Review History

All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.

Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.

View examples of open peer review.


  • The initial submission of this article was received on August 30th, 2021 and was peer-reviewed by 3 reviewers and the Academic Editor.
  • The Academic Editor made their initial decision on September 21st, 2021.
  • The first revision was submitted on November 12th, 2021 and was reviewed by 3 reviewers and the Academic Editor.
  • A further revision was submitted on January 4th, 2022 and was reviewed by the Academic Editor.
  • The article was Accepted by the Academic Editor on January 10th, 2022.

Version 0.3 (accepted)

· Jan 10, 2022 · Academic Editor


Dear Authors,
The current version of your MS has been improved and integrated, representing a good starting point to deeply investigate this important subject offering new points of view.

Best wishes for future research!

[# PeerJ Staff Note - this decision was reviewed and approved by Konstantinos Kormas, a PeerJ Section Editor covering this Section #]

Version 0.2

· Dec 16, 2021 · Academic Editor

Minor Revisions

The authors followed and supplemented most of the reviewers' suggestions and addressed many of the concerns raised.

The manuscript is now in a much improved form, however I am not fully satisfied with the level of depth of discussion of the data/results obtained using the FAPROTAX tool.

This aspect (i.e. the putative functionality of rare taxa) may further deepen your research perspectives, as also suggested by Rev # 2 and would deserve further comment in the discussion.

I would ask the authors to work a little more on the text to meet these requirements in order to produce a final version suitable for publication.
Moderate editing of English language and style required.

Reviewer 1 ·

Basic reporting

I am recommended this manuscript for publication.

Experimental design

Well explained

Validity of the findings



Basic reporting

I appreciated the efforts the authors made in reviewing the manuscript. I think most of the hints were adequately taken into account, as re-uploading the correct sequences, including the soil physiochemical parameters, and discussing more deeply some points. However, I still found the current version superficial in both reporting and deeply analyzing some available data/information.

Experimental design

In my concern, the putative functionality of rare taxa is the most engaging aspect of this manuscript. However, I believe this was not sufficiently explored although was previously suggested. Despite the authors employing the FAPROTAX tool, the functional prediction and, consequently, the distribution of the functional categories from the rare bacterial communities were not found out.

Validity of the findings

The authors reported that “the rare bacterial community was the key determinant of the soil fertility index, as is clearly shown by the supplementary data (figure S2 and 3). It would have been interesting to explore in which specific soil biogeochemical cycling processes (functional categories) are involved the prokaryotic phyla the authors found and their related proportion.

Additional comments

I strongly suggest a revision of the English language.


Basic reporting

The authors re-edited the reference format as requested. It is not reported in alphabetic order but the journal will edit it.

The authors re-uploaded the sequences as requested on NCBI SRA repository (accession number No. PRJNA766099). However, in the text (line 117) there is still the wrong number. Please, modify it.

Experimental design

The authors revised the manuscript according with all my previous comments.

Just a last comment: at Line 119, please cite “Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C., Al-Ghalith, G. A., ... & Caporaso, J. G. (2018). QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science (No. e27295v1). PeerJ Preprints ( instead of “Caporaso et al., 2010” for QUIIME2.

Validity of the findings

The authors added a table (Table S1), as requested. However, the units of the soil variables and the statistical meaning of the letters was not specified. Please, add them.

Additional comments

No comment

Version 0.1 (original submission)

· Sep 21, 2021 · Academic Editor

Major Revisions

Dear Authors,

You can see that while the reviewers appreciated the study, they raised a number of essential concerns by precluding acceptance in its current form on PeerJ, and requiring a major review.

I went through your work and, I believe, as pointed out by Ref # 3, that the focus on the spatio-temporal distribution of rare taxa across the depth of the soil is an intriguing element to explore further.

However, I found the current version of the manuscript quite superficial in many different aspects related to the quality/correctness of the data reported (rotation of corn or wheat?) (Sequence from a previously published study or from a new one?) (Shift of nutrient physiochemical parameters/land not reported).

On the basis of the reviewers' comments which are very constructive and helpful, I suggest you rethink and reorganize the whole manuscript in order to submit a completely revised version taking into account both the most critical points but also helpful suggestions.

I also suggest, as pointed by reviewer #2, the author using the Tax4fun or PicCrust or FAPROTAX tools, which could greatly improve the paper offering a new perspective of discussion which deserves to be less speculative and more deeply related and commented on the light of recent studies.

Regarding the references suggested by reviewer #1, I would ask you to choose only one or two from all of them to be cited appropriately in the new version of the discussion.

[# PeerJ Staff Note: It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors are in agreement that they are relevant and useful #]

Nevertheless, I do hope that you will be able to undertake the additional work on the paper and look forward to receiving a revised manuscript in due course.

Best Regards,

[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.  It is a common mistake to address reviewer questions in the response letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the response letter.  Directions on how to prepare a response letter can be found at: #]

Reviewer 1 ·

Basic reporting

The manuscript entitled “Vertical and temporal variations of soil bacterial and archaeal
communities in maize-soybean rotation agroecosystem” submitted by Yokota et al. aimed to study the variations in bacterial and archaeal population in surface/middle and deep soil. There is no novelty in this work. There are various corrections listed below.

1. Raw data for this manuscript have been submitted but it is already published in other paper. Disentangling the role of salinity-sodicity in shaping soil microbiome along a natural saline-sodic gradient DOI:10.1016/j.scitotenv.2020.142738.
2. Please remove the plagiarised words from the manuscript.
3. Please change the reference pattern in whole manuscript. It should be year wise first 2006 then 2007 and so on.
4. Please rewrite the abstract and mention how your study is better than others.
5. Line 260 improve the sentence; reference have repeated two-time Shade et al. Correct it.

Experimental design

6. In line 100 can bacterial population survived at -80℃??
7. Line 104-105 provide references for estimation of soil parameters (organic carbon, NPK etc.).

Validity of the findings

Discussion part is too short and discuss in details with recent references.
9. Discuss about the role of different phyla in soil how they involved in nutrient cycle.
10. Please add these two-reference related to this study in line 263
a) Chaudhary P, Khati P, Chaudhary A, Maithani D, Kumar G, Sharma A (2021d) Cultivable and metagenomic approach to study the combined impact of nanogypsum and Pseudomonas taiwanensis on maize plant health and its rhizospheric microbiome. PLoS ONE 16(4): e0250574. pone.0250574,
b) Chaudhary P, Sharma A, Chaudhary A, Khati P, Gangola S, Maithani D (2021b). Illumina based high throughput analysis of microbial diversity of rhizospheric soil of maize infested with nanocompounds and Bacillus sp. Applied Soil Ecology. 159: 103836. doi:
11. Add this reference in line 241.
Kukreti B, Sharma A, Chaudhary P, Agri U, Maithani D (2020). Influence of nanosilicon dioxide along with bioinoculants on Zea mays and its rhizospheric soil. 3Biotech. 10: 345.,
12. You can add these references in line 283 related to soil fertility.
a) Kumari S, Sharma A, Chaudhary P, Khati P (2020). Management of plant vigor and soil health using two agriusable nanocompounds and plant growth promotory rhizobacteria in Fenugreek. 3Biotech. 10: 461.,
b) Chaudhary P, Khati P, Gangola S, Kumar A, Kumar R, Sharma A (2021c) Impact of nanochitosan and Bacillus spp. on health, productivity and defence response in Zea mays under field condition. 3 Biotech. 11: 237.
c) Chaudhary P, Khati P, Chaudhary A, Gangola S, Kumar R, Sharma A (2021a) Bioinoculation using indigenous Bacillus spp. improves growth and yield of Zea mays under the influence of nanozeolite. 3Biotech. 11: 11.
13. Please discuss the outcome and how it benefits for others (its value).

Additional comments

Please check the accession number you have provided because it is already published in another paper. How is it possible to submit the information in two papers. Please remove the plagiarism in the manuscript.

Annotated reviews are not available for download in order to protect the identity of reviewers who chose to remain anonymous.


Basic reporting

In this paper, the authors examined in depth the possible vertical and temporal patterns of soil bacterial and archaeal communities in maize-soybean rotation agroecosystem. In particular, the authors pointed out that the bacterial and archaeal communities are impacted and shaped by the soil depth. Conversely, significant temporal patterns were not observed for both communities. The authors also focused on the rare taxa, identifying the rare bacterial community as the key determinants of the soil fertility index.
I find interesting the general concept of the work that incorporates temporal variation, in addition to vertical variation, as a putative determinant in influencing the distribution of soil microbes. However, I have some comments/suggestions on some points that I believe the authors should clarify and/or improved.

Experimental design

1) Soil characteristics (as TN, TC, etc.) obtained by the physiochemical analysis are not reported as supplementary results, as well as the methodologies are not explained in Materials and Methods. I think that these results, if available, should be reported as supplementary results. Otherwise, the authors should mention it only in the results sections as “data are not reported”. More important, are these parameters measured for the different sampling times? I think the authors should report this information.

Validity of the findings

2) The analysis was conducted in a maize-soybean rotation agro-ecosystem over one year. However, it seems to me that the agricultural context in which this analysis is carried out is little emphasized. For example, in the introduction, as well as in the discussion, the authors do not explicit/clarify why it is important to understand if (and eventually how) the soil depth influences the diversity and composition of soil microbial communities in agricultural soils especially when a crop rotation is performed. The deeper soils are important for crop yield, especially for cereal crops as maize. Therefore, the authors should explain how the information on the vertical patterns can help the sustainability of agricultural systems. Moreover, the soil prokaryotic community compositions are not linked to the agricultural context and the crops present in the different sampling times.
3) The authors should discuss more deeply why they did not detect a temporal variation in this particular crop rotation system. In particular, by Random forest analysis, the authors found the Total Nitrogen as one of the key determinants for bacterial richness and evenness. It is well known that the use of the leguminous plant in a crop rotation is crucial for increasing the total nitrogen in the soil. Concurrently, they found that the bacterial richness did not show temporal variations after the rotation with soybean, which certainly increased the Nitrogen content. I think that the authors should examine in-depth this point. Also, in the discussion section, the authors stated that “The temporal variations of the soil microbial community were attributable to two factors: the shift of soil nutrients and/or the plant growth stage (Yang, 2017)” (line 261-263) and justify their results saying that the soil samples were collected from only two plant individuals. What about the shift of soil nutrients? Again, did the authors verified if soil nutrients contents and, in general, soil properties were different among the sampling times? If not, I think that the phrase “The minimal impact may also be due to no apparent difference in soil environmental conditions among sampling times” (line 265-266) should be removed.

Additional comments

4) In general, the impression is that the authors glossed over the results, which are sometimes roughly reported. Moreover, It is often not clear to which figures (and to which panels of the figures) the authors were referring. Line 172- 174 for example.
5) The authors have confused Figure 3 with Figure 4.
6) I suggest the author using the Tax4fun software package, which can predict the functional profiles of bacterial and archaeal communities. This might shed a light on the functionality of rare bacterial and archaeal communities the authors found, then greatly improved the paper.


Basic reporting

Overall the manuscript is well written, according to the journal's instructions, except for the reference section. We recommend to remove the initial number from the list of references and adopt the following Journal reference format: List of authors (with initials). Publication year. Full article title. Full title of the Journal, volume: page extents. DOI (if available) (see author’s instructions here for more details)

Literature references are appropriate and figures/tables are well presented.

Regarding the raw data the authors affirmed having deposited the sequences in the NCBI SRA repository (accession No. SRP271579). However, those sequences do not seem to correspond to the sequences of this manuscript, being 121 samples (instead of 72) related to the microbiome of saline-sodic soils in west Songnen Plain. We recommend to carefully check and revise the info.

Experimental design

The authors presented a manuscript aiming to address the vertical and temporal patterns of soil bacterial and archaeal communities in maize-soybean rotation agroecosystem at a scale of millions of sequences per sample. The main goals were to address: (1) Which factor from soil depth and temporal fluctuations is the key determinant in shaping bacterial and archaeal communities; (2) Whether there exist differences in the vertical distribution pattern between soil bacteria and archaea; (3) Whether rare taxa occupy a larger proportion in the surface soil layer than in the deep soil layer.

Although both title and conclusions clearly refer to maize-soybean rotation, in the M&M section the authors described a wheat-soybean experimental design. This has to be carefully revised.

In general, the proposed methods were appropriate for the scope of the work. However, methods used to assess soil physicochemical characteristics were not described and no references were provided.

Considering the relevance of the "rare" bacterial taxa in this work, a better description of the criteria adopted for the selection of the "cut-off" value at 0.1% rather than 0.01% of the reads should be provided and possibly supported by literature or a clear motivation.

Validity of the findings

Overall, the topic of this work is not very innovative and many studies already addressed the distribution of soil microbial communities across soil depth during the last two decades (i.e. Eilers, K. G., Debenport, S., Anderson, S., & Fierer, N. (2012) Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biology and Biochemistry, 50, 58-65) as well as the role and temporal shifts of rare communities (i.e. Shade, A., Jones, S. E., Caporaso, J. G., Handelsman, J., Knight, R., Fierer, N., & Gilbert, J. A. (2014). Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio, 5(4), e01371-14). However, the focus put on the spatial-temporal distribution of rare taxa across soil depth represents an intriguing item to be better explored.

The authors claimed to have addressed a number of soil physiochemical parameters (es. TC, TN, DOC, pH, etc.) but their values were not included in the manuscript nor as results or into the supplemental materials. Considering their relevance for the interpretation of the work and that they have been used for microbial community analysis, it is highly recommended to include them in the main text as additional table.

The authors concluded that "we evaluated the effects of soil depth and sampling time on soil bacterial and archaeal community and co-occurrence networks in maize-soybean rotation agroecosystem at a depth of millions of sequences per sample". However, it's not maize but wheat and they did not get millions of sequences per sample.
Finally, the authors argued that "our study also revealed the potential of rare microbial taxa in soil biogeochemical function" but it was rather speculative and poorly supported by results. The discussion on this point should be significantly improved and supported by literature.

Additional comments

Minor comments:
Line 29: The reference of Caporaso et al.2011 seems to be poorly relevant here.
Line 56: bacterial diversity
Line 99: four sample sites?
Line 114: Qiime or Qiime2?
Lines 124-125: Relative abundances below 0.01% were defined as “rare” but above 0.1% as “abundant”. Are you sure that they were not the same value? Please, check it. In any case,
Line 172: the authors claim that the evenness index was significantly higher in October than in April (Fig.1). However, looking at the values reported in figure 1 (C), it does not seems to be true. Please, check it carefully.
Line 237: the authors affirmed that “we observed that bacterial richness and evenness in the middle soil layer were roughly equal to that in the surface”. However, the values of bacterial richness reported in Fig.1 show very different values between surface and middle soil samples. Please, check it. Moreover, one possible explanation proposed by the authors rely on the equal distribution of organic carbon in the two layers. However, the values of carbon distribution across soil layers is missing.
Lines 245-247: a comment/discussion on the eveness of archea is needed.
Lines 281-283: the authors claimed “We also found that rare taxa were key determinants of soil fertility, indicating that rare taxa had an over-proportional role in the soil biogeochemical cycling process”. However, it is not clear to me the results upon they based their speculation.

All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.