Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

In the reviewed article, the authors assessed the impact of cultivating cover crops following inoculation with Bacillus cereus on soil condition (including nitrate nitrogen content and the activity of CAT, IA, and UA). Based on the conducted research, the authors indicated that the applied treatments led to changes in soil pH, an increase in nitrogen and potassium content, as well as enhanced activity of the analyzed enzymes. I find the topic interesting and timely in the context of the deteriorating condition of soils (increasing degradation) resulting from agricultural intensification. Nevertheless, I recommend making revisions which, in my opinion, will enhance the scientific value of the manuscript. My comments are presented below:

1. In the section describing the preparation of the inoculum, the authors refer to two strains (4.7 and 4.8), whereas in the experimental design only variants ZB1 and ZB2 associated with strain 4.8 are mentioned. It is necessary for the authors to justify why strain 4.7 was not used in the experiment, despite being included in the description of the study.
2. On page 3 (line 125), the authors state that the initial soil organic matter content was 2 g/kg, whereas in Table 1 (also for CK) these values are drastically lower. Therefore, I expect the authors to address this issue in more detail in the manuscript, providing a more thorough analysis of the reasons for such a significant decrease in SOM content in the soil.
3. The results presented in this manuscript are based on a one-year experiment, whereas (as the authors themselves note in lines 308–309) more reliable conclusions regarding the impact of cultivation practices on soil condition can be drawn from longer-term (multi-year) studies. In light of this, why was the experiment not extended?
4. The quality of Figure 3 must be improved. The labels are illegible.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

After reviewing the article, I make the following comments:

The article presents a duplication of identical text in the results and discussion sections (specifically between lines 312-326 and 332-345).

Although the title mentions "Synergistic Effects," the article describes the benefits of plants and bacteria, but it could delve deeper into the biological mechanism of the interaction.

• How does B. cereus specifically help the nodulation or root growth of Medicago sativa under thermal stress in the valley?
• Is there any production of phytohormones by the bacteria that enhances the effect of the cover crop?

Since the study analyzes bacterial communities, including a network analysis would significantly strengthen the microbiology section. This would allow:

• Identifying "key species" (hub taxa) that maintain community stability.
• Visualizing whether inoculation with B. cereus increases the complexity and connectivity of microbial interactions compared to the control.

The article focuses on the soil microenvironment (chemical and biological indicators), which is valuable. However, adding data (even preliminary) or a broader discussion on how these soil improvements translate into coffee plant physiology (e.g., chlorophyll content, photosynthetic rate, or projected yield) would provide a much more comprehensive agronomic value.

To make the results more intuitive, a Pearson correlation Heatmap linking the most abundant bacterial genera to soil variables (pH, Total Nitrogen, Enzyme Activity) could be included. This would complement very well the redundancy analysis (RDA) that is already available. Since the sampling was carried out at a specific point in time (October 2023), the article would be more complete if the system's resilience to seasonal variations in the Dry-Warm Valley were discussed. Is it expected that these benefits will be maintained during the extreme drought season or do they require periodic reinoculations? In the abstract and results, there are phrases that seem truncated or with punctuation errors (e.g., line 34: "enriched in taxa including Xanthomonas and Redundancy analysis identified..."). Ensuring that each mentioned taxon is correctly linked to its functional impact will improve clarity.

Regarding the bibliography, the following technical details must be addressed:

• Consistency in Style: Ensure that all citations strictly follow the journal's format. This includes the correct use of journal abbreviations, bolding the year, and italicizing the volume.
• Incomplete References: In the text (lines 165 and 186) authors such as "Guan [24]" and "Gao [26]" are mentioned. It is crucial to verify that in the final reference list these numbers correspond exactly to those authors and that no data is missing (such as the DOI, which is highly recommended to include nowadays).
• Self-citations: The research group appears to be affiliated with Southwest Forestry University. It is acceptable to cite previous work from the group if relevant, but care must be taken not to overdo it to maintain the manuscript's objectivity.

Regarding the conclusions

• "Synergy" as a Key Concept: Although the title talks about synergistic effects, the conclusions could be a little more explicit in explaining why the combination is better than the parts separately. For example, briefly mentioning that the bacteria enhance nitrogen fixation in legumes or improve their heat resistance in the valley.
• Future Perspective: It is common and advisable to include a brief sentence about what comes next. For example: "These findings lay the groundwork for long-term studies that evaluate the final productivity of coffee beans under this management regime." This opens the door to future research.
• Writing Correction: In line 35, it reads: "...identified total nitrogen as the primary environmental driver...". It would be ideal that in the conclusion it is reinforced that Total Nitrogen is the factor that most influences the change in bacteria, to close the cycle of the redundancy analysis (RDA) mentioned in the results.
• Long-term Perspective: Since bacterial diversity did not show significant changes in one year, it would be valuable to add a brief discussion on how long the authors estimate it would take to observe a deep structural change in species richness.

Regarding the tables and figures:

• Duplication in the Text: As previously mentioned, the text describing these figures appears duplicated (lines 312-326 and 332-345). This should be corrected, even though the figures themselves are correct.
• Resolution and Legends: Ensure that the axis labels in the PCoA and RDA graphs are in a font size readable for the final printed version, as bioinformatics software sometimes generates very small letters.
• Although PCoA and Adonis analysis figures are mentioned, it would be beneficial to include a heatmap that specifically correlates the enriched bacterial genera with chemical variables (such as TN and pH).

In what concerns the introduction

• There is a small redundancy in the sentence "In summary, this study employs a meticulously designed field experiment..." (lines 102-108), which somewhat repeats what was said in the previous paragraphs. It could be condensed so that the transition to the Materials and Methods section is more direct.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors have provided comprehensive explanations for my comments and have made the necessary changes to the manuscript. Therefore, I believe the article can be accepted for publication in its current form.