PONE-D-22-17252Screening and identification of bacteria with biocontrol activity against ginseng root rot disease and their potential mechanism of actionPLOS ONE

Dear Dr. Li,

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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We look forward to receiving your revised manuscript.

Kind regards,

Rashid Nazir

Academic Editor

PLOS ONE

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Additional Editor Comments:

Please make the changes as per reviewers' comments and prepare the revised manuscript according to journal guidelines.

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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

Reviewer #3: No

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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

Reviewer #3: No

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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: Yes

Reviewer #3: Yes

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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 reviewed manuscript entitled "Screening and identification of bacteria with biocontrol activity against ginseng root rot disease and their potential mechanism of action." is generally clear and well written.

The study dealt with a promising scientific approach to inhibiting pathogens through plant growth-promoting rhizobacteria (PGPR). The authors were interested in studying the properties of growth-promoting bacteria and their effect on inhibiting the in vitro growth of pathogenic fungi.

However, the authors have not studied the effect of the bacteria in the pot experiment. It is important to complete the research by studying the effect of growth-stimulating bacteria in the in vivo trails rather than studying it on section cut of the Root.

In general, the research dealt with an important topic and reached promising results that could be applied in the field as an alternative to chemical pesticides. However, I have the following comments:

1. The novelty of the study needs to be highlighted compared to other similar studies.

2. Introduction part: Must contain the whole background regarding the targeted problem and how to solve that problem with a comparison with the literature review; please check and revise accordingly.

3. The discussion seems to be poor; it didn't give good explanations of the results obtained. I think that it must be really improved. Where possible, please discuss the potential mechanisms behind your observations. You should also expand the links with prior publications in the area but try to be careful not to over-reach. For the latter, you should highlight potential areas for future study.

Specific Comments:

Line 1-3: The title could be shortened, e.g. "The potential of novel bacterial isolates from healthy ginseng for the control of ginseng root rot disease (Fusarium oxysporum)".

Keywords: The selected keywords should not be mentioned in the title; please change them accordingly

Section 3.1 : No reference was cited on the different protocols you worked with; how is that? The section must contain recent and related references with more details to be beneficial to broad scientific readers.

Line 109: Spell out the abbreviation LB.

Line 115 : did the pathogen you worked with is identified? If yes, please provide the accession number of the sequence in the GeneBank. If not, the pathogen needs to be identified.

Line 140: Enter the full name "PCR" in the subsection heading.

In the section Phylogenetic Analysis of Antagonistic Bacteria:

Line 148- 151: Several modifications should be done to the text; you should add the information about the different software used for the treatment of sequences (Alignments, assembly.

About the phylogeny analysis and tree construction, you need to know that Neighbor-joining is a clustering algorithm that can make quick trees but is not the most reliable; the method is not acceptable for publication. You need to reconstruct your tree based on the Maximum likelihood using Kimura 2 method with 1000 bootstrap.

In the results section: 4.3 Taxonomic identification of the three bacterial isolates

The different bacterial isolates sequenced in the present study should be published in the GeneBank; the similarity is not enough; you should give accession numbers to your sequence.

The tables are represented by '+’ or ‘-‘, only the yes or no to each of these assays. However, each bacterial isolate will have a difference in the production of these lytic enzymes/ metabolites. This will be evident from the zones of inhibition. Include this data in the table to get a complete visual assessment of this aspect. This is included in the text for a few bacteria in the amylase, protease activity etc. Adding this to the table will give a clearer idea to the reader.

Another important aspect you should verify is the detection of lipopeptides by PCR; while you are working with only Three isolates, you should verify the different genes that may be involved in the potential of different bacteria.

In Figure 1: the phylogenetic tree should contain all the bacterial isolates with their references; not every isolate with its own tree.

In table 4, for IAA content: add the statistical analysis

It is necessary to detail the title of figure 3 and add the standard deviation for Fig.3a

Reviewer #2: The manuscript entitled “Screening and identification of bacteria with biocontrol activity against ginseng root rot disease and their potential mechanism of action” by Li. et al. deals with laboratory observation of bacterial isolates that exhibited biocontrol activity against ginseng root rot and potentially enhance the growth of ginseng plant. The manuscript contains precious laboratory data. However, the reviewer could not find any new insights of the finding due to many articles relating to the recent work were published already, except if the manuscript contains field data of efficacy validation of these bacterial against plant root rot and other soil borne diseases. Herewith, some suggestions.

Line (L) 80-90: Please only emphasis why this research important, rather than explain the result of the research.

L135. Please provide the accession number of the sequences YN-42, YN-43, and YN-59 and do re-construction of phylogenetic analysis by adding the accession numbers (Figure 1.).

In Figure 2, please provide the actual size (….micro meter?) of bacterial cells in SEM.

In table 3, Please rewrite the ghree bacterial strains…… to the three bacterial strains…….

Reviewer #3: The study sought to find possible biocontrol microorganisms for Ginseng root rot disease. The work is essential because it will give an alternate method of reducing foot rot diseases to chemical treatment.

(1) The writing must be thoroughly reviewed for grammatical and spelling errors.

(2) Method 3.6 -Detection of secreted hydrolytic enzymes and secondary metabolites requires additional explanation.

(3) The findings were not supported by evidence such as phylogenetic diagrams, gel photos, inhibitory test images, and so on.

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Reviewer #1: Yes: Nabil Radouane

Reviewer #2: Yes: Oslan Jumadi, Ph.D., Prof.

Reviewer #3: No

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PONE-D-22-17252R1The potential of novel bacterial isolates from healthy ginseng for the control of ginseng root rot disease (Fusarium oxysporum)PLOS ONE

Dear Dr. Li,

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 Dec 01 2022 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Estibaliz Sansinenea

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.

Additional Editor Comments:

The reviewers have commented about the Ms and reccommended minor revision

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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 #1: All comments have been addressed

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 #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

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 #1: Yes

Reviewer #2: Yes

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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

Reviewer #2: (No Response)

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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: the paper need to address the following comments before publishing

In section 3.2 (Gene bank sequence registration number AF077393.1), change it to

Accession number: AF077393

Change Similarity to Identity in all the text

Revise the sections on molecular and morphological identification sections numbering is missing

Reviewer #2: The manuscript was re-write well based on suggestion of reviewer, but reviewer think that the authors should be mention the accession number in the abstract and the methods.

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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 #1: Yes: RADOUANE Nabil

Reviewer #2: No

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[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: 2nd Reviwer.docx

The potential of novel bacterial isolates from healthy ginseng for the control of ginseng root rot disease (Fusarium oxysporum)

PONE-D-22-17252R2

Dear Dr. Li,

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.

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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,

Estibaliz Sansinenea

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have incorporated all recommendations made by the reviewers therefore the MS can be accepted in the current form

Reviewers' comments: