The Effect of Biofumigation on the Microbiome Composition in Replanted Soil in a Fruit Tree Nursery

Round 1

Reviewer 1 Report

I would recommend only a couple of minor changes for the ms to make the results more structured and easily understood by a wide range of readers. (see below):

 Recommends

1.     It would be good to supplement the Introduction chapter with a working hypothesis formulated explicitly, and the Discussion chapter - again, with an explicit definition of whether the hypothesis turned out to be correct.

2.     To fully understand the results of the work, as well as highlight the most important ones, I would recommend to add a figure with a kind of "graphic result".

Author Response

Dear Editor and Reviewers

“The Effect of Biofumigation on the Composition of the Microbiome in Replanted Soil in a Fruit Tree Nursery”, authors (Robert Wieczorek, Zofia Zydlik, Agnieszka Wolna-Maruwka, Alicja Niewiadomska, Dariusz Kayzer,), which Robert Wieczorek is a corresponding author

(email: [email protected]).

I have made every effort to improve this manuscript.

The entire manuscript was revised according to the reviewers' instructions.

Reviewer 1

1. We supplemented in the Introduction chapter hypothesis formulated explicitly, and the Discussion chapter - again, with an explicit definition of whether the hypothesis turned out to be correct.

2. To fully understand the work's results and highlight the most important ones, We added a figure with a kind of "graphic result".

Reviewer 2

1. We have changed the formulated purpose of the study to make it more understandable to the recipients
2. We have proposed criteria to show how to assess soil health in terms of microbial composition, providing a hypothesis at the end of the introductory chapter.
3. In the conclusions chapter, we proposed an appropriate planting scheme for soils after soil fumigation.

Reviewer 3

1. Lines 46, 62, 69, 177, etc. - change the style of literature citation, for example replace "[15, 16, 17, 18, 19, 20, 21, 22, 23]" with [15-23]. Please do this throughout the text

Was corrected

2. In the introduction section, it is desirable to reveal more the relevance of the biofumigation method and reduce general ideas about approaches to growing fruit trees

The introduction chapter supplements the knowledge about biofumigation using phytosanitary plants

3. Line 97 - please, remove the extra dot- was corrected

4. L 116-134 - This is a description of part of the results of the experiment. Materials and methods should contain only the methodological part.

The presented physical and chemical characteristics of the soil were research material, therefore they are included in this section: materials and methods, and not in the research results chapter. In microbiological research, the physicochemical properties of the soil are always included in the materials and methods section

5. Reviewer's suggestion in points 5-7 is indeed accurate and we thank you very much for it. However, we did not perform such analyses and cannot discuss the obtained results from this angle.

   However, in the introduction chapter, expanding the information about biofumigation, we highlighted what types of active substances may be released into the environment and how they may affect microbial communities.

   We will take this into account in the future during similar research

 I have prepared this manuscript according to the reviewers' instructions, but if you have any questions or suggestions regarding manuscript preparation, do not hesitate to contact me. I will do my best to correct the manuscript and send it to you quickly.

Best regards,

Alicja Niewiadomska

Author Response File: Author Response.doc

Reviewer 2 Report

The experiment is generally well-done, and the writing is acceptable. My main concern is the aim of the study. From the introduction, the aim is to investigate the difference in soil microbial compositions after planting different plant species. It is a well-known fact that different plants have their own rhizosphere characteristics, including microbial compositions. Therefore, the aim of the current study needs to be clear. It would be better if the authors can suggest a criteria showing how to evaluate the soil health condition from the aspect of microbial compositions. Or it could also help if the authors can propose a suitable planting scheme for soils after the soil fumigation treatment, after comparing microbial activities under different planting patterns. 

Author Response

Dear Editor and Reviewers

“The Effect of Biofumigation on the Composition of the Microbiome in Replanted Soil in a Fruit Tree Nursery”, authors (Robert Wieczorek, Zofia Zydlik, Agnieszka Wolna-Maruwka, Alicja Niewiadomska, Dariusz Kayzer,), which Robert Wieczorek is a corresponding author

(email: [email protected]).

I have made every effort to improve this manuscript.

The entire manuscript was revised according to the reviewers' instructions.

Reviewer 1

1. We supplemented in the Introduction chapter hypothesis formulated explicitly, and the Discussion chapter - again, with an explicit definition of whether the hypothesis turned out to be correct.

2. To fully understand the work's results and highlight the most important ones, We added a figure with a kind of "graphic result".

Reviewer 2

1. We have changed the formulated purpose of the study to make it more understandable to the recipients
2. We have proposed criteria to show how to assess soil health in terms of microbial composition, providing a hypothesis at the end of the introductory chapter.
3. In the conclusions chapter, we proposed an appropriate planting scheme for soils after soil fumigation.

Reviewer 3

1. Lines 46, 62, 69, 177, etc. - change the style of literature citation, for example replace "[15, 16, 17, 18, 19, 20, 21, 22, 23]" with [15-23]. Please do this throughout the text

Was corrected

2. In the introduction section, it is desirable to reveal more the relevance of the biofumigation method and reduce general ideas about approaches to growing fruit trees

The introduction chapter supplements the knowledge about biofumigation using phytosanitary plants

3. Line 97 - please, remove the extra dot- was corrected

4. L 116-134 - This is a description of part of the results of the experiment. Materials and methods should contain only the methodological part.

The presented physical and chemical characteristics of the soil were research material, therefore they are included in this section: materials and methods, and not in the research results chapter. In microbiological research, the physicochemical properties of the soil are always included in the materials and methods section

5. Reviewer's suggestion in points 5-7 is indeed accurate and we thank you very much for it. However, we did not perform such analyses and cannot discuss the obtained results from this angle.

   However, in the introduction chapter, expanding the information about biofumigation, we highlighted what types of active substances may be released into the environment and how they may affect microbial communities.

   We will take this into account in the future during similar research

 I have prepared this manuscript according to the reviewers' instructions, but if you have any questions or suggestions regarding manuscript preparation, do not hesitate to contact me. I will do my best to correct the manuscript and send it to you quickly.

Best regards,

Alicja Niewiadomska

 

Author Response File: Author Response.doc

Reviewer 3 Report

  1.  Lines 46, 62, 69, 177, etc. -  change the style of literature citation, for example replace "[15, 16, 17, 18, 19, 20, 21, 22, 23]" with [15-23]. Please do this throughout the text

2.  In the introduction section, it is desirable to reveal more the relevance of the biofumigation method and reduce general ideas about approaches to growing fruit trees

3. Line 97 - please, remove the extra dot

4. L 116-134 - This is a description of part of the results of the experiment. Materials and methods should contain only the methodological part.

5. Did you perform a physical and chemical analysis of the soil after fumigation? Perhaps it would be appropriate to determine the presence of certain bioactive compounds in soil samples that can cause the increase in the content of beneficial bacteria. For example, alpha-terthienyl as mentioned in the source [51].

6. Have the investigated plants been previously studied for their ability to synthesize secondary metabolites? 

7. The authors claim that the cultivation of the phytosanitary plants contributed to the change in the qualitative composition of the soil microbiome.  This is experimentally confirmed and described. However, a more detailed discussion of the mechanisms of the influence of phytosanitary plants used in this study on the creation of optimal conditions for the growth of beneficial bacteria is somewhat lacking. A short section with a description of substances that could affect the microbiome will expand the understanding of the mechanisms of the biofumigation method

Minor work needed to be done on articles and correction of minor technical errors

Author Response

Dear Editor and Reviewers

“The Effect of Biofumigation on the Composition of the Microbiome in Replanted Soil in a Fruit Tree Nursery”, authors (Robert Wieczorek, Zofia Zydlik, Agnieszka Wolna-Maruwka, Alicja Niewiadomska, Dariusz Kayzer,), which Robert Wieczorek is a corresponding author

(email: [email protected]).

I have made every effort to improve this manuscript.

The entire manuscript was revised according to the reviewers' instructions.

Reviewer 1

1. We supplemented in the Introduction chapter hypothesis formulated explicitly, and the Discussion chapter - again, with an explicit definition of whether the hypothesis turned out to be correct.

2. To fully understand the work's results and highlight the most important ones, We added a figure with a kind of "graphic result".

Reviewer 2

1. We have changed the formulated purpose of the study to make it more understandable to the recipients
2. We have proposed criteria to show how to assess soil health in terms of microbial composition, providing a hypothesis at the end of the introductory chapter.
3. In the conclusions chapter, we proposed an appropriate planting scheme for soils after soil fumigation.

Reviewer 3

1. Lines 46, 62, 69, 177, etc. - change the style of literature citation, for example replace "[15, 16, 17, 18, 19, 20, 21, 22, 23]" with [15-23]. Please do this throughout the text

Was corrected

2. In the introduction section, it is desirable to reveal more the relevance of the biofumigation method and reduce general ideas about approaches to growing fruit trees

The introduction chapter supplements the knowledge about biofumigation using phytosanitary plants

3. Line 97 - please, remove the extra dot- was corrected

4. L 116-134 - This is a description of part of the results of the experiment. Materials and methods should contain only the methodological part.

The presented physical and chemical characteristics of the soil were research material, therefore they are included in this section: materials and methods, and not in the research results chapter. In microbiological research, the physicochemical properties of the soil are always included in the materials and methods section

5. Reviewer's suggestion in points 5-7 is indeed accurate and we thank you very much for it. However, we did not perform such analyses and cannot discuss the obtained results from this angle.

   However, in the introduction chapter, expanding the information about biofumigation, we highlighted what types of active substances may be released into the environment and how they may affect microbial communities.

   We will take this into account in the future during similar research.

I have prepared this manuscript according to the reviewers' instructions, but if you have any questions or suggestions regarding manuscript preparation, do not hesitate to contact me. I will do my best to correct the manuscript and send it to you quickly.

Best regards,

Alicja Niewiadomska

 

Author Response File: Author Response.doc