PONE-D-23-22614Impacts of hurricanes and disease on Diadema antillarum in shallow water reef and mangrove locations in St John, USVIPLOS ONE

Dear Dr. Godard,

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 Oct 20 2023 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,

Jiang-Shiou Hwang, Ph.D.

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. Thank you for stating the following in the Acknowledgments Section of your manuscript: 

   "We thank Natasha Bestrom for help with field work and comments on a draft of the manuscript. We also thank Kristin Bell for help with map and Bonnie Bowers for advice on statistical analyses. We also thank Cheryl Taylor for technical support. We are grateful to Tom and Anna Lawson for funding support for this project as well as the various internal funding support from Hollins University. Finally, thanks to Thomas Kelley for help with obtaining research permits (VICR-2018-SCI-0001) to work in the Virgin Islands National Park and for the Virgin Islands Environmental Resource Station (VIERS) which provided support for research prior to the hurricanes in 2017."

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: 

  "Funding for this research was provided by the Paula Pimlott Brownlee and Janet Spear Professorships at Hollins University as well as support from Tom and Anna Lawson.  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

3. 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.

4. We note that Figure 1 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (a) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (b) remove the figures from your submission:

a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license.  

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

[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

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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: No

**********

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

**********

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 aimed to explore the bioactivity response to changes in bacterial community in coral mucus and compare the difference of the bioactivities between the conditions of coral health and bleaching.

The topic is interesting and important, but the manuscript content quality is not good enough. In addition, the manuscript needs to be edited further as at many places the manuscript lack clarity.

About the survey locations, I recommend the author to provide exact latitude and longitude in the materials and methods, or use a tale to present this information. In the figure 1, the map is not informative. The reader cannot know the location of the St John, USVI.

About the sampling time, I suggest the authors to provide a time scale to illustrate the events such as observation time, hurricanes and the disease outbreak.

About the observation species Diadema antillarum, the author should provide a photo to show the morphology of it. Also, Authors need to present reasons for choosing this species in the beginning of the introduction.

I would suggest the authors to be more cautious to prepare the manuscript. Therefore, this article would need a thoughtful and concise structure, which this manuscript would need to revise before considering.

Reviewer #2: PONE-D-23-22614 – Impacts of hurricanes and disease on Diadema antillarum in shallow water reef and mangrove locations in St John, USVI

This paper presents the results of several years (2017-2023) of surveys at nine reef and three mangrove locations around St. John, USVI. Within these fixed sites, initial surveys identified any areas of Diadema abundance and targeted transects were used to generated a maximum density estimate. Overall, the manuscript appears technically sound and data support the conclusions. The information provided is of value. Clarity could be improved and/or more information provided in several areas. It is my opinion that the manuscript could be acceptable for publication following a major revision in which the authors address the below general and specific comments.

General comments:

- The Methods section makes clear (and the first paragraph of Discussion addresses) that data were collected from targeted searches designed to capture the greatest number of Diadema possible. This appears to be in line with previous similar studies and is valid in my opinion given the sparse and patchy nature of this species’ distribution. I wonder if the authors might consider including this facet of the methodology in the Abstract and/or Introduction? As a reader, if not made explicit, I generally assume that field data collection to “survey” or “document” was done in some type of random or haphazard fashion. I think simply including the term “targeted surveys” or something analogous would be helpful early on to set the expectation.

- It is unclear why the total surface area of each surveyed site was calculated (lines 158-161) or how this information was used. Lines 144-145 suggest that the densities reported in this study are based on the average number of urchins found within each of three 20 square meter transects per site (e.g. an average of 10 urchins per transect would result in a reported density of 0.5 urchins per square meter for that site). In my opinion, adding in the total site area calculation and results to the Methods may confuse the reader on which area was used as the denominator in urchin density calculations. Unless the total site area data are going to be elsewhere reported/analyzed beyond the Methods section, the relative total size of reef vs. mangrove sites could be mentioned only in the Discussion if it affects the way results were interpreted.

- More detailed description of mangrove site characteristics would be appreciated in the Methods and/or Results. How far out from the red mangrove fringe were transects taken? Was the benthos qualitatively similar to or different from the reef sites?

- In my opinion, there is a bit too much blending of anecdotal or qualitative observations with quantitative, statistically analyzed, comparisons. It could be made clearer when one vs. the other is being presented/discussed.

- Was any data on urchin size collected or is any anecdotal information available? This could add some inference as to population dynamics at these sites or differences between mangrove fringe and reef. Mangroves serve as nursery grounds for many reef-associated animals, so it’d be interesting to know if there were any differences in size between the habitat types.

- Data availability – the authors provide a DOI with the submission, but I do not see this linked within the article such that readers will have access following publication. Also, the data provided are means of three transects per site and not the full raw dataset.

Specific comments:

lines 42 – Should be “…disease outbreak on populations of…”?

line 55 – 71 per square meter would be at the extreme high end of observed densities. Suggest noting that this would have been an exceptional density or perhaps using the more “average” figures that are often reported.

lines 57 – Should be “that” not “which”.

line 67 – Females can likely produce 10 million or more eggs per spawn. See Table 1 in Pilnick et al. (2021) A novel system for intensive Diadema antillarum propagation as a step towards population enhancement. Eggs were collected from captive spawned animals, but it nonetheless reflects the fecundity potential of the species.

line 90 – Should be “that” not “which”.

lines 123-124 – Wording could be improved for clarity here. It seems like annual surveys were conducted in January from 2017 to 2020 and then in May/June in 2022 and 2023.

line 186 – Suggest making percentage directionally explicit within the parentheses – “(96.4% reduction)”. Also, suggest being consistent with significant digits on decimals – 0.092 should be 0.09.

line 213-214 – Is this from contemporary surveys of “urchin zones” in various places or from pre 1980s die off levels? Would help the reader to make this explicit in the text.

line 228 – Comma after “cover”.

lines 251-252 – This is the first time I am catching that surveys in mangrove areas may have been conducted right along the fringe within the prop roots of the trees themselves, or is this just suggesting that adjacent habitat that could have supported Diadema was lost? Do the authors think that other areas of mangrove fringe on St. John may serve as a “refugia” for D. antillarum, or is there something special about Hurricane Hole?

lines 262-263 – Do the blue x’s in Figure 1 represent anecdotal observations that were not included in data reported in this study? This should potentially be made explicit in the Figure 1 caption or elsewhere. Up until these lines, I had misunderstood those X’s as being the location of particularly high-density transects.

line 277 – I would argue that this study presents an impact of the 2022 die-off of D. antillarum populations. In this sentence, perhaps add “full extent of impacts” or something along those lines.

**********

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

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.

Impacts of hurricanes and disease on Diadema antillarum in shallow water reef and mangrove locations in St John, USVI

PONE-D-23-22614R1

Dear Dr. Godard,

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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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,

Jiang-Shiou Hwang, Ph.D.

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

**********

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: N/A

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: In this revision, since the author provided enough data/explanation to all comments, the manuscript is acceptable. However, I would suggest the author to provide figures with higher resolution before publication.

Reviewer #2: Thank you for thoroughly addressing reviewer comments. It is my opinion that the article is acceptable for publication.

**********

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: Yes: Joshua Patterson

**********