Structure of Endophytes in the Root, Stem, and Leaf Tissues of Sweetpotato and Their Response to Sweetpotato Scab Disease Caused by Elsinoë batatas

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

1.         The abstract could benefit from a brief introduction outlining the importance or context of studying endophytes in sweet potatoes, especially in pathogenic infections.

2.         While the abstract mentions the use of high-throughput amplicon sequencing, providing a very brief mention of the methodological approach or data analysis could enhance the completeness of the abstract.

3.         The introduction provides a comprehensive overview of sweet potato's importance and scab disease's impact. However, it could benefit from a brief statement explicitly outlining the research gap or question that this study addresses.

4.         While the introduction mentions the susceptibility of the sweet potato variety 'Guangcaishu No. 5' to scab disease, it would be beneficial to briefly explain why this particular variety was chosen or its significance in sweet potato production.

5.         The paragraph on the role of endophytes in plant health and stress responses is informative. However, consider emphasizing how this relates to sweet potato and its susceptibility to scab disease.

6.         The introduction concludes by mentioning the study's aim to explore diversity changes in endophytic flora in healthy and diseased sweet potatoes. Consider adding a sentence highlighting this exploration's potential implications and how it could contribute to sweet potato scab prevention and control.

7.         The introduction provides a comprehensive overview of sweet potato's importance and scab disease's impact. However, it could benefit from a brief statement explicitly outlining the research gap or question that this study addresses.

8.         The introduction concludes by mentioning the study's aim to explore diversity changes in endophytic flora in healthy and diseased sweet potatoes. Consider adding a sentence highlighting this exploration's potential implications and how it could contribute to sweet potato scab prevention and control.

9.         The experimental setup and plant inoculation process description is well-detailed. However, providing a brief rationale for choosing the specific sweet potato variety, 'Guangcaishu No. 5', and why this location (Zhongluotan et al.) was selected would enhance the reader's understanding of the study context.

10.      The methods for sample collection are outlined clearly, but it would be helpful to elaborate on why specific parts of the plant (roots, stems, leaves) were chosen for analysis. A brief justification for choosing these plant parts could strengthen the experimental design.

11.      The steps involved in library construction and sequencing quality control are outlined well. However, briefly explain the rationale for using the NEXTFLEX Rapid DNA-Seq Kit and Illumina's Miseq PE300 platform.

12.      The manuscript generally provides a clear and organized presentation of the sequencing data and analysis. However, there are instances where the text could be further clarified. For example, in the description of dilution curves (lines 235-238), it would be beneficial to explicitly state the significance of the flattening slope in terms of sequencing depth and the sufficiency of the analysis.

13.      The description of endophytic species composition at the phylum and genus levels is informative. However, the biological implications of changes in the abundance of specific taxa should be discussed in more detail.

 

14.      The study's identification of Sphaceloma as a key pathogenic bacterium and its correlation with specific endophytes is a crucial discovery. Discuss in more detail how this information can be leveraged for potential biocontrol strategies and its implications for disease management.

Comments on the Quality of English Language

Moderate editing of the English language required

Author Response

Dear reviewer, we have addressed your comments point by point and made necessary corrections to the body of the text. Please check the attached PDF file for further details.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript of Shi-xin Wang et al. presents the results of high-throughput sequencing of endophytic flora of sweetpotato. The manuscript contains interesting findings and their discussion. Unfortunately, the quality of figures is low and must be greatly improved, text in many figures is not readable. In general, the manuscript is well written and relevant. The main issue with the manuscript is the lack of interpretation of the results and hypotheses.

 

Please check the punctuation in the manuscript, there are a lot of spaces between brackets, sentences, etc.

 

Check the formatting of figure captions.

 

Lines 139-132 Why was two-step amplification used? What technique did you use? Please clarify in the text.

 

Section 2.1: Why surface sterilised with ethanol? After all, ethanol does not destroy DNA; therefore, some of the DNA of exophytic bacteria could remain in the samples and end up in the DNA library. Comment in the text.

 

Section 2.1: What growing conditions did you use? What type of soil was it, what protection and nutrition system did they use? What were the agroclimatic conditions? This is quite important, since endophytes are exposed to various factors, including growing conditions. Information should be added.

 

Lines 757-759: the text should be rewritten. It is not entirely clear what is meant by trend. It should be added: a tendency to increase the diversity of endophytes in the root-stem-leaf.

 

Lines 763-764: what exactly has not changed: the number of bacterial species or from the biomass. Authors should be more specific in their discussions.

 

Lines 764: Ascomycota is not a mushroom, but a genus of mushrooms. Should be changed and clarified in the text.

 

Lines 771-772: Which pathogenic bacteria should be combated if your pathogen is of fungal etiology?

 

Section 2.1: How exactly was the presence of scab diagnosed? DNA analysis of the population DNA is not very informative, since the DNA of dead pathogen cells could get there. In addition, in phytopathological studies, the presence of a pathogen is diagnosed by at least 2 methods, one of which should be a pathogenicity text (Koch triad). Please comment on this in the text.

 

Discussion section: the authors should describe the research prospects in more detail, taking into account the information obtained in the article.

 

Discussion section: the authors should explain in more detail how exactly the change in endophytic composition occurred during infection with a pathogen (not just the species composition, but the metabalome, proteome and other components of the succession process).

 

 

Introduction section: information should be added on the effect of the pathogen on the yield and quality of the plant and product.

 

Author Response

Dear reviewer, we have addressed your comments point by point and made necessary corrections to the body of the text. Please check the attached PDF file for further details.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The paper reports a comparative metagenomic analysis of fungal and bacterial endophytes in healthy plants of Ipomoea batatas (sweetpotato) and plants experimentally infected with Elsinoë batatas, a fungal pathogen that causes major losses in sweetpotato production annually.  According to the authors, the results indicate that, compared with healthy controls, the diversity of fungal endophytes significantly decreased in the roots and increased in the leaves of infected plants, whereas the diversity of bacterial endophytes showed no significant variation in response to infection.

I have some problems with this paper, as reported below.

  1.   The authors refer to a former paper for details about the procedure followed to obtain infected plants. In my opinion, they need to include some details in the present paper. They probably used scab-infected plants as inoculum without knowing the exact nature of the pathogen. Their metagenomic analysis identified the pathogen with OTU87, a cluster of sequences associated with Elsinoë batatas (the right spelling includes a diaeresis on the “e”). Sphaceloma batatas is the asexual form of Elsinoë batatas and is no longer used in taxonomy (see Fan et al. 2017 http://dx.doi.org/10.1016/j.simyco.2017.02.001). Referring to OTU87 as Elsinoë in the title of the paper and the Abstract, and as Sphaceloma in Sections 3.4, 3.5 and 4 is most confusing.

     2. The fact that the composition of endophytic fungi changed in response to infection by Elsinoë is no evidence of a protective role against the pathogen. This inference should be tempered in Section 4 and deleted from the Abstract.

     3. The paper is exceedingly long and verbose. Substantial streamlining would make it easier to digest and more effective. Sections 4 and 5 repeat the same notions several times.

 

     Minor observations are included in the pdf attached.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Author Response

Dear reviewer, we have addressed your comments point by point and made necessary corrections to the body of the text. Please check the attached PDF file for further details.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript has been improved and can be published now.

Reviewer 3 Report

Comments and Suggestions for Authors

The authors satisfactorily addressed my comments and suggestions.