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Thank you for your resubmission, which was re-reviewed by the previous reviews. One of them has made just a few suggestions that should be incorporated into your revised manuscript.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
**PeerJ Staff Note:** Although the Academic and Section Editors are happy to accept your article as being scientifically sound, a final check of the manuscript shows that it would benefit from further English editing. Therefore, please identify necessary edits and address these while in proof stage.
The original concerns have now been well addressed.
Now much clearer following the additional information on samples and sample site selection
The updated methods have now resulted in clearer overall results
Thank you for sending me the revised version of this manuscript to review, and well done to the authors for a clear set of revisions for this work. The manuscript is now more robust as a result of the revisions.
Minor grammatical suggestions.
See attached.
Adequate
Meets standards
See attached.
Thank you for your submission to PeerJ. It was quickly reviewed by two experts in the field who have provided multiple suggestions for improvement (please note that they provided annotated manuscript files). I look forward to seeing a revised version of the manuscript.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
This is an interesting study of antibiotic resistance genes in soil microbiota. The study clearly has potential value to readers from both a human and animal health perspective, and the study is generally well supported by a range of relevant sources. There are several high quality figures provided, and a large number of additional supplementary figures. At current, it would be worth reviewing which of these are valuable and are of direct importance to the manuscript (and should therefore be placed in the main text) versus those that are in the appendix. The study provides a rationale, though at current it would benefit from strengthening, as it is now always clear what is novel and valuable with regards to this study.
The work fits the required structure as per a scientific paper, though some further restructuring may be needed for the methods and discussion / conclusion (i.e. a summary is provided immediately before the conclusion.
The study question could benefit from some clarity. The lack of clarity is in part due to a very concise introduction that does not fully flesh out the arguments and existing literature, which leaves questions regarding the importance of this work. This is also due in part to a rather limited initial soil sampling method, which makes it unclear where sampling took place and what methods were used.
The microbiome analysis was relatively robust, but there appears to be gaps in the explanation of data analysis (i.e. unexplained tests in the results, plus a lack of a data analysis section in the methods). This is complicated by the inappropriate use of the term significant throughout the work, which may lead to confusion where tests have(n't) been run.
There are previous soil microbiota studies, some of which are well cited in the work. However, the novelty of this study needs to be made implicit, whether it is novel locations or novel habitats and soil types that are being sampled.
Additional data files are provided.
This is an interesting and potentially useful study, but at current a bit more depth is needed to ensure that the questions being asked are meaningfully posed, and the sampling and statistical testing are clearly explained. This will result in a much clearer set of conclusions being drawn in a way that is meaningful for interested readers.
The writing is quite good. A few unusual phrases or confusing terminology noted in my notes.
The experimental design is adequate, even ambitious.
The findings appear to be valid. The authors were careful to not overstate conclusions. In fact, I think their discussion section could be stronger, rather than just mostly restating Results.
A worthwhile contribution to the databases on microbial communities, metagenome assembled genomes, and endogenous antibiotic resistance in the soil.
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