PWAT-D-24-00128

From bench to beach: Assessing the reliability of community-based qPCR monitoring for recreational water quality

PLOS Water

Dear Dr. Hanington,

Thank you for submitting your manuscript to PLOS Water. After careful consideration, we feel that it has merit but does not fully meet PLOS Water'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.

Your manuscript has been evaluated by two reviewers, and their comments are appended below.

Both reviewers have expressed positive opinions of your study, along with some matters that warrant further revision. Specifically, the reviewers have requested additional reporting of the characterization of the CBM partner, as well as revisions to the data presentation and discussion section. Please ensure you address each of the reviewers' comments when revising your manuscript.

Please submit your revised manuscript by Apr 06 2025 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 water@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pwat/ 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 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'.

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Hugh Cowley

Staff Editor

PLOS Water

Journal Requirements:

1. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why.

2. Please provide separate figure files in .tif or .eps format.

For more information about figure files please see our guidelines: https://journals.plos.org/water/s/figures  

https://journals.plos.org/water/s/figures#loc-file-requirements 

Additional Editor Comments (if provided):

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does this manuscript meet PLOS Water’s publication criteria ? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn 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 (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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 Water 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: You did a wonderful job with this study. it's very interesting. I'm not sure I'm so confident that the community group can be used for generating economically and use-disruption decisions at this stage but maybe in the future or with a sharper choice of the community group members. That stated, I feel there's a characterisation of the CBM partner missing. It's not clear what kind of people this partner is composed of. Technical students? from which area of study? with or without experience in a lab. I really need to see a characterisation of the group in the design of the study in materials and methods.

Reviewer #2: I deeply appreciated this paper. I agree wholeheartedly with the authors that qPCR is an extremely valuable tool for fecal indicator bacteria monitoring. One of its often-cited limitations is the need for highly trained staff. So, this paper exploring the validity of that stated limitation is very important.

We are increasingly recognizing the importance of including community members at all phases of a study, including design. The fact that new qPCR targets can be added to a monitoring plan with relatively minor changes in protocol for the new target, as the authors state, allows studies to be tailored to community needs. Community involvement at the laboratory research stage will lead to greater transparency and increased investment from the community partners.

Environmental research needs to move away from an extractive model, where community members’ environments are sampled but the people themselves may not know what happens to the samples and/or the data. This work moves forward the shift toward a reciprocal model.

Two things I would’ve like to see:

1. There is plenty of discussion on the fraction of samples for which there was agreement regarding a decision. A table is good b/c the numbers are important, but for this type of analysis I really like to see an x-y scatter plot where the x and y axes are the actual values determined by each lab. Then, a horizontal and a vertical line can be drawn at the level that corresponds to a decision threshold. This way, four quadrants are created, and each dot represents one sample. It’s a nice visual and I think it reveals more information than just the table.

2. I think there should be more discussion of the potential additional targets that could be added. For example, the Ebentier paper is discussed at length, but the fact that it analyzed agreement between labs for microbial source tracking isn’t emphasized. Microbial source tracking is one area where community based monitoring could be important. Also, the spread of antimicrobial resistance in the environment near industrial food animal production is a critical area for research.

Overall, it’s an excellent paper of wide interest that should be published with minimal changes.

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For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #1: Yes:  João Brandão

Reviewer #2: No

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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.

From bench to beach: Assessing the reliability of community-based qPCR monitoring for recreational water quality

PWAT-D-24-00128R1

Dear Dr. Hanington,

We are pleased to inform you that your manuscript 'From bench to beach: Assessing the reliability of community-based qPCR monitoring for recreational water quality' has been provisionally accepted for publication in PLOS Water.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow-up email from a member of our team. 

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

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 water@plos.org.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Water.

Best regards,

Guillaume Wright

Executive Editor

PLOS Water

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Additional Editor Comments (if provided):

Reviewer Comments (if any, and for reference):

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. Does this manuscript meet PLOS Water’s publication criteria ? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

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

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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 Water 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

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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: Thank you for addressing the description of the groups involved in the study.

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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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #1: Yes:  João Brandão

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