Analysis of the Fungi Community Variation during Rice Storage through High Throughput Sequencing

Round 1

Reviewer 1 Report

This manuscript is well-documented the changes in the fungi community during rice storage using high throughput sequencing analysis. This is a novel attempt. But few points are not well convincing

 

Positive points

• The title aptly explains the experiments performed by the researchers.
• The language is simplistic and clearly explains what they have attempted to do except few grammatical errors.

 Negative points

• “The orientation A” and “vertical position L1” in the abstract is mentioned first time with our prior information.
• The novelty of this work is poorly mentioned/ written.
• The physiological quality of each stored rice was not investigated in this work to find the collection of any deterioration rice quality with stored time and fungal abundance.
•  “Figure 7” can be reported as Supplementary data.
• The accession number of the NGS and isolates are not mentioned in the manuscript.
• Suggest the improvement of the discussion part.

Author Response

Dear Melinda Simon-Varhelyi,

Thank you for giving us this opportunity to submit a revised of the manuscript “Analysis of the fungi community variation during rice storage through high throughput sequencing” for publication in the Processes. We appreciate efforts that you and reviewers contributed to provide feedback on our manuscript and grateful for the insightful comments on our paper. As suggested by reviewers, certain experiments were operated. According to renewal experiments, we have rearranged the manuscript. Those changes are in red within the manuscript. Please see below, in red, for a point-by-point response to the reviewers’ comments and concerns.

Response to Reviewer 1 Comments:

This manuscript is well-documented the changes in the fungi community during rice storage using high throughput sequencing analysis. This is a novel attempt. But few points are not well convincing

Author response: Thank you!

Positive points

The title aptly explains the experiments performed by the researchers.

The language is simplistic and clearly explains what they have attempted to do except few grammatical errors.

Author response: Thank you!

 

Negative points

Point 1: “The orientation A” and “vertical position L1” in the abstract is mentioned first time with our prior information.

Response 1: Thank you for pointing this out. We have changed “The orientation A” into “Horizontal A”, while “vertical position L1” into “vertical L1”.

 

Point 2: The novelty of this work is poorly mentioned/ written.

Response 2: We have mentioned “This work comprehensively analyzed the fungi community variation in horizontal and vertical directions.” in abstract.

 

Point 3: The physiological quality of each stored rice was not investigated in this work to find the collection of any deterioration rice quality with stored time and fungal abundance.

Response 3: We haven’t put the physiological quality of each stored rice in this study due to the aim of the work, which focuses on the fungi variations by analyzing high throughput sequencing nor the quality variations.

 

Point 4: “Figure 7” can be reported as Supplementary data.

Response 4: As suggested by the reviewer, we have put the Figure 7 as Supplementary data.

 

Point 5: The accession number of the NGS and isolates are not mentioned in the manuscript.

Response 5: As suggested by the reviewer, we have put the accession number and isolates in the manuscript.

 

Point 6: Suggest the improvement of the discussion part.

Response 6: We agree with the reviewer’s assessment. Accordingly, the discussion was revised, where the change can be found in the revised manuscript.

 

Author Response File: Author Response.docx

Reviewer 2 Report

The present study identified the relative abundance of dominant fungal genera during rice storage and statistically analyze the patterns of fungi 
community changes in the horizontal orientation, vertical depth, and storage time

Abstract:

Line 14 And The Fungi ... reject And

I think that in the abstract are missing characteristics of samples and some relevant methods.

Introduction is very well described.

Material and methods:

In Rice samples is it necessary to write Latin names of the rice kind.

Statistics must be written as a separate chapter.

Results:

I don't understand the meaning: To investigate the composition of the fungal community from each sample, the valid sequences of 108 samples were clustered at 97% identity following the sequences annotation of OTUs with species.

Under table 1. It is necessary to explain what A,B,C etc. means.

Statistical differences must be written as the letters as upper index.

Phylum, genera is not written with italic. Only species and genus.

Figure 7 is illegible.

Discussions need more detailed description of results to compare with different authors.

Conclusion needs formatting.

Manuscript is very good and interesting, but still has some flaws, which is necessary change. Authors need to write some novelty of study.

Author Response

Dear Melinda Simon-Varhelyi,

Thank you for giving us this opportunity to submit a revised of the manuscript “Analysis of the fungi community variation during rice storage through high throughput sequencing” for publication in the Processes. We appreciate efforts that you and reviewers contributed to provide feedback on our manuscript and grateful for the insightful comments on our paper. As suggested by reviewers, certain experiments were operated. According to renewal experiments, we have rearranged the manuscript. Those changes are in red within the manuscript. Please see below, in red, for a point-by-point response to the reviewers’ comments and concerns. 

Response to Reviewer 2 Comments:

Abstract

Point 1: Line 14 And The Fungi ... reject And

Response 1: Thank you, the “And” was deleted.

 

Point 2: I think that in the abstract are missing characteristics of samples and some relevant methods.

Response 2:

 

Point 3: Introduction is very well described.

Response 3: Thank you!

 

Material and methods

Point 4: In Rice samples is it necessary to write Latin names of the rice kind.

Response 4: Thank you. As suggested by the reviewer, Latin name of rice species were removed.

 

Point 5: Statistics must be written as a separate chapter.

Response 5: As suggested by the reviewer, statistics were separated into “2.3.3. statistical analysis”.

 

Results

Point 6: I don't understand the meaning: To investigate the composition of the fungal community from each sample, the valid sequences of 108 samples were clustered at 97% identity following the sequences annotation of OTUs with species.

Response 6: To investigate the compositions of fungi in each sample, the species annotation was processed on OUTs through clustering at 97% identity of valid sequences from 108 samples.

 

Point 7: Under table 1. It is necessary to explain what A,B,C etc. means.

Response 7: Thank you for pointing this out. The meanings of A, B, C, etc. were explained below.

.

Point 8: Statistical differences must be written as the letters as upper index.

Response 8: As suggested by the reviewer, statistical differences were modified as superscripts.

 

Point 9: Phylum, genera is not written with italic. Only species and genus.

Response 8: As suggested by the reviewer, phylum, genera aren’t italicized.

 

Point 10: Figure 7 is illegible.

Response 10: Figure 7 is high-resolution that can be amplified to read, but due to the limited length it becomes illegible. Therefore, we have put the Figure 7 as Supplementary data.

 

Point 11: Discussions need more detailed description of results to compare with different authors.

Response 11: As suggested by the reviewer, we have redrafted the conclusions that [more detailed description of results to compare with different authors] have been added.

 

Point 12: Conclusion needs formatting.

Response 12: Thank you for pointing this out. The indention of conclusion section has been formatted.

 

Point 13: Manuscript is very good and interesting, but still has some flaws, which is necessary change. Authors need to write some novelty of study.

Response 13: Thank you. We have mentioned “This work comprehensively analyzed the fungi community variation in horizontal and vertical directions.” in abstract.

 

Author Response File: Author Response.docx

Round 2

Reviewer 2 Report

Authors accepted all comments.

It is there only few formal mistakes.

Author Response

Dear Melinda Simon-Varhelyi,

Thank you for proceeding our manuscript again. We appreciate your and the reviewers’ hard efforts on our paper to make it much more improving. Thanks a lot. As suggested by Reviewer 2, certain modifications were operated. Please see below, in red, for a point-by-point response to the reviewers’ comments and concerns.

Author’s Reply to the Review Report (Reviewer 2):

Point 1: It is there only few formal mistakes.

Response 1: As suggested by the reviewer, we have double checked the manuscript, and revised minor mistakes as italicizing genus, deleting or inserting blanks, changing numlist of supplementary materials, etc. 

Author Response File: Author Response.docx