Cooperative environmental engineering via biofilm formation can stabilize consumer-resource systems

Bryan K. Lynn; Patrick De Leenheer; Benjamin D. Dalziel

doi:10.1371/journal.pone.0337943

Peer Review History

Original SubmissionAugust 15, 2025
15 Aug 2025 Author Response Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. https://doi.org/10.1371/journal.pone.0337943.r001
22 Sep 2025 Decision Letter - Bashir Sajo Mienda, Editor PONE-D-25-44591Cooperative Environmental Engineering via Biofilm Formation Can Stabilize Consumer-Resource SystemsPLOS ONE Dear Dr. Lynn, 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 Nov 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 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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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 uploading your study's underlying data set. Unfortunately, the repository you have noted in your Data Availability statement does not qualify as an acceptable data repository according to PLOS's standards. At this time, please upload the minimal data set necessary to replicate your study's findings to a stable, public repository (such as figshare or Dryad) and provide us with the relevant URLs, DOIs, or accession numbers that may be used to access these data. For a list of recommended repositories and additional information on PLOS standards for data deposition, please see https://journals.plos.org/plosone/s/recommended-repositories. 3. Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. 4. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: Reviewer #1: [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know ****** 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 ****** 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 ****** 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: This manuscript addresses the classic cooperation problem in evolutionary and microbial ecology by examining how cooperative behavior can persist in consumer–resource systems despite the threat of social cheating and the tragedy of the commons. The paper’s main contribution is modeling biofilm formation as a form of environmental engineering that helps stabilize cooperation. It also shows that environmental modification is a collective ecological process that is both biologically important and not yet well studied. The article is well-written, however, I recommend the following revisions: • The manuscript could more explicitly engage with the literature on partially privatized public goods (e.g., Solutions to the Public Goods Dilemma in Bacterial Biofilms by Drescher et al., 2014; Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms by Otto et al., 2020) and niche construction theory (e.g., Niche Construction Theory: A Practical Guide for Ecologists by Odling-Smee et al., 2013; An Introduction to Niche Construction Theory by Laland et al., 2016). Without this integration, the manuscript’s novelty may appear overstated. • In lines 317–320, the authors introduce separate pools for enzymes in the fluid (E1) and biofilm (E2) but doesn’t fully justify this biologically. • Lines 317–333 describe cooperators, enzymes, and flow processes in detail, much of which is later repeated in Table 1 (lines 363–364). This is similar to lines 345–352, which discuss the assumptions for uptake functions. Present concise definitions in the text, and direct readers to Table 1 for full biological interpretations and units, rather than repeating these twice. • Lines 270–277 (Discussion): Link your findings to resilience theory, noting that biofilms provide structural feedbacks that increase system resilience by delaying or preventing collapse. • Lines 283–288 (Discussion): The authors should broaden the interpretation by connecting microbial biofilm resilience to general principles in social-ecological systems (e.g., A General Framework for Analyzing Sustainability of Social-Ecological Systems By Ostrom 2009). • The authors should conduct a careful proofread for typographical consistency and duplicate references (e.g., line 232 ‘liklihood’ → ‘likelihood’), remove duplicate or redundant references (e.g., line 582 and 588 Sandoz et al. 2007). ****** 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: Musa Hassan Muhammad ******** [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. Attachments Attachment Submitted filename: PONE-D-25-44591.docx https://doi.org/10.1371/journal.pone.0337943.r002
Revision 1
22 Oct 2025 Author Response Thank you for the careful review of our paper. We have attached a file with responses to each point addressed by the editor and reviewer, which is color-coded to separate our responses from their comments. The text from the file is repeated below: Academic Editor: 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 Necessary changes to file names and format have been completed to align with the PLOS ONE formatting style. 2. Thank you for uploading your study's underlying data set. Unfortunately, the repository you have noted in your Data Availability statement does not qualify as an acceptable data repository according to PLOS's standards. At this time, please upload the minimal data set necessary to replicate your study's findings to a stable, public repository (such as figshare or Dryad) and provide us with the relevant URLs, DOIs, or accession numbers that may be used to access these data. For a list of recommended repositories and additional information on PLOS standards for data deposition, please see https://journals.plos.org/plosone/s/recommended-repositories. We used Figshare as a repository, which is listed as an acceptable repository by PLOS ONE. We are unsure of what edits/changes need to be made here. 3. Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. We have updated our manuscript to be in a LaTeX file format. 4. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. We have added some citations that the reviewer recommended or were related to topics the reviewer suggested including. Reviewer 1: This manuscript addresses the classic cooperation problem in evolutionary and microbial ecology by examining how cooperative behavior can persist in consumer–resource systems despite the threat of social cheating and the tragedy of the commons. The paper’s main contribution is modeling biofilm formation as a form of environmental engineering that helps stabilize cooperation. It also shows that environmental modification is a collective ecological process that is both biologically important and not yet well studied. We appreciate your careful review of our manuscript and for the highly constructive comments. We responded to each comment below. The article is well-written, however, I recommend the following revisions: • The manuscript could more explicitly engage with the literature on partially privatized public goods (e.g., Solutions to the Public Goods Dilemma in Bacterial Biofilms by Drescher et al., 2014; Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms by Otto et al., 2020) and niche construction theory (e.g., Niche Construction Theory: A Practical Guide for Ecologists by Odling-Smee et al., 2013; An Introduction to Niche Construction Theory by Laland et al., 2016). Without this integration, the manuscript’s novelty may appear overstated. Thank you for the suggestion. We agreed that adding more discussion on these topics enhances the quality of the manuscript and arguments made within it. We’ve included additional text in the introduction expanding on partially public goods (lines 79-89) and how environmental engineering and Niche Construction Theory are related (lines 30-38). We also added text into the discussion highlighting how the results of Otto et al. 2020 relate to our results (lines 251-265). • In lines 317–320 (now 298-299), the authors introduce separate pools for enzymes in the fluid (E1) and biofilm (E2) but doesn’t fully justify this biologically. We agree that the rationale we included could have been more clear, and we have rewritten our justification (lines 299-301). • Lines 317–333 (now 297-310), describe cooperators, enzymes, and flow processes in detail, much of which is later repeated in Table 1 (lines 363–364). This is similar to lines 345–352 (now 329-344), which discuss the assumptions for uptake functions. Present concise definitions in the text, and direct readers to Table 1 for full biological interpretations and units, rather than repeating these twice. Thank you for pointing out the redundant text. The table was merely meant to be an easy reference guide for readers while parsing the text, as such, we have moved the table into supplemental materials (S1 Table) to reduce redundancy. • Lines 270–277 (now 209-217) (Discussion): Link your findings to resilience theory, noting that biofilms provide structural feedbacks that increase system resilience by delaying or preventing collapse. We agree that a more explicit connection to resilience theory is warranted. Lines 224-227 have been added to more directly link our results to resilience theory. • Lines 283–288 (now 222-232) (Discussion): The authors should broaden the interpretation by connecting microbial biofilm resilience to general principles in social-ecological systems (e.g., A General Framework for Analyzing Sustainability of Social-Ecological Systems By Ostrom 2009). Thank you for this compelling idea to strengthen our discussion. We have added a paragraph linking our system to Social-Ecological System Framework in lines 233-250. • The authors should conduct a careful proofread for typographical consistency and duplicate references (e.g., line 232 ‘liklihood’ → ‘likelihood’), remove duplicate or redundant references (e.g., line 582 and 588 Sandoz et al. 2007). Thank you for bringing these errors to our attention. A careful revision of the bibliography and text was done to resolve typographical errors. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0337943.r003
16 Nov 2025 Decision Letter - Bashir Sajo Mienda, Editor Cooperative Environmental Engineering via Biofilm Formation Can Stabilize Consumer-Resource Systems PONE-D-25-44591R1 Dear Dr. LYNN, 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. For questions related to billing, please contact billing support. 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, Bashir Sajo Mienda, 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: 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 ****** 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? 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) ****** 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 ****** 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) ****** 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: Musa Hassan Muhammad ******** https://doi.org/10.1371/journal.pone.0337943.r004
Formally Accepted
Acceptance Letter - Bashir Sajo Mienda, Editor PONE-D-25-44591R1 PLOS ONE Dear Dr. Lynn, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Bashir Sajo Mienda Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0337943.r005

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