From Anaerobic Digestion of Organic Waste to Soil: Digestate-Centered Inverse Engineering for Agroecosystem Sustainability

Anaerobic digestion offers promising solutions for both energy transition and sustainable soil management. By placing digestates at the heart of an inverse engineering approach, we aim to optimize process chains and balance energy production with the agronomic value of organic residues.

The anaerobic digestion sector is rapidly expanding in Europe and France, producing renewable biogas and nutrient-rich digestate for land application. This practice supports the recycling of organic matter and reduces reliance on mineral fertilizers. However, it can also generate environmental impacts, particularly through greenhouse gas emissions and contaminant transfers resulting from the agronomical use of digestates. Moreover, a mismatch can sometimes occur between the fertility needs of soils and crops and the actual quality of the digestates produced. Indeed, using anaerobic digestion as a tool for both energy and agroecological transitions requires a systemic optimization of the entire pathway. It is essential to consider both the transformation of organic matter into methane and the fate of digestates within agroecosystems. Digestates thus represent the intersection between the energy recovery process and the environmental performance of the resulting products in soils.
Our strategy focuses on placing digestates at the heart of the study and relying on an inverse engineering approach (Figure 1). By starting from the needs associated with the services provided by digestates, we aim to design and optimize the digestion pathway while managing compromises between energy production and agronomic valorization under environmental and sanitary constraints.

Figure 1 : Reverse Engeneering concept applied on Anaerobic Digestion Treatment chain
Given the diversity of feedstocks, management practices, and process conditions, evaluating the services provided and the associated impacts—and balancing these multiple objectives—remains challenging.

Our research focuses on identifying key action levers (feedstocks, process, post-treatments) to manage digestate quality, developing robust indicators for its assessment, understanding their influence on digestate behavior in agroecosystems (Figure 2), and implementing multiobjective optimization strategies to design sustainable anaerobic digestion pathways (Figure 3).

 Figure 2 : Matter and organic matter characterization-based indicators to explain the variability of digestates and feedstocks and understand the organic matter fate

 Figure 3 : Towards a plant-wide modelling approach based on organic matter indicators for multiobjective optimization

Publications and developed tools

Web site : digestate effects on agroecosystems
https://fertiliser-avec-des-digestats.fr/
Prediction tool :
https://shiny.biosp.inrae.fr/app/concept-dig).

Pérémé et al. (2025) https://doi.org/10.1016/j.biortech.2025.132369
Pérémé et al. (2023) https://doi.org/10.1016/j.wasman.2023.01.015
Fernandez-Dominguez et al. (2024), https://dx.doi.org/10.1007/s12649-023-02197-2
Fernandez-Dominguez et al. (2024), https://doi.org/10.1016/j.wasman.2024.03.031
Fernandez-Dominguez et al. (2023),  https://doi.org/10.1016/j.scitotenv.2023.162882
Fernandez-Dominguez et al. (2022), https://dx.doi.org/10.1007/s11157-022-09623-2
Zennaro et al. (2022), https://dx.doi.org/10.1016/j.jenvman.2022.115393  
Fernandez-Dominguez et al. (2021), https://doi.org/10.1016/j.wasman.2021.10.004
Jimenez et al. (2020), https://dx.doi.org/10.1016/j.wasman.2020.07.052
Guilayn et al. (2020), https://dx.doi.org/10.1007/s11157-020-09531-3
Guilayn et al., (2020), https://dx.doi.org/10.1016/j.wasman.2020.01.025
Guilayn et al. (2019), https://doi.org/10.1016/j.wasman.2019.01.032