Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Comments to authors

The manuscript titled “Potential of Paenibacillus dendritiformis as a plant growth-promoting bacteria of maize in infertile soil” lacks sufficient explanation for several aspects outlined in the comments below, particularly concerning the sampling sites, number of samples, and the isolation procedure of the strain of interest. The novelty of the work should be clarified, as well as the extent to which this study or strain provides advancements compared to previously published research.

line 30: “in vitro” should be italicized throughout the text

line 37: “(Zea mays)”  - remove brackets

line 86: add a full stop after “development”

Line 96-10: The sub-section 2.1 can be deleted

Line 102: use “coded as” instead of “identified as”

line 102: Rios-Reyes [27]

Line 103-104: Provide a strain code for the used Bacillus megaterium strain. Provide a reference to clarify why the strain was used as a control/what traits are characteristic (e.g., biocontrol, PGP..) for this strain. Where was the strain isolated from? Was it formulated into some biopesticide or similar?

lines 101-104: the sub-section 2.2. should be improved. The authors should explain the procedure of isolation (used medium, temperature/time for cultivation) of the strain of interest from the collected environmental sample. Also, what type of environmental sample do the authors refer to? How was the sample processed? How many samples were taken? The authors cited a certain manuscript; however, there is no information regarding the strain D28. Was it the only strain isolated? How was it the only one selected for work? Please provide more information.

Line 128: provide reference number for “Batista 2021”

Line 141: “Fusarium graminearum, F. oxysporum, and F. solani” – provide strain codes and references where the strains were published in order to confirm their identity. Are these the only fungal pathogens of maize in Mexico?

Line 185: “45 repetitions” – What did you mean by 45 repetitions? Please explain.

Figure 1 – Leave just “D28”, delete “isolated” on the phylogenetic tree

Line 240: “strains” - the authors analyzed just one strain. Please correct.

line 246: Different letters

Merge the sub-sections in Discussion into a single section.

Line 300: There is no need to refer to the results “Table 2” in the Discussion section

line 304: “This result” – what result? Please specify.

Author Response

For research article

 

Response to Reviewer X Comments
1. Summary
We sincerely appreciate your thorough review and constructive comments. All suggestions were carefully considered and incorporated into the revised manuscript. Below, we provide detailed responses to each point. In the revised version of the manuscript, all changes are highlighted in green.
2. Questions for General Evaluation	Reviewer’s Evaluation	Response and Revisions
Does the introduction provide sufficient background and include all relevant references?	Yes/Can be improved/Must be improved/Not applicable
Are all the cited references relevant to the research?	Yes/Can be improved/Must be improved/Not applicable
Is the research design appropriate?	Yes/Can be improved/Must be improved/Not applicable
Are the methods adequately described?	Yes/Can be improved/Must be improved/Not applicable
Are the results clearly presented?	Yes/Can be improved/Must be improved/Not applicable
Are the conclusions supported by the results?	Yes/Can be improved/Must be improved/Not applicable
3. Point-by-point response to Comments and Suggestions for Authors
Comments 1: The manuscript titled “Potential of Paenibacillus dendritiformis as a plant growth-promoting bacteria of maize in infertile soil” lacks sufficient explanation for several aspects outlined in the comments below, particularly concerning the sampling sites, number of samples, and the isolation procedure of the strain of interest. The novelty of the work should be clarified, as well as the extent to which this study or strain provides advancements compared to previously published research.
Response 1: We sincerely appreciate your valuable comments and observations. In the revised version of the manuscript, we have addressed all the issues you identified. Specifically, we added detailed explanations regarding the isolation and origin of the D28 strain. We also clarified the novelty of the study by expanding both the Introduction and the Discussion sections. Thank you for your constructive feedback, which has significantly contributed to improving the quality and clarity of the manuscript.
Comments 2: line 30: “in vitro” should be italicized throughout the text
Response 2: Thanks for the observation. The term in vitro has been italicized throughout the entire manuscript as suggested (Line 31).
Comments 3: line 37: “(Zea mays)” - remove brackets
Response 3: Thank you for the comment. The brackets around Zea mays have been removed as suggested (Line 38).
Comments 4: line 86: add a full stop after “development”
Response 4: Thank you for the observation. A full stop has been added after the word “development” as requested (Line 95).
Comments 5: Line 96-10: The sub-section 2.1 can be deleted
Response 5: Thank you for the suggestion. Sub-section 2.1 has been deleted from the manuscript as recommended.
Comments 6: Line 102: use “coded as” instead of “identified as”
Response 6: Thank you for the comment. The phrase “identified as” has been replaced with “coded as” in the manuscript as suggested (Line 114).
Comments 7: line 102: Rios-Reyes [27]
Response 7: Thank you for pointing this out. The author’s name has been corrected to “Ríos-Reyes” in the manuscript (Line 112).
Comments 8: Line 103-104: Provide a strain code for the used Bacillus megaterium strain. Provide a reference to clarify why the strain was used as a control/what traits are characteristic (e.g., biocontrol, PGP..) for this strain. Where was the strain isolated from? Was it formulated into some biopesticide or similar?
Response 8: We appreciate the reviewer’s observation and have substantially revised the text to improve clarity. The paragraph has been completely edited and new information added. We hope it is now clearer (118-122).
Comments 9: lines 101-104: the sub-section 2.2. should be improved. The authors should explain the procedure of isolation (used medium, temperature/time for cultivation) of the strain of interest from the collected environmental sample. Also, what type of environmental sample do the authors refer to? How was the sample processed? How many samples were taken? The authors cited a certain manuscript; however, there is no information regarding the strain D28. Was it the only strain isolated? How was it the only one selected for work? Please provide more information.
Response 9: We appreciate the reviewer’s careful observation. In response, sub-section 2.2 has been substantially expanded to include a clearer and more complete description of the origin and isolation of strain D28 (Line 1147-118).
Comments 10: Line 128: provide reference number for “Batista 2021”
Response 10: Thank you for noting this omission. The reference number for Batista (2021) has now been added in the revised manuscript, and the full citation has been included in the References section (Line 146).
Comments 11: Line 141: “Fusarium graminearum, F. oxysporum, and F. solani” – provide strain codes and references where the strains were published in order to confirm their identity. Are these the only fungal pathogens of maize in Mexico?
Response 11: Thank you for your valuable comment. In the revised manuscript, we have now added the corresponding strain codes and published references. To avoid misinterpretation, we also clarified in the text that these fungi were selected because they were accessible in the fungal collection of our institution (159-164).
Comments 12: Line 185: “45 repetitions” – What did you mean by 45 repetitions? Please explain.
Response 12: Thank you for pointing out this ambiguity. The term “45 repetitions” has now been clarified in the revised manuscript. Specifically, each treatment included 45 seeds (206-212).
Comments 13: Figure 1 – Leave just “D28”, delete “isolated” on the phylogenetic tree
Response 13: We appreciate the reviewer’s suggestion. The phylogenetic tree in Figure 1 has been updated accordingly: the label now displays only “D28,” and the word “isolated” has been removed.
Comments 14: Line 240: “strains” - the authors analyzed just one strain. Please correct.
Response 14: Thank you for the observation. The text has been corrected to refer to a single strain (264).
Comments 15: line 246: Different letters
Response 15: Thank you for your observation. The issue at line 246 has been corrected as suggested (Lines 270, 295, 311).
Comments 16: Merge the sub-sections in Discussion into a single section.
Response 16: The sub-sections in the Discussion have been merged into a single section as requested.
Comments 17:  Line 300: There is no need to refer to the results “Table 2” in the Discussion section.
Response 17: We appreciate the reviewer’s observation. The reference to “Table 2” in this sentence has been removed as requested. The text has been corrected accordingly.
Comments 18:  line 304: “This result” – what result? Please specify.
Response 18: Thank you for your comment. To address this issue, we revised the entire paragraph to improve clarity. The updated text now provides a more coherent explanation (Lines 331-332).
4. Response to Comments on the Quality of English Language
Point 1:
Response 1: No comments on the quality of English language
5. Additional clarifications
No additional clarifications

 

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors,

After reviewing the manuscript, I find the study valuable, but several key issues must be addressed before it can be considered for publication. The manuscript needs a clearer statement of novelty, stronger interpretation of physiological and plant-growth results, correction of data presentation inconsistencies, better integration of relevant literature, and more detailed methodological descriptions. With substantial revisions, the work has the potential to make a meaningful contribution.

1. Novelty and scientific contribution need clearer justification

 The novelty of using Paenibacillus dendritiformis as a maize PGPB remains unclear, as the species is already reported in maize and extreme soils. The Introduction must explicitly state the knowledge gap (e.g., no prior studies test volcanic-soil isolates for maize growth in infertile conditions), explain how volcanic origin may confer unique traits, and highlight relevance to sustainable agriculture amid climate-driven soil degradation. Currently, it provides background but fails to demonstrate how this work advances the field.

2. The physiological tolerance results are underinterpreted

The tolerance tests (temperature, pH, salinity) are well presented, but the Discussion lacks mechanistic explanations (e.g., membrane adaptations, osmolytes, extremozymes), comparisons with other Paenibacillus species, and implications for field use in degraded Mexican soils with high salinity or pH extremes. It currently repeats general PGPR concepts instead of interpreting this strain’s specific traits.

3. Biocontrol Results Contradict Claims in the Abstract and Introduction

The study found no biocontrol activity against Fusarium spp. through either direct antagonism or volatile organic compounds. However, the Abstract claims that “PGPB can mitigate this problem,” implying biocontrol capacity, while the Introduction strongly emphasizes biocontrol mechanisms of PGPB, creating a clear mismatch. To resolve this, the authors must explicitly state that biocontrol was tested but not observed, discuss possible reasons for the absence of antifungal activity despite reports in other Paenibacillus species, and avoid overstating the multifunctionality of the strain.

4. Vigor test data interpretation needs correction and clarification

Tables 4 and 5 reveal only very small differences between treatments (e.g., ~0.5 cm in root length), raising doubts about their biological or agronomic relevance despite statistical significance. Moreover, some reported “significant differences” appear numerically inconsistent, such as identical mean root lengths for uninoculated and inoculated treatments in Table 4. The manuscript fails to present effect sizes (e.g., Cohen’s d or percentage increase) and instead exaggerates the magnitude of plant growth promotion in the conclusions. The discussion and conclusions must be revised to acknowledge the modest magnitude of the effects and to discuss their realistic agronomic relevance more cautiously.

5. Several methodological limitations reduce the reliability and applicability of the results: no negative control was used for IAA production without tryptophan; high variability was observed despite an acceptable sample size; soil physicochemical changes were not assessed post-inoculation; and no multi-environment field trials were conducted. Consequently, because all experiments were in vitro or short-term pot trials, conclusions about practical agricultural use remain premature.
6. The manuscript contains several inconsistencies in data presentation, for example temperature tolerance results described in the text contradict Table 3, statistical annotations in tables are insufficiently explained, and Figure 1 lacks critical details such as scale bars and accession numbers; therefore, clearer, standardized, and more precise data presentation is required.
7. The reported IAA concentration (0.306 µg/mL) and phosphate-solubilization index (1.95) are considerably lower than values typically associated with effective PGPB, yet the Discussion interprets them as strong indicators of plant growth promotion; the authors should more accurately contextualize these low values and avoid overstating their biological significance.
8. The conclusion overgeneralizes the results by claiming high tolerance and strong PGPB potential, even though the strain exhibited low NF, PSI, and IAA values and no biocontrol activity, and the observed plant growth effects were modest; therefore, the conclusion should be revised to accurately reflect the study’s actual findings and limitations.
9. Although the manuscript cites many studies, several references are not directly relevant to the research questions, making the narrative unfocused; the authors should streamline the literature, keeping only studies that support the central novelty and ensuring better integration into the introduction and discussion.
10. The abstract lacks a clear statement of novelty, uses vague descriptions instead of key quantitative results, and does not clarify that biocontrol activity was absent. The conclusion overstates the strain’s potential despite limitations, and the abstract would benefit from being more concise and focused, with keywords that better reflect the study’s unique aspects.

Good Luck!

 

 

Author Response

Dear Reviewer,

We sincerely thank you for the time and effort dedicated to reviewing our manuscript. We carefully considered each of your comments and addressed them in detail throughout the revised version. Our team worked to correct the issues you highlighted, aiming to substantially improve the clarity, scientific depth, and methodological rigor of the work.

To facilitate your review of the updated manuscript, all modifications made in response to your comments have been clearly marked in red. This includes textual corrections, expanded methodological descriptions, and the incorporation of additional references and clarifications.

Specifically, we revised the sections you pointed out as deficient, strengthened the methodological description, and integrated additional and more recent literature to better support our findings and discussion. We believe these changes have significantly improved the quality of the manuscript.

We truly appreciate your valuable suggestions, which have contributed to enhancing the scientific merit of our study. Please feel free to let us know if further adjustments are needed—we remain at your disposal for any additional corrections or clarifications.

 

Thank you again for your constructive feedback.

Kind regards,

Dra. Ortiz-Sánchez

Dr. Cabral-Miramontes

Reviewer 3 Report

Comments and Suggestions for Authors

The article “Potential of Paenibacillus dendritiformis as a plant growth-promoting bacteria of maize in infertile soil” presents detailed laboratory studies of maize growth promoters under unfavorable conditions. The conducted studies aim to reduce the impact of climate change and soil degradation on maize cultivation.

 

Observations:

1. The article presents a detailed research methodology for determining the influence of the bacteria Paenibacillus dendritiformis on plant growth and soil. Valuable results were obtained confirming the positive effect of these bacteria, however:
2. a) It seems that the conducted studies are necessary to confirm the obtained laboratory studies in growing maize in field conditions.
3. b) There is a lack of results on the impact of growth-promoting bacteria on maize growth, yield increase, and grain quality.
4. c) It is unclear how long it will take for the positive effect of these bacteria on maize growth to be clearly noticeable (in the first and second years of maize cultivation). Therefore, it would be appropriate to present the results of at least several years of research on maize cultivation under real conditions.
5. d) It should also be mentioned what influence the growth-promoting bacteria Paenibacillus dendritiformis used will have on other bacteria in the soil.

The material presented in the article is very relevant and valuable. I suggest supplementing the article, taking into account the observations made.

Author Response

For research article

 

 

Response to Reviewer X Comments
1. Summary
Thank you very much for taking the time to review this manuscript. We sincerely appreciate your observations and the time you dedicated to evaluating our manuscript. Below, we provide a point-by-point response to each of the comments you raised.
2. Questions for General Evaluation	Reviewer’s Evaluation	Response and Revisions
Does the introduction provide sufficient background and include all relevant references?	Yes/Can be improved/Must be improved/Not applicable
Are all the cited references relevant to the research?	Yes/Can be improved/Must be improved/Not applicable
Is the research design appropriate?	Yes/Can be improved/Must be improved/Not applicable
Are the methods adequately described?	Yes/Can be improved/Must be improved/Not applicable
Are the results clearly presented?	Yes/Can be improved/Must be improved/Not applicable
Are the conclusions supported by the results?	Yes/Can be improved/Must be improved/Not applicable
3. Point-by-point response to Comments and Suggestions for Authors
Comments 1: It seems that the conducted studies are necessary to confirm the obtained laboratory studies in growing maize in field conditions.
Response 1: We fully agree with your assessment. Field trials are indeed necessary to confirm the results obtained under laboratory conditions. At this stage of the project, the objective was exclusively to evaluate the potential of Paenibacillus dendritiformis under controlled conditions; therefore, field experiments will be conducted in subsequent phases of the study.
Comments 2: There is a lack of results on the impact of growth-promoting bacteria on maize growth, yield increase, and grain quality.
Response 2: We appreciate your comment regarding the absence of yield and grain quality variables. Indeed, parameters such as grain weight, number of grains per row, cob weight and diameter, as well as yield per hectare, will be evaluated in future stages of the project. Since these results correspond to a different and broader phase of the study, we consider that they will be presented in a subsequent manuscript.
Comments 3: It is unclear how long it will take for the positive effect of these bacteria on maize growth to be clearly noticeable (in the first and second years of maize cultivation). Therefore, it would be appropriate to present the results of at least several years of research on maize cultivation under real conditions.
Response 3: Regarding the period required to observe sustained positive effects of the bacterium on maize cultivation, we have not yet assessed its long-term performance. These analyses will be carried out once the project advances to the field trial stage, where it will be possible to monitor its behavior over several growing cycles.
Comments 4: It should also be mentioned what influence the growth-promoting bacteria Paenibacillus dendritiformis used will have on other bacteria in the soil.
Response 4: We acknowledge the importance of evaluating the influence of Paenibacillus dendritiformis on other soil bacteria. In this study, it was not possible to perform such an assessment because we worked with sterilized soil, with the purpose of attributing the observed changes in maize growth exclusively to the interaction with the inoculated strain. Nevertheless, we plan to address this microbial interaction in future studies conducted under non-sterilized conditions. We once again appreciate your valuable comments. We fully agree with them and consider that your observations represent important opportunities to strengthen and broaden the scope of this work.
4. Response to Comments on the Quality of English Language
Point 1:
Response 1: (in red)
5. Additional clarifications
There´s no any other clarifications.

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

I do not have further comments. 

Author Response

06 December, 2025

We sincerely thank you for your time and for evaluating our revised manuscript. We appreciate your confirmation that no further comments are needed. Your contribution has been valuable in helping us improve the quality and clarity of this work.

Thank you once again for your time and consideration.

Kind regards,

Dra. Ortiz-Sánchez

Dr. Cabral-Miramontes

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors

Please revise the manuscript thoroughly by addressing all reviewer comments, including the major suggestions provided for each section from the Abstract through to the Conclusion. Additionally, please revise and improve the Keywords, as this was an extra comment raised in the latest review round.

Kindly ensure that the revised manuscript reflects substantial improvements and incorporates all recommendations in a clear and scientifically sound manner.

Author Response

06 December, 2025

 

Dear Reviewer,

We sincerely appreciate the time and effort dedicated to reviewing our manuscript and for providing valuable comments that helped us improve its quality. The suggestions have been carefully addressed and incorporated into the revised version.

We would also like to clarify that, during the first review round, we were not fully familiar with the MDPI submission system, and unfortunately, we did not notice the attached annotated file containing the detailed comments. In this second round, we have thoroughly reviewed that document and have made every effort to implement the recommendations provided in the ten points indicated by the reviewer.

We hope that the revisions made contribute to strengthening the scientific soundness and clarity of the manuscript. We appreciate your understanding and the opportunity to further improve our work.

Thank you again for your constructive feedback.

Kind regards,

Dra. Ortiz-Sánchez

Dr. Cabral-Miramontes