Examining the potential impacts of a coastal renourishment project on the presence and abundance of Escherichia coli

Jordan A. Lewis; Victoria J. Frost; Matthew J. Heard

doi:10.1371/journal.pone.0304061

Peer Review History

Original SubmissionJanuary 7, 2024
26 Feb 2024 Decision Letter - Md. Asaduzzaman Shishir, Editor PONE-D-24-00797Examining the potential impacts of a coastal renourishment project on the presence and abundance of Escherichia coli PLOS ONE Dear Dr. Lewis, 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 the revised version.============================== Please submit your revised manuscript by Apr 11 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. 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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 ******** 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: Yes ****** 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: Please mention the exact time/month of the sampling on page 7 line 144. Is there any seasonal influence on the presence and abundance of E. coli around beach area? How may the authors relate seasonal influence to this study? Reviewer #2: 1. As the impact of renourishment project was examined in terms of E. coli and its presence or absence, it might be insightful if the type of E. coli whether pathogenic or non-pathogenic was also detected. 2. The author suggests that following renourishment project the changes between microbial community and physical changes of the beach might be for short time. What might be the underlying reasons? Also required experimental evidence. 3. It would be intuitive if the work is conducted for longer period time (more years). Also is there any seasonal impact on microbial community there? 4. The asterisk should be in place in the graph. ****** 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: Yes: Umme Tamanna Ferdous 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. https://doi.org/10.1371/journal.pone.0304061.r001
Revision 1
7 Mar 2024 Author Response Manuscript Number: PONE-D-24-00797 Title: Examining the potential impacts of a coastal renourishment project on the presence and abundance of Escherichia coli Journal 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…………… Authors Response: We have gone through the manuscript and insured that the paper meets the style requirements of PLOS ONE. 2. 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. Authors Response: In the submission portal, we do not see distinct sections named Funding Information’ and ‘Financial Disclosure. Thus, we have added a section to the manuscript file called “Funding Sources” in order to compliment the financial disclosure section in the portal. 3. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. Authors Response: We have made the data associated with this manuscript available online via Dryad. The data can be found at https://datadryad.org/stash/dataset/doi:10.5061/dryad.zgmsbcchp 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). Authors Response: We have added the copyright information for the map used in figure 1 on page 5, lines 88-95. The map is available for use through ArcGIS. 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 ________________________________________ 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: Yes ________________________________________ 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 Authors Response to prompts I-IV: The authors would like to thank the reviewers for their time and effort reviewing the manuscript for publication in PLOS ONE. Please see specific responses to reviewer feedback below. ________________________________________ 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: 1. Please mention the exact time/month of the sampling on page 7 line 144. 2. Is there any seasonal influence on the presence and abundance of E. coli around beach area? How may the authors relate seasonal influence to this study? Authors Response to Reviewer I: 1. We have added the exact time and month of sampling in both years of our study to page 7, lines 139-141. 2. Seasonal influences may impact the presence and abundance of E. coli at this beach, as previous work has shown that levels of fecal indicators can fluctuate during the year. However, in this study we evaluated the beach during the same season and month of the year in back-to-back years, so this does not limit our ability to make comparisons between the summers. However, these fluctuations are a consideration and we have added brief conversation of this on page17, lines 351 to 354. Reviewer #2: 1. As the impact of renourishment project was examined in terms of E. coli and its presence or absence, it might be insightful if the type of E. coli whether pathogenic or non-pathogenic was also detected. 2. The author suggests that following renourishment project the changes between microbial community and physical changes of the beach might be for short time. What might be the underlying reasons? Also required experimental evidence. 3. It would be intuitive if the work is conducted for longer period time (more years). Also is there any seasonal impact on microbial community there? 4. The asterisk should be in place in the graph. Authors Response to Reviewer II: 1. We agree that determining the serotypes of E. coli isolated on the beach, and whether they are pathogenic or not, would add more clarity to this study. However, we chose the methods we did to attempt to approximate standard FIB monitoring procedures on a bacterium usually not tested for, in an environment where standards would typically be waived. FIB monitoring is inherently limited by its focus on abundance and distribution, and not serotype or pathogenicity. Our ultimate goal was to investigate the degree to which we could find E. coli in the sand, and if those numbers changed based on renourishment. As normal monitoring for enterococci (as is typically measured in marine environments) would not have indicated whether these strains were pathogenic or not before leading to a beach closure, we sought to use similar methods and compare our results. However, this limitation is still important and we now clarify that the ColiPlate™ does not identify strain or pathogenicity on page 8 lines 165-167. 2. We sampled the same locations on one beach in back-to-back years, with not relevant changes to the beach outside of the renourishment project. Ultimately, we are limited in our ability to directly address mechanisms behind this change without experimentation. However, we analyzed sand grains in an attempt to identify a mechanism given existing research on the effects of the sediment micro-environment on bacteria. Research has shown that biofilm formation and access to nutrients can be important for bacterial survival in these environments, as well as the normal competition, predation, and parasitism experienced by bacteria that could change with environmental perturbations (like a renourishment project). We discuss these possibilities throughout and attempt to find answers in the literature, however we now also provide more direct discussion on page 18 lines 390-392. 3. Please see the comment to Reviewer I above. In terms of the length of study, we agree more conclusions could be made if this had been done for longer than 2 years. However, this study was covered by a grant which lasted only two years and was conducted by someone who, at the time, was an undergraduate student and was limited in their ability to reassess the beach. These are limitations of the study and we have added note of these shortcomings on page 17, lines 341- 354. We also acknowledge that to fully understand the microbial community and how it is impacted, research must move past model species. We have included this on line 415 of page 19. 4. We have rechecked all of our figures and images and see all of the asterisk in place as we intended. We are unsure what the reviewer meant by comment 4, or if this reflects an error in the image they downloaded during review. https://doi.org/10.1371/journal.pone.0304061.r002
7 May 2024 Decision Letter - Md. Asaduzzaman Shishir, Editor Examining the potential impacts of a coastal renourishment project on the presence and abundance of Escherichia coli PONE-D-24-00797R1 Dear Dr. Lewis, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Md. Asaduzzaman Shishir, PhD 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: (No Response) 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: (No Response) Reviewer #2: Yes ****** 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 ****** 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 ****** 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) ****** 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: Umme Tamanna Ferdous Reviewer #2: Yes: Dr. Tamanna Zerin ******** https://doi.org/10.1371/journal.pone.0304061.r003
Formally Accepted
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