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Interaction Regulation Mechanism of Soil Organic Carbon Fraction and Greenhouse Gases by Organic and Inorganic Fertilization

Agronomy 2025, 15(9), 2166; https://doi.org/10.3390/agronomy15092166

by Jing Wang¹, Guojun Han^1,*, Chunbin Li¹, Mingzhu He² and Jianjun Chen³

Reviewer 1: Anonymous

Reviewer 2:

Ariel Villalolobos Olivera

Agronomy 2025, 15(9), 2166; https://doi.org/10.3390/agronomy15092166

Submission received: 4 August 2025 / Revised: 3 September 2025 / Accepted: 9 September 2025 / Published: 11 September 2025

(This article belongs to the Section Soil and Plant Nutrition)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

You have submitted a manuscript addressing the important issue of how food production and related soil fertilization affect soil carbon retention. Your work includes a large data set, but it presentation, description and discussion is not clear and clear discussed. The description of the results is very lengthy and does not highlight the most important achievements. The methodology contains numerous shortcomings, and the abbreviations used are often not explained, and sometimes in different, inconsistent ways. All of this makes the manuscript difficult to understand. I suggest carefully check and rebuild the manuscript. Some detailed comments are provided below.

Main comments
The manuscript is very lengthy. The description of the results and discussion is confusing, sometimes contradictory to the results, do not highlight the most important achievements and novelties of the work.

Did soil moisture change during the period studied? And could it have been a factor modifying the processes occurring in the soil?

All figures and tables should include a clear description of what they contain and what the abbreviations mean.

In “Discussion” section figures and tables should be also cited.

Detailed comments
Line 36
T0 was a control treatment?

Line 121, Tab. 1.
Table 1. What do the abbreviations in the table mean? Why do some appear twice (AN, AP), with different values presented underneath? Do they not refer to the same parameter?

Lines 125-128 and Table 2.
On what basis were the doses of organic fertilizer adopted?

Lines 138-141
Maybe the diagram would be clearer?

Lines 150-166
The entire fragment is repeated.

Line 183 – 184, 268-269
Why do you sometimes use capital letters and sometimes not when explaining abbreviations?

Line 192 – 198
Lack of source literature. The description is incomplete, and no measurement equipment is listed.

Line 205
What means “MAOC”?

Line 206
Incorrect citation.

Lines 218-219
Lack of citation, add source for this methodology.

Line 223-224
CO2 concentration was measured by using FID? Porapak Q chromatographic column was sufficient?

Line 250
“Total organic carbon (TOC)” - How was it determined?

Line 265, section “Results”
Be careful when using the word "significantly." This term should be supported by statistically significant differences. This is not always the case in manuscripts. The "Results" section needs to be reviewed and improved. A more concise and clear description of the results is needed.

Line 328, Fig. 1
What was the reason of increase e.g. TOC during flowering an fruiting stages?

Lines 338, 244
SOC or TOC? What abbreviation is correct?

Lines 258, 411-412, 418-419
What do CPI and CPMI actually mean?

Line 444-445
What does this sentence mean?

Line 463
Figure 3. What unit of time did CO2 and CH4 emissions occur in?

Figure 3 consist of 5 graphs, they should be additionally market by letters to be more clear. Why is methane represented as a negative value?

Lines 481-482, 767, 778, 903 and et cetera
Methane is produce by representatives of Archaea, that is not bacteria.

Line 513
NPK – what does it mean? How was it calculated?

Line 527
Not only correlation between soil organic carbon components and cumulative emissions of CH4 and CO2 are presented. Additionally, if these numbers in the tables represent correlation coefficients, haven't the colours been confused?

Lines 532-535
Rebuild this sentence to be more clear.

Line 582
Explain the role of tail grass in the experiment or correct the parts of the text where it is mentioned to make them clear?

Lines 547, 455
What mean HOC? And ROC?

Lines 591-594
“The negative correlation between stable carbon pools (e.g., MOC) and CO₂ emissions increased significantly (P < 0.01) during the bud stage, reflecting that the "negative contribution" of stable carbon pools to CO₂ emissions increased with the increase in fertilizer requirement of the crop”
I do not understand. Additionally, according to Figure 4, the mentioned correlation was statistically significant and positive in flowering and fruiting stages and positive but not statistically significant in buding stage..

Lines 765-767
According to this explanation, in the remaining variants, CH4 emissions should be at least equal to those in variant T0. Further explanation is needed as to how additional carbon (organic fertilizer) could reduce methanogenic activity?

Comments on the Quality of English Language

The sentences are too convoluted. Proofreading by a native speaker is necessary.

Author Response

Response to Reviewer 1 Comments

Dear reviewer:

Thanks for your letter and for reviewer's comments concern our manuscript entitled “Interaction regulation mechanism of soil organic carbon fraction and greenhouse gases by organic and inorganic fertilization” (Manuscript ID: agronomy-3828262). We are very grateful to the reviewers for their valuable comments and suggestions on our article, which has been of great help in our manuscript revision. The reviewer comments are laid out below in italicized font and specific concerns have been numbered. Our response is given in normal font and changes/additions to the manuscript are given in the green text.

Point-by-point response to Comments and Suggestions for Authors:

Comment 1:

The manuscript is very lengthy. The description of the results and discussion is confusing, sometimes contradictory to the results, do not highlight the most important achievements and novelties of the work.

Response 1:

Thank you for your careful review and constructive feedback on this manuscript. We greatly appreciate the time and effort you have invested in evaluating this manuscript and have carefully considered your comments regarding length, clarity, and emphasis on key innovations. We will revise the discussion and conclusions based on your specific comments below and streamline the entire manuscript to highlight the main findings of the study. After consolidating the entire text, we have shortened its length.

Comment 2:

Did soil moisture change during the period studied? And could it have been a factor modifying the processes occurring in the soil?

Response 2:

Thank you for raising this important issue regarding soil moisture dynamics. We appreciate your concern about environmental variables that may influence soil processes and would like to clarify the background of our experiment and the reasons for not explicitly analyzing soil moisture changes:

Although we acknowledge that precipitation variability inevitably led to spatiotemporal fluctuations in soil moisture during the study period, our experimental design did not include artificially designed soil moisture gradients. All treatments were conducted in adjacent plots within the same field, exposed to the same climatic conditions (including natural precipitation and irrigation practices). Therefore: Soil moisture dynamics were spatially uniformly distributed across all treatments, and temporal variations affected all plots to the same extent during the study period. Although soil moisture may regulate these processes in the soil, its consistent variability across treatments means it does not confound comparisons between different fertilization regimes. This allows us to attribute the observed differences primarily to fertilization practices rather than moisture variability.

We acknowledge that soil moisture may influence: microbial activity and decomposition rates; diffusion processes affecting gas emissions; and organic matter solubility and transport. However, under our experimental conditions, these mechanisms would act uniformly across all treatments, thereby minimizing their impact on the analysis of fertilizer effects.

In response to your valuable suggestion, we will introduce soil moisture sensors in future experiments to quantify their dynamic changes and study the interaction between fertilization regimes and controlled soil moisture gradients.

Your inquiry highlights the importance of environmental context in soil carbon research. We have added a brief note in the limitations section of the revised manuscript acknowledging that soil moisture may be a potential regulator of soil processes, while clarifying its experimental equivalence across different treatment groups.

Once again, thank you for your insightful feedback, which has further enhanced the rigor of our work.

Comment 3:

All figures and tables should include a clear description of what they contain and what the abbreviations mean.

Response 3:

Thank you for your valuable feedback. We have carefully revised all figures in the manuscript. Each figure now includes a concise caption explaining its content, and all abbreviations are clearly defined in the caption or upon their first appearance in the main text to avoid ambiguity.

Comment 4:

In “Discussion” section figures and tables should be also cited.

Response 4:

We sincerely appreciate your valuable feedback and for bringing this issue to our attention. We are deeply grateful for your careful review of the manuscript and constructive guidance, which have been instrumental in helping us improve the manuscript.

We sincerely apologize for failing to cite Figure 1 in the discussion section during the initial submission. During the discussion process, we directly quoted from the results analysis section, which is why the discussion did not include a citation for the figure. We have now thoroughly revised the manuscript to ensure that the discussion section appropriately cites all relevant figures.

Comment 5:

Line 36 T0 was a control treatment?

Response 5:

Thank you for your careful review and valuable comments on this paper. We sincerely apologize for the confusion caused by the ambiguous description of “T0” in line 36. To clarify, T0 is not treated as a control group but as an independent T0 treatment (100% chemical fertilizer application). We have revised the manuscript accordingly. Additionally, as you pointed out, the paper is quite lengthy, which may have affected clarity. We have completely restructured and simplified the abstract to succinctly highlight the core objectives, methods, and key findings of the study. The revised abstract now aligns more closely with the scope of the study and avoids unnecessary repetition.

Comment 6:

Line 121, Tab. 1. Table 1. What do the abbreviations in the table mean? Why do some appear twice (AN, AP), with different values presented underneath? Do they not refer to the same parameter?

Response 6:

Thank you for carefully reviewing and pointing out this issue. We sincerely apologize for the incorrect repetition of the abbreviations “AP” and ‘AN’ in the “Soil Background Values” section of Table 1. This was an unintentional error that occurred during data preparation, and we fully recognize the confusion that this error may have caused. The error has been corrected in the revised version. The revised Table 1 (attached below for your reference) clearly distinguishes these parameters and ensures that there are no duplicate entries. This table shows the soil nutrient content before fertilization. SOC, TN, TP, TK, AP, AN, and AK represent soil organic carbon, total nitrogen, total phosphorus, total potassium, available phosphorus, alkaline-hydrolyzable nitrogen, and available potassium.

Table 1. Soil background values

Indicator

SOC

(g·kg^-1)

(mg·kg^-1)

Value

8.12

8.32

0.56

0.82

28.00

117.40

76.42

237.70

Comment 7:

Lines 125-128 and Table 2. On what basis were the doses of organic fertilizer adopted?

Response 7:

Thank you for your insightful comments and for prompting us to further clarify the rationale behind our fertilizer application strategy. We appreciate your attention to detail, which has encouraged us to strengthen the explanation of our experimental design.

Regarding the fertilizer application rates, we initially adopted the amounts based on local farmers' practical experience to ensure relevance to real-world agricultural practices. For treatments T20–T80, the organic fertilizer doses were standardized relative to the nitrogen (N) content of the T0 control treatment. We would like to clarify that the organic fertilizer we used contained fixed ratios of N, phosphorus (P), and potassium (K), which prevented independent adjustment of individual nutrients.

Given this constraint, we prioritized aligning the total nutrient input across treatments by using N as the primary reference point. This approach was chosen because:

It ensured consistency in N supply, a critical factor for crop growth;

It resulted in near-balanced potassium (K) levels due to the proportional relationship between N and K in the fertilizer;

While phosphorus (P) levels showed slight discrepancies, these were relatively minor when scaled to our experimental plot sizes and did not compromise the overall validity of the nutrient balance.

We acknowledge that this method does not achieve perfect balance of all nutrients, but under experimental conditions, it is the most feasible and agronomically sound approach. To enhance transparency, we have included supplementary calculation tables below and calculated the fertilizer application rates within the plots.

Comment 8:

Lines 138-141. Maybe the diagram would be clearer?

Response 8:

Thank you for your constructive suggestion. We fully agree that a visual aid would enhance clarity. As recommended, we have added a schematic diagram to illustrate the experimental plot layout in Lines 128. This diagram explicitly shows the design and spatial arrangement of the treatment plots, ensuring the description is more intuitive and accessible. For your convenience, we have attached a schematic diagram below.

Comment 9:

Lines 150-166.The entire fragment is repeated.

Response 9:

Thank you for highlighting this issue. We sincerely apologize for the unintended repetition in Lines 150-166. As recommended, we have comprehensively reorganized and rewritten Section 1.2 (now corresponding to Lines 96-123 in the revised manuscript) to eliminate redundancies and enhance logical flow.

The revised section now presents a clear, concise description of the experimental design without overlapping content. We appreciate your careful review, which has helped us refine the manuscript’s structure and readability.

Comment 10:

Line 183 – 184, 268-269. Why do you sometimes use capital letters and sometimes not when explaining abbreviations?

Response 10:

We appreciate your attention to detail, which has helped us improve the manuscript’s professionalism and clarity. We sincerely apologize for the inconsistent use of capital letters when explaining abbreviations in Lines 183-184 and 268-269. As per your feedback, we have standardized all abbreviation explanations in the revised manuscript to use lowercase letters for consistency

We have thoroughly reviewed the entire text to ensure uniform formatting of abbreviations and avoid similar issues.

Comment 11:

Line 192 – 198.Lack of source literature. The description is incomplete, and no measurement equipment is listed.

Response 11:

We sincerely appreciate your feedback. This section describes the methods for measuring soil physical and chemical properties, which we have followed according to the methods outlined in the reference [22] (Bao, S. Soil agrochemical analysis. Beijing: China Agricultural Press, 2000: 30-34). This book is a textbook on soil indicator analysis for Chinese graduate students and members of the public, and it has a certain degree of authority. If we were to list the specific methods in detail, it would be too complicated, so we have not included them. We hope you understand. To help you understand, we have included the measurement table in this reply for your reference.

Detection indicators	Measurement methods	Main Instruments
Soil organic matter	Potassium dichromate oxidation by external heating	Oil bath digestion unit (including oil bath and wire cage), adjustable temperature electric furnace stopwatch, automatic temperature control regulator
Total soil nitrogen	Semi-micro Kjeldahl	Cooking Furnace, Automatic Nitrogen Determinator
Total soil phosphorus	HClO₄-H₂SO₄	Decoction Oven, Spectrophotometer Model 721
Total soil potassium	Sodium hydroxide melt-flame photometric	High-temperature muffle furnace, silver crucible, flame photometer
Soil alkaline nitrogen Decomposition	Alkaline diffusion	Diffusion dishes, semi-microburettes, thermostats
Soil effective phosphorus	0.5mol·L^-1NaHCO₃	Thermostatic oscillator, spectrophotometer or colourimeter
Soil fast-acting potassium	Ammonium acetate leaching - flame photometric	Thermostatic oscillator, flame photometer
pH	potentiometric	pH acidimeter or pH ionometer, pH glass electrode, reference electrode

Comment 12:

Line 205.What means “MAOC”?

Response 12:

Thank you for your careful review. We sincerely apologize for the typographical error "MAOC," which should have been consistently referred to as mineral-associated organic carbon (MOC), as defined earlier in the manuscript. This discrepancy has been corrected in the revised version to ensure terminology consistency(Line 162).

Comment 13:

Line 206.Incorrect citation.

Response 13:

Thank you for identifying the incorrect citation in our manuscript.

We agree that the previous citation (Reference 25) at this point was not appropriate. We have now replaced it with a more relevant and accurate reference that directly supports our statement.

The new citation is:

Zhang J.Y.; Zhang W.J.; Xu M.G.; Hunag, Q.H.; Luo, K. Response of red soil organic carbon and its particulate fractions to different fertilization patterns under long-term fertilization. Journal of Plant Nutrition and Fertilizers 2012, 18(04), 868-875.

We believe this reference provides a much stronger foundation for our argument. Thank you again for your careful review

Comment 14:

Lines 218-219.Lack of citation, add source for this methodology.

Response 14:

Thank you for pointing out this omission.

We agree that a citation was needed to credit the source of the methodology described in Lines 218-219. We have now added reference [7] to this sentence, as it provides a detailed elaboration of this specific method.

We appreciate your diligence in ensuring the completeness of our manuscript.

Comment 15:

Line 223-224. CO2 concentration was measured by using FID? Porapak Q chromatographic column was sufficient?

Response 15:

Thank you for your valuable feedback. We fully agree with your concern that the use of a FID detector and N₂ carrier gas alone is not sufficient for the effective detection of carbon dioxide (CO₂). We apologize for the lack of clarity in the previous wording and have made the necessary corrections in the revised version (lines 175-189).

In practice we use a stable catalyst gas analysis gas chromatography (GC) method developed by Agilent for the analysis of gases produced by the carbon dioxide technology.

The GC is a multi-dimensional design that uses thermal conductivity and a flame ionization detector (FID) combined with a nickel catalyst to analyse hydrogen (H₂), oxygen (O₂), nitrogen (N₂), methane (CH₄), carbon monoxide (CO), carbon dioxide (CO₂), and hydrocarbons from C1 to C6. The design is unique in its ability to measure both permanent gases and hydrocarbons. The system detects H₂, O₂, N₂, CH₄, CO, and CO₂ up to the 100 ppm limit using TCD, and detects CH₄, CO, CO₂, and hydrocarbons from C2 to C6 at the 0.1 ppm level using Catalyst-FID, allowing for greater detection range.

The catalyst-FID method we use uses two Agilent HP-PLOT Q PT columns for separation.

Comment 16:

Line 250.“Total organic carbon (TOC)” - How was it determined?

Response 16:

Thank you for raising this important question regarding the determination of organic carbon. We are pleased to clarify our methodology in this regard. In our study, the determination of soil organic carbon was performed using the potassium dichromate oxidation method (Walkley-Black method).

We will revise the manuscript to accurately describe the method as “potassium dichromate oxidation method” or “SOC” to avoid confusion with the term “TOC.” Once again, thank you for your rigorous review.

Comment 17:

Line 265, section “Results”.Be careful when using the word "significantly." This term should be supported by statistically significant differences. This is not always the case in manuscripts. The "Results" section needs to be reviewed and improved. A more concise and clear description of the results is needed.

Response 17:

Thank you very much for your valuable feedback. We fully agree with your perspective and apologize for any shortcomings in our manuscript.

Regarding the use of the term “significantly”: The issue you raised is very important. We will thoroughly review the entire manuscript (especially the results section) to ensure that the term “significant” is used exclusively to describe statistically significant differences (e.g., based on ANOVA or t-tests, p < 0.05). For instances where the term was previously used to describe larger numerical differences without statistical validation, we will replace it with more appropriate terminology, such as “substantial,” “marked,” “significantly increased (numerically),” or “notably.”

Regarding the clarity and conciseness of the results section: We will comprehensively revise this section to optimize its wording, making it clearer, more objective, and more concise. We will ensure that this section focuses solely on objectively presenting data results and statistical findings, avoiding any subjective interpretations or unnecessary repetition.

We believe these revisions will significantly enhance the quality and accuracy of our paper. Once again, thank you for your constructive feedback.

Comment 18:

Line 328, Fig. 1. What was the reason of increase e.g. TOC during flowering an fruiting stages?

Response 18:

Thank you for your insightful question regarding the increase in TOC during the flowering and fruiting periods. We are pleased to provide a more detailed explanation.

We believe that the increase in TOC observed during this critical reproductive period is primarily driven by a significant increase in carbon allocation to the underground parts of the plant. The specific reasons include:

Enhanced root exudation: The flowering and fruiting stages require substantial nutrients and water to support reproduction. To obtain these resources, plants increase the secretion of root exudates (such as sugars, organic acids, and amino acids) into the rhizosphere. These exudates serve as direct, readily available organic carbon sources, stimulating microbial activity and directly contributing to the SOC pool.

Increased microbial activity and residues: The abundance of available root exudates stimulates the growth and reproduction of soil microorganisms. The rapid turnover and death of these microbial cells (microbial residues) constitute an important and stable source of the soil organic carbon pool.

Root growth and turnover: Although root growth rates may slow compared to the vegetative growth stage, fine root turnover remains highly significant as plants optimize resource acquisition. The aging and decomposition of these fine roots add a large amount of particulate organic matter to the soil.

Mycorrhizal symbiosis: During fruit development, there is a high demand for phosphorus and other immobile nutrients. Plants typically enhance their symbiotic relationship with mycorrhizal fungi. Mycorrhizal fungi obtain carbon from the plant and transport it into the soil, further contributing to SOC.

Comment 19:

Lines 338, 244. SOC or TOC? What abbreviation is correct?

Response 19:

Thank you very much for your feedback. This was our mistake. As mentioned in response to comment 16, we initially intended to spell SOC as TOC, but failed to make the necessary corrections. Of course, as mentioned in comment 16, we have now corrected all instances to SOC.

Comment 20:

Lines 258, 411-412, 418-419.What do CPI and CPMI actually mean?

Response 20:

Thank you for pointing out this omission. We apologize for any confusion caused by not defining the abbreviations CPI and CPMI in the manuscript.

CPI stands for Carbon Pool Index. It is a ratio that compares the carbon pool in the treated soil to that in a reference soil (usually untreated or control soil). It is calculated as:

CPI = (Total Organic Carbon in Treatment Soil) / (Total Organic Carbon in Control Soil)

CPI > 1 indicates an increase in the total carbon pool relative to the control, while a CPI < 1 indicates a decrease.

CPMI stands for Carbon Pool Management Index. This is a comprehensive index that integrates both the size (CPI) and the lability (LI) of the soil organic carbon pool. It provides a single value to assess the overall effect of management practices on soil quality. It is calculated as:

CPMI = CPI × LI × 100(Where LI (Lability Index) = (Labile Carbon in Treatment / Non-labile Carbon in Treatment) / (Labile Carbon in Control / Non-labile Carbon in Control))

Higher CPMI value indicates a more favorable shift in soil organic matter quality towards a larger and more active (labile) pool, which is beneficial for nutrient cycling and soil health. (Lines 215-224)

Comment 21:

Line 444-445.What does this sentence mean?

Response 21:

Dear expert, We apologize for the unclear wording, We have revised this sentence in the revised draft(Lines 372-375).

This refers to: CH₄ cumulative emissions were reduced under all fertilization treatments, with a significant reduction trend observed compared to the T0, T40, T60, and T80 treatments. The T60 treatment reached the minimum value, indicating that the net absorption of CH₄ was highest under the T60 treatment.

Comment 22:

Line 463.Figure 3. What unit of time did CO2 and CH4 emissions occur in?

Figure 3 consist of 5 graphs, they should be additionally market by letters to be more clear. Why is methane represented as a negative value?

Response 22:

Thank you for this question. Figure 3 shows the cumulative emissions of CO₂ and CH₄, calculated based on the total emissions of CO₂ and CH₄ throughout the entire growing season. We have labeled each chart in Figure 3 with a letter.

The negative values for methane (CH₄) flux indicate that the soil ecosystem acted as a net sink for atmospheric methane, meaning it consumed methane from the atmosphere rather than emitting it.

This is a common convention in greenhouse gas flux studies:

Positive values denote net emissions from the soil to the atmosphere.

Negative values denote net uptake/consumption by the soil from the atmosphere

The Loess Plateau in Gansu Province has a relatively arid climate, with soil that is well-aerated most of the time and relatively high oxygen content. In this oxidizing environment, the soil contains a large number of methane-oxidizing bacteria, which can use methane as their sole carbon source and energy for growth and metabolism, oxidizing methane diffusing into the soil from the atmosphere into carbon dioxide and water. This results in the soil exhibiting net methane absorption, making soils with negative methane fluxes act as methane sinks, i.e., the soil absorbs methane from the atmosphere.

Comment 23:

Lines 481-482, 767, 778, 903 and et cetera. Methane is produce by representatives of Archaea, that is not bacteria.

Response 23:

Thank you very much for pointing out this critical error. You are absolutely correct. We sincerely apologize for the incorrect terminology used in the paper.

We mistakenly referred to all microorganisms involved in methane production as “bacteria.” As you correctly pointed out, the microorganisms responsible for methanogenesis are phylogenetically distinct from bacteria and belong to the domain Archaea, not Bacteria. This is a fundamental distinction in microbiology.

We will carefully revise the entire manuscript to correct this error. All instances where the term “bacteria” was incorrectly used (including but not limited to the paragraph you mentioned) will be replaced with the accurate terminology.

Thank you for your professional insights and thorough review, which have enhanced the scientific accuracy of our paper.

Comment 24:

Line 513.NPK – what does it mean? How was it calculated?

Response 24:

Thank you for raising this issue, which has helped us clarify an important statement in the manuscript.

In line 513, the use of the term “NPK” is not precise enough. We did not calculate a comprehensive NPK value. Our intention was to refer to the individual contents of total nitrogen (TN), available phosphorus (AP), total potassium (TK), and available potassium (AK) in the soil.

The correlation analysis was conducted separately for these nutrient elements (in relation to carbon content and gas emissions).

We apologize for any confusion caused by this oversight. We will revise the manuscript to clearly state: “The correlation between TP, TN, AK and AP content and carbon content and gas emissions at fruiting time tended to weaken, with most cases showing no significant relationship.”(Lines 428-429)

Comment 25:

Line 527.Not only correlation between soil organic carbon components and cumulative emissions of CH4 and CO2 are presented. Additionally, if these numbers in the tables represent correlation coefficients, haven't the colours been confused?

Response 25:

Thank you very much for your careful review of our data. We sincerely appreciate you pointing out this inconsistency.

You are absolutely correct. In the previous version, the color scheme for correlation coefficients was indeed reversed from that of ellipses and numerical values. Specifically, positive correlations were incorrectly displayed in the colors that should have been used for negative correlations, and vice versa.

We have corrected this error in the revised version. The color scheme for the new figures has been standardized:

Blue (or cool tones) now always represents positive correlation.

Red (or warm tones) now always represents negative correlation.

This correction ensures that the colors, the direction of the ellipses, and the signs of the correlation coefficients are fully consistent.

Once again, we sincerely thank you for this critical correction, which significantly enhances the clarity and accuracy of our presentation.

Comment 26:

Lines 532-535.Rebuild this sentence to be more clear.

Response 26:

We apologize for the lack of clarity in this passage and have rewritten it: “In this study, the analysis of results revealed that the replacement of chemical fertilizers with organic fertilizers made from vegetable waste had a significant regulatory effect on soil carbon pool dynamics, and that this effect varied significantly depending on the growth stage of the chili peppers.”

Comment 27:

Line 582.Explain the role of tail grass in the experiment or correct the parts of the text where it is mentioned to make them clear?

Response 27:

Thank you for your comment, which provides us with an opportunity to improve the clarity of our discussion.

The role of experimental tail grass (vegetable residues) as an organic amendment is indeed described in the introduction, where we explain its potential role as a source of organic matter that may affect soil carbon dynamics and greenhouse gas emissions.

However, we agree that re-stating its primary role in the discussion section will aid reader understanding without requiring them to refer back to previous content. We will revise the text near line 582 to include the following statement:

“As mentioned in the introduction, the application of tail grass provides an easily accessible source of organic carbon, which we hypothesize will stimulate microbial activity and thereby influence greenhouse gas emissions. Our results show...”（Lines 462-468）

This revision will directly link the discussion to the experimental setup and initial hypothesis. Thank you for suggesting this clarification.

Comment 28:

Lines 547, 455.What mean HOC? And ROC?

Response 28:

Thank you for your careful review and questions.

“HOC” and “ROC” are specific abbreviations used in the titles of the cited references (e.g., in those studies, “HOC” stands for “humified organic carbon”and “ROC” stands for “reactive organic carbon”). These concepts are not the subject of our analysis or discussion in this paper.

Based on your feedback, we acknowledge that these abbreviations could potentially cause confusion for readers. Therefore, to streamline the reference list and maintain a focus on the most relevant literature, we have removed these citations from the manuscript.

The revised manuscript now includes only content directly relevant to our research.

Comment 29:

Lines 591-594. “The negative correlation between stable carbon pools (e.g., MOC) and CO₂ emissions increased significantly (P < 0.01) during the bud stage, reflecting that the "negative contribution" of stable carbon pools to CO₂ emissions increased with the increase in fertilizer requirement of the crop”
I do not understand. Additionally, according to Figure 4, the mentioned correlation was statistically significant and positive in flowering and fruiting stages and positive but not statistically significant in buding stage.

Response 29:

We sincerely thank you for identifying this critical error in our interpretation. We sincerely apologize for this mistake in our writing, which significantly misrepresents the findings.

You are absolutely correct. The original meaning of this sentence is that there is a positive correlation between the bud stage, the flowering and fruiting setting stage, and the fruiting stage. Of course, there is indeed a misunderstanding here, and we have already corrected it in the revised draft. The corrected text is attached below. At the same time, we apologize for the error in the text. This is a positive correlation rather than a negative correlation, which was an error in our writing process.

Revised paragraph: “The positive correlation between stable carbon pools (e.g., MOC) and CO₂ emissions increased significantly (P < 0.01) during the flowering and fruit setting stage, reflecting that the "positive contribution" of stable carbon pools to CO₂ emissions increased with the increase in fertilizer requirement of the crop.”

Comment 30:

Lines 765-767. According to this explanation, in the remaining variants, CH4 emissions should be at least equal to those in variant T0. Further explanation is needed as to how additional carbon (organic fertilizer) could reduce methanogenic activity?

Response 30:

We sincerely thank you for this incredibly insightful comment. You have rightly pointed out a logical paradox that our original explanation failed to address: why would adding more organic carbon substrate reduce methane emissions?

We apologize for the overly simplistic and somewhat assertive initial explanation. Upon re-evaluation, we believe the phenomenon is better explained by a shift in microbial metabolic pathways driven by the quality of the organic fertilizer, rather than a direct inhibition of methanogens.

The addition of tail grass fertilizer provided a pulse of labile organic carbon, which primarily stimulated the activity of heterotrophic aerobic and facultative anaerobic microorganisms. This led to a competitive inhibition of methanogenesis. Specifically, other anaerobic microbes, such as sulfate-reducing bacteria (SRB) and iron-reducing bacteria (FeRB), which have a higher substrate affinity for common precursors (e.g., H₂, acetate), outcompeted methanogens for these resources. Thus, the carbon flow was diverted away from methane production towards other anaerobic respiratory pathways.

We have thoroughly revised the relevant section in the manuscript (Lines 761-771) to reflect this more nuanced and accurate interpretation based on microbial ecology principles. Thank you again for pushing us to improve the quality of our discussion.

Other clarifications:

Again, thank you very much for your valuable comments and suggestions. We hope that the revisions in the manuscript and our accompanying responses will be sufficient to make our manuscript suitable for publication in Agronomy.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

It is an honor for me to contribute to the manuscript review of the article titled “Interaction regulation mechanism of soil organic carbon fraction and greenhouse gases by organic and inorganic fertilization.”

Keywords
I suggest using terms that are not part of the title, as it is best practice in scientific writing for keywords. The current section reuses words that already appear in the title; selecting distinct keywords will improve indexing and readability.

Introduction
The introduction addresses several topics—fertilization, soil carbon, residues from leafy vegetables, greenhouse gas emissions, and CPMI (define the acronym when first used)—without a clear thread or an explicit research question. While it cites literature on fertilization, soil carbon, and emissions, the knowledge gaps that the study aims to fill are not clearly articulated. I recommend: (1) clearly stating the research question or hypotheses; (2) explicitly identifying the concrete gaps in knowledge these questions address; and (3) clarifying why the study is important for indoor horticulture soil management and for achieving lower emissions. Emphasizing these gaps will provide a stronger rationale and guide the reader through the study’s significance.

The introduction consists of two very long paragraphs, which hinder comprehension. Similarly, there are paragraphs that are overly lengthy and not conducive to this type of scientific article. I recommend using sentences that specify the results and, when possible, dividing long paragraphs into shorter sections.

There are several problems of redundancy and lack of coherence. I suggest reworking the introduction to move from the general context of the research to the specific aspects, highlighting the state of the art on the topic, the novelty, and the problem to be solved.

Materials and Methods
In the Materials and Methods section, there is, in general, redundancy and a lack of clarity in the methods. In addition, there are repetitions in the description of the organic fertilizer and its composition, which is repeated several times. I suggest describing the fertilizer once in the text.

Experimental design
Although a multifactorial block design with six treatments is stated, several critical details are missing. The size of the blocks and the number of plots per treatment within each replication should be described. Reference should be made to the randomization of plots and the method of treatment assignment. In addition, the total number of plots and their arrangement (experimental layout, blocks, etc.) should be described. I recommend including a diagram or table that outlines the experimental design, the total size of the experiment, and the randomization method.

In soil management, the description of fertilizer composition is repeated again, and the substitution between chemical and organic fertilizers remains unclear, as it does not specify which specific nutrients were substituted in each treatment beyond the general ratio. If you keep this structure, I suggest presenting a clear table with the exact amounts of N, P₂O₅, and K₂O supplied by each treatment, as well as the source of each nutrient and the date of each application. It should be specified whether the total N, P, and K input was constant across treatments.

Sampling details are lacking in several areas:

Soil sampling depth for organic carbon (OC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and mineral-associated organic carbon (MAOC).
Soil sampling methods (number of pits per plot, composite sampling).
Sampling frequency and sampling times throughout the crop cycle.
Plant sampling (if plant-dependent parameters were measured; sample size).

In this section, specify depths (e.g., 0–20 cm, 20–40 cm), the number of replications per plot, the sampling protocol, and the sampling schedule.

Analytical methods
I recommend greater brevity in the methods and citing specific references without detailing critical conditions (reagents, extraction conditions, times, temperatures, equipment).

At this stage, include key operational parameters for each method: solvents/reagents, volumes, temperatures, extraction times, result normalization, and any calibration or quality-control procedures, while also referencing the specific sources.

Measurement of greenhouse gases
You describe weekly measurements with static chambers and GC, but the following aspects are not addressed:

Chamber size, air volume, sampling rate, and sample volume.
Method calibration.
GC calibration details (gas standards, precision, detection limit).
How temporal variability was handled (time of day, meteorological conditions) and whether temperature corrections were applied.

I suggest adding complete equipment specifications, calibration protocols, and quality-control procedures, and a sampling scheme for CH4 and CO2 (number of replicates per plot, handling of weather conditions).

Calculations and formulas
Equations are presented but definitions of variables and units are missing. I suggest presenting equations with a clear list of symbols and units. Verify unit consistency throughout the manuscript and provide a calculation example to illustrate the procedure.

Statistical analysis
It is stated that Excel was used. If other statistical software was used, specify which ones and what analyses were performed, including the type of analysis for each case. Consider correcting for multiple comparisons if many tests are performed. Indicate whether standard errors or confidence intervals were reported.

Results
In Figure 1, there is no statistical analysis indicated in the figure caption. Additionally, the abbreviations are not described, and the information is generally incomplete. I recommend including in the figure caption: statistical analysis, sample size used, and a definition of what each abbreviation in the figures represents.

For Figure 2, I suggest adding the sample size and detailing what each abbreviation in the figure means.

For Table 3, propose including the type of statistical analysis in the table caption. Also, the abbreviations are not described, and the information is generally incomplete. I recommend adding in the table caption: statistical analysis, sample size used, and a definition of each abbreviation used in the figures.

Figure 3 should also include the sample size, definitions of all abbreviations used in the figures, and the statistical analysis employed. In the figure where GHGI is defined as the ratio of GWP to crop yield, more information is required to indicate whether statistical differences exist.

The presentation of the results is in a single, very long paragraph, which makes it difficult to grasp the results. I suggest reworking the paragraphs and dividing them into several sections, organizing the results to improve comprehension. The subsections below indicate where these issues occur:
3.1 Effect of fertilization practices on soil total organic carbon and its fractions
3.2 Effect of fertilization practices on the proportion of soil organic carbon fractions
3.3 Effect of fertilization practices on soil carbon pool management indices
3.4 Effect of fertilization practices on yield and cumulative CH4 and CO2 emissions
3.5 Correlation analysis of soil organic carbon fractions and nutrients with cumulative CH4 and CO2 emissions

Discussion
The discussion is not clear, and there are grammatical errors. Relevant research references should be used. Avoid statements that depend on unverified studies or studies not accessible to readers.

The presentation of the discussion is in very long paragraphs, which makes it difficult to grasp the results. I recommend reworking the paragraphs and dividing them into several sections, organizing the discussion so that it is easier to follow. The subsections below indicate where these issues occur:
4.1 Effect of fertilization practices on soil total organic carbon and its fractions
4.2 Effect of fertilization practices on the proportion of soil organic carbon fractions
4.3 Effect of fertilization practices on soil carbon pool management indices
4.4 Effect of fertilization practices on yield and cumulative CH4 and CO2 emissions
4.5 Correlation analysis of soil organic carbon fractions and nutrients with cumulative CH4 and CO2 emissions

Author Response

Response to Reviewer 2 Comments

Dear reviewer:

Point-by-point response to Comments and Suggestions for Authors:

Comment 1:

Keywords. I suggest using terms that are not part of the title, as it is best practice in scientific writing for keywords. The current section reuses words that already appear in the title; selecting distinct keywords will improve indexing and readability.

Response 1:

Thank you very much for your suggestion. Your suggestion is entirely reasonable. We have reorganized the keywords according to your suggestion, ensuring that they are consistent with the central meaning of the text and avoiding repetition with the title. We have revised the keywords to the following five:

Fertilizer substitution ratio; Soil organic carbon fractions; Carbon pool management index (CPMI); Greenhouse gas emissions; Organic-inorganic fertilizer synergy

Comment 2:

Introduction. The introduction addresses several topics—fertilization, soil carbon, residues from leafy vegetables, greenhouse gas emissions, and CPMI (define the acronym when first used)—without a clear thread or an explicit research question. While it cites literature on fertilization, soil carbon, and emissions, the knowledge gaps that the study aims to fill are not clearly articulated. I recommend: (1) clearly stating the research question or hypotheses; (2) explicitly identifying the concrete gaps in knowledge these questions address; and (3) clarifying why the study is important for indoor horticulture soil management and for achieving lower emissions. Emphasizing these gaps will provide a stronger rationale and guide the reader through the study’s significance.

Response 2:

Thank you for your valuable comments! We have systematically restructured the introduction section based on your suggestions, with the following key improvements:

Clearly stated research questions, objectives, and hypotheses: We have transformed the implicit research objectives in the original text into specific research questions and hypotheses, highlighting the research motivation and innovative points.

Rearranged and simplified the content structure to enhance logical coherence: We have broken down and summarized the original lengthy paragraphs, streamlined the narrative sequence of “background—problem—method—objective—significance,” and removed repetitive and distracting content.

Unified terminology and expressions, refined sentences: standardized the use of professional terminology, simplified lengthy sentences, merged similar literature citations, and improved the accuracy and readability of academic expression.

Thank you for your feedback, which has significantly enhanced the professional expression of our introduction section.

Comment 3：

Materials and Methods. In the Materials and Methods section, there is, in general, redundancy and a lack of clarity in the methods. In addition, there are repetitions in the description of the organic fertilizer and its composition, which is repeated several times. I suggest describing the fertilizer once in the text.

Response 3:

Thank you for your valuable comments on the “Materials and Methods” section. We fully agree with your observations regarding the redundancy and lack of clarity in the methods section, as well as the repetitive descriptions of organic fertilizers and their components. As you correctly pointed out, this repetition was also noted by the first reviewer.

To address these issues, we have revised this section to ensure that the description of the fertilizer appears only once, is clear and concise, and all redundant information has been removed. The modifications we have made are highlighted in green text rather than yellow for your reference(Line 96-123).

Comment 4：

Experimental design. Although a multifactorial block design with six treatments is stated, several critical details are missing. The size of the blocks and the number of plots per treatment within each replication should be described. Reference should be made to the randomization of plots and the method of treatment assignment. In addition, the total number of plots and their arrangement (experimental layout, blocks, etc.) should be described. I recommend including a diagram or table that outlines the experimental design, the total size of the experiment, and the randomization method.

Response 4:

In response to your suggestions, we have added a schematic diagram of the experimental plots to facilitate a clearer understanding for readers. Regarding the specific details you mentioned:

The size of the blocks is specified in line 116 of the original text.

The number of plots per treatment within each replication, which is 3 times for each treatment, can be found in line 101.

As for the randomization of plots and the method of treatment assignment, as well as the total number of plots (18 in total) and their arrangement, these aspects were indeed described in the original manuscript, though perhaps not as prominently as they should have been. We have now revised the relevant sections to make these details more explicit and easier to locate.

We hope these revisions adequately address your concerns and improve the overall quality and readability of our manuscript. Thank you again for your valuable input, which has been instrumental in refining our work.

Comment 5:

Response 5:

Thank you for your valuable feedback, which has prompted us to further clarify the rationale behind our fertilizer application strategy. We appreciate your attention to detail, which has prompted us to strengthen our explanation of the experimental design.

Regarding fertilizer application rates, we initially determined the application rates based on the actual experience of local farmers to ensure relevance to actual agricultural practices. For the T20–T80 treatment groups, the application rate of organic fertilizer was standardized relative to the nitrogen (N) content of the T0 control group. We need to clarify that the organic fertilizer we used contains a fixed ratio of nitrogen, phosphorus (P), and potassium (K), making it impossible to independently adjust the application rate of a single nutrient.

Given this limitation, we prioritized ensuring consistent total nutrient input across treatment groups by using nitrogen (N) as the primary reference point. The reasons for selecting this method include:

It ensures consistent nitrogen supply, a critical factor for crop growth;

Due to the proportional relationship between nitrogen and potassium in the fertilizer, potassium (K) levels are nearly balanced;

Although there are minor differences in phosphorus (P) levels, these differences are relatively small given the scale of the experimental plots and do not affect the effectiveness of overall nutrient balance.

At the same time, since reviewer 1 raised the same opinion, we marked the revisions with a green background in the revised draft.

Comment 6:

Sampling details are lacking in several areas:

Soil sampling depth for organic carbon (OC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and mineral-associated organic carbon (MAOC).
Soil sampling methods (number of pits per plot, composite sampling).
Sampling frequency and sampling times throughout the crop cycle.
Plant sampling (if plant-dependent parameters were measured; sample size).

In this section, specify depths (e.g., 0–20 cm, 20–40 cm), the number of replications per plot, the sampling protocol, and the sampling schedule.

Response 6:

We sincerely appreciate your valuable comments and detailed suggestions regarding the sampling details. We are deeply grateful for your efforts, which have played an important role in improving the quality of our paper.

In response to your feedback, we would like to clarify the following points:

Soil sampling depth: The soil sampling depth for all parameters mentioned (organic carbon (SOC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and mineral-associated organic carbon (MOC)) is uniformly set at 0–20 cm.

Soil sampling method: We conducted two soil samplings at each plot. Specifically, we used a five-point sampling method within each plot, followed by a quartering method to reduce the sample size to a representative composite sample.

Sampling frequency and timing: Soil samples were collected at four key crop growth stages: seedling stage, budding stage, flowering and fruit set stage, and fruit development stage. Within each stage, we conducted two samplings at one-week intervals to capture any temporal changes.

Plant Sampling: Currently, our research focuses solely on measuring final yield as a plant-dependent parameter, so we have not implemented detailed plant sampling protocols beyond yield measurement.

We have revised the relevant sections of the manuscript to more clearly incorporate these details, ensuring readers can easily access and understand our sampling procedures. Once again, thank you for your valuable feedback, which has made a significant contribution to improving our work.

Comment 7:

Analytical methods. I recommend greater brevity in the methods and citing specific references without detailing critical conditions (reagents, extraction conditions, times, temperatures, equipment).

Response 7:

We sincerely appreciate your insightful and valuable recommendations regarding the "Analytical methods" section. Your suggestion for greater brevity while ensuring the inclusion of key operational parameters is entirely reasonable and has significantly helped us refine our manuscript.

As per your guidance, in the revised version (lines 147 - 163), we have made the following improvements:

Brevity: We have carefully deleted unnecessary details that were previously included, such as some overly descriptive and non-essential steps, to streamline the methods section and make it more concise.

Key Parameters: We have retained and, in some cases, added crucial operational parameters for each analytical method.

Reference Citation: We have ensured that each method is properly referenced to specific sources, allowing readers to access more in-depth information if needed while keeping our manuscript focused on the essential aspects relevant to our study.

We believe these revisions have enhanced the clarity, readability, and scientific rigor of the "Analytical methods" section. Thank you again for taking the time to review our work and for providing such constructive feedback. We look forward to any further comments or suggestions you may have.

Comment 8:

Measurement of greenhouse gases. You describe weekly measurements with static chambers and GC, but the following aspects are not addressed:

Chamber size, air volume, sampling rate, and sample volume.

Method calibration.

GC calibration details (gas standards, precision, detection limit).

How temporal variability was handled (time of day, meteorological conditions) and whether temperature corrections were applied.

Response 8:

Thank you very much for your review. Your comments are entirely correct. We have supplemented and highlighted the chamber construction, gas volume, and sampling specifications: explicitly providing the specific dimensions of the static chamber, gas volume, sampling frequency, and schedule, while emphasizing parallel sampling and operational consistency.

We have refined the chromatographic analysis methods and detailed calibration/quality control procedures: expanded instrument configurations, calibration standard gas ranges, precision, detection limits, and flux calculation/correction methods. Additionally, we have included instructions for handling covariates such as repeat settings and weather conditions: specifying repetition counts, extreme weather response strategies, and data quality control measures. Revised version (lines 175-189).

Comment 9:

Calculations and formulas. Equations are presented but definitions of variables and units are missing. I suggest presenting equations with a clear list of symbols and units. Verify unit consistency throughout the manuscript and provide a calculation example to illustrate the procedure.

Response 9:

Thank you for your valuable feedback on the “Calculations and Formulas” section. We greatly appreciate your attention to detail and your efforts to ensure the manuscript's clarity and completeness.

Regarding the definition of variables and units, we clarify that these are explicitly stated in Section 2.4.1 of the manuscript. We understand that this information may have been overlooked due to its length, and we sincerely apologize for any inconvenience caused.

Regarding the suggestion to provide computational examples, given that the target audience consists of professionals proficient in such calculations, we believe adding examples would not significantly enhance comprehension and may instead result in an overly lengthy and cumbersome manuscript. For your convenience in reviewing, we have handwritten a sample calculation and included it below for your consideration.

Nevertheless, we fully recognize the importance of transparency and clarity in scientific communication. Should you believe computational examples are essential to understanding our methodology, we are open to reconsidering this position. If supplementation is deemed necessary, we will explore integrating relevant examples into existing sections without substantially increasing the manuscript length.

We thank you once again for your constructive feedback and look forward to your further comments and suggestions. We remain committed to ensuring our manuscripts meet the highest standards of scientific rigor and clarity of expression. For your convenience in reviewing, we have handwritten a sample calculation and included it below for your consideration.

Comment 10:

Statistical analysis. It is stated that Excel was used. If other statistical software was used, specify which ones and what analyses were performed, including the type of analysis for each case. Consider correcting for multiple comparisons if many tests are performed. Indicate whether standard errors or confidence intervals were reported.

Response 10:

Thank you for your valuable feedback on the statistical methods section. We have revised the “Data Analysis” section to provide a more comprehensive and precise description of the statistical software and procedures used in the study. The updated description is as follows:

Clarification of statistical tools and methodological details: The specific version number of R software is now listed, and additional details regarding the statistical methods employed (e.g., ANOVA, Tukey HSD test, Pearson correlation analysis) have been added.

Supplemented multiple comparison corrections and uncertainty representation: Clearly stated that Tukey HSD was used for multiple comparison corrections and indicated that data results are reported as “mean ± standard error (SE).”

Standardized and unified academic expression: Terminology and structure were standardized to ensure consistency with academic norms and international publication requirements.

Your suggestions have significantly enhanced the clarity and reproducibility of the methods description. Thank you again for your meticulous review.

Comment 11:

In Figure 1, there is no statistical analysis indicated in the figure caption. Additionally, the abbreviations are not described, and the information is generally incomplete. I recommend including in the figure caption: statistical analysis, sample size used, and a definition of what each abbreviation in the figures represents.

Response 11:

Thank you for your insightful comments on Figure 1. We acknowledge that the figure caption indeed lacks information regarding statistical analysis, and we appreciate you bringing this to our attention.

Regarding the concern about the caption becoming overly lengthy if all the additional information is included, we have opted to add a note beneath the figure caption instead. This note will elaborate on the relevant details without cluttering the caption itself.

As for the abbreviations, taking into account the suggestions from both you and Reviewer 1, we have decided to define the abbreviated terms at their first occurrence in the article. This approach ensures clarity while maintaining a reasonable length for the text.

With regard to the sample size, we have already provided a detailed description in the "Materials and Methods" section. Specifically, for soil samples, we collected samples twice during each of the four growth stages. With six treatments and three replicates, this amounts to a total of 2 * 4 * 6 * 3 = 216 samples. For gas samples, we collected samples every week throughout the entire growth period (on dates including 5.28, 6.04, 6.10, 6.18, 6.25, 7.04, 7.12, 7.19, 7.27, 8.05, 8.13, 8.21, 8.31, 9.06, 9.13, and 9.19). With six treatments and three replicates, this results in a total of 16 * 6 * 3 = 288 samples.

We believe that these adjustments will enhance the comprehensibility and completeness of our manuscript. Thank you once again for your valuable feedback.

Comment 12:

For Figure 2, I suggest adding the sample size and detailing what each abbreviation in the figure means.

Response 12:

Thank you for your insightful comments on Figure 2. Our response to this comment aligns with our reply to Comment 11. To avoid redundant explanations that may tire your review, we will not elaborate further. We appreciate your thorough review.

Comment 13:

Response 13:

We sincerely appreciate your valuable suggestions on Table 3. Your point about including the type of statistical analysis in the table caption is indeed very reasonable.

Considering that adding all the required information directly in the caption might make it excessively long, we have chosen to incorporate the statistical methods and the way to express significance in the notes section below the table. This way, readers can still access the crucial information without the caption becoming overly cumbersome.

As for the issue of undescribed abbreviations and incomplete information regarding sample size, we follow the approach we adopted in response to comment 11. That is, we define the abbreviated terms at their first occurrence in the entire text to ensure clarity. Regarding sample size, we have already provided a detailed description in the "Materials and Methods" section to maintain consistency throughout the manuscript.

We believe these adjustments will effectively address your concerns and enhance the overall quality and clarity of our table presentation. Thank you again for your constructive feedback.

Comment 14:

Response 14:

We greatly appreciate your valuable comments on Figure 3.

Regarding the sample size and the definitions of all abbreviations used in the figure, we have addressed them in accordance with our response to comment 11. As for the statistical analysis employed, we have included it in the notes section below the figure caption for ease of reference.

We admit that it was an oversight on our part not to indicate the statistical differences for GHGI (defined as the ratio of GWP to crop yield) in the original figure. Thanks to your reminder, we have now incorporated the statistical differences into Figure 3 in the revised manuscript. To facilitate your review, we have attached it below.

We once again express our gratitude for your meticulous review and constructive suggestions, which have been instrumental in improving the quality of our manuscript.

Comment 15:

3.1 Effect of fertilization practices on soil total organic carbon and its fractions

3.2 Effect of fertilization practices on the proportion of soil organic carbon fractions

3.3 Effect of fertilization practices on soil carbon pool management indices

3.4 Effect of fertilization practices on yield and cumulative CH₄and CO₂ emissions

3.5 Correlation analysis of soil organic carbon fractions and nutrients with cumulative CH₄and CO₂ emissions

Response 15:

Thank you for your valuable feedback; your comments are entirely correct. We have revised the entire Chapter 4, specifically the results analysis section, in the revised manuscript as follows:

Structural Decomposition and Clarification: Lengthy paragraphs have been restructured into multiple thematic sections, each focusing on a specific organic carbon fraction to enhance coherence and readability.

Academic Expression and Data Logic Enhancement: We have streamlined and standardized the presentation style, emphasizing the comparative relationships and significance among different fertilization treatments, growth stages, and components to facilitate reader comprehension of the data results.

Standardization of Terminology and Comparative Relationships: We have unified professional terminology and the sequence of data presentation, clearly illustrating the differences and trends between various treatments, periods, and components.

We appreciate your professional review and hope our revisions meet your requirements.

Comment 16:

Discussion

The discussion is not clear, and there are grammatical errors. Relevant research references should be used. Avoid statements that depend on unverified studies or studies not accessible to readers.

4.1 Effect of fertilization practices on soil total organic carbon and its fractions

4.2 Effect of fertilization practices on the proportion of soil organic carbon fractions

4.3 Effect of fertilization practices on soil carbon pool management indices

4.4 Effect of fertilization practices on yield and cumulative CH4 and CO2 emissions

4.5 Correlation analysis of soil organic carbon fractions and nutrients with cumulative CH4 and CO2 emissions

Response 16:

Your feedback is indeed spot-on, but we noticed that this section of the comment duplicates Comment 15. This may be an error in citation, though it does not affect our understanding.

We have carefully incorporated your suggestions and comprehensively revised the “Discussion” section as requested. The revisions encompass the following aspects:

First, we corrected grammatical errors to ensure more precise and fluent language.

Second, we incorporated relevant research literature to strengthen our arguments and provide a more solid theoretical foundation for our discussion. We ensured that only verifiable studies accessible to readers are cited, avoiding reliance on unverified or inaccessible sources.

Additionally, we restructured the presentation of the discussion section. Previously, lengthy paragraphs obscured key points; we have now divided the discussion into multiple, clearly organized subsections. This new structure enhances clarity and logical coherence, making our analysis and conclusions easier for readers to follow.

We believe these revisions significantly improve the quality and readability of the “Discussion” section. Thank you once again for your insightful comments—your valuable feedback has been crucial in refining our manuscript.

Other clarifications:

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

Your manuscript has been improved compared to the previous version, but it still contains inaccuracies.

Line 148

This sentence is a repetition of the previous one.

Lines 152, 156 and Figure 5

TOC or SOC?

Lines 395-427

In my previous review, I asked for verification of the accuracy of the results descriptions. The descriptions still don't match what's shown in the Figure 5.

(1)seedling stage

“During the seedling stage, AK and TP showed significant positive correlations with MOC and DOC (P < 0.05, P < 0.01).” – not significant in case of correlation: AK and DOC, TP and MOC, TP and DOC.

“EOC and MBC exhibited significant positive correlations with CO₂ (P < 0.01)” – according to Fig 5, Seedling stage:

EOC and CO2 – negative, not significant

MBC and CO2 – negative, not significant

(2) bud stage

“The positive correlations between EOC, MBC, and CO₂ continue but weaken” – correlation are positive while in previous stage were negative.

“MOC showed a stronger positive correlation with CO₂” – stronger in comparison to what? In previous stage the correlation was negative.

”AK maintained a negative correlation with CH₄ but exhibited a positive correlation with CO₂”

AK maintained a positive, statistically significant correlation with CO₂”

(3) flowering and fruit-setting stage

“Certain indicators (e.g., AK, TP, TN) show negative correlations with CO₂ and CH₄.”

According to results presented in Fig. 5 AK and CO2 – positive, not statistically significant correlation

TP and CO2 – negative, not statistically significant correlation

TN and CO2 – positive, not statistically significant correlation

TP and CH4 – positive, not statistically significant correlation

“Significant positive correlations between EOC, MBC, and CO₂ markedly strengthened (P < 0.01, high proportion)

EOC and CO2 – positive, not statistically significant correlation

MBC and CO2 – positive, not statistically significant correlation

“Particulate organic carbon (POC) showed a significant negative correlation with CO₂”

POC and CO2 – positive, not statistically significant correlation according Fig. 5.

“The negative correlation between AK and CH₄ disappears,”

AK and CH4 – positive, not statistically significant correlation according Fig. 5.

Line 470

Figure 4 or rather 5?

“The T40–T80 treatments showed a significant negative correlation between MOC and CO₂ emissions (P < 0.01)Figure 4”.

It is possible base of presented result inferring a trend in particular treatments? Analysis were carried out for growth stages not treatments.

Lines 484-485

At fruiting, T60–T80 treatments maintained higher MOC and POC with a stable negative correlation to CO₂, confirming the establishment of a high-sequestration, low-emission carbon equilibrium”.

It is possible base of presented result inferring a trend in particular treatments? Analysis were carried out for growth stages not treatments.

Lines 402, 530, 659

Use capital letter: „Archaea”

Author Response

Response to Reviewer 1 Comments ( Round 2 )

Dear reviewer:

Point-by-point response to Comments and Suggestions for Authors:

Comment 1:

Line 148. This sentence is a repetition of the previous one.

Response 1:

We sincerely apologize for the oversight, and we have made the necessary corrections by removing the repetitive sentence in the revised manuscript. Thank you for bringing this to our attention

Comment 2:

Lines 152, 156 and Figure 5 .TOC or SOC?

Response 2:

Dear Expert, We sincerely apologize for any inconvenience caused. Regarding your concerns about Figure 5 and lines 152 and 156, we have conducted a thorough review. For Figure 5, we have confirmed the previous error and corrected “TOC” to “SOC” in the revised manuscript. As for lines 152 and 156, our examination did not reveal any misuse of TOC or SOC. Thank you once again for your patient guidance and valuable feedback.

Comment 3:

Lines 395-427

In my previous review, I asked for verification of the accuracy of the results descriptions. The descriptions still don't match what's shown in the Figure 5.

(1)seedling stage

“During the seedling stage, AK and TP showed significant positive correlations with MOC and DOC (P < 0.05, P < 0.01).” – not significant in case of correlation: AK and DOC, TP and MOC, TP and DOC.

“EOC and MBC exhibited significant positive correlations with CO₂ (P < 0.01)” – according to Fig 5, Seedling stage:

EOC and CO2 – negative, not significant

MBC and CO2 – negative, not significant

(2) bud stage

“The positive correlations between EOC, MBC, and CO₂ continue but weaken” – correlation are positive while in previous stage were negative.

“MOC showed a stronger positive correlation with CO₂” – stronger in comparison to what? In previous stage the correlation was negative.

”AK maintained a negative correlation with CH₄ but exhibited a positive correlation with CO₂”

AK maintained a positive, statistically significant correlation with CO₂”

(3) flowering and fruit-setting stage

“Certain indicators (e.g., AK, TP, TN) show negative correlations with CO₂ and CH₄.”

According to results presented in Fig. 5 AK and CO2 – positive, not statistically significant correlation

TP and CO2 – negative, not statistically significant correlation

TN and CO2 – positive, not statistically significant correlation

TP and CH4 – positive, not statistically significant correlation

“Significant positive correlations between EOC, MBC, and CO₂ markedly strengthened (P < 0.01, high proportion)

EOC and CO2 – positive, not statistically significant correlation

MBC and CO2 – positive, not statistically significant correlation

“Particulate organic carbon (POC) showed a significant negative correlation with CO₂”

POC and CO2 – positive, not statistically significant correlation according Fig. 5.

“The negative correlation between AK and CH₄ disappears,”

AK and CH4 – positive, not statistically significant correlation according Fig. 5.

Response 3:

We sincerely apologize for failing to promptly address the discrepancy between the results description and Figure 5 in the previous revision. This was indeed an oversight on our part. We fully recognize that this error may have caused confusion for readers and extend our sincere apologies for the additional effort you had to exert during the review process.

The issue you raised is critical. Upon careful verification, we have confirmed that multiple instances exist where the descriptions do not align with the data in Figure 5. This primarily resulted from color interactions in the figures during writing, which led to misinterpretations of the data and consequently affected the accuracy of the textual descriptions. For example, the statement you mentioned—“some indicators (such as AK, TP, TN) showed negative correlations with CO₂ and CH₄”—was indeed imprecise. Our intended meaning was “Some indicators (AK and CH₄, TP and CO₂, TN and CH₄) showed negative correlations,” but this was not clearly conveyed.

For each issue you raised, we have made meticulous revisions to the original text and rechecked the data in Figure 5 to ensure descriptions align perfectly with the charts. Specific modifications include but are not limited to:

In the “seedling stage” section, we corrected the correlation descriptions between AK, TP, and MOC/DOC, as well as between EOC, MBC, and CO₂, ensuring consistency with Figure 5 data.

In the “bud stage” section, we have rephrased the changes in correlations between EOC and MBC with CO₂, as well as the correlations between MOC and AK with CO₂ and CH₄, resolving previous inconsistencies.

In the “flowering and fruit-setting stage” section, we have corrected the descriptions of correlations between AK, TP, and TN with CO₂ and CH₄, as well as the correlations between POC and CO₂, and AK and CH₄, ensuring all descriptions are accurate.

We fully recognize that scientific rigor demands unwavering attention, as even minor errors can undermine research credibility and value. We deeply regret this oversight and pledge heightened diligence and precision in future work to prevent recurrence.

We extend our sincere gratitude for your patient guidance and valuable feedback. Your professionalism and meticulousness are invaluable assets to us. Should you have further suggestions or identify any additional issues during subsequent review stages, please do not hesitate to inform us. We will cooperate fully to ensure the paper meets the highest standards of quality.

Comment 4:

Line 470

Figure 4 or rather 5?

“The T40–T80 treatments showed a significant negative correlation between MOC and CO₂ emissions (P < 0.01)Figure 4”.

It is possible base of presented result inferring a trend in particular treatments? Analysis were carried out for growth stages not treatments.

Lines 484-485

At fruiting, T60–T80 treatments maintained higher MOC and POC with a stable negative correlation to CO₂, confirming the establishment of a high-sequestration, low-emission carbon equilibrium”.

It is possible base of presented result inferring a trend in particular treatments? Analysis were carried out for growth stages not treatments.

Response 4:

We sincerely appreciate your meticulous review. The issues you pointed out in Line 470 and Lines 484–485 were indeed oversights in our presentation, for which we deeply apologize. Regarding the figure number citation error and the basis for inferring treatment group trends, we clarify as follows:

Figure citation issue: The reference to “Figure 4” in the original text should be “Figure 5.” The correlation analysis discussed here (e.g., relationships between the T40–T80 treatment group and MOC/CO₂) is indeed based on the correlation heatmap in Figure 5. This heatmap integrates nutrient data and greenhouse gas emission data across different treatments and growth stages. However, since the chart design did not explicitly label treatment group trends, our discussion lacked clarity.

Basis for Treatment Group Trend Inference: Your observation that “the analysis was conducted by growth stage rather than treatment group” is crucial. Our original text attempted to infer treatment group trends from the comprehensive dataset in Figure 5 without explicitly stating the data source, creating a logical leap. To avoid misleading readers, we have removed sentences such as “T40–T80 treatments showed...” and " T60–T80 treatments maintained..." and similar direct statements about treatment group trends, retaining only conclusions based on growth stage analysis.

For your review convenience, we have attached screenshots of the treatment group datasets not directly displayed in Figure 5 to this response letter. These data support our original inference of treatment group trends but were not charted separately to avoid figure duplication.

We fully recognize the impact of this error on the paper's rigor and have thoroughly revised the relevant content. Moving forward, we will place greater emphasis on precise wording and logical consistency. We sincerely appreciate your patient guidance and will fully cooperate to address any further suggestions you may have.

Data:

Comment 5:

Lines 402, 530, 659. Use capital letter: “Archaea”

Response 5:

We sincerely appreciate your meticulous review and valuable suggestions for revision. Regarding your observation that “archaea” should be capitalized as ‘Archaea’ in lines 402, 530, and 659 of the original text, we have carefully verified and made comprehensive corrections. All relevant references throughout the document have now been uniformly changed to “Archaea” to ensure compliance with academic standards and terminological accuracy.

Once again, thank you for your support and encouragement. It is a privilege to have our research evaluated by such a distinguished expert in the field.

With our warmest regards !

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

Translation with grammar corrections:
"In this way, the article is understood more clearly. Thank you for taking my suggestions into account."

Author Response

Dear Reviewer,

We sincerely appreciate your valuable suggestions! We thank you for your guidance on the manuscript and for your approval of our first round of revisions. We will make further adjustments to the manuscript's grammar.

Thank you again for your professional guidance!

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