PONE-D-25-04924

Integration of FTIR-based soil degradation indices with stochastic modelling to assess spatial patterns of organic matter-sediment dynamics in a Mediterranean watershed

PLOS ONE

Dear Dr. La Licata,

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.

Manuscript presents a valuable and methodologically sound case study integrating FTIR-based soil characterisation with spatial modelling. Reviewer 1 recommends acceptance, while Reviewer 2 requests minor revisions regarding title precision, figure quality, and clarification of erosion processes. In addition to these points, I require the authors to address several editorial concerns:

(1) avoid overgeneralisation of results beyond the studied catchment;

(2) moderate the interpretation of FTIR indices as direct erosion proxies, clearly stating their indirect nature;

(3) discuss the potential sampling bias due to post-event sediment collection;

(4) critically reflect on model uncertainties and limitations; and

(5) better integrate lithological and geomorphological controls into the analysis.

These revisions are necessary to meet PLOS ONE’s standards of scientific transparency and accurate interpretation.

Please submit your revised manuscript by Jun 29 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.

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,

Przemysław Mroczek, Dr. hab.

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 note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

3. 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.

4. Thank you for stating the following financial disclosure:

“This research was conducted with the financial support of the Earth and Environmental Sciences PhD-PON program (Research & Innovation, 2014e2020, Education and research for recovery - REACT-EU, DOT1322534-4) of University of Pavia, Department of Earth and Environmental Sciences. This research was also funded by the PRIN 2022 project by the Italian Ministry of University and Research, entitled: ”Full cOveRage, Multi-scAle and multi-sensor geomorphological map: a practical tool for TerrItOrial plaNning – FORMATION” (2022C2XPK7_004). This research was also supported by the Polish National Agency for Academic Exchange - Urgency Grants program project contract no. BPN/GIN/2024/1/00008.”

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.

5. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.

6. We note that Figures 1 and 4-7 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:

 1. You may seek permission from the original copyright holder of Figures 1 and 4-7  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].”

 2. 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/

7. 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:

Dear Authors,

Thank you for submitting your manuscript entitled “Integration of FTIR-based soil degradation indices with stochastic modelling to assess spatial patterns of organic matter-sediment dynamics in a Mediterranean watershed” to PLOS ONE. I appreciate the considerable effort invested in this interdisciplinary study, which integrates FTIR spectroscopy with geomorphological and statistical modelling approaches to investigate organic matter and sediment dynamics in a Mediterranean catchment.

The manuscript has been reviewed by two external referees. Reviewer 1 provided a very positive evaluation, stating that your research is technically sound, the data are sufficient and appropriately analysed, and the manuscript is clearly written. They commended the scientific relevance of your study and acknowledged the improvements made since the initial submission. Reviewer 2 also recognised the value of your work but raised several points requiring attention. Specifically, they suggested that the manuscript’s title should be more precise, explicitly reflecting the study area rather than implying a broader regional scope. They noted deficiencies in figure quality, particularly Figure 1, and recommended improvements in visual presentation, including the addition of geological and land use maps, as well as photographs of typical lithologies. Furthermore, they pointed out inconsistencies in figure referencing within the text and encouraged a more nuanced discussion of erosion processes, especially regarding the role of hydrophobicity in soil stability.

In addition to the reviewers' comments, I would like to draw your attention to several further issues that require careful consideration. While your integration of FTIR-derived indices with Random Forest modelling is methodologically sound, the interpretation of these proxies as direct indicators of erosion susceptibility appears overstated. The manuscript lacks empirical validation linking the FTIR indices to actual erosion measurements, sediment yields, or field-observed processes. This disconnect should be addressed with a more cautious interpretation of your findings, clearly acknowledging the proxy-based and indirect nature of your assessments.

Moreover, your conclusions frequently extrapolate results from a relatively small catchment in the Northern Apennines to “Mediterranean watersheds” in general. Such generalisations are not sufficiently substantiated and should be carefully delimited to the specific physiographic and climatic context of your study area. A more balanced formulation that frames your findings as case-study insights rather than general regional conclusions is recommended.

Another aspect requiring attention concerns the sampling strategy. Given that samples were collected following a significant rainfall event, it would be pertinent to discuss how this may have influenced sediment composition and whether such conditions are representative of the typical sediment dynamics in the catchment. This context is essential for interpreting your results.

Additionally, while your Random Forest models are well described, there is little discussion of model uncertainties, potential overfitting, or limitations. Providing a critical reflection on the robustness of your models and discussing the possible influence of dataset characteristics would enhance the scientific transparency of your work.

Finally, the integration of lithological controls and the role of mass movements in sediment connectivity and SOM dynamics are not fully explored. Although mentioned in the text, these factors are not quantitatively assessed nor sufficiently linked to your FTIR-based analyses. A more detailed examination of how different lithologies and geomorphological processes affect your observed patterns would significantly strengthen the study.

I therefore invite you to revise your manuscript by addressing both the reviewers’ comments and the editorial concerns outlined above. I believe these improvements will enhance the clarity, scientific rigour, and overall impact of your work.

Yours sincerely,

Przemysław Mroczek

Academic Editor

PLOS ONE

[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

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: 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: Yes

Reviewer #2: 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

**********

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: I believe that authors put sufficient data in order to explain their approach and to enable reproducibility. This is a a valuable contribution for the study of landscape evolution in Mediterranean watersheds. I also understand that the MS went through one round of review with different reviewers and authors made significant changes.

Reviewer #2: The title of the article suggests research in the Mediterranean region, whose coastline is very long, extensive, and is based on many countries, regions, etc. Meanwhile, when reading the text, we read that the authors are basically studying the catchment area of one river flowing into the Adriatic Sea, which concerns the region of Emilia-Romagna, northern Italy, the Arda River. This means that the title should be changed, precisely defining the area.

Fig. 1. The quality of these images is low, it needs to be improved. The hatching also raises concerns because the maximum height of 1300m is marked as if it were a height of over 5000m.

Line 134 and others: I suggest writing Roman numerals with a capital letter.

The authors described the catchment area of the studied river, also showing the lithology of the bedrock. They indicate in the text that mass movements occur there. Maybe it would be worth including a geological and soil map in this place? It would be good to explain why mass movements occur, whether it is the effect of soil instability resulting from heavy rains, the arrangement of rocks in the subsoil, or improper use of soils. This information has an impact on the rest of the text, especially since the authors themselves indicate that mass movements destroy soils (line 149). It is also worth considering how fields are ploughed, which can facilitate or hinder surface runoff of water on slopes.

Table 3 is interesting, but the authors could include photographs of typical examples of rocks and a map of agricultural use of the research area.

After Fig. 5, the authors describe Figure 7 (line 439) in the text, so it should be moved so that the order of citation of graphics in the text is maintained. There is no description of Figure 6 in this paragraph. This needs to be supplemented. There is only one reference in line 473, but it is too little for the information contained there.

Line 571, requires consideration, the hydrophobicity of matter alone does not have to stop erosion, which can be caused by, for example, soil instability and mechanical washing out. In addition, chemical compounds can appear in polluted waters that cause emulsification of such compounds.

**********

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: Yes:  Bülent Arıkan

Reviewer #2: Yes:  Miłosz Huber

**********

[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.

PONE-D-25-04924R1Integration of FTIR-based soil degradation indices with stochastic modelling to assess spatial patterns of organic matter-sediment dynamics in a Mediterranean watershed – A case study from the Northern ApenninesPLOS ONE

Dear Dr. La Licata,

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.

The manuscript now fully meets PLOS ONE’s methodological and data requirements and addresses all major reviewer and editor concerns. A minor revision is requested solely to streamline the title and refine the keywords to avoid unnecessary repetition and ensure better indexing. No further substantive changes are required, and I recommend acceptance once these final editorial points have been implemented.

Please submit your revised manuscript by Aug 02 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.

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,

Przemysław Mroczek, Dr. hab.

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 :

Dear Dr La Licata and Co-authors,

Thank you very much for submitting the revised version of your manuscript entitled “Integration of FTIR-based soil degradation indices with stochastic modelling to assess spatial patterns of organic matter–sediment dynamics in a Mediterranean watershed – A case study from the Northern Apennines” to PLOS ONE. I sincerely appreciate the significant effort you have devoted to addressing the reviewers’ and editorial comments. The manuscript has improved considerably in terms of methodological transparency, a more balanced interpretation of proxy-based findings, and an overall clearer presentation of the research context.

Before I can proceed with a final decision, I would kindly ask you to address two small but important editorial points to ensure that your manuscript meets the journal’s best practice for clarity and discoverability. Firstly, while your current title correctly reflects the study’s scope and regional focus, it is rather long and includes redundant wording that makes it unnecessarily complex. PLOS ONE encourages concise titles that convey the essential elements without superfluous phrases. I therefore strongly recommend shortening it to the following form: “FTIR-derived soil degradation indices and stochastic modelling of organic matter–sediment dynamics in a Mediterranean catchment: a Northern Apennines case study.” This version preserves all key terms but removes the overly extended structure and the phrase “to assess spatial patterns”, which is implicit in your methods and discussion.

Secondly, I encourage you to refine your set of keywords to avoid repeating phrases already present in the title. For example, “Organic matter indices”, “Mediterranean watershed”, and “Geomorphological modelling” duplicate core title terms and thus reduce the added value of the keywords for search engines and indexing. A more effective set could include terms that highlight important aspects of your study not directly stated in the title. I suggest the following as an example: Soil erosion risk, FTIR spectroscopy, Soil organic matter composition, Random Forest modelling, Watershed connectivity, and Sediment transport processes. This selection emphasises the main processes, analytical approach, and spatial system interactions central to your manuscript.

Once you have adjusted the title and keywords accordingly, I will be pleased to proceed with the final acceptance. No further substantive revisions are needed. Thank you again for your thoughtful and thorough response to the peer review process and for choosing PLOS ONE for the publication of your work. I look forward to receiving your final version soon.

With best regards,

Przemysław Mroczek, Dr hab.

Academic Editor, PLOS ONE

[Note: HTML markup is below. Please do not edit.]

[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.

FTIR-derived soil degradation indices and stochastic modelling of organic matter–sediment dynamics in a Mediterranean watershed: a Northern Apennines case study

PONE-D-25-04924R2

Dear Dr. La Licata,

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. For questions related to billing, please contact billing support .

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,

Przemysław Mroczek, Dr. hab.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you for your thorough revision and for addressing the editorial suggestions with care and clarity. The changes made to the title, keyword selection, and data availability statement are appropriate and fully in line with the previous guidance. I appreciate the effort to enhance the clarity and coherence of the manuscript.

However, I note that the revised version labelled as "tracked changes" does not actually contain any visible change markings. While the clean version appears to incorporate the necessary revisions, the absence of a tracked version prevents a straightforward verification of specific edits. I recommend ensuring that such a file is included in future submissions where applicable.

I would like to thank you and your co-authors for your constructive engagement throughout the editorial process. I believe the manuscript is now in a form suitable for publication.

Reviewers' comments: