A Review of Plant–Microbe Interactions in the Rhizosphere and the Role of Root Exudates in Microbiome Engineering
Round 1
Reviewer 1 Report
Comments and Suggestions for Authors
Comments to the Authors
The manuscript titled: “Plant-Microbe Interactions in the Rhizosphere and the Role of Root Exudates in Chemical Signaling and Microbiome Engineering”- Manuscript ID: applsci-3701660 is very interesting.
This review article discusses the role of rhizosphere microorganisms in plant health and immunity, with a particular focus on plant growth-promoting microorganisms (PGPM), such as bacteria and mycorrhizal fungi. It describes the importance of root exudates as carriers of chemical signals that shape the composition of the soil microbiome and enable the recruitment of beneficial microbes in response to stress. The paper also presents the prospects for the use of microbiome engineering and synthetic microbial communities (SynComs) as tools to support sustainable agriculture.
In my opinion, a few shortcomings could be corrected in some chapters of the manuscript.
SPECIFIC COMMENTS
Comments 1
I think the title is too long. In fact, the role of root exudates concerns plant-microorganism interactions. I suggest a more concise title.
Abstract
Comments 2
The abstract accurately reflects the main themes of the manuscript, highlighting the importance of plant-microorganism interactions and the role of root exudates and microbiome engineering in sustainable agriculture. It would be advisable to emphasize the bidirectionality of signals in the plant-soil microbiome relationship.
Introduction
Comments 3
The introduction comprehensively presents the context of climate change and its impact on agriculture, as well as the importance of soil health and plant-microorganism interactions. It interestingly combines classical approaches with modern microbiome engineering (SynCom), which indicates the need to address this topic. I know that Chapter 10 is devoted to this, but I think it would be worth including brief information about existing research gaps, which would emphasize the importance of further research and justify the purpose of the publication. I also suggest placing greater emphasis on the innovative nature of the topic.
Chapter 2
Comments 4
In my opinion, this chapter could include brief information on the quality assessment procedure for selected articles and the number of articles found and ultimately selected, reflecting the work put in by the authors in preparing the manuscript.
Chapter 3
Comments 5
The only thing I suggest is to standardize the terminology, mainly with regard to the words: “microorganisms,” “microbiome,” "PGPR
Chapter 4
Comments 6
I suggest dividing the content of this chapter into subsections to organize it thematically. It seems to me that information can be extracted here on the composition of exudates (1); types of microorganism interactions and the role of chemotaxis (2); and the impact of PGPR on plant immunity.
In my opinion, some of the content overlaps too much, especially regarding the role of PGPR, and such content should be eliminated.
Comments 7
I think that when abbreviations are used for the first time in individual chapters, they should be expanded. I am referring to PGPR – plant growth-promoting bacteria, or AMF – arbuscular mycorrhizae.
Chapter 5
Comments 8
“...taxifolin promotes the recruitment of beneficial Bacillus spp. in the tomato rhizosphere.”
I think the word “taxifolin” should be briefly defined, e.g., “a flavonol with antioxidant properties.” In addition, there are several statements that secretions affect the recruitment of microorganisms. These passages should be rewritten.
Chapter 6
Comments 9
In some places, general or vague expressions appear, e.g., “others, such as phosphorus-solubilizing and drought-adaptive microbes...” – it is worth indicating at least some examples of types or taxa to make this information more credible.
Comments 10
The description of the impact of abiotic stresses (drought, salinity) is very detailed, while the section on biotic stress is treated briefly. It is worth expanding this section by providing more examples of plant defense mechanisms induced by microorganisms.
Comments 11
It is worth explaining lesser-known terms (e.g., DIMBOA).
Chapter 7
Comments 12
In my opinion, a brief explanation of how “microbial vaccines” (i.e., inoculants) differ from classic biopreparations or microbial fertilizers should be added to the introduction of the chapter.
Comments 13
I suggest separating the subheadings or at least highlighting the different groups of physiological and molecular inoculant mechanisms in the text.
Comments 12
To increase the substantive value, I suggest developing at least one experimental example with a specific description of the test conditions and effects (e.g., % yield increase, changes in IAA levels, etc.).
Comments 13
Although the title suggests general stress resistance, it would be worth clarifying the title or expanding the content to include the impact of microbial vaccines on plant resistance to pathogens (e.g., through SAR/ISR induction).
Chapter 8
Comments 14
In the sentence: “Microbial inoculants, including single strains or multi-species consortia...” I would consider adding a short example (e.g., “e.g., Bacillus spp., Azospirillum spp.”).
Comments 15
“biological vaccines”
It would be better to simply use the term “microbial vaccines.”
Comments 16
In the sentence “...improvement of physiological responses such as photosynthesis and stomatal conductance,” I suggest indicating whether these effects are documented in model plants, agricultural plants, or both.
Comments 17
In the sentence “...as can be seen in the example of tomatoes, where microbiological inoculation led to an improvement in biochemical stress markers...”, please specify which biochemical markers were analyzed (e.g., proline, MDA, SOD?).
Chapter 9
Comments 18
The information on “core taxa” is valuable, but it would be worth briefly explaining what characterizes them or giving an example.
Chapter 10
Comments 19
SIREM, please explain briefly whether this abbreviation refers to transport or a new type of metabolite...
Comments 20
It is worth separating knowledge gaps from future directions by dividing them into 2–3 distinct sections, e.g., “Main research gaps,” “New technologies in research,” and “Practical applications.”
Conclusions
Comments 21
The authors' conclusions are very well structured — precise, substantive, and consistent. They summarize the most important points from the previous chapters. In my opinion, it would be good to add a sentence emphasizing that understanding and implementing SynComs is not only a research challenge but also a huge opportunity for sustainable agriculture and environmental protection.
Comments 22
The selection of references is appropriate to the content of the manuscript.
Comments for author File: 
Comments.pdf
Author Response
Comments to the Authors
The manuscript titled: “Plant-Microbe Interactions in the Rhizosphere and the Role of Root Exudates in Chemical Signaling and Microbiome Engineering”- Manuscript ID: applsci-3701660 is very interesting.
This review article discusses the role of rhizosphere microorganisms in plant health and immunity, with a particular focus on plant growth-promoting microorganisms (PGPM), such as bacteria and mycorrhizal fungi. It describes the importance of root exudates as carriers of chemical signals that shape the composition of the soil microbiome and enable the recruitment of beneficial microbes in response to stress. The paper also presents the prospects for the use of microbiome engineering and synthetic microbial communities (SynComs) as tools to support sustainable agriculture.
In my opinion, a few shortcomings could be corrected in some chapters of the manuscript.
SPECIFIC COMMENTS
Comments 1
I think the title is too long. In fact, the role of root exudates concerns plant-microorganism interactions. I suggest a more concise title.
Response: Thank you for your suggestion. The title has been revised to:
“A Review of Plant-Microbe Interactions in the Rhizosphere and the Role of Root Exudates in Microbiome Engineering”
Abstract
Comments 2
The abstract accurately reflects the main themes of the manuscript, highlighting the importance of plant-microorganism interactions and the role of root exudates and microbiome engineering in sustainable agriculture. It would be advisable to emphasize the bidirectionality of signals in the plant-soil microbiome relationship.
Response: Thank you. We have revised the abstract to clearly highlight the bidirectional nature of the signaling between plants and soil microbes. The updated version will be reflected in the revised manuscript.
Introduction
Comments 3
The introduction comprehensively presents the context of climate change and its impact on agriculture, as well as the importance of soil health and plant-microorganism interactions. It interestingly combines classical approaches with modern microbiome engineering (SynCom), which indicates the need to address this topic. I know that Chapter 10 is devoted to this, but I think it would be worth including brief information about existing research gaps, which would emphasize the importance of further research and justify the purpose of the publication. I also suggest placing greater emphasis on the innovative nature of the topic.
Response: We appreciate this insightful recommendation. We have added a paragraph toward the end of the introduction summarizing key research gaps in SynCom stability, exudate-microbiome specificity, and scalable applications, emphasizing the novelty of the review topic.
Chapter 2
Comments 4
In my opinion, this chapter could include brief information on the quality assessment procedure for selected articles and the number of articles found and ultimately selected, reflecting the work put in by the authors in preparing the manuscript.
Response: Thank you. A brief quality assessment criterion has been added to the Search Methodology section.
Chapter 3
Comments 5
The only thing I suggest is to standardize the terminology, mainly with regard to the words: “microorganisms,” “microbiome,” "PGPR
Response: We agree and have reviewed the entire manuscript to standardize terminology. “Microorganisms” is used broadly, while “microbiome” refers to the community context. The abbreviation “PGPR” is consistently applied to “plant growth-promoting rhizobacteria.”
Chapter 4
Comments 6
I suggest dividing the content of this chapter into subsections to organize it thematically. It seems to me that information can be extracted here on the composition of exudates (1); types of microorganism interactions and the role of chemotaxis (2); and the impact of PGPR on plant immunity.
In my opinion, some of the content overlaps too much, especially regarding the role of PGPR, and such content should be eliminated.
Response: Thank you for your comment. The repetitive part of the paragraph has been removed and reorganized.
Comments 7
I think that when abbreviations are used for the first time in individual chapters, they should be expanded. I am referring to PGPR – plant growth-promoting bacteria, or AMF – arbuscular mycorrhizae.
Response: We ensured that all abbreviations (e.g., PGPR, AMF) are expanded at their first mention in the main text.
Chapter 5
Comments 8
“...taxifolin promotes the recruitment of beneficial Bacillus spp. in the tomato rhizosphere.”
I think the word “taxifolin” should be briefly defined, e.g., “a flavonol with antioxidant properties.” In addition, there are several statements that secretions affect the recruitment of microorganisms. These passages should be rewritten.
Response: The word taxifolin has been defined.
Chapter 6
Comments 9
In some places, general or vague expressions appear, e.g., “others, such as phosphorus-solubilizing and drought-adaptive microbes...” – it is worth indicating at least some examples of types or taxa to make this information more credible.
Response: Thank you. We have replaced vague phrases with examples for clarity and specificity.
Comments 10
The description of the impact of abiotic stresses (drought, salinity) is very detailed, while the section on biotic stress is treated briefly. It is worth expanding this section by providing more examples of plant defense mechanisms induced by microorganisms.
Response: The section has been expanded to include a few examples of biotic stresses.
Comments 11
It is worth explaining lesser-known terms (e.g., DIMBOA).
Response: Thank you for noting. The terms have been defined and explained in the revised version of the manuscript.
Chapter 7
Comments 12
In my opinion, a brief explanation of how “microbial vaccines” (i.e., inoculants) differ from classic biopreparations or microbial fertilizers should be added to the introduction of the chapter.
Response: An explanation has been added at the start of Chapter 7 to clarify that microbial vaccines refer to inoculants with immune-priming effects, distinct from nutrient-focused biofertilizers.
Comments 13
I suggest separating the subheadings or at least highlighting the different groups of physiological and molecular inoculant mechanisms in the text.
Response: Thanks for the suggestion. We made the changes.
Comments 14
To increase the substantive value, I suggest developing at least one experimental example with a specific description of the test conditions and effects (e.g., % yield increase, changes in IAA levels, etc.).
Response: Thanks for the suggestion. A study has been added.
Comments 15
Although the title suggests general stress resistance, it would be worth clarifying the title or expanding the content to include the impact of microbial vaccines on plant resistance to pathogens (e.g., through SAR/ISR induction).
Response: I am sorry, but I am confused. Which title need to be modified.
Chapter 8
Comments 16
In the sentence: “Microbial inoculants, including single strains or multi-species consortia...” I would consider adding a short example (e.g., “e.g., Bacillus spp., Azospirillum spp.”).
Response: Examples have been added.
Comments 17
“biological vaccines”
It would be better to simply use the term “microbial vaccines.”
Response: I did not find the term “biological vaccines”
Comments 18
In the sentence “...improvement of physiological responses such as photosynthesis and stomatal conductance,” I suggest indicating whether these effects are documented in model plants, agricultural plants, or both.
Response: The manuscript now specifies that effects were documented in both model plants and crops.
Comments 19
In the sentence “...as can be seen in the example of tomatoes, where microbiological inoculation led to an improvement in biochemical stress markers...”, please specify which biochemical markers were analyzed (e.g., proline, MDA, SOD?).
Response: The sentence has been revised to indicate specific biomarkers.
Chapter 9
Comments 20
The information on “core taxa” is valuable, but it would be worth briefly explaining what characterizes them or giving an example.
Response: The term has been explained in the revised manuscript.
Chapter 10
Comments 21
SIREM, please explain briefly whether this abbreviation refers to transport or a new type of metabolite...
Response: SIREM has been clarified as a transport process that describes how microbial colonization at one plant site (e.g., leaves or roots) triggers systemic changes that result in the transport and exudation of specific metabolites.
Comments 22
It is worth separating knowledge gaps from future directions by dividing them into 2–3 distinct sections, e.g., “Main research gaps,” “New technologies in research,” and “Practical applications.”
Response: We have divided this section into two subsections, Research gaps, and need of new technologies.
Conclusions
Comments 23
The authors' conclusions are very well structured — precise, substantive, and consistent. They summarize the most important points from the previous chapters. In my opinion, it would be good to add a sentence emphasizing that understanding and implementing SynComs is not only a research challenge but also a huge opportunity for sustainable agriculture and environmental protection.
Response: Thanks. The information has been added.
Comments 24
The selection of references is appropriate to the content of the manuscript.
Response: Thank you!
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsI have carefully reviewed the manuscript entitled “Plant-Microbe Interactions in the Rhizosphere and the Role of Root Exudates in Chemical Signaling and Microbiome Engineering” submitted by Wankhade et al. to a MDPI journal Applied Sciences. Rhizosphere microbial interactions are fundamental to plant health, influencing nutrient availability, stress tolerance, and pathogen resistance. Beneficial microbes, such as PGPR and AMF, enhance plant resilience through nutrient solubilization, phytohormone production, and pathogen suppression via antimicrobial compounds and siderophores. Root exudates, composed of sugars, organic acids, and secondary metabolites, act as chemoattractants that shape the rhizosphere microbiome by recruiting beneficial microbes. Stress conditions alter exudate composition, enabling plants to attract specific microbes that aid in stress mitigation. The dynamic interactions between plants and microbes are central to sustainable agriculture, as they can reduce dependency on chemical fertilizers and pesticides. Advancements in microbiome engineering have led to the development of synthetic microbial communities (SynComs) tailored to enhance plant productivity and disease resistance. Recent studies have highlighted the potential of engineered microbiomes to establish stable, beneficial microbial consortia that support plant growth under diverse environmental conditions.
Rhizosphere microbial interactions and microbiome engineering are central topic in achieving modern sustainable agriculture and ensuring sustainable land use. This review discusses the role of microbial interactions in plant health, the influence of root exudates on microbiome composition, and the emerging potential of SynComs in optimizing plant-microbe associations for sustainable agriculture. The topic of this manuscript is very interesting. Besides, the manuscript is well-written and well-structured. This review will broaden the understanding about how to use rhizosphere microbial interactions to improve agricultural production. Therefore, I suggest accepting this manuscript for publication after minor revision. Regarding this manuscript, I have only two questions.
- Deepen research significance through linking the content of the manuscript with one earth and one health.
- One of field applications related to beneficial microorganisms is bio-organic fertilizer. I advise supplementing the content associated with beneficial microbes-enriched bio-organic fertilizer production and application.
Author Response
Reviewer 2
I have carefully reviewed the manuscript entitled “Plant-Microbe Interactions in the Rhizosphere and the Role of Root Exudates in Chemical Signaling and Microbiome Engineering” submitted by Wankhade et al. to a MDPI journal Applied Sciences. Rhizosphere microbial interactions are fundamental to plant health, influencing nutrient availability, stress tolerance, and pathogen resistance. Beneficial microbes, such as PGPR and AMF, enhance plant resilience through nutrient solubilization, phytohormone production, and pathogen suppression via antimicrobial compounds and siderophores. Root exudates, composed of sugars, organic acids, and secondary metabolites, act as chemoattractants that shape the rhizosphere microbiome by recruiting beneficial microbes. Stress conditions alter exudate composition, enabling plants to attract specific microbes that aid in stress mitigation. The dynamic interactions between plants and microbes are central to sustainable agriculture, as they can reduce dependency on chemical fertilizers and pesticides. Advancements in microbiome engineering have led to the development of synthetic microbial communities (SynComs) tailored to enhance plant productivity and disease resistance. Recent studies have highlighted the potential of engineered microbiomes to establish stable, beneficial microbial consortia that support plant growth under diverse environmental conditions.
Rhizosphere microbial interactions and microbiome engineering are central topic in achieving modern sustainable agriculture and ensuring sustainable land use. This review discusses the role of microbial interactions in plant health, the influence of root exudates on microbiome composition, and the emerging potential of SynComs in optimizing plant-microbe associations for sustainable agriculture. The topic of this manuscript is very interesting. Besides, the manuscript is well-written and well-structured. This review will broaden the understanding about how to use rhizosphere microbial interactions to improve agricultural production. Therefore, I suggest accepting this manuscript for publication after minor revision. Regarding this manuscript, I have only two questions.
- Deepen research significance through linking the content of the manuscript with one earth and one health.
Response: Thank you. We have modified the contents.
- One of field applications related to beneficial microorganisms is bio-organic fertilizer. I advise supplementing the content associated with beneficial microbes-enriched bio-organic fertilizer production and application.
Response: Thank you. The information has been added.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsI sincerely appreciate the opportunity to review this engaging and well-prepared manuscript. It was a rewarding experience to contribute to the editorial process.
It is recommended that the authors provide clarification regarding the nature of the article in its title. The content of the work in fact corresponds to a structured literature review (a compilation of recent studies in the field of plant interactions with synthetic microbial communities). It is recommended that this aspect be clearly indicated in the title (for example, by adding the phrase "literature review," "systematic review," or simply "review") to enhance the informativeness of the title for potential readers and improve the article's indexing in relevant databases.
The abstract would benefit from further refinement. The present abstract is composed primarily of well-established, generic information concerning microbial interactions in the rhizosphere and the potential of synthetic microbial communities. However, the text does not conform to the conventional structure expected of a scientific abstract, particularly in that it does not clearly formulate the objective of the review, does not describe how the literature selection and analysis were conducted (which is especially important for review articles), and does not highlight the main findings or key conclusion of the review. It is hypothesised that the clarification of the structure of the abstract in this manner would result in a substantial enhancement of its informativeness and alignment with scientific publishing standards.
The Introduction section provides a comprehensive overview of the critical challenges confronting agricultural production in the context of global climate change, with a particular emphasis on the mounting pressures faced by agricultural systems due to rising temperatures, extreme weather events, water scarcity, and the depletion of natural resources. The authors provide a cogent rationale for the necessity of a transition towards more sustainable agricultural approaches, which extend beyond the mere intensification of yields. Significant attention is given to soil health, with particular emphasis on plant–microbe interactions in the rhizosphere. These interactions have the potential to enhance the resilience of agroecosystems. In this context, the relevance of studying the role of root exudates in chemical signalling and shaping the soil microbiome is well substantiated. The contribution of research into plant–microbe interaction is presented as a key direction for developing climate-adaptive, sustainable agriculture. This scientific focus facilitates a re-evaluation of the utilisation of microbial inoculants and microbiome engineering approaches directed towards enhancing crop productivity and reducing reliance on chemical fertilisers and pesticides.
The final paragraph of the Introduction, which, in principle, should state the aim of the present review, currently reads more as a statement of perspectives for future research – a component more typical for a conclusion section. It is imperative that the Introduction clearly articulates the rationale behind this particular review, including the identification of contentious or under-researched areas in the existing literature. This rationale should also elucidate the selection of sources and the structure of the review. Such clarification would assist readers in comprehending the focus and novelty of the review, thereby contributing to a more coherent perception of the material presented.
As stated in the Search Methodology section, the literature review encompasses publications from 2020 to 2025. It can be hypothesised that this lower time boundary is related to the fact that the term "SynCom" (synthetic microbial communities) was first introduced in 2019. However, this rationale is not explicitly stated in the text. It would be beneficial to explicitly state in the Search Methodology section that the selected timeframe was influenced by the recent emergence of the term and concept of SynComs in the scientific discourse. This would serve to enhance the clarity and transparency of the review's structure for its readers.
The authors correctly observe that in order to enhance the readability and coherence of the text, they employed an AI-powered language platform. The utilisation of such tools represents a significant and promising trajectory in contemporary scientific research, and the authors' experience with these tools may prove invaluable to other researchers. In this regard, it would be beneficial to elaborate on this point within the text. In order to facilitate further discussion on this matter, it would be beneficial to clarify the following points:
The purpose of this study is to ascertain the meaning of the term 'draft'. In order to achieve this objective, it is necessary to establish at which stage of manuscript preparation or editing the language platform was used.
The objective of this study is to ascertain which specific sections or parts of the manuscript were edited using artificial intelligence (AI).
It is imperative to ascertain whether the authors conducted a subsequent review of the final text following the implementation of artificial intelligence to ensure the veracity of the content and the preservation of the academic style.
The provision of such clarification would serve to enhance the transparency of the authors' approach to the utilisation of AI, thereby providing a valuable exemplar for other researchers in the field.
Another salient issue pertains to the selection of literature sources for the review. The authors state that they selected relevant publications "to compile relevant literature for this review." However, utilising the fundamental search query "synthetic AND microbial AND communities" in the Scopus database alone results in the retrieval of over 4,000 documents. In order to comprehend the rationale behind the selection of specific works included in the review, it is imperative to understand the methodology employed by the authors in this regard. The selection criteria employed in this process are of particular interest. Could the selection process be clarified, with details of the thematic relevance, the type of publication, the journal impact, and the novelty of the approaches taken? The provision of more detailed explanations of this step in the Search Methodology section would greatly enhance the transparency and reproducibility of the authors' approach to building the literature base, and would facilitate the interpretation of the review's conclusions.
The third section of the text is entitled '…'. Microbial Interactions in Plant Microbiomes, there is no introductory paragraph that would justify the inclusion of the particular aspects covered in its subsections. This renders the logic of the section's structure and the interconnections between its parts more opaque. Furthermore, it has been observed that some subsection titles appear to exceed the scope of the paper's title, thereby creating a discernible imbalance between the scale of the subsection titles, the focus of the section, and the stated aim of the review. In order to ensure a coherent and well-structured argument, it is advisable to align the scope and orientation of the subsections with the overall aim and title of the paper. Furthermore, it is essential to clearly state in the introduction to the section which aspects will be addressed and why they are key to this review.
In order to enhance the clarity and organisation of the presented information, it may also be beneficial to consider incorporating a graphical block diagram that visually represents the primary interrelationships among the discussed aspects. It is my opinion that the incorporation of such a diagram would serve to significantly enhance the clarity and readability of the manuscript, particularly in light of the intricacy of the subject matter. It is acknowledged that the appropriateness and format of such a figure is at the discretion of the authors.
The Conclusion, in its current form, primarily reiterates well-known facts and emphasizes the importance of further research — an element more characteristic of the Introduction when justifying relevance, rather than of a conclusion section in a review article. Since the authors have deliberately analyzed literature from the past five years, it would be extremely valuable for readers if the Conclusion clearly outlined what conceptual or methodological breakthroughs have occurred in this field during that period. For example: was there the development of a new methodology (a new class of methods for studying microbial interactions), a breakthrough concept (a new model of interactions), or a practical technological solution (effective approaches to constructing SynComs for specific crops)? Such a synthesis would significantly strengthen the closing section of the review and more clearly convey the contribution this review makes to the understanding of the current state of the field.
The manuscript presents significant interest and demonstrates a high scientific standard. In my opinion, it can be accepted for publication after minor revisions
Author Response
Reviewer 3
Comments and Suggestions for Authors
I sincerely appreciate the opportunity to review this engaging and well-prepared manuscript. It was a rewarding experience to contribute to the editorial process.
It is recommended that the authors provide clarification regarding the nature of the article in its title. The content of the work in fact corresponds to a structured literature review (a compilation of recent studies in the field of plant interactions with synthetic microbial communities). It is recommended that this aspect be clearly indicated in the title (for example, by adding the phrase "literature review," "systematic review," or simply "review") to enhance the informativeness of the title for potential readers and improve the article's indexing in relevant databases.
Response: Thank you. The title has been revised to include “A Review,” making the article’s nature explicit.
The abstract would benefit from further refinement. The present abstract is composed primarily of well-established, generic information concerning microbial interactions in the rhizosphere and the potential of synthetic microbial communities. However, the text does not conform to the conventional structure expected of a scientific abstract, particularly in that it does not clearly formulate the objective of the review, does not describe how the literature selection and analysis were conducted (which is especially important for review articles), and does not highlight the main findings or key conclusion of the review. It is hypothesised that the clarification of the structure of the abstract in this manner would result in a substantial enhancement of its informativeness and alignment with scientific publishing standards.
Response: The abstract has been restructured to clearly state the objective of the review, the methods of literature selection, and the key findings and contributions
The Introduction section provides a comprehensive overview of the critical challenges confronting agricultural production in the context of global climate change, with a particular emphasis on the mounting pressures faced by agricultural systems due to rising temperatures, extreme weather events, water scarcity, and the depletion of natural resources. The authors provide a cogent rationale for the necessity of a transition towards more sustainable agricultural approaches, which extend beyond the mere intensification of yields. Significant attention is given to soil health, with particular emphasis on plant–microbe interactions in the rhizosphere. These interactions have the potential to enhance the resilience of agroecosystems. In this context, the relevance of studying the role of root exudates in chemical signalling and shaping the soil microbiome is well substantiated. The contribution of research into plant–microbe interaction is presented as a key direction for developing climate-adaptive, sustainable agriculture. This scientific focus facilitates a re-evaluation of the utilisation of microbial inoculants and microbiome engineering approaches directed towards enhancing crop productivity and reducing reliance on chemical fertilisers and pesticides.
Response: Thank you!
The final paragraph of the Introduction, which, in principle, should state the aim of the present review, currently reads more as a statement of perspectives for future research – a component more typical for a conclusion section. It is imperative that the Introduction clearly articulates the rationale behind this particular review, including the identification of contentious or under-researched areas in the existing literature. This rationale should also elucidate the selection of sources and the structure of the review. Such clarification would assist readers in comprehending the focus and novelty of the review, thereby contributing to a more coherent perception of the material presented.
Response: The final paragraph of the Introduction has been revised to clearly state the aim of the review, knowledge gaps, and its focus on recent advances in SynComs and exudate-mediated microbial recruitment.
As stated in the Search Methodology section, the literature review encompasses publications from 2020 to 2025. It can be hypothesised that this lower time boundary is related to the fact that the term "SynCom" (synthetic microbial communities) was first introduced in 2019. However, this rationale is not explicitly stated in the text. It would be beneficial to explicitly state in the Search Methodology section that the selected timeframe was influenced by the recent emergence of the term and concept of SynComs in the scientific discourse. This would serve to enhance the clarity and transparency of the review's structure for its readers.
Response: The Search Methodology section now explains that 2020–2025 was chosen to capture research following the conceptual emergence of SynComs post-2019.
The authors correctly observe that in order to enhance the readability and coherence of the text, they employed an AI-powered language platform. The utilisation of such tools represents a significant and promising trajectory in contemporary scientific research, and the authors' experience with these tools may prove invaluable to other researchers. In this regard, it would be beneficial to elaborate on this point within the text. In order to facilitate further discussion on this matter, it would be beneficial to clarify the following points:
The purpose of this study is to ascertain the meaning of the term 'draft'. In order to achieve this objective, it is necessary to establish at which stage of manuscript preparation or editing the language platform was used.
The objective of this study is to ascertain which specific sections or parts of the manuscript were edited using artificial intelligence (AI).
It is imperative to ascertain whether the authors conducted a subsequent review of the final text following the implementation of artificial intelligence to ensure the veracity of the content and the preservation of the academic style.
The provision of such clarification would serve to enhance the transparency of the authors' approach to the utilisation of AI, thereby providing a valuable exemplar for other researchers in the field.
Response: AI tools were used for sentence restructuring during the editing stage. Only grammatical and spelling suggestions were applied. All content was manually reviewed to maintain accuracy and scientific tone
Another salient issue pertains to the selection of literature sources for the review. The authors state that they selected relevant publications "to compile relevant literature for this review." However, utilising the fundamental search query "synthetic AND microbial AND communities" in the Scopus database alone results in the retrieval of over 4,000 documents. In order to comprehend the rationale behind the selection of specific works included in the review, it is imperative to understand the methodology employed by the authors in this regard. The selection criteria employed in this process are of particular interest. Could the selection process be clarified, with details of the thematic relevance, the type of publication, the journal impact, and the novelty of the approaches taken? The provision of more detailed explanations of this step in the Search Methodology section would greatly enhance the transparency and reproducibility of the authors' approach to building the literature base, and would facilitate the interpretation of the review's conclusions.
Response: The Search Methodology now includes criteria: relevance to SynCom/exudate-microbiome interaction, peer-reviewed articles, journal impact factor, novelty, and focus on recent advancements.
The third section of the text is entitled '…'. Microbial Interactions in Plant Microbiomes, there is no introductory paragraph that would justify the inclusion of the particular aspects covered in its subsections. This renders the logic of the section's structure and the interconnections between its parts more opaque. Furthermore, it has been observed that some subsection titles appear to exceed the scope of the paper's title, thereby creating a discernible imbalance between the scale of the subsection titles, the focus of the section, and the stated aim of the review. In order to ensure a coherent and well-structured argument, it is advisable to align the scope and orientation of the subsections with the overall aim and title of the paper. Furthermore, it is essential to clearly state in the introduction to the section which aspects will be addressed and why they are key to this review.
Response: Thank you for the suggestion. The information has been added.
In order to enhance the clarity and organisation of the presented information, it may also be beneficial to consider incorporating a graphical block diagram that visually represents the primary interrelationships among the discussed aspects. It is my opinion that the incorporation of such a diagram would serve to significantly enhance the clarity and readability of the manuscript, particularly in light of the intricacy of the subject matter. It is acknowledged that the appropriateness and format of such a figure is at the discretion of the authors.
Response: Thank you for the suggestion. A schematic diagram has been added to the manuscript showing key interactions between root exudates, microbial consortia, and plant responses.
The Conclusion, in its current form, primarily reiterates well-known facts and emphasizes the importance of further research — an element more characteristic of the Introduction when justifying relevance, rather than of a conclusion section in a review article. Since the authors have deliberately analyzed literature from the past five years, it would be extremely valuable for readers if the Conclusion clearly outlined what conceptual or methodological breakthroughs have occurred in this field during that period. For example: was there the development of a new methodology (a new class of methods for studying microbial interactions), a breakthrough concept (a new model of interactions), or a practical technological solution (effective approaches to constructing SynComs for specific crops)? Such a synthesis would significantly strengthen the closing section of the review and more clearly convey the contribution this review makes to the understanding of the current state of the field.
Response: Thank you for your suggestions. The modifications have been made to the revised manuscript.
The manuscript presents significant interest and demonstrates a high scientific standard. In my opinion, it can be accepted for publication after minor revisions
Response: Thank you.
Author Response File: Author Response.pdf
