A Two-Way Street: How Are Yeasts Impacted by Pesticides and How Can They Help Solve Agrochemical Contamination Problems?

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I have thoroughly reviewed the manuscript, and while it contains basic information available in the literature, it reads more like a book chapter rather than a review article. To strengthen it as a review, I recommend providing more in-depth information under various headings and subheadings.

The author should also include a section on the future perspectives of this work before the conclusion.

Introduction
The introduction is quite brief and lacks depth. I suggest adding more insights into the topic, supported by relevant data. Additionally, it would be helpful to provide a clear research gap that this review aims to address.

Methodology
The methodology section is missing. Please specify whether the author followed PRISMA or other guidelines for selecting the published articles reviewed in the manuscript.

Tables
The tables provided are basic, with limited data and insufficient citations. I recommend expanding the information in the tables and ensuring the captions clearly reflect their content.

Please consider adding a table in Section 5 that highlights the potential of yeasts in the bioremediation of pesticides.

Figures
In Figure 1, the bread-like structures representing roots with yeast presence should be labeled similarly to the other elements in the figure, explicitly mentioning the yeasts for clarity.

Specific Line Edits

• Line 63: The abbreviation for salicylic acid should be "SA," or if referring to the commercial form, it must be ASA (acetylsalicylic acid), not AS.
• Line 67: Provide more specific details about the changes in the soil environment.
• Line 82: Please include a reference for the claim made in this line.
• Line 92: The sentence "generating an increase of 80.31% and 50.90%" should be reconsidered for clarity.
• Line 160: "Secondary metabolites" would be more appropriate than "secondary compounds."
• Line 185: The sentence "or even survives within the gastric tract during periods when there is no flowering" is unclear and should be reworded for better explanation.
• Line 282: Please specify the name of the compound in the sentence "this last compound accumulates."

Citations
The citations between paragraphs are inconsistent. Please review and correct the citation format throughout the manuscript.

 

Author Response

"I have thoroughly reviewed the manuscript, and while it contains basic information available in the literature, it reads more like a book chapter rather than a review article. To strengthen it as a review, I recommend providing more in-depth information under various headings and subheadings."

Response We sincerely appreciate the reviewer's input on the manuscript. We believe that the manuscript has significantly improved due to the reviewer's comments.

 

"The author should also include a section on the future perspectives of this work before the conclusion."

Response: We thank the reviewer for this suggestion. The last section has been split. Challenges and avenues have been added before the conclusion.

 

"The methodology section is missing. Please specify whether the author followed PRISMA or other guidelines for selecting the published articles reviewed in the manuscript."

Response: Since our manuscript is a review, we preferred to add a paragraph at the end of the introduction outlining the procedure we used for the literature review rather than creating a new section titled "methodology".

 

"The tables provided are basic, with limited data and insufficient citations. I recommend expanding the information in the tables and ensuring the captions clearly reflect their content."

"Please consider adding a table in Section 5 that highlights the potential of yeasts in the bioremediation of pesticides."

Response: We thank the reviewer for these comments. All the tables have been improved, and an additional table was inserted in section 5.

 

"In Figure 1, the bread-like structures representing roots with yeast presence should be labeled similarly to the other elements in the figure, explicitly mentioning the yeasts for clarity."

Response: We agree with the reviewer; Figure 1 has been entirely redesigned.

 

"Line 63: The abbreviation for salicylic acid should be "SA," or if referring to the commercial form, it must be ASA (acetylsalicylic acid), not AS."

Response: The reviewer is right; we have now corrected the abbreviation.

 

"Line 67: Provide more specific details about the changes in the soil environment."

Response: We appreciate the reviewer's comment. Additional details have been added (please see lines 98–103 in the revised version).

 

"Line 82: Please include a reference for the claim made in this line."

Response: A reference has been properly included.

 

"Line 92: The sentence "generating an increase of 80.31% and 50.90%" should be reconsidered for clarity."

Response: The sentence has been rewritten (please see lines 129–130 in the revised version).

 

Line 160: "Secondary metabolites" would be more appropriate than "secondary compounds."

Response: The reviewer is correct; we have replaced the term "compounds" with "metabolites."

 

"Line 185: The sentence "or even survives within the gastric tract during periods when there is no flowering" is unclear and should be reworded for better explanation."

Response: The sentence has been rewritten (please see lines 224–225 in the revised version).

 

"Line 282: Please specify the name of the compound in the sentence 'this last compound accumulates.'"

Response: This paragraph has been rewritten, and the compound's name is now specified (please see line 320 in the revised version).

 

"The citations between paragraphs are inconsistent. Please review and correct the citation format throughout the manuscript."

Response: The citations have been revised throughout the manuscript.

Reviewer 2 Report

Comments and Suggestions for Authors

Manuscript ID: processes-3264321
"A two-way street: how are yeasts impacted by pesticides, and how can they help solve agrochemical contamination problems?"

The paper provides valuable insights into the effects of biopesticides on yeast and engineered yeast uses for the degradation of biopesticides via genetic Engineering techniques in improving sustainability in agriculture. However, I suggest the following major revisions before considering this manuscript for publication.

Please find below my comments:

-  Restructure the abstract to emphasize the implications of biopesticides on yeast and highlight the benefits of engineered yeast in addressing agrochemical challenges.

- The authors are suggested to include descriptions of the novelty and significance of the review in the introduction, which is currently too short and needs to be elaborated.

- The authors have not included the implications of biopesticides on yeast cells in the form of a table or figure. It is suggested that they include the information.

- The manuscript would benefit from a more comprehensive review of the literature. Add more recent references from 2022, 2023, and 2024 to strengthen the background and context of the present study.

 

 - The manuscript should be checked thoroughly for grammatical and typing mistakes. 

Comments on the Quality of English Language

Overall the manuscript requires major English language correction in expressing research scientifically.

Author Response

"The paper provides valuable insights into the effects of biopesticides on yeast and engineered yeast uses for the degradation of biopesticides via genetic Engineering techniques in improving sustainability in agriculture. However, I suggest the following major revisions before considering this manuscript for publication."

Response: We sincerely appreciate the reviewer's input on the manuscript. We believe that the manuscript has significantly improved due to the reviewer's comments.

 

"Restructure the abstract to emphasize the implications of biopesticides on yeast and highlight the benefits of engineered yeast in addressing agrochemical challenges."

Response: The reviewer is right; the abstract has been improved.

 

"The authors are suggested to include descriptions of the novelty and significance of the review in the introduction, which is currently too short and needs to be elaborated."

Response: The reviewer is correct; the introduction has been improved.

 

"The authors have not included the implications of biopesticides on yeast cells in the form of a table or figure. It is suggested that they include the information."

Response: We thank the reviewer for this comment. A new figure has been included in the manuscript in this regard.

 

"The manuscript would benefit from a more comprehensive review of the literature. Add more recent references from 2022, 2023, and 2024 to strengthen the background and context of the present study."

Response: We believe the relevant recent references have already been addressed.

 

"The manuscript should be checked thoroughly for grammatical and typing mistakes."

Response: We appreciate the reviewer's comment. The manuscript has been completely proofread for English language accuracy. All changes made to the text are highlighted in red.

Reviewer 3 Report

Comments and Suggestions for Authors

This manuscript entitled "A two-way street: how are yeasts impacted by pesticides, and how can they help solve agrochemical contamination problems?", focuses on the dual role that yeasts play in agriculture, particularly their interactions with pesticides. It explores how yeasts are affected by pesticide use and also how these microorganisms can be utilized to remediate soils contaminated by agrochemicals. The review covers various yeast species that not only support plant growth but also contribute to the breakdown of harmful substances in the environment. Additionally, the paper touches on the potential of genetically engineered yeasts to enhance these bioremediation processes.

Strengths

1. Relevance and Timeliness:

The topic of pesticide contamination and bioremediation is highly relevant, particularly in the context of sustainable agriculture. This paper takes a novel approach by focusing on yeasts, an often-overlooked group of microorganisms, to address environmental challenges. The dual role of yeasts as both impacted by and beneficial for managing agrochemical contamination makes this review innovative.

2. Comprehensive Literature Review:

The authors do an excellent job of reviewing the current state of research. They cite a broad range of studies, which strengthens the scientific foundation of their arguments. The paper dives deep into the ecological and biochemical roles of yeasts, offering insights that are well-supported by existing literature.

3. Detailed Discussion of Biochemical Pathways:

The discussion of yeast metabolism, particularly concerning plant growth promotion and pesticide degradation, is thorough. The authors explain the biochemical pathways involved, adding a valuable technical dimension to the review. Readers will appreciate this level of detail with a background in biochemistry or microbiology.

4. Potential for Real-World Application:

The paper goes beyond theoretical concepts, suggesting practical applications for using yeasts in organic agriculture and bioremediation. This makes it highly relevant for industry stakeholders as well as academic researchers.

Areas for Improvement

1. Clarity and Readability:

   - Abstract: While the abstract provides a good summary, it could be made more concise. Simplifying the language and directly stating the main conclusions would make it more accessible.

   - Flow of Information: The sections on pesticide impacts and yeast bioremediation could be structured better for clarity. Breaking them into smaller, clearly titled subsections might help guide the reader through the complex concepts being discussed.

 

2. Emphasis on Practical Applications: Although the review includes real-world applications, it could benefit from a stronger emphasis on how these yeast-based bioremediation strategies can be implemented in practice. Discussing the logistical challenges of using yeasts on a large scale, including costs and potential obstacles, would provide a more comprehensive picture.

3. Addressing Research Gaps: The paper could more explicitly point out where gaps in current research exist. While it does a good job reviewing what has been done, highlighting specific areas that need further study would be a useful addition. This could guide future research and spark interest among readers in investigating these gaps.

Technical and Terminology Suggestions

- Some of the more technical terms could be explained for readers who may not have an extensive background in molecular biology or biochemistry. Simplifying the language in certain parts would make the paper more accessible to a broader audience.

- The section on genetic engineering is particularly dense and would benefit from a brief explanation of the techniques mentioned, such as CRISPR. This would help readers unfamiliar with these concepts to better understand the implications of using genetically engineered yeasts for bioremediation.

Conclusion and Future Directions

Overall, this review provides a valuable and comprehensive examination of how yeasts can both be affected by and help mitigate the environmental impacts of pesticides. Its detailed exploration of biochemical pathways and real-world applications is commendable. However, with minor improvements in clarity, structure, and practical focus, the paper could become more widely accessible and impactful, reaching both academic and industry audiences.

Language and Style Review:

Many sentences are quite long and dense, which can make the article difficult to read. Breaking down complex sentences into simpler, more direct ones would improve clarity. For example:

Page 7, lines 228-232. Rewrite "The repeated use of products ....." as "Repeated use of products with similar mechanisms of action leads to resistance in target organisms. As a result, these pathogens are no longer affected by the chemicals, rendering them ineffective. This also harms beneficial organisms, leaving crops vulnerable to resistant pathogens."

Page 9, lines 332-334. Revise "The degradation of 2,4-D involves different...." as "Different metabolic pathways degrade 2,4-D. Most bacteria start by cleaving the side chain, whereas fungi typically use hydroxylation of the aromatic ring."

The transitions between sections and ideas could be smoother. At times, the article jumps from one topic to another without sufficient transition, making it harder to follow the logical flow. For instance, the shift from discussing the negative impacts of pesticides on yeast to yeast’s role in bioremediation could use a clearer transition.

- Suggested Transition: "While pesticides pose significant challenges to yeast populations, these microorganisms also have a remarkable ability to adapt and mitigate environmental damage. In the next section, we explore the potential of yeasts as bioremediation of contaminated soils."

Figures are used in the article but could be better integrated into the text. Referencing figures explicitly and explaining their significance in the context of the discussion would help readers understand their purpose. For example, Figure 1 could be introduced like this:

"As shown in Figure 1, yeasts provide various ecological services in the soil, including nutrient cycling and pathogen suppression."

There are a few minor grammatical issues that should be addressed, such as misplaced commas and missing articles. Here are a few examples:

Page 2, lines 48-50. Revised "Yeasts also play ...." as "Yeasts also play a prominent role in nutrient cycling (biogeochemical cycles) and contribute significantly to the digestive and immune systems of herbivores, pollinivores, and nectarivores.

 

Page 9, lines 339-341. Revise "These enzymatic processes ...." as "These enzymatic processes and their resulting metabolites are crucial for understanding and optimizing the bioremediation of herbicide-contaminated environments."

Comments on the Quality of English Language

The quality of English will be better after minor revisions.

Author Response

"This manuscript entitled 'A two-way street: how are yeasts impacted by pesticides, and how can they help solve agrochemical contamination problems?', focuses on the dual role that yeasts play in agriculture, particularly their interactions with pesticides. It explores how yeasts are affected by pesticide use and also how these microorganisms can be utilized to remediate soils contaminated by agrochemicals. The review covers various yeast species that not only support plant growth but also contribute to the breakdown of harmful substances in the environment. Additionally, the paper touches on the potential of genetically engineered yeasts to enhance these bioremediation processes."

Response: We are deeply thankful for the reviewer's comments and suggestions to the manuscript. The reviewer was very thoughtful in pointing out the strengths of our manuscript (which we are not reproducing in this response letter). We believe that the manuscript has significantly improved thanks to the reviewer's suggestions.

 

"Abstract: While the abstract provides a good summary, it could be made more concise. Simplifying the language and directly stating the main conclusions would make it more accessible."

Response: The abstract has been improved.

 

"Flow of Information: The sections on pesticide impacts and yeast bioremediation could be structured better for clarity. Breaking them into smaller, clearly titled subsections might help guide the reader through the complex concepts being discussed."

Response: The manuscript has been substantially modified according to suggestions from three reviewers. We thus believe that new subheadings would no longer be necessary.

 

"Emphasis on Practical Applications: Although the review includes real-world applications, it could benefit from a stronger emphasis on how these yeast-based bioremediation strategies can be implemented in practice. Discussing the logistical challenges of using yeasts on a large scale, including costs and potential obstacles, would provide a more comprehensive picture."

Response: We agree with the reviewer's comment; these challenges have now been addressed (please see lines 599–608 in the revised version).

 

"Addressing Research Gaps: The paper could more explicitly point out where gaps in current research exist. While it does a good job reviewing what has been done, highlighting specific areas that need further study would be a useful addition. This could guide future research and spark interest among readers in investigating these gaps."

Response: We agree with the reviewer's comment; these research gaps have now been addressed (please see lines 588–598 in the revised version).

 

"Technical and Terminology Suggestions

- Some of the more technical terms could be explained for readers who may not have an extensive background in molecular biology or biochemistry. Simplifying the language in certain parts would make the paper more accessible to a broader audience.

- The section on genetic engineering is particularly dense and would benefit from a brief explanation of the techniques mentioned, such as CRISPR. This would help readers unfamiliar with these concepts to better understand the implications of using genetically engineered yeasts for bioremediation."

Response: The reviewer is correct; the revised version of the manuscript has these points clarified (please see lines 494–508 in the revised version).

 

"Overall, this review provides a valuable and comprehensive examination of how yeasts can both be affected by and help mitigate the environmental impacts of pesticides. Its detailed exploration of biochemical pathways and real-world applications is commendable. However, with minor improvements in clarity, structure, and practical focus, the paper could become more widely accessible and impactful, reaching both academic and industry audiences."

Response: We sincerely appreciate the reviewer's comments.

 

"Many sentences are quite long and dense, which can make the article difficult to read. Breaking down complex sentences into simpler, more direct ones would improve clarity."

Response: We agree with the reviewer. The manuscript has been completely proofread for English language accuracy. All changes made to the text are highlighted in red.

 

"Page 7, lines 228-232. Rewrite 'The repeated use of products .....' as 'Repeated use of products with similar mechanisms of action leads to resistance in target organisms. As a result, these pathogens are no longer affected by the chemicals, rendering them ineffective. This also harms beneficial organisms, leaving crops vulnerable to resistant pathogens.'"

Response: The paragraph has been rewritten accordingly (please see lines 267–270 in the revised version).

 

"Page 9, lines 332-334. Revise 'The degradation of 2,4-D involves different....' as 'Different metabolic pathways degrade 2,4-D. Most bacteria start by cleaving the side chain, whereas fungi typically use hydroxylation of the aromatic ring.'"

Response: The sentences have been rewritten accordingly (please see lines 388–389 in the revised version).

 

"The transitions between sections and ideas could be smoother. At times, the article jumps from one topic to another without sufficient transition, making it harder to follow the logical flow. For instance, the shift from discussing the negative impacts of pesticides on yeast to yeast’s role in bioremediation could use a clearer transition.

- Suggested Transition: 'While pesticides pose significant challenges to yeast populations, these microorganisms also have a remarkable ability to adapt and mitigate environmental damage. In the next section, we explore the potential of yeasts as bioremediation of contaminated soils.'"

Response: We appreciate the reviewer's suggestion; it has been included in the revised version of the manuscript. Similarly, we have added another paragraph for the transition between sections 3 and 4.

 

"Figures are used in the article but could be better integrated into the text. Referencing figures explicitly and explaining their significance in the context of the discussion would help readers understand their purpose. For example, Figure 1 could be introduced like this: 'As shown in Figure 1, yeasts provide various ecological services in the soil, including nutrient cycling and pathogen suppression.'"

Response: We appreciate the reviewer's comment. We believe the issue raised does not apply to every figure. For Figure 1, we have included a sentence similar to the one suggested by the reviewer (see lines 88–89 in the revised version). We have also added an introductory sentence for Figure 4 (Figure 5 in the revised version, see lines 558–559).

 

"There are a few minor grammatical issues that should be addressed, such as misplaced commas and missing articles."

Response: The manuscript has been completely proofread for English language accuracy. All changes made to the text are highlighted in red.

 

"Page 2, lines 48-50. Revised 'Yeasts also play ....' as 'Yeasts also play a prominent role in nutrient cycling (biogeochemical cycles) and contribute significantly to the digestive and immune systems of herbivores, pollinivores, and nectarivores.'"

Response: We couldn't understand the reviewer's comment. That is how it is written. Moreover, the English proofreading didn't detect any problem with this sentence.

 

"Page 9, lines 339-341. Revise 'These enzymatic processes ....' as 'These enzymatic processes and their resulting metabolites are crucial for understanding and optimizing the bioremediation of herbicide-contaminated environments.'"

Response: This sentence has been rewritten through the English proofreading process (please see lines 395–396 in the revised version).

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Authors have incorporated all the suggestions.

Comments on the Quality of English Language

Use premium software to improve the English.

Author Response

"Authors have incorporated all the suggestions."

Response We sincerely appreciate the reviewer's input on the manuscript. We believe that the manuscript has significantly improved due to the reviewer's comments.

"Use premium software to improve the English."

Response: In revision 1 (R1), our manuscript was kindly proofread by a native English-speaking colleague who suggested several changes, which are highlighted in red in R1. Anyway, we have now analyzed the manuscript using Grammarly with a premium subscription plan. The last changes made are highlighted in blue (in R2).

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have uploaded the response to the reviewer's document, but they have not uploaded the revised manuscript file. The manuscript Version-1 and version-2 documents (i.e., revised manuscript) are the same.

- Update the manuscript with recent references (i.e., 2022, 2023, and 2024) to provide more insights into the current work.

Comments on the Quality of English Language

Still, the manuscript needs to be checked thoroughly for grammatical and typing mistakes.

Author Response

"The authors have uploaded the response to the reviewer's document, but they have not uploaded the revised manuscript file. The manuscript Version-1 and version-2 documents (i.e., revised manuscript) are the same."

Response: Actually, we, the authors, uploaded the correct revised version. We do not know what may have happened. However, the reviewer can now see the changes made to the manuscript: revisions marked in red refer to revision 1, and those in blue indicate revision 2.

"Update the manuscript with recent references (i.e., 2022, 2023, and 2024) to provide more insights into the current work."

Response: During revision 1, we added 27 new references to the manuscript. We believe we covered all the significant references to the aim of our review.

"Still, the manuscript needs to be checked thoroughly for grammatical and typing mistakes."

Response: In revision 1 (R1), our manuscript was kindly proofread by a native English-speaking colleague who suggested several changes, which are highlighted in red in R1. Additionally, following reviewer #1's recommendation, we have now analyzed the manuscript using the software Grammarly with a premium subscription plan. The last changes made are highlighted in blue (in R2).

Round 3

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have addressed the comments very well.