Microbial Allies in Agriculture: Harnessing Plant Growth-Promoting Microorganisms as Guardians against Biotic and Abiotic Stresses

Reviewer 1

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Title: replace microbes with microorganisms

- Corrected

Line 66: add bibliography

-A reference was added in the revised manuscript.

Line 74: remove capitalized phytohormones

-Corrected

Line 75: remove double space

-Removed

Line 76: remove the space before the paragraph

-Removed

Line 81: replace microbes with microorganisms in the whole document.

-The word is replaced in the whole manuscript.

Table 1 and 3: capitalize Zinc; Pseudomonas fluorescens. Remove the period; unify the whole table, capital letters, and periods. Add in references the meaning of abbreviations

-The word zinc is capitalized in the modified manuscript.

-The whole tables 1 and 3 is unified in the revised manuscript.

Line 111: use the abbreviation clarified above, or the word without clarifying the abbreviation again.

-The entire word is removed in the revised version

Table 4: Add the bacteria's name in italics, and unify periods.

-The bacteria name was added in italic form and the period is unified.

Line 143: put the word or the abbreviation, as previously clarified (ROS).

-The word is removed from the revised manuscript.

Apply throughout the document: where an abbreviation is clarified, do not clarify it again where you continue speaking, put the abbreviation (ABA, ROS, Ga, etc.). Unify tables, place abbreviations, clarify references, or place the complete words.

-The tables are unified in the whole manuscript.

Line 196: italicize the scientific name

-The scientific name is italicized in the modified version.

Line 224: italicize the gene name

-The gene name is italicized in the modified version.

Line 313 and throughout the document: change microbes to bacteria or microorganisms.

-The word is replaced in the whole manuscript.

Heading 6.3: capitalize the name of the gene

-The first word (not a gene) in the heading is capitalized in the revised manuscript.

Line 350: insert the full name of S. officinalis

-The full name is added to revised manuscript.

Line 418: The author's last name is all capitalized

-The mistake is modified in the revised version.

Line 451: place subscript to the "2" in hydrogen peroxide.

-The number is placed in subscript form in the revised version.

Beginning by questioning the absence of the section dedicated to identifying areas for further research, despite being one of the stated objectives, this aspect remains unaddressed throughout the article. Furthermore, with respect to the proposed objective focusing on the importance of Plant Growth-Promoting Bacteria (PGPB), there is a recurrent mention of fungi and yeasts, which are not bacteria. If the intention is to include these microorganisms in the study, the objectives should appropriately reflect this, and crucial information regarding the benefits they confer is notably absent. Consider, for instance, the example of mycorrhizal associations. Conversely, if the primary focus is exclusively on bacteria, issues arise when organisms such as Trichoderma, Pichia, Candida, Rhodotorula, etc., are mentioned.

We sincerely appreciate the reviewer's insightful comment. We agree that our research contributes to the growing body of evidence supporting the critical role of microbial communities in boosting plant growth under various stress conditions. While our primary focus lies on exploring the beneficial effects of PGBP bacteria, we have not neglected the potential contributions of other microbial players. We have indeed highlighted the importance of antagonistic interactions between PGBPs and other microorganisms throughout the manuscript, particularly in Tables 2, 4, and 6.

We have focused on the crucial role of PGBPs, we have also acknowledged and discussed the potential roles of other microorganisms to offer a more holistic perspective. We believe our approach strikes a balance between highlighting the key contributions of PGBPs and acknowledging the broader context of plant-microbe interactions under stress.

The introduction provides scant context for the work, specifically lacking a comprehensive overview of the current state of the art. Only one paragraph addresses drought, leaving other abiotic stress factors largely unexplored. Subsequently, a paragraph begins with the statement, "Plant disease is a biotic stress..." which is not entirely accurate. Plant diseases can indeed result from biotic factors such as fungi or bacteria, among others, but they can also stem from abiotic factors like nutrient deficiencies or excesses in the soil. In essence, plant diseases are not exclusively caused by biotic stress factors. Consequently, relevant information is missing, and the existing content requires careful revision. In the final paragraph of the introduction, focused on PGPB, it is stated that "PGPB employ a variety of mechanisms to alleviate stressors and boost plant resilience, including: (I) Nutrient assimilation (...) and (II) Production of metabolites." The way the article is presented, it appears that point (I) has been somewhat overlooked or lost in the discussions related to point (II).

We deeply appreciate the reviewer's insightful comment. We acknowledge that abiotic stress on plants can stem from diverse factors, making it challenging to comprehensively address each type and the corresponding roles of microorganisms. Indeed, attempting to cover all potential stresses could lead to a considerably larger research scope. Therefore, the present work intentionally focuses on specific types of biotic and abiotic stress, particularly drought, which allows for a more focused and in-depth exploration of the topic. This approach enables us to provide a more comprehensive and nuanced understanding of the complex interactions between microorganisms and plants under these specific stressors. We believe this targeted approach ultimately contributes to a clearer and more impactful research contribution, allowing us to delve deeper into the mechanisms and implications of PGBP roles in combating drought stress. We would be happy to discuss this further and explore the potential for future research that could address a broader range of abiotic stress factors.

- The statement " Plant disease is abiotic stress" in line 46 is changed in the revised manuscript to "Plant disease may result by abiotic stress".

-  The biotic (especially microbial) causes of plant diseases are mentioned in lines 46-49.

- The mechanisms were detailed in lines 560-587.

-As mentioned earlier, it is difficult to mention all the different types of plant disease causes (biotic and abiotic), and it is out of the scope for this review article.

The topic "4. Phytohormones" is particularly confusing. Much attention is given to discussing phytohormones, what they are, and what they do, without overlooking the fact that they are inherently produced by plants. Little attention is given, or few examples are provided, of bacteria that produce these substances. At times, the text contradicts itself, such as in the section "4.2. Cytokinin," where it is stated that "CKs can also increase the content of reactive oxygen species (ROS), which are signalling molecules that play a role in plant immunity," while previously in section "3. Antioxidant activity", it is indicated that "reactive oxygen species (ROS) are potential indicators of plant stress and cause progressive oxidative damage by damaging lipids, proteins, and nucleic acids." Thus, following this logic, how can this be considered positive? Moreover, specific cases addressing PGPB in this context are not provided. Another example of this contradiction is seen in section "4.6. Ethylene," where several benefits of this compound are listed, but it concludes with an example in which bacteria reduce its production, stated as having a positive effect. In essence, the various subtitles within section 4 present very little relevant information. They could simply be condensed into a single section that combines all relevant information and focuses solely on the bacteria's impact through these compounds, rather than spending considerable time explaining plant hormones. The emphasis should remain on bacteria.

We appreciate the reviewer's insightful comment. We agree that the research incorporated a concise introduction to plant hormones and their vital roles. As is often the case in research, aiming to avoid an excessively large volume of material, the focus shifted towards the specific roles of microorganisms, particularly PGBP, in either producing these hormones or amplifying their effects within plants. This targeted approach allowed for a more in-depth exploration of these specific interactions, delving deeper into the mechanisms by which PGBPs influence plant hormone levels and contribute to plant resilience under stress. We believe this focused approach ultimately yields a more impactful contribution to the field, providing valuable insights into the complex interplay between PGBPs and plant hormone regulation under stress conditions. We are open to discussing this further and exploring the potential for future research that could address broader aspects of plant hormone regulation and its interaction with various microbial communities.

- About the reactive oxygen species (ROS) part there are no contradicts, as the ROS play a good role as signaling molecules and activate signal transduction processes in response to various stresses, but contrarily the imbalance between ROS generation and safe detoxification generates oxidative stress and the accumulating ROS cause harmful effect to the plants Lines 580-581.

In addition to the examples mentioned, there are several other contradictions throughout the text. The proposed topic has the potential to be interesting, but the presented work needs a comprehensive revision. Given that it is a review paper, it should include thorough contextualization and focus on examples and practical cases that substantiate the potential of Plant Growth-Promoting Bacteria (PGPB). The subchapters of the text would also benefit from a revision. I feel that there is certain content inherent to specific points that would make more sense if consolidated instead of subdivided (as seen, for instance, in points 6 and 7). In reality, a significant portion of point 6 does not align with the overall context of the paper; for example, subpoint 6.3 does not provide relevant information concerning bacteria that promote plant growth.

While we appreciate the reviewer's insights and concerns, we respectfully hold a different opinion on the clarity and coherence of the research topic. The topic focuses on the crucial roles beneficial plant growth-promoting bacteria (PGBP) play in enhancing plant resilience against both biotic and abiotic stress factors, which we believe constitutes a highly relevant and coherent research area.

Nevertheless, we acknowledge the reviewer's feedback and have undertaken a thorough review of the research, including content review, paragraph revision, and linguistic review. We believe these revisions have further strengthened the manuscript and addressed any potential concerns regarding clarity and coherence.

We are confident that the revised manuscript presents a valuable contribution to the field of plant growth promotion and stress resistance, and we hope the reviewer will find the revised version more satisfactory.

1

I suggest another title may be more sound "Microbial Allies in Agriculture: Harnessing Plant Growth-Promoting Microbes as Guardians Against Biotic and Abiotic Stresses"

Done as suggested

2

There is much grammatical, punctuation, syntax errors, so English language editing is needed. For example:

-  Line #35 –write (poses) instead of (posing).

-  Line #36 –write (predicted) instead of (predictable).

-  Line #43 –write (is biotic) instead of (is a biotic).

-  Line # 70 –write (employs) instead of (employ).

And others in all article. Please check it and correct

A linguistic revision has been done and all mistakes have been removed in the modified manuscript

3

- Write paragraphs about Induced Systemic Resistance (ISR) and attempt to include a discussion of the mechanisms and signaling pathways that plants use to develop systemic resistance to diseases as a result of PGPMs. Please, if it's feasible.

Done as suggested in lines 560-587

4

- it's important to mention mechanisms of Nutrient Uptake and Availability and Examination of PGPMs' role in nutrient solubilization and fixation. and gave Examples of microbial strains enhancing nutrient availability to plants and insert examples in tables

Done as suggested in lines 592-603

5

-  Add more examples on PGPB phytohormones impact under biotic stress table 6.

Done in Table 6

6

-  You have to Illustrate interactions Between Biotic and Abiotic Stress Responses and the interconnectedness between responses to biotic and abiotic stresses. and gave Examples of PGPMs that confer dual stress tolerance in plants

Done as suggested in lines 521-558

7

-  Why you didn't write Field Applications and Challenges? Insert Review of successful field applications of PGPMs in different crops and also you have to discuss challenges such as formulation, stability, and large-scale implementation

A dedicated paragraph outlining the most significant successful field applications and the most critical challenges faced was incorporated into the document, beginning on line 591-616.

This section highlights the demonstrably effective real-world implementations of the proposed approach and acknowledges the key obstacles that require further research and development efforts to overcome.

8

-  The paper lacks novelty

We appreciate the reviewer's comment. We have added three more sections and have further reviewed the literature to provide the new insight to the existing work. We believe that this revised work is important for new researchers and provided a overall idea about the current state of art and could be a good point for young researchers to start gaining information for there future research in the area.

No.

Comment

Reply

1

Overall, several changes and corrections have been incorporated to enhance the overall content of the presented article. However, there are still some points that require attention. Despite the attempt to balance the mention of non-bacterial organisms by altering the title, the primary focus remains on PGPB. Consequently, this aspect should be reflected in the article's objectives, adjusting to something similar "This review aims to elucidate the impact of PGPM, with a particular focus on PGPB, and their mechanisms of action on plants under varying stressors, while also identifying areas for further research". 

We sincerely appreciate the reviewer's insightful feedback. We fully agree that the focus on PGPB remains the primary thrust of the article, even after adjusting the title. We have revised the objectives to better reflect this focus, as suggested: "This review aims to elucidate the impact of PGPM, with a particular focus on PGPB, and their mechanisms of action on plants under varying stressors, while also identifying areas for further research in both PGPB and other non-bacterial organisms".

2

In "Table 4. Models of antioxidant activities studies of PGPB under biotic stress," microorganisms listed under the first column "Microorganism" (specifically Pichia, Candida, and Rhodotorula) should be excluded since they are not PGPB. Alternatively, the table title and corresponding text could be adjusted to reflect PGPM instead of PGPB.

Thank you for pointing out this inconsistency. You are absolutely right, Pichia, Candida, and Rhodotorula are not PGPB. I've incorporated your suggestion and updated the table title. Please check Table 4.

3

In section "4.2. Cytokinin," practical examples supporting the statements are absent. Additionally, the issue of ROS presented here (also in the 4.1 section) should be briefly explained, as the authors did in the rebuttal, to prevent readers from misunderstanding it as a contradiction, when compared to what is stated in section 3.

Thank you for pointing out the lack of practical examples in section 4.2 on cytokinin. We agree that this would strengthen the section and provide better context for readers. We added relevant examples of cytokinin-mediated plant growth promotion and stress tolerance in the revised manuscript (lines 190-202). Also, ROS issue was explained in section 3 Lines 118-133 and Lines 165-167.

4

The wording of the text in L246-L248 needs clarification. As currently written, it suggests that the bacterial strains Achromobacter xylosoxidans (SF2) and Bacillus pumilus (SF3 and SF4) are causing abiotic stress to sunflower seedlings. A possible rephrasing could be: Salicylic acid (SA) was identified as the predominant phytohormone in the shoots of sunflower seedlings subjected to abiotic stress, particularly when inoculated with bacterial strains Achromobacter xylosoxidans (SF2) and Bacillus pumilus (SF3 and SF4).

Thank you for your insightful feedback on the wording in lines 246-248. Your suggested rephrasing is excellent, and implemented in the revised manuscript (lines 279-281)

5

In the section "6.1. VOC-mediated interactions in the Rhizosphere," an example of a Plant Growth-Promoting Bacterium (PGPB) should be included in addition to the already provided fungal example. This addition would further enrich the content by showcasing the specific potential of PGPB.

We appreciate the reviewer's suggestion for enriching the section on VOC-mediated interactions in the Rhizosphere by including an example of a PGPB alongside the fungal example. We agree that this would be valuable for showcasing the diverse roles of microorganisms in plant growth promotion. Please check lines 366-374.

6

In section "7.6. Rhizoremediation," practical examples supporting the presented information are currently lacking.

Thank you for your insightful feedback regarding the lack of practical examples in section 7.6 on rhizoremediation. We fully agree that adding concrete examples would strengthen the section and provide greater context for readers. Please check lines 563-575.

7

The article is generally well-written, but there are some minor writing style errors that need to be reviewed. Similarly, there are formatting issues and a lack of italics in scientific designations, such as L118 "Juglans regia" or L187 "Microbacterium, Rhizobium, Mycobacterium, and Sphingomonas," that require attention and correction throughout the text.

Thank you for your positive feedback on the overall quality of our article and for pointing out the minor writing style errors and formatting inconsistencies. We greatly appreciate your attention to detail. We thoroughly reviewed the manuscript for any stylistic errors and ensured consistent formatting throughout, including proper italicization of scientific designations