PONE-D-24-05844Subsurface microbial community structure shifts along the geological features of the Central American Volcanic ArcPLOS ONE

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PONE-D-24-05844R1Subsurface microbial community structure shifts along the geological features of the Central American Volcanic ArcPLOS ONE

Dear Dr. Lloyd,

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.

The review process has now been completed for your manuscript, the reviewers have raised critical comments that you need to pay attention and revise your work accordingly.

Please submit your revised manuscript by Jun 27 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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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.

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Academic Editor

PLOS ONE

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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: (No Response)

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: Yes

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Reviewer #1: No

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: Basili et al. built upon previous understandings of across-arc microbial community variations in the Central American Volcanic Arc and investigated the microbial community variations *along* the convergent margin. The study is a useful addition to our understanding of biosphere-geosphere interactions. The study appears to be technically sound and associated methods are described in sufficient details. However, the current presentation is somewhat difficult to follow especially when reading for the first time. I suggest the following improvements:

1. Please clarify the relationship between the microbial sample set in this manuscript and in other companion papers, e.g. Fullerton et al. 2021 Nat. Geosci.: Were any of the microbial samples used in this study published before? If so, please specify which one(s) were downloaded data and add citations; if not, please describe whether or how the sampling/sample processing/resulting data differ between samples that appear to have the same names across papers.

2. I suggest clarifying what direction is meant by "across-arc" and "along arc" in earlier sections of the manuscript. It might be helpful to add arrows to Fig.1 to help readers comprehend along which direction are you analyzing microbial variations. Currently, the first instance where this is clarified seems to be in the Results section, line 198-199.

3. Lines 196-197: Please make the naming of these subgroups of regions consistent with those in Figs 1A, S1, etc. Please also add the number of samples per region to the Figures where appropriate.

4. Lines 222-226 & Fig. 2B&C: Can you map the regions (arc, forearc, backarc, Panama slab window, etc.) onto Fig. 2B&C? e.g. by using different shapes? It is hard to follow the descriptions here for readers unfamiliar with which samples were from "outer forearc" or "forearc" or "flank geothermal sites". Same for Fig. S3.

5. Lines 277-279 & Fig. S11: Fig S11 is hard to interpret and doesn't seem to support what is said here based on its current presentation. Please map different regions and sample types onto Fig S11 by using different colors, shapes, etc.

6. Line 266-269 & Fig. 3: The interpretation of the hierarchical clustering is not quite straightforward. It looks like most sample pairs have Jaccard dist. close to 1, so it is hard to see many obvious "clusters". What is the rationale behind choosing Jaccard distance? Have you considered/tried other distance metrics?

Other minor issues:

- Line 103: the word "active" is duplicated.

- Line 252: by "dark blue" do you mean purple?

- Line 262: Based on Jensen-Shannon Divergence or Jaccard distance? The caption of Fig 4 says Jaccard distance.

- Line 302: Please cite the figure(s) that support what you said here.

- Line 346: Please cite the figure(s) that support what you said here.

- Line 346: by "Costa Rica backarc" do you mean Costa Rica outer forearc?

- Fig S4: Please explain what is meant by the dendrogram on the left side of the heatmap.

Reviewer #2: This manuscript is a very interesting paper, which presents microbial community changes across the Central American Volcanic Arc, and discusses underling mechanisms controlling the shifts in microbial composition in each sites along the arc. The paper is well written, and the results support their conclusion overall. As there are some many data and parameters considered, the authors need to revise their paper by presenting their discovery and point of views more clearly. My major concerns are:

(1) The authors suggest that bacterial community composition shifts across-arc with distance from the trench in addition to changes in pH and temperature, without giving further explanation as to what kind of change leads to such shifts in bacterial community (Line 299-314). They gave an interpretation that such changes in sampling location relative to the cross-arc may result in a shift in deep volatile delivery, without further evidence to support this notion. In their discussion part, the authors need to give evidence to support and explain this clearly.

(2)

Another main point of the manuscript is that microbial community composition shifts significantly according to geological changes along the CAVA, supporting the fundamental role that tectonic processes play in shaping subsurface microbial ecosystems. Again the authors need to explain more about this geological change. From their Line 315-354, I tried to guess that such geological change include deep volatile and bedrock composition, which I am not so sure. This is because the formal (volatile) has interacted with overriding crust, through which to change fluid geochemical composition. What is the relationship between overriding crust and bedrock? Are they the same stuff? The authors need to revise their discussion and present their notions more clearly. Also If geological change has something to do with deep volatile, then this has been mentioned in their Line 312-314. If the two paragraphs were discussing the same thing, the authors can try to revise the contents concisely.

Details of the sampled section need to be added.

Line 59-61: Rephrase.

Line 63: Be specific of what “geological setting” means?

Line 72-73: Previous sentence did not mention that scientist names. Thus, I cannot understand what these authors mean.

Line 78: along-arc differences of what?

Line 101-104: Rephrase.

Line 103: Delete one “active”.

Line 126: Detailed methods of what tests?

Line 309: Please be specific of what kind of change in bacterial community have changed across-arc.

Line 311-314: I did not get the logic here. How does the author come up with this conclusion based on previous discussion?

Line 316: What do you mean by geological change? Bedrock composition and volatile?

Line 246 Rephrase. The similarity in microbial community between these two sites?

Figure and figure captions

Fig. 4: font size within figure are too small to read.

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Reviewer #1: No

Reviewer #2: No

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Subsurface microbial community structure shifts along the geological features of the Central American Volcanic Arc

PONE-D-24-05844R2

Dear Dr. Karen Lloyd,

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,

Rizwan Sarwar Awan

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: (No Response)

Reviewer #2: Yes

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

Reviewer #1: (No Response)

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: (No Response)

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 #1: (No Response)

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: (No Response)

Reviewer #2: (No Response)

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Reviewer #1: No

Reviewer #2: No

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