Peer Review History
| Original SubmissionSeptember 24, 2021 |
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PONE-D-21-30855Compatible interaction of Brachypodium distachyon and endophytic fungus Microdochium bolleyiPLOS ONE Dear Dr. Matušinsky, 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. The paper has been revised by two experts who both suggested major revision in order to improve the ms and render it acceptable for publication in PlosOne. Authora are invited to carefully follow reviewers' suggestion and to submit a revised version of their work. Please submit your revised manuscript by Dec 29 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:
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, Sabrina Sarrocco 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. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: - https://www.frontiersin.org/articles/10.3389/fpls.2019.00979/full The text that needs to be addressed involves the Discussion section. In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. 3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 4. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels.
In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. [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: 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 ********** 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: Dear corresponding author, The manuscript number PONE-D-21-30855 titled “Compatible interaction of Brachypodium distachyon and endophytic fungus Microdochium bolley” investigate the effect of this endophytic fungus on the intensity of the attack by pathogen Fusarium culmorum in B.distachyon and wheat and tested changes in expression of genes (in B. distachyon: BdChitinase1, BdPR1, BdLOX3, BdPAL, BdEIN3, and BdAOS; and in wheat: TaB2H2(chitinase), TaPR1, TaLOX, TaPAL, TaEIN2, and TaAOS) involved in defense against pathogens. The nature of the subject studied and the results obtained are worthy to be taken into account for publication in PLOS ONE. However, some aspects need to be clarified and a revision is necessary to increase the article quality. For this reason, I provided a revision list. I hope that my considerations could be useful to improve your study and its clarity to the reader. Revision list: 1) Lines 1-2: About the title, I was wondering if is possible to speak of “compatible interaction” between a host and an endophytic fungus such as Microdochium bolleyi. In addition why you did not mention also wheat? 2) ABSTRACT: please avoid the excessive use of “we” in the abstract section as well as in other parts of the manuscript; 3) Line 23: Please change infestation with infection, infestation is not correct for pathogenic fungi; 4) Line 26-29: Please reword this sentence because is not clear to the reader; 5) Line 52: Please describe better the distribution of F. culmorum in the different world regions; 6) Lines 65-67: Please provide more details of the activity of Microdochium bolleyi especially against F. culmorum; 7) Lines 68-73: The aim of the work is not clear. Please reformulate it; 8) Line 82: Please add more detail about Microdochium bolleyi isolates, in particular, host of origin and country of origin; 9) TABLE 1: What are MbPOLII? Is this the first time that this abbreviation or name appears, please explain; 10) Line 108: Please provide more details of inoculum preparation, because is not enough what has been provided; 11) Line 109: Why you used the word “variants”? 12) Line 137: Fungal mycelia of what species? Please specify; 13) Line 139: Only roots or also leaves? 14) Lines 147-148: I suggest inserting the results of the preliminary screen in the main text and not as supporting information because is very important for primer pairs design; 15) Line 159: please change the expression “vis-à-vis”; 16) Lines 174-175: please explain the choice of plant defense genes, in other words, why did you choose these genes? 17) Lines 205-206: Again please insert in the main text this information (see comment number 14); 18) Lines 211-212: Where these results are reported? 19) Lines 231-278: All the paragraph “expression levels of genes involved in plant-pathogen interaction in Bd and wheat” is not clear. Please try to re-organize sentences and table clearer; 20) Lines 294: Please mention briefly these examples; 21) Lines 300-301: Please provide an accurate hypothesis relative to other mechanisms involved in the phenotypic resistance observed in this study; 22) Lines 391-392: Please be sure about this sentence; 23) Lines 412-413: The last sentence of the paper implies that all the sections relative to the Microdochium bolleyi identification method should be more accurate. So please also based on previous comments (for example 14 and 17) edit with more attention all aspects of Microdochium bolleyi identification because you are going to propose a method of identification that should be very accurate and precise. Best regards. Reviewer #2: The manuscript from Matušinsky et al. studies the impact of Microdochium bolleyi (Mb) on both Brachypodium and wheat leaves infection by Fusarium culmorum (Fc). First, the authors aim establish the endophytic status of Mb in roots both through microscopic observations and by molecular methods. Then, using a set of defense marker genes, they try to decipher whether Mb induces the expression of defense genes. The study is overall well conducted with appropriate controls and replicates. The manuscript is clear and well-structured. Nevertheless, there are two weak points in the manuscript that prevent acceptance of the manuscript and which should be improved. The first point concerns whether Mb is a true endophyte in Brachypodium (or wheat) roots. The second point is the relationship between Mb potential endophytism and the induction of defense genes. Endophytism of Mb in roots is, to my opinion, insufficiently demonstrated. Indeed, microscopic observations are not fully convincing. Pictures (Fig1) are not sufficient to fully demonstrate the colonization of Brachypodium roots by Mb or the presence of chalmydospores within host root cells. The authors should provide cross-sections to fully demonstrate that Mb is truly inside the roots. In the same part, the authors claim they manage to detect Mb by PCR. If PCR results using pure Mb DNA and primers MbPOLIIF/R are indeed statisfying, no data are presented on roots. Moreover, in the Material and Methods section, the authors do not mention any surface sterilization, which is a very important step in endophytism studies. This part should be strengthened to fully demonstrate that Mb is indeed an endophytic fungus. The second aspect that needs to be improved concerns the study of defense genes expression. The first point is that the authors seem not to use the same biological material to test endophytism (in roots) and defense gene expression (in leaves). Indeed, they mention that Fc inoculations are performed “In the phase of the second offshoot in Bd and third leaf of wheat » which, albeit not being very precise, means rougly three-week old plants, whereas endophytism was tested 90 days after sowing that is much later. In this context, it is very difficult to compare expression analysis with the putative endophytic status of Mb as no result establishes that Mb is truly endophytic at the stage of inoculation by Fc. Additional comments Lines 240-256: the whole paragraph is unclear. The authors should first describe the induction of gene expression by Fc infection then describe how Mb presence may modify gene expression. Lines 242-243: BdChitinase1 and TaPR1.1 do show differential expression in the presence of Mb at 1 dpi. Why do the authors claim no statistical difference in gene expression Minor revisions Line 85: the 6 isolates were mixed together, detail in which proportion Lines 234-235: gene names should be revised as used in the cited references (e.g. BdPR1 is BdPR1.1 in Kouzai et al. 2016) ********** 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.] 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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Compatible interaction of Brachypodium distachyon and endophytic fungus Microdochium bolleyi PONE-D-21-30855R1 Dear Dr. Matušinsky, 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, Sabrina Sarrocco Academic Editor PLOS ONE Additional Editor Comments (optional): 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: 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: (No Response) ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) ********** 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: (No Response) ********** 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: (No Response) ********** 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: (No Response) ********** 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 |
| Formally Accepted |
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PONE-D-21-30855R1 Compatible interaction of Brachypodium distachyon and endophytic fungus Microdochium bolleyi Dear Dr. Matušinsky: 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 Sabrina Sarrocco Academic Editor PLOS ONE |
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