Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition

Nazia R. Zaman; Umar F. Chowdhury; Rifath N. Reza; Farhana T. Chowdhury; Mrinmoy Sarker; Muhammad M. Hossain; Md. Ahedul Akbor; Al Amin; Mohammad Riazul Islam; Haseena Khan

doi:10.1371/journal.pone.0257863

Peer Review History

Original SubmissionJune 6, 2021
30 Jun 2021 Decision Letter - Abhay K. Pandey, Editor PONE-D-21-18655 Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through multiple modes of action PLOS ONE Dear Dr. Islam, 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 Aug 14 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. 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Discussion must focus the critical analysis of literature and should be condensed. Conclusion summarizes the findings of research. [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: Yes Reviewer #2: Yes ******** 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: 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: On the basis of what the authors reported in the manuscript, the present study was aimed to "Plant growth promoting endophyte Burkholderia contaminants NZ antagonizes phytopathogen Macrophomina phaseolina through multiple modes of action". To gain these aims, the authors developed series of experiments devoted to re-culturing, identify pathogen and growth promoting bacterial isolates using GC-MS and whole genome sequencing and the information in results is clear and concise but need to be checked again as there are few grammatical error and used a few long sentences that should be summarized. Materials and methods should be more attractive if the sequencing and analysis be placed before the in-vivo and in-vitro studies; over all the manuscript is written well and have valuable information for the readers. The whole manuscript should be proofread for English language editing and grammatical errors. Discussion section of the manuscript is should be improved by using a few latest references. Reviewer #2: 1. Objective of the study should be more clearly defined. 2. Replicates used in the experiments are very few, so my question is why the authors did not repeat the experiments. If they did, then it requires proper elaboration. and How will authors justify the findings and their reproducibility? 3. Discussion is very very long, it should be précised. 4. Conclusion section is lacking impressiveness in its expression. I will suggest authors to put an extra effort in improving it. 5. There is also an suggestion about the title, I think it should be more specific as it is very generalized in its current form. ****** 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:** Raees Ahmed 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. Attachments Attachment Submitted filename: APAP.docx https://doi.org/10.1371/journal.pone.0257863.r001
Revision 1
29 Jul 2021 Author Response Responses to the Editor and Reviewers’ comments 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf The format has been changed according to PLOS ONE’s style. 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: We would like to address the funding information as stated below: This project is funded by Higher Education Quality Enhancement Project (HEQEP) (Grant number: CP-3250), a World Bank financed development project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 3. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. "Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. There are no ethical or legal restrictions to sharing our data publicly. Data Availability statement has been corrected to ‘The authors have no objection to make the data set underlying the results described in our manuscript to be fully available.’ In the revised cover letter the accession no of the bacterial whole genome sequence (This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession QRBC00000000) and data availability statement have been included. 4. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ An ORCID iD was generated and validated in Editorial Manager 5. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. The results have been included in the Supporting Information (S2 Fig and S5 Table) 6. We note that Figures 1, 2, and 3 in your submission contain copyrighted images. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. There is no chance of copyright issue for Figures 1, 2 and 3. They have been produced in this study and have not been used in any other article or report. Additional Editor Comments (if provided): The English language must be addressed with the help of a native speaker or English language editing service. Furthermore, the manuscript lacks detailed experimental procedure; at least three replications and one repetition of experiment are required, failing which MS will be rejected. Discussion must focus the critical analysis of literature and should be condensed. Conclusion summarizes the findings of research. [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: Yes Reviewer #2: Yes ________________________________________ 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: 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: On the basis of what the authors reported in the manuscript, the present study was aimed to "Plant growth promoting endophyte Burkholderia contaminants NZ antagonizes phytopathogen Macrophomina phaseolina through multiple modes of action". To gain these aims, the authors developed series of experiments devoted to re-culturing, identify pathogen and growth promoting bacterial isolates using GC-MS and whole genome sequencing and the information in results is clear and concise but need to be checked again as there are few grammatical error and used a few long sentences that should be summarized. Materials and methods should be more attractive if the sequencing and analysis be placed before the in-vivo and in-vitro studies; over all the manuscript is written well and have valuable information for the readers. The whole manuscript should be proofread for English language editing and grammatical errors. Discussion section of the manuscript is should be improved by using a few latest references. Changes has been made according to the suggestions. Reviewer #2: 1. Objective of the study should be more clearly defined. The objective has been clearly defined. 2. Replicates used in the experiments are very few, so my question is why the authors did not repeat the experiments. If they did, then it requires proper elaboration and How will authors justify the findings and their reproducibility? All the experiments were done with three replications as stated in the Materials and Method section (lines 119 and 172) and all tests were performed in triplicate if not mentioned otherwise. 3. Discussion is very long, it should be précised. Discussion has been modified accordingly. 4. Conclusion section is lacking impressiveness in its expression. I will suggest authors to put an extra effort in improving it. This has been modified accordingly. 5. There is also an suggestion about the title, I think it should be more specific as it is very generalized in its current form. The title has been edited as suggested. ________________________________________ 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: Raees Ahmed Reviewer #2: No Reviewer Recommendation Term: Major Revision 1. Is the manuscript technically sound, and do the data support the conclusions? Yes 2. Has the statistical analysis been performed appropriately and rigorously? Yes 3. Have the authors made all data underlying the findings in their manuscript fully available? Yes 4. Is the manuscript presented in an intelligible fashion and written in standard English? Yes 6. Review Comments to the Author The data itself is good, but the manuscript need to be improved in terms of writing. There are so many small mistakes that can easily be fixed by just reading it through a few more times. Here I listed a portion of the problems, but I recommend the authors to go over carefully for each sentence and craft it again. Also, I didn't like the red background for some figures. Although I won't say this is mandatory, I think red is probably not the best background color for those figures. Overall, this paper presents solid data sets and I recommend it to be published after major revisions. Abstract Line 40- Secondary metabolites, catechols and ergotaman (that has been found through what?) They were found through GC-MS analysis as mentioned in line 35. Introduction Line 58- be specific of what 'They' indicates (ex: the beneficial effects of endophytes) Revised accordingly Line 61-63 biocontrol activity including competition for iron, nutrient and space, production of antibiotics, lytic enzymes and volatile compounds, and induction of systemic resistance. Corrected accordingly Line 63-65 Many studies have emphasized the ability of these microorganisms for possible roles for promoting plant growth and protection through additive/synergistic effects. Corrected accordingly Line 66 B. subtilis [9], Pseudomonas parafulva, and Pantoea agglomerans are a few examples. Not so sure about "recent developments". What developments? Corrected accordingly Line 68 Full scientific name for Jute Throughout its life cycle, Corrected accordingly Line 81 human environment? Like inside of human body? If so, "a widespread presence in water, soil, plants, and animals including human" Corrected accordingly Line 84 & 86 Space between (Bcc) and [17] / [18] and . Corrected accordingly Line 90 Don't start a line with "but" Corrected accordingly Line 94-96 I think this line can be written shorter and clearer. Changed accordingly Overall, introduction is good, but can be better by reorganizing and rewriting sentences. Line 105 Delete "used in this study ... collection of" Corrected accordingly Materials and methods Line 108-109 and throughout manuscript Use full scientific names including authroties if possible. These should be okay. Line 117 Fix 'NZ' (italic) Corrected accordingly Line 123 At first, TSB media? Full names should be mentioned when first introduced. Instead of that, full name was introduced in line 199 Corrected accordingly Line 124 At the same time, Corrected accordingly Line 134 and MgSO4.7H2O Corrected accordingly Line 137 Thirty instead of 30 Corrected accordingly Line 152 (10x coverage) Corrected accordingly Line 158 server [29] Corrected accordingly Line 198 and throughout manuscript Authors should be consistant for number+unit (ul, degree, etc) combination. For example, I can see inconsistancies such as 20ml (no space) vs 20 ml (space between number+unit). Just go with one. Corrected accordingly Line 205-206 For HPLC and LC-MS analysis, a seperate 1000ml of B. contaminans NZ was cultured under similar conditions described above. Corrected accordingly Line 208 Delete 'together' since co-culture already contains the meaning. Corrected accordingly Line 209 filtered thorough 'what'? Corrected accordingly Line 213-215 Recommend to rephrase it. Hard to understand. Revised accordingly Line 220 One µL is awkward. What about one microliter? Corrected accordingly Line 221 Helium was used as the carrier gas with the flow rate set at 1.0 mL/min Also, be comsistant with ml or mL (chose one) Corrected accordingly Line 224 respectively, and Corrected accordingly Line 235 temperature: Corrected accordingly Line 251-252 The capillary voltage was maintained at 4000 V, and dry gas temperature was set at 350°C. Corrected accordingly Line 256 biosynthesis; among those, Corrected accordingly Results Table 1. Adding chromosomal locations for the genes would be beneficial. Has been added in S4 Table Line 334 and (f) Rhizoctonia solani Corrected accordingly Table 3. Xylaria sp. Nigrospora sphaerica 52.99 ± 3.67 Corrected accordingly Line 403-404 , and their 404 corresponding homologues in M. phaseolina were identified through a BLAST search Corrected accordingly Discussion Line 416 Delete , Corrected accordingly Line 440 Delete But and replace with 'however' or similar word. Corrected accordingly Line 458 The Burkholderia genome Corrected accordingly Line 459 M. phaseolina Corrected accordingly Line 461 and Rhizoctonia solani Corrected accordingly Line 481 Space issue Corrected accordingly Line 530 , and scytalone dehydratase Corrected accordingly Line 547 downregulation Corrected accordingly Attachments Attachment Submitted filename: Responses to the reviewers comment.docx https://doi.org/10.1371/journal.pone.0257863.r002
16 Aug 2021 Decision Letter - Abhay K. Pandey, Editor PONE-D-21-18655R1 Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition PLOS ONE Dear Dr. Islam, 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 Sep 30 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled '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. 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, Abhay K. Pandey Academic Editor PLOS ONE Additional Editor Comments (if provided): This manuscript is an improvement over the previously submitted version. Although all reviewers recommended publication of the MS, however, The MS still needs improvement in terms of clarity and quality. I recommended in my last review that the authors find someone fluent in scientific writing in English to correct the many grammar, terminology, and sentence structure errors in the manuscript. While, some effort was made to correct these errors, the current manuscript is still filled with errors that make the article very difficult to read. I have noted a few of these errors on the manuscript, but there are many errors per page that need to be addressed. The level of writing is not up to the standard required for publication in PLoS series journals. At this point, the authors should consider employing a professional editor experienced in scientific writing. In abstract, background of research and aim of the study are missing, please revise abstract to make it more focused. What is NZ in abstract, this is a wrong way of presentation please revise, do you mean Burkholderia contaminans, if it is, then it is not properly cited. Page 2 lines 34 compounds or molecules not substances, and overall the MS need thorough English revision failing which MS will be not accepted. Overall, abstract is very poorly written, please revise it to make more focused. Page 3 line 65 line 85 species not italic correct in whole MS Line 77 space Line 92 to 101 it should described objective of your research and why it needed and then what are you presenting in this paper. Did you check pathogenicity of Macrophomina phaseolina before conducting experiments? Line 120 it was not grown in shaker, you incubated in incubator shaker, how long old culture you used for DNa isolation Line 157 spore density was adjusted ??? revise sentence Line 172, the experiment was repeated three times, if it is the case, how you handled the data from repeated experiments it is not described in the statistical section. Also this section does not show you used original data or transformed data for analysis. Petri dish, P should be capital Line 193 35 and 36 why two reference, anyway this paper contains more references, more than we require for a research paper, please reduce the number of references upto 50. Remove statistical part from each section and put it in the last of material and method in the single section describing the details how u analyzed the data as I mentioned. Line 259 ascomycota group of fungi Line 272 (P<0.05) Table1 I think name of genes should be italic, follow in all tables Mention CD, MSS and F values in table 3. Coulumn one Fungal Species Line 342 full name Macrophomina phaseolina should start follow in whole in whole MS same trend Table 4 can be given as supplementary table Line 441 strains Conclusion should be short and easily understandable Some of the references not follow the journal trends. [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: All comments have been addressed Reviewer #2: All comments have been addressed Reviewer #3: 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 Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: Yes ****** 5. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: I have received and checked critically the revisions from the author on the the manuscript with title "Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition" and found satisfactory. On the light of this my recommendation is to accept the manuscript keeping in view the decision of other experts. Reviewer #2: (No Response) Reviewer #3: Authors corrected listed errors/problems, and this MS looks a lot better now. Just a few recommendations: Based on track change file Line 81: There is a space between [14] & . Line 125-126: What rpm? ****** 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: Raees Ahmed Reviewer #2: Yes:** Adnan Akhter Reviewer #3: 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.0257863.r003
Revision 2
10 Sep 2021 Author Response Responses to the Editor and Reviewers’ comments Additional Editor Comments (if provided): This manuscript is an improvement over the previously submitted version. Although all reviewers recommended publication of the MS, however, The MS still needs improvement in terms of clarity and quality. I recommended in my last review that the authors find someone fluent in scientific writing in English to correct the many grammar, terminology, and sentence structure errors in the manuscript. While, some effort was made to correct these errors, the current manuscript is still filled with errors that make the article very difficult to read. I have noted a few of these errors on the manuscript, but there are many errors per page that need to be addressed. The level of writing is not up to the standard required for publication in PLoS series journals. At this point, the authors should consider employing a professional editor experienced in scientific writing. The revised manuscript has been corrected by professional editing company. In abstract, background of research and aim of the study are missing, please revise abstract to make it more focused. Made changes according to the suggestions What is NZ in abstract, this is a wrong way of presentation please revise, do you mean Burkholderia contaminans, if it is, then it is not properly cited. Changed all instances of NZ to B. contaminans NZ Page 2 lines 34 compounds or molecules not substances, and overall the MS need thorough English revision failing which MS will be not accepted. Changed according to the suggestions Overall, abstract is very poorly written, please revise it to make more focused. Revised according to the suggestions Page 3 line 65 line 85 species not italic correct in whole MS Revised accordingly Line 77 space Revised accordingly Line 92 to 101 it should described objective of your research and why it needed and then what are you presenting in this paper. Revised accordingly Did you check pathogenicity of Macrophomina phaseolina before conducting experiments? We have checked the pathogenicity of Macrophomina phaseolina on jute seedlings and found jute seedlings dies after few days of infection, and turns brown. This result has been included in our recent paper by Zaman NR et al. (2020) Ref: 1. Zaman NR, Kumar B, Nasrin Z, Islam MR, Maiti TK, Khan H. (2020) Proteome Analyses Reveal Macrophomina phaseolina's Survival Tools When Challenged by Burkholderia contaminans NZ. ACS Omega. 5(3):1352-1362. doi:10.1021/acsomega.9b01870 Line 120 it was not grown in shaker, you incubated in incubator shaker, how long old culture you used for DNA isolation The statement was corrected according to the suggestion. It is mentioned in the same line that the bacterium was grown overnight and DNA was isolated from that culture. Line 172, the experiment was repeated three times, if it is the case, how you handled the data from repeated experiments it is not described in the statistical section. Also this section does not show you used original data or transformed data for analysis. The average shoot length, average root length and average height from the three repeated experiment was taken for statistical analysis shown in supplementary table 1. Petri dish, P should be capital Revised accordingly Remove statistical part from each section and put it in the last of material and method in the single section describing the details how you analyzed the data as I mentioned. Revised accordingly Line 259 ascomycota group of fungi Revised accordingly Line 272 (P<0.05) Revised accordingly throughout the MS Table1 I think name of genes should be italic, follow in all tables Revised accordingly Coulumn one Fungal Species Revised accordingly Line 342 full name Macrophomina phaseolina should start follow in whole in whole MS same trend Revised accordingly Table 4 can be given as supplementary table Revised accordingly Line 441 strains Revised accordingly Conclusion should be short and easily understandable Changed accordingly Some of the references not follow the journal trends. Changed accordingly Attachments Attachment Submitted filename: Response to the Editors Comments.docx https://doi.org/10.1371/journal.pone.0257863.r004
14 Sep 2021 Decision Letter - Abhay K. Pandey, Editor Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition PONE-D-21-18655R2 Dear Dr. Islam, 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, Abhay K. Pandey Academic Editor PLOS ONE Additional Editor Comments (optional): authors addressed all comments Reviewers' comments: https://doi.org/10.1371/journal.pone.0257863.r005
Formally Accepted
22 Sep 2021 Acceptance Letter - Abhay K. Pandey, Editor PONE-D-21-18655R2 Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition Dear Dr. Islam: 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. Abhay K. Pandey Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0257863.r006

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