Effects of Different Proportions of Organic Fertilizer in Place of Chemical Fertilizer on Microbial Diversity and Community Structure of Pineapple Rhizosphere Soil

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

• The manuscript provides a detailed investigation into the effects of different fertilization methods on the microbial diversity and community structure of pineapple rhizosphere soil. Overall, the manuscript is well-structured and informative. Here are some suggestions for improvement:

• 1. In the abstract, clarify the term "cluster analysis" in line 13. Is it hierarchical clustering, k-means, or another method?

• 2. In the introduction, consider providing a brief overview of the key findings and objectives of the study.

• 3. In the results, when discussing differences in bacterial diversity (line 142), provide a more in-depth interpretation of the ecological implications of these differences.

• 4. In the discussion, consider discussing the limitations of the study and potential sources of variability in the results.

• 5. When discussing functional differences (line 230), elaborate on the ecological significance of these functions in the context of soil health.

• 6. Provide more details on the interpretation of LEfSe results, specifically explaining why certain bacterial groups are enriched in different treatments.

• 7. Clarify the term "Chemoheterotrophy" and other functional types in the context of their significance in soil ecosystems.

• 8. In the conclusion, emphasize the key practical implications of the findings for agriculture or soil management.

Comments on the Quality of English Language

• Consider breaking down long sentences for better readability.
• Ensure that each paragraph focuses on a specific aspect or result, making it easier for readers to follow.

Author Response

Dear editor:

1. The hierarchical clustering method used.
2. The introduction has been modified.
3. The significance of differences in bacterial diversity is stated in the Discussion.
4. Discussion has been modified.
5. Chemoheterotrophic functions are involved in soil carbon cycling, as explained in the Discussion.
6. According to the LEfse analysis, different treatments had different enrichments of bacterial groups, and the reasons are explained in the Discussion.
7. Discussion has highlighted the importance of chemoheterotrophy.
8. The experimental results and follow-up work have been explained in the conclusion, aiming to provide reference for production practice.
9. Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

Brief Summary

The manuscript agronomy-2751665 entitled “Effects of Organic Fermentation Substitution for Chemical Fermentation on Microbial Diversity and Community Structure of Pineapple Rhizosphere Soil” has to be revised with major revisions to improve the quality of the manuscript and a future publication. In general, the authors have to underline the workin hypothesis and be careful to grammar errors in the text. The authors carried out interesting analysis, but the methodologieas and the presentation of the results need relevant imrpovment. See specific comments below.

Specific comments

·        Title: Do you mean organic/chemical fertilization? Please, change the title and make sure it reflects the meaning of the work.

·        Abstract: The abstract has to be revised in order to introduce some lines about the contest of the work and the objective of the same. After you can add the information about the methodologies and the results. In the present way, the abstract seems incoherent and it not weel explained the whole work.

·        Introduction: The introduction places the study in a broad context and highlights why the study was needed. However, I suggest to improve the quality inserting more references. Furthermore, the working hypothesis are not described. See below the specific comments:

§  L34: use italic for scientific name “Ananas comosus”

§  L42: revise the grammar of the sentence.

§  L43: replace With to with

§  L68-76: in this part it is not clear the working hypothesis of the work. Please, revise it.

§  L76: delete a dot

 

·        Materials and Methods: The description of the methods is too poor and more references have to be provided. Still, the following elements needs to be added:

 

§  L79-81: add more details about the samplings site. Where did you collect the samples? Please, after dot use case letter and revise the English of the whole paragraph.

§  L83-93: add more details about the chemical properties of the soil and about the experimental design (planting method, duration and period of pineapple plantation, application of the treatments … ).

§  L95-97: this sentence has no meaning as it appears. Please, revise. Furthermore, you have to add more details and information about the DNA extraction, PCR amplification and sequencing. For the DNA extraxtion which kit did you use? Did you check the DNA concentration and purity before to proceed with the amplification? Regarding the PCR, which primers did you use for the amplification? Specify also the regions amplified of the 16SrRNA. Please, insert more detail about the PCR cycle. Please, insert also more information about the platform used for the sequencing.  

 

·       Results: The results section should be improved for the following aspects:

§  L151: correct bydiversity in biodiveersity you should carry out the phylogenetic analysis and provide the ohylogenetic tree for the Bacillus glycinifermentans MGMM1.

§  L195: replace the comma with a dot

§  Figure 2: please, revise the figure using only English language in the labels.

§  Figure 5: please, revise the figure using only English language in the labels. Revise the section of the label avoiding any signs (see Chemoheterotrofy).

·        Discussion: The section is too generalized. The relevance of this section needs to be updated in light of the significance of the results. The writers looked into a number of characteristics. These should be thoroughly explored, highlighting the significance of their findings and incorporating the references and comparisons with other studies.

·        Conclusions: An overview of the study was given by the writers. The significance of the results should be emphasized more, and the authors should provide more information about the directions for future research.

Other comments

All the sections need improvements for the English language. Please, revise the manuscript avoiding grammar errors. 

Author Response

Dear editor:

1. The title has been changed
2. Abstract has been changed
3. The introduction adds references and working hypothesis:

（1）"Ananas comosus" is italicized.

（2）With replaced with.

（3）The working hypothesis of this study has been modified.

4. Materials and methods.

(1) Added sampling details, soil chemistry indicators, as well as planting methods, pineapple planting cycles and treatment applications.

(2) Added information on DNA extraction, PCR amplification and sequencing.

5. Results.

   （1）Phylogenetic tree constructed.

   （2）All pictures use English labels.

6. Discussion has been revised
7. The conclusion adds the next research direction
8. Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Manuscript No. 2751665: Effects of Organic Fermentation Substitution for Chemical Fermentation on Microbial Diversity and Community Structure of Pineapple Rhizosphere Soil

The authors, Wanying Chen et al., researched the effects of organic fermentation substitution for chemical fermentation on the microbial diversity and community structure of pineapple rhizosphere soil. I have highlighted below the areas that need corrections.

Line 42: Why a special banana?

Line 47: Why actinomycetes and not fungi?

Lines 47–48: Needs a supporting reference

Line 56: Delete 2022 and insert a reference number in brackets. Do similar to the subsequent section below.

Lines 56–59: Not clear

Lines 61–62: Not clear

Lines 68-69: Rephrase

Lines 69–76: Rephrase

 

Materials and methods

This section is missing a lot of key information!

Line 79: Where did you source pineapple fruit?

Line 92: What was the pineapple spacing?

Lines 95–97: How was DNA extracted?

What kind of DNA extraction kit was used? How was the purity of the DNA determined? Was the extracted DNA stored before sequencing? If so, where was the storage, and under what conditions? Were amplicons purified? If yes, how?

 

How did you do the sequencing?

Bioinformatics for the bacterial composition is missing.

 

Statistical analysis

How did you do the correlation and multiple regression?

How are alpha, observed, and Shannon diversity indexes done?

What statistical analyses were done between the groups for the alpha-diversity and beta-diversity indexes?

 

Results

The authors need to present the results without discussing them.

Discussions

The discussion should focus on the presented results in a logical manner and not repeat the explanations given in materials and methodologies.

Comments on the Quality of English Language

Language for presenting methodology, results, and discussion needs improvement.

Author Response

Dear editor:

1. In Hainan, bananas and pineapples are the four major tropical fruits in tropical areas. There are many experts studying bananas, there are many documents, and the scope is wide. Therefore, I prefer to consult the literature on bananas to extract useful information to write about pineapple.
2. Having more bacteria and actinomycetes is good for the soil, while having more fungi and less bacteria is bad for soil health.Confirmed that Actinomycetes and Bacteria were greatly reduced and their activity was decreased due to soil acidification, while fungi were less affected by soil acidification.

Chen X,Wei H,Zhang J. Nitrogen and Sulfur Additions Improved the Diversity of  nirK - and  nirS -Type Denitrifying Bacterial Communities of Farmland Soil. Biology (Basel). 2021;10 (11).

Cai Jie, Zhang Jie, Yu Shan, et al.  Effects of fertilization methods on bacterial diversity and community structure characteristics of cassava rhizosphere soil [J].  Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 2022, 51(1):15- 20.

3. Lines 56–59: Not clear

        Lines 61–62: Not clear

       Chen, J., & Zeng, H. Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation. PeerJ,2022.

      Wang, B., Sun, M., Yang, J., Shen, Z., Ou, Y., Fu, L., Shen, Q et al. Inducing banana fusarium wilt disease suppression through soil microbiome reshaping by pineapple–banana rotation combined with biofertilizer application. Soil,2022, 8(1), 17-29.

       Yang, J., Wu, Q., Wang, Y., Chen, X., Gao, W., Zhao, Y. Ruan, Y. et al. Suppression of banana fusarium wilt disease with soil microbial mechanisms via pineapple rotation and residue amendment. Agronomy, 2013,13(2), 377.

      4.Lines 68-76 have been modified

      5.Materials and methods: Added pineapple source, pineapple row spacing, DNA extraction and related information, bioinformatics of bacterial composition

     6.Statistical analysis:

• Mothur software was used to calculate the ɑ-diversity index and beta diversity of the bacterial community.
• PCoA and NMDS using R language.
• ɑ-Diversity index analysis Simpson, shannon, Invsimpson, ACE, Chao1.
• Beta-diversity analysis PCoA and NMDS

7. Discussion has been revised
8. The conclusion adds the next research direction
9. Please see the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Dear authors,

the manuscript agronomy-2751665 entitled “Effects of Organic Fermentation Substitution for Chemical Fermentation on Microbial Diversity and Community Structure of Pineapple Rhizosphere Soil” has to be revised with minor revisions to improve the quality of the manuscript and a future publication.

Specific comments

·        Introduction

§  L42-44: these sentences still remain unclear. Please revise them in order to create a sentence with a logical meaning.

§  L78: add a space before the new paragraph

 

·        Materials and Methods

 

§  L122-125: The period is too long. Please, be careful also to the logical meaning of the sentences.  

·        Discussion

 

§  L310-330: This part needs more improvement as of the quality of the writing and several typos. 

Author Response

Dear editor:

1. L42-44 has been modified.
2. L78 Spaces have been added.
3. L122-125 has been rewritten.
4. L310-330 has been rewritten.
5. Please see the attachment

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Authors have improved the document to my satisfaction

Comments on the Quality of English Language

N/A

Author Response

Please see the attachment

Author Response File: Author Response.pdf