PONE-D-24-15257Microbial community succession mediated by planting patterns in the loess beam-shaped hilly region of ChinaPLOS ONE

Dear Dr. Cai,

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

Academic Editor

PLOS ONE

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“The authors wish to express their sincere thanks to the Ningxia Hui Autonomous Region Natural Science Foundation�2022AAC03453�, and the Ningxia Hui Autonomous Region Key R&D Project(2023BEG02042). In addition, this work also is supported by the special project of Ningxia Academy of Agriculture and Forestry Science with foreign (DW-X-2020002), the Ningxia Hui Autonomous Region Sci-Tech innovation demonstration program of High-quality agricultural development and ecological conservation (NGSB-2021-11-01). The authors thank Biomarker Technologies for the support of tests.”

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“The authors wish to express their sincere thanks to the Ningxia Hui Autonomous Region Natural Science Foundation�2022AAC03453�, and the Ningxia Hui Autonomous Region Key R&D Project(2023BEG02042). In addition, this work also is supported by the special project of Ningxia Academy of Agriculture and Forestry Science with foreign (DW-X-2020002), the Ningxia Hui Autonomous Region Sci-Tech innovation demonstration program of High-quality agricultural development and ecological conservation (NGSB-2021-11-01). The authors thank Biomarker Technologies for the support of tests.”

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

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

Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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

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

Reviewer #1: Yes

Reviewer #2: Yes

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

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

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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

Reviewer #1: The manuscript submitted to the journal titled “Microbial community succession mediated by planting patterns in the loess beam-shaped hilly region of China”. The succession of microbial community structure and function in ecologically fragile areas is a core ecological issue for solving the problem of ecological degradation. This research focuses on the functional dynamics of microbial communities in soil sample sequences of different planting areas in ecologically degraded areas. It is important and contributes with information about the succession of microorganisms in the loess beam-shaped hilly region of China. However, there are some suggestions as follows:

1. About the co-author, why “Tianning WANG” NOT “Tianning Wang”�

2. In abstract, you mentioned “we studied the functional dynamics……” but I can not find any “dynamics”.

3. Lack of lots of necessary data in abstract, such as in Line 19-21, “Bacteria showed higher succession variability than fungi, and changes in bacterial and fungal communities were related to soil vegetation type and physical, chemical, and enzyme activity characteristics.” So, what physical, chemical, and enzyme activity parameter�and how these parameters influence microbial community?

4. Line 80, Change "Therefor" for "In this study".

5. Line 90, Change “Materials and methods” for “Materials and Methods”.

6. In “2.1 Study area and soil sampling”, the author introduced the research site, including latitude and longitude. Please add a figure to show this site will be better.

7. In “2.2 Soil sampling……” has “soil sampling” repeated with 2.1, so delete “soil sampling” in 2.1.

8. Line 108-109 what “+” in “forest +” “shrub +”means?

9. Line 127, Please confirm the wavelength in the molybdenum blue method? “700 nm” or “880 nm”?

10. Line 134, change “2.4.1 Extraction of DNA from soil bacteria and fungi” for “2.4.1 Extraction of DNA from soil samples”

11. Why do you did “qRT-PCR quantitative analysis”?

12. Line 144, what is “H O “ mean? Maybe the author want to write “H2O”?

13. There is so much blank between Line 175 and Line 176.

14. Line 176, change “3. Analysis of results” for “3. Results and Discussion”.

15. Line 176-183. These two sentences belong to “Materials and Methods”, not belong here.

16. The title of table 2 is not proper. Suggest change to “soil physical and chemical characteristics”.

17. Line 212-214, plus bacteria and fungi, archaea, and virus is not 100%?

18. Table 3 is not necessary for results, put it in the “Supplement Materials”.

19. From the Figure 3, it seems it is the same of all the samples, has no difference. How to interpret?

20. The font size seems strange. It is bigger of the title of figures compare to main body.

21. In Figure 5, why (c) use red? And what are “A,B,C,D,E” mean? It not clear.

22. In Figure 9, this network figure is a little disordered? What is the main factor?

23. The figures quality should be improved especially Figure 3, Figure 4, Figure 6, Figure 7 and so on.

24. Line 407, Line 442, Line 481, What is the 7th, 21th, 36th reference going on? And the font size in references are different, please check one by one.

Reviewer #2: Review Report has been added as an attachment since it exceeds 20000 characters. I recommend major revisions to address clarity, enhance ecological relevance, and expand on the practical applications of the research. With these improvements, the manuscript has strong potential for publication.

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Reviewer #1: No

Reviewer #2: Yes:  BRIGHT FAFALI DOGBEY

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Attachments

Attachment

Submitted filename: PLOSone review (Autosaved).docx

PONE-D-24-15257R1Microbial Community Succession Mediated by Planting Patterns in the Loess Plateau, China: Implications for Ecological RestorationPLOS ONE

Dear Dr. Cai,

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 Apr 05 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 . 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,

Massimiliano Cardinale, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: (No Response)

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

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

Reviewer #1: Yes

Reviewer #2: (No Response)

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

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

Reviewer #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:  (No Response)

Reviewer #2:  Thank you for your efforts in revising the manuscript. Your study presents important insights into the role of mixed planting systems in shaping soil microbial diversity and stability. The revisions have improved the clarity and depth of the manuscript; however, there are still areas that require further refinement. Below are my detailed comments to help enhance the manuscript before publication.

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

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

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

Reviewer #1: No

Reviewer #2: Yes:  Bright Fafali Dogbey

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[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: Plos One_Revision_Review_Microbial_123 (Autosaved).docx

Microbial Community Succession Mediated by Planting Patterns in the Loess Plateau, China: Implications for Ecological Restoration

PONE-D-24-15257R2

Dear Dr. Cai,

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

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

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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,

Massimiliano Cardinale, PhD

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 #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 #2: Yes

**********

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

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 #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 #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 #2: The review report has been attached. Please refer to the document named Microbial Community Succession Revision Review Report

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

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

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

Reviewer #2: Yes:  Bright Fafali Dogbey

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Attachments

Attachment

Submitted filename: Microbial Community Succession Revision Review Report.docx