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Acceptable for publication. The authors diligently addressed all concerns raised by the reviewers. I agree with the reviewers to accept the revised version for publication. Thank you, authors, for your scholarly contribution and for finding PeerJ as your journal of choice. Looking forward to your next manuscript submission. Congratulations :)
[# PeerJ Staff Note - this decision was reviewed and approved by Ann Hedrick, a PeerJ Section Editor covering this Section #]
no comment
no comment
no comment
Thank you for the thorough revisions.
Authors have addressed all my comments
Authors have addressed all my comments
Authors have addressed all my comments
NA
Thank you, authors, for your patience. Reviewers have raised important concerns, ranging from experimental study/structure to other specifics. Make sure to strengthen the hypothesis, and make sure you upload Figure 2, ok. Please, kindly address them in great detail, and respond, not only in the revised manuscript, but also to the comments raised, point by point. Look forward to your revised 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.
My biggest issue is that figure 2 wasn't shown. Also some issues with phrasing (i.e., no significant difference vs we did not find significant differences). There were also some inconsistencies between the references in the text and in the works cites section.
Study was a bit underpowered to find differences. Unsure if question is well defined, currently presented as hypothesis but would be preferable as questions.
Good support for ongoing work in this area. Sequence data should be available from public repository (NCBI, etc)
29: This reads like a matter of opinion. Can you rephrase to be more objective?
38: Citation?
53: Can you include a brief sentence here on why rare taxa are important?
62: Why one month?
66: These are really more predictions than hypotheses, could you be more specific about the mechanism or rephrase as questions?
81: Do you think the parafilm would change the gas composition of the jars? Also, was there enough time for the samples to “air-dry” before starting the experiment?
83: Why not test the frozen sample over time?
106: Specify forward and reverse?
113: *fewer
117: How was this distinction made?
121: Did you check to ensure your data met assumptions of the statistical test?
Results: Not finding differences is not the same as there being now differences, especially with low sample size. I think phrasing is important here, as your study may be under powered to find differences if they are relatively small.
140: confusing wording “similar and no significant difference”
141: I don’t think you actually included figure 2 in this document
160: *could stem, you don’t know this for a fact
173: It is quite difficult to evaluate this study without seeing figure 2.
179: Vague statement, not sure it really contributes much.
References: I think some of the citations may be misattributed or missing from the text. Please check to ensure all citations are full and included both in the text and references section.
The manuscript is well-written and easy to follow. Literature references are sufficient but there are two points that need to be addressed:
1. Line 42-43: Authors should be more specific about the storage timeline when they state that Kushwaha et al. (2024) showed that storage time shapes the bacterial diversity. According to Kushwaha et al. (2024), bacterial/archaeal richness and community composition remained stable over 9-weeks and it was fungal diversity that was impacted more by storage.
Kushwaha et al. :“Though microbial richness remained stable, Shannon diversity indices decreased significantly at W6 for bacteria/archaea and W3 for fungi. Bacterial/archaeal community composition also remained stable, whereas the fungal community changed significantly during the first 3 weeks.”
2. Line 67: I appreciate that the authors have tested different methods but why only air-drying was included in the hypotheses regarding the bacterial community.
The experimental design used three different soil types and tested the impact of soil storage over a month. Since there are some differences across the three soil types tested, having replicates for each soil type per timepoint would have provided a better assessment. Also to clarify, DNA was extracted the same day it was collected? (Lines 82-83).
The topic is highly relevant to researchers studying soil microbiomes, especially those involved in multi-day field sampling who need to ensure that microbial community profiles remain representative of the original field conditions during sample transit and storage, prior to the DNA extraction. The findings contribute valuable insights into this area. However, the manuscript could be further strengthened by addressing the following points:
1. Results need to be elaborated some more. Although Shannon Diversity is not significantly different, the temporal trends can still be described from Fig 1. Similarly, in Fig S1, the clay loam soil tends to have lower diversity under certain storage methods. I do not completely agree that Shannon diversity in different soil types showed limited influence from storage methods (L137).
2. As stated in the results, the three soils tested in this study had different community compositions. Results from Fig S2 should be described in the results and not just referenced in the Discussion.
3. Results from Table 1 are not described in the manuscript and they are not cited within the text
4. One important aspect the manuscript fails to highlight well is that all three soil types had different community composition, but they were stable over time under the tested storage methods.
Other minor comments:
1. Fig 2 is missing. Based on the results and Figure caption, this Figure was supposed to have community composition differences. Please include the corresponding Fig.
2. Line 135: Change to Table 2
3. Line 175-177: It might be beneficial to describe the taxonomic distribution of the rare taxa.
4. Fig 1: I wonder if the better representation of data would be to have the samples grouped by different storage methods rather than time. This would make it easier to follow the temporal trends of storage methods. The points added for the soil types could be more streamlined so they are in the center. Lastly, the points inside the square legend makes it harder to see the colors of the legend.
5. In Fig 1 and Fig S1, the soil types are: Silty loam, Sandy, and Clay loam, but in Fig S2, the soil types are Silty loam, Sandy, and Sandy loam. Based on the methods, they should be Silty loam, Sandy, and Clay loam. Please verify.
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