PONE-D-24-32365

Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzae

PLOS ONE

Dear Dr. Shan,

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 22 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,

Yunzhou Li

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match.

When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

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

Reviewer #1: Yes

**********

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

Reviewer #1: 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: Yes

**********

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

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

Reviewer #1: Yes

**********

5. Review Comments to the Author

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

Reviewer #1: After carefully reviewing the manuscript titled "Isolation, Identification, and Whole-Genome Sequencing of Streptomyces rochei FE-3-1 Against Pyricularia oryzae" (Manuscript ID: PONE-D-24-32365), I find the research both relevant and timely, particularly in terms of its implications for biocontrol and antibiotic discovery. The genome analysis and biocontrol potential of Streptomyces rochei FE-3-1 represent significant contributions to the field.

However, before recommending the manuscript for publication, I would like to suggest a few points for revision and clarification. Below, I outline the questions and recommendations that could help improve the depth and clarity of the manuscript:

1. Lines 87-99: You mention the potential use of Streptomyces rochei FE-3-1 as a biopesticide or biofertilizer. Could you expand on the next steps in product development or field trials? This would help position the findings for practical, real-world applications.

2. Lines 111-121: Please provide more details on the statistical methods used to validate the inhibition rates observed in the antagonistic activity assay against Pyricularia oryzae. Including specific statistical tests will add rigor to the data and help readers assess the reliability of the results.

Additionally, have you assessed the ability of Streptomyces rochei FE-3-1 to control Pyricularia oryzae-caused disease in actual rice plants, beyond the in vitro antagonistic assays? If so, please provide detailed information on these trials, as it would greatly enhance the practical relevance of your findings.

3. Lines 229-237: The identification of heavy metal resistance genes is intriguing, but it would be beneficial to discuss how these genes enhance the strain’s survival and effectiveness in agricultural environments that are subject to pollution or heavy metal contamination.

4. Lines 240-253: Could you clarify how the genes related to plant growth promotion, such as those for phosphorus and potassium solubilization, enhance the biocontrol efficiency of Streptomyces rochei FE-3-1? Understanding the synergy between plant growth and pathogen inhibition would be valuable.

5. Lines 257-274: The manuscript identifies several biosynthetic gene clusters, such as those for candicidin and streptothricin, which are related to antimicrobial activity. Expanding on how these clusters contribute to the biocontrol properties of Streptomyces rochei FE-3-1 would strengthen the link between the genomic data and the biological functions of the strain.

6. Lines 257-277: It would be helpful to include a comparison of the identified secondary metabolites with known commercial biocontrol agents in terms of their effectiveness and range of activity. This could give a clearer perspective on the potential competitive advantage of Streptomyces rochei FE-3-1.

7. Lines 333-362: The manuscript mentions unique homologous genes found in Streptomyces rochei FE-3-1. It would be beneficial to discuss how these genes might contribute to the strain’s unique abilities or adaptations, especially in comparison with other Streptomyces species.

8. Lines 364-374: Finally, your study contributes significantly to microbial genome mining. Could you emphasize how your findings advance the field of genome-guided discovery of biocontrol agents and antibiotics?

9. Introducing biocontrol agents into agricultural systems carries some risk. Have you considered any potential environmental impacts or risks associated with using Streptomyces rochei FE-3-1? If so, how might these be mitigated?

**********

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

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

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

Reviewer #1: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step.

PONE-D-24-32365R1Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzaePLOS ONE

Dear Dr. Shan,

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 Feb 01 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,

Yunzhou Li

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: 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 author has made corrections according to the suggestions, but minor errors remain, such as the need to italicize the scientific name Streptomyces. It is therefore recommended that the author thoroughly check the manuscript for accuracy.

**********

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

**********

[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.

PONE-D-24-32365R2Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzaePLOS ONE

Dear Dr. Shan,

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.

==============================

After carefully reviewing the manuscript titled "Isolation, Identification, and Whole-Genome Sequencing of Streptomyces rochei FE-3-1 Against Pyricularia oryzae" (Manuscript ID: PONE-D-24-32365), I find the research both relevant and timely, particularly in terms of its implications for biocontrol and antibiotic discovery. The genome analysis and biocontrol potential of Streptomyces rochei FE-3-1 represent significant contributions to the field.

However, before recommending the manuscript for publication, I would like to suggest a few points for revision and clarification. Below, I outline the questions and recommendations that could help improve the depth and clarity of the manuscript:

1. Lines 87-99: You mention the potential use of Streptomyces rochei FE-3-1 as a biopesticide or biofertilizer. Could you expand on the next steps in product development or field trials? This would help position the findings for practical, real-world applications.

2. Lines 111-121: Please provide more details on the statistical methods used to validate the inhibition rates observed in the antagonistic activity assay against Pyricularia oryzae. Including specific statistical tests will add rigor to the data and help readers assess the reliability of the results.

Additionally, have you assessed the ability of Streptomyces rochei FE-3-1 to control Pyricularia oryzae-caused disease in actual rice plants, beyond the in vitro antagonistic assays? If so, please provide detailed information on these trials, as it would greatly enhance the practical relevance of your findings.

3. Lines 229-237: The identification of heavy metal resistance genes is intriguing, but it would be beneficial to discuss how these genes enhance the strain’s survival and effectiveness in agricultural environments that are subject to pollution or heavy metal contamination.

4. Lines 240-253: Could you clarify how the genes related to plant growth promotion, such as those for phosphorus and potassium solubilization, enhance the biocontrol efficiency of Streptomyces rochei FE-3-1? Understanding the synergy between plant growth and pathogen inhibition would be valuable.

5. Lines 257-274: The manuscript identifies several biosynthetic gene clusters, such as those for candicidin and streptothricin, which are related to antimicrobial activity. Expanding on how these clusters contribute to the biocontrol properties of Streptomyces rochei FE-3-1 would strengthen the link between the genomic data and the biological functions of the strain.

6. Lines 257-277: It would be helpful to include a comparison of the identified secondary metabolites with known commercial biocontrol agents in terms of their effectiveness and range of activity. This could give a clearer perspective on the potential competitive advantage of Streptomyces rochei FE-3-1.

7. Lines 333-362: The manuscript mentions unique homologous genes found in Streptomyces rochei FE-3-1. It would be beneficial to discuss how these genes might contribute to the strain’s unique abilities or adaptations, especially in comparison with other Streptomyces species.

8. Lines 364-374: Finally, your study contributes significantly to microbial genome mining. Could you emphasize how your findings advance the field of genome-guided discovery of biocontrol agents and antibiotics?

9. Introducing biocontrol agents into agricultural systems carries some risk. Have you considered any potential environmental impacts or risks associated with using Streptomyces rochei FE-3-1? If so, how might these be mitigated?==============================

Please submit your revised manuscript by Jul 17 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,

Sujata Singh Yadav

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: 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 author has revised the MS “Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzae” in several aspects as suggested.

**********

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

**********

[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.

PONE-D-24-32365R3Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzaePLOS ONE

Dear Dr. Shan,

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 Sep 27 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,

Chetan Keswani, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

1. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 

2. 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: All comments have been addressed

Reviewer #2: (No Response)

**********

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: The author has addressed the suggested revisions in multiple sections of the manuscript titled 'Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzae.

Reviewer #2: This manuscript reports the isolation of Streptomyces rochei FE-3-1 from rice rhizosphere, its antifungal activity against rice blast fungus and a detailed genomic analysis elucidating its biocontrol and plant growth-promoting potential. The study includes classical microbiological approaches, genome mining, and comparative genomics including comparisons with related Streptomyces species. The use of whole-genome sequencing, functional annotation, and the practical insight into biocontrol product development align well its aim.

Relevance and novelty of this paper.

The biocontrol of rice blast is a problem of global agricultural importance. The study addresses a significant challenge in sustainable crop protection by focusing on a native rhizosphere Streptomyces strain. The complete genome sequence for S. rochei FE-3-1 is newly reported, including genome mining for secondary metabolites and resistance genes, and there is thoughtful discussion of the translational path toward product development (biopesticide/biofertilizer).

Both the main text and the cover letter clarify that the whole genome sequence and detailed comparative genomics of S. rochei FE-3-1 are first reported in this study. The NCBI accession numbers are provided for verification. There is no indication of prior publication of these data elsewhere.

Experimental design and logic.

The experimental provides a comprehensive workflow. The work combines phenotype assays, genome sequencing, mining for beneficial traits, and comparative genomics. All relevant data (accession numbers for GenBank, etc.) are made available in accordance with PLOS ONE standards.

Experimental replication and statistical methods are clearly described for laboratory inhibition data, and the connection between detected biosynthetic gene clusters and mechanisms of pathogen inhibition is explicitly made.

Standard microbiological, genetic, and bioinformatics approaches (antiSMASH, Prokka, phylogenetic analysis) are applied. The main claims (FE-3-1's antagonism in vitro, genomic potential for biocontrol and growth-promotion, biosynthetic gene clusters) are directly supported by experimental/genomic data.

Though I believe that limitations of this study, e.g., using in vitro data only, should be acknowledged more clearly. The environmental risk assessment is limited which is another weak point.

1. The supplementary table (S6) provides an overview of commercial benchmarks. It might be helpful to briefly discuss in the main text how the observed inhibition rates and genomic potential of FE-3-1 compare quantitatively, where possible, to those products. Also it is unclear which of references 1-4 relates to respective preparation.

2. English: there are minor issues with grammar and phrasing throughout the text. A careful editing may be necessary. Although my judgment may be subjective due to the fact that I’m not a native speaker.

Suggestions

• If possible, reference supporting data (statistical outputs, graphical results) directly in the main text rather than relying on supplementary figures.

• In the discussion, clearly differentiate between what is demonstrated (in vitro/in silico) and what is still hypothetical or future work (in planta, field results, compound isolation, commercial development).

• Reinforce the conclusion with perspective on how this genome resource could contribute to the mining of new actinobacterial biocontrol strains.

Overall conclusion:

Minor revisions are recommended

**********

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.

Isolation, identification, and whole-genome sequencing of Streptomyces rochei FE-3-1 against Pyricularia oryzae

PONE-D-24-32365R4

Dear Dr. Shan,

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. For questions related to billing, please contact billing support .

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,

Chetan Keswani, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

NIL

Reviewers' comments: