The Bacterial Composition and Diversity in a Eucalyptus pellita Plantation in South Sumatra, Indonesia

Round 1

Reviewer 1 Report

Lelana et al. submitted their manuscript entitled “The microbial composition and diversity in a Eucalyptus pellita plantation in South Sumatra, Indonesia” to Diversity. The manuscript is well written, however, I have some major concerns about the statistics and think that the data could be analyzed and discussed in more detail.

In the introduction, the Authors ask three questions about the properties of microbiomes, differing microbial population diversities and the correlation between microbiomes and chemical soil properties. The manuscript tries to answer those questions in a very descriptive way. I do not see any novelty in the discussed results as the connection between physicochemical properties and soil microorganisms is already discussed in many papers and there is no evidence that the type of forest influenced the data. However, I think the manuscript could provide relevant results if the data would be analyzed further.

 

Per site, only one pooled sample was taken and it seems like the sites that were grouped together are quite different from each other. What causes those considerable differences within plantation forest samples?

I do not find any accession number for the raw sequences. If they have not been uploaded yet, please upload them and add the accession number to the manuscript.

Some of the figures have to small labels. It is almost impossible to read them.

Please revise the conclusion and avoid repetitions of results.

 

On line 122 “… using primers 515F and 806R with the barcode.” What is meant with barcode? please add the amplified target.

On line 225 authors start writing about differential abundant taxa. Was that statistically tested?

Fig 3 is missing statistics. At least all the data should be shown. Here the authors presented “sample groups” without giving a number of replicates or deviation.

Line 241 “This means that the richness of the entire microbiome decreased from natural forests to plantation forests” Is the difference significant? How can the difference between the estimators and Shannon/simpson be explained?

On line 246 “However, two-way ANOVA for ACE, Chao1, Shannon, and Simpson indicated no significant differences among soil samples in the observed species” this clearly contradicts line 241. Why is the anova not shown?

Fig 4: Statistics is missing. The labels are very small. How many replicates?

Line 263 the anova is not shown.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

This article reported microbial composition and diversity in a Eucalyptus pellita plantation in South Sumatra. Some relationships between chemical properties of soils and richness or biodiversity of microbiota were also explored. Overall, the manuscript is well structured and the contents of this study is quite suitable for the scope of the journal. I would like to recommend its publication after some minor revisions.

Introduction

Literature citation should be subject by subject in the introduction section. Below are just some examples.

1. Line 63, I suggest using biogeochemical cycles rather than ecologcial processes, which are too wide. Relevant references can be seen in Meng et al. 2022, DOI: 10.1128/msphere.00936-21 and Liu et al. 2021, DOI: 10.1016/j.csbj.2021.01.013.
2. Line 71, References should be cited subject by subject. For example, Zhou et al. 2020, DOI: 10.1021/acssuschemeng.9b07288 for 'Fusarium wilt disease' and Xiao et al. 2018, DOI: 10.1007/s00253-018-8757-3 for 'tobacco bacterial wilt disease'.
3. Lines 72-73, provide the references for this statement, such as Siong et al. 2021, DOI: 10.1016/j.scitotenv.2021.148797.

M & M

1. Figure 1 is no clear to read, especially the lattitude and longitude.
2. Why and how did you select the sample sites?
3. For '2.3. Soil DNA Extraction', did you check the DNA purity and concentration? 
4. It seems you have not deposited your sequence data in any public gene database, such as NCBI?  

Results

1. Figure 6, the names of phyla are overlapped and thus can not be read. Moreover, the percentage explained should be added on both axes. 
2. Line 274, no Table 4 present in the text.

Discussion

1. I suggest using 'bacterial diversity' rather than 'microbial diversity' as you only detected bacteria in this study. Change microbial as bacterial over the text including the title.
2. Are you sure N2 cycling? If so, please explain the specific processes and list the relevant references.
3. Lines 374-380, it should further discuss the relationship between soil chemical properties and your results, rather than repeating your results. What implications did you have based on your results?

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Soils sampled and analyzed in this study showed exceptional uniformity with respect to their chemical and microbial characteristics. It would be interesting and important to add also some information about physical structure (sand, silt, clay content) of the soils.

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

 

Even though the Figures 2 and 5 are still difficult to read and the statistics is still not included in the figures, all the issues have been addressed by the authors. I would suggest showing statistics within the figures; however, it might be enough to have them in the supplements.

I have one last comment

In line 406 “In conclusion, this study clearly showed that the soil microbiomes in Eucalyptus pellita plantation and natural forests in South Sumatra had similar relative abundances.” Are you refer to abundance of phyla?

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

All my comments have been addressed and I recommend its publication.

Author Response

Dear reviewer,

Thank you for the consideration of this manuscript for publication

Sincerely yours,

Authors