Diversified Cropping Modulates Microbial Communities and Greenhouse Gas Emissions by Enhancing Soil Nutrients

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

In their manuscript the authors present a quantitative bibliometric analysis of major findings regarding maize/legume intercropping (which has been selected as father search key) and its connections to: soil physicochemical properties, microbial diversity, GGE (I suggest using the acronym GHGs), crop yield (which has been selected as secondary search key). Moreover, the maize/legume rotation has been also searched in the Web of Science database. The submitted review aims at suggesting most prosing and consistent management practices and inspiring future research directions which focus not only on crop yield, but also comply with the aspects related with environmental issues, such as finite resource conservation and environmental risks. I found the submitted manuscript very well written, structured, concise and clearly focused, and shows the potential to provide a significant contribution to the advancements of our knowledge in the field.

However, the way results are shown and discussed is intimately depending on the strategy the literature survey and selection of cited papers has been conducted. I found that 59% of cited papers are from scientists/researchers from People’s Republic of China, thus rendering the result shown in Fig. 1A not really surprising. Moreover, reference to some titles can be questionable (i.e. reference 10, 11, 12, 34, 37, 38, 39, 62, 67, 75). It is also true that a number of well known highly cited contributing papers on the subject have been ignored. Even though the main conclusions are consistent with the evidence and arguments presented and do they address the main question posed, it is also true that underrepresented selection of selected article during the bibliometric analysis would affect major finding of the analysis, and provide only a partial view of this ambitious topic. So, references are not appropriate and should be expanded. I therefore suggest that the authors revise and widen their research strategy in order to provide a more comprehensive and internationally representative view of the topic.

Additional comments:

In their captions Figure 1 and 2 should report a more detailed explanation so as to make it easier for readers who might not be familiar with such approach to catch the meaning and the strength of the relations (and how they were structured).

Authors contributions (line 473-480) are missing.
Data availability (line 483-487) is missing.
Acknowledgments (line 488-490) are missing

Author Response

We appreciate the thoughtful review and constructive feedback provided by the reviewers. We agree with the reviewers' suggestions and wilincorporate the recommended changes into the manuscript.

Comments 1: Reference to some titles can be questionable (i.e. reference 10, 11, 12, 34, 37, 38, 39, 62, 67, 75). It is also true that a number of well known highly cited contributing papers on the subject have been ignored. Even though the main conclusions are consistent with the evidence and arguments presented and do they address the main question posed, it is also true that underrepresented selection of selected article during the bibliometric analysis would affect major finding of the analysis, and provide only a partial view of this ambitious topic. So, references are not appropriate and should be expanded.

Response 1: We have partially deleted controversial references to improve readability, and we appreciate this valuable suggestion. Regarding the issue of high-profile, highly cited related papers being overlooked, we have added references to Breza et al. (2023) and briefly discussed them as suggested (see revised pages 16-19).

Comments 2: In their captions Figure 1 and 2 should report a more detailed explanation so as to make it easier for readers who might not be familiar with such approach to catch the meaning and the strength of the relations (and how they were structured).

Response 2: As suggested, we have provided more detailed explanatory notes for Figures 1 and 2 (see revised pages 4 and 7).

Comments 3: Authors contributions (line 473-480) are missing.
Data availability (line 483-487) is missing.
Acknowledgments (line 488-490) are missing

Response 3: We have supplemented the missing Authors contributions, Data availability, and Acknowledgments sections and appreciate this valuable suggestion (see revised pages 15 and 16).

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript titled "Diversified Cropping Modulate microbial communities and greenhouse gas emissions by enhancing soil nutrients” by Wang et al., is well-organized and presents relevant and valuable information for the reaadership of Agronomy. The introduction is well-supported and effectively highlights the importance of studying cropping system diversification, particularly intercropping and crop rotation.

The authors state that diversified cropping systems effectively mitigate crop pests and diseases. However, no specific keywords related to these terms appear to be included in the reported search criteria. To maintain consistency, this claim should either be supported by one of the documented search criteria (perhaps nested within broader terms) or removed from the manuscript entirely.

It would be very helpful to present the number of articles retrieved overall, as well as those identified for each management type (e.g., intercropping and crop rotation) or even for each subcategory analyzed. This information is essential to assess the scope of the effort described in the statement: “Crop rotation and intercropping-related documents were downloaded individually, and their contents were then examined.” These data should be included either in the results section or as part of the supplementary tables detailing the search criteria.

Given the broad nature of the search terms used, it is important to discuss the potential magnitude of bias introduced by including journals outside the core disciplines of agronomy, agriculture, or environmental sciences, such as those in social or economic fields. Similarly, the lack of a filter based on journal impact factor raises concerns. Without this filter, the analysis may include less influential publications, which could dilute the relevance of the findings. Article volume alone is not a reliable indicator of research quality or trends. The Discussion section should briefly address these decisions regarding the search methodology.

Figures 1 and 3 should be presented better, as the scale is not clearly visible either in the legend or within the rings. Enhancing their clarity will aid the reader's interpretation of the data.

The Discussion section should more explicitly reflect the findings of the bibliometric analysis. At present, it reads more like a general literature overview rather than a synthesis based on the specific nodes and trends identified in the systematic and comprehensive review.

Additionally, the discussion remains too general in places, and some statements do not meaningfully contribute to the manuscript. For example, lines 246–249 state: “Different cropping patterns and management practices have different effects on soil microbial communities and crop growth, and appropriate integration with other agricultural practices can improve soil quality and biodiversity.” Such broad statements should be revised or replaced with insights derived directly from the bibliometric results.

Author Response

We appreciate the thoughtful review and constructive feedback provided by the reviewers. We agree with the reviewers' suggestions and wilincorporate the recommended changes into the manuscript.

Comments 1: The authors state that diversified cropping systems effectively mitigate crop pests and diseases. However, no specific keywords related to these terms appear to be included in the reported search criteria. To maintain consistency, this claim should either be supported by one of the documented search criteria (perhaps nested within broader terms) or removed from the manuscript entirely.

Response 1: Based on the reviewer's comments, we have removed the relevant description regarding ‘diversified cropping systems can effectively alleviate crop pests and diseases’ from the manuscript, and we appreciate this valuable suggestion.

Comments 2: It would be very helpful to present the number of articles retrieved overall, as well as those identified for each management type (e.g., intercropping and crop rotation) or even for each subcategory analyzed. This information is essential to assess the scope of the effort described in the statement: “Crop rotation and intercropping-related documents were downloaded individually, and their contents were then examined.” These data should be included either in the results section or as part of the supplementary tables detailing the search criteria.

Response 2: We have provided the total number of articles retrieved in the Materials and Methods section as recommended (see lines 99-102).

Comments 3: Given the broad nature of the search terms used, it is important to discuss the potential magnitude of bias introduced by including journals outside the core disciplines of agronomy, agriculture, or environmental sciences, such as those in social or economic fields. Similarly, the lack of a filter based on journal impact factor raises concerns. Without this filter, the analysis may include less influential publications, which could dilute the relevance of the findings. 

Response 3: We have partially deleted controversial references to improve readability, and we appreciate this valuable suggestion. Regarding the issue of high-profile, highly cited related papers being overlooked, we have added references to Breza et al. (2023) and briefly discussed them as suggested (see revised pages 16-19).

Comments 4: Figures 1 and 3 should be presented better, as the scale is not clearly visible either in the legend or within the rings. Enhancing their clarity will aid the reader's interpretation of the data.

Response 4: We have improved the clarity of Figures 1 and 3 as suggested (see revised pages 4 and 8).

Comments 5: The Discussion section should more explicitly reflect the findings of the bibliometric analysis. At present, it reads more like a general literature overview rather than a synthesis based on the specific nodes and trends identified in the systematic and comprehensive review.

Response 5: We have added relevant discussions to the discussion section to more clearly reflect the results of the bibliometric analysis, making it a review based on specific nodes and trends identified in the systematic comprehensive review (see revised pages 13).

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

the manuscript had been improved significantly and according to my requests.

I can now recommend it for publication in Agronomy.

Best wishes.