Peer Review History
| Original SubmissionApril 2, 2026 |
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Dear Dr. liu, 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 Jul 08 2026 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 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. 3. Thank you for stating the following financial disclosure: “This work was supported by the National Natural Science Foundation of China (grant No. 32172978 to XB; https://www.nsfc.gov.cn/english/site_1/index.html), the Natural Science Foundation of Tianjin (grant No. 25JCYBJC00800 to XB; https://kjgh.tj.gov.cn/), the Tianjin Science and Technology Planning Project (grant No. 24ZYCGSN00140 to XB; https://kjgh.tj.gov.cn/), the Gansu Science and Technology Project (grant Nos. 24CXNP011 and 24CXNP005 to XB; https://kjt.gansu.gov.cn/), and the Innovation Training Program Project for College Students of Tianjin Agricultural University (grant No. 202410061160 to XB; https://www.tjau.edu.cn/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” We note that one or more of the authors is affiliated with the funding organization, indicating the funder may have had some role in the design, data collection, analysis or preparation of your manuscript for publication; in other words, the funder played an indirect role through the participation of the co-authors. If the funding organization did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of authors' salaries and/or research materials, please do the following: 1. Review your statements relating to the author contributions, and ensure you have specifically and accurately indicated the role(s) that these authors had in your study. These amendments should be made in the online form. 2. Confirm in your cover letter that you agree with the following statement, and we will change the online submission form on your behalf: “The funder provided support in the form of salaries for authors [insert relevant initials], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. 4. Please amend the manuscript submission data (via Edit Submission) to include author Jingjing Zhang, Rui Chen, Wenjie Zhao, Dajuan Zhang, Qian Wang and Xinyu Wang. 5. 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. Additional Editor Comments: After careful evaluation of the manuscript entitled “Mechanism of anaerobic microcystin (MC) degradation by microbial community enriched in shrimp pond sediment”, and considering the comments provided by the reviewers, I recommend a Major Revision before the manuscript can be considered further for publication. The study addresses an important topic related to anaerobic degradation of microcystin by sediment-associated microbial communities and has potential scientific significance in the field of environmental microbiology and bioremediation. The experimental approach and overall findings are promising. However, several important concerns regarding methodological clarity, data interpretation, presentation of results, and discussion need to be adequately addressed. Reviewer 1 has raised substantial issues that require detailed revision and clarification, particularly regarding experimental design, mechanistic interpretation, microbial community analysis, and supporting evidence for the proposed degradation pathways. Reviewer 2 has also provided valuable suggestions for improving the manuscript presentation and scientific clarity. The authors are therefore requested to carefully address all reviewer comments point-by-point and revise the manuscript accordingly. Additional clarification, improved data presentation, and strengthening of the discussion section will significantly enhance the overall quality and impact of the manuscript. [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? 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 Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ********** Reviewer #1: This manuscript investigates the anaerobic degradation mechanism of microcystin-RR (MC-RR) by a microbial community enriched from shrimp pond sediments, integrating LC–MS/MS with metagenomic and metatranscriptomic analyses. The integration of isotope tracing with multi-omics provides a potentially valuable framework for understanding anaerobic toxin attenuation in sediment environments, and the findings may have practical implications for developing in situ bioremediation strategies targeting cyanotoxins. However, I have major concerns that should be addressed before this paper can be considered for publication. 1. The manuscript heavily relies on correlations between metatranscriptomic upregulation and inferred enzymatic functions to propose a “novel anaerobic degradation pathway.” However, no direct biochemical or genetic validation (e.g., enzyme assays, gene knockouts, or heterologous expression) is provided to confirm the roles of U32, M23, or S9 peptidases in MC-RR degradation. The conclusions should be supported with functional evidence. 2. Although LC-MS identifies multiple candidate products, only three are tentatively assigned, and many peaks remain unresolved. The proposed degradation pathway is therefore incomplete and lacks structural confirmation (e.g., MS/MS fragmentation patterns, NMR validation). Inferring specific cleavage sites (Arg–Adda or Ala–Arg) based on limited evidence is not sufficiently convincing and may be misleading. 3. The authors claim activation of the DNRA pathway and carbon–nitrogen coupling; however, this conclusion is based solely on gene expression data. No measurements of nitrogen species (NO₃⁻, NO₂⁻, NH₄⁺) or isotope tracing of nitrogen flux are provided. Without quantitative biogeochemical data, the assertion of DNRA-driven nitrogen recycling is speculative and overextended. 4. the initial MC-RR concentration (1 μg/mL) is not representative of most natural environments. This raises concerns about the ecological relevance and scalability of the findings. The absence of comparison with environmental concentrations undermines the claimed application value. 5. The role of QS in the anaerobic conditions Bioresour. Technol., 2026, 442, 133668 should be covered. The manuscript attributes a central regulatory role to multiple QS systems (AI-2, AHLs, DSF, c-di-GMP), yet provides no experimental validation (e.g., QS inhibition, signal quantification, or gene knockout). The observed transcriptional upregulation does not demonstrate functional involvement in MC-RR degradation. This section is largely speculative and should be significantly reduced or experimentally supported. 6. The authors propose a “syntrophic fermentation–respiration network” between Citrobacter and Shewanella, but this is inferred solely from genomic annotation and transcriptional contribution. No co-culture experiments, metabolite exchange measurements, or electron transfer analyses are conducted. The claim of syntrophy is therefore not justified and reflects conceptual overreach. 7. Although the study emphasizes a “novel anaerobic pathway,” similar observations, such as mlr-independent degradation, involvement of diverse peptidases, and community-level degradation, have been reported previously. The manuscript does not clearly delineate how its findings fundamentally advance beyond prior studies, particularly in terms of mechanistic resolution. 8. The manuscript frequently uses strong claims such as “novel mechanism,” “precise division of labor,” and “efficient carbon–nitrogen coupling,” which are not fully supported by the data. This rhetorical inflation detracts from scientific credibility and should be revised to reflect actual evidence. 9. The abstract is overly dense and contains excessive mechanistic claims not fully supported in the main text. 10. Figures (especially pathway diagrams) are conceptual and lack quantitative support. Reviewer #2: This manuscript investigates the anaerobic degradation of Microcystin-RR in shrimp pond sediments using a combination of stable isotope labeling and multi-omics to propose a synergistic metabolic pathway between Citrobacter and Shewanella. While the technical approach is sophisticated and the findings regarding non-canonical enzyme systems are intriguing, the manuscript required revisions before publication and contextualize the findings against several very recent 2024/2025 studies that propose alternative anaerobic pathways and taxonomic roles in the same ecological niche. − The manuscript fails to engage with critical contemporary literature, such as Yang et al. (2025), which identifies a different set of functional genes and pathways for anaerobic MC degradation, potentially overstating the novelty or universality of the proposed peptidase system. − The novelty of identifying Shewanella as a key anaerobic microcystin degrader in shrimp pond sediments is diminished by a failure to reference Zhao et al. (2025), which reports nearly identical findings in the same ecological niche. − Major portions of the manuscript, including the Introduction and Materials and methods, are currently empty or contain only submission template instructions rather than scientific content. − The Results section contains malformed molecular formulas (e.g., separating element counts from symbols) and tables missing clear column headers, which obscures the presentation of the core chemical data. − The theoretical framing of the quorum sensing and DNRA results lacks grounding in established literature, such as failing to cite prior work establishing the AI-2 regulatory patterns in the Shewanella genus. − How do the identified non-canonical peptidases (U32, M23, S9 families) reconcile with the alternative anaerobic degradation genes (mblH, ridA, paaA) and intermediates identified by Yang et al. (2025)? − What specific novel mechanistic insights does this study provide regarding the Citrobacter–Shewanella synergy that differentiate it from the recently published work by Zhao et al. (2025), which also identified Shewanella as a key anaerobic MC-degrader in shrimp pond sediments? − Can the authors clarify the molecular formula formatting issues in the Results section (e.g., C H15N2O7 17 34) and provide a corrected, standard list of identified 15N intermediates? − Could the authors provide a version of the manuscript that populates the currently empty Introduction and Materials and Methods sections and removes the editorial placeholders and instructional text? ********** 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: Partha Sarathi Tripathy ********** [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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. |
| Revision 1 |
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Putative anaerobic transformation pathway of microcystin-RR inferred from ¹⁵N labeling and multi-omics in an enriched shrimp pond sediment microbial community PONE-D-26-16301R1 Dear Dr. Liu, 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, Bijay Kumar Behera, Ph.D. Academic Editor PLOS One Additional Editor Comments (optional): Dear Dr. Liu, Thank you for submitting the revised version of your manuscript entitled, "Putative anaerobic transformation pathway of microcystin-RR inferred from ¹⁵N labeling and multi-omics in an enriched shrimp pond sediment microbial community" to PLOS ONE. The revised manuscript has now been evaluated in light of the reviewers' comments and your detailed responses. I appreciate the considerable effort you and your co-authors have made in addressing the concerns raised during the initial review. The revisions have substantially improved the clarity, scientific rigor, and overall quality of the manuscript. Both reviewers have evaluated the revised version positively and recommend acceptance. The responses to the reviewers are comprehensive, and the revisions satisfactorily address the major and minor issues identified during the previous review round. The study presents a valuable contribution by elucidating the putative anaerobic transformation pathway of microcystin-RR through the integration of stable isotope labeling (¹⁵N) and multi-omics approaches in an enriched shrimp pond sediment microbial community. The findings enhance our understanding of anaerobic cyanotoxin biodegradation and provide important insights with potential implications for environmental remediation and aquaculture ecosystem management. Based on the positive reviewer recommendations and my own assessment of the revised manuscript, I am pleased to inform you that your manuscript is accepted for publication in PLOS ONE. Congratulations to you and your co-authors on this excellent work. Thank you for choosing PLOS ONE to publish your research, and I look forward to seeing your article published. Sincerely, Bijay Kumar Behera, Ph.D. Academic Editor PLOS ONE Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: (No Response) Reviewer #2: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> 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 Reviewer #1: (No Response) Reviewer #2: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: (No Response) Reviewer #2: Yes ********** Reviewer #1: The comments raised by the reviewers have been addressed, thus can be accepted for possible publication. Reviewer #2: All the comments have been addressed properly by the authors and the manuscript can be accepted in the present form ********** 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: Partha Sarathi Tripathy ********** |
| Formally Accepted |
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PONE-D-26-16301R1 PLOS One Dear Dr. Liu, 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. Bijay Kumar Behera Academic Editor PLOS One |
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