PONE-D-20-07320

Bacillus simplex treatment promotes soybean defense against soybean cyst nematodes: A metabolomics study using GC-MS

PLOS ONE

Dear Dr. Kang,

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.

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Hon-Ming Lam, Ph.D.

Academic Editor

PLOS ONE

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

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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

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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

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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: The article : Bacillus simplex treatment promotes soybean defense against soybean cyst

nematodes: A metabolomics study using GC-MS is well written. The content is easy to follow and the methodologies are clearly stated. However, feature extractions of metabolites (relatively low coverage nowadays but acceptable) could be improved.

Reviewer #2: This manuscript reports the results from a pot experiment and revealed the effects of Bacillus inoculation on root metabolic changes in soybean plants infected with cyst nematodes (SCN). The findings showed that the bacterial inoculation functioned in three different aspects: reduced food source, produced nematocidal substances and improved disease-resistance ability. The main concern is that only one soybean cultivar, one bacterial strain, and one isolate of cyst nematode were used in this study. Another concern is the language writing which needs further improvements throughout the manuscript (lots of typos and grammatical errors). Some other specific comments:

L. 47-50: the objective is quite general. It would be good to add hypotheses of this study.

L. 59: not clear of how the bacteria inoculum were coated to the seeds

L. 67: not clear of the seedling age or growth stage at the time of inoculation with SCN

L. 70: plants were assessed at 5 and 10 days after inoculation: not sure if such short period was enough for observing interactions between the bacteria and SCN

L. 81: samples of roots?

L. 74: ‘Liaodou15’ here, but ‘Liao15’ in L. 58. Use one and be consistent throughout the manuscript

L. 77-78: last sentence on data analysis can be removed to the “Data analysis” section

L. 107-114: put this section last, i.e. before the ‘Results’ section to include all acquired data in this study in addition to the spectrometry data, such as ANOVA for nematode numbers etc.

L. 129: significant level? The statistical analysis was not mentioned in the M&M section.

L. 130-131: delete this sentence and move it to Discussion section.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-07320R1

Bacillus simplex treatment promotes soybean defence against soybean cyst nematodes: A metabolomics study using GC-MS

PLOS ONE

Dear Dr. Kang,

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 2020 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

We look forward to receiving your revised manuscript.

Kind regards,

Hon-Ming Lam, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

This manuscript needs a thorough English polishing. The authors may consider to get professional English editing service.

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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 #2: (No Response)

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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 #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: 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 #2: 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 #2: 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 #2: The authors have attended all comments and carefully revised the manuscirpt. Higher resolution / better quality of figures are required for the publications. The writing language has been largely imporved in the R1. However, there are still many language problems requiring further improvements. Let's take the first paragraph of the Introduction section as examples:

L. 33: change "Soybean has a high protein and oil content" to "Soybean seeds contain high protein and oil content".

L. 34 "which place high importance on its production yield" is not clear.

L. 36 "can hinder its growth and production": not clear of "its" - just use "soybean", and can be changed to "can hinder the growth and production of soybean".

L. 39-40: "Plant growth-promoting rhizobacteria (PGPR) colonises the rhizosphere of" should use "colonise".

L. 42-44: replace "Our past studies have discovered the Sneb545 strain of Bacillus simplex that can enhance soybean resistance to SCN" with "Our past studies have discovered that the Sneb545 strain of Bacillus simplex enhanced soybean resistance to SCN"

.....

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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 #2: Yes: Yinglong Chen

[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.

Bacillus simplex treatment promotes soybean defence against soybean cyst nematodes: A metabolomics study using GC-MS

PONE-D-20-07320R2

Dear Dr. Kang,

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.

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Kind regards,

Hon-Ming Lam, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: