Research topics & Projects

Research topics & Projects

The Unit's projects fall into two application areas:

Biomolecules & Biomaterials: How to design and produce biomolecules & biomaterials?

Agrosystems and the environment: How can biomass be mobilised and managed to ensure the closure of biogeochemical cycles?

They are organised into 3 Themes:

Theme 1 - Biomass properties: What are the properties of plant biomass and biobased products?

Theme 2 - Process/process efficiency: How efficient are plant biomass transformation processes?

Theme 3 - Modelling transformations: What models and digital tools are needed to understand and predict plant biomass transformations and the associated impacts?

The projects below are classified by type of funder, with the FARE correspondents for each project.

France 2030 - PEPR

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Carbon in continental ecosystems: levers and trajectories for carbon neutrality


The Priority Research Programmes and Equipments (PEPR) FairCarboN aims to bring together the entire French scientific community studying carbon in continental ecosystems. FairCarboN will help to determine the possible contribution of continental ecosystems to climate change mitigation.

FARE contributes to two targeted FairCarboN projects (ALAMOD and SLAM-B) and leads a laureate project (CANETE) from the first open call for projects (2023) of FairCarboN.



Contact FARE : Gwenaëlle LASHERMES



Towards carbon dynamics models in ecosystems validated on a key benchmark tool

ALAMOD will capitalize on the data produced and the know-how of several research infrastructures that will be heavily involved in the project. It will also mobilize the French community and partners notably in Southern countries that use and develop simulation models of C stock evolution in terrestrial ecosystems. The realization of this federative project will allow the provision of an unprecedented tool for the evaluation of models and of very powerful models, which will guarantee ALAMOD to have very strong impacts in the academic field and beyond.



Co-coordinator : Bernard KUREK


Scénarios labs pour concevoir et évaluer les trajectoires de bioéconomie des territoires vers la neutralité carbone

The SLAM-B project aims to structure the French research community working on IAM (Integrated Assessment and Modelling) approaches to support the development of a sustainable bioeconomy based on agroecology. SLAM-B will consider various components of the bioeconomy and has three main scientific objectives: (i) develop generic IAM approaches to simulate a variety of transitions towards sustainable bioeconomy systems and anticipate their consequences, (ii) validate these IAM approaches through their application within prospective Scenario Labs and, (iii) produce knowledge for public decision-makers at national and European levels.



Coordinator : Gwenaëlle LASHERMES


Efficiency of microbial use of soil carbon and nutrients in human-managed terrestrial ecosystems

The CANETE project aims to assess and predict the physiological responses of microbes to agricultural and forest management practices in different pedoclimatic contexts, with particular focus on the consequences for the coupling/decoupling of C and nutrients (N and P) and the impacts on C and nutrient storage in soil, the nutrient supply to plants, and plant production. The project will identify the ways in which soil microbial communities can be more effectively managed to promote the efficient use of C and nutrients in terrestrial ecosystems. The project will generate open data and model frameworks for simulation of the main microbial mechanisms involved, and will produce improved tools and methodology for projections of C and N stocks.


Biomass, biotechnologies, green chemistry and renewable energy technologies2023-2029

The B-BEST PEPR (Biomass, biotechnologies, technologies for green chemistry and renewable energies) is being developed from 2023 to 2029 with a budget of €70 million, and is co-directed by IFPEN and INRAE. Its aim is to bring together the scientific community to lay the foundations for the technical, organisational and social innovations that will make it possible to understand and activate the levers for the efficient transformation of biomass to produce bio-based products and sustainable fuels.



Contact FARE :  Gabriel PAËS


Approach combining analytical tools and machine learning to identify markers and predict bioMass reactivity in enzymatic hydrolysis.

The aim of the project is to combine the skills of experts in the fields of data analysis and science to identify markers of enzymatic hydrolysis reactivity and propose a model for predicting the reactivity of lignocellulosic biomass of various origins.



Contact FARE :  Gabriel PAËS


An operational website for the production of biobased products

The aim of this project is to provide generic and shared tools and resources for designing, executing and monitoring the projects of the PEPR B-BEST axes. To this end, a centralised website will provide software tools as well as computing and storage resources.



Coordinator : Gabriel PAËS


Biomass at all scales to understand its properties

The aim of the project is to develop multi-scale approaches, for representative biomass species, in order to establish relationships between scales and highlight markers of biomass properties and reactivity.



Contacts FARE : Sofiène ABDELLAOUI & Ludovic BESAURY


Optimisation of the metabolic network of the electrochemically assisted MICrobiale community for the biorefinery of organic waste

The aim of the ElectroMIC project is to develop a bioelectrochemical device using microorganisms capable of converting the organic matter present in wastewater and agricultural by-products into high added-value molecules.

European Projects




Zero Waste Ligno-Cellulosic Bio-Refineries

Contact : Bernard KUREK

2016         -       2022The ZELCOR project aims to demonstrate the feasibility of converting recalcitrant lignocellulosic residues from biorefineries into high value-added bioproducts. The project concept is to combine chemical and enzymatic catalysis with insect-based bioconversion. It covers three types of recalcitrant materials: lignocellulose from ethanol production, lignins dissolved during the pulping process and humins formed by sugar conversion. A transversal platform will be set up to identify bioproducts of commercial interest among multifunctional nanoparticles, phenolic antioxidants, chitosans of entomological origin and aromatic intermediates. It will improve our knowledge of the structure-function relationships and mechanisms involved in the catalytic depolymerisation and bioconversion of recalcitrant residues.

Improved estimation and mitigation of nitrous oxide emissions and soil carbon storage from crop residues

Contacts :
Sylvie RECOUS,

2017         -       2021Crop residues provide significant inputs of carbon (C) and nitrogen (N) to soils and contribute to the net GHG balance of soils. N2O emissions from crop residues vary considerably depending on the quality of the residues, their management and the soils and climate. This situation is currently not reflected in the methodology of national emission inventories. The European ResidueGas project (co-fund FACCE ERA-GAS call) will propose an improved methodology for quantifying N2O emissions from the management of agricultural crop residues, for a wide range of crops, taking into account their biochemical composition and their management in the field, for a diversity of soils and climate in Northern Europe. The project is based on the collection of published data, laboratory and field experiments, and modelling. ResidueGas will also propose improved crop residue management practices to improve their net GHG balance.

Carnot Projects

Logo 3BCAR






Engineering microbial consortia in microfluidic droplet bioreactors

Contact : Véronique AGUIE-BEGHIN


Microbial communities (or microbial consortia) play a key role in most fundamental biogeochemical processes. But, surprisingly, their application to biotechnological processes is limited because most biotechnological conversions have favoured single-strain approaches. In this context, the aim of the Eco-Drop project, coordinated by TBI in collaboration with TWB Toulouse and FARE, is to develop a new approach for building simplified microbial consortia that efficiently perform complex functions, instead of using monocultures, and to develop new cell factories.


Optimised extraction of anthocyanins from distillers' ground and improvement of their functionality as colour agents and antioxidants

Contact : Caroline Rémond


The ColorANTH project aims to develop a process for extracting anthocyanins from grape marc by combining microwaves and the use of enzymes. One of the objectives will be to enzymatically modulate the composition and structure of anthocyanins to increase their stability and properties. The spin-offs of the ColorANTH project will be both fundamental (better knowledge of the mechanism of extraction of anthocyanins from grape marc and their structure-properties relationships) and technological (development of a process combining microwaves and enzymes for the extraction of anthocyanins and development of a biocatalytic process for the functionalization of anthocyanins).

National Research Agency Projects




Design of moLecular AssemBliEs to assess gLycosylation role on hemicellulases activity

Contact: Véronique AGUIE-BEGHIN

2023-2026LABEL project aims to tackle the unexplored question of substrate targeting by post-translational glycosylation of enzymes. LABEL will devise solutions to overcome the experimental challenges and perform experiments to investigate the targeting function. Through this proposal at the interface of enzyme engineering and bioorthogonal chemistry applied to biomass active hemicellulases, we propose an innovative and original approach to generate trackable post-translational modified proteins to provide functional tools required to understand complex biological systems, such as enzymatic biomass deconstruction.

Lignin VALorization by BIO-ELECtro-refinery

Contact :Sofiène ABDELLAOUI

2022-2025The VALBIOELEC (Lignin VALorizations by BIO-ELECtro-refinery) project aims to overcome some  limitations constraining lignin valorizations through the design and development of bio-electrochemical reactors operating with redox ligninolytic enzymes combined with electrodes. These systems will allow the coupling of enzymatic and electrochemical redox reactions through heterogeneous electron transfers. This coupling will catalyze both the depolymerization and the refining of lignins in order to release homogeneous aromatic molecules. In addition, these reactors will operate as enzymatic fuel cells capable of producing electrical energy. This project will be carried out in collaboration with Michigan State University and the Fungal Biodiversity and Biotechnology Laboratory of Marseille.

Multiscale Analysis and Spatio-temporal Modelling of Deconstruction of Lignocellulosic Biomass

Contact : Yassin REFAHI


2020-2023The conversion of lignocellulose into products such as biofuels and bio-based molecules can be a solution to concerns over growing energy demand and contribute to climate change mitigation. However, lignocellulosic biomass (LB) is naturally recalcitrant to enzymatic deconstruction. Extensive research for understanding the parameters underlying LB recalcitrance has led to the identification of several chemical and physical parameters which not universal and are specific to LB species and/or pretreatment type. Goal of BIOMOD project is to develop an original combination of confocal time-lapse imaging of LB samples during enzymatic hydrolysis, 4D (space + time) image processing, and spatio-temporal modelling to identify universal key structural parameters at cellular and tissular scales correlated with hydrolysis yield.

Proof of concept for the functionalization of lignins by applying laccase-deshydrogenase enzymatic treatments in biobased materials applications

Contact : Véronique AGUIE-BEGHIN


2020-2023FuncLIPRO project aims to increase our knowledge of lignin-degrading enzymes (LDEs) and the mechanism of lignin deconstruction and modification. It also aims to provide proof of concept for the use of LDEs to transform these lignins into green adhesives, protective films and new agro-sourced composites.

Nanoscale investigations of water effects on wood S2 layer and wood-inspired polymeric nano-systems, combining MD and advanced experiments

Contact : Brigitte CHABBERT

2019- 2022The aim of this project is to understand the hygromechanical behavior of moisture-sensitive materials like cellulose-based materials. We use wood as the base natural model and synthetize different wood polymer systems, in order to quantify the physical impact of micro-climatic conditions. We probe the systems systematically, combining experimental characterization and atomistic modeling, and pioneering a meticulous match of the scales of the experimental and in-silico investigations


Grand-Est Region, Feder, Fondation Paris-Reims, URCA Projects




Manufacture of bio-based multifunctional materials using ternary mixtures

Doctoral student : Bao Anh HUYNH

Supervisors: Trystan Domenech; Françoise Berzin


This project aims to develop biobased multifunctional materials using a ternary blending approach, where nano to macro-sized lignocellulosic particles are dispersed in thermoplastic polymers using melt blending processes. The strategy envisaged includes ternary blends of two immiscible polymers with colloidal particles, as well as ternary blends of two types of particles in a single polymer matrix.
The research will be carried out within the framework of the FAREMAT chair, recently awarded to the University of Reims Champagne-Ardenne to develop its activity in the field of low environmental impact biomaterials.


Multi-scale Modelling of Lignocellulosic Biomass Deconstruction

PhD Student : Solmaz HOSSEIN              

Supervisors : Yassin REFAHI and Gabriel PAËS

2022-2025The project initially aims to develop a pipeline of computational tools to extract the dynamics of the voxel intensity (volumetric pixel) representing the enzymatic deconstruction of lignocellulosic biomass. The extracted values will then be used to estimate the parameters of a spatialized hierarchical kinetic model. A correlation analysis between the temporal evolution of voxel intensities and cell wall composition will allow to propose hypotheses on the mechanisms underlying the recalcitrance of lignocellulose. The genericity of the proposed hypotheses and the model predictions will be studied on different biomass species.

Spatialization and dynamics of the physical and chemical properties of crop residues by airborne imaging.

PhD Student : Noémie Lafouge                           Supervisors : Sylvie RECOUS and Brigitte CHABBERT

2019-2022The RESAERO project aims to explore and compare methods for measuring the physico-chemical characteristics of biomasses and the rate of soil cover by these biomasses, by airborne imagery in the field. Three spectral domains associated with different spatial resolutions are explored in semi-controlled and field conditions.  Collaboration INRAE, CReSTIC, TERRALAB

CARActerisation by Electrochemical Methods of Bacterial Ligninolytic Enzymes and their implementation in the valorisation of lignocellulosic biomass

PhD Student : Issa Fall                                 Supervisor : Harivoni Rakotoarivonina

2019-2022The main objective of this thesis is to develop an efficient enzymatic process to release aromatic molecules from lignins. The adapted strategy is to produce thermostable bacterial enzymes, to thoroughly characterise the properties of these enzymes (by electrochemical methods in the presence of aromatic molecules or biomimetic membranes of lignins) to determine their potentialities, and finally to implement the identified and characterised enzymes in the presence of lignins and to evaluate the released aromatic molecules.

Study of the production of natural smicrobial pigments during the fractionation of lignocellulosic biomass

PhD Student : Matthieu Cassarini                      Supervisors :  Ludovic Besaury and Caroline Rémond 

2019-2022Natural microbial pigments have many advantages compared to synthetic pigments of petrochemical origin (low environmental impact of their production, non-toxicity). Pigments are widely used in the medical and cosmetic sectors, as bio-indicators of pollution or as anti-microbial agents.)  The use of lignocellulosic biomasses is of interest for the microbial production of microbial metabolites such as pigments. The aim of the thesis project is to develop innovative white biotechnology approaches to produce pigments of interest by growth on lignocellulosic substrates.

Other projects


Collect and valorization “open science” of data of organic resources recycled in soil

Contact : Gwenaëlle LASHERMES

2018-2022...Efforts have been made over the last 30 years to study the soil organic matter decomposition process. The COLLECT-OR project aims at capitalizing, organizing and sharing as "open data" the data that INRAE scientists agree to share. The COLLECT-OR project brings together scientists from the FARE, Agroécologie, BioEcoAgro, Eco&Sols, SAS, EcoSys, ISPA, UREP at INRAE and CIRAD (Recycling and Risk) laboratories for their data, and the VSoil modeling platform (EMMAH). This project will make it possible the data meta-analysis, the calibration of numerical tools or the acquisition of references easily mobilized and opened to all.

Modification date : 15 April 2024 | Publication date : 24 April 2013 | Redactor : V. Aguié-Béghin