The Role of Bacillus sp. in Reducing Chemical Inputs for Sustainable Crop Production
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe newer vistas of Bacillus use in agriculture beyond phytohormones, Nitrogen and phosphorus, should be discussed in a separate section and should be given prime focus.
The MS can be improved further by discussing perspectives on the commercial formulations also, as the content present in the MS has been written several times. There is nothing new.
There are challenges in the regulation of the Bacillus bioformulations under different categories like biostimulants, biopesticides, etc. A section should discuss this also.
Another concern is repetitiveness, spend less words on the aspects of N, P and phytohormones, as it has been described widely in thousands of papers
Write a section on the complicated and changing Bacillus taxonomy, and recent changes that has been made in this regard
Bacillus in the metagenomic era: Write something in this line considering the data available from omics analysis, the kind of diversity and functions has been interpreted in last 10 years is huge and could be accommodated in a section.
Author Response
Reviewer 1
Answer: The authors express their gratitude to the reviewers for the opportunity to improve the manuscript. We appreciate your contributions.
Reviewer 1: The newer vistas of Bacillus use in agriculture beyond phytohormones, Nitrogen and phosphorus, should be discussed in a separate section and should be given prime focus.
Answer: The manuscript has been entirely revised based on the reviewers' suggestions. Initially, we focused on reducing nitrogen and phosphorus using Bacillus sp. inoculation. This version covers additional aspects: changes in Bacillus sp. classification, the importance of Omics technology to Bacillus sp., and its mode of action, Consistency in Field Performance , Reduction of nitrogen and phosphorous fertilization,
Reviewer 1: The MS can be improved further by discussing perspectives on the commercial formulations also, as the content present in the MS has been written several times. There is nothing new.
Answer: The discussion about perspectives on the commercial formulation has been addressed.
Reviewer 1: There are challenges in the regulation of the Bacillus bioformulations under different categories like biostimulants, biopesticides, etc. A section should discuss this also.
Answer: Thank you for your suggestions. An section about Formulation and Delivery Methods has been added.
Reviewer 1: Another concern is repetitiveness, spend less words on the aspects of N, P and phytohormones, as it has been described widely in thousands of papers
Answer: Initially, we focused on reducing fertilizer usage. Acknowledging the repetitiveness, we explored other aspects of Bacillus utilization.
Reviewer 1: Write a section on the complicated and changing Bacillus taxonomy, and recent changes that has been made in this regard
Answer: It has been done.
Reviewer 1: Bacillus in the metagenomic era: Write something in this line considering the data available from omics analysis, the kind of diversity and functions has been interpreted in last 10 years is huge and could be accommodated in a section.
Answer: It has been done.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsI have been assigned to review the perspective with the title "The Role of Bacillus sp. in Reducing Chemical Inputs for Sustainable Crop Production " showing the perspective that;
1. Bacillus sp., the gram-positive bacterium most commonly found in the rhizosphere, has several abilities related to promoting plant growth.
2. Currently, agricultural production faces great challenges in producing food, reducing production costs and environmental impact without reducing productivity.
3. Thus, Bacillus sp. is a promising alternative to achieve this goal. However, is it possible to effectively reduce the input in food production using Bacillus sp.
In this review, the authors have addressed addressed the utilization of Bacillus sp. to reduce nitrogen and phosphorus fertilizers through mechanisms of nitrogen fixation, phosphorus solubilization, and phytohormone production for reducing production costs and environmental impact without reducing productivity of crop.
Authors have written this review in intellectual manner however, there are several major issues that has to be addressed by the authors to cover the comprehensive knowledge and latest information of the filed.
1. First of all, its better if authors provide the graphical abstract of their prospective as it surely will be easier and perceivable manner for making this perspective more and thoroughly understandable for the readers.
2. In addition to this, authors should include the graphical summaries of the mechanisms of each aspect they have addressed in this perspective for example Bacillus sp to reduce phosphorous fertilization and other too,
3. Moreover, authors should present the literature and role of different Bacillus sp in tabular form. So that readers feel it feasible to find it in proper robust manner.
4. Authors should include new references.
5. Grammatical and formatting issue should be rectified by authors.
Comments on the Quality of English LanguageExtensive editing of English language required.
Author Response
Reviewer 2:
Reviewer 2: I have been assigned to review the perspective with the title "The Role of Bacillus sp. in Reducing Chemical Inputs for Sustainable Crop Production " showing the perspective that; 1. Bacillus sp., the gram-positive bacterium most commonly found in the rhizosphere, has several abilities related to promoting plant growth. 2. Currently, agricultural production faces great challenges in producing food, reducing production costs and environmental impact without reducing productivity. 3. Thus, Bacillus sp. is a promising alternative to achieve this goal. However, is it possible to effectively reduce the input in food production using Bacillus sp.
Reviewer 2: In this review, the authors have addressed the utilization of Bacillus sp. to reduce nitrogen and phosphorus fertilizers through mechanisms of nitrogen fixation, phosphorus solubilization, and phytohormone production for reducing production costs and environmental impact without reducing productivity of crop.
Reviewer 2: Authors have written this review in intellectual manner however, there are several major issues that has to be addressed by the authors to cover the comprehensive knowledge and latest information of the filed.
Answer: The authors express their gratitude to the reviewers for the opportunity to improve the manuscript. We appreciate your contributions.
Reviewer 2: 1. First of all, its better if authors provide the graphical abstract of their prospective as it surely will be easier and perceivable manner for making this perspective more and thoroughly understandable for the readers.
Answer: Figure 1 showing some aspects of the Bacillus sp inoculation has been added.
Reviewer 2: 2. In addition to this, authors should include the graphical summaries of the mechanisms of each aspect they have addressed in this perspective for example Bacillus sp to reduce phosphorous fertilization and other too,
Answer: In the Figure 1 is shown the fertilizer reduction.
Reviewer 2: 3. Moreover, authors should present the literature and role of different Bacillus sp in tabular form. So that readers feel it feasible to find it in proper robust manner.
Answer: New sections on other aspects of Bacillus sp inoculation have been added.
Reviewer 2: 4. Authors should include new references.
Answer; New references have been added.
Reviewer 2: 5. Grammatical and formatting issue should be rectified by authors.
Comments on the Quality of English Language
Extensive editing of English language required.
Answer: thanks for mentioning this. The English has been revised.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsIntroduction
L.67: mixture of microorganisms and chemicals? generally the commercial biostimulant composed only by microoganisms. otherwise cite an example.
L76-78: It's too long sentence, re-write and divide into 2 sentences.
L.79, L. 130 and L. 143: correct as "sp."
L. 112: delete space before "The study".
L. 131: correct as "biofertilizer".
L. 139-L. 141: re-write the sentences to be more more clear and reduce redondancy.
L. 164: correct as "by-products".
L. 180: add the author name before [30].
L. 206 to L. 208: improved only protease, urease, acid phosphomonesterase and glucosidase? what about alkaline phosophatase? several benefical bateria are known by their ability to enhance alkaline phosphatase activity in the soil. Look for benefits and add this information especially as this enzyme is crucial in P cycling.
L. 223 and L. 241: add references.
L. 257: B. subtilis in italic and delete (BS).
L. 260 and L. 262: B. subtilis in italic.
L. 274 and L. 275: correct as "..high amount of IAA" and delete "a phytohormone that plays..." to avoid rodondancy.
L. 275: replace "The prodution range for IAA" by "Its production range from...to....by these bacteria."
L. 276 to L. 278: delete "However, ....pathogens" it's non necessary informations.
L. 279: Follow authors instructions and correct the reference style in the text.
L. 283: Incomplete sentence.
L. 288 to L. 291: re-write the sentences.
Conclusion
L. 313: Bacillus in italic.
To summarize, add a table that contains Bacillus species with their aptitude to fix nitrogen, solublize the phsopahte and to prodcue IAA and which harbor a plant growth-promoting aptitude in different plant species (cite them) and add references for each study.
Author Response
Reviewer 3
Answer: The authors express their gratitude to the reviewers for the opportunity to improve the manuscript. We appreciate your contributions.
Answer: The manuscript has been entirely revised based on the reviewers' suggestions. Initially, we focused on reducing nitrogen and phosphorus using Bacillus sp. inoculation. This version covers additional aspects: changes in Bacillus sp. classification, the importance of Omics technology to Bacillus sp., and its mode of action, Consistency in Field Performance , Reduction of nitrogen and phosphorous fertilization,
Introduction
L.67: mixture of microorganisms and chemicals? generally the commercial biostimulant composed only by microoganisms. otherwise cite an example.
Answer: This sentence has been deleted.
L76-78: It's too long sentence, re-write and divide into 2 sentences.
Answer: This sentence has been deleted.
L.79, L. 130 and L. 143: correct as "sp."
Answer: This sentence has been deleted.
- 112: delete space before "The study".
Answer: This sentence has been deleted.
- 131: correct as "biofertilizer".
Answer: This sentence has been deleted.
Answer: This sentence has been deleted.
- 139-L. 141: re-write the sentences to be more more clear and reduce redondancy.
Answer: This sentence has been deleted.
- 164: correct as "by-products".
Answer: This sentence has been deleted.
- 180: add the author name before [30].
Answer: This sentence has been deleted.
- 206 to L. 208: improved only protease, urease, acid phosphomonesterase and glucosidase? what about alkaline phosophatase? several benefical bateria are known by their ability to enhance alkaline phosphatase activity in the soil. Look for benefits and add this information especially as this enzyme is crucial in P cycling.
Answer: This sentence has been deleted.
- 223 and L. 241: add references.
Answer: This sentence has been deleted.
- 257: B. subtilis in italic and delete (BS).
Answer: This sentence has been deleted.
- 260 and L. 262: B. subtilis in italic.
Answer: This sentence has been deleted.
- 274 and L. 275: correct as "..high amount of IAA" and delete "a phytohormone that plays..." to avoid rodondancy.
Answer: This sentence has been deleted.
- 275: replace "The prodution range for IAA" by "Its production range from...to....by these bacteria."
- 276 to L. 278: delete "However, ....pathogens" it's non necessary informations.
Answer: This sentence has been deleted.
- 279: Follow authors instructions and correct the reference style in the text.
Answer: It has been done.
- 283: Incomplete sentence.
Answer: This sentence has been deleted.
- 288 to L. 291: re-write the sentences.
Conclusion
- 313: Bacillus in italic.
Answer: It has been done.
To summarize, add a table that contains Bacillus species with their aptitude to fix nitrogen, solublize the phsopahte and to prodcue IAA and which harbor a plant growth-promoting aptitude in different plant species (cite them) and add references for each study.
Author Response File: Author Response.pdf
Reviewer 4 Report
Comments and Suggestions for Authorssee attachment
Comments for author File: Comments.pdf
I suggest minor editing of the English language
Author Response
Reviewer 4
Answer: The authors express their gratitude to the reviewers for the opportunity to improve the manuscript. We appreciate your contributions.
Answer: The manuscript has been entirely revised based on the reviewers' suggestions. Initially, we focused on reducing nitrogen and phosphorus using Bacillus sp. inoculation. This version covers additional aspects: changes in Bacillus sp. classification, the importance of Omics technology to Bacillus sp., and its mode of action, Consistency in Field Performance , Reduction of nitrogen and phosphorous fertilization,
General comments
The manuscript focuses on the great potential of microorganisms of the genus Bacillus to reduce the administration of chemicals in agriculture. This choice would make crops much more sustainable by avoiding soil impoverishment. The authors report several related studies to define whether this alternative is possible. The work appears well structured, even if some repetitions could be avoided. The manuscript is of appropriate length.
Answer: The authors express their gratitude to the reviewers for the opportunity to improve the manuscript. We appreciate your contributions.
Specific comments
Answer: Many sentences were deleted as the manuscript was restructured to incorporate reviewers' suggestions.
Line 262: "Bacillus subtilis contributes to soil fertility by improving nutrient availability and..." From this point on, the word Bacillus is often written regularly. Please fix.
Answer: This sentence has been deleted.
Lines 257-258: "A previous study demonstrated that B. subtilis (BS) produces indole-3-acetic acid (IAA) via both L-tryptophan (L-Trp)-dependent and independent pathways." The reference to the work is not mentioned.
Answer: This sentence has been deleted.
Line 278: "(Singh et ai., 2024). The references are shown with the progressive number. Please correct.
Answer: This sentence has been deleted.
Lines 282-285: "A study evaluated a mixture of both A. brasilense and B. subtilis and found two important abilities in both. The capacity to produce phytohormones, fix nitrogen, and solubilize phosphorus. Notably, the production of phytohormones and nitrogen fixation are complementary mechanisms employed by bacteria to enhance plant growth [34]." lt is written that both strains show two important properties, but in the following sentence, three are mentioned. Also, if the reference of the cited work is 34, it would be clearer if the number was put first.
Answer: This sentence has been deleted.
Lines 285-291: "lndeed, the promotion of plant growth is significant for bacteria, as it enhances root area and volume, facilitating bacterial colonization of the rhizosphere and increasing the release of carbohydrates and energy from plants through rhizodeposition. lndeed, it is challenging to differentiate between the quantity of fertilizers in the plant provided by the increased availability of nutrients and that provided by enhanced root development, which consequently increases nutrient uptake." This partis redundant and repeats concepts already expressed several times.
Final comments
1 suggest reviewing the manuscript and trying to avoid repeating concepts already stated. 1 also recommend adding tables describing the results of the different works cited. Tables are much more usable by readers.
Answer:
Finally, in my opinion, it is essential that in a review, there are at least two figures/schemes that graphically illustrate the mechanisms of growth promotion. The figures must be original and well-finished from a graphic point of view.
Answer: Thank you so much for your suggestions. One figure has been added.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThe changes has been incorporated
Author Response
The authors express their gratitude to reviewer2 for providing the opportunity to enhance the manuscript.
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsI have been assigned to review the "Perspective" entitled "The Role of Bacillus sp. in Reducing Chemical Inputs for Sustainable Crop Production".
The current perspective discusses the role of Bacillus species as promising agents for reducing chemical input in sustainable crop production such as nitrogen and phosphorus fertilizers. The authors have shown three main areas of concern as given below.
Firstly, the authors discuss that Bacillus sp. improves crop yields, however, their field performance may be inconsistent, highlighting the need for further research to optimize formulations and delivery methods.
In addition, compatibility with other agricultural inputs varies depending on the specific chemicals and conditions involved.
Secondly, Bacillus sp. can significantly 16 affect the soil microbiome, potentially promoting plant growth and microbial diversity as strain specificity and host compatibility play crucial roles in determining the success of host-microbe interactions.
Moreover, the authors also showed their reservations about the safety usage of Bacillus according to the Integrated Pest Management and Integrated Crop Management principles for the successful implementation of Bacillus in agricultural practices.
Reviewing this perspective, I have the following comments and reservations that the authors need to rectify.
Table 1, "Aspects related to the use of Bacillus sp in agricultural production," is unclear and ambiguous. It needs elaborative and more specific information.
There are several typos and formatting mistakes to be corrected by the authors.
The use of abbreviations should be correct throughout the text. What is FDA's GRAS? this information is completely missing.
The use of scientific names is not consistent.
Comments on the Quality of English Language
Extensive English corrections are required.
Author Response
Reviewer2
Answer: We, the authors, thank the reviewer for the opportunity to improve our manuscript. We greatly appreciate your work and patience.
Reviewer2: Table 1, "Aspects related to the use of Bacillus sp in agricultural production," is unclear and ambiguous. It needs elaborative and more specific information.
Answer: The reviewer is right. Table1 was deleted.
Reviewer2: There are several typos and formatting mistakes to be corrected by the authors.
Answer: This has been revised accordingly.
Reviewer2: The use of abbreviations should be correct throughout the text. What is FDA's GRAS? this information is completely missing.
Answer: The reviewer is right. This sentence has been added to the text. “ Although B. subtilis and certain other species are classified as Generally Recognized As Safe (GRAS) by the Food Drug Administration (FDA) [87], the safety of new strains or genetically modified Bacillus species used in industrial applications must be thoroughly evaluated.”
Reviewer2: The use of scientific names is not consistent.
Answer: This has been revised accordingly.
Author Response File: Author Response.pdf
Round 3
Reviewer 2 Report
Comments and Suggestions for AuthorsDear Editor,
Thanks for sending me this prospect to evaluate and review it for publication in this journal.
In this version, I still have major concerns about Table 1 which has been removed instead of improving the ambiguities in the table. I suggest improving table 1 before submitting it for publication.
Secondly, I suggest that all authors get an idea from other prospects published in the field. Several prospects on the role of Bacillus have been published that may help to provide you with ideas on how to write and improve your version for publication in this journal. Several latest reports are missing in this review article.
Review articles and prospects should be clear enough for readers in the scientific community.
Thank you very much.
Comments on the Quality of English Language
Extensive editing of English language required.
Author Response
Reviewer2
Answer: The authors express their gratitude to reviewer2 for providing the opportunity to enhance the manuscript.
Reviewer2: In this version, I still have major concerns about Table 1 which has been removed instead of improving the ambiguities in the table. I suggest improving table 1 before submitting it for publication.
Answer: The table 1 has been improved and it has been incorporated to review.
Reviewer2
Secondly, I suggest that all authors get an idea from other prospects published in the field. Several prospects on the role of Bacillus have been published that may help to provide you with ideas on how to write and improve your version for publication in this journal. Several latest reports are missing in this review article.
Review articles and prospects should be clear enough for readers in the scientific community.
Answer: We, the authors, sincerely thank the reviewer for their thorough consideration and support of our manuscript. This manuscript has addressed the current subjects suggested by the reviewers, including changes in the classification of Bacillus sp.; the importance of Omics technology to Bacillus sp.; mode of action; consistency in field performance; reduction in nitrogen fertilization; reduction in phosphorus fertilization; compatibility with other inputs; impact on the soil microbiome; formulation and delivery methods; and integration into crop management systems.
Could the reviewer please suggest a study or subject to add to this review? We, really appreciate you help.
Author Response File: Author Response.pdf
