Synergistic evolution of soil microaggregates biogeochemical processes driven by elevation gradients in Tongbai Mountain

Chunjie Li; Shili Guo; Songhao Shang

doi:10.1371/journal.pone.0325425

Peer Review History

Original SubmissionJanuary 29, 2025
29 Jan 2025 Author Response https://doi.org/10.1371/journal.pone.0325425.r001
10 Mar 2025 Decision Letter - Erika Kothe, Editor Dear Dr. Li, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Apr 24 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Erika Kothe Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Thank you for stating the following financial disclosure: National Nature Science Foundation of China [grant number 41601614]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. We note that you have indicated that there are restrictions to data sharing for this study. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Before we proceed with your manuscript, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., a Research Ethics Committee or Institutional Review Board, etc.). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories. You also have the option of uploading the data as Supporting Information files, but we would recommend depositing data directly to a data repository if possible. We will update your Data Availability statement on your behalf to reflect the information you provide. 5. We note that your Data Availability Statement is currently as follows: All relevant data are included within the manuscript and its Supporting Information files. Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition). For example, authors should submit the following data: - The values behind the means, standard deviations and other measures reported; - The values used to build graphs; - The points extracted from images for analysis. Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories. If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access. 6. We note that Figure 1 in your submission contain copyrighted images. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. 7. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” b . If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ Additional Editor Comments : The reviewers gave helpful comments. Especially the remark about generalization being very limited if only one time sampling was used is a severe shortcoming for a journal that hopes to attract readers interested in general microbiology. Only if the data can be compared to other publications, or preferably, a second time point, the manuscript can become acceptable for PlosOne. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: I Don't Know ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: The study used a variety of advanced analytical techniques to comprehensively characterize the mineral composition, soil organic carbon (SOC), and heavy metal element distribution of soils at different altitudes in Mount Tongbai. The manuscript proposes a comprehensive scoring method to evaluate the sensitive factors of soil biogeochemical characteristics. This method has some innovation and practicality in ecological data analysis. The data is detailed, and the methods are scientific. It is believed that reliable research results can be provided. Although the research scope is limited to this specific region, it may limit the generalizability and generalizability of the research results. Moreover, based solely on one-time sampling and analysis, lacking long-term monitoring data, it may not fully reflect the dynamic changes in soil biogeochemical processes. I suggest the authors check the details of the manuscript carefully. For example, what does the “SThe structure” in Line 230 mean? In addition, the discussion part should be improved, and some similar previous studies should be cited and discussed. Reviewer #2: Dear Authors I have several comments regarding the X-ray fluorescence analysis. 1. If you used reference materials to construct calibration curves for determining elements, you should list them, including manufacturers and analyte ranges. If the calculation was carried out using a standardless approach, it should also be indicated how exactly this was done. However, in this case, an analysis of the reference material is also necessary to estimate the accuracy of applied technique (reference materials are quite available for soil composition). 2. Table 3 is unclear to me. What does 0.00±1.12 mean? Why is the confidence interval for Mg so large, while for Al these values are several times smaller? Was Na which is also a major element for soils, analyzed? 3. Before Table 5, the LOD values for each element and how they were calculated must be indicated. Was fluorine analyzed? Some values, for example, for barium 435±399, also raise questions. What conclusions can be made if the standard deviation is almost 100 percent? Are you sure that barium is present in these samples? Why is iron not classified as a major element and the accuracy of its determination (according to the table) is significantly higher than, for example, for calcium? I recommend describing in more detail the X-ray fluorescence method, as well as critically approaching obtained results. ****** what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0325425.r002
Revision 1
31 Mar 2025 Author Response Response to Editor Comments Dear Editor, Thank you for providing us with valuable feedback and suggestions, which have significantly improved the quality of our manuscript. Here we submit a revised manuscript with the title “Synergistic Evolution of Soil Microaggregates Biogeochemical Processes Driven by Elevation Gradients in Tongbai Mountain”, which has been modified according to the suggestions carefully. The followings are point-to-point responses to the comments. Comment 1: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response 1: We have revised the manuscript according to the PLOS ONE formatting style, including the main text structure and file naming requirements. All revised files conform to the templates provided in the formatting guidelines. Comment 2: In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. Response 2: We have added a statement in the Methods section indicating that field sampling was carried out with the approval of the Tongbai Mountain National Nature Reserve Administration Bureau. (line 242-243). No special permits were required as the study did not involve protected species or private land. Comment 3: Thank you for stating the following financial disclosure: National Nature Science Foundation of China [grant number 41601614]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Response 3: We have included the following statement in the manuscript and cover letter: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Comment 4a & 5: Clarify data access restrictions or upload data to a repository. Confirm data availability. Response4a & 5: There are no ethical or legal restrictions on sharing the data. All relevant raw data, including values behind graphs and statistical measures, have now been uploaded as Supporting Information files and to an open repository [repository link/DOI to be inserted upon upload]. The Data Availability Statement has been updated accordingly. All relevant data are contained within the article. Comment 6 & 7: Figure 1 includes copyrighted [map/satellite] images. You must obtain permission or replace them. Response 6 & 7: We have removed the previously used copyrighted image in Figure 1 and replaced it with a schematic diagram titled “Schematic diagram of vertical vegetation zonation along an altitudinal gradient in Tongbai Mountain.” The updated figure complies with the CC BY 4.0 license, and the figure caption has been revised to include appropriate attribution. Sincerely, Chunjie LI Response to Reviewer 1 Comments Dear Reviewer, Thank you for providing us with valuable feedback and suggestions, which have significantly improved the quality of our manuscript. Here we submit a revised manuscript with the title “Synergistic Evolution of Soil Microaggregates Biogeochemical Processes Driven by Elevation Gradients in Tongbai Mountain”, which has been modified according to the suggestions carefully. The followings are point-to-point responses to the comments. Comment 1: The study used a variety of advanced analytical techniques to comprehensively characterize the mineral composition, soil organic carbon (SOC), and heavy metal element distribution of soils at different altitudes in Mount Tongbai. The manuscript proposes a comprehensive scoring method to evaluate the sensitive factors of soil biogeochemical characteristics. This method has some innovation and practicality in ecological data analysis. The data is detailed, and the methods are scientific. It is believed that reliable research results can be provided. Although the research scope is limited to this specific region, it may limit the generalizability and generalizability of the research results.. Response 1: Thank you for recognizing the innovation and scientific merit of our methodology. We acknowledge that focusing solely on Tongbai Mountain may limit the generalizability of our results. To address this, we have significantly expanded the Discussion section by comparing our findings with studies from various mountain ranges—including the Tatra Mountains, the Andes, the Helan Mountains, the Lushan Mountains, the Dabie Mountains, the Bamtou Mountains, the Karakorum Mountains, Mount Everest, the Alps, Luoji Mountain, and the Hengduan Mountains—and by citing multiple studies (e.g., Cao et al., 2024; Du et al., 2014; Li et al., 2018; Magnani et al., 2018; Ouyang et al., 2021; Shedayi et al., 2016; Sun et al., 2023; Tsozué et al., 2019; Wu et al., 2023; Zechmeister, 1995) to provide a broader ecological and geochemical context for our results. (line 525-532; line 543-557; line 566-587; line 611-615). Through these efforts, we aim to enhance the broader applicability of our research outcomes and provide a replicable analytical framework and theoretical support for future studies in similar settings. Comment 2: Based solely on one-time sampling and analysis, lacking long-term monitoring data, it may not fully reflect the dynamic changes in soil biogeochemical processes. Response 2: Thank you for your important comment regarding the one-time sampling and the absence of long-term monitoring data. We acknowledge that our study is based on a single sampling event, and we have added a statement in the Discussion section to underscore that long-term monitoring is essential for capturing the temporal variability in soil biogeochemical processes. In future work, we plan to conduct multi-year sampling campaigns to address this issue more effectively. Although our results from Tongbai Mountain show similarities with observations from other mountain ranges—suggesting that our conclusions may have broader applicability—we caution against extrapolating these findings to different geographical contexts without further investigation. It is also important to note that the distributions of soil organic carbon (SOC) and heavy metals may exhibit distinct dynamic characteristics over various timescales. For example, SOC levels can respond rapidly (within years to decades) to changes in vegetation or management practices, whereas heavy metal distributions tend to remain relatively stable, reflecting historical deposition patterns that span hundreds to thousands of years. (line 711-722).Therefore, incorporating time-series data or radiocarbon dating techniques in future research will be essential for further elucidating the turnover rates and long-term stability of SOC and heavy metals. Comment 3: I suggest the authors check the details of the manuscript carefully. For example, what does the “SThe structure” in Line 230 mean? Response 3: We thank the reviewer for spotting this typographical error. The text "SThe structure" is a typo and has been corrected to "The structure" in the revised manuscript (Section 2.3, SEM Analysis). (line 274). Comment 4: The discussion part should be improved, and some similar previous studies should be cited and discussed. Response 4: We agree with the reviewer and have expanded the Discussion section accordingly. In the revised version, we compare our findings with studies from other mountainous regions, including the Tatra Mountains and the Andes. We now reference multiple studies (e.g., Cao et al., 2024; Du et al., 2014; Li et al., 2018; Magnani et al., 2018; Ouyang et al., 2021; Shedayi et al., 2016; Sun et al., 2023; Tsozué et al., 2019; Wu et al., 2023; Zechmeister, 1995) to provide a broader ecological and geochemical context for our results. (line 525-532; line 543-557; line 566-587; line 611-615). These additions help to highlight both the uniqueness and the generality of the elevation-driven patterns observed in our study. Sincerely, Chunjie LI Response to Reviewer 2 Comments Dear Reviewer, Thank you for providing us with valuable feedback and suggestions, which have significantly improved the quality of our manuscript. Here we submit a revised manuscript with the title “Synergistic Evolution of Soil Microaggregates Biogeochemical Processes Driven by Elevation Gradients in Tongbai Mountain”, which has been modified according to the suggestions carefully. The followings are point-to-point responses to the comments. Comment 1: If you used reference materials to construct calibration curves for determining elements, you should list them, including manufacturers and analyte ranges. If the calculation was carried out using a standardless approach, it should also be indicated how exactly this was done. However, in this case, an analysis of the reference material is also necessary to estimate the accuracy of applied technique (reference materials are quite available for soil composition). Response 1: We appreciate the reviewer’s detailed and professional feedback. In the revised manuscript (Section 2.5), we have clarified that XRF measurements were conducted using a PANalytical AXIOS WDXRF spectrometer. This instrument is equipped with SuperQ 4.0 quantitative analysis software, which automatically handles peak intensity calculations, Compton scatter internal standard correction, spectral interference correction, and matrix correction before displaying the analysis results. Calibration was performed using certified reference materials (GBW07401 and GBW07404 from the Chinese National Institute of Metrology) that encompass the major and trace element concentration ranges relevant to soil. The analytical accuracy was verified by repeatedly testing these reference materials and comparing the results with their certified values, yielding recovery rates generally between 90% and 110%. This additional information has been included to enhance transparency and ensure data quality. (line289-303). Comment 2: Table 3 is unclear to me. What does 0.00±1.12 mean? Why is the confidence interval for Mg so large, while for Al these values are several times smaller? Was Na which is also a major element for soils, analyzed? Response 2: We appreciate the reviewer’s insightful comments regarding the presentation of our results. MgO and similar compounds were also measured using XRF. Compared with high atomic weight elements, XRF exhibits lower sensitivity for low atomic weight elements due to their low characteristic X-ray energies, weak fluorescence yields, and the ease with which their signals are absorbed by air and detector windows. As a result, elements such as Na, Mg, and Al have higher detection limits and greater measurement uncertainties. The values, such as 0.00 ± 1.12 reported in Table 3, indicate that the measured concentrations of MgO in some samples were close to or below the instrument’s detection limit, leading to high uncertainty. The large standard deviation reflects the very low MgO concentrations in those specific samples (near 0%). In contrast, Al₂O₃ levels were consistently higher and fell within the instrument’s optimal detection range, resulting in lower variability. Regarding sodium (Na), due to limitations in our XRF setup—specifically, its low fluorescence yield and high volatility—Na was not analyzed. This explanation has been added to the Methods section. (line304-316). Comment 3: Before Table 5, the LOD values for each element and how they were calculated must be indicated. Was fluorine analyzed? Some values, for example, for barium 435±399, also raise questions. What conclusions can be made if the standard deviation is almost 100 percent? Are you sure that barium is present in these samples? Why is iron not classified as a major element and the accuracy of its determination (according to the table) is significantly higher than, for example, for calcium? Response 3: We thank the reviewer for the insightful comments. By repeatedly measuring the reference materials and comparing the results with their certified values, we achieved recovery rates generally between 90% and 110%, indicating that the method has high analytical precision, although its accuracy for trace elements is limited. The limit of detection (LOD) for each element was determined using the 3σ criterion (three times the standard deviation of blank measurements). The high standard deviation observed for barium (e.g., 435 ± 399) reflects both significant spatial variability in its concentration and the fact that some samples were near the detection limit; we have acknowledged this uncertainty in the revised discussion. Furthermore, the XRF results for trace elements should be considered qualitative. Although iron (Fe) is typically classified as a heavy metal, it also functions as a major oxide-forming element in soil. We have now clarified in both the Methods and Discussion sections that, despite Fe not being grouped under "major elements," its role and high analytical accuracy (due to its strong fluorescence yield and abundant concentration) render it comparable to the major oxides. (line304-316). Sincerely, Chunjie LI Attachments Attachment Submitted filename: Author to respond Editor - PLOS One.docx https://doi.org/10.1371/journal.pone.0325425.r003
15 Apr 2025 Decision Letter - Erika Kothe, Editor Dear Dr. Li, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by May 30 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Erika Kothe Academic Editor PLOS ONE Additional Editor Comments: The answers to the reviewers query did not completely meet the expectations. Please be very careful to commit to diligent following standard procedures. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: I Don't Know ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes ****** Reviewer #2: Dear Authors I still have some comments. Presenting the results as 0.00±1.12 is completely unacceptable. If this content (or the content of any other element being determined) was close to the detection limit, you should write <lod, better="" or="" yet=""> Despite the adequacy of your answer, I recommend adding information about the analysis of certified reference materials to the text. The part of your answer is quite acceptable for it.</lod,> ****** what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0325425.r004
Revision 2
16 Apr 2025 Author Response Dear Reviewer, Thank you for your insightful feedback and valuable suggestions, which have greatly contributed to improving the quality of our manuscript. We are pleased to submit a revised version of our manuscript titled “Synergistic Evolution of Soil Microaggregates Biogeochemical Processes Driven by Elevation Gradients in Tongbai Mountain”. The manuscript has been carefully revised in accordance with your comments. Below are our point-by-point responses to your suggestions. Comment 1: Presenting the results as 0.00±1.12 is completely unacceptable. If this content (or the content of any other element being determined) was close to the detection limit, you should write. Response 1: Thank you for your valuable comment. We acknowledge that presenting results as "0.00±1.12" without specifying the detection limit (LOD) can be misleading. In our revised manuscript, we have now clearly indicated that these values are below the detection limit (LOD), and we have revised the results accordingly to reflect this. (line309-315). The relevant results are now presented as “< LOD” (below the limit of detection) to better align with scientific reporting standards for data close to the detection limit. We have made these changes in both the manuscript text and Table 3 to avoid any potential misinterpretation. We appreciate your suggestion, which helps to improve the accuracy of our presentation. Comment 2: Despite the adequacy of your answer, I recommend adding information about the analysis of certified reference materials to the text. The part of your answer is quite acceptable for it. Response 2: We have included details in the manuscript on the calibration of our methods using certified reference materials (GBW07401 and GBW07404 from the Chinese National Institute of Metrology), which cover major and trace element concentrations, as well as major element oxide concentrations relevant to soil analysis. The analytical accuracy was validated through repeated testing, with recovery rates typically ranging from 90% to 110%. This information has been added to the Methodology section (lines 303-308) of the manuscript for transparency and clarity. The specific text added is as follows: “Calibration was carried out using certified reference materials (GBW07401 and GBW07404 from the Chinese National Institute of Metrology), which cover the major and trace element concentration ranges relevant to soil. The analytical accuracy was validated through repeated testing of these reference materials, with the results compared to their certified values, yielding recovery rates typically ranging from 90% to 110%.” We believe that this addition strengthens the rigor of our study and addresses your concern regarding the quality assurance of our analytical methods. We would like to thank you for your invaluable feedback, which has helped improve the manuscript. We believe that the revisions made in response to your suggestions have significantly enhanced the quality of our work. We look forward to your further feedback. Sincerely, Chunjie LI Attachments Attachment Submitted filename: Author to respond reviewer 2 - PLOS One.docx https://doi.org/10.1371/journal.pone.0325425.r005
13 May 2025 Decision Letter - Erika Kothe, Editor <p>Synergistic Evolution of Soil Microaggregates Biogeochemical Processes Driven by Elevation Gradients in Tongbai Mountain PONE-D-25-05130R2 Dear Dr. Li, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Erika Kothe Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0325425.r006
Formally Accepted
Acceptance Letter - Erika Kothe, Editor PONE-D-25-05130R2 PLOS ONE Dear Dr. Li, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Prof. Dr. Erika Kothe Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0325425.r007

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .