Organic Farming Allows Balanced Fungal and Oomycetes Communities
Round 1
Reviewer 1 Report
The results of this article consist of three parts. The first part involves the collection of fungi and oomycetes from different cultivated soils. However, the number of strains obtained was very small, and there was a significant amount of repetition. The conclusion drawn by the authors that no fungi or oomycetes were collected from YCC or MPO, raising questions about the experimental procedure. Additionally, it is unclear what the purpose and significance of collecting cultivable strains of fungi and oomycetes in the first part of the results are. The second and third parts of the results compare the fungal and oomycetes communities in different cultivated soils, respectively. The analysis is somewhat dry and uninteresting, consisting mostly of simple comparisons between the relative abundances of different microbial groups. Overall, the results lack the necessary logical structure and fail to support the implications of the article's title.
Author Response
Comments from Reviewer 1
Question 1: The results of this article consist of three parts. The first part involves the collection of fungi and oomycetes from different cultivated soils. However, the number of strains obtained was very small, and there was a significant amount of repetition.
Answer 1: Thank you very much for your comments that were really relevant and helped us improve this manuscript. The authors have added detailed explanations about a filtering process to sort out fungal and oomycetes isolates to the part of materials and methods. After grouping the colonies by their cultural and morphologic characteristics, one or two representative isolates with different phenotypes were selected from each plate for DNA barcoding (114-121).
Q2: The conclusion drawn by the authors that no fungi or oomycetes were collected from YCC or MPO, raising questions about the experimental procedure.
A2: In this study, we discovered predominant taxa in YCC and MPO soil samples. The YCC farm soil was dominated by Globisporangium, an oomycete group. Its rapid growth may have hindered other taxa from thriving, resulting in no fungal isolates obtained from the YCC farm. Conversely, in the MPO farm soil, Linnemannia and Mortierella were unexpectedly dominant. These fast-growing genera are thought to suppress oomycete growth. Since culture-based approaches can be biased towards species that produce the most spores or grow the fastest, competitive species may cause misrepresentation. To address these potential biases, we supplemented our findings with next-generation sequencing (NGS) analysis.
Q3: Additionally, it is unclear what the purpose and significance of collecting cultivable strains of fungi and oomycetes in the first part of the results are.
A3: Although culture-based studies show limited diversity, these results complement culture-independent eDNA metabarcoding. In addition, the authors believe that the resources of fungal and oomycetes cultures obtained from the present study could contribute to their morphological, physiological, biochemical, and ecological characterization. We are planning to apply some beneficial strains to agriculture in the next study.
Q4: The second and third parts of the results compare the fungal and oomycetes communities in different cultivated soils, respectively. The analysis is somewhat dry and uninteresting, consisting mostly of simple comparisons between the relative abundances of different microbial groups. Overall, the results lack the necessary logical structure and fail to support the implications of the article's title.
A4: The community analysis section of our study was thoroughly revised to enhance our understanding of the differences in fungal and oomycetes communities between organic and conventional tomato farms. We have tried to present the results in an easily comprehensible manner, emphasizing the key findings. This community analysis aids in understanding the factors that govern the distribution and diversity of fungi and oomycetes in tomato farms and their subsequent effects on the environment. Microbial diversity is critical for the health and functioning of any ecosystem, as microbes significantly contribute to soil health, plant growth, and crop yield. The community analysis in the present study including the composition analysis and diversity evaluation of fungi and oomycetes provided relevant information for maintaining the sustainability of the ecosystem by reducing the use of chemical fertilizers and pesticide (204-227, 248-254, 275-281).
Reviewer 2 Report
The paper is well written, and the results are logical given the adequate methodologies used.
Comments for author File: 
Comments.pdf
Author Response
Answer: Thank you for reviewing our manuscript and agreeing with us on the intention of this manuscript.
Reviewer 3 Report
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General comments |
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The manuscript, presenting results of the study of fungi and oomycetes on tomato farms under different management practices (organic and conventional, mature and young) is very interesting for specialists in many fields, ranging from agronomy to soil microbiology. However, I believe the manuscript cannot be published in its current version due to some major drawbacks, namely a) not clear description of experimental design; b) not adequate discussion of the obtained results, and c) no data or reference to the yields, which makes all the statements about relatedness between fertility and fungal diversity unsubstantiated. |
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Line # |
Original |
Comment/suggestion |
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Major comments |
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50-52 |
However, many studies have revealed that organic farming can positively affect soil microbial communities. |
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94 |
five replicate plots (1 m apart) on each farm were sampled |
Does it mean that one farm has only MPO plots (5 replicates), the other farm only MIO, also five replicates, and so on? |
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173-174 |
No fungal isolates were found at the YCC farm. |
How do you explain it? It does seem strange, does it not? |
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207 |
inhabited only the organic farms… |
Here I got quite confused about how many organic farms/plots were studied? |
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236 |
on the MCC farms |
Here I got once again quite confused about how many MCC farms/plots were studied? |
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The Figure between 241-242 |
No Figure number (I assume it is Fig 2) and no proper caption. The rarefaction curves show different farms only: what about treatments/plots/replicates? |
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294 |
Soil from the mature pure organic farm had the highest fertility level. |
How can you prove it? Where are tables/references with tomato yields? |
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368-371 |
This study… provides essential information for future research to …replenish soil fertility... |
There is nothing in the paper about fertility per se, i.e. the ability to produce crop yields. Therefore the statements about fertility on the studied farms are totally unsubstantiated. |
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Minor comments |
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95 |
farm |
Farm or plot? Please, check, otherwise it is confusing. |
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322-323 |
Fusarium oxysporum and F. solani, which are the most common tomato wilt diseases |
Not diseases, but causing agents of the disease. Correct, please. |
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Technical comments |
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18 |
practises |
practiсes |
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23 |
eDNA |
Environmental DNA (it is the beginning of a sentence!) |
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101, 178, 185, 196, elsewhere |
Error! Reference source not found.. |
Check and correct, please. |
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171 |
fungal |
fungi |
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Comments for author File: Comments.pdf
Author Response
Comments from Reviewer 3
General comments: The manuscript, presenting results of the study of fungi and oomycetes on tomato farms under different management practices (organic and conventional, mature and young) is very interesting for specialists in many fields, ranging from agronomy to soil microbiology. However, I believe the manuscript cannot be published in its current version due to some major drawbacks, namely a) not clear description of experimental design; b) not adequate discussion of the obtained results, and c) no data or reference to the yields, which makes all the statements about relatedness between fertility and fungal diversity unsubstantiated.
Answer: We sincerely thank you for your insightful comments that have guided us in enhancing this manuscript. We've included further details in the materials and methods section to better explain the experimental design. Additionally, we've thoroughly revised the results and discussion sections to effectively present the key findings and ensure a comprehensive analysis. We have meticulously reviewed and rectified any unclear statements, including those concerning the relationship between fertility and fungal diversity.
Major comment 1
Original: However, many studies have revealed that organic farming can positively affect soil microbial communities (50-52)
Comment/suggestion: --
Answer: The authors have incorporated relevant references to substantiate this point within the manuscript (50-52).
Major comment 2
Original: five replicate plots (1 m apart) on each farm were sampled (94)
Comment/suggestion: Does it mean that one farm has only MPO plots (5 replicates), the other farm only MIO, also five replicates, and so on?
Answer: The authors collected five soil samples from each of four distinct farming practices, maintaining a 1 m distance between samples. To clarify the experimental design in detail, we have described it in materials and methods (93-99).
Major comment 3
Original: No fungal isolates were found at the YCC farm (173-174)
Comment/suggestion: How do you explain it? It does seem strange, does it not?
Answer: Thank you for your question. Soil from the YCC farm was dominated by Globisporangium spp. belonged to oomycetes. Globisporangium grew fast that might preclude other taxa from growing. Since the media will be dominated by the species that produces the largest number of spores or grows the fastest, a bias toward this competitive species can lead to a misrepresentation in culture-based approaches. Our culture-independent approach could overcome the underestimated diversity of the culture-based approaches alone.
Major comment 4
Original: inhabited only the organic farms… (207)
Comment/suggestion: Here I got quite confused about how many organic farms/plots were studied?
Answer: The authors have studied two organic farms, and five plots for each farm. The authors have improved the description about the experimental design (93-99).
Major comment 5
Original: on the MCC farms (236)
Comment/suggestion: Here I got once again quite confused about how many MCC farms/plots were studied?
Answer: See the above answer 4. The entire manuscript was generally revised to better understand, and we tried to make the text easy to read.
Major comment 6
Original: The Figure between 241-242
Comment/suggestion: No Figure number (I assume it is Fig 2) and no proper caption. The rarefaction curves show different farms only: what about treatments/plots/replicates?
Answer: We have carefully checked all figures and fixed all errors regarding all figures.
Major comment 7
Original: Soil from the mature pure organic farm had the highest fertility level (294)
Comment/suggestion: How can you prove it? Where are tables/references with tomato yields?
Answer: The authors agree that information about the level of mineral content, organic matter and carbon is insufficient to indicate soil fertility, without tomato yields. We have corrected all ambiguous statements about soil fertility and relatedness between fertility and fungal diversity (307-315).
Major comment 8
Original: This study… provides essential information for future research to …replenish soil fertility... (368-371)
Comment/suggestion: There is nothing in the paper about fertility per se, i.e. the ability to produce crop yields. Therefore, the statements about fertility on the studied farms are totally unsubstantiated.
Answer: The authors agree that further research is needed to provide certain information to replenish soil fertility. We have corrected all ambiguous statements about it (382-385).
Minor comment 1
Original: farm (95)
Comment/suggestion: Farm or plot? Please, check, otherwise it is confusing.
Answer: We have added detailed description to the part of materials and methods to clarify the experimental design (93-99).
Minor comment 2
Original: Fusarium oxysporum and F. solani, which are the most common tomato wilt diseases (322-323)
Comment/suggestion: Not diseases, but causing agents of the disease. Correct, please.
Answer: We have revised this sentence (338-339).
Technical comments 1
Original: practises (18)
Comment/suggestion: practices
Answer: We have corrected this (18).
Technical comments 2
Original: eDNA (23)
Comment/suggestion: Environmental DNA (it is the beginning of a sentence!)
Answer: Thank you for commenting this. We have added a full name for eDNA in the sentence where it was mentioned initially (17).
Technical comments 3
Original: Error! Reference source not found (101, 178, 185, 196, elsewhere)
Comment/suggestion: Check and correct, please.
Answer: We have carefully reviewed the table and all figures, rectifying all errors that resulted from technical issues.
Technical comments 4
Original: fungal (171)
Comment/suggestion: fungi
Answer: We have corrected this (178).
