PONE-D-25-12060Seasonal changes in the structure of river fish communities in temperate Japan depicted using quantitative eDNA metabarcodingPLOS ONE

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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: 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: No

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 authors detected fish species in Isazu river and its tributary Ikeuchi river using quantitative environmental DNA metabarcoding, and detected 78 species (or operational taxonomic units) across the seasons. The found that the fish community structure varied spatially and temporally. I believe that this work appeals to a broad scientific community particularly those ae interested in fish biology and coastal/marine science. I have some minor suggestions that might improve the presentation of the manuscript.

Minor comments:

L19. This study does not go beyond fish species detection, and does not study ecosystem services per se.

L267. Comprised.

L294. Space-time -> Spatio-temporal

L298. The spring and the fall; delete ‘pair’

L305. The authors should present degree of freedom of F statistics in Table1

L322. Independent -> dissimilar?

L461. Nitrogen deposition from yellow sand impact different fish species equally. I’m not sure why does this factor come into play.

Figure 3. Distance dependence. It is known that Shannon diversity index recovers its doubling property and the exponentiated Shannon index can thus be better linked with distance from the river mouth. I suggest that the current version s fine, but merits redrawing the figure using exponentiated index; then the authors fid exponential decay more clearly.

See the Equation (B3) of the following article by Roswell et al. 2021.

Reference: https://nsojournals.onlinelibrary.wiley.com/doi/10.1111/oik.07202

Reviewer #2: In the manuscript titled “Seasonal changes in the structure of river fish communities in temperate Japan depicted using quantitative eDNA metabarcoding,” the authors have employed an eDNA metabarcoding approach to examine spatial and seasonal variations in fish communities within the Isazu River.

The manuscript is well-written, clearly organized, and easy to follow. The analyses appear sound, with no major methodological flaws identified. The conclusions are well supported by the data presented. However, one significant concern is the limited sampling effort used to assess seasonal changes in fish diversity. The authors collected samples only once per season, which is insufficient to draw robust conclusions about seasonal variation in fish communities.

Another concern pertains to the quality of the figures. In several instances, the text within the figures is blurry and difficult to read. I recommend that the authors improve the resolution and overall quality of the figures.

Minor Comments:

• Line 85: Please delete the word “so.”

• Line 146: Likely a typo—please correct “10 mL” to “10 μL.”

• Line 159: Include the DNA concentration in ng/μL. Listing only the volume (1 μL) is not informative.

• Line 193: Clarify how the value of 200 was determined to convert copy number/μL to copy number/L.

• Line 279: Replace “Benn” with “Venn.”

• Line 293: Remove the space between “H′” and “during.”

• Line 310: The “4” in “PO4-P” should be subscripted.

• Line 337: Change “2 copy/L” to “2 copies/L.”

• Lines 342–343: The use of two-letter abbreviations for Le. torrentis and Li. reinii seems unnecessary, as there is no apparent ambiguity in these taxa. Please explain the rationale or correct it consistently throughout the manuscript.

• Line 355: Add the word “in” before “the.”

• Line 410: The phrase “in other studies” is used, but only one reference is cited. Please include additional references.

• Line 426: Remove the extra comma.

• Line 437: “The” should begin with a lowercase “t.”

• Line 462: Clarify what is meant by “continent” in the phrase “yellow sand transported from the continent.”

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Reviewer #1: No

Reviewer #2: Yes:  Girish Kumar

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Seasonal changes in the structure of river fish communities in temperate Japan depicted using quantitative eDNA metabarcoding

PONE-D-25-12060R1

Dear Dr. Ito,

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.

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Kind regards,

Qing Wang

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

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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 #2: Yes

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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

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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 #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 #2: (No Response)

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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: No

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