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.
I appreciate your careful incorporation of the reviewer's comments. Regards, Michael
[# PeerJ Staff Note - this decision was reviewed and approved by Valeria Souza, a PeerJ Section Editor covering this Section #]
The revised version of manuscript has been improved considerably.
Experimental design are perfect as per my knowledge.
Findings are valid
Congratulate the authors for their effort for the improvement of the manuscript.
Everything is OK
Everything is OK
Everything is OK
The manuscript was generally well received by the three reviewers but they identified some major and minor revisions that I suggest you consider. I have added a few comments below. Consider these as examples, not a comprehensive list. Look for other cases that require similar revisions following the examples. If you choose to resubmit, please provide a point-by-point response to these comments.
Line 20. Provide a justification for this work. Why is looking at the microbes associated with soil formation an important topic? Also, consider this revision “Parent rock material appeas more important in forming rendzic leptosols from on limestone bedrock than climate but little is known about the role microbes and human activities play…
Line 26. Avoid empty phrases like “The results showed that..” unless you are specific about the methods that generate the results. For examples, “Whole genome sequencing showed that…”
Line 33. Replace “Their microbiomes were characteristic of oligotrophic..” with “Oligiotrophic bacteria dominated the microbiome of…”
Line 40. Write more directly. Replace “CCA analysis, in combination with PERMANOVA, showed that differences in microbiomes could be linked to the joint change of all soil chemical parameters.” With “CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to soil chemical parameters.”
Line 52. Replace “One example of such a chronosequence is a series of coastal bars in Lake Ladoga (Russia), formed by a gradual lowering of the water level (Ivanova et al., 2020). This study showed that in the process of pedogenesis..” With “Coastal bars formed by a gradual lowering of Lake Ladoga showed that, in the process of pedogenesis,…”
Line 59. Replace “photosynthetic bacteria able to survive using a limited..” with “photosynthetic bacteria can survive with limited…”
Line 60. Avoid the passive voice. Replace “Technosols become populated by copiotrophic bacteria…” with “copiotrophic bacteria populate technosols…”
Line 64. Replace “is dependent” with “depends”
Line 76. Avoid fillers like “Some studies have shown that” unless you introduce contrasting studies that show something else.
Line 83. Do not use variation and various in the same sentence. Revise to “Origins, texture and chemical composition of parent material varies…”
Line 86. Delete “resulted in”
Line 99. Provide a sucking statement of the key result at the end of Introduction.
Line 206. Replace “Quantitative PCR was conducted to estimate the quantity of three microorganism groups across all samples (Fig. 2). Results showed that the number of bacteria ribosomal operons per 1g of soil was high...” With “Quantitative PCR showed that bacterila abundance was high across all soils sampled but archaeal and fungal abundance varied with…”
Line 268. Replace “PERMANOVA was used to assess the significance of individual factor impact on beta diversity. The maximum coefficient of determination was shown by soil horizon (Table 2).” With “PERMANOVA showed that soil horizon controlled beta diversity..”
Line 370. Delete “described as”
Line 371. Revise to “Withing this phylum, Chitinophagaceae in particular, are essential for carbon…”
Line 375. Replace “They are reported to be sensitive…” with “This phylum is sensitive…”
Line 456. Do not provide issue, just volume:page-page (Geoderma. 19:11-19.)
Line 461. Only cap proper nouns in article titles “Applications of the soil, plant and …”
Line 467. Cap all words in journal titles “Scientific Reports”
Figure 2. Use box or violin plots for visualization of means. Most of the bar has no data.
Table 1. Be consistent in number of significant figures (0.67 vs 11.7).
[# PeerJ Staff Note: Please ensure that all review comments are addressed in a rebuttal 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 rebuttal 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 rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
Clear, unambiguous, professional English language used throughout.
The manuscript is well written and easy to read when it comes to language. To my understanding there aren't many problems in this regard.
Intro & background to show context
The line of reasoning used by the authors for the construction of the Introduction is not clear or continuous throughout the text. The authors start from a remarkably interesting premise addressing how the different aspects of pedogenesis (parental material and age or time) can shape the microbiome of different soils and horizons. In my opinion, this is the original aspect of the work and it should permeate the entire text (from Introduction to Discussion and Conclusions). In the Introduction section, the authors add different elements to this logic (pedogenesis shaping microbiome) (e.g. mining, liming, anthropic impacts) that cause the Introduction to lose its focus, organization, and clarity.
Literature well referenced & relevant
References are current and appropriate.
Figures are relevant, high quality, well labelled & described
With regard to the figures, I suggest that Figure 1, where the sampling points were located, be made with a different base map, perhaps a geological map since this is an information used by the authors in the Introduction and in the Discussion. In the case of Figures 4 and 5 I suggest that the authors increase the size of the letters.
Original primary research within Scope of the journal
The manuscript fits well within the scope of PeerJ (Environmental Sciences).
Research question well defined, relevant & meaningful. It is stated how the research fills an identified knowledge gap
As previously mentioned about the Introduction, I feel that the authors have chosen a very original and poorly explored subject by trying to link aspects of soil pedogenesis with the shaping of their microbiome. However, as observed for the Introduction section, the text did not maintain this focus on the presentation of the results, nor on its discussion. I feel that this original aspect was lost throughout the manuscript. In this case I suggest the authors to reorganize the manuscript throughout and further explore central aspect.
As regards the M&M, my main concern regards the description of the structure of the study. I understand that for the authors the structure of the study must be clear but it is not for those who read the manuscript. The way that the different study sites (soils) were described in the item "Study sites and sample collection", must be improved and different important aspects are unclear.
1. Are all the soils Technosols? If not, how do the authors defend the fact that they have used both Technosols and natural soils in the same sequence of soils?
2. How exactly did the authors have established the supposed chronosequence? Is it based on different durations of anthropic activity? If so; these activities would have had to be able to "reset the pedogenesis clock" at different times; if that’s the case please explain how. The establishment of this chronosequence must be much better explained and described in the manuscript.
3. Are there any dating data or another technique that confirms or corroborates the alleged soil ages?
4. Are all soils originated from limestone? If so, are these rocks part of the same geological formation and with the same characteristics? It is known that because of its sedimentary origin, limestones can vary widely in their composition on small spatial scales. The geology, climate, vegetation cover and geomorphology (the other soil forming factors) from each location must be described in much more detail.
5. In the case of the Technosol, the authors mention a "reclaimed sandy quarry"; this fact indicates the occurrence of a contrasting geology in relation to the soils developed from limestone. In this is case; if there are different parent materials the authors would not be working with a chronosequence.
Regarding the results section, I suggest that the authors reorganize it and present the data respecting the structure of the work (that is, the chronosequence). In addition some of the parts of the results section are actually discussions of the data (for example, lines 196 to 198; lines 202-203; 273-274; 278-279).
On the other hand, in the discussion section, (between lines 338-356) there of parts that fit more appropriately either in the Introduction or in the Material & Methods sections. Therefore, I suggest a reorganization.
Another important point regarding the Discussion is that until line 412, the authors practically limit themselves to describing which groups of microorganisms were found, the most and least frequent ones in the different areas, in the horizons and describe the characteristics of these groups without effectively discussing their presence (and abundance) in the actual context of the study.
Conclusions are well stated, linked to original research question & limited to supporting results.
Regarding the conclusions, as was mentioned for the previous sections, the authors mix parts of results in this item (for example, line 443 "The microbiome of the Technosol of the K6 site was also similar in composition to benchmark soil but was higher in alpha-diversity "). Few real conclusions can be identified.
In this item, the authors mention in line 435 - 436 "Our research demonstrated that soil type on a limestone rock is the driving force behind microbiome shaping, without any apparent influence of its age"; I suggest that the authors try to structure their article more clearly in these direction (Introduction and hypotheses); i.e. around the effects of material factors of origin and time on the microbiome.
Finally the authors, in my opinion, have created a great ammount of interesting data but failed in connecting them into a cohesive, clear and objective text. Given the points highlighted, I consider that the authors should seek the restructuring of the manuscript (perform a major revision) before its acceptance by the journal.
Major Comments:
1. Abstract; line no 19-21, while the author’s mentioned that Rendzic Leptosols area the most important factor than the climate in shaping soil properties. However the literature suggests climate as the crucial factor for the same. Please check the statement.
2. Your results show Acidobacteria as the third most abundant phyla (Fig 3), as you also mentioned it in the abstract, line no. 27. However in the very next line (28), you mentioned low representation of Acidobacteria. Check the data or change in the abstract.
3. Again in the conclusion section line no 436-437, it is mentioned that the sites were deficient in Acidobacteria due to the alkalinity of the environment. This indicates doubt in your results, clarify this statement.
4. All the supplementary figures and tables are missing in the pdf file.
5. While the author’s have represented the data in heat map/ tabular form that make it difficult for the readers to understand. Better to represent the data in graphical form.
6. The author’s have chosen 4 study sites with 8 sampling horizons, site K1 (O, AY, C), site K2 (AY, C), site K3 (AY, C), site K6 (AY). Can the author’s mention the possible reason for choosing varying number of sampling sites from the 4 study areas? Like for K1 there are 3, K2 and K3 have 2 and K6 1, why.
7. While the authors have performed the Quantative analysis of fungal diversity by performing qPCR. The study does not seem much impactful, better would have been if the authors have done ITS sequencing as well. Any specific reason ?
Minor Comments:
1. Overall the article seems very nice and presents an interesting read. However, some points need a focus. Grammar need attentions, references need focus.
e.g., references needs a particular some where the references seem incomplete
Like line no. 670, reference seems incomplete.
Similarly line no702, reference seems incomplete.
2. Line no 34 add “old” after years
3. Line no 38 again add “old” after years
4. I think could have been should be replaced by “could be”.
5. Spelling needs proper focus
Major Comments:
1. Abstract; line no 19-21, while the author’s mentioned that Rendzic Leptosols area the most important factor than the climate in shaping soil properties. However the literature suggests climate as the crucial factor for the same. Please check the statement.
2. Your results show Acidobacteria as the third most abundant phyla (Fig 3), as you also mentioned it in the abstract, line no. 27. However in the very next line (28), you mentioned low representation of Acidobacteria. Check the data or change in the abstract.
3. Again in the conclusion section line no 436-437, it is mentioned that the sites were deficient in Acidobacteria due to the alkalinity of the environment. This indicates doubt in your results, clarify this statement.
4. All the supplementary figures and tables are missing in the pdf file.
5. While the author’s have represented the data in heat map/ tabular form that make it difficult for the readers to understand. Better to represent the data in graphical form.
6. The author’s have chosen 4 study sites with 8 sampling horizons, site K1 (O, AY, C), site K2 (AY, C), site K3 (AY, C), site K6 (AY). Can the author’s mention the possible reason for choosing varying number of sampling sites from the 4 study areas? Like for K1 there are 3, K2 and K3 have 2 and K6 1, why.
7. While the authors have performed the Quantative analysis of fungal diversity by performing qPCR. The study does not seem much impactful, better would have been if the authors have done ITS sequencing as well. Any specific reason ?
Minor Comments:
1. Overall the article seems very nice and presents an interesting read. However, some points need a focus. Grammar need attentions, references need focus.
e.g., references needs a particular some where the references seem incomplete
Like line no. 670, reference seems incomplete.
Similarly line no702, reference seems incomplete.
2. Line no 34 add “old” after years
3. Line no 38 again add “old” after years
4. I think could have been should be replaced by “could be”.
5. Spelling needs proper focus
No problem with the findings.
Major Comments:
1. Abstract; line no 19-21, while the author’s mentioned that Rendzic Leptosols area the most important factor than the climate in shaping soil properties. However the literature suggests climate as the crucial factor for the same. Please check the statement.
2. Your results show Acidobacteria as the third most abundant phyla (Fig 3), as you also mentioned it in the abstract, line no. 27. However in the very next line (28), you mentioned low representation of Acidobacteria. Check the data or change in the abstract.
3. Again in the conclusion section line no 436-437, it is mentioned that the sites were deficient in Acidobacteria due to the alkalinity of the environment. This indicates doubt in your results, clarify this statement.
4. All the supplementary figures and tables are missing in the pdf file.
5. While the author’s have represented the data in heat map/ tabular form that make it difficult for the readers to understand. Better to represent the data in graphical form.
6. The author’s have chosen 4 study sites with 8 sampling horizons, site K1 (O, AY, C), site K2 (AY, C), site K3 (AY, C), site K6 (AY). Can the author’s mention the possible reason for choosing varying number of sampling sites from the 4 study areas? Like for K1 there are 3, K2 and K3 have 2 and K6 1, why.
7. While the authors have performed the Quantative analysis of fungal diversity by performing qPCR. The study does not seem much impactful, better would have been if the authors have done ITS sequencing as well. Any specific reason ?
Minor Comments:
1. Overall the article seems very nice and presents an interesting read. However, some points need a focus. Grammar need attentions, references need focus.
e.g., references needs a particular some where the references seem incomplete
Like line no. 670, reference seems incomplete.
Similarly line no702, reference seems incomplete.
2. Line no 34 add “old” after years
3. Line no 38 again add “old” after years
4. I think could have been should be replaced by “could be”.
5. Spelling needs proper focus
The manuscript needs to improve some mistakes in the language (minor corrections).
- Methods are described with sufficient information to be reproducible by another investigator.
- The research question is well defined, relevant, and meaningful.
- All data have been provided; they are robust, statistically sound, and controlled.
- Conclusions are well stated, linked to the original research question and limited to supporting results.
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.