Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas

ABSTRACT Soil microbial communities are key to material cycling and energy exchange in forest soils. As the Tianshan Mountains in Xinjiang are rich in tree species, it is important to understand the impact of tree species composition on soil microbial community structure and co-occurrence networks in arid mountain habitats. In this study, soil microbial community structure of five typical vegetation types in the Tianshan Mountains of Xinjiang, China, was investigated using bacterial 16S rRNA and fungal ITS sequences. The results showed that the relationship between the fungal community and tree species was strong, while the bacterial community was mainly affected by soil carbon. The dominant bacterial composition was Ascomycota, which had the highest relative abundance in herbaceous soils (27%–41%); the dominant fungal phylum was Ascomycota (50.22%–63.95% of the total sequences), followed by Stramonium (8.99%–28.09%). The fungal community structure of mixed coniferous and broadleaf forests was similar to that of conifers, while the bacterial community structure was similar to that of pure broadleaf forests. Mixed forests (mean connectivity: 812.50, clustering coefficient: 8.89) showed a more complex co-occurrence network and a significant increase in microbial structure related to soil carbon and nitrogen than pure forests (broad: mean connectivity: 710.69, clustering coefficient: 6.94; coniferous: mean connectivity: 730.79, clustering coefficient: 7.76). The results contribute to the understanding of the interactions between soil microorganisms and soil factors in different forest ecosystems and provide new insights into the interactions among forest microorganisms in arid zones. IMPORTANCE The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.

2. Material and methods for soil parameters need to be explained in more detail with the instruments being used.Microbial data analysis also needs to be explained in more detail with the pipeline used for analysis and taxonomy annotation databases.3.In the result section, figures need a little more explanation.4. Discussion needs to explain with the key microbial process performed by the dominant fungal and bacterial phyla in the soil in the current study.Specific comments Introduction 1. Table 1.Here are two times removed.Is given in the very beginning.Place it properly somewhere in the main text.2. Many typographical and spacing errors.L1. ( forest,mixed), L63 (2013)have), L 66 (properties(Xue) and so on...... M & M: 3. L103-105, L120-122 (Give sampling Coordinates).Re-write this sentence.4. L124.Scientific names should be italics.(apply throughout the MS) Reviewer #3 (Comments for the Author): Comments, suggestions and questions are described in paper for the author.It's important that figure captions with descriptive content should be added to the paper.
Reviewer #5 (Comments for the Author): This article has ignored the microbial interactions.So it focused on bacteria and fungal community as an individual factors.However in conclusion, they wrote that " Our research further elucidates the factors that affect the structure of microbial communities and can be applied to forest management, ecosystem processes, and ecosystem services."

Preparing Revision Guidelines
To submit your modified manuscript, log onto the eJP submission site at https://spectrum.msubmit.net/cgi-bin/main.plex.Go to Author Tasks and click the appropriate manuscript title to begin the revision process.The information that you entered when you first submitted the paper will be displayed.Please update the information as necessary.Here are a few examples of required updates that authors must address: • Point-by-point responses to the issues raised by the reviewers in a file named "Response to Reviewers," NOT IN YOUR COVER LETTER.
• Upload a compare copy of the manuscript (without figures) as a "Marked-Up Manuscript" file.
• Each figure must be uploaded as a separate file, and any multipanel figures must be assembled into one file.For complete guidelines on revision requirements, please see the journal Submission and Review Process requirements at https://journals.asm.org/journal/Spectrum/submission-review-process.Submissions of a paper that does not conform to Microbiology Spectrum guidelines will delay acceptance of your manuscript." Please return the manuscript within 60 days; if you cannot complete the modification within this time period, please contact me.If you do not wish to modify the manuscript and prefer to submit it to another journal, please notify me of your decision immediately so that the manuscript may be formally withdrawn from consideration by Microbiology Spectrum.
If your manuscript is accepted for publication, you will be contacted separately about payment when the proofs are issued; please follow the instructions in that e-mail.Arrangements for payment must be made before your article is published.For a complete list of Publication Fees, including supplemental material costs, please visit our website.
Corresponding authors may join or renew ASM membership to obtain discounts on publication fees.Need to upgrade your membership level?Please contact Customer Service at Service@asmusa.org.
Thank you for submitting your paper to Microbiology Spectrum.
A manuscript titled "Compared with pure forest, mixed forests alter microbial diversity and increase the complexity of inter-domain networks in arid areas" studied the soil microbial community structure of five typical vegetation types in Tianshan, Xinjiang, China, using bacterial 16S rRNA and fungal ITS sequences.It has been stated that bacterial community is more related to soil C and fungal community to forest type.Overall manuscript is well-written and the conclusion is supported by the data.My comments on the manuscript and supporting information document are detailed below.
Introduction needs a paragraph where the microbial role is explained for soil processes such as degradation, mineralization and transformation.

2.
Material and methods for soil parameters need to be explained in more detail with the instruments being used.Microbial data analysis also needs to be explained in more detail with the pipeline used for analysis and taxonomy annotation databases.

3.
In the result section, figures need a little more explanation.

4.
Discussion needs to explain with the key microbial process performed by the dominant fungal and bacterial phyla in the soil in the current study.Table 1.Here are two times removed.One of the tables is given in the very beginning.Place it properly somewhere in the main text.

4.
L124.Scientific names should be italics.(apply throughout the MS) Thank you for your letter.I really appreciate all your comments and suggestions!These suggestions have enabled us to improve our work.Based on the instructions provided in your letter, we uploaded the file of the revised manuscript.Accordingly, we have uploaded a copy of the original manuscript with all the changes highlighted by using the track changes mode in MS Word.Appended to this letter is our point-by-point response to the comments raised by the reviewers.The comments are reproduced and our responses are given directly afterward in a different color (yellow).We would like also to thank you for allowing us to resubmit a revised copy of the manuscript.Thanks again!Reviewer comments: Reviewer #1 (Comments for the Author): A manuscript titled "Compared with pure forest, mixed forests alter microbial diversity and increase the complexity of inter-domain networks in arid areas" studied the soil microbial community structure of five typical vegetation types in Tianshan, Xinjiang, China, using bacterial 16S rRNA and fungal ITS sequences.It has been stated that bacterial community is more related to soil C and fungal community to forest type.Overall manuscript is well-written and the conclusion is supported by the data.My comments on the manuscript and supporting information document are detailed below.General comments: 1. Introduction needs a paragraph where the microbial role is explained for soil processes such as degradation, mineralization and transformation.Answer: We thank the reviewer for the indicating this crucial point.We have added one more paragraph about the microbial role from the text Line 78 to Line 90. 2. Material and methods for soil parameters need to be explained in more detail with the instruments being used.Microbial data analysis also needs to be explained in more detail with the pipeline used for analysis and taxonomy annotation databases.Answer: Thanks for such important suggestion.Specific methods have been added to the text, in L160 to L167. 3. In the result section, figures need a little more explanation.Answer: Thanks for highlighting this point.We have added more explanatory content in the part of the result section.4. Discussion needs to explain with the key microbial process performed by the dominant fungal and bacterial phyla in the soil in the current study.Answer: We thank the reviewer for the suggestion.Has been added in the discussion section,in L443 to L469.Specific comments Introduction 1. Table 1.Here are two times removed.Is given in the very beginning.Place it properly somewhere in the main text.Answer: Thanks for this suggestion.The table 1 has been placed appropriately.
2. Many typographical and spacing errors.L1. ( forest,mixed), L63 (2013)have), L 66 (properties(Xue) and so on...... M & M: Answer: We are thankful to the reviewer for this suggestion.We have done several format revisions of the full text.3. L103-105, L120-122 (Give sampling Coordinates).Re-write this sentence.Answer: Thank you very much for this important suggestion.We have re-written the sentence, and added more detailed information about the sampling sites in the new text Line 126 -Line 129.For the former manuscript L 103-105, it refers to the range of Tianshan Mountains, which is a potentially disputed issue.Given this, we tend to give no coordinates about it.4. L124.Scientific names should be italics.(apply throughout the MS) Answer: We thank the reviewer for highlighting this point.All species names have been changed to Italics in the full text.
Reviewer #3 (Comments for the Author): Comments, suggestions and questions are described in paper for the author.It's important that figure captions with descriptive content should be added to the paper.Answer: In the light of your suggestion, the descriptive content in figure captions have been added in the text.

Reviewer #5 (Comments for the Author):
This article has ignored the microbial interactions.So it focused on bacteria and fungal community as an individual factors.However in conclusion, they wrote that " Our research further elucidates the factors that affect the structure of microbial communities and can be applied to forest management, ecosystem processes, and ecosystem services."Answer: Thanks for such an insightful suggestion.We have revised the content changed the sentence to "This study further investigated the mechanism of interaction between microorganisms and soil in natural stands, which has positive implications for exploring the ecological processes of forest ecosystems."InL511.Thank you for the privilege of reviewing your work.Below you will find my comments, instructions from the Spectrum editorial office, and the reviewer comments.
Please return the manuscript within 60 days; if you cannot complete the modification within this time period, please contact me.If you do not wish to modify the manuscript and prefer to submit it to another journal, notify me immediately so that the manuscript may be formally withdrawn from consideration by Spectrum.

Revision Guidelines
To submit your modified manuscript, log into the submission site at https://spectrum.msubmit.net/cgi-bin/main.plex.Go to Author Tasks and click the appropriate manuscript title to begin.The information you entered when you first submitted the paper will be displayed; update this as necessary.Note the following requirements: • Upload point-by-point responses to the issues raised by the reviewers in a file named "Response to Reviewers," NOT IN YOUR COVER LETTER • Upload a compare copy of the manuscript (without figures) as a "Marked-Up Manuscript" file • Upload a clean .DOC/.DOCX version of the revised manuscript and remove the previous version • Each figure must be uploaded as a separate, editable, high-resolution file (TIFF or EPS preferred), and any multipanel figures must be assembled into one file • Any supplemental material intended for posting by ASM should be uploaded separate from the main manuscript; you can combine all supplemental material into one file (preferred) or split it into a maximum of 10 files, with all associated legends included For complete guidelines on revision requirements, see our Submission and Review Process webpage.Submission of a paper that does not conform to guidelines may delay acceptance of your manuscript.
Data availability: ASM policy requires that data be available to the public upon online posting of the article, so please verify all links to sequence records, if present, and make sure that each number retrieves the full record of the data.If a new accession number is not linked or a link is broken, provide Spectrum production staff with the correct URL for the record.If the accession numbers for new data are not publicly accessible before the expected online posting of the article, publication may be delayed; please contact production staff (Spectrum@asmusa.org)immediately with the expected release date.
Publication Fees: For information on publication fees and which article types are subject to charges, visit our website.If your manuscript is accepted for publication and any fees apply, you will be contacted separately about payment during the production process; please follow the instructions in that e-mail.Arrangements for payment must be made before your article is published.

ASM Membership:
Corresponding authors may join or renew ASM membership to obtain discounts on publication fees.Need to upgrade your membership level?Please contact Customer Service at Service@asmusa.org.
The ASM Journals program strives for constant improvement in our submission and publication process.Please tell us how we can improve your experience by taking this quick Author Survey.
Thank you for submitting your paper to Spectrum.

Sincerely, Diyan Li Editor Microbiology Spectrum
Reviewer #7 (Comments for the Author): In this study, authors have investigated the impacts of pure forest and mixed forest types on the soil microbial dynamics.Overall, this study is worthy of investigation and having some environmental significance.However, the reviewer has provided additional comments for further improvement of the quality.

Comments:
Abstract: Include some quantitative data in the abstract, Also, at the end, add a statement on the important implications of this work.Several studies have reported about the changes of abundance and dynamics of soil microbial communities with plant root exudates.A brief discussion is needed on this topic.In the Introduction, the novelty and importance of this study with respect to existing knowledge in literature should be clearly highlighted.At the end of discussion, add a section discussing the major implications and limitations of this work.Delete all the pronouns like "we, ours, etc." and change the text accordingly.The plant name and microbial species name should be written in italic text.Table 1: In the footnote, explain all the abbreviations reported in the table.Figure 4: In addition to this figure, is it possible to show the strength of correlation in a table containing the quantitative information.
There are several issues related to spacing errors throughout the manuscript, e.g.line 67 "diversity [3].", line 68: "small scale [1,4].",etc.To improve readers understanding and readability, the legends of all figures should be well written with explanation of the abbreviations representing the samples info.
Authors have carefully revised the manuscript according to the comments, and the quality of the manuscript has improved.Although the authors have done a great deal of work, there are still some issues to be resolved before publication.Thus, I suggest some minor revisions and expect the revised paper published in the AEM journal.
The line numbers in the "Response to Reviewer Comments" do not match the line numbers of the highlighted content in the Marked Up Manuscript or the Manuscript Text File.The following suggestions are given based on the Marked Up Manuscript.Line130-145: Suggested change the formatting of entire paragraphs in Result 2.1 so that the entire text is typographically consistent.
Line181-184: The writing format of symbols needs to be unified.Please revise "broad-leaved forest>coniferous forest" to "broad-leaved forest > coniferous forest" and revise similar content accordingly.
Dear Editor, Dear reviewers Thank you for your letter.I really appreciate all your comments and suggestions!These suggestions have enabled us to improve our work.Based on the instructions provided in your letter, we uploaded the file of the revised manuscript.Accordingly, we have uploaded a copy of the original manuscript with all the changes highlighted by using the track changes mode in MS Word.Appended to this letter is our point-by-point response to the comments raised by the reviewers.The comments are reproduced and our responses are given directly afterward in a different color (yellow).We would like also to thank you for allowing us to resubmit a revised copy of the manuscript.Thanks again!Reviewer comments: Reviewer #7 (Comments for the Author): In this study, authors have investigated the impacts of pure forest and mixed forest types on the soil microbial dynamics.Overall, this study is worthy of investigation and having some environmental significance.However, the reviewer has provided additional comments for further improvement of the quality.

Comments:
Abstract: Include some quantitative data in the abstract, Also, at the end, add a statement on the important implications of this work.Response: Thanks for such important suggestion.As requested, the abstract has been revised with additional quantitative results added to it and the implication of this work supplemented.
Several studies have reported about the changes of abundance and dynamics of soil microbial communities with plant root exudates.A brief discussion is needed on this topic.Response: Thanks for such an insightful suggestion.The content has already been added in lines 92 -95 of the text.
In the Introduction, the novelty and importance of this study with respect to existing knowledge in literature should be clearly highlighted.

Response:
We are thankful to the reviewer for this suggestion.This content has already been included in the text in lines 83 -89.
At the end of discussion, add a section discussing the major implications and limitations of this work.

Response:
We thank the reviewer for the suggestion.This part has already been supplemented in lines 440-450 of the text.Delete all the pronouns like "we, ours, etc." and change the text accordingly.Response: Thanks for mentioning this point.That type of inappropriate wording in the text has been corrected.
The plant name and microbial species name should be written in italic text.Response: We thank the reviewer for highlighting this point.All species names have been revised to Italics in the full text.Response: Thanks for such important suggestion.However, since the amount of data is quite large, we processed it into the form of a heat map.A graph (Figure 5) has been added to clearly demonstrate the quantitative levels of correlation between the results.
There are several issues related to spacing errors throughout the manuscript, e.g.line 67 "diversity [3].", line 68: "small scale [1,4].",etc. Response: We thank the reviewer for the indicating this crucial point.All spacing errors throughout the manuscript have been corrected.
To improve readers understanding and readability, the legends of all figures should be well written with explanation of the abbreviations representing the samples info.Response: In the light of your suggestion, we have added footnotes for all tables and figures of this manuscript.
November 22, 2023 2nd Revision -Editorial Decision Re: Spectrum02642-23R2 (Compared with pure forest,mixed forest alter microbial diversity and increase the complexity of interdomain networks in arid areas) Dear Dr. lu gong: Your manuscript has been accepted, and I am forwarding it to the ASM production staff for publication.Your paper will first be checked to make sure all elements meet the technical requirements.ASM staff will contact you if anything needs to be revised before copyediting and production can begin.Otherwise, you will be notified when your proofs are ready to be viewed.
Data Availability: ASM policy requires that data be available to the public upon online posting of the article, so please verify all links to sequence records, if present, and make sure that each number retrieves the full record of the data.If a new accession number is not linked or a link is broken, provide production staff with the correct URL for the record.If the accession numbers for new data are not publicly accessible before the expected online posting of the article, publication may be delayed; please contact ASM production staff immediately with the expected release date.
Publication Fees: For information on publication fees and which article types have charges, please visit our website.We have partnered with Copyright Clearance Center (CCC) to collect author charges.If fees apply to your paper, you will receive a message from no-reply@copyright.com with further instructions.For questions related to paying charges through RightsLink, please contact CCC at ASM_Support@copyright.com or toll free at +1-877-622-5543.CCC makes every attempt to respond to all emails within 24 hours.
ASM Membership: Corresponding authors may join or renew ASM membership to obtain discounts on publication fees.Need to upgrade your membership level?Please contact Customer Service at Service@asmusa.org.
PubMed Central: ASM deposits all Spectrum articles in PubMed Central and international PubMed Central-like repositories immediately after publication.Thus, your article is automatically in compliance with the NIH access mandate.If your work was supported by a funding agency that has public access requirements like those of the NIH (e.g., the Wellcome Trust), you may post your article in a similar public access site, but we ask that you specify that the release date be no earlier than the date of publication on the Spectrum website.

Embargo Policy:
A press release may be issued as soon as the manuscript is posted on the Spectrum Latest Articles webpage.The corresponding author will receive an email with the subject line "ASM Journals Author Services Notification" when the article is available online.
The ASM Journals program strives for constant improvement in our submission and publication process.Please tell us how we can improve your experience by taking this quick Author Survey.
Thank you for submitting your paper to Spectrum.

Sincerely, Diyan Li Editor Microbiology Spectrum
-23R1 (Compared with pure forest,mixed forest alter microbial diversity and increase the complexity of inter-domain networks in arid areas) Dear Dr. lu gong:

Figure 4 :
Figure 4: In addition to this figure, is it possible to show the strength of correlation in a table containing the quantitative information.Response: Thanks for such important suggestion.However, since the amount of data is quite large, we processed it into the form of a heat map.A graph (Figure5) has been added to clearly demonstrate the quantitative levels of correlation between the results.
• Manuscript: A .DOC version of the revised manuscript • Figures: Editable, high-resolution, individual figure files are required at revision, TIFF or EPS files are preferred

Table 1 :
In the footnote, explain all the abbreviations reported in the table.Response: Following your suggestion, we have revised footnotes and explained all the abbreviations reported in in the tables and figures.