https://orcid.org/0000-0001-5914-6440
Peer Review History
| Original SubmissionMay 22, 2022 |
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PONE-D-22-14818Rotational fishing enables biodiversity recovery and provides a model for oyster (Ostrea edulis) habitat restoration PLOS ONE Dear Dr. Kennon, 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 Sep 05 2022 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:
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Fernández Robledo, 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 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: "This research was supported by The Glenmorangie Company and Scottish Enterprise as part of the Dornoch Environmental Enhancement Project: A project that seeks to restore native oysters to the Dornoch Firth. We are very grateful to Heriot-Watt Scientific Divers, especially Hamish Mair, Dan Harries, Owen Paisley, Hannah Lee and Stephanie Lapidge for additional field support, as well as Rab Lamont and John Mills of Vital Spark. We would also like to thank Richard Shucksmith for the use of his imagery and Siôn Williams for creating the biodiversity infographic. 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: "The project received funding from The Glenmorangie Company (https://www.glenmorangie.com/en-gb) and Scottish Enterprise (https://www.scottish-enterprise.com/) as part of the Dornoch Environmental Enhancement Project (WGS: D18R11697). 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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: No 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: The approach of using a rotational fishery to study reef recovery and biodiversity is insightful, and this study will serve as a useful resources for restoration practitioners. I have a number of comments below, which would help with the clarity have some sections of the manuscript. Lines 59-61 - Would benefit from references about the risks to shellfish reefs. Also surprised that climate change (and synergistic effects) not listed among the risks in the long-term. The manuscript would benefit from a clearer description of the methods used in a few areas. Specifically: Lines 115-117 (study site) - Suggest adding more site description. For instance - What are the depths of the reefs being surveyed? Other than a rotational system, how does the Loch Ryan Oyster Fishery Company operate (e.g., gear type, season, etc.)? Lines 120-121 - The four replicate transects in each plot are arranged quite differently (treatment 1 – in a rectangle, treatment 2 – in a line spread out, treatment 3 – clustered together). How were the locations of the four transects in each plot selected, and what if any impact might that have on the results? Do the characteristics of each transect vary at all? Lines 123-125 - Clearer description of the photo quadrat layout. The picture of the quadrats in figure 2 depicts a grid of 25 quadrats. Were a random sample of those selected at each location along the transect, or just one .5x.5m quadrat photographed/counted at each location, randomly selected along the 25m transect? Figure 3 is missing axis labels/titles, making it hard to interpret Figure 4 - In the plot with 6 years since disturbance, why might the shell density vary so much between the four transects? More generally, can the authors provide any more description of the variability within each treatment, across different metrics? Lines 189-190 - What is the relationship between shell cover and diversity/richness? Reported as strongly related but the correlation/significance is not specified. Line 198 - Where did the recovery trajectory of ten years come from? Is this from the literature (if so, needs citation) or the study? Line 213-215 - Minor clarification, would suggest adding "after 6 years" after "allowing macrofauna biodiversity to recover by 60%". As currently written, could be misinterpreted to mean that biodiversity recovers by 60% after each fishing season. Data availability - Data on percent oyster shell cover were not available, but the remaining data were. Reviewer #2: Line 22: Change to “percent cover”--also, is this percent cover of benthos that is shells? To make clearer, the authors could consider changing this metric to ‘benthic shell cover’? Line 23: Since there are multiple plots within each treatment, I would replace the word “plot” with treatment. If the authors made this edit they could then rephrase the following sentence to “Shell density was 8.5 times higher in the six-year treatment compared to the one-year treatment, whilst…”. Line 26: Change “percentage” to “percent” Line 31: Rephrase slightly, perhaps by starting with the result and deleting the first section of the sentence and start with something like-- “Here we show that the likely scale of biodiversity gain….”. The authors end with how this can be used for conservation and management so the first half of the sentence is unnecessary. Line 35: I suggest the authors open with a broader introduction to restoration and the need for reference sites, data, etc. This would provide more context for the first paragraph which would follow and would make the paper applicable to a broader audience. This is a huge issue/topic of interest in the field of restoration and could be fleshed out more. The authors could then use their study to help provide that reference data that is so critical for evaluating project outcomes. Line 35: Define reference model. “Reference” is typically reserved for a natural, un-impacted site but no reference was mentioned in the abstract so from this point on the reader could be thinking that the 6-year treatment is the reference. If there is a reference site included, that should be mentioned in the abstract as the “target”. Line 40: What does “familiar” mean here? I would rephrase. Who is the audience for this paper? If managers, as was set up in the abstract, these individuals would know of rocky reefs biogenic reefs. Also, since most bivalves require some hard substrate upon which to settle, maybe rephrase to emphasize instead that reef structural complexity can be constructed from bedrock, but (often overlooked) bivalves too can provide (more?) intricate microhabitats. Lines 46-49: Strongly encourage the authors to integrate natural, undisturbed reefs into the abstract given that this has been the focus thus far of the introduction. Line 50: Replace “As well as” with “In addition to providing physical…” Line 52: Need comma after psuedofaeces Line 54: Remove “an” Lines 56-58: Rephrase to make more concise. Unless introducing monetary value of the services, I’d rephrase to “importance”. Something like “The importance of ecosystem services supported by bivalve-built reefs is gaining recognition by government entities and industry.” It would be great if the authors could point to an example of this increased recognition, there are certainly numerous examples. Perhaps the authors could cite a few papers that lay out examples that support the sentence. When editing this sentence, I recommend the authors remove the last portion of the sentence “for the benefits…” since that is implied when mentioning ecosystem services in the beginning of the sentence. Line 76: should read “including” not “included” Line 79: Rephrase to something like “Coincidence with the increased understanding of how important and vulnerable biogenic shellfish reefs are, actions to protect this now rare habitat are now also on the rise.” Line 81: I would clarify that oyster restoration is a relatively new approach--in terrestrial and (less so) marine habitats, it is not a new approach. If the authors choose to keep this sentence as is, I suggest clarifying the conservation/management strategy they are comparing restoration to that validates restoration as “relatively new”. I encourage the authors to re-write this sentence since I do not think it is accurate, as written. Line 83: Sometimes restoration plans include plans for chronic intervention (if necessary) so I would add “often” to the sentence--“This often requires building a self-sufficient…”. Additionally, a sentence on passive restoration to encourage natural recovery could be included here. Line 85: Topic sentence is very similar to previous sentences above. I would rephrase. Line 93: Remove first clause of sentence, start paragraph with “Oyster restoration is…” Line 98: Replace “articulate” with “re-construct” and revise sentence--“…it is extremely difficult to re-construct the biodiversity characteristics of a fully restored reef, given how rare pristine habitats have become” Lines 99-101: Rephrase to better transition from previous sentence. It’s my understanding that the authors are trying to state that studies that compare biodiversity in restored and less disturbed/somewhat natural habitats is necessary for measuring progress towards reaching biodiversity goals. I would re-write this last sentence to reflect this study goal, that will also lead into study aims nicely. Line 106: Rewrite slightly--Something like…“The implications of this work extend from identifying likely expectations for biodiversity development post-restoration to the management of fished biogenic habitats and the biodiversity they support.” Line 111: Could rephrase Hypothesis 2 to clarify language -- “Recovery of macrofaunal community biodiversity is influenced by time since disturbance” Hypothesis Question: The authors have not defined biodiversity yet and this term is often overused or misused. It may be nice to define this in the introduction so the reader is aware ahead of time whether you are talking about biodiversity as species richness and evenness (using H’) or some other variable like species density, which is being used as a proxy for biodiversity. Since biodiversity is a key part of this study, the authors could add more to the introduction and discussion as to why biodiversity is ecologically important. Provide specific examples, cite relevant literature, etc. The majority of the intro was focused on ecosystem services and the importance of biogenic habitats but the ecological importance of the diverse assemblage of species that these habitats support could be strengthened and made more prominent in the intro. Line 118: I’d remove the term “plots” and only refer to them as Treatment 1, 2, and 3, each with four replicate transects. Ideally, the authors would have tracked each Treatment as it evolved since there may be differences between treatments unrelated to treatment (i.e., distance to shore, hydrology, relief of bedroom, depth, turbidity, etc.). Authors should address the above (and other) potential confounding factors. If these factors were not evaluated during the study period, their omission should be acknowledged as a potential explanation that could weaken the strength of the findings. Looking at Figure 1 the Treatments are not interspersed and are clumped, so the potential confoundment of the results due purely to environmental factors and not treatment needs to be addressed (if the data was not collected and shown to be similar across treatments). If this environmental data exists, it should be highlighted in the section that outlines the details for all the various treatments. Is there no reference habitat? Is Treatment 3 serving as the reference habitat? Since this was a prominent topic in the introduction, I suggest aligning the experimental design to the motivation outlined in the intro. Line 124: Why were quadrats placed randomly instead of at some standardized interval? Could the authors elaborate on this? Were they opportunistically sampling along the transect line on whatever side had the most biogenic habitat? I suggest the authors justify the sampling design. Line 135: “were taken for…” Figure 2 Caption: “Scientific divers taking photo…” Line 146: Add Figure 3 for NMDS? Missing caption from this section? Figure 3: Add legend. Match symbols between Fig 1 and 3 Line 142-143: I’ll defer to the other reviewers here to verify, but I don’t believe Pielou’s evenness should be run on transformed data. If the data were transformed for evaluating evenness, what was the justification? Line 179: Evenness (add “n”) Line 197: Replace “probably” with “likely” Line 198: How are the authors defining recovery trajectory? The curve plateauing? What if the plateau in the fished areas is still below what would have been the biodiversity “target” of a natural undisturbed oyster reef? This has not been addressed yet but is critical. If ten years is the “recovered” state, Fig 4 should extend to 10 like Fig 5 does since shell density, which covaries with time since harvesting, is stated as the ultimate cause of increased biodiversity. Line 199: Replace “accepted” with “supported”. Line 200: The authors have yet to acknowledge that what they may be witnessing is a version of the intermediate disturbance hypothesis. What if natural reefs have lower biodiversity? It’s important to acknowledge that the 10-year “recovery” is based on a disturbed system. The authors should include text that acknowledges 1) no reference included, 2) confounding factors could explain differences in biodiversity, 3) have not tracked individual treatments over time, only a snapshot in time so can’t rule out #2. Line 206: I don’t think this is an issue at all actually since the level of detail in sampling was the same across all treatments. Line 224: Why inevitably? Line 225: What is several years? 2-3 or 5-6? Please specify. Lines 223-225: Is this where the ten years comes from? Lines 223-225: The study results show that recovery begins as early as 1 year post-harvest and increases over time as shell density increases, but without knowing what biodiversity would be without any harvest, it’s unclear that the recovery would be on a ten year cycle when the fished system is on a 6-year cycle. Oysters would be recruiting throughout that 6-year period and the contributions of each cohort to overall shell density would be staggered. It’s also possible there is a benefit to biodiversity when the size structure of the oyster reef is varied and that’s what’s driving the pattern (another confounding factor that should be mentioned in the discussion). Treatment 3 is going to have a broader size frequency distribution than Treatment 2 or 1. Since this data was not collected, the contributions of a reef composed of different sized individuals should be addressed. Figure comment: Have symbols match across all figures, when applicable. Line 233: remove “aspects of the” Line 236: This sentence about the indices of different components of diversity should be included in the introduction under study aims as well in the discussion (see above comment on this) Lines 237-240: Could this be due to the down-weighting of abundances when transformed? Please clarify whether the data used for the evenness index was transformed. If it was transformed, justify. If it was not transformed, include text that distinguished what data was vs was not transformed. Line 242: “recently fished plots (Treatment 1) and those that had been fished six years previously (Treatment 3)” Line 244: “less recently fished plot” replace with Treatment 3 Line 255: The biodiversity gain is relative to Treatment 1, correct? Line 257: Figure 8 should not be cited here since this is an infographic showing change in six years. I recommend moving the reference to Fig 8 to Line 256 after “that can be achieved as oyster habitats develop”. Line 260: Replace “simultaneous” with “concurrent” Line 260: Remove “per se” Line 261: Is 1701 the age of the Loch Ryan Company? If so, that detail should be in Intro or Methods. Discussion Comment: I strongly encourage the authors to address the limits of the data they collected. Without environmental data, their findings could be confounded by factors outlined in previous comments above. Additionally, the authors did not track each individual Treatment over time so there is no way to know whether Treatment 1 in 2025 would look like Treatment 3 did in 2019. This assumption, given that their locations do not overlap, needs to be laid out in the main text. Overall, the paper was well-written and easy to follow. The findings were compelling but the limitations of the study, given the limited data collected, need to be acknowledged in the main text. It would be great if the authors could apply their findings and more strongly recommend management options for oyster aquaculture and more fully flesh out the benefits of allowing a biodiverse community to develop both ecologically and economically (for the fishery). Great work! With these revisions, this paper will be a valuable contribution to the field. -Kat Beheshti ********** 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: Yes: Kathryn Beheshti ********** [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. |
| Revision 1 |
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PONE-D-22-14818R1Rotational fishing enables biodiversity recovery and provides a model for oyster (Ostrea edulis) habitat restorationPLOS ONE Dear Dr. Kennon, 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 18 2022 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:
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, José A. Fernández Robledo, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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. [Note: HTML markup is below. Please do not edit.] 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 #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 #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #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 #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 #2: The authors addressed all of the comments and suggested edits. I have a few remaining comments and suggestions that should be addressed. Most of these revisions focus on improving language and clarity of the main text. FIGURE 2 - consent for photos is typically for those pictured in the photo. I believe PLOS ONE policy is that those scientific divers submit a consent form for their photo to be included in the paper. An exception to this may be if the scientific divers are also co-authors on the manuscript. I would defer to the Editor on this though. Line 13: Rephrase, shouldn’t end the sentence with “in”. I suggest, “European oyster habitat are now considered rare and there are few examples of undisturbed reefs from which restoration sites could be compared.” Line 15: I suggest rephrasing--I don’t consider oyster restoration a “feature” or marine conservation practice. Perhaps rephrase to…”…oyster restoration efforts are on the rise, becoming a more prominent component of Europe’s portfolio for marine conservation practices” or something along those lines? Revised Line 35: I appreciate the authors editing the introduction to make it more applicable to a broader audience. I have indicated line edits in all caps to the revised text below. Deleted “making them rare or endangered”. The authors could emphasize that rarely do we have the data or historical knowledge of the pre-degraded state to set a desired target for a restored habitat. Often, the best we can do is compare restored habitats to ambient conditions of nearby, less impacted, sites (reference sites). I suggest the author re-phrase the third sentence--it’s often a lack of data (not only studies) that make it difficult to determine what condition/historical state you are targeting for restoration. I attempted to provide an option for revision to better connect the last two sentences in the revised paragraph, the authors should review and consider how to best communicate their point here which I believe to be that 1) success requires a fundamental understanding of how a particular ecosystem functions, 2) we lack the data necessary to understand how a restored habitat should function given many of these habitats are rare or degraded and don’t function how they “should”, 3) the best we can do is compare a restored habitat to a nearby reference habitat that for the location, local stressors, etc. serves as the most appropriate target for evaluating restoration outcomes. “Habitat and biodiversity restoration is becoming an increasingly popular conservation practice around the world in both terrestrial and aquatic habitats [1][2][4][5]. Many of these habitats have been lost or degraded due to anthropogenic activities [3]. EFFECTIVE RESTORATION REQUIRES an ecological understanding of the TARGETED habitat, but in many cases, due to the degradation or rarity of the habitat, WE LACK THE DATA NEEDED TO DETERMINE THE DESIRED CONDITION AND ECOLOGICAL FUNCTIONING FOR A RESTORED HABITAT. A reference habitat (analogous in terms of community composition, niche fulfilment and provision of ecosystem services)[6] can provide a baseline against which restorative progress can be judged and expectations of biodiversity outcomes clarified (see [7]).” Line 48: Common since when? I would rephrase this sentence. It could be made more clear. I would start with something like “In Europe, native oyster restoration projects have been increasing over the past XYZ”. By providing the approximate time from which oyster restorations became more common, the authors will get at their earlier point in their original draft that it is a relatively new field that lacks data. Line 50: Composition of what? Species composition? How is this different from biodiversity in many ways they are components of one another. Perhaps add in a reference that highlights the lack of knowledge on other reef functions (i.e. water filtration, habitat provisioning) and replace “composition” with whatever function you’d like to highlight along with biodiversity. Line 69-70: Replace “to account for” with “mitigate the impacts of organic waste from the distillery’s discharge water”. Line 90: Revise. “importance” should be “important” Line 109: Revise. The revised sentence is still disjointed and hard to follow. What is an ‘ecological understanding’? The authors use this phrase frequently throughout but are mostly concerned with biodiversity. The authors could clarify by better communicating the link between biodiversity and ecosystem functioning. The language is very broad here and should be revised. Line 139: Authors should state in the methods that the sampling was opportunistic. Line 143: A supplemental figure of the transect survey layout would be helpful. Line 217: “Furthermore, the scale and trend in the observed relationships are consistent with successional differences (ADD CITATION HERE) not spatial patterns.” Figure 3: Add axis 1 and axis 2 labels as suggested by authors. Line 217: List/acknowledge potential confounding factors that were not co-monitored in this sentence “Potential confounding environmental factors (LIST HERE), were not included in the study.”. Line 217: Explain what the authors mean by “out of proportion” with any environmental gradients? Also, this added language makes many sweeping statements without acknowledging what environmental gradients, factors, etc. may be at play. The authors should add specificity to the main text about the potential confounding factors that they did not evaluate. Line 219: Add citations after “In keeping with most biodiversity studies,…” Line 239: Remove the word “consequential”. Revise “is potentially decadal in nature”--this language could be much improved. The authors should revise this section slightly for conciseness. The data supports that reef recovery begins within a year post disturbance and reaches reference levels within ten years. ********** 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 #2: Yes: Kathryn Beheshti ********** [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.
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| Revision 2 |
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PONE-D-22-14818R2Rotational fishing enables biodiversity recovery and provides a model for oyster (Ostrea edulis) habitat restorationPLOS ONE Dear Dr. Kennon, 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 Dec 24 2022 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:
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, José A. Fernández Robledo, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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: Dear Dr. Kennon, please proceed addressing the reviewer's concerns and comments. Sincerely, José A. Fernández Robledo AE PLoS ONE [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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. |
| Revision 3 |
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PONE-D-22-14818R3Rotational fishing enables biodiversity recovery and provides a model for oyster (Ostrea edulis) habitat restorationPLOS ONE Dear Dr. Kennon, 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 Feb 09 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:
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, José A. Fernández Robledo, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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 (if provided): Dear Dr. Kennon, as the reviewer mentioned, they are a few minor edits that need to be addressed. Happy Holidays. -j [Note: HTML markup is below. Please do not edit.] 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 #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 #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #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 #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 #2: The revised manuscript is much improved--great work. I appreciate how the authors approached edits suggested by my previous reviews. This paper is going to be a valuable contribution to the field of oyster conservation and management. That said, I had a suite of minor revisions I suggest the authors consider. My final suggested edits and comments are below. Abstract: In the last sentence--“indicate the likely scale of biodiversity gain” is unclear. The authors could consider replacing with “indicate the probable biodiversity benefits of oyster habitat restoration…”. The authors should also replace “tool” with “metric”, as shell density is a metric not a tool. Line 40: Rephrase; “Habitat restoration to enhance biodiversity is becoming…” Line 42: Delete “making them rare or endangered” or add a citation. Line 72: Replace “bottom-contacting fishing gear” with “Bottom towed fishing gear” to match the following sentence. Line 74: If correct, the better reflect the destruction of these practices, could consider replacing “some” with “many”. Line 77: Replace “with” with “and a significant reduction in biodiversity” Lines 79-81: Need citation Line 85: Replace “around” with “in” Line 92: Replace “disruption” with “disturbance” Lines 97-98: Remove “From 2021” and start the sentence with “The UN Decade on…” Line 101: Replace restoration projects with restoration practitioners since you’re naming entities/stakeholders in this sentence. Line 119: Hypothesis 1 does not address the live vs. dead shell component described above. This should be integrated into the hypothesis. Line 135: I recommend removing “geographic gradient” as this would suggest there are environmental conditions that vary along that gradient (different reef rigosity, depth, etc. could impact flow, temperature, light penetration). If the authors are convinced that environmental conditions were similar across transects, it’d be best to remove “geographic gradient” and have the sentence read as “Sampling was conducting along X (put number of transects here) 25 m transects that ran parallel to shore.” Lines 143-145: Did the divers count the shells in the field or was all counting down using ImageJ--please clarify. Line 154: Replace “within” with “by” Line 164: Should MDS be nMDS? Lines 172-173: Rephrase to - (“diminishing rate of increase as reef approaches ‘recovered’ condition”) Line 173: The authors should explain why year was log-transformed. Lines 177-178: Should be in methods Line 181: Replace “a very good” with “is an accurate representation” Line 192: Table 1 -- Referring now to the treatments and treatment sites is confusing to the reader, I suggest maintaining the naming system above and referring to Treatments 1 and 3 (removing “site”). Lines 195-197: It’d be great if in the methods, the authors wrote a quick few sentences about the strengths and weaknesses of Shannon-Wieners, Margalef’s and Pielou’s evenness so the reader can better make sense of the results and what each of these values means. Line 198: Average oyster shell density increased between what treatments? Only 1 and 3? Need to specify. Line 217: Rephrase--“…is expected to represent community-wide patterns” Line 218: This is great, I think it’s really important to acknowledge the data that wasn’t collected for this study and could have (but are unlikely to have) influenced results. Instead of “included in the study” replace with “were not evaluated”. Line 230; 233: Replace bottom-contacting with bottom towed. Unless the authors are referring to other fishing practices (shrimp pots, lobster traps, bottom trawling)--if this is the case, some examples in parentheses would be helpful. Line 246: Rephrase to “…that trophic cascades could ultimately transform the benthic community and affect oyster reef recovery” Line 247-249: I suggest the authors improve the text in this sentence here as it’s unclear what they are trying to say is the reasoning behind why their study is not evidence of intermediate disturbance hypothesis. Also, intermediate disturbance hypothesis appears out of nowhere so perhaps the authors could add a sentence before the current one that addresses other potential explanations to support their findings and then follow it up with why it doesn’t apply (as they’ve done, but with slight editing to make clearer). Line 250: What kind of relationship? Positive? Negative? This type of information is important for guiding the reader. Lines 250-258: The authors should indicate the directionality of all of the relationships in this paragraph to help guide the reader. Lines 260-263: Great! Line 278: Rephrase slightly: “perhaps the most direct evidence yet quantifying the potential biodiversity gain…” Line 280: Replace “would probably double in a decade” to “would likely double within a decade” Line 281: Make more concise; “the present findings demonstrate the benefits of restoration and the trajectory of restoration success as it relates to biodiversity.” Then, the authors could start a new sentence “Our data showed a link between increased shell material and increased biodiversity.” Line 283: Missing a period. Line 284: Rephrase; “rare example from a long-term dredge fishery whose practices appear to have allowed rare oyster habitat and the associated community to persist, thereby providing a valuable insight into the recovery of biodiversity by balancing sustainable fishery practices with European oyster habitat recovery efforts”. Since this study did not track restoration over time but recovery post disturbance, distinguishing between the two is critical. ********** 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 #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. |
| Revision 4 |
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Rotational fishing enables biodiversity recovery and provides a model for oyster (Ostrea edulis) habitat restoration PONE-D-22-14818R4 Dear Dr. Kennon, 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, José A. Fernández Robledo, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-22-14818R4 Rotational fishing enables biodiversity recovery and provides a model for oyster (Ostrea edulis) habitat restoration Dear Dr. Kennon: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. If we can help with anything else, please email us at plosone@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. José A. Fernández Robledo Academic Editor PLOS ONE |
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