Tissue-specific synergistic bio-priming of pepper by two Streptomyces species against Phytophthora capsici

Sakineh Abbasi; Naser Safaie; Akram Sadeghi; Masoud Shamsbakhsh

doi:10.1371/journal.pone.0230531

Peer Review History

Original SubmissionNovember 1, 2019
6 Dec 2019 Decision Letter - Marie-Joelle Virolle, Editor PONE-D-19-30373 Tissue-specific synergistic bio-priming of pepper by two Streptomyces species against Phytophthora capsici PLOS ONE Dear Dr Naser Safaie, Thank you for submitting your manuscript to PLOS ONE. After careful consideration by unfortunately a single reviewer (10 were approached), 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 variouspoints raised by the reviewer, that should help you to improve your manuscript. Be aware that I will try to find other reviwers besides this unique reviewer to juge your revised manuscript. We would appreciate receiving your revised manuscript by mid january 2020. 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled '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, Marie-Joelle Virolle, PhD 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 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. 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Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. Additional Editor Comments (if provided): [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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: 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: Comments on the manuscript: “Tissue-specific synergistic bio-priming of pepper by two Streptomyces species against Phytophthora capsica” This manuscript reports studies on protection of pepper plant from the fungal plant pathogen, Phytophthora capsici. The investigators have examined in-vitro inhibition of the pathogen by the selected strains of Streptomyces spp. Subsequently they have the experimental pepper plant with the Streptomyces spp. and challenged them with the pathogen. Parameters of the plant, like, shoot length, fruit length and weight etc. were measured as an indication of the health condition of the plant. Further, effect of Streptomyces strains on treated plants in respect of accumulation of H2O2 and transcription level of defense related genes were examined. While the subject of study is interesting, the paper is not suitable for publication in its present form. The authors require to address the following queries before the manuscript can be considered further. 1. The manuscript needs major improvement in English language. It should re-written for clarity and accuracy of language. 2. Name of the organisms must be in italicized throughout the text. 3.The method section does not provide clear description of experimental procedure. This needs to be appropriately revised. 4. Please clarify how cfu/ml suspension of Streptomyces strains were achieved by using cells and spores? 5. Whether the Streptomyces strains were able to colonize the root, leaf or fruit of the plant following treatment with the culture? 6. What was the level of expression of plant defense genes during the 7-days period following treatment of the plant with the Streptomyces spp. but before inoculation of the P. capsici into the plant? 7. Table 1 seems unnecessary and should be removed. Necessary information may be included in the materials and methods. 8. There is no description of Fig. 1 in the text?? 9. Superscripts in Table 3 should be explained in note under the table. 10. What was the rational for measuring shoot length 30 days after inoculation and plant weight on 80 dai? Whether these measurements were done only once during the entire period of experiment? 11.Results pertaining to Phytophthora fruit blight assay of treatments, contained in Fig. 6 should be moved at the end of the result section after description of Fig 5. 12. Since several Streptomyces spp. are reported to induce systemic acquired resistance in plants and protect them against phytopathogenic fungi, what is novel in this study? ****** 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: Ashok K. Dubey [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. https://doi.org/10.1371/journal.pone.0230531.r001
Revision 1
14 Jan 2020 Author Response Authors are grateful for reviewing the manuscript and good comments. We tried to improve and correct the manuscript according to the reviewer's comments. The answers (R) to the questions (Q) are as follow: Q1. The manuscript needs major improvement in English language. It should re-written for clarity and accuracy of language. R. Major improvements and changes were made in the manuscript, grammatical errors were corrected and conclusion was rewritten. Q2. Name of the organisms must be in italicized throughout the text. R. The name of the organisms italicized throughout the text. Q3.The method section does not provide clear description of experimental procedure. This needs to be appropriately revised. Q4. Please clarify how cfu/ml suspension of Streptomyces strains were achieved by using spores? R. Method section was revised and clearly explained. We suppose all the questions are answered accurately. We cultivated one plug of seven days old bacterial strains in ISP2 media supplemented with 10 mM NaCl, then the spores were counted with hemocytometer. Q5. Whether the Streptomyces strains were able to colonize the root, leaf or fruit of the plant following treatment with the culture? R. Indeed, we only noted the effect of soil treatment by these two species and reported that Streptomyces were able to colonize the root plant following re-isolation and culturing. We did not examine leaf and fruit colonization. Q6. What was the level of expression of plant defense genes during the 7-days period following treatment of the plant with the Streptomyces spp. but before inoculation of the P. capsici into the plant? R. Just, soil drench with chemical inducer BABA (10mM) was performed 48 h before P.capsici inoculation. After seven days of bacterial treatment (to establish), plants were inoculated with the pathogen. The first disease symptoms were observed on pepper plants seven days after pathogen inoculation. So, after seven days of P.capsici inoculation leaves and fruits (by length 1 cm) were harvested for study. We have two groups of treatments inoculated and non-inoculated with pathogen. Q7. Table 1 seems unnecessary and should be removed. Necessary information may be included in the materials and methods. R. Table 1 was removed and included in the content of material and methods anywhere needed. Q8. There is no description of Fig. 1 in the text?? Q9. Superscripts in Table 3 should be explained in note under the table. R. subscription into note and description of Fig 1 were done. Q10. What was the rational for measuring shoot length 30 days after inoculation and plant weight on 80 dai? Whether these measurements were done only once during the entire period of experiment? All of them were conducted during 30-80 days after treatment in two time repeats of experiments. We observed difference in plant height promotion after 30 days of treatment. At the end of study we observed some treatments have less reproductive promotion but more vegetative growth promotion, so we measured plant weight. Q11. Results pertaining to Phytophthora fruit blight assay of treatments, contained in Fig. 6 should be moved at the end of the result section after description of Fig 5. R. The results of fruit rot assay was moved after Fig 5. Q12. Since several Streptomyces spp. are reported to induce systemic acquired resistance in plants and protect them against phyto-pathogenic fungi, what is novel in this study? The results showed that phosphate solubilizing Streptomyces strain has the potential to induce systemic resistance and reduce the effects of leaf blight disease in compatible combinations in the greenhouse but expression analysis in two different tissues was distinct. Such findings are important, as they open doors to study the mechanisms and the interactions between the genetic background and priming in different tissues of the host plant. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0230531.r002
7 Feb 2020 Decision Letter - Marie-Joelle Virolle, Editor PONE-D-19-30373R1 Tissue-specific synergistic bio-priming of pepper by two Streptomyces species against Phytophthora capsici PLOS ONE Dear Dr Naser Safaie, Thank you for submitting your manuscript to PLOS ONE. After careful consideration by unfortunately a single reviewer, 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 various points raised during the review process. Be aware that efforts would be made by the editor to find more than one reviewer for your revised version. We would appreciate receiving your revised manuscript by end of february. 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled '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, Marie-Joelle Virolle, PhD 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) ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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: (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 ****** 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: Major revision of English language is still required. Authors should highlight the changes made in the revised version for a quick reference and review. ****** 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 [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. https://doi.org/10.1371/journal.pone.0230531.r003
Revision 2
21 Feb 2020 Author Response Dear Marie-Joelle Virolle, I am grateful for reviewing the manuscript and good comments. We tried to improve and correct the manuscript according to the reviewer's comments and the revised manuscript is submitted. C2. The manuscript needs major improvement in English language. It should re-written for clarity and accuracy of language. R. Major improvements and changes were made in the manuscript, grammatical errors were corrected and conclusion was rewritten. Best regards, Naser Safaie Attachments Attachment Submitted filename: Response to Reviewers R2.docx https://doi.org/10.1371/journal.pone.0230531.r004
3 Mar 2020 Decision Letter - Marie-Joelle Virolle, Editor Tissue-specific synergistic bio-priming of pepper by two Streptomyces species against Phytophthora capsici PONE-D-19-30373R2 Dear Dr. Naser Safaie, 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, Marie-Joelle Virolle, PhD 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: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: Queries and concerns raised during the review process have been addressed adequately by the authors. The revised version of the manuscript can now be accepted for publication. ****** 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: Yes: Ashok K. Dubey, https://doi.org/10.1371/journal.pone.0230531.r005
Formally Accepted
5 Mar 2020 Acceptance Letter - Marie-Joelle Virolle, Editor PONE-D-19-30373R2 Tissue-specific synergistic bio-priming of pepper by two Streptomyces species against Phytophthora capsici Dear Dr. Safaie: 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. Marie-Joelle Virolle Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0230531.r006

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