Agroecosystem edge effects on vegetation, soil properties, and the soil microbial community in the Canadian prairie

Mariah Aguiar; Alexandra J. Conway; Jennifer K. Bell; Katherine J. Stewart

doi:10.1371/journal.pone.0283832

Peer Review History

Original SubmissionAugust 15, 2022
9 Nov 2022 Decision Letter - RunGuo Zang, Editor PONE-D-22-22877Living on the edge: fungal community strongly influenced by land management at perennial grassland-cropland edgesPLOS ONE Dear Dr. Stewart, 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. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This research was supported by a Natural Sciences and Engineering Research Council of Canada Strategic Partnership Grant entitled “Understanding resilience in agroecosystems: landscapes in transition" with Agriculture and Agri-Food Canada. Thank you to Alix Schebel for assistance in the laboratory; and Megan Horachek, Raidin Brailsford, Lauren Reynolds, Lukas Smith, and Trang Nguyen for their help with field sampling. Lastly, thank you to Steve Mamet for providing a review of the manuscript.” We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that 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: “This research was supported by a Natural Sciences and Engineering Research Council of Canada Strategic Partnership Grant entitled “Understanding resilience in agroecosystems: landscapes in transition" with Agriculture and Agri-Food Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. 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. 5. 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: Although the two referees have some concerns on the manuscript,they are generally positive to it.You can refer to the comments of the refees and revise the manuscript accordingly. [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: 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: Edge effects in agroecosystems is crucial for maintaining ecosystem function. This study examine impacts of land management on aboveground and belowground edge effects, which would help our better understanding of Edge effects . Title: Living on the edge might be unnecessary. What kinds of fungal community? Unclear. What and how about the land management? Could you be specific? I think perennial grassland-cropland also too large, which place? global of national? Abstract: It reports "soil fungal and bacterial community composition", so I think the title using fungal community might not cover all subjects the authors conducted. "Soil total nitrogen and carbon significantly decreased across the edge, " it might need P value and R2 for it, how to prove "significantly"? Line 39: Can you be specific what "properties" here? Line 60: Can you list the references for each of the four "essential mechanisms"? All the essential mechanisms from the same reference [6]? Figures，better put the figure into the text where the legends are so that reviewers can read the text and figures at the same time. No need to go and forth from the start to the end. Each figure should stand independently. Better with different color for all figures. Figure 1, lines in the sampling are not clear, why three 33 m lines existed? for control? Each 33 m line are conducted the same sampling as the upper one? Figure 2, why there are no values in the structural equation models? All are positive? I suggest combine Figure 3 and 6 together? Figure 4 and 5 into one plate, if not, could one of them putting in the appendix? Seven figures are too many I think. Figure 7 is fine, might put it as appendix for Figure 2? Reviewer #2: This manuscript investigated the plant and soil communities along the grassland-cropland edge, generally the experiment was well designed, however, I am cofused about the analysis about different sites, for the organizing of the results and figures. As you selected two sites to represent the edges, shall they be considered as replications? why you analyze them individually? The three transect in each site was not real replicate. So I think the authors should considered carefully about their experiment design and analyze the data properly. The figures should be improved, especially for Figure 1 and 2, could be combined as one composite figure. Another concerns is about the soil parameters, why you only select soil C and N to link with the microbial communities? have you think about the C/N ratios? ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Hua-Feng Wang 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. https://doi.org/10.1371/journal.pone.0283832.r001
Revision 1
26 Dec 2022 Author Response Manuscript PONE-D-22-22877 Dear Editor, Thank you for the opportunity to revise our manuscript formerly entitled Living on the edge: fungal community strongly influenced by land management at perennial grassland-cropland edges (revised title: Agroecosystem edge effects on vegetation, soil properties, and the soil microbial community in the Canadian prairie). The reviewer’s comments and feedback were valuable and helpful in improving the manuscript. We have carefully read all comments and have revised the manuscript based upon the reviewer’s suggestions. Below we provide our responses to each comment in italics, and we have uploaded a revised manuscript with tracked changes as requested. Please also note that we have now uploaded our data to Federated Research Data Repository with the following DOI: https://doi.org/10.20383/103.0623. We hope you will now find our manuscript suitable for publication in PLOS ONE. Regards, Dr. Katherine Stewart Editor Comments Comment 1: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style requirements were reviewed, and we have ensured that the manuscript meets them, including the file naming requirements. Comment 2: In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. Information regarding the authorization for the field sampling was added in the Methods section. The field sampling was authorized by the St. Denis National Wildlife Area and the Conservation Learning Centre. Comment 3: 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: “This research was supported by a Natural Sciences and Engineering Research Council of Canada Strategic Partnership Grant entitled “Understanding resilience in agroecosystems: landscapes in transition" with Agriculture and Agri-Food Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” We have removed funding information from the acknowledgement section. Comment 4: 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. The data has been uploaded to a repository, the doi is: https://doi.org/10.20383/103.0623, we have also provided this information in our cover letter. Comment 5: 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. References have been reviewed to ensure it is complete and correct. No papers that were cited have been retracted. Reviewer 1 Comment 1: Title: Living on the edge might be unnecessary. What kinds of fungal community? Unclear. What and how about the land management? Could you be specific? I think perennial grassland-cropland also too large, which place? global of national? Abstract: It reports "soil fungal and bacterial community composition", so I think the title using fungal community might not cover all subjects the authors conducted. We have reviewed the title and altered it to be more reflective to the study. The title was modified to “Agroecosystem edge effects on vegetation, soil properties, and the soil microbial community in the Canadian prairie” Comment 2: "Soil total nitrogen and carbon significantly decreased across the edge, " it might need P value and R2 for it, how to prove "significantly" The significance was denoted in Supplemental table S2, but we have now also included the P value in the abstract as per your suggestion. Comment 3: Line 39: Can you be specific what "properties" here? We have updated the text to specify the soil properties. Comment 4: Line 60: Can you list the references for each of the four "essential mechanisms"? All the essential mechanisms from the same reference [6]? The essential mechanisms were discussed at length in the reference [6] as it was the primary paper in which these mechanisms were identified. The authors present a conceptual model of edge dynamics based on previous studies. Comment 5: Figures, better put the figure into the text where the legends are so that reviewers can read the text and figures at the same time. No need to go and forth from the start to the end. Each figure should stand independently. Better with different color for all figures. We agree that figures would be better left in the text for the ease of reading. However, PLOS ONE guidelines state “Do not include figures in the main manuscript file. Each figure must be prepared and submitted as an individual file.” Figure colours were chosen based on their legibility. All panels within a figure have the same color scheme for coherence as it is the same analyses. Comment 6: Figure 1, lines in the sampling are not clear, why three 33 m lines existed? for control? Each 33 m line are conducted the same sampling as the upper one? The same sampling procedure occurred on each 33m transect line. Three transect lines were chosen to capture the range of variability in these areas. To account for the 3 transects at each edge site (note: two edge sites per location -St. Denis and Conservation Learning Centre), transects were nested within site and considered a random factor during our analyses. A supporting explanation of the sampling design is provided in the figure legend. We have also revised our terminology throughout to improve the clarity of our sampling design. Comment 7: Figure 2, why there are no values in the structural equation models? All are positive? This was a conceptual structural model; thus it has no values. The actual SEM models with values can be found in the last figure (now figure 4). Comment 8: I suggest combine Figure 3 and 6 together? Figure 4 and 5 into one plate, if not, could one of them putting in the appendix? Seven figures are too many I think. Figure 7 is fine, might put it as appendix for Figure 2? We thank the reviewer for their suggestion and agree seven figures was too many. In examining our figures again, we have focused the paper on four figures and placed the others (2,4,5) into the supplementary document. Reviewer 2 Comment 1: This manuscript investigated the plant and soil communities along the grassland-cropland edge, generally the experiment was well designed, however, I am confused about the analysis about different sites, for the organizing of the results and figures. As you selected two sites to represent the edges, shall they be considered as replications? why you analyze them individually? The three transect in each site was not real replicate. So, I think the authors should considered carefully about their experiment design and analyze the data properly. We appreciate the reviewer’s comments and provide clarification on our design, analyses, and reasoning here. In our mixed linear model used to analyze biomass and all soil parameters, location (i.e., the St. Denis and Conservation Learning Centre) and site (i.e. two edge sites sampled per location) and their interaction were included as fixed factors. Therefore, for these measurements all data were analyzed together. Furthermore, at each site within a given location, three transects were sampled for a total of six transects per location. Due to our design the transects were nested within site and included as a random factor in the mixed model. We have revised the terms used throughout the methods section to better clarify the design and explain the mixed linear model in the statistics section. NMDS analyses for the plant, bacteria and fungal communities, were originally analyzed including both locations in one analysis. However, due to strong differences in the plant community and management regimes between the two locations we found that analyzing each site separately provided more information regarding changes across the edge, which is the focus of our paper. The separation of the locations for the NMDS analyses was also supported by the differences in soil parameters found between the two locations. Comment 2: The figures should be improved, especially for Figure 1 and 2, could be combined as one composite figure. We have placed Figure 2 into the supplementary document and Figure 1 remains in the main document, as per reviewer 1’s suggestion. Comment 3: Another concerns is about the soil parameters, why you only select soil C and N to link with the microbial communities? have you think about the C/N ratios? Your comment is greatly appreciated as soil C:N ratios are important when considering microbial communities. Initial exploratory analyses did not reveal strong trends with C:N ratios and we decided to include C and N only. We have added a point in the discussion regarding this topic to highlight the potential importance of C:N ratios. Attachments Attachment Submitted filename: Reponse to Reviewers (1).docx https://doi.org/10.1371/journal.pone.0283832.r002
20 Mar 2023 Decision Letter - RunGuo Zang, Editor Agroecosystem edge effects on vegetation, soil properties, and the soil microbial community in the Canadian prairie PONE-D-22-22877R1 Dear Dr. Stewart, 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, RunGuo Zang Academic Editor PLOS ONE Additional Editor Comments (optional): accept Reviewers' comments: https://doi.org/10.1371/journal.pone.0283832.r003
Formally Accepted
28 Mar 2023 Acceptance Letter - RunGuo Zang, Editor PONE-D-22-22877R1 Agroecosystem edge effects on vegetation, soil properties, and the soil microbial community in the Canadian prairie Dear Dr. Stewart: 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 Professor RunGuo Zang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0283832.r004

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