Impacts of cellulase and xylanase addition on antibiotic resistance and microbial community during dairy manure composting

Ping Gong; Yuan Zhou; Daoyu Gao; Pingmin Wan; Zhiyong Shao; Erguang Jin

doi:10.1371/journal.pone.0328055

Peer Review History

Original SubmissionDecember 4, 2024
10 Mar 2025 Decision Letter - Shweta Sharma, Editor Dear Dr. Jin, 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. Dear Authors, Your manuscript, "Impacts of Cellulase and Xylanase Addition on Antibiotic Resistance and Microbial Community During Dairy Manure Composting," has been reviewed by two reviewers. One reviewer has suggested major revisions, while the other has recommended minor revisions. Please address the comments accordingly to improve the quality of your manuscript. Best regards, Please submit your revised manuscript by Apr 24 2025 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 . 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We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.-->--> -->-->5. Please amend either the abstract on the online submission form (via Edit Submission) or the abstract in the manuscript so that they are identical.-->?> Additional Editor Comments: Dear Erguang Jin, Your submission Impacts of cellulase and xylanase addition on antibiotic resistance and microbial community during dairy manure composting has been reviewed and we would like to encourage you to submit revisions that address the reviewers' comments. An editor will review these revisions and if they address the concerns adequately, your submission may be accepted for publication. The reviewers' comments are included at the bottom of this email. Please respond to each point in the reviewers' comments and identify what changes you have made. If you find any of the reviewer's comments to be unjustified or inappropriate, please explain your perspective. We look forward to receiving your revised submission. Kind regards, Editor, PLOS One [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? Reviewer #1: Yes Reviewer #2: Yes ******** 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 Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: Comments to Authors: Major points 1- In results: you wrote many sentences as discussion!!! The rule of manuscripts’ writing is to avoid using any discussing points in the results chapter, so you should transfer those sentences to discussion part. 2- You should add conclusion part at the end of discussion chapter. Minor points 1- In this manuscript; you wrote (5 times Our)!!! The rule of manuscript writing is to avoid using (Our). So you should delete (Our) and use academic scientific words such as (This study or The current study or The present study). Kind regards Reviewer #2: Thanks for all Researchers for this research psper. The paper is well written and acceptable for publication after addressing some comments More details needed on Mann whiteny test used to assess differece of what tukey used in anova need to be added in the Figure legend ****** 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-24-53884 reviewed.pdf https://doi.org/10.1371/journal.pone.0328055.r001
Revision 1
9 Apr 2025 Author Response Response to reviewers, PONE-D- 24-53884 Dear Editor, We are grateful for the opportunity to revise our manuscript entitled “Impacts of cellulase and xylanase addition on antibiotic resistance and microbial community during dairy manure composting” in light of the editorial and reviewer comments. Below, we have provided a point-by-point response. Academic editor's comments 1.When submitting your revision, we need you to address these additional requirements. 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: We have ensured that our manuscript meets PLOS ONE's style requirements. 2.Thank you for stating in your Funding Statement: This work was supported by the Tibet Autonomous Region Key R&D Project (XZ201801NB34) and the Wuhan Academy of Agricultural Sciences Scientific and Technological Innovation Project (XTCX2021002). Please provide an amended statement that declares all the funding or sources of support (whether external or internal to your organization) received during this study, as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Please include your amended Funding Statement within your cover letter. We will change the online submission form on your behalf. Response: We have provided the following amended Funding Statement: “This work was supported by the Tibet Autonomous Region Key R&D Project (XZ201801NB34) and the Wuhan Academy of Agricultural Sciences Scientific and Technological Innovation Project (XTCX2021002). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” Please see line 451-456 in manuscript. 3.In the online submission form, you indicated that The original contributions presented in the study can be contacted to the corresponding author. All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either a. In a public repository, b. Within the manuscript itself, or c. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval. Response: We have provided the data in an Excel uploaded as “Supporting Information files.xlsx”, all relevant data except for sequence data are in the file. 4.When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. Response: We have uploaded our 16S-DNA sequence data to NCBI and revised the “Data Availability Statement” section. Please see Line 435-439. 5.Please amend either the abstract on the online submission form (via Edit Submission) or the abstract in the manuscript so that they are identical. Response: We have carefully re-read and revised our manuscript, and we didn’t revise the abstract of manuscript. Response to Reviewer #1 We sincerely appreciate your time and effort in reviewing our manuscript. Your insightful comments and constructive suggestions have been invaluable in improving the quality and clarity of our work. We are grateful for your thoughtful feedback and have carefully addressed each point in our revised manuscript. Major points 1- In results: you wrote many sentences as discussion!!! The rule of manuscripts’ writing is to avoid using any discussing points in the results chapter, so you should transfer those sentences to discussion part. Response: Thank you for your insightful comment. We appreciate your guidance on the proper structure of the manuscript. Upon reviewing the Results section, we identified and relocated sentences that contained interpretative or discussion-like content to the Discussion section. The Results section now strictly presents the findings without interpretation. We have revised the manuscript accordingly, and the changes can be found at line 242, line 314-316, line 318-320, line 357-360, line 371-373, line 379-380. 2- You should add conclusion part at the end of discussion chapter. Response: Thank you for your valuable suggestion. We agree that a conclusion section would enhance the clarity and impact of our manuscript. Accordingly, we have added a conclusion at the end of the Discussion section, summarizing the key findings and their implications. The revised manuscript now includes this section at line 427-434. Minor points 1- In this manuscript; you wrote (5 times Our)!!! The rule of manuscript writing is to avoid using (Our). So you should delete (Our) and use academic scientific words such as (This study or The current study or The present study). Response: Thank you for your careful review and valuable suggestion. We acknowledge that using more formal academic expressions enhances the clarity and professionalism of the manuscript. Accordingly, we have replaced instances of "Our" with more appropriate terms such as "This study," "The current study," or "The present study" throughout the manuscript. These revisions can be found at line 91-92, line 318, line 371 and line 407. We appreciate your insightful feedback, which has helped us improve the quality of our manuscript. Response to Reviewer #2 We sincerely appreciate your thorough review of our manuscript. Your thoughtful feedback and detailed suggestions have greatly contributed to improving the clarity and rigor of our work. We highly value your time and effort in evaluating our study, and we have carefully considered and addressed all your comments in our revision. Comment: More details needed on Mann whiteny test used to assess differece of whattukey used in anova need to be added in the Figure legend Response: Thank you for your positive feedback and for recognizing the quality of our manuscript. We appreciate your constructive suggestions for improvement. Regarding your comment on the Mann-Whitney test and Tukey’s test in ANOVA, we have now clarified their specific applications in the manuscript and we made a mistake for writing “Mann-Whitney test” was used. Additionally, we have revised the figure legend to explicitly describe the use of these statistical tests in assessing the differences. The corresponding changes can be found at line 190-192, line 633-636, line 644, line 653 and line 671-672. Thank you again for your valuable insights and constructive input, which has helped us improve the quality of our manuscript. Attachments Attachment Submitted filename: Response to Reviewer.docx https://doi.org/10.1371/journal.pone.0328055.r002
26 Jun 2025 Decision Letter - Shweta Sharma, Editor Impacts of cellulase and xylanase addition on antibiotic resistance and microbial community during dairy manure composting PONE-D-24-53884R1 Dear Dr. Jin, 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, Shweta Sharma, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> 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 Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes ****** Reviewer #1: (No Response) ****** 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.0328055.r003
Formally Accepted
Acceptance Letter - Shweta Sharma, Editor PONE-D-24-53884R1 PLOS ONE Dear Dr. Jin, 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 You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Shweta Sharma Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0328055.r004

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