A standardised protocol for measuring farmland biodiversity outcomes across European Farmer Cluster landscapes

Rachel N. Nichols; Graham S. Begg; Lisette Cantú-Salazar; John M. Holland; Youri Martin; John Tzilivakis; Sarah Vray; Douglas J. Warner; Alon Zuta; Niamh M. McHugh

doi:10.1371/journal.pone.0345691

Peer Review History

Original SubmissionJuly 4, 2025
4 Jul 2025 Author Response Attachments Attachment Submitted filename: response to reviewers.docx https://doi.org/10.1371/journal.pone.0345691.r001
25 Dec 2025 Decision Letter - RunGuo Zang, Editor Dear Dr. Nichols, 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 revised the manuscript according to the comments of the reviewers. Please submit your revised manuscript by Feb 08 2026 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 letter that responds to each point raised by the academic editor and reviewer(s). 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Additional Editor Comments: Please respond to the concerns of the referees and revised the manuscript accordingly [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: N/A 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: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: Comments on MS PONE-D-25-36303 entitled “A standardised protocol for measuring farmland biodiversity outcomes across European Farmer Cluster landscapes” by Nichols et al. 1. General comments: This paper proposes a standardized protocol for monitoring farmland biodiversity in European Farmer Cluster landscapes. The protocol is designed to evaluate and unify methods for assessing biodiversity across different farming systems. It provides practical guidance on selecting survey squares and transects, as well as detailed procedures for surveying birds, pollinators, and vegetation. Comprising a suite of standardized sub-protocols, the framework is adaptable to diverse agricultural contexts. Finally, the authors evaluate the effectiveness of these biodiversity indicators and survey methods. This paper is of good scientific quality, thus may interest the readers of PLoS One. However, there are some aspects that could be improved for me. Therefore, I recommend this paper to have a major revision. After this major revision, the paper may contribute to the field. 2. Specific comments 1) Is it necessary to include some indicators of biodiversity pressures such as the annual application of pesticides, annual application of fertilizers, per capita annual net income of rural households and so on. These indicators could facilitate the subsequent analysis after biodiversity investigation. 2) Is it necessary to include some indicators of ecosystem services such as water purification, reducing pesticide needs and so on. 3) Some biodiversity indicators at landscape scale could be derived from satellite remote sensing data such as forest cover, productivity and so on. 4) This protocol aims to monitor biodiversity of farm cluster. The pro 5) I suggest to compare this protocol with similar protocols in discussion mentioned in the paper like biodiversity indicators for organic and low-input farming systems (BioBio), Farm4Bio, and European Monitoring of Biodiversity in Agricultural Landscapes. Reviewer #2: This research holds significant value for both ecological science and practical agricultural conservation in Europe. It directly addresses the critical challenge of farmland biodiversity loss by developing and rigorously evaluating a standardized, scalable monitoring protocol. The core innovation lies in its application within the "Farmer Cluster" model—a bottom-up, collaborative conservation approach. By creating a robust methodology to assess biodiversity outcomes across these clusters, the study provides an essential tool for empirically testing whether community-led agricultural initiatives can effectively reverse biodiversity decline at a meaningful landscape scale. The use of a Before-After-Control-Impact (BACI) experimental design significantly strengthens the potential to attribute observed changes in biodiversity to the interventions themselves, moving beyond mere observation to causal inference. However, I do not believe this is a research article. It strikes me more as a research proposal or a work guideline. This depends on the journal's positioning. In terms of strengthening practical guidance and feasibility, greater consideration should be given to the following issues—although these may not necessarily need to be addressed within the scope of the present study, but rather as key priorities for the authors’ future follow-up research. From the perspective of the work itself, I think at least three additional points need to be considered in its actual implementation. 1. The monitoring methods, although well-documented, can be labor-intensive and require significant expertise, potentially limiting their long-term application outside well-funded research projects. The BACI design, while robust, also depends heavily on the availability of suitable control sites, which may be difficult to maintain over time due to changing land-use practices. 2. Integrate adaptive elements into the monitoring framework, allowing limited customization to regional conditions without compromising comparability. Incorporating remote sensing or automated monitoring tools could reduce costs and labor demands, making the protocol more scalable. 3. Stronger integration of socio-economic indicators—such as farmer engagement and management changes—would help link ecological outcomes more directly to decision-making processes within farmer clusters. ****** 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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. https://doi.org/10.1371/journal.pone.0345691.r002
Revision 1
26 Feb 2026 Author Response 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 >> We have made edits to meet the style requirements. 2. Thank you for stating the following financial disclosure: “This Project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 862731” 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. >> We have included the updated statement in our cover letter. 3. We note that you have referenced Nichols et al.” and “McHugh et al.” which has currently not yet been accepted for publication. Please remove this from your References and amend this to state in the body of your manuscript: “Nichols et al., unpublished” and “McHugh et al., unpublished” as detailed online in our guide for authors http://journals.plos.org/plosone/s/submission-guidelines#loc-reference-style >> These papers are now published, so the reference list and citations have been updated to include them correctly. 4. We note that Figures 1 and 2 in your submission contain map and 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(s) [#] to publish the content specifically under the CC BY 4.0 license. 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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/ >> Both figures have now been revised, and contain maps that do not require copyright statements, or that have been correctly cited and can be used. 5. We note that Figures 3 and s10 in your submission contain copyrighted images. 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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. >> We do not believe that any of the photographs used in Figure 3 are under any copyright laws. They were all take by project partner members and have been provided for use in this paper. If one of these has been highlighted as copyright, please tell us which one and where it is published, as we are unaware that they have been published elsewhere. 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General comments: This paper proposes a standardized protocol for monitoring farmland biodiversity in European Farmer Cluster landscapes. The protocol is designed to evaluate and unify methods for assessing biodiversity across different farming systems. It provides practical guidance on selecting survey squares and transects, as well as detailed procedures for surveying birds, pollinators, and vegetation. Comprising a suite of standardized sub-protocols, the framework is adaptable to diverse agricultural contexts. Finally, the authors evaluate the effectiveness of these biodiversity indicators and survey methods. This paper is of good scientific quality, thus may interest the readers of PLoS One. However, there are some aspects that could be improved for me. Therefore, I recommend this paper to have a major revision. After this major revision, the paper may contribute to the field. >> Thank you for your comments and providing suggestions for improvement. 2. Specific comments 1) Is it necessary to include some indicators of biodiversity pressures such as the annual application of pesticides, annual application of fertilizers, per capita annual net income of rural households and so on. These indicators could facilitate the subsequent analysis after biodiversity investigation. 2) Is it necessary to include some indicators of ecosystem services such as water purification, reducing pesticide needs and so on. 3) Some biodiversity indicators at landscape scale could be derived from satellite remote sensing data such as forest cover, productivity and so on. >> Thank you for your suggestions. We agree that other environmental pressures are highly important, and were indeed considered. However, they were considered separately, as part of the Farmer Cluster sustainability analysis, and Farmland Ecosystem Assessment Support Tool (FEAST), so were not included in this methods protocol directly. We have added this text to the discussion: L578-579: “Although other environmental indicators, services, and pressures were considered and are ecologically important…” L588-594: “Additionally, environmental pressures such as pesticide use, fertiliser applications, water quality, and area of semi-natural habitat are all important indicators that were considered through a separate FC sustainability analysis (48), and ecosystem service indicators along with habitat suitability metrics were considered through the Farmland Ecosystem Assessment Support Tool (FEAST; (103)). These could be combined alongside the biodiversity indicators suggested above, should the FC have the funding and resources to include them.” 4) This protocol aims to monitor biodiversity of farm cluster. The pro >> I emailed the editor to ask if the reviewer could send the full comment – I received the following text from the editor: “The reviewer's comments are as follows: The purpose of this protocol is to monitor biodiversity within farm clusters. It encompasses multiple taxon-specific subprotocols (e.g., for birds, insect pollinators, and vegetation). The current descriptions can be made more concise by increasing cross-references to these individual subprotocols.” In response to this, we are struggling to see how the descriptions could be made more concise by cross-referencing. What the referee is proposing is unclear, and in the absence of an example, we don’t feel we can address this. 5) I suggest to compare this protocol with similar protocols in discussion mentioned in the paper like biodiversity indicators for organic and low-input farming systems (BioBio), Farm4Bio, and European Monitoring of Biodiversity in Agricultural Landscapes. >> We have now added references of similar projects throughout the discussion, highlighting similarities and differences between our methods. Some examples: L450-454: “The European Farmland Bird Indicator (EFBI) was created by Gregory et al. (51), and since then it has been used to predict that multiple European countries would witness a decline in farmland bird species in response to agricultural land-use change (52), making farmland birds a significant landscape-scale biodiversity indicator to monitor, hence their inclusion in many similar projects (16,24,25).” L466-477: “Similar transect line surveys are already conducted as part of national bird census initiatives across Europe (56–58), with the data often used in large-scale biodiversity monitoring projects (20) and collated through the Pan-European Common Bird Monitoring Scheme, hence this method was chosen to be implemented in the FCs. However, some landscape-scale projects opt for different methods, such as “area searching” (mapping all birds that were seen or heard; (25)) or point counts, the latter with the potential to be used in place of transect walk. For example, the Zeeasterweg, Lelystad FC in the Netherlands conducted a point count for each transect/survey square to align more closely with their country’s national monitoring scheme (59). Additionally, the Bass-Durance FC in France began their breeding bird surveys earlier than the protocol specified to capture migratory species Attachments Attachment Submitted filename: Response_to_Reviewers_auresp_1.docx https://doi.org/10.1371/journal.pone.0345691.r003
9 Mar 2026 Decision Letter - RunGuo Zang, Editor A standardised protocol for measuring farmland biodiversity outcomes across European Farmer Cluster landscapes PONE-D-25-36303R1 Dear Dr. Nichols, 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, RunGuo Zang Academic Editor PLOS One Additional Editor Comments (optional): accept Reviewers' comments: https://doi.org/10.1371/journal.pone.0345691.r004
Formally Accepted
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