Seasonal Changes in Soil Microbial Community and Co-Occurrence Network of Species of the Genus Corylus

Round 1

Reviewer 1 Report

See attached file.

Comments for author File: Comments.pdf

Author Response

Dear Editors and Reviewers:

Thank you for your letter and for the reviewers’ comments concerning our manuscript entitled “Seasonal changes in soil microbial community and co-occurrence network of species of the genus Corylus” (microorganisms-1380492). Those comments are all valuable and very helpful for revising and improving our paper, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. Revised portion are used the “Track Changes” function in the paper. The main corrections in the paper and the responds to the reviewer’s comments are as the attached file.

We tried our best to improve the manuscript and made some changes in the manuscript. These changes will not influence the content and framework of the paper. And here we did not list the changes but used the “Track Changes” function in revised paper.

We appreciate for Editors/Reviewers’ warm work earnestly, and hope that the correction will meet with approval.

Once again, thank you very much for your comments and suggestions.

Thank you and best regards.

Yours sincerely,
Corresponding author:
Tiantian Zhao
[email protected]

Author Response File: Author Response.pdf

Reviewer 2 Report

The manuscript ID: microorganisms-697889 by Ma et al., entitled “Seasonal changes in soil microbial community and co-occurrence network of species of the genus Corylus” aim to reveal microbial diversity, co-occurrence network and seasonal variation in the soil microbial community of species of genus Corylus.

General remarks:

Dear authors,

the manuscript is well written. However, my biggest concern is the usage of the very old version of Mothur (1.30.1) while for the experimental period (2019) the newer version 1.42 was already available. Each new version has improved algorithms and thus provide greater reliability of the results. So using the initial version 1.30.1 seems to be a methodological error. I don't know Mothur very well, but I would expect that using the current software would give much better results. In my research I used QIIME, and now QIIME 2 with improved ASV -amplicon sequence variant analyzes rather than OTU.

My second major comment is that in my opinion the diversity and co-occurrence analyzes should be done for the lowest reliable taxonomical level, which in your case considering the length of amplicon and technology used (Illumina) should be family/genus level. This approach is targeted for greater differentiation of samples, suggesting the possible function of specific genera, functions not represented by all taxa of given phylum/class.I am also a bit surprised that the PCR products were cut/purified from the gel and not the purification of raw PCR product mixture for example, with the use of magnetic beads. To my knowledge, excision is much less efficient and while bacteria usually have one product size, fungal communities often produce several sizes of amplicons (required larger excision of the gel amount). The cutting/cleansing of the gel seems to be a possible bias point of library preparation. Can you present the image of your PCR products?

Other:

It is recommended to prepare figures to be sufficient for standalone analysis – abbreviations explained.

Taxonomical names of bacteria and fungi should be written in italics

Augmentation (inoculation) by ectomycorrhizal microbial communities or specific taxa seem to be an interesting approach for greater productivity of hazelnut.

Minor comments:

Line 18 16S rDNA because you have worked with DNA not RNA

Line 128 Add information to the methodology that the amplicons were sequenced with Illumina (Miseq?)

Figure 3 and 4,  if the x-axis is described by “Percent of community abundance…” then the scale should be 20, 40, 60,80, 100 rather than fractions up to 1

Figure S5 hard to read, poor quality

Line 400-… at this point of discussion it is worth reminding readers what the sample abbreviations mean (adden on first appearance also in the results and discussion sections)  The use of abbreviations (C. heterophylla (CH), C. kweichowensis (CK), C. avellane (CA), and C. heterophylla × C. avellane (CHA or CP).) seems more logical but maybe there were other reasons

Author Response

Dear Editors and Reviewers:

Thank you for your letter and for the reviewers’ comments concerning our manuscript entitled “Seasonal changes in soil microbial community and co-occurrence network of species of the genus Corylus” (microorganisms-1380492). Those comments are all valuable and very helpful for revising and improving our paper, as well as the important guiding significance to our researches. We have studied comments carefully and have made correction which we hope meet with approval. Revised portion are used the “Track Changes” function in the paper. The main corrections in the paper and the responds to the reviewer’s comments are as the attached file.

We tried our best to improve the manuscript and made some changes in the manuscript. These changes will not influence the content and framework of the paper. And here we did not list the changes but used the “Track Changes” function in revised paper.

We appreciate for Editors/Reviewers’ warm work earnestly, and hope that the correction will meet with approval.

Once again, thank you very much for your comments and suggestions.

Thank you and best regards.

Yours sincerely,
Corresponding author:
Tiantian Zhao
[email protected]

Author Response File: Author Response.pdf