The Preliminary Research on Shifts in Maize Rhizosphere Soil Microbial Communities and Symbiotic Networks under Different Fertilizer Sources
Round 1
Reviewer 1 Report
Review
The work „ Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties unde different fertilizer sources“ is interesting and concerns an important ecological aspect, namely – impact various types of fertilization on the basic chemical and microbiological properties of soils.
A main shortcoming of this experiment is the fact that research is being carried out for only one year, which decreases the credibility and repetition of results.
In my opinion, the authors draw too far-reaching conclusions from a one-year field experiment. I suggest changing the topic to, for example, preliminary research on...
After an analysis of the Manuskript, I have the following comments, that are required to pass to the next stage of procedure:
· please provide the correct soil taxonomy according to WRB 2022 (line 112)
· line 143- please briefly describe the analytical methods used
- round results - see attached PDF file
· in my opinion, some analyzes are redundant, such as total potassium, while the lack of basic analysis, such as soil texture, soil reaction and determination of electrical conductivity as a measure of salinity
Comments for author File: 
Comments.pdf
Author Response
Responses to Reviewer and Editor’s Comments
Manuscript Number: agronomy-2500002
Manuscript Title: Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources
Article Type: Original article
Firstly, we are thankful to the reviewers for their valuable time and effort used to review our manuscript. We appreciate the reviewers’ comments, which certainly improved the quality of the manuscript. The responses to the reviewers’ comments are provided point-by-point below. The revisions and other minor corrections made were highlighted in red for easy reference. Please find below the responses to the corrections raised by the reviewers, along with the list of changes that we have made in the revised manuscript.
Reviewers’ comments:
Reviewer #1:
GENERAL COMMENTS
The work “Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources” is interesting and concerns an important ecological aspect, namely – impact various types of fertilization on the basic chemical and microbiological properties of soils.
Comments 1- A main shortcoming of this experiment is the fact that research is being carried out for only one year, which decreases the credibility and repetition of results.
Response: Thank you for the suggestion. We have been conducting our experiment for the third year, which have not been written before. Now, it is as been supplemented in “2.1 The Study site and field experience design”, please refer to Line 114 for specific details.
Comments 2- In my opinion, the authors draw too far-reaching conclusions from a one-year field experiment. I suggest changing the topic to, for example, preliminary research on...
Response: Thank you for the suggestion. We have changed the topic to “The preliminary research on shifts in maize rhizosphere soil microbial communities and symbiotic networks under different fertilizer sources”.
After an analysis of the Manuscript, I have the following comments, that are required to pass to the next stage of procedure:
Comments 3- please provide the correct soil taxonomy according to WRB 2022 (line 112)
Response: Thank you for the suggestion. What we want to express is that the soil texture is silty alkaline clay loam, and we have now changed the “soil taxonomy” to “soil texture” in Line 110 of the revised manuscript.
Comments 4- line 143- please briefly describe the analytical methods used
Response: Thank you for the suggestion. The analytical methods used have been supplemented in “2.3. Soil chemical analysis”, please refer to Lines 141-146 for specific details.
Comments 5- round results - see attached PDF file
Response: Thank you for the suggestion. We have carefully revised the ones that need to be rounded. Please refer to the revised manuscript for specific details.
Comments 6- in my opinion, some analyzes are redundant, such as total potassium, while the lack of basic analysis, such as soil texture, soil reaction and determination of electrical conductivity as a measure of salinity
Response: Thank you for the suggestion. We fully agree with your opinion, but due to some reasons, these analyses cannot be supplemented in the short term. However, we will focus on considering and analyzing these basic indicators in our future research.
Author Response File: Author Response.pdf
Reviewer 2 Report
A manuscript entitled " Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources " submitted to Agronomy presented research on the soil microbiome after the application of organic and inorganic fertilizers at different doses. The research presented is not a novel approach and is similar to others on the effects of different organic fertilizers on the microbiome of the rhizosphere zone of corn. Overall, the manuscript is well written, but requires major revisions. The authors should rewrite the introduction and indicate the innovative element of the study. Detailed comments can be found below:
Introduction
1. Please indicate the novelty of your research
Materials and methods
1. Please present graphically (e.g., a map) the place where the experiment was established
2. What were the mineral and organic fertilizer dosages based on?
3. Please explain what rhizosphere soil was?
4. Line 152: please delete one of „Illumina”
Results
1. Line 220: In fig. S2 there is no correlation presented between the variables mentioned.
2.Please improve the quality of the figures in the supplementary material (Fig. S4 and S5)
3. Table S2: Please correct the table caption. It involves fungi.
Discussion
1. Lines 370, 393, 407: Please do not quote tables and figures in the discussion part of the manuscript
2. Lines 438-439: Microplastic was not studied in the presented research, I think this sentence can be removed.
3.The obtained results should be discussed more with the results of other scientists.
4. The discussion should be rewritten and be more supported by the findings of other authors. The discussion should only concern the results presented.
Conclusion
1. The conclusion is very general and should be rewritten.
2. Please indicate whether the research objective was achieved or the research question was answered. Please suggest also what still needs to be studied in the future and emphasize why the research conducted is important compared to others.
Author Response
Responses to Reviewer and Editor’s Comments
Manuscript Number: agronomy-2500002
Manuscript Title: Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources
Article Type: Original article
Firstly, we are thankful to the reviewers for their valuable time and effort used to review our manuscript. We appreciate the reviewers’ comments, which certainly improved the quality of the manuscript. The responses to the reviewers’ comments are provided point-by-point below. The revisions and other minor corrections made were highlighted in red for easy reference. Please find below the responses to the corrections raised by the reviewers, along with the list of changes that we have made in the revised manuscript.
Reviewers’ comments:
Reviewer #2:
A manuscript entitled " Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources " submitted to Agronomy presented research on the soil microbiome after the application of organic and inorganic fertilizers at different doses. The research presented is not a novel approach and is similar to others on the effects of different organic fertilizers on the microbiome of the rhizosphere zone of corn. Overall, the manuscript is well written, but requires major revisions. The authors should rewrite the introduction and indicate the innovative element of the study. Detailed comments can be found below:
Comments 1- Introduction: Please indicate the novelty of your research
Response: Thank you for the suggestion. We have added the novelty of your research in the Introduction section, as follows: However, up to now, the establishment of soil microbial community network in maize field under different fertilizer sources is still in the primary stage, so it is of great significance to further establish the network of soil microbial community for the interaction between microorganisms. Moreover, the effects of fertilizer sources on maize soil microbial communities and their symbiotic networks in arid irrigated areas of Ningxia have not been revealed. Here, a field trial was carried to investigate the impact of fertilizer sources on rhizosphere soil bacterial and fungal communities in maize using amplicon sequencing and network analysis.
Comments 2- Materials and methods
2.1 Please present graphically (e.g., a map) the place where the experiment was established
Response: Thank you for the suggestion. We have remade the graphically (e.g., a map) to present the place where the experience was established, as detailed in “2.1. Study site and field experiment design”.
2.2 What were the mineral and organic fertilizer dosages based on?
Response: Thank you for the suggestion. The dosages of inorganic and organic fertilizer were set according to the local common dosages applied by farmers.
2.3 Please explain what rhizosphere soil was?
Response: Thank you for the suggestion. Rhizosphere soil refers to the local micro domain soil directly affected by plant roots, which is unique in the soil system and has significant differences in physical, chemical, and physicochemical properties compared to the soil itself (non-rhizosphere soil).
2.4 Line 152: please delete one of „Illumina”
Response: Thank you for the suggestion. We have deleted one “Illumina”. For specific details, please refer to Line 155 of the revised manuscript.
Comments 3- Results
3.1 Line 220: In fig. S2 there is no correlation presented between the variables mentioned.
Response: Thank you for the suggestion. Fig. S2 in Line 220 has been removed in revised manuscript. Please refer to the Line 223 of revised manuscript for specific details.
3.2 Please improve the quality of the figures in the supplementary material (Fig. S4 and S5)
Response: Thank you for the suggestion. We have improved the quality of the figures in the supplementary material. Please refer to the revised supplementary material for specific details.
Fig. S4 Results of LEfSe analysis showing bacterial taxa that significantly differed in the four treatments (a). Cladogram plotted from LEfSe analysis showing the significant differences (p <0.05) in relative abundance of bacterial taxon among four treatments (b).
Fig. S5 Results of LEfSe analysis showing fungal taxa that significantly differed in the four treatments (a). Cladogram plotted from LEfSe analysis showing the significant differences (p <0.05) in relative abundance of fungal taxon among four treatments (b).
3.3 Table S2: Please correct the table caption. It involves fungi.
Response: Thank you for the suggestion. We have made corrections, and the caption of Table S2 is correct, while Table S3 is incorrect. However, we have carefully checked and modified it. Please refer to the relevant content.
Comments 4- Discussion
4.1 Lines 370, 393, 407: Please do not quote tables and figures in the discussion part of the manuscript
Response: Thank you for the suggestion. We have removed all quoted tables and figures in the Discussion part of the manuscript. Please refer to the Discussion section of the revised manuscript for specific details.
4.2 Lines 438-439: Microplastic was not studied in the presented research, I think this sentence can be removed
Response: Thank you for the suggestion. This sentence can be removed. That is to say, the relevant content of reference 68 cited has been removed.
4.3 Table S2: The obtained results should be discussed more with the results of other scientists.
Response: Thank you for the suggestion. The obtained results in Table S2 have been discussed more with the results of other scientists. Please refer to the Discussion section of the revised manuscript for specific details.
4.4 The discussion should be rewritten and be more supported by the findings of other authors. The discussion should only concern the results presented.
Response: Thank you for the suggestion. The discussion has been rewritten carefully, and please refer to the Conclusion section of the revised manuscript for specific details.
Comments 5- Conclusion
5.1 The conclusion is very general and should be rewritten.
Response: Thank you for the suggestion. The conclusion has been rewritten carefully, and please refer to the Conclusion section of the revised manuscript for specific details，as follows: In this work, a field trial was carried to investigate the impact of fertilizer sources on rhizosphere soil bacterial and fungal communities in maize using amplicon sequencing and network analysis. Our results showed that different fertilizer sources significantly shifted soil chemical properties and microbial community in maize farm after water irrigation. Network analysis also suggested that fertilization caused fewer interaction among bacterial and fungal taxa in the microbial community, especially in the combination of NPK and OF, indicating it can decrease microbial competition among them through im-proving soil fertility, etc. Moreover, redundancy analysis combined with Mantel test further revealed soil OM and available N and P were main soil fertility factors driving microbial community variation. Above all, the results indicated that the application of NPK combined with OF is the most appropriate method of fertilization, which can affect soil biogeochemical cycles through significantly affecting soil C, N, and P as well as microbial community in maize rhizosphere. In short, this study can provide important methods and data support for further research on the improvement of soil quality and yield in the future, as well as the green development of agriculture.
5.2 Please indicate whether the research objective was achieved or the research question was answered. Please suggest also what still needs to be studied in the future and emphasize why the research conducted is important compared to others.
Response: Thank you for the suggestion. The conclusion has been rewritten carefully, and relevant questions have been answered and resolved. Please refer to the Conclusion section of the revised manuscript for specific details，as follows: Above all, the results indicated that the application of NPK combined with OF is the most appropriate method of fertilization, which can affect soil biogeochemical cycles through significantly affecting soil C, N, and P as well as microbial community in maize rhizo-sphere. In short, this study can provide important methods and data support for further research on the improvement of soil quality and yield in the future, as well as the green development of agriculture.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Review 2
The authors corrected most of the inaccuracies and errors. The field experiment was conducted on soil. The reader does not know what kind of soil it is, please provide the correct taxonomy according to WRB 2022 - I have suggested it before. (IUSS Working Group WRB. 2022. World Reference Base for Soil Resources. International soil classification system for naming soils and creating legends for soil maps. 4th edition. International Union of Soil Sciences (IUSS), Vienna, Austria).
Line 111 - the soil texture is silty alkaline clay loam - there is no such texture group
In my opinion the lack of basic analysis, such as soil texture, soil reaction and determination of electrical conductivity as a measure of salinity makes the work unattractive to the reader and does not comprehensively address the topic.
Author Response
Responses to Reviewer and Editor’s Comments
Manuscript Number: agronomy-2500002
Manuscript Title: Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources
Article Type: Original article
Firstly, we are thankful to the reviewers for their valuable time and effort used to review our manuscript. We appreciate the reviewers’ comments, which certainly improved the quality of the manuscript. The responses to the reviewers’ comments are provided point-by-point below. The minor revisions were highlighted in red for easy reference. Please find below the responses to the corrections raised by the reviewers, along with the list of changes that we have made in the revised manuscript.
Reviewers’ comments:
Reviewer #1:
GENERAL COMMENTS
Comments 1- The authors corrected most of the inaccuracies and errors. The field experiment was conducted on soil. The reader does not know what kind of soil it is, please provide the correct taxonomy according to WRB 2022 - I have suggested it before. (IUSS Working Group WRB. 2022. World Reference Base for Soil Resources. International soil classification system for naming soils and creating legends for soil maps. 4th edition. International Union of Soil Sciences (IUSS), Vienna, Austria).
Response: Thank you for the suggestion. According to previous research and statistics, the local Soil type belongs to gray desert soil.
Comments 2- Line 111 - the soil texture is silty alkaline clay loam - there is no such texture group.
Response: Thank you for the suggestion. The sentence has been revised to “the soil texture is silty clay loam”. Please refer to Line 111 for specific details.
Comments 3- In my opinion the lack of basic analysis, such as soil texture, soil reaction and determination of electrical conductivity as a measure of salinity makes the work unattractive to the reader and does not comprehensively address the topic.
Response: Thank you for the suggestion. We greatly appreciate the reviewer's profound suggestions and believe that presenting basic analysis, such as soil texture, soil reaction, and determination of electrical conductivity would be useful. However, the determination of soil texture usually uses the sieving method, using a standard sieve group for sieving, and classifying and weighing particles of different sizes, ultimately determining the soil texture based on the percentage of particles; soil reaction refers to the acidity and alkalinity of the soil, generally expressed as soil pH; use a conductivity meter to measure soil conductivity. Unfortunately, the soil sampled in this field in 2019 was no longer available. Therefore, we regret not being able to provide these indicators in this study. We will consider this suggestion in future research.
Author Response File: Author Response.pdf
Reviewer 2 Report
Thank you for responding to my comments. The article can be published in the present form.
Author Response
Responses to Reviewer and Editor’s Comments
Manuscript Number: agronomy-2500002
Manuscript Title: Shifts in maize rhizosphere soil microbial communities and networks are correlated with soil chemical properties under different fertilizer sources
Article Type: Original article
Firstly, we are thankful to the reviewers for their valuable time and effort used to review our manuscript. We appreciate the reviewers’ comments, which certainly improved the quality of the manuscript. The responses to the reviewers’ comments are provided point-by-point below. The minor revisions were highlighted in red for easy reference. Please find below the responses to the corrections raised by the reviewers, along with the list of changes that we have made in the revised manuscript.
Reviewers’ comments:
Reviewer #2:
Comments 1- Thank you for responding to my comments. The article can be published in the present form.
Response: Thank you for your comments.
Author Response File: Author Response.pdf
