PONE-D-24-34035Fungal community and taxa specialization to host and environment interactions in two temperate forestsPLOS ONE

Dear Dr. Benitez Ponce,

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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: Partly

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

Reviewer #1: Yes

Reviewer #2: No

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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: Review of the Manuscript Submitted to PLOS ONE by Ponce and Colleagues, Titled: “Fungal Community and Taxa Specialization to Host and Environment Interactions in Two Temperate Forests”

Summary

In this study, the authors tested the hypothesis that fungal host specialization occurs at both the individual fungus and fungal community levels and is influenced by environmental conditions. They evaluated the effects of various environmental factors on structuring seedling-associated fungal communities in temperate tree species, taking into account both the Janzen-Connell (JC) hypothesis and the impacts of climate warming.

To achieve their objective, the authors surveyed seedling-associated fungal communities from experimental sites in two temperate forests. The experimental design incorporated treatments involving light availability, elevated temperature, and distance to and density of conspecifics. The seedling mycobiome fungal communities were characterized using high-throughput sequencing, and the data were analyzed using generalized joint attribute models.

The results showed that host species, distance to conspecifics, and conspecific density were the strongest factors in shaping seedling fungal communities. The authors also identified specific fungal taxa that responded to these predictors. Overall, their findings support the concept of fungal host specialization at the community level and highlight particular fungal taxa that may contribute to density- and distance-dependent regulation of plant species diversity in the studied forests.

General Comments

The manuscript is well-written, with a high-quality experimental design, methods, and interpretation of results. I found it enjoyable to read. It makes a solid and significant contribution to our understanding of fungal-host-environment dynamics, which will be especially valuable for future models considering these dynamics in the context of global environmental changes. The results are likely to be of broad interest to the scientific community.

Specific Comments

My comments below are also available on the pdf copy of the manuscript.

1. Supplementary Materials and Methods (Page 5): Please add the similarity cutoff value used in “UPARSE algorithm implemented in USEARCH version 7 [10] was used for OTU calling at XX% similarity cutoff.”

2. Page 8, Line 165: I suggest including the expected size range for the amplicons generated with primers LR0R and LR3 of LSU. This information will help readers understand why short-read sequencing technology (e.g., Illumina) could have been used alongside long-read 454 pyrosequencing. Please also clarify the rationale for using both platforms.

3. Page 8, Line 168: Please provide the URL for Qiita.

4. Page 9, Line 182: Readers unfamiliar with the domain might not know what SILVA is. Please provide the URL for SILVA.

5. Table 1: The authors state, “Host species names in bold indicate hosts for which models of host and density and host and distance interaction were analyzed.” However, no species names are in bold. Please revise this accordingly.

6. Page 13, Lines 246–248: Please clarify what the numbers (e.g., Sordariomycetes_186) refer to.

7. Supplementary Figure S4: Please check the format and rendering of this figure. There seems to be an issue with the graph labels and lines. Additionally, the sequencing labels should distinguish between the two platforms used.

8. Table S8: Please add lines to the table for clarity.

9. Figure 3D: I suggest writing out "Duke Forest Eno West" for consistency, as "Harvard Forest" is written out in Figure 3C. Alternatively, use a complete acronym for "Harvard Forest ST."

10. Figure 4: The graph is difficult to interpret. It appears to show that more than 150 taxa had zero responses, which seems incorrect given that 247 minus 109 equals 138. Additionally, the tick marks should be placed in the middle of the bars to improve readability.

11. Page 19, Lines 382–388 (Page 20): This section reads like a figure legend, and the writing style differs from the preceding text. I suggest revising it to report specific observations and use past tense. The same applies to the next paragraph (Lines 390–399).

12. Discussion Section: I recommend removing references to figures and tables in the discussion, as they have already been addressed in the results section. Additionally, some sentences read like results and should be moved to the appropriate section. For example, “Most taxa responded to a limited number of predictors, but a small subset responded to more than ten (Fig. 4)” (Lines 425–426) should be placed in the results section.

Reviewer #2: Please see my comments in the methods section. Unclear and cryptic description of methods does not allow evaluation of statistical power of the experiments nor of the results. Please list the number of samples that represented each statistical test. There are a host of 'treatments' in the study and these should be listed clearly along with the 'n' that represented each test.

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Reviewer #1: Yes:  Martin Petrus Albertus Coetzee

Reviewer #2: No

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Attachments

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Submitted filename: PONE-D-24-34035 reviewer.pdf

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Submitted filename: PONE-D-24-34035_reviewer_.pdf

Fungal community and taxa specialization to host and environment interactions in two temperate forests

PONE-D-24-34035R1

Dear Dr. Benitez Ponce,

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. It was noted by reviewers that the manuscripts lacks NCBI accession numbers and other raw data links. Please address this.

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Kind regards,

Theodore Raymond Muth

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

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

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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

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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 authors have adequately addressed my comments in my previous review. I, therefore, feel that this manuscript is now acceptable for publication pending the comments from the second reviewer (if applicable).

Reviewer #2: (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:  Martin Petrus Albertus Coetzee

Reviewer #2: No

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