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The authors have addressed the reviewers' questions and concerns with a point-by-point response. I hereby endorse the publication of the manuscript, and no further peer review is required.
[# PeerJ Staff Note - this decision was reviewed and approved by Konstantinos Kormas, a PeerJ Section Editor covering this Section #]
Please revise the manuscript by following the reviewer's remaining comments.
Dear authors, after the second round of revisions on the manuscript, I confirm that I am satisfied with the work done, understanding that the authors have made most of the suggested corrections and justified others less serious. Having said that, I believe that no additional comments are necessary regarding the other fields of the article and that it is now suitable for publication.
Sincerely
The Revisor
no comment.
no comment.
no comment.
Please, find my comments on additional comments for the authors.
no comment.
Please, find my comments on additional comments for the authors.
This resubmission has addressed most of my previous comments satisfactorily. However, there are still some additional points I would like to address to the authors.
Line 59: From my understanding, authors use “FT” for freeze-thawing. Should authors introduce the acronym 'FT' for freeze-thawing, considering it appears for the first time in the introduction?
Line 73, 90, 97, 99, 101 and 102: For the FT, authors refer to FT cycles or FT intensity or both?
Line 116: Add a comma after (Liu et al., 2024).
Line 125: Add "of" after "200 g" and "5 g". Plus, add “maize” before “straw stalks” for clarity.
Line 126: Add a comma after “pot”.
Line 211, 212, 220 and 222: Please, check the Peerj jounal guidelines regarding using acronyms.
For me, if the acronyms for soil nutrient availabilities and soil enzyme activities were already introduced in the Materials and Methods section, there’s generally no need to reintroduce them in the Results section, unless it's specified by the journal's guidelines.
Line 215: “Among soil enzyme indices, BG (increased by 49.2%), XYL (20.1%) and LAP (7.7%) were enhanced by residue retention,” Authors might change to “Among the soil enzyme indices, BG, XYL, and LAP were enhanced by residue retention by 49.2%, 20.1% and 7.7%, respectively,”
Line 127: Delete “.” after the “Table”.
Line 233-236: The text mentioning Fig. 2A, Fig. 2B, and Fig. 2C is currently placed before Fig. 1D, Fig. 1E, and Fig. 1F, which disrupts the sequence. To improve coherence, authors should think about moving this content to the end of the paragraph to match the order of the figures more accurately. Additionally, they may need to adjust the wording to better align with the details provided in the paragraph.
Line 326-327: Please, see comment line 211, 212, 220 and 222. You can directly use the abbreviations for AK, AP and TN.
Line 356: Delete Freeze-thawing (FT), and then add “FT”.
Line 364: Delete freeze-thawing, and then add “FT”. This is because authors use FT for freeze-thawing.
Line 408: For BG and XYL, authors have already introduced them in the Materials and Methods section. Authors can now directly use BG and XYL.
Line 439: For the FT, authors refer to FT cycles or FT intensity or both?
Please revise the manuscript based on the reviewers' comments. During the revising stage, please respond to the reviewers' comments and suggestions point-by-point. When re-submitting your manuscript for re-consideration, please make sure a response letter is provided, together with the revised manuscript (track-change mode on).
**Language Note:** The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
The article titled “Maize residue retention shapes soil microbial communities and co-occurrence networks upon freeze-thawing cycles” presents interesting findings. However, it requires extensive revision before it can be considered for publication. Although the results are relevant and the hypotheses have been proven, the authors should consider a careful review of the English, considering grammar, punctuation, and use of inappropriate expressions for scientific text. The bibliographic references are up to date and the article has an adequate structure for the defense of its hypotheses and the achievement of its objectives, presenting the group data, information on the deposit of genetic sequences, and appropriate tables and figures. However, they need to improve the presentation of the results and the quality of the figures. For this, an extensive review was carried out and several observations were made about the original manuscript to allow the authors to adequately review and substantially improve the work.
The experimental design proved appropriate for obtaining the results, as well as the number of samples proved sufficient to prove the hypotheses, but many points of the methodology need to be explained to allow reproduction and adequate interpretation of the results. All improvement needs were reported in the attached file
I believe that most of the conclusions are in accordance with the results, but I recommend a full review of the results regarding the concept of multifunctionality adopted throughout the manuscript.
Given the previous considerations, I recommend a major revision of the manuscript before it is considered for publication. Before that, I emphasize the need for a new presentation for the approval of the reviewers. Sincerely,
The revisor
This study focuses on the effects of maize residue retention (maize residue retention and control), freeze-thawing intensities (no FTC, moderate FTCs, and severe FTCs) and number of freeze-thawing cycles (1, 3, 6, and 12 FTCs) on soil microbial communities and co-occurrence networks. The findings contain valuable information that could benefit both farmers and researchers, enhancing their knowledge in the field. However, there are several issues need to be addressed.
• The manuscript contains several unclear and excessively long sentences, making it challenging to understand. Therefore, it is advisable to have the manuscript reviewed by a professional service before resubmission.
• There are mistakes in inserting citations, and some of the literature referenced may not be relevant. Hence, it is crucial to ensure that all sources are relevant and correctly cited throughout the manuscript.
• The overall structure of the manuscript is well-organized, but there seems to be a discrepancy in the order of figures cited in the text. Specifically, figures are referenced out of alphabetical order, such as explaining figures 1D-F before 1A-C. Additionally, the figures are consistently cited as groups, for instance "figure 1D-F," throughout the manuscript. It might be clearer to break them down individually (e.g., Fig. 1A, Fig. 1B, and Fig. 1C) and cite them after the relevant text.
• Text should align left according to the PeerJ guidance.
• The figures exhibit good quality. However, there is a concern regarding overcrowding, as multiple small figures are grouped under a single figure title. This could potentially compromise the clarity and comprehensibility of the visuals. To address this issue, it may be beneficial for the authors to consider breaking down the small figures and assigning them new figure numbers. This approach could improve the overall effectiveness of the visual representation.
• The titles of the figures and tables could be clearer, especially in supplementary figures and tables. Abbreviations used within the figures and tables, as well as letters indicating statistics, might need additional explanation to ensure comprehension.
• The raw data provided includes only soil chemical and respiration parameters.
The experimental design is generally clear and well-explained. However, there are some points that could be clarified, as noted in the general comments.
The findings provide informative insights into the effects of maize residue retention and freeze-thawing intensities. However, the factor of freeze-thawing cycle number lacks clear explanation in the text, particularly in the results, discussion, and conclusion sections. Clarifying the significance and impact of freeze-thawing cycle numbers would enhance the comprehensibility and depth of the study findings.
Please note that the line numbers correspond to the version of the Word document that was submitted.
Line 35: Before using the abbreviation "FT," it should be introduced.
INTRODUCTION
Line 49: Mitchell et al., (2016) conducted the experiment on sandy soil in sub-tropical Australia. It seems unrelated to the statement.
Line 51: Dai et al., (2017)’s study doesn't relate to improving soil water use efficiency, preventing erosion, or enhancing soil fertility.
Line 58: There is an error in citing (Yaoand, 2017). It should be (Yao et al., 2017).
Line 69: There is an error in citing (Yanaiand, 2011).
Line 103: The authors have hypotheses, but they might not be very clear. Adding the study's objectives or making them clearer would be helpful.
MATERIALS AND METHODS
Line 110: The methods should be described with sufficient detail and information to allow for replication.
Line 127: What was the weight of maize straw used for each treatment?
Line 128: Authors stated that the water content of the maize was 92.48%. Dry maize straw typically contains a very low moisture content. Please double-check.
Line 130: In formal academic writing, it is more appropriate to use 'approximately' instead of abbreviations like 'ca.'
Line 135-148: For soil physiochemical variables and enzyme activities determination, it would be beneficial to briefly mention the methods used for analyzing soil physiochemical properties and soil enzymes, along with citations referencing the specific methods employed. Moreover, did authors use air-dried or wet soil for conducting analyses on soil physiochemical variables and enzyme activities? This question also applies to soil DNA extraction procedures.
RESULTS
Line 202-211: The authors should provide clarity by including the actual values or the magnitude of changes for all parameter like soil physiochemical properties, enzyme activities and respiration. For instance, it would be helpful to specify how much TN, AK, and AP increased for each treatment. Plus, I would recommend putting the p-value in-text as well.
There are some other issues:
Line 202: For title 3.1, what are the results for soil ammonium-N, soil nitrate-N, and soil pH? While the p-values for pH suggest no significant differences among treatments, Table S1 shows that soil pH decreased after the FTC cycles. Please double-check the soil pH data and statistical tests for accuracy. Considering that soil pH and nutrients can impact shifts in soil microbial communities, investigate deeper into these soil chemical properties result could provide valuable insights and help connect them with changes in the soil microbial community.
Line 205-206: In Table 1, the p-values indicate that AK, TC, and soil enzymes (XYL, LAP, and PPO) respond to the FTC cycle. However, the authors did not report this factor.
Line 219: “For fungi, Ascomycota, Zygomycota and Basidiomycota dominate” What are the percentage values for each fungal phylum?
Line 221: The author should avoid using figure references like "Fig. 1D-F". Instead, they can break them down and cite them individually as "Fig. 1D, Fig. 1E, and Fig. 1F" after each relevant context. The figure citations should be placed after each specific parameter mentioned. Additionally, the figures should be arranged in alphabetical order (A, B, C, D, E, F). For example, you initially reference Fig. 1D-F, followed by Fig. 1A-C later in the paragraph.
Line 223: How author define 'weaker'? Add (Fig. 2A) after archaea. Add (Fig. 2B) after bacteria. Delete Fig.2A-C.
Line 229: Are you confident that the abundance of Acidobacteriota, Firmicutes, and Crenarchaeota is significantly reduced? The data from Fig. S2D and S2E suggests that they are not significantly reduced by moderate or severe FTC intensity.
Line 235-236: The archaeal community also showed no significant difference, as indicated by the P-value (P=0.098) in table S2. Please check.
Line 236: The authors have omitted reporting the effect of the FTC cycle. The results from table S2 demonstrate that the FTC cycle significantly impacted the compositions of bacteria (P=0.02) and fungi (P=0.027).
Line 238: Could you provide details on the extent of decrease and increase observed? For example, how much they decrease or increase?
Line 238-239, 247, 253, 259, 268: Please place the corresponding individually figure directly after the relevant text.
Line 249: The authors excluded the results of the FTC cycle effect. Figures 2D-F indicate that there is no significant difference among FTC cycles for bacterial, fungal, and archaeal communities.
Line 270: Use this figure as an example to present the figure in the document.
Line 302: Please verify if this is Module #1 for prokaryotic organisms.
DISCUSSION
Line 309: Additional references are needed to bolster the support for your findings.
Line 309: Since you say a large number of studies, you should provide more literatures.
Line 310: “Xu et al. (2023) reported” where was the research conducted, and what type of soil was studied?
Line 328: What is the significance of saprotrophs in straw decomposition, and in your study, which group of microorganisms represents the saprotrophs?
Line 334: Could authors provide additional studies to support your explanation? On average, how many freeze-thaw cycles typically occur in farms in that region?
Line 344: In this sub-title, is "FTCs" referring to FTC intensity or the number of FTC cycles? Clarification is needed.
Line 357: Could these nutrients come from soil organic matter? Have authors tested the soil organic matter?
Line 362: “The shift of soil microbial communities under FTCs may be reflected at the gene expression level but not at the DNA replication level.” Authors can provide relevant works/studies to support your spectacular?
Line 399: I would recommend including detailed information about soil physicochemical and enzyme properties in the result report and discussion because these parameters are closely linked to the composition of soil microorganisms.
Line 401: “Recently, a large number of research have recorded”. The authors should include citations to this statement.
Line 406: “Module #3 and prokaryotic Module #1 were the most important determinants for soil multifunctionality, supporting our third hypothesis” Could you explain how the modules support the third hypothesis?
Line 422: “unfavorable condition created by maize residue retention” I recommend providing a more detailed explanation of how maize residue creates unfavorable conditions and incorporating relevant literatures.
CONCLUSIONS
Line 424: Authors should ensure that the main three factors following the hypotheses are included in the conclusion. It is evident that only two factors have been stated.
Line 433-435: “Another contribution of the….” The authors should provide further clarification on this statement.
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