Climate, Soil, and Microbes: Interactions Shaping Organic Matter Decomposition in Croplands

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

 

General comments

I have read the manuscript “Climate, Soil, and Microbes: Interactions Shaping Organic Matter Decomposition in Croplands”. Authors addresses soil organic matter decomposition in relation to the climate soil and microbes. This review paper is quite interesting and obviously has potential to address the problems how organic matter improve in various croplands. In this sense the manuscript is valuable. However, I found some lacking information especially in the abstract, introduction and literature. I found the lack of potential mechanisms and the latest reference to support their findings. I request to author for Major revision of this manuscript.

1. Need to add data table or figure on temporal and spatial scale to strength your study
2. Potential mechanism missing how temperature and seasonal variations in moisture play a critical role in microbial activity and enzyme kinetics?
3. How soil mineralogy affects the microbial habitat and protects SOM? Need to draw a schematic figure
4. Draw a figure on the role and feedback of microbial communities as well as necromass in forming stable SOM and CUE? Also need to add the role of microbial C pump in enhancing SOC sequestration. Add more mechanism in the text considering climate-soil and microbes’ interaction.
5. Need further explanation to address the cycling of organic matter at multiple scales, ranging from molecular to landscape
6. Add more details on how microbial functional ecology mediates decomposition outcomes
7. How C:N (increase or decrease) affects decomposition rate
8. Role of POC and MAOC regarding climate, soil and microbes interaction in forming stability of SOM is lacking
9. Table 2; Key microbial groups involved in decomposition processes addresses with regards to agricultural practices, that’s OK and why not include your claim- “climate variables, soil characteristics/types, must include
10. Draw a figure on temperature and moisture sensitivity on microbial processes and enzyme kinetics, and CUE under combined climate soil and microbes interaction.
11. In the first lines of conclusion need to revise
12. Conclusion is not upto the mark, revise and give a clear message.
13. The development of science based…..is not suitable revise.
14. Lack of suggestion/recommendation in the end of conclusion, add future perspective

 

 

Author Response

I found some lacking information especially in the abstract, introduction and literature. I found the lack of potential mechanisms and the latest reference to support their findings. 

Thanks for your detailed feedback. We took guidance from all your comments and have incorporated them. Regarding this comment, it is "Done." The changes has been incoroporated in red color throughout abstract and introduction sections. 

1. Need to add data table or figure on temporal and spatial scale to strengthen your study

Response: Thank you so much for your valuable suggestion. We have included a data table on temporal and spatial scale (Table 3; Page No. 16, Lines 616–618). This addition provides concrete evidence of how environmental factors and microbial processes vary across different timeframes and locations.

2. Potential mechanism missing how temperature and seasonal variations in moisture play a critical role in microbial activity and enzyme kinetics?

Response: Indeed, this is an important area for clarification. Per your suggestion, we have included data on the potential mechanism of how temperature and seasonal variations in moisture play a critical role in microbial activity and enzyme kinetics (Page No. 8, Lines 270–286).

3. How soil mineralogy affects the microbial habitat and protects SOM? Need to draw a schematic figure

Response: We are very thankful for your valuable suggestion. We have worked on the schematic representation of the effect of soil mineralogy on microbial habitat and SOM protection and have included it in the form of Figure 2 (Page No. 11–12, Lines 421–437). This single figure integrates the requested information, also encompassing the broader role and feedbacks of microbial communities and necromass in SOM stabilization.

4. Draw a figure on the role and feedback of microbial communities as well as necromass in forming stable SOM and CUE? Also need to add the role of microbial C pump in enhancing SOC sequestration. Add more mechanism in the text considering climate-soil and microbes’ interaction.

Response: We really appreciate your kind response and valuable suggestion. We have included the recommended figure in Figure 2 (Page No. 11–12, Lines 421–437). This consolidated figure comprehensively illustrates the role and feedbacks of microbial communities, necromass, and the microbial carbon pump in stable SOM formation, also covering how soil mineralogy affects microbial habitat and SOM protection.

5. Need further explanation to address the cycling of organic matter at multiple scales, ranging from molecular to landscape

Response: Thanks, based on your suggestion, we have included the data on organic matter cycling at multiple scales (Page No. 15, Lines 587–609).

6. Add more details on how microbial functional ecology mediates decomposition outcomes

Response: We appreciate this insightful suggestion. Based on your suggestion, we have included a detailed process on how microbial functional ecology mediates decomposition outcomes (Page No. 4, Lines 143–161).

7. How C:N (increase or decrease) affects decomposition rate

Response: Thank you, we found this suggestion very useful and have added data on how variations in C:N affect decomposition rate (Page No. 13, Lines 499–504; Page No. 13–14, Lines 510–523).

8. Role of POC and MAOC regarding climate, soil and microbes interaction in forming stability of SOM is lacking

Response: Thank you so much for your kind suggestion. We agree that a more explicit focus on particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) significantly enhances our discussion. We have therefore integrated specific data and insights on their roles in SOM stability, especially regarding their interactions with climate, soil properties, and microbial communities, at multiple instances throughout the article (Page No.3, Lines 93–110; Page No. 16–17, Lines 632–647)."

9. Table 2; Key microbial groups involved in decomposition processes addresses with regards to agricultural practices, that’s OK and why not include your claim- “climate variables, soil characteristics/types, must include

Response: We appreciate your kind suggestion. Data related to “climate variables” has now included in the Table 1 on “key microbial groups involved in decomposition processes (Page No. 4–5; Lines 162–164).

10. Draw a figure on temperature and moisture sensitivity on microbial processes and enzyme kinetics, and CUE under combined climate soil and microbes interaction.

Response:  We are grateful for this constructive feedback and have thus included a detailed Figure on temperature (Figure 1a; Page No. 6–7, Lines 226–240) and moisture (Figure 1b; Page No. 7–8, Lines 241–251).

11. In the first lines of conclusion need to revise

Response: Thank you so much for your critical review of our manuscript. Following implementation of your insightful suggestions throughout the article, we have now revised the whole conclusion of the manuscript to better reflect the review outcomes (Page No. 21, Lines 828–856).

12. Conclusion is not upto the mark, revise and give a clear message.

Response: Your insightful suggestion is appreciated. We have now revised the conclusion to ensure clarity (Page No. 21; Lines 828–856).

13. The development of science based…..is not suitable revise.

Response: We are very thankful for your valuable feedback. Based on your suggestion, we have revised this particular statement (Page No. 21; Lines 844–850).

14. Lack of suggestion/recommendation in the end of conclusion, add future perspective

Response: We have added sentences on recommendations and future perspectives in the conclusion (Page No. 21; Lines 844–856).

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript entitled "Climate, Soil, and Microbes: Interactions Shaping Organic Matter Decomposition in Croplands" presents a comprehensive literature review on the complex interplay between climate, soil properties, and microbial communities in determining soil organic matter (SOM) decomposition in agricultural systems. The topic is timely and relevant to sustainable agriculture, especially under climate change pressures. The manuscript compiles a vast body of recent literature, integrates diverse mechanistic insights, and outlines conceptual advancements in microbial-driven carbon cycling. However, the review currently lacks a clear conceptual synthesis, suffers from structural inefficiencies, and includes repetitive and long passages that reduce its readability. The manuscript would benefit from practical reorganization and refinement to improve its scientific impact and reader engagement. The following major comments highlight areas where improvement is required.

1. Page 2, Lines 41–75: The introduction, while informative, devotes considerable space to general background and reiterates points about SOM and microbial necro mass that are repeated later. This section should be revised to clearly define the review’s scope, objectives, and structure. Additionally, streamline the background to avoid redundancy with Section 2.3 and later discussions on microbial necro mass.
2. Lines 105–124 and Table 1: The detailed listing of microbial groups is useful, but the section overlaps conceptually with content in Lines 155–165 and others like 239–279 as well. Merge or condense these redundant discussions on microbial community function, and instead consider presenting a visual summary (e.g., a schematic or functional wheel) that better illustrates how microbial taxa contribute to specific decomposition processes under different environmental contexts.
3. Section 2.3: The importance of microbial necro mass is discussed in an isolated and overly detailed manner. Since necro mass is a recurring theme throughout the manuscript, it would be more effective to integrate this section into a broader framework of SOM stabilization mechanisms, alongside mineral association and aggregate protection. Additionally, clarify the transition from live biomass to necro mass and its quantifiable contributions across different management regimes.
4. Section 3.1: The section on temperature sensitivity is overly long and fragmented. Numerous studies are cited without clearly distinguishing their unique contributions. Consolidate the discussion around a central conceptual model, perhaps supported by a figure showing enzyme Q10 ranges and microbial CUE responses across temperature gradients. Avoid repeating the same observations on intracellular vs extracellular enzyme sensitivity in multiple places.
5. Lines 239–291, section 3.2: While the role of soil moisture is well described, this section lacks a clear distinction between aerobic and anaerobic processes in cropland systems. The discussion would benefit from more targeted examples of how waterlogging or drought affects SOM decomposition and microbial shifts. Additionally, condense the discussion of moisture thresholds and aggregate feedbacks, as these are again covered in later sections.
6. Further in section 4: The influence of soil structure and pH on microbial habitats is discussed across multiple fragmented subsections. Consider integrating the discussion of soil aggregation, texture, and porosity into one cohesive subsection with better conceptual flow. Furthermore, the role of pH should be presented with stronger linkage to microbial community shifts and enzyme functionality, rather than general soil chemistry.
7. Page 11, Lines 421–474: The treatment of nutrient availability and mineralogy is well referenced but includes excessive detail on specific ions (e.g., calcium, aluminum, potassium) and microbial groups without tying back to a central hypothesis. Streamline this content by focusing on the overall impact of nutrient stoichiometry on microbial enzyme expression, CUE, and SOM stabilization.
8. Lines 498–512: The landscape-scale implications of microbial decomposition are mentioned but remain underdeveloped. Strengthen this section by including concrete examples or studies that link micro-scale decomposition processes (e.g., rhizosphere respiration) to macro-scale carbon dynamics. This would also be a good place to introduce spatial modeling frameworks or geospatial tools if available.
9. Lines 571–630: This section on agricultural practices contains many valuable insights but reads like a list of disconnected effects. Reorganize by grouping the practices (e.g., tillage, cover cropping, fertilization) and discussing their combined impact on microbial traits (e.g., CUE, enzyme activity) and SOM fate. Eliminate repetitive examples already presented in earlier sections (e.g., Lines 94–104 and 140–152).
10. Lines 631–644: The future directions are currently unclear and overly generic. Refine this section to propose concrete and prioritized research gaps such as standardizing microbial trait measurements, integrating omics and soil physical models, or scaling lab findings to field trials. Avoid generic calls for interdisciplinary research unless coupled with specific tools or methods.
11. The conclusion lacks a clear synthesis of the review’s main messages. Revise this section to concisely restate the major findings, the functional roles of microbes in decomposition, and the implications for climate-smart agriculture. A closing paragraph highlighting how the review informs both theory and practice would add value.
12. Throughout the manuscript: There is a lack of conceptual diagrams, summary tables, or illustrative figures to organize and synthesize complex information. Adding 2–3 well-designed visuals (e.g., a model of climate-soil-microbe interactions, a comparison of SOM stabilization pathways, or a CUE-based feedback diagram) would significantly enhance the paper's utility for readers.

Comments on the Quality of English Language

The English is generally clear but could be improved for precision and conciseness. Many sentences are excessively long and contain redundant or unclear phrasing. The manuscript would benefit from a thorough language edit by a native English-speaking scientist or professional editor. Special attention should be given to verb tense consistency, article usage, and reducing repetition in multi-clause sentences.

Author Response

The English is generally clear but could be improved for precision and conciseness. Many sentences are excessively long and contain redundant or unclear phrasing. The manuscript would benefit from a thorough language edit by a native English-speaking scientist or professional editor. Special attention should be given to verb tense consistency, article usage, and reducing repetition in multi-clause sentences. The review currently lacks a clear conceptual synthesis, suffers from structural inefficiencies, and includes repetitive and long passages that reduce its readability. The manuscript would benefit from practical reorganization and refinement to improve its scientific impact and reader engagement. The following major comments highlight areas where improvement is required.

Thanks for your detailed feedback. We really appreciate it. Keeping in view your comment, we have proofread the whole manuscript multiple times to fix grammar, syntax, and redundancy issues. Moreover, long passage were also fixed. The connections between ideas, flow, and cohesion was also improved. All such changes were incorporated in red color throughout the manuscript. 

1.           Page 2, Lines 41–75: The introduction, while informative, devotes considerable space to general background and reiterates points about SOM and microbial necro mass that are repeated later. This section should be revised to clearly define the review’s scope, objectives, and structure. Additionally, streamline the background to avoid redundancy with Section 2.3 and later discussions on microbial necro mass.

Response: We truly appreciate your detailed and constructive feedback on the introduction. We have carefully reviewed and revised this section to clearly define the review's scope, objectives, and structure. Furthermore, we have revised the entire Section 2.3 to enhance overall clarity and conciseness and to ensure that any redundancy or repetition of the same information is eliminated (Page No. 2, Lines 65–73; Page No. 5–6, Lines 177–218).

2.           Lines 105–124 and Table 1: The detailed listing of microbial groups is useful, but the section overlaps conceptually with content in Lines 155–165 and others like 239–279 as well. Merge or condense these redundant discussions on microbial community function, and instead consider presenting a visual summary (e.g., a schematic or functional wheel) that better illustrates how microbial taxa contribute to specific decomposition processes under different environmental contexts.

Response: We are very grateful for this insightful comment. We recognize the initial redundancy concerning microbial community function across various sections. Per your valuable suggestion, we have thoroughly condensed and merged these discussions to eliminate overlap between Lines 105–124 (Page No. 4, Lines 123–161 in revised manuscript), Table 1, and subsequent sections. Furthermore, we have incorporated a dedicated functional wheel (Figure 3; Page No. 18, Lines 703–719), which now visually summarizes and better illustrates how specific microbial taxa contribute to decomposition processes across different environmental contexts (pH, moisture, temperature, nutrients, and oxygen), providing a clear and comprehensive overview.

3.           Section 2.3: The importance of microbial necro mass is discussed in an isolated and overly detailed manner. Since necro mass is a recurring theme throughout the manuscript, it would be more effective to integrate this section into a broader framework of SOM stabilization mechanisms, alongside mineral association and aggregate protection. Additionally, clarify the transition from live biomass to necro mass and its quantifiable contributions across different management regimes.

Response: Thank you for your valuable suggestion. We have now revised Section 2.3 to integrate the importance of microbial necromass within a broader framework of SOM stabilization mechanisms, discussing its interplay with mineral association and aggregate protection. Furthermore, we have clarified the transition from live biomass to necromass and, where possible, highlighted its quantifiable contributions across different management regimes (Page No. 5–6, Lines 177–218).

4.           Section 3.1: The section on temperature sensitivity is overly long and fragmented. Numerous studies are cited without clearly distinguishing their unique contributions. Consolidate the discussion around a central conceptual model, perhaps supported by a figure showing enzyme Q10 ranges and microbial CUE responses across temperature gradients. Avoid repeating the same observations on intracellular vs extracellular enzyme sensitivity in multiple places.

Response: We really appreciate your insightful review on Section 3.1. We have thoroughly revised this section, streamlining the fragmented discussion and emphasizing a central conceptual model. Crucially, we have incorporated Figure 1a (Page No. 6–7, Lines 226–240) to illustrate generalized enzyme Q10 ranges and microbial CUE responses across temperature gradients, effectively summarizing key insights. Furthermore, we have ensured to avoid redundant observations on enzyme sensitivity, thereby enhancing the clarity and flow of the section.

5.           Lines 239–291, section 3.2: While the role of soil moisture is well described, this section lacks a clear distinction between aerobic and anaerobic processes in cropland systems. The discussion would benefit from more targeted examples of how waterlogging or drought affects SOM decomposition and microbial shifts. Additionally, condense the discussion of moisture thresholds and aggregate feedbacks, as these are again covered in later sections.

Response: Thank you for your valuable feedback. We have amended section 3.2 based on your suggestion and included data on waterlogging (Page No. 9, Lines 326–327) and drought (Page No. 9, Lines 340–342) effects on SOM decomposition and microbial shifts. Additionally, we slightly condensed the discussion of moisture to avoid redundancy or repetition (Page No. 10, Lines 356–364).

6.           Further in section 4: The influence of soil structure and pH on microbial habitats is discussed across multiple fragmented subsections. Consider integrating the discussion of soil aggregation, texture, and porosity into one cohesive subsection with better conceptual flow. Furthermore, the role of pH should be presented with stronger linkage to microbial community shifts and enzyme functionality, rather than general soil chemistry.

Response: Based on your suggestion, we have revised the subsections 4.1 and 4.2 by integrating the discussion into a single subsection “4.1. Soil aggregation, texture, and porosity: regulators of microbial habitat and OM protection” (Page No. 11–12, Lines 409–461). Moreover, we have revise the role of pH to focus more on microbial community shifts and enzyme functionality (Page No. 13, Lines 471–475; 477–479; and 482–483).

7.           Page 11, Lines 421–474: The treatment of nutrient availability and mineralogy is well referenced but includes excessive detail on specific ions (e.g., calcium, aluminum, potassium) and microbial groups without tying back to a central hypothesis. Streamline this content by focusing on the overall impact of nutrient stoichiometry on microbial enzyme expression, CUE, and SOM stabilization.

Response: We really appreciate your comprehensive analysis of our review paper. We have thoroughly revised the section on nutrient availability and mineralogy, streamlining the content to focus on the overall impact of nutrient stoichiometry on microbial enzyme expression, CUE, and SOM stabilization, ensuring more direct alignment with our main hypotheses (Page No. 13–14, Lines 484–522).

8.           Lines 498–512: The landscape-scale implications of microbial decomposition are mentioned but remain underdeveloped. Strengthen this section by including concrete examples or studies that link micro-scale decomposition processes (e.g., rhizosphere respiration) to macro-scale carbon dynamics. This would also be a good place to introduce spatial modeling frameworks or geospatial tools if available.

Response: Thank you for your valuable comment on strengthening the landscape-scale implications. We have accordingly included concrete examples and studies that link micro-scale decomposition processes, such as rhizosphere respiration, to broader carbon dynamics at the macro-scale. This expanded discussion now better highlights the cross-scale interactions driving carbon cycling and, where appropriate, introduces relevant spatial modeling frameworks (Lines 498–512, now Page No. 15, Lines 586–608).

9.           Lines 571–630: This section on agricultural practices contains many valuable insights but reads like a list of disconnected effects. Reorganize by grouping the practices (e.g., tillage, cover cropping, fertilization) and discussing their combined impact on microbial traits (e.g., CUE, enzyme activity) and SOM fate. Eliminate repetitive examples already presented in earlier sections (e.g., Lines 94–104 and 140–152).

Response: We appreciate your valuable feedback. We have comprehensively reorganized this section based on your suggestion (Lines 571–630, now Page No. 18–20, Lines 720–792), with specific amendments related to focusing on their combined impact on microbial CUE and enzyme activity and SOM fate on Page No. 18, Lines 722–723 and Page No. 19, Lines 730–734, 737–741, 752–755, 769, and 779–784.

10.         Lines 631–644: The future directions are currently unclear and overly generic. Refine this section to propose concrete and prioritized research gaps such as standardizing microbial trait measurements, integrating omics and soil physical models, or scaling lab findings to field trials. Avoid generic calls for interdisciplinary research unless coupled with specific tools or methods.

Response: We really appreciate your insightful suggestion regarding the future directions. Based on your suggestion, we have revised the entire “Future Directions” section to ensure that research gaps are clearly proposed, including the standardization of microbial trait measurements, the integration of omics technique and soil physical models, and the scaling of laboratory findings to field trials (Page No. 20–21, Lines 793–720). This section now offers actionable directions for future research, avoiding generic calls for interdisciplinary studies.

11.         The conclusion lacks a clear synthesis of the review’s main messages. Revise this section to concisely restate the major findings, the functional roles of microbes in decomposition, and the implications for climate-smart agriculture. A closing paragraph highlighting how the review informs both theory and practice would add value.

Response: We are very thankful for your constructive review of the conclusion of the article. We have revised the conclusion section completely to provide a clearer synthesis of the review's main messages. The conclusion now concisely restates our major findings, explicitly highlights the functional roles of microbes in decomposition, and discusses their critical implications for climate-smart agriculture. Additionally, we have added a closing paragraph that underscores how this review contributes to both theoretical understanding and practical applications in the field (Page No. 21, Lines 828–856).

12.         Throughout the manuscript: There is a lack of conceptual diagrams, summary tables, or illustrative figures to organize and synthesize complex information. Adding 2–3 well-designed visuals (e.g., a model of climate-soil-microbe interactions, a comparison of SOM stabilization pathways, or a CUE-based feedback diagram) would significantly enhance the paper's utility for readers.

Response: We are truly grateful for this feedback regarding the lack of conceptual diagrams, summary tables, and illustrative figures throughout the manuscript. In direct response to this and other specific comments, we have substantially enhanced the visual components of the manuscript, including the followings:

Figures 1a and 1b (Page No. 6–8, Lines 226–251), a conceptual model illustrating enzyme Q10 ranges and microbial CUE responses across temperature (Figure 1a) and moisture (Figure 1b) gradients, which directly addresses climate-microbe interactions.

Table 1 (Page No. 4–5, Lines 162–163), an improved table with a new column for “Influence of Climate and Soil Type)” on decomposition activity of key microbial groups.

Figure 2 (Page No. 11–12; Lines 421–437), illustrates the effects of soil mineralogy on microbial habitat and SOM protection, while also integrating the feedbacks and role of microbial communities and necromass in SOM stability.

Figure 3 (Page No. 18, Lines 703–719), a comprehensive functional wheel diagram that elucidates how microbial taxa contribute to specific decomposition processes under various environmental contexts.

These additions collectively serve to visually synthesize complex information on climate-soil-microbe interactions, SOM stabilization pathways, and CUE-based feedback, thereby significantly strengthening the review’s clarity.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Authors have effectively addressed my concerns/suggestions. I have no more comments. The manuscript can be accepted for publication

Reviewer 2 Report

Comments and Suggestions for Authors

Overall, this is a valuable and timely contribution to the field of soil biogeochemistry and sustainable agriculture. I recommend acceptance with minor editorial polishing.

Comments on the Quality of English Language

While the manuscript is now much clearer, there are still a few overly long sentences and areas where word choice and syntax could be polished further. A final round of language editing by a native English speaker or professional editor would further enhance readability.