Peer Review History
| Original SubmissionJune 24, 2019 |
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PONE-D-19-17858 Multi-trophic level responses of belowground nematode communities to stage dependent removal strategies of an invasive tree PLOS ONE Dear Miss Peralta, 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. We would appreciate receiving your revised manuscript by Oct 04 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript:
Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Martin Schädler Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. 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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 3. We noted in your submission details that a portion of your manuscript may have been presented or published elsewhere: "Part of the data has been used in a previous publication, as explained in the cover letter and in the manuscript (introduction and material and methods)." Please clarify whether this [conference proceeding or publication] was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript. Additional Editor Comments: Both reviewers are pretty positive regarding the study itself and the results but both recommend substantial text work in more or less all parts 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? 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 #2: Yes ********** 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: No Reviewer #2: No ********** 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: No ********** 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 reviewed manuscript describes the results of an experiment examining the responses of soil nematode communities to an invasive plant (Pinus contorta) management intensity gradient. I am always excited to see new studies examining the responses of soil nematodes to plant invasion and management. The results presented here are interesting and highlight the importance of considering soil community responses to plant invasion and management. This manuscript presents data from an experiment originally described in Dickie et al. 2014 (AoB Plants). I remain at least marginally concerned about potential overlap between this MS and Dickie at al. 2014, which also presents some soil nematode data. Dickie et al. 2014 reports abundance data of nematode feeding guilds (bacterial-feeding, fungal-feeding, etc.), but community composition and diversity/richness data were not reported. Thus in my opinion, the data presented here are a substantial expansion of the Dickie et al. 2014 paper, though not entirely independent. That being said, I would recommend restructuring the Introduction to better frame this work as a direct expansion of Dickie et al. 2014. That paper is cited six times prior to the reveal that this MS is an in-depth assessment of nematodes initially reported in that paper. Over that same stretch of MS, no other paper is cited more than twice. So this MS relies heavily on Dickie et al. 2014. For the sake of transparency, I’d recommend acknowledging that upfront. Additionally, maintaining similar terminology between Dickie et al. 2014 and this MS would facilitate an easier comparison between the two. For example, Dickie et al. 2014 refers to the four treatments as 1) seedling-removal, 2) sapling-removal, 3) no-removal, and 4) tree-removal. In this MS, the four groups are 1) uninvaded, 2) sapling-removal, 3) tree-removal, and 4) invaded. Additional methodological details are needed to fully assess experimental rigor. I also recommend new analyses to provide insights into nematode community responses to invasion and management. Abstract: -No direction or magnitude of invasion or management effects are included in the abstract. I recommend adding statements along the lines of “Invaded plots had XX% lower richness than seedling removal plots.” Introduction: -The hypotheses focus primarily on nematode richness and community composition. Composition data typically includes taxon abundance, which may be encroaching on the abundance data presented in Dickie et al. 2014. Methods: -The phrasing ‘we selected‘ plots (line 118) sounds strange. Were these not the same 24 plots established in Dickie et al. 2014? -Is removal of seedlings twice a year often enough to be considered ‘uninvaded’? I’d like to see more data on the number of seedlings removed. Early removal of 3 vs. 3000 seedlings would be an important factor in determining if you are maintaining this area as uninvaded, or if it is well into the early stages of invasion. -Why no removal of invasive plant biomass from the site (line 127)? I need some justification for this. With herbaceous plant biomass, it is more typical to remove the biomass since its decomposition will alter soil nutrients and soil fauna. -Sampling occurred three years after removal treatments, but more details are needed. Was sampling three years after the initiation of removal treatments if removal treatments were a one-time event? Seedling removal seems like it would need to be recurring regularly, which it may have been (line 121), but I’m still not clear on this. If reinvasion as occurred (lines 128-129) has this shifted plots from one group to another? -I have some concerns about the designation of trophic groups T1, T2, and T3. As presented, it invokes a linear food chain with T1 being directly associated with the plant (by feeding on the plant) with T2 and T3 being sequentially further removed from direct plant interactions. In reality, these are two pathways of energy transfer from the plant, either to 1) plant-feeding nematodes directly, or to 2) microbial-feeding nematodes indirectly via root exudation and root turnover stimulating bacteria and fungi, which are then consumed by nematodes. Predatory nematodes may serve to bridge these two energy pathways by feeding on plant-feeding, bacterial-feeding, and fungal-feeding nematodes. I’d argue that the term ‘trophic level’ is not appropriate, and perhaps use ‘trophic group’. -Were nematode analyses run on genera or morpho-species data? Line 172 states that number of species were used, but nematodes were only identified to genus or morpho-species (lines 144-146). -It seems that relative abundance data was used for the ordinations and PERMANOVA (line 181). Is this correct? I highly recommend use of absolute abundance data, since differences can be caused by both changes in species identity but also abundance, though use of abundance data might overlap more with the Dickie et al. 2014 paper. -Following up on my earlier comment regarding the designated trophic levels, I think the SEM needs justification for including a direct effect of plants on TL3. In a soil food web, effects of plants on predaceous nematodes would likely be modulated by the lower trophic levels (TL1 and TL2). Direct effects of management could still exist on TL3, likely through habitat disruption, and could be included in the SEM. Results: -My biggest concern with the Results is that no data are presented to show which nematode species, or trophic groups, are driving the observed changes in composition. The PERMANOVA is great for testing for differences between groups, and the PCoA is one method for visualizing differences among groups, but for food webs it is important to know which genera/trophic groups are driving the observed changes. Without these data, we have an incomplete picture of the soil nematode responses to invasion and management. Ideally, inclusion of additional analyses, such as an indicator species analysis, or at minimum, a breakdown of feeding groups and/or trophic levels by treatment are needed. Discussion: -The Discussion generally lacks comparison of these results to previously published studies examining soil nematode responses to invasive plant management (lines 289-308). -Are there comparisons you can make with other published studies examining the timing of invasive plant management on other organisms? Comparisons to aboveground fauna may also be of interest to assess the generality of invasion and management effects in higher trophic levels. Data accessibility: -No database is listed where data will be deposited upon successful publication. Minor comments: -line 253: remove extra period after Invaded -line 304: change ‘same area’ to ‘same experiment’ -line 330: change ‘than’ to ‘to’ Reviewer #2: 1. The manuscript reports changes of soil nematode community structure in response to ontogenic removal of an invasive tree species. The study was well designed and the methodology was proper to address the concerns. However, this manuscript is overall poorly written and may need reorganization. 2. The title is confusing (e.g. stage-dependent, what stages?) and not informative enough as the authors estimated the responses of soil nematodes both at community (composition, indices etc.) and trophic level to the management strategies. I suggest it could be changed like “Community- and trophic-level responses of soil nematodes to removal of an invasive tree species at different invasion stages”. 3. Sap- and tree-removal are the two comparable management strategies (treatments) employed in this study. However, in the introduction I did not read any information about “why the two strategies were comparably tested” or “what are the potential difference in responses of soil food webs to sap- and tree-removal”. 4. The hypotheses need to be adjusted: (1) Line 92-93: I could not read how the nematode species richness will increase if invasions reduce the abundance and alter the composition of native plant communities. I guess the authors attempted to highlight the invasions may reduce the abundance and diversity of native plant communities, right? (2) I understand that removal of invasive trees would results in the recolonization of herbs, which may help restore the nematode communities…However, I am confused by the following sentence “We expect uninvaded communities to have more complex structure, with higher abundance of long-life cycle nematode taxa…”. Does that mean uninvaded habitat will have more complex structure or higher abundance of nematodes than “invaded habitat”? 5. The authors claimed that the removal management strategies influence the soil nematodes via effects on plant community, such as indicated in Fig. 4, but I could not find any data or related analysis on plant community. I strongly suggest them to include data on plant community composition they scored (percentage of coverage). Otherwise, I could not see the value of Fig. 4 in this study. 6. I would change the structure of the manuscript, showing the community- and trophic- level responses separately. Fig. 1a, b and Fig. 3 showed tree species invasion indeed resulted in a different nematode community responses from uninvaded soil, and both sap- and tree-removal could reverse this disturbance of invasion to the level of uninvaded treatment. On the other hand, at the trophic level, it seems only sap-removal of the invasive tree species could reverse the disturbance (represented as nematode community responses) back to the level of the uninvaded treatment (Fig. 1c and Fig. 2), suggesting different trophic levels would respond to management strategies in different ways. 7. I found the results were not fully discussed in the current version. I would like to read discussion on (1) invaded vs. uninvaded: tree invasion indeed alter soil nematode communities; (2) removal of these invasive trees could reverse these invasion influences; (3) the extent of removal of invasive trees recovering nematode communities depends on the invasion stage of removal. 8. Specific comments: L62: what functional traits? L73: NOT a sentence L83-86: not logic L90: “changes” should be “differs” L100-102: confusing. What is the comparison? L128-129: what do you want to say by mentioning “with some reinvasion…”? L143: where is the data of soil moisture? L167: more details are needed on SI to introduce this index. L172: “total number of species”? I thought authors mostly identify the nematodes at genus level L319-321: not understandable L329: “have” should be “result in” L331: “both” should be “all three” L334: “perturbations” should be “perturbations, such as plant invasions” L340: should be “soil nematode communities” instead of “communities” ********** 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: 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 1 |
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PONE-D-19-17858R1 Community- and trophic-level responses of soil nematodes to removal of a non-native tree at different stages of invasion PLOS ONE Dear Miss Peralta, 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. We would appreciate receiving your revised manuscript by Dec 27 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols Please include the following items when submitting your revised manuscript:
Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Martin Schädler Academic Editor PLOS ONE Additional Editor Comments (if provided): The manuscript is much improved. There are only few minor comments. However, I think some changes to the new Figure 4 are warranted prior to publication. In its current form, it is not immediately intuitive how the data are depicted. [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 #2: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: I appreciate the efforts of the authors to revise this manuscript. The manuscript is much improved, particularly regarding the new analyses and restructuring of the Introduction and Discussion. The authors have highlighted the original Dickie et al. 2014 paper in AoB Plants, and how this manuscript builds upon that published work. Additionally, the authors provide greater methodological details and justification for the tree, sapling, and seedling removal management treatments. Specific plans for making the data publicly available have now been stated, complying with the PLOS data policy. I have only a few concerns to be addressed, outlined below. Results: S2 Table: Table caption isn’t overly informative. This table appears to summarize results comparing the seedling removal treatment to the other treatments, so should be stated in the table caption. Figure 4: I’m a bit confused by this figure. For relative abundance data, figures are normally shown in percentages. Since an unequal number of nematodes were identified per sample ('approximately 100'), standardizing those to values to percentages would be most appropriate. A quick glance at Figure 4 reveals that adding up the bars of relative abundance for T1, T2, and T3 do not appear to sum to 100. That makes it harder to attribute differences to treatments versus sampling effort. It may be worthwhile to offer a more thorough explanation in the figure legend as well. Minor comments: Line 78: change ‘removal or…’ to ‘removal of…’ Line 329: I think you mean ‘were’ not ‘where’ Line 350: change ‘completed’ to ‘completely’ Reviewer #2: The authors have considered my and other reviewer comments and made satisfactory and considerable changes in the new version of the manuscript "Community- and trophic-level responses of soil nematodes to removal of a non-native tree at different stages of invasion". The text has been edited significantly and the readability and flow of the manuscript has greatly improved. The change of an informative title and the reanalysis of the data, the addition of associated visual elements have resulted in a more interesting manuscript. Overall, this manuscript has been improved significantly. ********** 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 #2: Yes: Minggang Wang [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 be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 2 |
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Community- and trophic-level responses of soil nematodes to removal of a non-native tree at different stages of invasion PONE-D-19-17858R2 Dear Dr. Peralta, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Martin Schädler Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-19-17858R2 Community- and trophic-level responses of soil nematodes to removal of a non-native tree at different stages of invasion Dear Dr. Peralta: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Martin Schädler Academic Editor PLOS ONE |
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