2.3.1. Under both RCPs, this is an in-silico experiment and no observation can be compared to simulated future performance under climate change conditions. Under such conditions, no R2 can be computed. C19. Whether different sources of composts (elemental composition) were analyzed or not? R19. The types of composts were analyzed for elemental composition, a table was added (Table 2). C20. In this study, date of sowing of cotton is July 01, 2021, Generally, application of compost 2-3 week before sowing is recommended, but in this study application in mid-May emphasized therefore proper discussion is required indicating to show why application of this model is important rather than going for general recommendation R20. Thank you for your comment. The reference 28 specifies that organic manure is usually applied between March and April in Mali. In addition, an unpublished survey of farmers producing organic cotton in Mali has identified that compost is also commonly applied in March or April but rarely after. Our work highlights the need for a change of practice. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0308736.r002
29 May 2024 Decision Letter - Sudeshna Bhattacharjya, Editor PONE-D-23-33999R1Optimizing type, date, and dose of compost fertilization of organic cotton under climate change in Mali: A modeling studyPLOS ONE Dear Dr. Loison, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it still needs some minor revision to 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 Jul 13 2024 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, Sudeshna Bhattacharjya, 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. [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #2: 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 Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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: General comments they have worked on which is fin but still the research gap part is lacking. They have added only a paragraph that to not ensuring why application of compost and their timing of application is important for Mali cotton farmers. I understand that application of manure organics undoubtedly improves the soil and crop performance. But it has to come in the manuscript. Without highlighting any potential gap or requirement of this research how we are going to justify that our work is the need of the hour. I request authors to include these things. What is the objective here. What they are trying to address by optimizing the date dose and timing of manure application and how it is going to address the climate change issues. Ultimately, if they address these things then it would be good. Reviewer #2: Accepted for publication The study on optimizing the type, timing, and dosage of compost fertilization for organic cotton in Mali under climate change conditions is crucial As climate change alters growing conditions, finding the best composting practices ensures that organic cotton farming remains resilient and sustainable. By determining the optimal composting strategies, farmers can maximize their cotton yields, contributing to economic stability. findings can inform agricultural policies and practices, helping to develop guidelines for compost use under changing climatic conditions, ****** 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 Reviewer #2: Yes: Rahul Mishra ******** [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. Attachments Attachment Submitted filename: Reviewer sheet_PONE-D-23-33999_R1.docx https://doi.org/10.1371/journal.pone.0308736.r003
Revision 2
15 Jul 2024 Author Response The authors are grateful to the reviewer for his comment. In the revised manuscript with track changes, revisions are highlighted in green. Reviewer #1: C1. General comments they have worked on which is fin but still the research gap part is lacking. They have added only a paragraph that to not ensuring why application of compost and their timing of application is important for Mali cotton farmers. I understand that application of manure organics undoubtedly improves the soil and crop performance. But it has to come in the manuscript. Without highlighting any potential gap or requirement of this research how we are going to justify that our work is the need of the hour. I request authors to include these things. What is the objective here. What they are trying to address by optimizing the date dose and timing of manure application and how it is going to address the climate change issues. Ultimately, if they address these things then it would be good. R1. Thank you. The introduction has been augmented a second time to present better the gap in knowledge and the study's objective. Please kindly check the introduction. Attachments Attachment Submitted filename: Response to Reviewers second round.docx https://doi.org/10.1371/journal.pone.0308736.r004
30 Jul 2024 Decision Letter - Sudeshna Bhattacharjya, Editor Optimizing type, date, and dose of compost fertilization of organic cotton under climate change in Mali: A modeling study PONE-D-23-33999R2 Dear Dr. Romain Loison, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Sudeshna Bhattacharjya, 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: The authors have updated the manuscript quite satisfactorily. The manuscript is publication ready. Thank you. ****** 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.0308736.r005
Formally Accepted
5 Aug 2024 Acceptance Letter - Sudeshna Bhattacharjya, Editor PONE-D-23-33999R2 PLOS ONE Dear Dr. Loison, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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 Dr. Sudeshna Bhattacharjya Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0308736.r006

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