Rhizospheric Fungal Diversities and Soil Biochemical Factors of Fritillaria taipaiensis over Five Cultivation Years
Round 1
Reviewer 1 Report
I have reviewed the manuscript entitled, “Rhizospheric fungal diversities and soil bio-chemical factors of Fritillaria taipaiensis over five cultivation years”. The manuscript is well organized and well written. It presents an important aspect of evaluation of dynamics and change of soil factors and microbial communities over the years, which affect the growth of Fritillaria taipaiensis. The introduction is well set and presents the aim of the manuscript well. The results are well presented and finely discussed. The only problem that I could find is that the manuscript has many grammatical mistakes, some sentences need to be refined for better understanding, and at places a better word choice would significantly improve the manuscript. Please find my comments in the .pdf file attached
Comments for author File: 
Comments.pdf
Author Response
Dear Reviewer:
Thank you for your letter and for the comments concerning our manuscript entitled “Rhizospheric fungal diversities and soil biochemical factors of Fritillaria taipaiensis over five cultivation years” . 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 marked in the paper. The main corrections in the paper and the responds to the editor and reviewer’s comments are as flowing:
Reviewer #1: I have reviewed the manuscript entitled, “Rhizospheric fungal diversities and soil bio-chemical factors of Fritillaria taipaiensis over five cultivation years”. The manuscript is well organized and well written. It presents an important aspect of evaluation of dynamics and change of soil factors and microbial communities over the years, which affect the growth of Fritillaria taipaiensis. The introduction is well set and presents the aim of the manuscript well. The results are well presented and finely discussed. The only problem that I could find is that the manuscript has many grammatical mistakes, some sentences need to be refined for better understanding, and at places a better word choice would significantly improve the manuscript. Please find my comments in the .pdf file attached.
Response: Thank you very much for your valuable suggestion. We have revised the manuscript carefully and invited a native English speaker to improve the language expression. In addition, we made some other revisions in the article, please find them in the revised version.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Line 27: ... in the family Liliaceae
Line 28: which can decrease body temperature in humans
Line 31: italicize F. taipaiensis
Line 32: What is "Pharmacopoie"? Please use a word that everyone knows
Line 38: "might post"? What does it mean? Choose another verb
Line 40: "positively/negatively affect its production." Add the appropriate one (positively or negatively).
Lines 52-55: Delete "Thus" and split up the single sentence into at least 2 sentences, clearly defining the goals in one sentence and background info in another one.
Line 58: "Sampling was conducted in Lanying Village, ..."
Line 64: Delete "the" in front of F. taipaiensis
Line 78 (and everywhere else throughout the manuscript, including the title): "biochemical" is one word! Please change throughout the manuscript.
Line 97: Do not start the sentence with an abbreviation!
Line 102: ITS stands for the internal transcribed spacer fungal barcode region. Please fix!
Lines 101-102: Please cite the papers in which these primers were originally developed.
Lines 110-111: This is very confusingly written. Simplify as follows: "Raw forward and reverse sequence reads were assembled using FLASH ..."
Line 112-113: Remove "after removed the Barcode sequence and PCR amplification primer sequence to obtain the Raw date"
Lines 113, 114, 116, elsewhere: Raw "date", Clean "date" -> data are always plural. Please change to Raw "data" and Clean "data" throughout.
Line 119: "Operational Taxonomic Units (OTUs) were assigned and clustered..."
Lines 134-135: What was the purpose of the "single factor (one-way ANOVA) and Duncan for variance analysis and multiple comparisons"? Please write down WHY these analyses were done. Should be something like: "To study the difference among ....., we applied the following statistical methods ..."
Lines 189, 190, and elsewhere: Taxon names should not be preced by "the". Please change where necessary.
So: "The dominant fungal phylum, with a maximum relative abundance of up to 68.23%, was Ascomycota."
I suggest a change in that same statement, because it can be presented better: "The dominant fungal phylum, with a maximum relative abundance of up to 68.23%, was Ascomycota, whereas the relative abundance of Chytridiomycota ranged between 11.12% in Y1 190 and 0.69% in Y3 (Table 2)."
Lines 215-231: Genus names must be italicized. Please check and change where necessary throughout the manuscript.
In general, I would also like to know what is the "core community" of the rhizosphere and whether this "core community" is more stable than the total fungal community. See these papers for a discussion on core communities: https://doi.org/10.3390/jof7040277 and https://doi.org/10.1016/j.funeco.2015.05.007. In our work, we have found that total community and core community are two different things, and there are some interesting aspects that can be pulled out from the core communities, especially if there are larger similarities among different years.
I would like to see subtitles in the Discussion, to guide the reader through. It is currently difficult to follow the discussion of this manuscript, and be able to understand its significance.
Consider citing the following papers on rhizosphere fungi and the impact of environmental variables, including soil depth, which I don't believe was considered here. These papers are on other systems, but may be helpful in the general Introduction and Discussion sections.
https://doi.org/10.1007/s11104-009-9991-3
https://doi.org/10.1038/ismej.2008.87
https://doi.org/10.1016/j.envpol.2017.11.037
https://doi.org/10.1038/s41598-019-43110-z
Finally, please have the manuscript carefully revised throughout by an English-native speaker. I started making some edits but it's not my job as a reviewer to provide feedback on the English writing, but it has to be improved at this stage before the manuscript is ready for publication.
Author Response
Dear Reviewer:
Thank you for your letter and for the comments concerning our manuscript entitled “Rhizospheric fungal diversities and soil biochemical factors of Fritillaria taipaiensis over five cultivation years” . 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 marked in the paper. The main corrections in the paper and the responds to the editor and reviewer’s comments are as flowing:
Reviewer #2:
- Line 27: ... in the family Liliaceae
Response: We have made the correction according to the reviewer’s advise to add a “family” before the “Liliaceae” (1. Introduction, L30).
- Line 28: which can decrease body temperature in humans
Response: We have made the correction according to the reviewer’s advise to replace that part with “which can decrease body temperature in humans” (1. Introduction, L32).
- Line 31: italicize F. taipaiensis
Response: We have made the correction according to the reviewer’s advise to italicize F. taipaiensis (1. Introduction, L34).
- Line 32: What is "Pharmacopoie"? Please use a word that everyone knows
Response: Pharmacopoeia of the People’s Republic of China is a national standard for traditional Chinese medicine, here we replaced the word “Pharmacopoie” with “a national standard for traditional Chinese medicine” according to the reviewer’s advise (1. Introduction, L35-36).
- Line 38: "might post"? What does it mean? Choose another verb
Response: We have made the correction according to the reviewer’s advise to replace the word “post” with “appear” (1. Introduction, L42).
- Line 40: "positively/negatively affect its production." Add the appropriate one (positively or negatively).
Response: We are very sorry for the unclear expression, the germplasm degradation can negatively affect the production of F. taipaiensis (1. Introduction, L43).
- Lines 52-55: Delete "Thus" and split up the single sentence into at least 2 sentences, clearly defining the goals in one sentence and background info in another one.
Response: We have made the correction according to the reviewer’s advise (1. Introduction, L54-57).
- Line 58: "Sampling was conducted in Lanying Village, ..."
Response: We have made the correction according to the reviewer’s advise (2.1 Experimental Site location, L60).
- Line 64: Delete "the" in front of F. taipaiensis
Response: We have made the correction according to the reviewer’s advise (2.1 Experimental Site location, L64).
- Line 78 (and everywhere else throughout the manuscript, including the title): "biochemical" is one word! Please change throughout the manuscript.
Response: We have made the correction according to the reviewer’s advise to replace “bio-chemical” with “biochemical” throughout the manuscript.
- Line 97: Do not start the sentence with an abbreviation!
Response: We are very sorry for our negligence, We have made the correction according to the reviewer’s advise (2.4 Soil DNA Extraction and High-throughput Sequencing, L89).
- Line 102: ITS stands for the internal transcribed spacer fungal barcode region. Please fix!
Response: We are very sorry for our negligence, we have made the correction according to the reviewer’s advise (2.4 Soil DNA Extraction and High-throughput Sequencing, L92-93).
- Lines 101-102: Please cite the papers in which these primers were originally developed.
Response: We are very sorry for our negligence, we have made the correction according to the reviewer’s advise (2.4 Soil DNA Extraction and High-throughput Sequencing, L93; Reference [17]).
- Lines 110-111: This is very confusingly written. Simplify as follows: "Raw forward and reverse sequence reads were assembled using FLASH ..."
Response: We have made the correction according to the reviewer’s advise to simplify it as “Raw forward and reverse sequence reads were assembled using FLASH ...” (2.5 Data Analysis, L99).
- Line 112-113: Remove "after removed the Barcode sequence and PCR amplification primer sequence to obtain the Raw date"
Response: We have made the correction according to the reviewer’s advise to remove that part (2.5 Data Analysis).
- Lines 113, 114, 116, elsewhere: Raw "date", Clean "date" -> data are always plural. Please change to Raw "data" and Clean "data" throughout.
Response: We have made the correction according to the reviewer’s advise to remove that part (2.5 Data Analysis, L101).
- Line 119: "Operational Taxonomic Units (OTUs) were assigned and clustered..."
Response: We have made the correction according to the reviewer’s advise to replace that part with (2.5 Data Analysis, L103-104).
- Lines 134-135: What was the purpose of the "single factor (one-way ANOVA) and Duncan for variance analysis and multiple comparisons"? Please write down WHY these analyses were done. Should be something like: "To study the difference among ....., we applied the following statistical methods ..."
Response: We are very sorry for the unclear expression, we have made the correction according to the reviewer’s advice. To study the difference among the alpha diversity indices, fungal taxonomic compositions, soil biochemical factors in the F. taipaiensis rhizospheric soils with different cultivation years and the effect of cultivation year on the core community, we applied the one-way ANOVA and the Duncan for variance analysis and multiple comparisons via SPSS 22.0 and Excel 2003 (α=0.05). (2.5 Data Analysis, L114-117)
- Lines 189, 190, and elsewhere: Taxon names should not be preced by "the". Please change where necessary. So: "The dominant fungal phylum, with a maximum relative abundance of up to 68.23%, was Ascomycota." I suggest a change in that same statement, because it can be presented better: "The dominant fungal phylum, with a maximum relative abundance of up to 68.23%, was Ascomycota, whereas the relative abundance of Chytridiomycota ranged between 11.12% in Y1 190 and 0.69% in Y3 (Table 2)."
Reponse: We have made the correction according to the reviewer’s advise to remove “the” before the taxon names throughout the manuscript.
- Lines 215-231: Genus names must be italicized. Please check and change where necessary throughout the manuscript.
Response: We have made correction according to the reviewer’s advice to italicize genus names throughout the manuscript. But the italicized genus names may not be showed when the Word file convert into PDF.
- In general, I would also like to know what is the "core community" of the rhizosphere and whether this "core community" is more stable than the total fungal community. See these papers for a discussion on core communities: https://doi.org/10.3390/jof7040277 and https://doi.org/10.1016/j.funeco.2015.05.007. In our work, we have found that total community and core community are two different things, and there are some interesting aspects that can be pulled out from the core communities, especially if there are larger similarities among different years.
Response: Thank you for your your valuable comments. We checked the 181 common OTUs shared by the samples with different cultivation year and found 13 genera (Pseudogymnoascus, Fusarium, Mortierella, Colletotrichum, Laetinaevia, Gibberella, Synchytrium, Lysurus, Trichocladium, Volutella, Monoblepharis, Aquamyces and Trichoderma) in the genera with the top 20 relative abundance exist in all the samples. These 13 genera could be considered as the core community in the F. taipaiensis rhizosphere. For the core community, the effect of cultivation year on the number of OTUs was not significant (t = 2.384, p = 0.121). (3.2 Fungal Taxonomic Composition, L207-212; Table S1)
- I would like to see subtitles in the Discussion, to guide the reader through. It is currently difficult to follow the discussion of this manuscript, and be able to understand its significance.
Response: We have made correction according to the reviewer’s advice to add subtitles to the Discussion.
- Consider citing the following papers on rhizosphere fungi and the impact of environmental variables, including soil depth, which I don't believe was considered here. These papers are on other systems, but may be helpful in the general Introduction and Discussion sections.
https://doi.org/10.1007/s11104-009-9991-3
https://doi.org/10.1038/ismej.2008.87
https://doi.org/10.1016/j.envpol.2017.11.037
https://doi.org/10.1038/s41598-019-43110-z
Response: Thank you for your your valuable comments. We cited these papers in the Discussion to discuss the effect of cultivation years on the biochemical factors (4.3 Analysis on the Effect of Cultivation Years on the Biochemical Factors in the F. taipaiensis rhizosphere, L381-383; References [58-61]).
- Finally, please have the manuscript carefully revised throughout by an English-native speaker. I started making some edits but it's not my job as a reviewer to provide feedback on the English writing, but it has to be improved at this stage before the manuscript is ready for publication.
Response: Thank you for you valuable advice. We have revised the manuscript carefully and invited a native English speaker to improve the language expression.
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
I appreciate the efforts that the authors put in to improve the manuscript.
