Partial substitution of chemical fertilizer by organic fertilizer increases yield, quality and nitrogen utilization of Dioscorea polystachya

Chao Sun; Hua Zheng; Shuxia He; Qing Zhao; Yuxi Liu; Hai Liu

doi:10.1371/journal.pone.0301108

Peer Review History

Original SubmissionJuly 16, 2023
6 Sep 2023 Decision Letter - Sofia Isabel Almeida Pereira, Editor PONE-D-23-21993 Partial Substitution of Chemical Fertilizer with Organic Fertilizer Increases Yield, Quality and Nitrogen Utilization of Dioscorea polystachya PLOS ONE Dear Dr. Liu, 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 Oct 21 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. 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For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. Additional Editor Comments: The material and methods section must be carefully revised and improved. References must be added to the methods. Please revise the statistical analysis. Captions of Tables and Figures should be self-explanatory. Please include the explanation of each treatment. The discussion section must be improved based on the reviewer's comments. [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: Partly Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: No ****** 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 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: No 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: 1. The study has no novelty or authors should state the novelty 2. Authors are economical with major information needed in the materials n methods 3. Authors needs to include one more treatment i.e. 75%OM + 25%CF 4. Authors claimed to carry out correlation analysis in section 2.5 but there is no correlation matrix/table to show 5. See more corrections in the attached text Reviewer #2: The manuscript provides valuable information. However, some points need to be clarified and improved. More description of the material used for vermicompost production is needed. The experimental design is deficient. The statistical analyses are incomplete. More discussion is needed. Some references are cited in the text. All observations are noted in the paper. ****** 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: Yes: Aboyeji, C. M Reviewer #2: 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. Attachments Attachment Submitted filename: PONE-D-23-21993.pdf Attachment Submitted filename: PONE-D-23-21993 Rev.pdf https://doi.org/10.1371/journal.pone.0301108.r001
Revision 1
3 Nov 2023 Author Response Thank you very much for your positive comments on our manuscript entitled “Partial Substitution of Chemical Fertilizer with Organic Fertilizer Increases Yield, Quality and Nitrogen Utilization of Dioscorea polystachya” (PONE-D-23-21993). All the comments are valuable and helpful for improving our paper. We substantially revised our old version based on the reviewer’s comments. Thereafter, the manuscript was revised and edited by a native speaker and we hope the revised manuscript can meet the requirements. In this thoroughly revised version, changes in our manuscript within the document were highlighted by using red-colored text. Point-by-point responses to the reviewers are included, and the line number based on the attached file named “Revised Manuscript with track changes”. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0301108.r002
29 Nov 2023 Decision Letter - Sofia Isabel Almeida Pereira, Editor PONE-D-23-21993R1Partial Substitution of Chemical Fertilizer with Organic Fertilizer Increases Yield, Quality and Nitrogen Utilization of Dioscorea polystachyaPLOS ONE Dear Dr. Liu, 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 Jan 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, Sofia Isabel Almeida Pereira 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. Additional Editor Comments: Minor corrections: Title - replace "with organic fertilizer" by "by organic fertilizer. Abstract - Please rephrase this sentence - "Although there were no significant differences in tuber length and marketable yield among the fertilizer treatments, 25%OM + 75% CF exhibited the highest values at 69.23 cm and 75.86%, respectively, representing a 3.14% and 1.57% increase compared to CF. If there is not significant differences the authors could not state increases compared to control. - Please rephrase the following sentences, as the infomration is repeated : The total sugar, starch, crude protein, total amino acid, and ash contents of D. polystachya significantly increased in all fertilizer treatments compared to the control (except for ash content between CK and OM). When compared to CF, the substitution of different ratios of organic fertilizer for chemical fertilizer increased the total sugar, starch, crude protein, total amino acid, and ash contents to varying degrees." Line 137- The following sub-heading should be changed: " Measuring items and methods"? Not clear, please rephrase for clarity. Line 177 - Please replace by "Data analysis" Discussion - Data regarding yam's quality are not discussed. Please imporve the discussion section. The manuscript must be revised by a Native English speaker as it contains several grammatical faults. [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: All comments have been addressed 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: Partly Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A 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: Kindly do some minor corrections as specified in the attached text nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Reviewer #2: The corrections and observations made in the first review were correctly modified, and some suggestions were also addressed. ****** 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: 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. Attachments Attachment Submitted filename: PONE-D-23-21993_R1_reviewer-1.pdf https://doi.org/10.1371/journal.pone.0301108.r003
Revision 2
13 Jan 2024 Author Response 1. Title - replace "with organic fertilizer" by "by organic fertilizer. Response: revised. 2. Abstract - Please rephrase this sentence - "Although there were no significant differences in tuber length and marketable yield among the fertilizer treatments, 25%OM + 75% CF exhibited the highest values at 69.23 cm and 75.86%, respectively, representing a 3.14% and 1.57% increase compared to CF. If there is not significant differences the authors could not state increases compared to control. Response: We have rephrased this sentence. 3. - Please rephrase the following sentences, as the infomration is repeated : The total sugar, starch, crude protein, total amino acid, and ash contents of D. polystachya significantly increased in all fertilizer treatments compared to the control (except for ash content between CK and OM). When compared to CF, the substitution of different ratios of organic fertilizer for chemical fertilizer increased the total sugar, starch, crude protein, total amino acid, and ash contents to varying degrees." Response: Rephrased. 4. Line 137- The following sub-heading should be changed: " Measuring items and methods"? Not clear, please rephrase for clarity. Response: Revised. Changed into “Methods of index determination”. 5. Line 177 - Please replace by "Data analysis" Response: Changed into "Data analysis". 6. Discussion - Data regarding yam's quality are not discussed. Please imporve the discussion section. Response: We have added the yam quality discussion, and also improved the presentation. 7. The manuscript must be revised by a Native English speaker as it contains several grammatical faults. Response: Revised. Attachments Attachment Submitted filename: Response to Reviewers0113.docx https://doi.org/10.1371/journal.pone.0301108.r004
18 Jan 2024 Decision Letter - Sofia Isabel Almeida Pereira, Editor PONE-D-23-21993R2Partial Substitution of Chemical Fertilizer with Organic Fertilizer Increases Yield, Quality and Nitrogen Utilization of Dioscorea polystachyaPLOS ONE Dear Dr. Liu, 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 Mar 03 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, Sofia Isabel Almeida Pereira 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. Additional Editor Comments:============================== ACADEMIC EDITOR:The manuscript needs to be revised by a native English speaker. Several grammar faults and unclear sentences are found throughout the text.============================== [Note: HTML markup is below. Please do not edit.] [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.0301108.r005
Revision 3
6 Mar 2024 Author Response Response: Thanks a lot for your suggestion. I have taken the necessary steps to enhance the linguistic quality of our manuscript. I engaged the assistance of a faculty member from the University of Florida, who provided valuable insights and refined the language throughout the paper. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0301108.r006
12 Mar 2024 Decision Letter - Sofia Isabel Almeida Pereira, Editor Partial Substitution of Chemical Fertilizer with Organic Fertilizer Increases Yield, Quality and Nitrogen Utilization of Dioscorea polystachya PONE-D-23-21993R3 Dear Dr. Liu, 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 http://www.editorialmanager.com/pone/ 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, Sofia Isabel Almeida Pereira Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0301108.r007
Formally Accepted
1 Apr 2024 Acceptance Letter - Sofia Isabel Almeida Pereira, Editor PONE-D-23-21993R3 PLOS ONE Dear Dr. Liu, 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. Sofia Isabel Almeida Pereira Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301108.r008

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