Application of synthesized metal-trimesic acid frameworks for the remediation of a multi-metal polluted soil and investigation of quinoa responses

Amir Zarrabi; Reza Ghasemi-Fasaei; Abdolmajid Ronaghi; Sedigheh Zeinali; Sedigheh Safarzadeh

doi:10.1371/journal.pone.0310054

Peer Review History

Original SubmissionMay 5, 2024
24 Jun 2024 Decision Letter - Zhongchuang Liu, Editor PONE-D-24-18022Application of the synthesized metal-trimesic acid frameworks for the remediation of a multi-metal polluted soil: Investigation of crop responsesPLOS ONE Dear Dr. Ghasemi-Fasaei, 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 Aug 08 2024 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. Please include the following items when submitting your revised manuscript: 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, Zhongchuang Liu, Ph.D. 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. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. Additional Editor Comments : Please refer to the following article during the revision process. Liu, Z.C., Wang, L.A., Zeng, F.T., Al-Hamadani, S.M.Z.F., 2015. The Absorption and Enrichment Condition of Mercury by Three Plant Species. Polish Journal of Environmental Studies. 24, 887-891. Liu, Z.C., Wang, L.A., Xu, T.T., Deng, X.J., Zhang, H.L., 2014. Research on the effect of Na2S2O3 on mercury transfer ability of two plant species. Ecological Engineering. 73, 649-652. [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? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes Reviewer #3: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: No Reviewer #2: Yes Reviewer #3: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: No ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Considerably improve the quality of images and captions to convey the message clearly (self-sufficient) to the reader without relying on support from the text. Observe the writing of scientific names of plants in italics, for example: Chenopodium quinoa Nicotiana tabacum Morus alba Davidia involucrata Reviewer #2: Title The title is clear and accurately reflects the content and scope of the study. It effectively highlights the use of metal-trimesic acid frameworks for soil remediation and the investigation of crop responses. Abstract The abstract provides a concise summary of the study, including the background, methodology, key results, and conclusions. However, it lacks a clear statement of the study's objectives at the beginning and does not sufficiently highlight the significance and implications of the findings for environmental remediation practices. Introduction The study provides a comprehensive background on the issue of heavy metal contamination in soils and clearly states the importance of using MOFs for soil remediation. It also introduces quinoa as a relevant crop for studying metal uptake. However, the introduction could benefit from more recent references to support the claims and provide a broader context. The rationale for choosing quinoa as the test crop could be further elaborated, particularly in the context of its properties relevant to heavy metal uptake. Materials and methods The statistical analysis section lacks detail on the methods used for data analysis including specific tests used and software employed. Some procedural steps could be described with more clarity to ensure replicability. Results and discussion The section does not adequately address potential limitations of the study, such as any assumptions made, limitations of the experimental setup, and potential sources of error. It also lacks suggestions for future research directions to build on the findings, such as exploring different types of MOFs or testing in different soil conditions. Conclusion Include a brief statement on the broader implications of the study's findings for environmental remediation practices, particularly in urban areas with high levels of heavy metal pollution. References Update the reference list to include more recent studies, particularly those published in the last five years, to provide a broader context and support for the study's findings. General Comments The manuscript presents a well-conducted study on the application of metal-trimesic acid frameworks for soil remediation. The findings are significant and contribute to the field of environmental science. With some minor revisions and additional explanations, the manuscript will be suitable for publication in PLOS ONE. I recommend the manuscript for publication after the authors address the specific and general comments outlined above. Reviewer #3: 1. Suggested Topic: Application of the synthesized metal-trimesic acid frameworks for the remediation of a multi-metal polluted soil and investigation on Quinoa responses. 2. Abstract, Results etc. : Authors should replace "belongs to" with 'is for' or any other appropriate replacement 3. Authors should define abbreviation at the first use to aid comprehension, e.g. FTIR 4. It may be good to benchmark the HMs present in Quinoa in this research with the daily acceptable dosage from literature. 5. Authors have done a good first draft of reporting this interesting study however, further corrections have to be done. Some prepositions are missing and some sentences need restructuring. Editing tools should be employed to correct syntax, semantics and grammatical errors. ****** 6. PLOS authors have the option to publish the peer review history of their article (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 Reviewer #3: 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.0310054.r001
Revision 1
22 Jul 2024 Author Response Dear professor Zhongchuang Liu Academic Editor of PLOS ONE Thank you very much for considering our article. The revisions have been done according to what you and reviewers asked. ******* Dear professor Zhongchuang Liu 1. The manuscript has met PLOS ONE's style requirements, including those for file naming and the PLOS ONE style templates. 2. The captions for Supporting Information files were included at the end of our manuscript according to Supporting Information guidelines. Your suggested articles have been used in the present article in the sections of Introduction and Materials and methods and they have been marked with green font color in the text. Dear Reviewer #1 • The quality of the images has been adjusted by PLOS ONE Pace Image Tool. However, the length and width of the images have been increased again as much as possible. • The scientific names of plants have been written in italics and marked in light orange font color in the text. Dear Reviewer #2 Your recommended revisions have been marked with purple font color in the text: • The study's objectives at the beginning, the significance and implications of the findings for environmental remediation practices have been more clearly stated in the Abstract section. • The reason for choosing quinoa for this study is given in the Introduction section. Old references have been replaced with new references (2024) in this section. • Statistical analysis is described in more detail in the Materials and Methods section. • The limitations and problems of conducting the experiment are explained under the heading of Potential limitations of the study and suggestions in the Results and discussion section. The significant role of copper in the production of high-performance MOFs is also mentioned. The use of copper MOFs in acidic contaminated soils has been mentioned. Also, the use of other organic ligands to synthesis MOFs is suggested for future studies. • In the conclusion section, the high efficiency of copper MOF is mentioned due to its unique structure, especially for the removal of Pb in polluted urban soils. • A number of new references (2024) have been replaced with old references or added in References section. Dear Reviewer #3 Your recommended revisions have been marked with light blue font color in the text: • The previous title of the article has been changed according to your recommendation. • "belongs to" has been replaced by other appropriate words throughout the text. • Heavy metal absorption by quinoa in this study has been compared to other studies. • Many grammatical corrections have been made in the text, marked by Track Changes. Best regards Dr. Reza Ghasemi-Fasaei Corresponding author Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0310054.r002
7 Aug 2024 Decision Letter - Zhongchuang Liu, Editor PONE-D-24-18022R1Application of synthesized metal-trimesic acid frameworks for the remediation of a multi-metal polluted soil and investigation of quinoa responsesPLOS ONE Dear Dr. Ghasemi-Fasaei, 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 Sep 21 2024 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. Please include the following items when submitting your revised manuscript: 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, Zhongchuang Liu, Ph.D. Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: The plant names that need to be italicized in the references have not been modified. The name of the vertical axis in Fig.1 is unclear. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #3: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #3: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: (No Response) ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #3: (No Response) ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #3: (No Response) ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #3: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (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 #3: 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.0310054.r003
Revision 2
15 Aug 2024 Author Response Dear professor Zhongchuang Liu Academic Editor of PLOS ONE Thank you very much again for considering our article. The second round of revisions have been done according to what you recommended. ******* Dear professor Zhongchuang Liu • There was a retracted reference that was replaced by another reference. In reference number 35, Haseeb et al. 2022 was replaced by Bamagoos et al. 2022. • The scientific names of plants that were not written in Italic in the references section were corrected. • Fig 1 was edited and the name of the vertical axis is now clear. Best regards Dr. Reza Ghasemi-Fasaei Corresponding author Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0310054.r004
19 Aug 2024 Decision Letter - Zhongchuang Liu, Editor Application of synthesized metal-trimesic acid frameworks for the remediation of a multi-metal polluted soil and investigation of quinoa responses PONE-D-24-18022R2 Dear Dr. Ghasemi-Fasaei, 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, Zhongchuang Liu, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0310054.r005
Formally Accepted
27 Aug 2024 Acceptance Letter - Zhongchuang Liu, Editor PONE-D-24-18022R2 PLOS ONE Dear Dr. Ghasemi-Fasaei, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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 Dr. Zhongchuang Liu Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0310054.r006

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