This study used a soil microcosm experiment to investigate the effects of straw incorporation on the relationship between soil fertility and greenhouse gas (GHG) fluxes, as well as the underlying microbial mechanisms. These are relevant and timely topics in the context of straw return and GHG mitigation. However, several issues need to be addressed before the manuscript can be considered for publication.

Introduction

1, The introduction mainly lists the effects of straw incorporation on CO2, CH4, and N2O emissions, but lacks a sufficient synthesis of the underlying regulatory mechanisms, particularly the microbially mediated processes involved in greenhouse gas production and consumption. As a result, the knowledge gap identified in the current version remains rather broad.

2, Although the study objective is stated at the end of the introduction, it has not been further distilled into clear scientific questions, and corresponding hypotheses are also lacking. The authors are therefore encouraged to explicitly state the scientific questions addressed in this study and to propose relevant hypotheses at the end of the introduction.

3, This study further conducted an indoor incubation experiment based on a 5-year field trial; however, the necessity of this design and its advantages over field observations have not been sufficiently explained in the introduction. The authors are advised to clarify the logical connection between the long-term field background and the subsequent indoor mechanistic investigation.

Materials and Methods

1, It is suggested that Section 2.1 be divided into two subsections: 2.1 Site description and experimental design and 2.2 Soil and straw sampling and preparation.

2, Line 64: Please clarify the physical condition of the straw (e.g., whether it was chopped or crushed, and its length range) and the depth at which it was incorporated. In addition, please explain why the rice straw was sieved through a 1 mm mesh during the incubation experiment (Line 73), and why the straw was fully mixed with the 0-15 cm soil layer (Line 89) instead of following the actual field situation.

3, Line 71: Please specify the temperature conditions used during the pre-incubation period.

4, Line 77: It would be helpful to add a photo of the experimental setup in the Supplementary Materials. Together with the schematic diagram, this would make the experimental procedure clearer.

5, Line 84: Why was 1.27 kg of soil used? Please clarify whether this amount was determined according to the actual field bulk density.

6, Line 96: Was the sampling conducted at a fixed time each day, for example, 9:00–10:00 a.m.? Please specify the sampling time and briefly explain the reason for this setting.

7, Line 99: Please clarify the purpose of taking 1 mL of gas from the silicone tube buried at the bottom, including what parameter it was used to measure or what role it played in the experimental design.

Results

1, According to the study objectives, soil fertility is one of the core concerns. However, the related results are currently mainly included under 3.1 Soil properties, where they are not sufficiently highlighted. The authors are suggested to strengthen the presentation of soil fertility-related results and consider reflecting this aspect more clearly in the subsection title.

2, No correlation analysis was conducted, yet terms such as “positively related to” and “negatively related to” are used in the Results section. Such wording is not rigorous without statistical support. The authors are advised to either perform correlation analysis or revise these statements to more descriptive expressions.

3, The incubation experiment included both flooding and drainage periods, and Fig. 1 shows that both CO2 and CH4 emissions peaked in each stage. However, the Results section does not describe these two periods separately. Since the experimental design clearly distinguished them, the authors are encouraged to further compare the emission patterns between the flooding and drainage periods. In addition, it is suggested that cumulative emissions in Table 2 be calculated separately for the two stages to better reflect their differences.

Discussion

1, The expression “We hypothesized that …” in Line 264 is not appropriate in the Discussion section. Research hypotheses should normally be presented in the Introduction rather than introduced for the first time in the Discussion. The authors are advised to move the hypothesis to the end of the Introduction and then discuss whether it is supported by the results.

2, The discussion of soil fertility is still insufficient. At present, the effect of ST1 on soil fertility is only briefly mentioned in one sentence (Line 266), which does not fully respond to the study objectives. The authors are encouraged to specify which soil fertility-related indicators were improved by ST1 and to further analyze the possible reasons based on the results.

3, The reason why ST1 did not significantly increase GWP is not clearly discussed. According to Table 2, although ST1 significantly increased the cumulative emissions of CO2 and CH4, it also significantly reduced N2O emissions, which likely explains why GWP did not increase markedly. This point should be stated more explicitly in the Discussion, together with the relative contributions of different gases to GWP. At present, the manuscript only discusses the reason for the increase in N2O under CK, while the overall effect of ST1 is not sufficiently addressed.

4, If the authors intend to emphasize the regulatory role of microbial changes in GHG or GWP, corresponding correlation analyses are recommended.

5, Line 293: There is a grammatical problem in this sentence. “Such as” should not be followed by a complete sentence, and the sentence structure should be revised.

6, Line 294: The phrase “The question is why …” is rather colloquial and adds little information. It is suggested to delete this expression.

Introduction

1, L38–45: The reported effects of rice straw incorporation on CH₄, CO₂, and N₂O emissions vary substantially across studies. As currently written, it is unclear whether this variability is primarily driven by differences in the amount of straw incorporated or by other environmental and management factors (e.g., soil properties, water management, climate, or fertilization practices). While the introduction indicates that reducing straw input may be a promising strategy for mitigating GHG emissions, it would be helpful to briefly discuss the mechanisms through which straw incorporation influences GHG fluxes. Providing this background would strengthen the rationale for investigating straw application rates and help justify the objectives of the study.

2, Please add hypotheses to the end of the introduction section.

Materials and Methods

L64-65: If available, it would be useful to include the depth of rice straw incorporation in the field plots from which soils were collected.

L65: The word “Besides” is not needed in this sentence.

L70-71: It is unclear whether plant residues and gravel were removed manually or by sieving. If sieving was used, please specify the sieve size.

L84: Please provide justification for the use 1.27 kg (dry weight) per pot – it seems it may be to reach 10 cm in depth, but the way it is written it is not entirely clear.

Results

L162-163: The relationships between TN, TC, available nutrients and CEC and straw incorporation rate are described as being ‘positive’, while BD was described as ‘negatively related’ to the rate. This terminology implies correlation – if a correlation analysis was conducted, it should be included in the Materials and Methods section.

Discussion

L263: The hypothesis should be moved to the Introduction section. It should also be stated more explicitly. In addition, the hypothesis would benefit from greater specificity. For example, were any of the treatments expected to improve soil fertility while minimizing increases in global warming potential (GWP)? Providing specific predictions would strengthen the rationale of the study.