Plant–Soil Microbial Interaction: Differential Adaptations of Beneficial vs. Pathogenic Bacterial and Fungal Communities to Climate-Induced Drought

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This paper highlights key information regarding the adaptation of microbial communities in soil during drought stress. Furthermore, it provides knowledge on the effects of such adaptive responses to the plants. The authors have done a very comprehensive study and compiled relevant information. However, the flow of information is confusing with a lot of redundancies. The paper feels like a jumbled mess of good information without a definitive flow. This confuses the readers. Please reorganize so that there is good flow to show what has been studied and how that applies to the statements made in the conclusion.

Major comments:

The flow of the introduction and most of the paragraphs is not clear. For example: Line 650 to 652 & 703 – 705 Repetitive information; needs reorganization to make the flow of information appropriate.

The topic: “Microbial community structure affected by drought”, does not contain sufficient information about the bacterial communities using 16S rRNA gene-based comparisons.

The figures are not of a good standard. The authors should consider compiling data from reviewed papers to show comparisons in different experimental or environmental conditions. Such as comparison of gene expression or microbial abundances.

Minor comments:

Line 52 “?” is not required. The statement is bold and comprehensive, therefore, instead of citing another review article, it is suggested that the authors find original papers leading to those conclusions within that article or another article.

Line 119: “This paper addresses several critical aspect”: The wording is inappropriate. The paper reviews those aspects instead of providing a solution.

Line 178: The conclusion “in the rhizosphere zone, drought enhances the fungal microbiota by suppressing virus and algal populations” was derived from a study in the chickpea fields. Please, specific the results instead of generalizing them.

Line 255: “PGPR for short” is not necessary. Adding letters in parentheses should suffice.

Line 332: What are the values in the parentheses?

Line 406 to 410: “Each study emphasizes the flexibility of AMF communities in adapting to water stress and discusses the potential effects of drought on plant-mycorrhizal associations under changing climatic conditions. Changes in AMF communities, especially those involved in nitrogen (N) and phosphorus (P) cycling, can negatively affect other beneficial microbial taxa, which may ultimately lead to the degradation of some ecosystems”: There is an inappropriate direct generalization for the research in controlled conditions with climatic conditions. Rephrase the sentences to show a proper correlation with the sentences above.

Comments on the Quality of English Language

The sentences are clear and easy to read. However, the manuscript lacks a proper organization causing the flow of information to be confusing.

Author Response

Reviewer 1

This paper highlights key information regarding the adaptation of microbial communities in soil during drought stress. Furthermore, it provides knowledge on the effects of such adaptive responses on plants. The authors have done a very comprehensive study and compiled relevant information. However, the flow of information is confusing, with a lot of redundancies. The paper feels like a jumbled mess of good information without a definitive flow. This confuses the readers. Please reorganize so that there is good flow to show what has been studied and how that applies to the statements made in the conclusion.

 

Thank you for the observation. We have reduced the length of the review and changed its structure to make it more understandable.

 

Major comments:

The flow of the introduction and most of the paragraphs is not clear. For example: Line 650 to 652 & 703 – 705 Repetitive information; needs reorganization to make the flow of information appropriate.

We completely redesigned the introduction, shortened some paragraphs and structured the rest. We removed repetitive information.

 

The topic: “Microbial community structure affected by drought”, does not contain sufficient information about the bacterial communities using 16S rRNA gene-based comparisons.

 

We considered this topic as an introductory one, designed to highlight the most general information on the subject, so we did not "weight" this paragraph with additional details related to genetics.

 

The figures are not of a good standard. The authors should consider compiling data from reviewed papers to show comparisons in different experimental or environmental conditions. Such as comparison of gene expression or microbial abundances.

We've revised and improved the contents and quality of all three figures.

 

Minor comments:

Line 52 “?” is not required. The statement is bold and comprehensive, therefore, instead of citing another review article, it is suggested that the authors find original papers leading to those conclusions within that article or another article.

 

We have completely rewritten the introduction, removing this statement.

 

Line 119: “This paper addresses several critical aspect”: The wording is inappropriate. The paper reviews those aspects instead of providing a solution.

 

We have changed the wording of that phrase.

Line 178: The conclusion “in the rhizosphere zone, drought enhances the fungal microbiota by suppressing virus and algal populations” was derived from a study in the chickpea fields. Please, specific the results instead of generalizing them.

We have added a clarification to this sentence regarding "chickpeas".

 

Line 255: “PGPR for short” is not necessary. Adding letters in parentheses should suffice.

Thank you for the comment, we have removed that section.

 

Line 332: What are the values in the parentheses?

 

We removed the unnecessary values in brackets, now it's clearer.

 

Line 406 to 410: “Each study emphasizes the flexibility of AMF communities in adapting to water stress and discusses the potential effects of drought on plant-mycorrhizal associations under changing climatic conditions. Changes in AMF communities, especially those involved in nitrogen (N) and phosphorus (P) cycling, can negatively affect other beneficial microbial taxa, which may ultimately lead to the degradation of some ecosystems”: There is an inappropriate direct generalization for the research in controlled conditions with climatic conditions. Rephrase the sentences to show a proper correlation with the sentences above.

 

We have removed this phrase completely and written a new conclusion to this section.

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript provides a comprehensive review of the response mechanisms and patterns of interactions among bacteria, fungi, and pathogens to drought stress in soil-plant systems, The manuscript is very informative and well-written. I think it can be published in this journal after revision. However, the manuscript as a whole is too long. It will take a long time to finish reading it, and some sentences are too long and difficult to understand. I suggest that the author needs to further concisely improve some of its contents. Please refer to specific comments:

1.      Line 160: Many literatures categorize Actinobacteria phylum as copiotrophic bacteria rather than oligotrophic bacteria, so there may be controversy here

2.      Line 188-189: Here you mention that several environmental factors can also modulate bacterial response strategies to drought, such as soil composition, pH, and presence of heavy metals, but these environmental factors are not further described later in the article, so I would suggest that you add a description of them.

3.      Line 198-218: These two paragraphs are mainly descriptions of bacteria in the rhizosphere, which are not very relevant to the title of section 2.1, and it is suggested that this section should be transferred to section 2.2.

4.      Line 261-264, Line 266-268: These two parts of the sentence seem to contradict each other.

5.      Line 273: Section 3.0 is too long and many of the subsections could be streamlined appropriately and then merged.

6.      Line 282: Please make sure that the term "gene expression" is used correctly, as only RNA-based transcriptomics analyses are allowed to use this term.

7.      Line 288-302: You gave a lot of examples of gene expression in this section, but what do these changes in gene expression indicate?

8.      Line 342-356: Here you have listed several strains of bacteria that have been reported to be drought tolerant, but through your investigation, can you identify any similarities or patterns in these bacteria? For example, do they mainly belong to a particular bacterial phylum? or family?

9.      Line 376: “stress gene expression”, Please specify which genes and what are their functions.

10.   Line 381: What is “AMPs”? Is it AMF?

11.   Line 412-434: You mentioned the “Distinct adaptation strategies” in the title of section 3.5, but, the subsequent paragraphs seem to emphasize the similarities without specifying what the " distinct" are.

12.   In section 3.6 you emphasize "Distinct adaptive strategies", but by reading later I don't see "distinct" adaptive strategies for pathogenic bacteria, which seem to be similar to those in section 3.5 for rhizosphere bacteria and AMF. I think you should focus more on whether pathogenic bacteria are still pathogenic under drought conditions. Are their interactions with beneficial bacteria and plants affected by drought stress? When beneficial and pathogenic bacteria coexist, which one is more likely to survive drought stress?

13.   Line 562: What is “PGPBs”? Is it PGPR?

14.   Line 593: What does the “EPSs” mean? You should explain the abbreviations when first mentioned.

15.   Line 621-622: What are the types of these metabolites? What about the functions?

Comments on the Quality of English Language

none

Author Response

Reviewer 2

This manuscript provides a comprehensive review of the response mechanisms and patterns of interactions among bacteria, fungi, and pathogens to drought stress in soil-plant systems, The manuscript is very informative and well-written. I think it can be published in this journal after revision. However, the manuscript as a whole is too long. It will take a long time to finish reading it, and some sentences are too long and difficult to understand. I suggest that the author needs to further concisely improve some of its contents.

 

Thank you very much for your comments. The text of the review has been shortened and systematized.

 

Please refer to specific comments:

1. Line 160: Many literatures categorize Actinobacteria phylum as copiotrophic bacteria rather than oligotrophic bacteria, so there may be controversy here

We have inserted an additional phrase in the text that this statement applies only to oligotrophic representatives of the phylum Actinobacteria

2. Line 188-189: Here you mention that several environmental factors can also modulate bacterial response strategies to drought, such as soil composition, pH, and presence of heavy metals, but these environmental factors are not further described later in the article, so I would suggest that you add a description of them.

 

Thanks for the offer. But the purpose and main ideas of our review are not related to this topic. In this case, the mention of environmental factors was made for a general understanding that there are additional factors that can also affect the response of microorganisms during drought. Coverage of this issue could be the topic of a stand-alone review. In addition, as you yourself have pointed out, our review is already large and needs to be shortened. Therefore, we apologize, but we did not insert additional information on these facts.

 

3. Line 198-218: These two paragraphs are mainly descriptions of bacteria in the rhizosphere, which are not very relevant to the title of section 2.1, and it is suggested that this section should be transferred to section 2.2.

 

You're right. We removed the second paragraph from the review because it is a repetition of information in other sections. We left the first paragraph about the help that plants give to "their" microorganisms, but changed the wording slightly.

 

4. Line 261-264, Line 266-268: These two parts of the sentence seem to contradict each other.

Thank you for the observation. We removed this section altogether in the process of shortening the text of the review.

5. Line 273: Section 3.0 is too long and many of the subsections could be streamlined appropriately and then merged.

 

We have shortened this section and split it into 2 sections.

 

6. Line 282: Please make sure that the term "gene expression" is used correctly, as only RNA-based transcriptomics analyses are allowed to use this term.

In this case, the term is used correctly.

7. Line 288-302: You gave a lot of examples of gene expression in this section, but what do these changes in gene expression indicate?

 

We have inserted an explanation in the text to make it clearer.

 

8. Line 342-356: Here you have listed several strains of bacteria that have been reported to be drought tolerant, but through your investigation, can you identify any similarities or patterns in these bacteria? For example, do they mainly belong to a particular bacterial phylum? or family?

Unfortunately, no such patterns could be identified.

9. Line 376: “stress gene expression”, Please specify which genes and what are their functions.

We've corrected.

10. Line 381: What is “AMPs”? Is it AMF?

We’ve corrected.

11. Line 412-434: You mentioned the “Distinct adaptation strategies” in the title of section 3.5, but, the subsequent paragraphs seem to emphasize the similarities without specifying what the " distinct" are.

We've corrected the title of the section, now it's clearer.

12. In section 3.6 you emphasize "Distinct adaptive strategies", but by reading later I don't see "distinct" adaptive strategies for pathogenic bacteria, which seem to be similar to those in section 3.5 for rhizosphere bacteria and AMF. I think you should focus more on whether pathogenic bacteria are still pathogenic under drought conditions. Are their interactions with beneficial bacteria and plants affected by drought stress? When beneficial and pathogenic bacteria coexist, which one is more likely to survive drought stress?

We have taken into account all of your comments and made corrections to several sections.

13. Line 562: What is “PGPBs”? Is it PGPR?

We've corrected.

14. Line 593: What does the “EPSs” mean? You should explain the abbreviations when first mentioned.

We've corrected.

15. Line 621-622: What are the types of these metabolites? What about the functions?

These 245 metabolites are very diverse and have very different functions that are very difficult to list in the format of this review.  Therefore, we have simply emphasized that the spectrum and activity of metabolites is highly variable under these conditions.

Reviewer 3 Report

Comments and Suggestions for Authors

The review article titled “Plant-Soil Microbial Interaction: Differential Adaptations of Beneficial vs. Pathogenic Bacterial and Fungal Communities to Climate-Induced Drought and Desiccation Stresses” submitted by Nataliya Loiko and M. Nazrul Islam describing interactions between plant roots and soil microbes under drought stress, reporting adaptive strategies of bacterial and fungal communities in response to drought and exploring soil microbiomes mediate plant defense mechanism under drought stress. This is a well-written article and I anticipate that the manuscript should be of great interest to the researchers working on plant-microbe interaction under stress conditions. I considered the manuscript suitable for publication subject to following improvements.

1.      The title should be revised, I would suggest to remove the word “desiccation” from the title.

2.      Revise the statement Line 23-26: “This review synthesizes the current knowledge on the contrasting adaptive mechanisms utilized by different groups of plant soil microorganisms focusing on beneficial and pathogenic bacterial and fungal communities in response to drought and desiccation stresses.” Also remove the word “synthesizes”.

3.      I would suggest to remove the word “desiccation” from the manuscript and add different types of drought “Short term and Long term”.

4.      What is the deference between desiccation and drought? Add in the abstract section or first paragraph of introduction section.

5.      Revise the concluding remarks at the end of the abstract section “This review provides insights into the divergent survival strategies of soil microorganisms in response to drought and desiccation, for managing the resilience of agroeco-systems to climate change.”

6.      Line 47-51: Revise the statement, divide it into two shot sentences and why did you add sign of interrogation? “In one gram of soil, there are thousands of microbial taxa: viruses, bacteria, archaea, protists, and fungi, which form stable microbial communities that participate in nutrient cycling, transformation of organic matter, modification of biochemical and biophysical properties of soil, bioaccumulation of inorganic compounds, bioremediation of contaminated soils, and other activities or functions?”.

7.      Delete the statement Line 65-66 “Mankind is accustomed to the idea that drought is a common natural phenomenon that occurs periodically in almost all climatic zones.”

8.      Lack of coherence and flow of information, I would suggest revising the introduction section fully. Make it reader-friendly.

9.      Indicate research gaps in the introduction to increase its merit for citations.

10.  Add a short table on soil microbiomes that mediate plant defense mechanism under drought, covering both rhizobacteria and AMF.

 

11.  It is suggested to add a cartoon figure, which illustrates Horizontal Gene Transfer (HGT) within pathogenic and non-pathogenic/beneficial soil microbes.

Author Response

Reviewer 3

The review article titled “Plant-Soil Microbial Interaction: Differential Adaptations of Beneficial vs. Pathogenic Bacterial and Fungal Communities to Climate-Induced Drought and Desiccation Stresses” submitted by Nataliya Loiko and M. Nazrul Islam describing interactions between plant roots and soil microbes under drought stress, reporting adaptive strategies of bacterial and fungal communities in response to drought and exploring soil microbiomes mediate plant defense mechanism under drought stress. This is a well-written article and I anticipate that the manuscript should be of great interest to the researchers working on plant-microbe interaction under stress conditions. I considered the manuscript suitable for publication subject to following improvements.

 

1. The title should be revised, I would suggest to remove the word “desiccation” from the title.

Thank you for the observation. Indeed, much of our review is devoted to drought. We have removed the term " desiccation" from the title of the review and further text.

2. Revise the statement Line 23-26: “This review synthesizes the current knowledge on the contrasting adaptive mechanisms utilized by different groups of plant soil microorganisms focusing on beneficial and pathogenic bacterial and fungal communities in response to drought and desiccation stresses.” Also remove the word “synthesizes”.

 

We have redone the text of the abstract, starting at line 23. Accordingly, we have revised this statement.

 

3. I would suggest to remove the word “desiccation” from the manuscript and add different types of drought “Short term and Long term”.

 

Thank you, that's what we did.

 

4. What is the deference between desiccation and drought? Add in the abstract section or first paragraph of introduction section.

We have removed the term "desiccation", so there is no need to explain it now.

5. Revise the concluding remarks at the end of the abstract section “This review provides insights into the divergent survival strategies of soil microorganisms in response to drought and desiccation, for managing the resilience of agroeco-systems to climate change.”

 

We changed that phrase.

 

6. Line 47-51: Revise the statement, divide it into two shot sentences and why did you add sign of interrogation? “In one gram of soil, there are thousands of microbial taxa: viruses, bacteria, archaea, protists, and fungi, which form stable microbial communities that participate in nutrient cycling, transformation of organic matter, modification of biochemical and biophysical properties of soil, bioaccumulation of inorganic compounds, bioremediation of contaminated soils, and other activities or functions?”

We removed that statement and completely reworked the introduction.

 

7. Delete the statement Line 65-66 “Mankind is accustomed to the idea that drought is a common natural phenomenon that occurs periodically in almost all climatic zones.”

We removed that statement and completely reworked the introduction.

 

8. Lack of coherence and flow of information, I would suggest revising the introduction section fully. Make it reader-friendly.

Completely redid the introduction. It was made smaller and more understandable.

 

9. Indicate research gaps in the introduction to increase its merit for citations.

Pointed out gaps in the research.

10. Add a short table on soil microbiomes that mediate plant defense mechanism under drought, covering both rhizobacteria and AMF.

 

Thanks for the advice. We limited ourselves to adding a large conclusion so as not to "weigh down" the review. As it is not the main task of our review to consider plant protection mechanisms. It is well covered in other reviews, so we did not want to repeat ourselves.

11. It is suggested to add a cartoon figure, which illustrates Horizontal Gene Transfer (HGT) within pathogenic and non-pathogenic/beneficial soil microbes.

 

We decided that such a figure would be superfluous, as it would not provide additional information, but would increase the scope of the view. Moreover, the figure 3 related to HGT is now revised and improved based on the new texts and information added in section 6.0 on HGT.

Reviewer 4 Report

Comments and Suggestions for Authors

This review deals with the plant/soil interaction and the differential adaptation of communities to stresses. The paper cited a lot of articles and is well organized however some modifications are needed prior to publication. 

Authours should explain one time AMF, PGPR at the beginning of the review. 

As drought and dessication are key components of the review, authours should explain these two components in the introduction part and why it is relevant. Sometimes in the paper, the limit between drought and dessication is not clear, authours should check this point. 

In the second part and in the third part of the review (part 2 and part 3), authors should add a figure/a conclusion with the main informations after each paragraph (2.1 and 2.2, 3.1 and 3.2, 3.7) as a lot of information are listed to highlight the main conclusions. 

Figures 1 and Figures 2 are not easy to read. Authors should try to present the results with more readability. 

 

Author Response

Reviewer 4

This review deals with the plant/soil interaction and the differential adaptation of communities to stresses. The paper cited a lot of articles and is well organized however some modifications are needed prior to publication.

Thank you for your valuable comments.

 

Authors should explain one time AMF, PGPR at the beginning of the review.

 

We explained these terms at the beginning of the review.

 

As drought and dessication are key components of the review, authours should explain these two components in the introduction part and why it is relevant. Sometimes in the paper, the limit between drought and dessication is not clear, authours should check this point.

 

At the suggestion of other reviewers, removed the term "desiccation" from the title and text, and described the term drought at the beginning of the introduction.

In the second part and in the third part of the review (part 2 and part 3), authors should add a figure/a conclusion with the main informations after each paragraph (2.1 and 2.2, 3.1 and 3.2, 3.7) as a lot of information are listed to highlight the main conclusions.

Added a conclusion to each paragraph.

 

Figures 1 and Figures 2 are not easy to read. Authors should try to present the results with more readability.

 

We've revised and improved the quality of all three figures.