Impacts of anaerobic digestion on biodiversity and ecosystem services - State of play and levers to better take them into account

Synthesis

Disclaimer: The content of this publication is based on the state of knowledge and the regulatory framework in force at the time of publication of the documents.

Context and objectives of the study

In response to energy challenges, methanisation offers a solution for producing renewable energy from organic matter and bio-waste. In France, there will be more than 1,600 methanisation plants by 2023, producing electricity via cogeneration or biomethane by injecting it into natural gas networks. 

In the average French input mix, agricultural inputs currently account for the majority of biogas plant supplies, at 76% of used substrates, with livestock manure as the main resource (ADEME, PRODDige 1 and 2 projects). With the sector's shift towards injection-type methanisation units and the ambitions for green gas production by 2030 and 2050, the input mix is undergoing significant change and is turning mainly towards the use of intermediate crops for energy purposes (CIVE). The installation of methanisation units in different regions generally results in agricultural changes ranging from the adaptation of practices to the transformation of cropping systems. These changes can have an impact on biodiversity and ecosystem services, which need to be assessed and monitored over time. 

The aim of this study is to assess the impact of these practices based on an in-depth analysis of the scientific and technical literature available as of 1 August 2025. The study also proposes to establish a selection of indicators that will enable changes in pressures on agricultural biodiversity in connection with the installation of a methanisation unit to be reported. These indicators will be integrated into a simplified diagnostic tool that will enable stakeholders in the sector to better adapt methanisation projects and associated agricultural practices for the balanced and sustainable development of French methanisation.

Methodology and results

Methodology

In order to identify and analyse the available scientific knowledge, a literature review was conducted following the main steps of systematic review methods. This simplified approach was chosen in view of the time allocated to the study in the call for projects and in relation to the resources and time required to conduct this type of review. The literature review is based on structured research, founded on explicit criteria. It has the advantage of minimising selection bias while ensuring transparency and reproducibility (Koutsos, Menexes and Dordas, 2019). This review is based on the method proposed by Mengist, Soromessa and Legese (2020), which is based on the PSALSAR methodological framework (see Figure 1), which will be detailed in the following sections.

Figure 1: PSALSAR framework used and adapted as the overall methodology for the study (Record, 2025)

The figure below shows the overall approach to selecting indicators and the link with the bibliometric and bibliographic analyses conducted previously.

Figure 2: General approach guiding the selection of indicators (Record, 2025)

Initially, bibliometric analysis was used to identify the main ‘populations’ studied in relation to the impact of methanisation. The bibliographic analysis complements this initial analysis by identifying more precisely the sources of these impacts and the associated risk practices. The objective is therefore to propose indicators covering all the main impacts of methanisation on biodiversity with a view to managing these impacts, and thus focusing on promoting favourable practices or reducing the risk practices identified in the bibliographic analysis.

To this end, we focus the selection of indicators on ‘Pressures’ indicators as described in the DSPIR (Driving Forces, Pressures, States, Impacts, Responses) model, as illustrated in Figure3.

Figure 3: DPSIR model and choice of indicator type used in the study (adapted from European Environment Agency, 1999)

The advantage of pressure indicators is that they are good proxies for impacts on biodiversity and ecosystem services, while remaining operational and easier to deploy than monitoring state indicators. In addition, they enable the various stakeholders to easily identify the practices to be implemented in order to reduce their impacts.

Finally, an analysis grid was constructed in order to select the most relevant indicators for the sector. This grid is based on the work carried out by Van Oudenhoven et al., 2018, which was then incorporated into the work of Casdar APPRIVOISE (Appropriating biodiversity indicators in relation to expected ecosystem services, 2023-2027). The analysis framework is based on four main categories for analysing the indicators:

• Credibility (shared by scientists and experts, quantifiable, valid representation of phenomena).
• Relevance (assesses changes over time, valid at multiple scales and transferable, meets needs). 
• Feasibility (accessibility of tonnes, availability of target audience, cost of accessing data/indicators). 
• Legitimacy (broad acceptance by legislative actors, particularly in relation to the regulations studied, or by economic actors).

Results

The study led to the selection of the 12 indicators presented in the figure below. These indicators measure pressures on biodiversity rather than direct impacts on biodiversity. Each indicator has been linked to one of the four major pressures on biodiversity defined by IPBES and identified in the literature review: land use change, climate change, resource exploitation and pollution. The set of indicators proposed here was designed to cover, in chronological order, all practices presenting risks, as identified in the literature review: (i) crop rotation and intercropping; (ii) use of inputs; (iii) feeding substrates to the methanisation unit; (iv) production of biogas and digestate; and (v) recovery of digestate. Furthermore, it has been designed so as not to be limited to negative impacts alone.

Figure 4: Selected indicators and links between key drivers of biodiversity pressures and agricultural practices (Record, 2025)

Farmers and biogas plant managers each have at least one indicator related to each pressure factor. It is important to note that some of these indicators are actually cross-cutting and relate to several pressure factors simultaneously. The use of mineral nitrogen, for example, is both a source of pollution for aquatic environments and a source of greenhouse gas emissions contributing to climate change. Similarly, the factor ‘Land use change’ is very often intertwined with other pressures, even though, for the sake of clarity, it is associated with a single colour in the figure above. This is particularly the case for the indicator on soy imports, which, beyond land use change through deforestation, is intrinsically linked to climate change and pollution. 

The development of the calculator was guided by the objective of limiting the amount of data to be entered, both for unit managers and farmers, while ensuring the production of operational indicators. The models are not intended to determine which type of anaerobic digestion unit would have the least impact, nor do they reflect the diversity of real-life anaerobic digestion situations. Consequently, these results cannot be extrapolated. For managers, the impact of methanisation units depends heavily on the composition of the feed used, while for farmers, the situation before and after methanisation is based on numerous assumptions about farming practices and crop rotation.

The tool is structured with:

- A ‘User Guide’ tab that presents the tool's objectives, its architecture and the data entry procedures for both stakeholders.

- Two data entry tabs:

• A ‘Manager’ tab: this is used to collect and organise the data needed to calculate indicators relating to the pressure exerted on biodiversity by the anaerobic digestion unit.
• A ‘Farmer’ tab: this spreadsheet is specially designed for farmers involved in the operation of a methanisation unit by providing inputs and/or receiving digestate. It is used to collect and organise the data needed to calculate indicators relating to the pressures exerted on biodiversity according to agricultural practices.

- A ‘Results’ tab: this spreadsheet lists all the indicator results, whether they are intended for farmers or biogas plant managers. Each indicator is accompanied by a note specifying the actor primarily concerned by the result, whether a farmer or a manager, and a note concerning the type of indicator: annual or progressive. 

• Annual indicator: this type of indicator provides an overview of results over a one-year period. It mainly concerns managers. 
• Progressive indicator: this type of indicator shows changes in practices over time by comparing practices before and after methanisation. It concerns farmers exclusively.

- ‘References’ tabs that ensure overall functionality. These contain references needed to calculate indicators, databases and lists. These tabs are hidden and cannot be modified by the user. In order to analyse and isolate as much as possible the impact of methanisation on farms, a comparative approach between a ‘pre-methanisation’ reference year and a ‘post-methanisation’ reference year was chosen to calculate most of the indicators, as was done in the MéthaLAE project (op. cit.). It is therefore necessary to choose a reference situation as close as possible to the year in which the cropping system was modified before the arrival of methanisation, but to exclude exceptional years that are not representative of the cropping system. Similarly, for the reference year after methanisation, it is important to choose the most recent year possible that is representative. For indicators targeting managers, there is no comparison before/after the methanisation project, but comparisons are made with the results of other units. 

Analysis

It is difficult to establish a direct and unambiguous causal link between an agricultural practice, monitored by one of the 12 indicators, and the status of a particular taxon. Most agricultural practices exert diffuse pressures that affect all components of biodiversity. On the other hand, the links between these same indicators and ecosystem services, such as soil fertility or climate regulation, are clearer and are shown in the table below. This table shows that all the ecosystem services in the study are covered by the indicators and that each of the actors has several indicators for each category of ecosystem service.

Table 1: Synthesis of ecosystem services addressed by the selected set of pressure indicators on biodiversity (Record, 2025)

Dark blue: indicators targeting farmers - Light blue: indicators targeting anaerobic digestion plant managers

Important note: As the results are based on modelling hypothetical cases, they cannot be extrapolated and interpreted for every anaerobic digestion plant. However, certain observations can be described as follows.

Conclusion and perspectives

Conclusion

The legislative and regulatory framework relating to biodiversity has been significantly strengthened over the last five years, in line with the ambitions of the European Green Deal. Despite a marked ecological backlash in 2024-2025, which is pushing for a simplification of these regulatory requirements (e.g. omnibus law), the momentum for sustainability is still having a long-term impact on all agricultural and energy sectors. The methanisation sector in particular is increasingly being questioned about its impact on biodiversity and the ecosystem services provided by agricultural systems. In this context, players in the methanisation sector will be required to report on these impacts, whether negative or positive, and to adapt their practices accordingly.

An analysis of the main regulatory texts relating to biodiversity has identified the key issues that need to be addressed by the anaerobic digestion sector in order to anticipate possible future changes to the regulatory framework and reduce transition risks by adapting today. One of the priority areas is reducing the pressure on biodiversity exerted by agricultural production and biomass production in particular. Limiting land use change through the introduction of ZAN (Zero Net Land Take) in different regions will also have an impact on the construction of new anaerobic digesters in the coming years. This regulatory analysis has confirmed the four main factors of pressure on biodiversity that need to be addressed by the sector – land use change, climate change, resource exploitation and pollution – in order to align with the ambitions of current public policies (most of which are non-binding) and respond to potential coercive measures in the future.

The state of the art in the literature on this subject confirms the need for further long-term scientific studies, under real spreading digestat conditions and on certain taxa, particularly earthworms and nematodes. The results presented vary and depend on the type of soil and digestate, encouraging further long-term experimentation that would also take into account agricultural practices related to the implementation of a methanisation unit.

A panel of 12 pressure indicators was selected to report on the effects of changes in practices on these pressures before and after the installation of a methanisation unit. These indicators were selected according to a set of specific criteria such as credibility, relevance, feasibility and legitimacy.

Modelling these indicators in a simplified diagnostic tool (Excel) applied to hypothetical cases of anaerobic digestion units (cogeneration, on-farm injection and regional injection). It should be noted that these indicators were calculated on the basis of average data and modelling assumptions for each case. The results obtained cannot under any circumstances be extrapolated and interpreted for each anaerobic digestion case. Nevertheless, the development of this diagnostic tool offers interesting prospects, which are presented on the following page.

Perspectives

The tool developed is operational with a simplified user interface. However, the results obtained are not yet usable without application to real-life methanisation cases. It would be possible to continue developing this tool by deploying it across a pool of methanisation plants representative of the sector in France. In this case, a more in-depth analysis would make it possible to assess the sensitivity of each indicator to changes in practice. This is essential if the tool is to become a decision-making aid that enables farmers or managers to adapt their practices in line with changing pressures on biodiversity.

In the case of a larger-scale deployment, it would be possible to analyse, interpret and draw sufficiently reliable conclusions about each type of biogas plant by specifying the tool's scope of applicability and the uncertainty associated with each indicator. The accumulation of data obtained through these assessments would make it possible to specify impact thresholds for each indicator in order to assess the level of impact on biodiversity. This would not only enable the sector to acquire objective knowledge of its overall impacts, but also provide local stakeholders with diagnostic tools to adjust their practices and optimise the co-benefits between renewable energy production and ecosystem preservation.

This tool also aims to raise awareness among farmers/managers from the design stage of the anaerobic digestion project by modelling the potential impacts of the project according to the changes in practices envisaged. To this end, it would be useful to collect user feedback during its deployment and ensure a process of continuous improvement of the tool.

The assumptions validated in the indicator calculation methods can be clarified, and it would be possible to take new criteria into account in each indicator (see identified areas for improvement) to further increase the robustness of the scientific approach while maintaining a pragmatic approach that is easy for farmers/managers to use.