PONE-D-24-16486Endophytic and epiphytic metabarcoding reveals fungal communities on cashew phyllosphere in KenyaPLOS ONE

Dear Dr. Mbinda,

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PLOS ONE

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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: I Don't Know

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: No

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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 titled " Endophytic and epiphytic metabarcoding reveals fungal communities on cashew phyllosphere in Kenya" is comprehensive and interesting, especially contribute to the understanding of the microbiome of cashew. Here are the comments:

1. Please provide details in the M&M section, such as the replications of each tissue sample; they should be sufficiently supplied.

2. What’s the portion of your DNA regarding microbes and plants? How to deal with this in this study?

3. Could the term “phyllosphere” cover your study about different plant organs?

4. The authors use both ITS and 28S rRNA to barcode the presence of the fungi in and on the plants. Why you use this approach? What’s the pros and cons? How to interpret the difference? It is better to further discussed in this article

Other suggestions:

5. L130: The term “Isolation” should be replaced since the microbes were not isolated and cultured.

6. L137-143: How large are the samples? How many samples? Please provide enough details in the M&M section.

7. L154: It seems like “county”, not “country”.

8. L155: NL4, instead of NL

9. L202: b ITS?

10. L200: OTSs

11. L213: 28S rRNA

12. L218, L222: phy Incertae sedis or Phy Incertae sedis? Make sure they are the same, check the entire article.

13. L224, L225: Saccharomycetes, italicized or not? Make sure they are the same, check the entire article.

14. L273: sp. Check the entire article.

15. L277: sp. Should not be italicized.

16. L281: Saccharamycetales, Helotiales

17. L366: “Candid sp” is incorrect.

18. Make sure the reference style follow the Submission Guidelines. Some of the writing is inconsistent.

19. Legend of Supplementary 7 is not consistent, check the entire article.

Reviewer #2: The research work presented in this manuscript is rigorously designed, with experiments conducted meticulously and data analysis performed appropriately. However, I would like to offer some constructive feedback regarding the clarity and accessibility of the writing style.

It is advisable for the authors to aim for precision in their writing and adopt a more accessible language, particularly in the Abstract, Introduction, Discussion, and Conclusion sections. This would make the content more understandable to a broader audience, minimizing the use of excessive technical jargon.

For instance, the Introduction should concentrate more on the issues related to cashew cultivation and the potential roles of microbiota. It should also discuss previously isolated endophytes from this or similar plant species, setting the stage for proposing potential solutions. Typically, an effective introduction outlines a problem, proposes a solution, and previews the methods used to explore that solution.

In the Conclusion, the key takeaways are somewhat vague concerning the specific causes of problems in cashew trees, such as pathogens. I recommend revising parts of the manuscript to enhance clarity and digestibility for the general reader.

A more direct approach would be to clearly state that cashew production faces significant challenges, primarily due to fungal pathogens and the overuse of agricultural land. The manuscript should then detail how the conducted meta-analysis addresses these challenges, presenting findings such as the structures of endophytic and epiphytic mycobiome communities and subsequently proposing practical solutions for the identified issues in cashew cultivation.

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Reviewer #1: Yes: Yuan-Min Shen

Reviewer #2: Yes: Mahmoud W. Yaish

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Endophytic and epiphytic metabarcoding reveals fungal communities on cashew phyllosphere in Kenya

PONE-D-24-16486R1

Dear Dr. Mbinda,

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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Kind regards,

Eugenio Llorens

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

Reviewer #1: All comments have been addressed

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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

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

Reviewer #1: N/A

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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

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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

**********

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)

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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: Yes: Yuan-Min Shen

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