Culturomics and Amplicon-Based Metagenomic Insights into the Bacteria of Soils with High Yield of Oryza sativa L. subsp. Japonica

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

1.    The main question addressed by the research is the role of bacterial communities in the growth and adaptability of rice in paddy field agroecosystems, particularly in the context of high-yield and low-yield rice fields. The research aims to understand the differences in bacterial community composition and abundance between these two types of fields and explores the potential applications in promoting an efficient strategy of rice growth.
2.    The topic is both original and relevant in the field of agriculture and microbiology. It addresses a specific gap by focusing on the microbiota of paddy fields and their influence on rice yield, which is of great importance for food production. The study also introduces culturomics as a technique, contributing to the methodological innovation in the field.
3.    The research adds to the subject area by providing insights into the specific microbial composition and abundance differences between high-yield and low-yield rice fields, shedding light on potential microbial markers for rice field productivity. It also highlights the presence of Exiguobacterium and its potential applications, which can be considered a novel contribution to the field.
4.    Methodological Improvements: Description of how soil and root samples were collected is clear and follows established methods. The description of the methods for analyzing bacterial diversity is quite detailed. The use of MALDI-TOF MS for bacterial identification and the reference to 16S rRNA gene sequencing in cases of low scores are standard practices. This section is adequately described. A rice growth experiment is described clearly, including the process of soaking and germinating rice seeds.

 

The authors analyzed the bacterial community  composition of  the rhizosphere and non-rhizosphere soil samples of rice in high-yield and low-yield fields of Japonica Chu 54 by advanced techniques of  culturomics and amplicon sequencing in order to promote efficient strategy of rice growth and its agroenvironment.

It is a scientifically sound paper,based on a heavy methodology as explained for analysing bacterial diversity and species identification. Results are well investigated and presented in marvelous schematic representations.

A rice growth promotion experiment was also done.

THeir results are extensively discussed based on the up to date bibliography .The paper will contribute to develop efficient strategies and culture techniques for rice growth .

As it is a scientifically sound paper,well written.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors,

The corrections are attached.

Best regards,

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Dear Authors,

The corrections are attached.

Best regards,

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 3 Report

Comments and Suggestions for Authors

Dear Authors,

 

Thank you for your manuscript submission “Culturomics and Amplicon-Based Metagenomic insights into the bacteria of soils with high yield in Oryza sativa L.subsp. Japonica.” The manuscript compared the difference in bacterial community structure composition of rhizosphere and non-rhizosphere soil samples between in-yield and low-yield fields using amplicon sequencing techniques, which will help to improve the growth adaptability strategy of rice. Here are my specific comments:

 

-          The quality of English language is low. There are many typos and grammar errors in the abstract and main context. Extensive editing of English language required

-          Line 37 (page 1), FAO link should be put in the reference list and this citation place should be renamed as [1]. There are some typos in the first paragraph

-          Line 48-52, references are required

-          Line 82-90 (page 2), this paragraph is confusing and hard to understand. Rewriting it should be considered

-          Why are Oryza sativa L.subsp. Japonica selected in this study? What are their advantages over others? Similar question to culturomics and amplicon-based metagenomic method

-          What is the innovation and significance of this study compared with previous studies? More details are required

-          More details should be given for the specific objectives of this study in the introduction

-          Line 141-144 (page 3), why the title of section 2.2 and 2.3 is the same? Section 2.2 is too short and should be removed or combined with other sections

-          Line 145-153, how are these experimental conditions selected? If you got the numbers from other sources, references are required

-          Line 179 (page 4), omicstudio link should be put in the reference list

-          Section 2.4 and 2.5, the information for primers should be put in the appendix to reduce the length of main context

-          Data analysis section should be included in the materials and methods

-          Are there any equations or assumptions for the experimental conditions and data analysis?

-          Figure 1, axis unit is missing. What is the meaning of colorful shape covering each box plot in figure 1a and 1b?

-          Line 236-238 (page 5), from figure 1a, the difference between bacterial richness and low yield in high-yield rice soil is significant, which conflicts with your comments. How do you explain this observation?

-          Figure 2, the figures are too small and difficult to see the content. Changing new figures or removing some figures should be considered.

-          Figure 3 and 5, the figures are too small and difficult to see the content. Changing new figures or removing some figures should be considered. Axis titles for small figure are missing

-          Figure 4, axis titles and units are missing

-          More explanations and proofs with proper citations are expected instead of showing numbers/observations from the figures

-          A comparison of results in this study with previous papers is expected

-          In summary, what is the meaning of all results? More explanations/details are required to explain the meaning of all results.

-          The connection between results should be clarified to emphasize the importance of results

-          The conclusion should focus more on the objectives mentioned in the introduction

-          Are there any limitations for the method in this study?

-          Future research is missing

 

Comments on the Quality of English Language

The quality of English language is low. There are many typos and grammar errors in the abstract and main context. Extensive editing of English language required

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 4 Report

Comments and Suggestions for Authors

agronomy-2699101

In this manuscript, a combination of culturomics and high-throughput sequencing technology was described, for the first time, to explore the bacterial community (rhizosphere, non-rhizosphere). The aim of the research was to highlight bacteria diversity from soils sampled from super-rice in both high-yield and low-yield rice, using both culturomics and V3-V4 amplicon sequencing approaches.

Culturomics along with amplicon sequencing approaches allow isolation of large-scale bacteria and identification of new species, with a broad view in bacterial diversity of a study area.

Bacterial strains were isolated from suspended soil and root by using a total of 180 cultivation conditions, and bacterial diversity was analised based on amplicon seuencing, followed by species identification. Experiments of rice growth promotion in laboratory conditions were moreover carried out.

This manuscript is well written, it is innovative and can give important insights for future research. In the discussion section, the authors should include some considerations on the soil ecology, on the role of bacteria in biogeochemical cycles and the importance for soil conditions and on advantages for agriculture, with a view on the use of plant growth promoting bacteria to improve agriculture in a sustainable way.

Revisions

Lines 3, 33, 48 and aling the text of the manuscript: ‘L. subsp.’ Change not in Italic style;

line 22 and in the text: ‘HSB_0F53_F07’ chanche not in Italics;

line 38: ‘in the past 27 years’, maybe change to ‘a period of 27 years from 1994 to 2021’;

lines 40-41: please explain better this concept;

line 59: ‘Bryobater’ change to ‘Bryobacter’;

lines 63, 67 and in the text: ‘sp. and the letters and numbers indicating a strain’, change not in Italic strains;

line 67: ‘18’ ?;

line 249: ‘Actinobacteriol’ change to ‘Actinobacteria’ or ‘Actinomycetota’;

line 269 and in legend of Figure 2: ‘candidate phylum MBNT15’ change not in Italic style;

Table S4: ‘subsp’ change not in Italics;

Figure S2: ‘EU786131’: not in Italics;

Table S1: Concerning column of ‘chemical composition’ of components of culturomics media, two formulae have been reported, (K2HPO4 and MgSO47H2O) only, and the others are names of the compounds, except complex substrates as yeast extract and others, standardize writing formulae and/or names of compounds. For “Dipotassium Hydrogen Phosphate” the formula is the same as reported above ‘K2HPO4’, or the compound is ‘Monopotassium Phosphate’?;

line 350 and Figure S3: ‘LGIW_s’ change not in Italics. 

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 3 Report

Comments and Suggestions for Authors

 

Dear Authors,

 

Thank you for your manuscript submission. All of my concerns have been carefully considered. In my opinion, the revised manuscript meets the criteria to publish in Agronomy. Therefore, I recommend to accept this manuscript.