PONE-D-24-52526Influence of Landscape Structure on Carbon Storage in Agroforestry Systems with Cacao and Silvopastoral Systems in the Colombian AmazonPLOS ONE

Dear Dr. Diaz Chaux,

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 authors conducted a systematic review of the effects of Conservation Reserve Program in USA. They systematically searched for studies dealing with Soil/vegetation/wildlife/social and other aspects that were affected by CRP. They also conducted spatial analyses to show which states participating in the program have conducted studies to assess the effects of CRP. The study was done well and summaries have been provided on how many studies were conducted on different habitat/organismal factors affected by CRP. However, the authors did not provide good syntheses in the Discussion. For example, there is good summaries on how many studies covered soil improvement and from which State(s), but there are limited or no syntheses extracted from these studies as discussion points. The same is true of vegetation, wildlife, social studies etc. I feel the paper would improve a lot more if such information is summarized and synthesized from the substantial numbers of papers to enrich the discussion. I suggest major review and i have appended a marked up version of the manuscript where I propose these changes need to be incorporated.

Please submit your revised manuscript by Apr 14 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,

Marcela Pagano, Ph.D, M.D.

Academic Editor

PLOS ONE

Journal Requirements:

1. When submitting your revision, we need you to address these additional requirements.

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 a complete copy of PLOS’ questionnaire on inclusivity in global research in your revised manuscript. Our policy for research in this area aims to improve transparency in the reporting of research performed outside of researchers’ own country or community. The policy applies to researchers who have travelled to a different country to conduct research, research with Indigenous populations or their lands, and research on cultural artefacts. The questionnaire can also be requested at the journal’s discretion for any other submissions, even if these conditions are not met.  Please find more information on the policy and a link to download a blank copy of the questionnaire here: https://journals.plos.org/plosone/s/best-practices-in-research-reporting. Please upload a completed version of your questionnaire as Supporting Information when you resubmit your manuscript.

3. Thank you for stating the following financial disclosure: [Beca de excelencia doctoral Bicentenario otorgada por Minciencias Colombia (código BPIN 2021000100036)].

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 your Data Availability Statement is currently as follows: [Todos los datos relevantes están dentro del manuscrito y de sus archivos de información de apoyo]

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.

5. 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:

 1. 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].”

 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/

Additional Editor Comments:

Dear authors, please, revise your manuscript according to reviewer suggestions.

[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: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: I Don't Know

**********

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

Reviewer #3: No

**********

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: 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: In the manuscript, the authors did not include much data and objective in the abstract.

There is also a need to incorporate the objective in the introduction section.

Please write the aim and applicability of the study.

There is a need to include study site photographs for authentication and to clarify the hypothesis of this study.

Please add many more recent references related to the study.

I strongly suggest that the author edit and rewrite the sentences for language editing, which is the most useful criterion of any scholarly research article.

Discussion of the manuscript needs to elaborate by including some recent literature.

Reviewer #2: I reviewed the manuscript titled "Influence of Landscape Structure on Carbon Storage in Agroforestry Systems with Cacao and Silvopastoral Systems in the Colombian Amazon" for consideration in PLOS ONE. This study addresses a critical issue in the conservation of Amazonian ecosystems by evaluating the influence of landscape structure and configuration on carbon storage in cacao agroforestry systems (SAFc) and silvopastoral systems (SSP). The study provides valuable insights into the role of agroforestry mosaics in carbon regulation, highlighting their potential for climate change mitigation. The research suggests strategies to enhance connectivity and increase carbon sequestration capacity in productive landscapes, which has significant implications for land-use planning. However, I do have some suggestions and areas for improvement for the manuscript:

• Biomass and carbon storage may vary depending on the floristic composition within SAFc and SSP, suggesting the need for further studies on the contribution of key species.

• Differences in management practices within agroforestry systems could affect carbon dynamics, which could be explored in greater depth.

• The statistical analysis and results section presents valuable insights, but there are several areas where clarity, coherence, and interpretation could be improved.

• The results section presents p-values and F-statistics but lacks biological or ecological interpretation of the findings. I suggest adding means and SD of each variable to give a better perspective of the values and differences and explain the ecological significance of significant and non-significant results.

• Add a brief explanation of why each statistical method was chosen and how it aligns with the study objectives.

• The manuscript does not mention whether key assumptions for ANOVA (normality, homogeneity of variance) and regression analyses (linearity, multicollinearity) were checked.

• Some tables and figures lack clear captions or explanations, making it difficult for readers to interpret the data. Please improve the clearly label significant results with asterisks or superscripts in tables. Ensure figure legends describe all abbreviations and variables. For example, table 3 presents mean carbon storage values across different vegetation covers. Add a legend indicating that values with the same letter are not significantly different (Tukey’s HSD test, p > 0.05).

• The results do not mention potential confounding factors that could influence carbon storage variability (e.g., soil type, elevation, past management). Please address potential confounders and, if applicable, describe how they were controlled.

• The PCA and PLS regression results are presented with numerical outputs do not have a clear biological interpretation. Please explain what the principal components represent and how the regression findings contribute to the study’s conclusions.

• The discussion section provides a general overview of the findings, but it would benefit from a more in-depth interpretation of the observed patterns.

• I suggest explicitly addressing how different landscape metrics influence carbon sequestration and why certain patch configurations lead to higher/lower storage.

• The discussion includes citations to previous studies but lacks a critical comparison that highlights the novelty of the current research. Clearly articulate how the results confirm, contradict, or expand on prior studies.

• Although different landscape mosaics are analyzed, microclimatic and edaphic factors that may influence carbon capture are not explored in detail.

• The discussion would benefit from explicitly acknowledging limitations and suggesting future research directions.

• The discussion highlights the importance of landscape connectivity but does not explicitly state how land-use policies should integrate these findings. Please expand the implications by providing concrete recommendations for conservation planning

Reviewer #3: #Revisor

The manuscript deals with an interesting subject involving landscape metrics and measurements of biomass and carbon in vegetation in the field. The authors indicate that this type of study is a pioneer in the region. However, I found the article difficult to understand for a general audience, and it had a weak connection between the objectives, the methodology, and the results. I have tried to highlight some of the critical points below. A conceptual issue that seems important to me is the classification of silvopastoral systems, which involve trees, pastures, and animals. The system closest to the silvopastoral system (PAD) is poorly represented. So, it does not seem easy to relate landscape metrics to the carbon stored in production systems (SAF; SPP). In addition, some results are conflicting, such as the carbon in the aerial biomass of grasses being higher than in secondary tropical forests; estimation of carbon stored in the biomass of trees, herbaceous, and litter in LAG=lagoons; use of biomass equations for fruit species, but they are not highlighted in any production system. In addition, the manuscript needs to reorganize the text and its writing. I could not recommend the acceptance of the manuscript in its present form.

Material and methods

The separation of the M&M item could be redone. Line 148 onwards should not be part of the study area.

L148-149. Could it include the main species that make up the SSP? Does SAF with cocoa present high or low plant diversity?

L170-173. What would be the area of each of the 78 plots? How were the plots within each mosaic systematized?

L99-211. This topic is confusing. How was the carbon stored in each plot converted to SAF, SPP, and mosaic model scale? Did the authors use the same equation to convert aerial biomass into root biomass for all vegetation types?

Why were landscape metrics classified as descriptive to use in PCA if they are quantitative in regression? Moreover, why do linear regression and PLS? Are the authors using the same metrics as Table 1 for all cases (PCA, LR, SLS)? How did the authors deal with the different measurement scales to do the PCA? In general, PCA can be influenced by high and low values.

Results

A more coherent separation of the results into topics would facilitate understanding.

It is unclear what type of ecosystem fits the silvopastoral systems (SPP) classification. The only one that could fit is the PAD model, represented only by the ES Mosaic. So, I asked how it was possible to statistically test the effects of the SAF and SPP models on the stored carbon. Also, how did the authors calculate the carbon stored in trees in LAG, RIO, PEN, PPH, PPL, RTT, and RTV?

Table 3. The table is cut off, and I cannot see all the information. Furthermore, what is the unit of values? Is the size of the area in ha, m2, km2? Why isn't there SD in some of the information? Why are the letters that indicate statistical results only in CAC and PPL?

L230-245. The authors indicate the different landscape metrics in the PCA, but it would be easier to relate them to Table 1. For example, which metrics are related to "complexity in patch shape, while the negative end associates with mosaics featuring larger, more aggregated patches" "mosaics with irregular, aggregated patches, while the negative end is characterized by mosaics with larger patches that have smoother, less irregular contours".

L255-264. This paragraph should be in the M&M. In addition, the authors could go into more detail about this type of information:

"The cover type with the highest number of plots was early fallow (RTT), followed by old fallow (RTV) and agroforestry cacao cultivation (CAC). A total of 2,846 individual plants were surveyed across both systems: 1,505 trees in the SAFc mosaics, including 330 cacao shrubs, 105 rubber trees (H. brasiliensis), 29 palms, thirteen fruit trees, and 1,028 saplings."

L266-276. Given the diversity of ecosystems and the very different number of replicates, comparing the SAF and SPP systems seems difficult. In addition, it seems strange to me that the biomass of grasses is greater than forest (BSE). The carbon stored in the soil could be higher in grass than in secondary forest, but I had not yet seen biomass.

Fig.3. The figure does not show ANOVA, but rather the average carbon values in biomass. A period is used and not a comma to separate the numbers in English.

L289. How did the authors arrive at this value of stored carbon?

L305-303. Is carbon stored in biomass equal to total carbon? Usually, grasses have a lot of root biomass.

Discussion

L419. This connectivity metric is unclear. Where is this result?

L 428-432. This relationship was weak many times for some metrics. Could you explain which metrics might be most important for estimating carbon relative to Table 1? Although the linear regression was significant, the data distribution in Fig 4 does not appear linear.

**********

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.

Influence of Landscape Structure on Carbon Storage in Agroforestry Systems with Cacao and Silvopastoral Systems in the Colombian Amazon

PONE-D-24-52526R1

Dear Dr. Jenniffer Diaz Chaux,

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,

Marcela Pagano, Ph.D, M.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: