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I would like to thank you for accepting the referees' suggestions and improving your article based on their suggestions. Your article is ready to publish. We look forward to your next article.
[# PeerJ Staff Note - this decision was reviewed and approved by Valeria Souza, a PeerJ Section Editor covering this Section #]
All the questions are well addressed.
The inquiries presented have been thoroughly reviewed and addressed with precision in their current form, ensuring clarity and comprehensive responses.
Accept in the current form.
Medicinal plants have great potential as sources of new medicines. Therefore, I believe your study could offer valuable insights to growers regarding habitat changes after transplantation. However, to improve the clarity of your article, certain technical aspects need to be addressed. I strongly encourage you to carefully review the reviewers' suggestions and thoughtfully consider each recommendation. If you disagree with any suggestion, providing clear and well-reasoned justifications would be beneficial. Additionally, your article would benefit from linguistic refinement. I recommend seeking assistance from a colleague or using our editing service to ensure polished and professional language.
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services if you wish - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Your revision deadline is always extended while you undergo language editing. #]
The English language is in the majority of the manuscript of good quality, although I am not a native speaker. Nevertheless, in some instances, it is not acceptable. I have a feeling that the manuscript was translated into English by a non-agronomist/biologist, as some terms are rarely used in biology or agronomy. Need to improve sentence formation and grammar.
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Comments and Suggestions for Authors
The English language is in the majority of the manuscript of good quality, although I am not a native speaker. Nevertheless, in some instances, it is not acceptable. I have a feeling that the manuscript was translated into English by a non-agronomist/biologist, as some terms are rarely used in biology or agronomy. Need to improve sentence formation and grammar.
Minor Comments
Line 48, 79. Please change "Umbelliferae" to the italics "Umbelliferae."
Line 91. Usually, at the end of the Introduction, there is some sort of hypothesis that researchers were investigating. Some questions that were interesting to you and because of which you performed this research. Please add
Line 102. Please change "cultivation(Fig. 1)" to "cultivation (Fig. 1)"
Line 105. Plant samples
Line 106. Please change "A. Sinensis" to "A. sinensis"
Line 107. Could you clarify what you mean by "celler, and medicinal stage"? Are you referring to a specific stage in the cell biology of medicinal plants, a certain process in cell culture, or perhaps a particular step in drug development?
Line 113. Change "ultra-clean bench" to "laminar flow hood"
Line 116. Soil samples
Lines 117-122. Is the described method a standard approach to collect rhizosphere soil samples? Need reference. How many plants are used to collect rhizosphere soil? What were the replicates of each treatment?
Line 223, 240, 259, 273. Change "VENN" to "Venn"
Line 229, 243. Change "eight" to "8"
Line 233. Change "twenty-eight" to "28"
Line 245. Change "six" to "6"
Line 266. Change "twenty" to "20"
Line 410. "This process" should be more specific. It is unclear which process is being referred to (the microbial reorganization or something else).
Line 414. The term "cellar stage" is ambiguous. Does it refer to a specific stage in growth or a specific environment?
Line 415. The phrase "creates favorable conditions" is vague. What specific conditions are being created by transplanting? Is it the altered soil microbiota, temperature, or nutrient availability that is favorable? Be more specific in identifying what aspects of the environment are being influenced.
All Figures need to improve in terms of text size and resolution.
This study explores the reorganization of the microbial community in Angelica sinensis across different transplanting stages, investigating how soil microbial communities influence the structure of plant endophytic microbiomes. Overall, the structure of the article is clear, and the research objectives are well defined. However, certain sections of the text are repetitive, particularly in the discussion of the relationship between plant endophytic microbiomes and soil microbial communities. I suggest that the authors streamline this part to avoid redundancy, ensuring a more concise and impactful expression. In the literature review, although relevant studies are cited, the discussion of existing theories is somewhat general. In particular, the discussion on how transplanting modes specifically affect microbial community changes is lacking depth. It would be beneficial for the authors to incorporate more recent findings from the field, particularly on plant-microbe interactions and the mechanisms underlying ecological reorganization, to strengthen the theoretical depth and novelty of the article.
The research question is clear and has practical significance, especially the study of the impact of A. sinensis transplanting modes on microbial communities. However, the experimental design could be further refined. The details regarding the specific time points and methods for microbial community sampling during the transplanting process are not fully explained. In particular, the sampling methods and processing protocols for microbial samples at different transplanting stages (e.g., alpine seedling stage, cellar planting stage, and dam cultivation stage) need to be clearly described. For the sake of reproducibility and methodological rigor, I recommend that the authors provide a more detailed explanation of the sample collection time points, sampling strategies, and sample handling procedures.
The study provides sufficient data to demonstrate changes in the endophytic microbial communities of A. sinensis during the transplanting process, along with preliminary statistical analysis. However, the discussion of the results lacks depth, especially in analyzing the actual impacts of microbial community changes on plant health and yield. For example, while the article mentions that transplanting helps reduce disease threats in dam cultivation, it does not explore how the reorganization of microbial communities after transplanting might affect plant resistance to diseases or stress over the long term. Furthermore, the study does not provide enough data to support the long-term stability of these microbial community changes or to discuss how these changes influence plant growth and health over time. I recommend that the authors expand the discussion by adding long-term tracking data on microbial community dynamics and their relationship with plant physiological parameters (e.g., growth rate, disease incidence). Additionally, a more detailed analysis of the microbial community reorganization mechanisms at different transplanting stages, supported by more data, would be beneficial to clarify how these microbial communities affect the plant's ecological adaptability.
In discussing the reorganization of microbial communities due to transplanting and its effect on plant health, the authors have not adequately explored the direct relationship between microbial community structure and disease occurrence. Although the article mentions that transplanting helps reduce disease threats in dam cultivation, it lacks sufficient empirical data to support this claim, particularly with respect to the changes in pathogen species and their relative abundance. Additionally, the long-term stability of the microbial community changes and their relation to plant health have not been sufficiently addressed. The authors should consider incorporating more specific data on changes in pathogen species before and after transplanting, as well as a comparison of pathogen abundance to provide stronger evidence for their conclusions.
The manuscript entitled “Microecological recombination of Angelica sinensis driven by the transplanting of "alpine seedling - cellar planting – dam cultivation"” used high-throughput sequencing to analyze microbial community structure and microecological recombination of A. sinensis during the transplanting process of “alpine seedling - cellar planting - dam cultivation” at two concurrent field experiments. The study found that fungi showed more pronounced recombination than bacteria during the transplanting process, and soil microbial communities are crucial drivers of this recombination. Most parts of this submission are presented satisfactorily, minor revisions are still needed prior to publish. The comments and suggestions are listed as follows.
Comments:
1. Line 90: Please change Min A. sinensis into 'Min A. sinensis'.
2. Line 97: Please add more details of the Xizhai Town (XZ) and Qingshui Town (QS), such as climate or altitude.
3. Line 136: Please change “uL” into “μL”, verify and revise in the full text.
4. Line 191: In Fig. 3e and Fig. 3g, the information at QS town is missing, please add clarification or explanation.
5. Line 203: Fig. 4a and Fig. 4b are the same. It is recommended to verify and modify.
6. Line 223: Based on the article, it is suggested that Fig 9 be placed after Fig 6.
7. Line 233: Please change “p < 0.01” into “p < 0.01”. p should be italic.
8. Line 319: In Fig. 12a, the content is incomplete, please revise it.
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