Peer Review History
| Original SubmissionJanuary 30, 2021 |
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PONE-D-21-03306 Two new Nothophytophthora species from streams in Ireland and Northern Ireland: Nothophytophthora irlandica and N. lirii sp. nov. PLOS ONE Dear Dr. O'Hanlon, 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. While both reviewers agreed that the manuscript is well written and adds to our knowledge of an important new genus (Nothophytophthora), Reviewer #1 does express some valid concerns about the framing of the discussion. The manuscript could therefore be improved with any additional data you may have on pathogenicity/virulence of your new isolates, host range, and frequency of isolation. The addition of these supporting details, and appropriate text in the discussion, will increase the impact of your careful and otherwise thorough work on these two new species. Thank you for addressing these concerns in a revised manuscript. Please submit your revised manuscript by Apr 16 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Jaime E. Blair, PhD 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. 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. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files 3. Thank you for submitting the above manuscript to PLOS ONE. During our internal evaluation of the manuscript, we found significant text overlap between your submission and the following previously published works. - https://doi.org/10.3767/persoonia.2017.39.07 We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable, even for works which you authored. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications. Please revise the manuscript to rephrase the duplicated text, cite your sources, and provide details as to how the current manuscript advances on previous work. Please note that further consideration is dependent on the submission of a manuscript that addresses these concerns about the overlap in text with published work. We will carefully review your manuscript upon resubmission, so please ensure that your revision is thorough. Additional Editor Comments: Thank you for your submission. Please carefully address the comments of Reviewer #1 in your revision. [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: N/A 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: 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: This is a well-performed study and a well-written and rigorous manuscript that reports on the isolation and identification of two new Nothophytophthora spp. in Ireland, including their formal description. Generally, there are no major issues and the species descriptions are complete, well-illustrated and thoroughly performed. The only point that leaves a feeling of disappointment to the reviewer is the fact that the question of pathogenicity of the genus/ the new species does not receive the amount of (practical) attention that it would deserve, in particular when comparing with the huge number of details given for the phylogenetic analyses, the tree topologies and the morphological description. Line 411 states that “the question arises whether the two new Nothophytophthora species are native or introduced…”. While academically, such question could of course be of interest for any microbe found anywhere in the world, in the present context it is clear that this question is of interest only in a phytopathological sense. Much of the last two pages of the discussion refers to questions of invasive microorganisms and their potential threat to plant health. Given all this, it is hard to understand why not a single, simple, and basic test of pathogenicity has been performed during the study, e.g. a leaf inoculation test with Rhododendron, instead of manoeuvring around this issue on two pages of discussion. Compared to the analysis of 8 genes, state-of-the-art phylogenetics, and the detailed description of every single aberrant form of sporangial shape, this is really a bit disappointing – while on the other hand the authors’ effort and the accurateness of the study are of course highly appreciated. Similar to that, the point “hosts and distribution” is also only briefly covered, and the reader only gets very short information on isolation success (i.e. were the new species regularly found, or only rarely?, how many leaves were actually infected as compared to the Phytophthora spp.?, how many leaves were analysed?…). I feel that this would also contribute to the full picture that the reader should get of the new species. Also, the info in line 448 ff. could have been described somewhat more prominently (i.e., in the results). The fact that Rhododendron leaves were not infected is explained here by a proposed equilibrium of host and pathogen, as proposed for P. ramorum in Vietnam (line 453). In this case, however, this contradicts what is stated in lines 416 ff (origin in South America). In particular, the association with Rhododendron would be of such great interest, as this genus obviously grows wild in Ireland, and was an effective bait plant! – again a case for a pathogenicity test! Minor/ other issues: - line 20/21: something went wrong with this sentence - line 107: why two different primer pairs for cox? - line 243 and elsewhere (see below): please check Figure legends, 4i does not show sympodia - line 255: two decimal places suggest a degree of accuracy that does not exist. - line 257 ff/ 317 ff: has this result been repeated? Might this be due to some unknown external factor? Is this also observed in other species? What might be the background/ reason? What might be the effect? Should this be mentioned in the discussion (or otherwise just left out completely)? - line 266: there is no Fig. 4s - line 266/267: this is purely hypothetical. Here, a chlamydospore “becomes” a hyphal swelling, while there seems to be no big difference to a sporangium becoming a hyphal swelling in line 315. This is not convincing - line 296: Fig. 7l is not unbranched - line 297: sporangiophores - line 315: see above, purely hypothetical - line 321: structure in Fig. 7t is much larger and defined differently above (in line 315) - line 384: Than et al. to be replaced by [5] - line 427: Reference to be replaced by [number] Reviewer #2: Dear Dr. O'Hanlon Corresponding author PONE-D-21-03306, PLOS ONE I hope this message finds you well. It was my great honor to review the manuscript ID: PONE-D-21-03306, entitled "Two new Nothophytophthora species from streams in Ireland and Northern Ireland: Nothophytophthora irlandica and N. lirii sp. nov.". I really enjoyed reading it describing two new Nothophytophthora species. The manuscript has written well and I believe it really falls within the scope of PLOS ONE. Therefore, my recommendation would be "Accept" without any revision. Best regards, Sonia ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: SONIA AGHIGHI [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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Two new Nothophytophthora species from streams in Ireland and Northern Ireland: Nothophytophthora irlandica and N. lirii sp. nov. PONE-D-21-03306R1 Dear Dr. O'Hanlon, 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, Jaime E. Blair, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Thank you for your very careful revision and for addressing the reviewer comments. Your manuscript is now acceptable for publication. 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-21-03306R1 Two new Nothophytophthora species from streams in Ireland and Northern Ireland: Nothophytophthora irlandica and N. lirii sp. nov. Dear Dr. O'Hanlon: 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. Jaime E. Blair Academic Editor PLOS ONE |
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