PONE-D-20-33816

If you flood it, they will come: prokaryote and microeukaryote communities in passively restored wetlands approach reference conditions

PLOS ONE

Dear Dr. Rachel Rubin,

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Ashwani Kumar, Ph.D.

Academic Editor

PLOS ONE

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Dear Authors,

I have received the response from the reviewers and they recommended this manuscript for revision. Please revise in track change carefully with point to point answers to their queries. I would like to see the revise manuscript.

Thanks

Sincerely

ashwani

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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: No

Reviewer #2: Yes

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

Reviewer #1: No

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: PONE-D-2033816

The manuscript is generally written very clearly and concisely. I am very grateful to the authors for that! The subject matter is also very interesting. Unfortunately, as the manuscript currently reads, I cannot recommend publication because 1) the analyses reflect pseudoreplication, 2) the soil sampling may have been flawed, and 3) age differences among sites of different treatments may prohibit comparisons among treatments.

Pseudoreplication

Lines 118-123. As far as I can tell, there is a single reference wetland, 2 actively restored sites, 3 passively restored sites, an unknown number of retired sites and an unknown number of active farms. The authors need to be clearer about replication for each treatment. This information and site descriptions should probably be made available in a table. Despite the limited replication at the site level, each individual soil sample was apparently analyzed as if it were independent of the other samples. I do not see how the authors can justify this pseudoreplication. The unit of replication is the SITE, not the SOIL SAMPLE because the treatments were applied at the level of the site, not the level of the soil sample. Therefore, these analyses are incorrect.

Soil sampling

Line 140. If the ratio of muck to sand varies from site to site, then one will probably see corresponding variation in microbial community structure, SOM concentration, CEC, etc. that has more to do with the relative amounts of muck and sand rather than anything to do with restoration effort. In other words, the properties of the muck may be highly similar in ALL sites, and the differences and similarities among sites may be explained simply by the amount of sand vs. muck in the soil samples, not necessarily by the level of restoration.

Age effects

Lines 118 – 123. Obviously, it is difficult to find retired farms, passively restored sites, and actively restored sites that are similar to each other except in the way they have been managed following farm retirement. But clearly time may affect many of the variables that were assessed. There are 3 replicate passively restored sites of the same age (4 y), but the actively restored sites were 1 and 6 years old, and the retired farms were newly retired (1-4 y) or “old retired”: (17-20 y). Which of the active farms, which of the actively restored sites, which of the retired farms, and which of the passively restored sites can logically be compared to the reference wetland? The authors will have to take age into consideration in drawing conclusions. On line 244, the authors remove site age as a “nuisance variable”. I do not understand the justification for doing so. I do not see how you can remove the effect of age from among, for example, the actively restored sites, of which there are only two. Presumably every variable is modeled as a linear function of age, but how can that be justified if there are only two replicates of given treatment? Moreover, there is but a single reference wetland. Such a justification is possible only if each soil sample is considered an independent variable, and I have already indicated above why this is not so.

Smaller editorial comments:

Line 74. The word “ditches” is used twice.

Line 102. It is not immediately clear what the difference is between retired farms and flooded sites because flooded sites are presumably retired farms.

Lines 101 – 103. Are these really the only questions? Certainly, these are important but, judging from the rest of the introduction, an important underlying management question concerns the effectiveness of passive flooding as a restoration strategy. Shouldn’t that be included?

Line 106. Yes, but what basis is there for thinking that simply because “extensive action” was taken, active restoration would be the best strategy? Is there any evidence for this expectation? One could possibly propose another even more logical, opposing hypothesis, which is that active restoration would result in less SOM accumulation because of the greater level of disturbance.

Line 115. Describing the length of the perimeter is not helpful at all unless we know the shape.

Lines 128-129. Previously the authors used the term “flashboard”, but here they use the term “wooden board”. Keep it simple and use just one term.

Line 141. “…at a depth of 10 cm” is not clear. Do the authors mean “…to a depth of 10 cm”?

Line 141. What does “Soil samples (50 cm3)” mean? Does this mean that 50 cm3 samples were taken at 10 cm depth?

Line 142. Were all 8 samples homogenized together, or do you mean each of the 8, 50 cm3 samples was homogenized?

Reviewer #2: The manuscript presented by Rubin et al is an interesting example of how restoration processes have effects on microbial soil communities. The paper is well written, and I think it is easy to understand. I agree with the conclusions obtained here; however, I have some concerns about the data showed here and the data that the authors did not show.

Please, show at least in supplementary data, a table containing number of raw reads, reads per sample after filtering, taxonomy… those data showed in most of papers, that I believe is mandatory.

Authors refer ASVs correspond to unique taxonomic assignments to genus and species level for 16S (lines 173-175). Which genera within the identified Classes are the most abundant? Same question remains unanswered for microeukaryotic populations.

How the authors removed chimeras and sequences from plants/algae in the 16S analyses?

Some minor comments:

Line 74, remove one ditches

Line 149-154, please identify the regions for 16S and 18S (V3-V5, V4…)

The elimination of the R2 raw reads represents here an issue. Please, explain pros and cons of using only R1 or give more reasons/discussion about how this affects the data quality. This is a limitation of the study.

Data regarding to sequencing must be presented at least as supplementary data.

Line 181, Charophytes refers only to green algae, why the authors remove this taxon if they form part of the microbial communities as a whole?

Please, upload raw reads to SRA NCBI for better data accessibility. MG-RAST showed no results for the number provided.

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Reviewer #2: No

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PONE-D-20-33816R1

Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

PLOS ONE

Dear Dr. Rachel Rubin,

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 06.05.2021. 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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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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: http://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,

Luigimaria Borruso

Academic Editor

PLOS ONE

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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.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #3: (No Response)

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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: Partly

Reviewer #3: Yes

**********

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

Reviewer #1: I Don't Know

Reviewer #3: 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: Yes

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: PONE-D-20-33816R1

In general, this manuscript is very much improved over the first iteration. My main concern is Table 1, which appears to list the wrong values for n. I hope it is just an oversight and that the authors did not really perform incorrect analyses. In addition, the following are some other things to consider.

Line 68. “Data” is a plural word. Thus, “data that are…” is correct.

Lines 99-101. I do not understand the reasoning here. If flooding produces comparable results to restoration, why use flooding merely as an intermediate step, or as an alternative only when restoration is NOT an option? If it is comparable, why not use it ALL the time, particularly if it is easier, faster and cheaper than restoration?

Line 120. I do not seem to have access to the S1 file. I looked for this file because I do not see a good description of the natural sites. In fact, they are not described as wetlands in the text, only that “natural reference sites have no history of cranberry farming (Fig 1).”

Line 144. What does this mean: “For the MAJORITY of cases”? It might be better to state how many cases out of how many cases so the reader can make the judgement as to whether the procedure justifies what was done.

Lines 144-146. This sentence seems to be missing something.

Line 154. “spaced 30 m apart” is not clear. In a straight line? Often non-random sampling schemes like this are not easily justified. The point is for the sampling to best represent the kind of real variability likely to exist at the site.

Line 155. What kind of sampling device was used? It seems like a cylindrical soil probe was used, in which case the width should be given as the diameter.

Lines 233-234. How did you control for spatial autocorrelation?

Lines 234-235. It is probably more accurate to write “spatial correlation is unavoidable in many ecological studies”. But this still does not eliminate the potential problems interpreting this dataset. The interpretations have to take this potential confounding into consideration.

Line 242. Explain ASV.

Table 1. I do not understand the values for n. The unit of replication is the site, not the soil sample. Therefore, I am not confident that the statistical analyses were done properly.

Reviewer #3: The present article investigates the effects of retiring cranberry farms, and compares how retiring alone, flooding and active restoration are affecting soil microbial communities.

Although numbers of real replicates are low, appropriate efforts such as statistical power tests have been applied to compensate for this drawback. Moreover, individual soils have been sampled intensively to account for within-soil heterogeneity. Certainly, it is not easy to find and sample suitable sites for these five(!) treatments. The ecological conclusions are important for restoration politics and can contribute to a site melioration during the time leading up to restoration.

I do have some minor points that should be addressed before publication:

INTRODUCTION

Do soil variables explain microbial communities or vice versa? You mentioned this point that is especially true for denitrification in the discussion (l445) but I suggest to pronounce it more in the introduction.

l58: reference is missing

METHODS

l144: Unfortunately, FigS2 doesn’t show any data, at least in my file.

l151: please include the projection type that you used in this map.

l191: At this point, the reader is not familiar with the identifier M3. I suggest either to reference the position where these identifiers are explained, or to shortly state what kind of site it was. e.g. restored site M3

I 201: Being new to this method, I would appreciate some more information on how this extraction works in the main text.

l205: Please include a reference for your spectrometry.

l241: Paradis and Schleip 2018 is not included in the reference list

l263-264: this statement is not easy to understand. Above you stated that your environmental data didn’t show a relationship between geography and soil variables but here you mention short environmental gradients. Please explain more carefully.

RESULTS

l316 + l 337(+figure caption of fig 3): Adding up both percentages in fig. 3A/B I am not getting the 45% /44% mentioned in the text (36.5/28%). Whether this is due to the forward selection of paricular variables or due to other reasons, please explain more carefully.

Table S1 is missing many values for sample ER.2.5: It is not clear, however, if this is a real artefact, or if it is only missing by mistake. If values were not obtained for this sample, plese state something like n.d. in the excel file.

l350-352: In order to complete this information, I suggest to include two columns indicating the importance of each variable for microeucariotes/procaryotes, and to shorten the table caption accordingly.

Fig. 4: I really like those graphs, they are very informative! However, you should stay consistent in what you are labelling and what you don’t. Please include Methanobacteria labeling that is missing in the graph depicting differences between natural and restored areas. Other labels of significant differences are also missing (same in fig. 5) and I am wondering why. Were they not as important or did you choose to label only the once with a certain log2 ratio of median proportions?

l379: …whereas taxa that are more abundant in retired, flooded, and restored… here, farm sites are missing from the description.

DISCUSSION

l391-392: Wasn’t this class (kathablepharidae) MORE abundant in flooded and restored sites (orange) as compared to natural sites? If this is the case, they seem to represent a species that gains importance in succession stages such as flooded and restored sites, but is not as important in the natural reference sites. Please correct also in the discussion.

Fig. 5: Nucletmycea are labelled as Nucleomycea in some graphs, please correct.

l408: This procedere has not been described in the methods. How did you define “standouts”?

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Reviewer #1: No

Reviewer #3: Yes: Magdalena Nagler

[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.

PONE-D-20-33816R2

Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

PLOS ONE

Dear Dr. Rachel Rubin,

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 29.07.2021. 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:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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: http://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,

Luigimaria Borruso

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.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #3: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: No

Reviewer #3: Yes

**********

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

Reviewer #1: No

Reviewer #3: 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: Yes

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: PONE-D-20-33816R2

I believe we have a fundamental disagreement about the unit of replication in this study. The authors believe that the soil sample is the unit of replication. Thus, in Table 1, n = 24 or n = 48. On the other hand, I believe the unit of replication is the farm or the flooded site or the restored site, etc. The reason for this is that the unit of replication is the unit to which the treatment is applied. Individual soil samples from a single farm do not represent units of replication simply because the treatment was not individually applied to each soil sample. Therefore, I must insist that the authors perform their statistical analyses correctly.I mentioned this in my last review.

Reviewer #3: The authors addressed most of my comments. The only critcial point, which may be addressed, however, by the publishing team is that FIG S2 in file S2 still doesn’t display any data.

L62: I have the feeling that “are” needs to be removed

L449: The effect of treatments was stronger,

L452: isn’t it the S2 File?

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Reviewer #1: No

Reviewer #3: Yes: Magdalena Nagler, PhD

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PONE-D-20-33816R3Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmlandPLOS ONE

Dear Dr. Rachel Rubin,

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. I gently ask you to consider the comments regarding the statistics approach the review#I arose since the objection from her/his original review still stands (see below).

Please submit your revised manuscript by Dec 02 2021 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:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
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• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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,

Luigimaria Borruso

Academic Editor

PLOS ONE

[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 #1: (No Response)

Reviewer #3: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: No

Reviewer #3: Yes

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

Reviewer #1: No

Reviewer #3: Yes

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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: Yes

Reviewer #3: Yes

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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

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I am not satisfied that the authors have handled the statistical analyses correctly. The objection from my original review two iterations ago still stands.

Reviewer #3: The authors addressed all issues raised in the former revision and I am happy with how the manuscript improved. Before publication, fig. S2 needs to be re-formatted as in my version I can see the graphs with x- and y-axes, but those graphs are not displaying any data.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

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 #3: Yes: Magdalena Nagler

[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.

Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

PONE-D-20-33816R4

Dear Jason,

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,

Luigimaria Borruso

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: