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[hal-05802715] Microscale Morphometric Dynamics as Predictive Biomarkers of Plant Cell Wall Hydrolysis Yield
Efficient conversion of lignocellulosic biomass into fermentable sugars remains a bottleneck for sustainable biorefineries due to the recalcitrance of plant cell walls. Predicting sugar conversion yields during enzymatic hydrolysis remains challenging due to complexity of mechanisms underlying hydrolysis and labor-intensive conventional analyses. We used fluorescence confocal microscopy to image spruce (Picea abies) wood cell walls throughout enzymatic hydrolysis. We developed an innovative 4D (3D + time) image analysis pipeline that quantifies cell wall autofluorescence intensity and morphological descriptors from the collected images. The pipeline includes an adaptive drift compensation strategy that adjusts dynamically to the extent of deconstruction. Subsequently, enzyme-driven autofluorescence intensity dynamics together with dynamics of cell wall volume and accessible surface area were computed. In parallel, dynamics of conversion yields of monosaccharides were measured. A correlation analysis revealed strong negative correlations between conversion yields and both the dynamics of autofluorescence intensity and morphological descriptors. Phase-specific analysis uncovered distinct correlation patterns dependent on hydrolysis stage and sugar type. In addition, the results revealed distinct dynamics of cell wall volume and surface area, demonstrating an asynchronous structural response to hydrolysis with volume reduction preceding surface area reduction. Consequently, for the first time we are able to quantify the cell wall structural erosion during hydrolysis. Taken together, the results established morphological descriptors and autofluorescence intensity as real-time biomarkers for predicting sugar release, offering a robust alternative to conventional assays. The approach offers substantial potential to accelerate the optimization of biotechnological strategies for efficient biomass conversion by selecting enzymes specific to deconstruction targets.
ano.nymous@ccsd.cnrs.fr.invalid (Yassin Refahi) 16 Oct 2026
https://hal.science/hal-05802715v1
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[hal-05802701] BioModLab: an integrated software platform for investigating and modelling plant cell wall enzymatic deconstruction
Utilising abundant biopolymers embedded in plant cell walls to produce bioproducts can form a cornerstone of sustainable bioeconomy and help reduce our reliance on fossil-derived carbon. However, an economically viable biotechnological conversion of plant cell walls requires a deeper knowledge of enzymatic deconstruction to successfully address cell wall recalcitrance to enhance biorefinery process competitiveness. Innovative tools are essential for deciphering the underlying complex mechanisms of enzymatic hydrolysis. In this context, we have developed BioModLab, a software platform that integrates cutting-edge image-processing algorithms and mathematical modeling to investigate enzymatic cell wall deconstruction. We have also addressed the computational challenges associated with timelapse image processing by devising versatile 4D image-analysis algorithms that track cell walls during enzymatic hydrolysis and generate virtual 4D representations of cell wall deconstruction. In parallel, we have developed mechanistic mathematical models of the enzymatic hydrolysis that incorporate key phenomena such as enzyme adsorption, product inhibition, and other enzyme-substrate interactions, and that faithfully reproduce experimentally measured saccharification. By unifying virtual datasets, computational models, advanced image-processing algorithms, and high-performance visualization together with a user-friendly graphical interface, BioModLab enables researchers to efficiently process, analyze, and interpret new experimental datasets. Overall, BioModLab offers an integrative software platform that combines state-of-the-art image-processing algorithms with mechanistic mathematical models, facilitating in-depth investigation of cell wall deconstruction and supporting the development of innovative strategies to optimize plant cell wall conversion.
ano.nymous@ccsd.cnrs.fr.invalid (Yassin Refahi) 16 Oct 2026
https://hal.science/hal-05802701v1
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[hal-05788702] Time Matters More than Cryoprotectants: Storage Duration Selects for Dormancy-Competent Lineages in Cathodic Microbiomes
Microbial electrosynthesis (MES) converts CO₂ into acetate using electroactive microbial communities. Optimizing these communities is important for industrial application. However, little is known about how to preserve and reactivate these complex communities over time. This study investigated how storage duration and preservation strategy affect the reactivation, electrochemical performance, microbial composition, and functional potential of electrosynthetic cathodic communities. Cathodic communities were first enriched in three-chamber bioelectrochemical reactors for 44 days. The biomass was then preserved using three approaches: (i) freezing without cryoprotectant at −80°C, (ii) freezing with glycerol at −80°C, and (iii) lyophilization with a maltodextrin–trehalose stabilizer, with the dried material stored at room temperature in sealed containers. These preservation strategies were adapted from standardized protocols developed for the conservation of complex microbial communities, such as those used for stool samples in fecal microbiota transplantation studies (Burz et al., 2019; Cammarota et al., 2017). Communities were stored for 39 days or 174 days before reactivation. Reactors were then operated for 85–90 days under identical conditions. Current density, carboxylate production, and coulombic efficiency were measured. Microbial structure and activity were analyzed using 16S rRNA gene sequencing on DNA and cDNA. In addition, metagenome-assembled genomes (MAGs) were reconstructed and functionally annotated to assess metabolic potential. Storage duration had a strong impact on performance. After 39 days, mean current density was about 2.8 times higher than after 174 days. Acetate concentration reached 6.1 ± 1.3 g·L⁻¹ after 39 days of storage, but only 1.8 ± 0.9 g·L⁻¹ after 174 days. Coulombic efficiency averaged 75% after short-term storage and decreased to 43% after long-term storage. Preservation method had a limited effect and mainly influenced short-term recovery. Short-term storage favored the dominance of Acetobacterium, which strongly correlated with acetate production. After long-term storage, Acetobacterium nearly disappeared. Communities became more taxonomically diverse and enriched in alternative acetogens such as Sporomusa and poorly classified taxa. Multivariate and differential analyses confirmed that storage duration was the main factor shaping community structure. Functional analysis of MAGs supported these results and showed a shift from a specialized electroacetogenic potential toward a broader and less targeted metabolic profile after prolonged storage. Unexpectedly, storage duration emerged as the main driver of functional and ecological changes in electrosynthetic cathodic communities. Even though preservation was performed under conditions generally considered highly protective for microbial communities (e.g., storage at −80 °C), prolonged storage still led to a marked decline in electroacetogenic performance and to significant shifts in community structure and metabolic potential. While short-term storage largely preserved the electroacetogenic specialization of the community, long-term storage resulted in reduced performance and a functional diversification of the community. Preservation methods adapted from complex microbiota conservation protocols therefore improve short-term stability but do not fully prevent long-term functional drift. These findings highlight the unexpected sensitivity of electrosynthetic communities to storage duration and provide important insights for the development of reliable inoculum banks for microbial electrosynthesis.
ano.nymous@ccsd.cnrs.fr.invalid (Louise Rigaud) 09 Oct 2026
https://hal.science/hal-05788702v1
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[hal-05788677] Hypersaline microbial electrolyser for the energy efficient production of carboxylates from biowaste
Microbial electrochemical technologies (METs) represent a promising approach to valorizing organic waste by separating oxidation at the bioanode from bio-based chemical synthesis at the biocathode. The taxonomic composition of microbial communities directly influences the spectrum of multicarbon compounds synthesized. Electrolyte salinity is a key performance parameter, reducing internal resistance and optimizing energetic yields. Hypersaline conditions might also constitue a lever for steering microbial selection and metabolic functionality in METs. This research aims to evaluate the selection, adaptation, and functional characterization of electrosynthetic microbial communities under hypersaline conditions. It focuses on the impact of contrasted electrolyte salinity on microbial assembly and metabolic specialization, targeting the efficient bioconversion of CO2 into carboxylates. A microbial electrochemical system was designed with three compartments: (i) a bioanode for organic matter oxidation, (ii) a biocathode for electrotrophic CO2 reduction, and (iii) an intermediate compartment for selective extraction and concentration of carboxylates via electrodialysis. Two inoculation strategies were compared in triplicated labscale reactors: hypersaline communities from salt marsh sediments and industrial digester sludge as a reference non-saline inoculum. The cathode inoculum was heat-treated to enrich homoacetogenic Clostridia while eliminating methanogenic archaea. The anode was configured as a flat carbon cloth to maximize electrocatalytic activity, while the cathode consisted of carbon granules to enhance microbial adhesion and electron transfer. Experiments demonstrated that the nature of salts in the electrolyte significantly influences catalytic performance. NaCl-based saline conditions enhanced electrochemical efficiency; achieving current densities up to 8 A.m-² as daily averages with real biowaste hydrolysates as substrate and promoting carboxylate synthesis at the biocathode. 16S rDNA sequencing confirmed taxonomic shifts between conditions with Alkalibaculm dominated cathodic communities versus Sporomusa dominated ones, under saline and non-saline conditions, respectively. Our findings reveal how selective pressures exerted by ionic environment finaly translated into in contrasted microbial community and carboxylate electrosynthesis patterns. Shotgun metagenomics and metabolic modeling from metagenome-assembled genomes (MAGs) are underway to further resolve underlying metabolic processes and community interactions. This study provides insights into microbial selection in bioelectrochemical systems, demonstrating that salinity-driven adaptation can be used to steer microbial community structure and associated metabolic pathways. Metabolic models of engineered hypersaline electrosynthesis communities are being designed to further optimize the efficiency of CO2-to-carboxylate conversion.
ano.nymous@ccsd.cnrs.fr.invalid (Louise Rigaud) 09 Oct 2026
https://hal.science/hal-05788677v1
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[hal-05785578] Trends in C2−C4 Alcohols Dehydration Catalyzed by the γ‐Alumina (100) Surface: The Isobutanol Puzzle
The monomolecular dehydration of alcohols into olefins catalyzed by the (100) surface of γ‐alumina is investigated by DFT simulations. The transition states (TS) and mean energy paths are determined for C2 to C4 alcohols through the intrinsic reaction coordinate (IRC) method. The reaction occurs through a non‐ideal E2‐type mechanism: the Cα─O bond stretching takes place before the Cβ─Hβ stretching along IRC. Quantitative structural and energetic trends are recovered: primary alcohols are the least reactive with the lower (respectively larger) Cα─O (respectively Cβ─Hβ) stretching, while secondary and tertiary are the most reactive with the larger (respectively lower) Cα─O (respectively Cβ─Hβ) stretching. However, the calculated dehydration kinetic constant of isobutanol underestimates the experimental one. By analyzing structural and charge descriptors along the IRC path and at TS, we identify that the TS of isobutanol dehydration is subject to steric hindrance between the two methyl groups present on and the (100) surface, which destabilizes the TS during the elimination. This destabilization is confirmed by the Bader charge analysis of the TS carbocationic alkyl moiety. We finally question the relevance of the Al site located on the (100) surface for catalyzing the dehydration of alcohols containing hindered mathematical equation atom.
ano.nymous@ccsd.cnrs.fr.invalid (Pierre Marmey) 08 Oct 2026
https://ifp.hal.science/hal-05785578v1
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[hal-05720737] Structure and Function of the Type IX Secretion System for Protein Secretion and Cellular Motility
The type IX secretion system (T9SS) is a Bacteroidota -specific multiprotein machine that supports a wide range of biological processes, from nutrient acquisition and surface modification to host interaction and gliding motility. T9SS effectors represent a structurally diverse repertoire of enzymes, adhesins, and surface proteins that all possess a C-terminal domain that addresses them to their final destination. Recent structural and mechanistic information has revealed the modular organization of the T9SS and molecular details governing effector selection, transport, processing, and sorting. In motile Bacteroidota , the T9SS has been co-opted, evolved, and specialized for gliding motility. In this review, we summarize current knowledge on T9SS architecture and function, describe the embedded gliding machinery, and highlight conceptual advances and open questions regarding the mechanisms, dynamics, and ecological implications of this unique system.
ano.nymous@ccsd.cnrs.fr.invalid (Yaëlle Aouizerate) 24 Sep 2026
https://hal.science/hal-05720737v1
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[hal-05761385] Pareto Suboptimal Resource Allocation and Microbial Growth
Abstract Microbial growth has often been analyzed under the assumption that microorganisms have evolved to optimize phenotypic characteristics of interest, such as growth rate and growth yield. This assumption has been useful, for example, for the genome-scale modeling of metabolism and the study of the allocation of cellular resources to physiological processes. In many experimental situations of interest, however, microorganisms are found to be suboptimal with respect to phenotypic characteristics that are thought to be favorable in that situation. Whereas a strong theoretical framework exists to mathematically relate cellular resource allocation strategies to Pareto optimality of microbial growth and other biological processes, much less is known about the consequences of Pareto suboptimality. We extend the framework to the latter case and show that a given Pareto suboptimal phenotype can be explained by a range of underlying resource allocation strategies, each corresponding to a different growth physiology and biomass composition. We test the predictions with the help of a coarse-grained model of microbial growth and published experimental data, which relate Pareto suboptimal rate-yield phenotypes of Escherichia coli and the microalga Tisochrysis lutea to the macromolecular composition of the cells (storage metabolite and total protein contents). Changing the focus from Pareto optimality to suboptimality provides interesting leads to exploring the diversity of growth strategies that can support a given phenotype. This change of perspective is of practical interest, because some of the growth physiologies within this range may be important for biotechnological applications. Author summary Many methods for the analysis of metabolism and growth are based on the assumption that, under the pressure of natural selection, microorganisms have evolved towards phenotypes that are optimal with respect to ecologically important characteristics. In mathematical terms, this assumption can be formulated as Pareto optimality of microbial growth and related to underlying resource allocation strategies that shape cellular physiology. Based on the observation that this assumption is often not satisfied in practice, we investigate the consequences of adopting the opposite assumption, namely that microbial growth and cellular resource allocation are suboptimal. We extend an existing mathematical framework to the case of Pareto suboptimality, which allows us to make predictions on the diversity of the macromolecular composition of microbial cells. These predictions are shown to correspond with experimental data on growth rate, growth yield, and macromolecular composition of the model bacterium Escherichia coli and the microalga Tisochrysis lutea . Our results thus associate suboptimality with observed metabolic diversity in microorganisms.
ano.nymous@ccsd.cnrs.fr.invalid (Valentina Baldazzi) 23 Sep 2026
https://hal.inrae.fr/hal-05761385v1
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[hal-05758238] Assessing the reproducibility of a bioimage analysis workflow characterising tissue flow in Drosophila
Abstract Reproducibility challenges in bioimage analysis are common. The proliferation of tools and workflows creates a complex ecosystem that is difficult to reproduce without deliberate, explicit reporting and support. We assess the reproducibility of Gehrels et al.(2023) as a representative bioimage analysis workflow. We do not evaluate the biological claims; instead, we examine the reproducibility of the bioimage analysis methods used and the implications for current peer‐review practices in the field. Although some data were deposited in the BioImage Archive and code was available on GitHub, the materials were insufficient to completely reproduce the analysis. Moreover, the repository lacked the configuration to enable straightforward replication of the workflow or results. This case study highlighted how incomplete reporting can significantly hinder the reproduction of bioimage analysis workflows. Because scientific progress relies on verifiable replications, insufficiently reproducible results can erode confidence in the scientific record.
ano.nymous@ccsd.cnrs.fr.invalid (Mélodie Ambroset) 22 Sep 2026
https://hal.inrae.fr/hal-05758238v1
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[hal-05755030] Photosynthesis for industrial biotechnology: mechanisms to bioprocesses
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ano.nymous@ccsd.cnrs.fr.invalid (Filipa Lopes) 18 Sep 2026
https://hal.science/hal-05755030v1
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[hal-05751999] Adaptative evolution of Escherichia coli in continuous culture for improved resistance to acrylic acid toward future biocatalytic applications
Acrylic acid is a promising bio-based platform molecule but exhibits strong toxicity toward microbial hosts, severely limiting its biological production. In this study, Escherichia coli K12 wt strain MG1655 was monitored for growth kinetics, lag phase duration, and survival at high acrylate concentrations using Bioscreen assays and plate-based selection methods. A MIC of 80 mM was recorded for populations grown for 18 hours in flasks. Further cultivation resulted in dense growth after 72 hours, pointing to acrylate adaptation of these cells. Growth in the presence of acrylate concentrations of up to 300 mM was observed. Cellular isolates were obtained from these cultures and found to exhibit different growth efficiencies; the best performing isolate was chosen for inoculation of a GM3 continuous culture device in order to further enhance acrylic acid tolerance and identify robust phenotypes of interest for future biocatalytic applications.
ano.nymous@ccsd.cnrs.fr.invalid (Pauline Daclin) 16 Sep 2026
https://hal.science/hal-05751999v1
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[hal-05744889] PHOTOSYNTHETIC BIOFILMS: FROM MECHANISMS TO BIOPROCESSES
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ano.nymous@ccsd.cnrs.fr.invalid (Filipa Lopes) 10 Sep 2026
https://hal.science/hal-05744889v1
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[hal-05733568] Natural phenolic autofluorescence reveals cell wall-specific distribution of hydroxycinnamates in Brachypodium distachyon
Abstract p-Coumaroyl-CoA:monolignol transferase has been demonstrated to be involved in the coumaroylation of lignins in Brachypodium distachyon. However, the specific localization of acylation remains poorly documented at the tissue and cell wall levels in this species. Detecting molecules that are sometimes present at levels <1% in the cell wall remains a challenge, especially when suitable antibodies are not always available. In this work, we applied fluorescence microscopy methods, including large-beam excitation scanning at the SOLEIL synchrotron, to detect variations induced by hydroxycinnamic acids within B. distachyon stems. Using principal component analysis (PCA), fluorescence microscopy imaging effectively distinguished genotypes differing subtly in phenolic composition. The results were supported by immunolabeling, which confirmed that p-coumarate co-localizes with S-unit lignin in lignified tissues, while ferulate is broadly distributed. Strong autofluorescence in the mestome sheath and metaxylem pit area indicated a potential functional role for p-coumaric acid in these tissues. Finally, autofluorescence-based imaging and PCA proved to be a robust, non-destructive tool for visualizing lignin and phenolic compounds, offering valuable insights into cell wall specialization and phenolic function.
ano.nymous@ccsd.cnrs.fr.invalid (Laura Vimenet) 01 Sep 2026
https://hal.inrae.fr/hal-05733568v1
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[hal-05732668] Life cycle assessment of bilirubin oxidase production and its use for enzymatic solubilization of lignin at neutral pH
Lignin is the largest renewable source of aromatic building blocks, yet it remains largely underutilized due to its structural complexity and poor water solubility. Enzymatic lignin treatment under mild, solvent-free conditions has emerged as a promising alternative to conventional chemical methods, but its environmental performance has not yet been assessed from a life cycle perspective. This study presents a cradle-to-gate life cycle assessment of bilirubin oxidase production and its application for enzymatic lignin solubilization at neutral to basic pH. Using laboratory-scale data, environmental impacts were quantified across eighteen midpoint categories to identify the main process contributors to environmental impacts. The results show that enzyme production dominates the environmental profile, primarily due to electricity consumption and the upstream impacts of growth media and chemical reagents. Treatment of lignin with the enzyme contributes a relatively smaller but significant share of impacts, mainly through auxiliary inputs such as oxidant supply. Sensitivity analyses highlight the strong influence of the electricity mix and demonstrate that substituting pure oxygen with ambient air could reduce oxidant-related impacts under the laboratory assumptions considered without altering the reaction chemistry. By extending life cycle assessment to enzymatic lignin treatment, this work addresses a gap in the lignin LCA literature, which has been focused predominantly on extraction and thermochemical valorization. The findings emphasize the importance of energy sourcing and process integration in the sustainable development of biocatalytic lignin technologies.
ano.nymous@ccsd.cnrs.fr.invalid (Anish Koyamparambath) 31 Aug 2026
https://hal.science/hal-05732668v1
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[hal-05728633] Comprendre l’aptitude au fractionnement des bioressources : de la variabilité des plantes cultivées aux différentes fonctionnalités des fractions via la modélisation des structures et de leur déstructuration. Application au maïs
L’aptitude à la transformation des ressources végétales est fortement impactée par la composition et structure des matières premières. Dans le cadre du projet FillingGaps l’aptitude à l’hydrolyse enzymatique/dégradation ainsi que l’aptitude au broyage sont plus particulièrement étudiées. Cette étude focalise sur le maïs, plante fourragère et substrat modèle pour les graminées pour laquelle une diversité de structure et composition est obtenue via les leviers génétiques ou conditions de culture. L’aptitude au broyage des tiges de maïs peut être estimée et sa variabilité peut être reliée, selon l’échelle de dissociation, à la composition et à l’organisation à l’échelle microscopique. L’exploration de la diversité structurale est abordée in planta via des techniques d’imagerie optique permettant de quantifier la morphologie tissulaire et cellulaire et de révéler des différences de composition chimique (colorations histologiques, imagerie multispectrale). La modélisation de la microstructure est réalisée afin de construire des échantillons virtuels représentatifs dont le comportement à la rupture peut être étudié.
ano.nymous@ccsd.cnrs.fr.invalid (Cecile Barron) 27 Aug 2026
https://hal.inrae.fr/hal-05728633v1
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[hal-05717355] New workflow for multimodal and multiscale analysis of the parietal structure of maize stem, combining AFM, Raman, and MSI.
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ano.nymous@ccsd.cnrs.fr.invalid (Oriane Morel) 14 Aug 2026
https://hal.inrae.fr/hal-05717355v1
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[hal-05715231] CO2-mediated conversion of furfuryl alcohol to 4-hydroxycyclopentanone and its toxicological assessment
Through a combined chemical-toxicological study, this report reexplores the Piancatelli rearrangement of furfuryl alcohol into 4-hydroxycyclopentenone (4-HCP), a key building block for the synthesis of bio-based solvents. In this context, we demonstrate that (1) in aqueous media, the addition of CO<sub>2</sub> results in a fivefold increase in the rate of the Piancatelli rearrangement of furfuryl alcohol to 4-HCP, even at temperatures as low as 120&nbsp;°C, and (2) 4-HCP exhibits pronounced cyto-and genotoxicity, approximately 200 times higher than that of furfural. Based on these results, we recommend avoiding the isolation of 4-HCP and instead converting it in situ into cyclopentanone or cyclopentanol, two identified safer downstream target chemicals through toxicological studies.
ano.nymous@ccsd.cnrs.fr.invalid (Ana Franco) 11 Aug 2026
https://hal.inrae.fr/hal-05715231v1
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[hal-05713233] Integration of experimental protocols into the Galaxy platform to support FAIR experimental workflows
The sharing of experimental protocols remains challenging, limiting their accessibility and reuse, due to the variability of experimental practices and the lack of standardized protocol representation. To address this issue, it is critical to apply FAIR principles (Findable, Accessible, Interoperable, and Reusable) to improve protocol management. This work focuses on integrating experimental protocols into the open-source Galaxy platform, providing a standardized, executable, and fully traceable environment consistent with FAIR principles. As this represents a relatively novel approach, it was first essential to establish a robust methodology consistent with the platform’s capabilities to ensure effective implementation. At this stage, this approach has been applied to a selected set of key non-confidential laboratory protocols used in biomass transformation (biomass material grinding, chemical composition, and enzymatic hydrolysis), demonstrating its feasibility and practical applicability. For each protocol, key steps involving critical decisions and parameters for reproducibility were identified and implemented into a dedicated Galaxy tool. Users are invited to provide the required inputs through the tool interface and execute the process, generating a structured record of the entered parameters and decisions for traceability.The structured record from the first tool is used by a second tool to generate a final report, with optional inclusion of supplementary results such as images or comments. This automated reporting captures all critical decisions and parameters, enabling clear documentation, easy sharing and reuse of experimental protocols. The method ensures that experimental protocols are traceable, reusable and aligned with FAIR principles. By structuring and recording essential protocols steps, the approach ensures that all critical elements are captured, supporting reproducible experiments. The strategy could be further revised and optimized to generalize the method, enabling efficient integration of numerous protocols across different domains in Galaxy.
ano.nymous@ccsd.cnrs.fr.invalid (Fanny Demange) 07 Aug 2026
https://hal.science/hal-05713233v1
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[hal-05704575] Carbonic anhydrase activity under low zinc in Phaeodactylum tricornutum largely depends on metal-free iota-carbonic anhydrase
Carbonic anhydrases (CA) typically possess a Zn2+-cofactor, and are involved in a wide range of adaptative metabolisms involving pH and dissolved inorganic carbon homeostasis. In photosynthetic microorganisms, they are involved in CO2 concentrating mechanisms (CCM) that supply CO2 to Rubisco. Here we show that the model diatom Phaeodactylum tricornutum possesses a CA from the newly identified iota class (Pt-ιCA) that exhibited catalytic activity without a metal cofactor, in contrast to most CAs. Metal-free Pt-ιCA activity was two orders of magnitude lower than that the Zn2+ containing bovine erythrocyte CA, yet still in the range of expected value for CA. Zn2+ concentrations on the picomolar range induced the expression of Pt-ιCA in P. tricornutum, together with the Zn2+/Co2+ responsive protein A. Zn2+ scarcity did not prevent the induction of Zn2+-containing CAs involved in biophysical CCM when the cells were transferred from high pCO2 to very low pCO2 conditions. The induction of CCM at very low pCO2 and low Zn2+ conditions was concomitant to induction of light harvesting complex and remodeling of the pentose phosphate pathways. The total cellular CA activity decreased in Pt-ιCA deletion mutant (ΔιCA) compared to control cells, indicating that Pt-ιCA is active in P. tricornutum under low Zn2+ conditions. P. tricornutum adapted to the absence of Pt-ιCA by a morphometric change, without affecting photosynthesis or growth rate. The newly identified metal-free Pt-ιCA represents an evolutionary advantage for diatoms that live in metal-limited environments.
ano.nymous@ccsd.cnrs.fr.invalid (Luisana Avilan) 27 Jul 2026
https://hal.science/hal-05704575v1
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[hal-05704510] Approximating committor functions: Objective functions and enhanced sampling
Many molecular dynamics simulations aim at studying transitions between two states (from reactants to products). In this context, the committor function (which gives for a given molecular configuration the probability to reach the product state before the reactant state) is a pivotal quantity, in particular because it is the optimal importance function for rare event simulation methods such as importance sampling or splitting techniques. These methods are used to sample the reactive path ensemble, and estimate for example the transition rate. However, learning such a function is generally a challenging task due to the high dimensionality of the configuration space. In this work, after reviewing the existing methodologies to construct approximate committor functions, a new loss function based on the application of Itō's formula is proposed to learn the committor function with a minimization procedure on the parameters of a neural network. After comparing this novel approach to existing procedures on the Müller-Brown potential, we introduce a coupling strategy with the Adaptive Multilevel Splitting method to better approximate the committor function using a better sampling of the reactive trajectories. This methodology in which the committor function is iteratively learned only requires initially the knowledge of the reactant and product states.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Pigeon) 27 Jul 2026
https://hal.science/hal-05704510v1
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[hal-05694938] Galaxy-BioProd: An Integrated FAIR Platform for Synthetic Biology, Biotechnology and Life Cycle Analysis
The "Bioproductions (B-BEST): Biomass, Biotechnologies, and Sustainable Technologies for Chemistry and Fuels" research program is part of the national acceleration strategy "Bio-based Products and Industrial Biotechnologies - Sustainable Fuels" under the France 2030 plan. Co-led by INRAE and IFPEN, this program supports the transition from a petrochemical economy to bio-based products and services by aiming to better understand and utilise biomass to produce bio-based products and sustainable fuels. A secondary objective is to establish common practices for bio-refineries, which are currently not implemented at national level, thereby limiting the efficiency and reproducibility of developments. To address these issues, the Galaxy-BioProd project aims to develop a centralised portal providing standardised digital tools and resources to simplify, connect and accelerate industrial biotechnology projects. The tools and pipelines are developed by the members of the project. Based on the Galaxy environment and adhering to FAIR principles, the B-BEST Galaxy lab deployed on usegalaxy.fr offers an accessible and unified platform that can serve various communities in the fields of synthetic biology, biocatalysis and industrial biotechnology. Seventeen tools ranging from synthetic biology to Life Cycle Analysis are currently under development and will be deployed on B-BEST lab of usegalaxy.fr. Galaxy-BioProd project is part of the PEPR Bioproductions (B-BEST) program, supported by the France 2030 investment plan and co-led by INRAE and IFPEN [ANR-22-PEBB-0008].
ano.nymous@ccsd.cnrs.fr.invalid (Anthony Pragassam) 16 Jul 2026
https://hal.science/hal-05694938v1
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[hal-05693548] Lignocellulose-powered bioelectrochemical systems: microbial communities, controlling factors, and enhancement strategies
Lignocellulosic biomass (LCB) is the world’s most abundant renewable carbon source, yet its potential to drive a circular bioeconomy remains largely untapped. Microbial electrochemical technologies (METs) offer a promising route for converting this complex feedstock into electricity or valuable chemicals. However, LCB-MET advancement is hindered by a fundamental challenge: LCB recalcitrance necessitates depolymerization, a process mismatched with the metabolic capabilities of most electroactive microorganisms (EAMs). While EAMs excel at oxidizing simple substrates, most lack the hydrolytic machinery to break down LCB, creating a critical performance bottleneck. Addressing this requires a multi-disciplinary approach. At the heart of the biological challenge lie two core paradigms, each drawing on microorganisms sourced from nature or artificially engineered: (i) specialized strains capable of both hydrolytic and electrogenic functions, or (ii) synthetic consortia establishing division of labor between fermentative microbes and EAMs. These strategies do not operate in a vacuum; their performance is constrained by materials and environment. To evaluate the progress and potential of these interdependent biological, material, and engineering strategies, this review examines the landscape of LCB utilization in METs. It synthesizes recent advances in coupling depolymerization with extracellular electron transfer, critically evaluate microbial players from pure strains and mixed communities to genetically modified organisms and synthetic consortia, and assesses the key operational parameters, challenges, and potential solutions that define this field. Moving beyond, the review provides graphic representations and statistical analyses of recent publications to establish quantitative performance benchmarks.
ano.nymous@ccsd.cnrs.fr.invalid (Animut Assefa Molla) 15 Jul 2026
https://hal.inrae.fr/hal-05693548v1
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[hal-05692403] Caproate production from electro-fermentation of wine lees and waste activated sludge under applied potential
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ano.nymous@ccsd.cnrs.fr.invalid (Luisa Barbonaglia) 15 Jul 2026
https://hal.inrae.fr/hal-05692403v1
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[hal-05676003] Teindre durable sans se tromper de ton. Représentations des professionnels et consommateurs sur l'adoption de colorants biosourcés dans l'industrie de la mode
La couleur, critère clé dans le choix des vêtements, engendre une forte pollution liée aux teintures textiles, rendant indispensable une transition vers une mode plus éthique et durable (Lara et al., 2022; Niinimäki et al., 2020). Alors que les colorants synthétiques pétrosourcés dominent encore le marché, des alternatives biosourcées issues de biotechnologies émergent et peuvent s’inscrire dans une démarche circulaire en valorisant des biodéchets (Fried et al., 2022; Mazotto et al., 2021). Ces solutions innovantes offrent un potentiel environnemental et social important pour la mode, mais les perceptions des professionnels et consommateurs restent peu étudiées, tant concernant la teinture que les biotechnologies « vertes » (Mabuza et al., 2023). Cette recherche vise à comprendre comment les colorants biosourcés issus de biotechnologie peuvent s’intégrer dans la chaîne de valeur tout en conciliant les intérêts divergents des acteurs, des intermédiaires aux consommateurs. Elle mobilise deux cadres théoriques complémentaires : le modèle TOE pour analyser les déterminants de l’adoption par les professionnels (Tornatzky et Fleischer, 1990) et la théorie de la résistance à l’innovation (TRI) pour étudier les freins à l’acceptation chez les consommateurs (Ram et Sheth, 1989). Une enquête qualitative par entretiens semi-directifs a été réalisée auprès de professionnels de la filière (n=11) et de consommateurs ou influenceurs de mode (n=18), à partir de guides adaptés à leurs pratiques mais incluant un tronc commun sur la mode durable et les colorants biosourcés. Les entretiens, enregistrés et analysés thématiquement avec MAXQDA, ont permis d’identifier les bénéfices et obstacles perçus selon les cadres du modèle TOE pour les professionnels et de la théorie de la résistance à l’innovation (TRI) pour les consommateurs. Les professionnels perçoivent les colorants biosourcés comme un levier potentiel de différenciation et de communication, mais doutent de leurs réels bénéfices environnementaux et soulignent plusieurs obstacles techniques, économiques et structurels. Leur adoption semble conditionnée à la compatibilité avec les procédés existants et à des gains mesurables en efficacité (eau, énergie, coûts). Enfin, les contraintes réglementaires et la pression contradictoire des consommateurs entre durabilité et prix limitent encore leur déploiement. Les consommateurs accordent une grande importance à la couleur mais peu au type de colorant utilisé, exprimant globalement une confiance dans les procédés industriels et la réglementation. Si l’aspect circulaire des colorants biosourcés est perçu positivement, certaines réticences subsistent face à l’usage de biodéchets et à une technologie jugée compatible avec la surconsommation. Enfin, la valorisation de procédés traditionnels perçus comme plus “propres” peut constituer une barrière culturelle à l’adoption. Ces résultats impliquent que le développement de ces biocolorants doit répondre aux attentes environnementales des consommateurs et aux contraintes techniques et économiques des professionnels, la seule circularité ne suffisant pas sans impacts environnementaux positifs clairement identifiés. L’adoption de vêtements bio-colorés passerait surtout par des stratégies de marque, compte tenu du faible intérêt direct des consommateurs pour les colorants.
ano.nymous@ccsd.cnrs.fr.invalid (Arnaud Lamy) 01 Jul 2026
https://hal.science/hal-05676003v1
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[hal-05674613] Isobutanol Dehydration to Linear Butenes on Ferrierite: Mechanistic Insights from operando FTIR, Chemometrics and Kinetic Modelling
The selective dehydration of isobutanol to linear butenes catalyzed by acidic ferrierite (H-FER) has been investigated by operando IR spectroscopy under close batch conditions and along a temperature ramp. The employed apparatus permits to alternatively acquire spectra of both the gas phase composition and the species adsorbed on the H-FER surface, thus providing fundamental insights onto the products formation and the reaction intermediates formed on the catalyst surface. In the gas phase, the high selectivity for linear butenes was confirmed in the first phases of the reaction, followed by a slower isomerization to isobutene and by the formation of heavier compounds due to secondary processes. Detailed MCR-ALS analysis of the adsorbed species’ spectra permitted to also identify and quantify adsorbed 2-butanol and trans-2-butene on the H-FER surface, providing a first indication of the alcohol isomerization as a key step in the reaction mechanism. The proposed mechanism was evaluated by microkinetic modelling of both gas phase and surface concentration profiles, showing that the consecutive isomerization of isobutanol to adsorbed 2-butanol followed by its dehydration to trans-2-butene is more favorable than the one-step dehydration-isomerization of isobutanol. In contrast, the direct dehydration of isobutanol to isobutene was found to be slower over the entire investigated temperature range.
ano.nymous@ccsd.cnrs.fr.invalid (Eleonora Vottero) 30 Jun 2026
https://hal.science/hal-05674613v1
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[hal-05674426] Enzymatically treated lignin as a water-soluble polymer for the stabilization of carbon inks and emulsions
Lignin is an abundant aromatic biopolymer with high potential for sustainable material applications, but its limited water solubility restricts its use as a molecular dispersant or surfactant. Here, we report the use of enzymatically modified kraft lignin, obtained via bilirubin oxidase (BOD) oxidation, as a water-soluble amphiphilic polymer for the stabilization of carbon black dispersions and oil-in-water emulsions. The enzymatic treatment yields a low-sulfur and high molecular weight lignin fraction readily soluble at neutral pH. Interfacial tension measurements demonstrate adsorption at both air-water and oil-water interfaces. Stable carbon black dispersions are obtained over a broad concentration window, with a defined phase boundary controlled by the carbon black/lignin ratio. The dispersions exhibit rheological properties compatible with printing technologies. Dried films display electrical conductivity of 35 S m -1 , confirming the formation of percolated carbon networks. In parallel, the modified lignin stabilizes oil-in-water emulsions with remarkable resistance to thermal aging and centrifugation, outperforming sodium dodecyl sulfate under identical conditions. These results demonstrate that enzymatically treated lignin combines amphiphilicity and colloidal stabilization, providing a sustainable alternative to synthetic surfactants for emulsions and advanced carbon-based formulations.
ano.nymous@ccsd.cnrs.fr.invalid (Ashish Kumar Rajayan) 30 Jun 2026
https://hal.science/hal-05674426v1
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[hal-05673913] Isobutanol dehydration catalyzed by bridging OH groups at the (100) surface of ferrierite: From static DFT to machine learning accelerated molecular dynamics
Ferrierite is industrially used as a catalyst for the dehydration of isobutanol into butenes and the critical part of this transformation is presumably catalyzed by Brønsted acid (BA) sites located on its external surface. In this work, we present a DFT investigation of a complete reaction network over the T1O3 BA site at the (100) surface of this zeolite. Exploration of reaction mechanisms by means of the static approach revealed that the transformation towards all products proceeds in two steps - dehydration and deprotonation - with the former step being rate determining for all competing reaction channels. Free energetics of the dehydration reaction was therefore investigated using ab initio molecular dynamics accelerated by machine-learned force fields with accuracy controlled via a correction scheme based on machine learning perturbation theory. The activation free energies for transformations towards branched and linear products computed using the PBE+D2 functional (111.3 and 125.7 kJ/mol, respectively) suggest a preference of the former reaction channel. This conclusion was found to be independent of the dispersion correction used with the PBE functional (no correction, D3, D3(BJ), and D4) and of the choice of bridging OH group, as shown for the alternative T3O1 and T4O7 sites. Interestingly, our results are in agreement with our previous investigation of analogous reactions catalyzed by bulk chabazite. At the same time, however, they do not reproduce the experimental selectivities observed for ferrierite, which suggests that the bridging OH groups are not at the origin of the specific selectivity of ferrierite for linear alkenes.
ano.nymous@ccsd.cnrs.fr.invalid (Katarína Skladanová) 30 Jun 2026
https://ifp.hal.science/hal-05673913v1
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[hal-05673026] Open data for publication : Isobutanol Dehydration to Linear Butenes on Ferrierite: Mechanistic Insights from operando FTIR, Chemometrics and Kinetic Modelling
Dataset associated with the analysis described in the paper "Isobutanol Dehydration to Linear Butenes on Ferrierite: Mechanistic Insights from operando FTIR, Chemometrics and Kinetic Modelling". The folder includes: raw spectra of the operando FTIR experiment under batch conditions reference spectra measured in situ the python script containing the MCR-ALS analysis of the spectra associated with the species adsorbed on H-FER the measured concentration profiles of all quantified species the python script containing the kinetic model fit calculations
ano.nymous@ccsd.cnrs.fr.invalid (Eleonora Vottero) 29 Jun 2026
https://hal.science/hal-05673026v1
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[hal-05673023] Open data for publication: Multivariate analysis coupled to infrared spectroscopy unravels the diversity of adsorption sites and strengths of a zeolite surface.
Raw IR spectra and scripts for their processing and MCR analysis
ano.nymous@ccsd.cnrs.fr.invalid (Reda Aboulayt) 29 Jun 2026
https://hal.science/hal-05673023v1
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[hal-05662647] A Nanocatalyst‐Based Approach to Sustainable HMF Oxidation
In the urgent shift toward fossil-free chemistry, 5-hydroxymethylfurfural (HMF) stands out as a pivotal bio-based platform molecule for producing high-value furanic derivatives, including 2,5-furandicarboxylic acid (FDCA), a key precursor for next-generation bio-plastics like polyethylene furanoate (PEF). However, conventional FDCA synthesis often relies on harsh conditions (high pressure, toxic oxidants, or complex catalytic systems), limiting scalability and/or sustainability. In this study, we demonstrated that colloidal Pd nanoparticles enable efficient HMF oxidation under mild conditions (atmospheric air, 80°C), achieving full HMF conversion with 80% FDCA selectivity, a competitive performance under milder conditions. Through detailed mechanistic investigations, we elucidated the catalytic cycle of Pd nanoparticles while demonstrating the critical role of the soluble base, which generates hydroxyl groups with water to drive the reaction. Our findings conclusively established that the base must be introduced stoichiometrically to achieve optimal performance. Colloidal Pd system overcomes the limitations of traditional heterogeneous catalysts by eliminating support interference, providing clear mechanistic insights. Its scalable and tunable nature allows for future immobilization to enhance recyclability and ensures a controlled oxidation reaction. These advantages, mild conditions, mechanistic insights, and tunability, position our system as a promising, sustainable alternative for FDCA production, paving the way for industrial high-value-added biobased chemicals production.
ano.nymous@ccsd.cnrs.fr.invalid (Lénaïck Hervé) 25 Jun 2026
https://hal.science/hal-05662647v1
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[hal-05667759] Production of biopolymers from denitrifying microorganisms in granular sequencing batch reactor
Granular sequencing batch reactors allows aggregation of microorganisms through granule shape thanks to high selection pressure [1]. These granules are aggregates of microorganisms embedded in a network of highly cohesive exopolymers (EPS). The cohesive property of these polymers called structural EPS (sEPS) led to develop extraction protocols [2] and understand their properties [3] which allows to develop a new pathway for matter recycling inside wastewater treatment field. We aim to increase our knowledge in this field by studying the role of specific populations in the production of sEPS. The case of PAOs having been studied recently [4]and we focus here on denitrifying populations. This study aims to link sEPS production and characteristics to GSBR operating conditions and sludge properties. Based on the work from a previous thesis, [5], a 17L GSBR was operated during 3 months with alternating anoxic/aerobic conditions and a 4 carbon sources synthetic effluent composed of volatile fatty acids (Acetate and propionate), glucose and peptones. Nitrates were added to ensure anoxic conditions during non-aerated phase. The reactor followed 3.5-hour operating cycles consisting of 25 minutes of anoxic feed, 20 minutes of additional anoxic phase under slow agitation, 155 minutes of aerobic phase under rapid agitation, 6.5 minutes of decantation and 3.5 minutes of purging. The Volume Exchange Ratio (VER) was 50%. Typical ratios encountered in urban wastewater were applied: COD/P and COD/NTK ratios of 48 and 8, respectively. After inoculating with an activated sludge, the denitrifying microorganisms were selected by injecting the substrate during the non-aerated phase, allowing maximum COD consumption by the denitrification reaction in the anoxic phase and only slow growth in the aerated phase. In order to assess the activity and proportion of denitrifying populations, COD and nitrate balances were carried out in the anoxic and aerobic phases. The properties of the sludge in terms of settling and treatment of carbon, nitrogen and phosphorus were monitored dynamically. The stability and robustness of EPS production was assessed by quantifying the dynamics of polymer extraction yields, as well as their structures and rheological qualities. This made it possible to relate the structure of the aggregates to the production of sEPS. Ultimately, we hope to compare the results of this study with those obtained from the selection of other dominant populations and pure cultures. References [1] E.Morgenroth, T.Sherden, M.C.M Van Loosdrecht, Water Research, volume 31 (1997), p3191-3194). [2] Y.Lin, M. De Kreuk, M.CM. Van Loosdrecht, Water research, volume 44 (2010), p3355-3364 [3] T.Seviour, B.Donose, M.Pijuan, Z.Yuan, Environmental Science &amp; Technology, vol44 (2010) [4] L.B.Guimaraes, N.R Gubser, Y.Lin, preprint (2024) [5] A.Filali, A. Mañas, M. Mercade, Y.Bessière, Biochemical Engineering Journal, vol. 67 (2012), p. 10-19
ano.nymous@ccsd.cnrs.fr.invalid (Lucas Berti) 24 Jun 2026
https://hal.science/hal-05667759v1
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[hal-05667005] An extended 1D dynamic model of biological methanation considering water production, variable height and maintenance heterogeneity
Numerical simulation of biological methanation remains challenging due to the strong coupling between mass transfer, hydrodynamics, and bioreaction in such gas-fed bioreactors. This work presents an extension of a 1D spatio-temporal gas-liquid model for bubble columns to the case of biological methanation. To this end, three major improvements are added to the previously published model: (i) the consideration of water production due to the biological methanation reaction, (ii) the implementation of an additional equation for the liquid height, (iii) the introduction of a variable maintenance model based on the spatial heterogeneity of the H2 mass transfer. The model was validated with experimental data from literature. Results indicate that water production acts as a dilution term, as revealed by simulations performed under both constant and variable height conditions. This led to a reduced biomass concentration while preserving methane production owing to a redistribution of H2 consumption between maintenance and growth. These intriguing results were confirmed by analytical solutions at steady-state. The variable maintenance model further allows connecting the decrease in performances through scale-up to increased local deviations between H2 mass transfer and cell demand. Also, a basic moving mesh method now extends the gas-liquid dynamic 1D model capabilities to any fed-batch (bio) reactor.
ano.nymous@ccsd.cnrs.fr.invalid (Julian Federico Sanchez Caldas) 23 Jun 2026
https://hal.inrae.fr/hal-05667005v1
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[hal-05662964] MetExplore 3: a web solution for network-based interpretation of metabolomics data
Introduction: Metabolomics experiments routinely generate lists of metabolites (metabolic profiles), but transforming these results into biologically interpretable metabolic mechanisms remains challenging. Existing workflows or web solutions often rely on disconnected tools for identifier search, pathway enrichment, network extraction, visualization, and dissemination of results. Aim: We developed MetExplore 3 to provide an integrated web platform for the exploration, contextualization, visualization, and sharing of graphical representation of metabolomics data mapping within genome-scale metabolic networks. Methods: MetExplore 3 is an open access web server based on modern web components that provides interactive tools for metabolic network analysis and visualization. The platform includes published curated genome-scale metabolic networks for several organisms and also allows users to import their own metabolic networks from SBML files. A dedicated metabolite identification module maps experimental metabolites onto metabolic networks using ChEBI identifiers. Once mapped, metabolites can be analyzed through pathway overrepresentation approaches and used to extract biologically contextualized subnetworks. These subnetworks can then be interactively visualized, edited, and shared through reproducible graphical representations. In addition to the graphical interface, MetExplore 3 provides an API enabling access to data structures and analytical methods from external environments and programming languages, facilitating integration into custom bioinformatics workflows. Results: MetExplore 3 enables users to move from metabolite identification to interpretable and shareable metabolic network representations within a unified environment, providing an alternative to widely used pathway enrichment interpretations. The platform integrates metabolite mapping, pathway overrepresentation, subnetwork extraction, and interactive visualization into a unique web solution. The ability to save and share curated network layouts facilitates collaborative interpretation of metabolomics data. Conclusion: By integrating analytical, visualization, and sharing functionalities within the same web solution, MetExplore 3 helps bridge the gap between metabolite lists and biologically meaningful network interpretations. The platform provides the metabolomics community with an accessible and extensible environment for network-based analysis of metabolomics data.
ano.nymous@ccsd.cnrs.fr.invalid (Ludovic Cottret) 19 Jun 2026
https://hal.inrae.fr/hal-05662964v1
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[hal-05661923] Volatile Fatty Acids (VFAs) as a sustainable carbon source for bioproduction by unconventional yeasts
In order to answer the major societal and environmental challenges of our time, we strive to replace fossil-derived molecules with sustainable alternatives. Biotechnological approaches offer promising opportunities but require sustainable, low-cost, and renewable carbon sources to achieve an economically viable and sustainable bioeconomy. One such alternative carbon source of great interest are volatile fatty acids (VFAs), produced naturally during the anaerobic digestion (AD) of organic waste. Although inexpensive and readily available, VFAs have long been overlooked as substrates for bioproduction due to their general toxicity towards microorganisms. However, recent insights into unconventional yeasts have revealed the potential of their diverse metabolisms to efficiently utilize VFAs as sole carbon sources and convert them into molecules of higher value. This review synthesizes the latest advancements in VFAs utilization by unconventional yeasts, focusing on VFAs production and composition, the diversity of unconventional yeasts, metabolic optimization, and bioproduction. It further discusses the current limitations in strain engineering and process integration for certain unconventional yeasts, while highlighting the emerging perspectives in process engineering and co-culture systems. Together, these insights shed light on the potential for unconventional yeasts to become established platforms for the revalorization of organic wastes, adding a crucial building block to the future circular bioeconomy.
ano.nymous@ccsd.cnrs.fr.invalid (Erik Habek) 18 Jun 2026
https://hal.science/hal-05661923v1
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[hal-05598191] Advancing Fast-Track Genome Engineering in Bacillus subtilis Phages
Phage genome engineering methods accelerate the study of phage biology, the discovery of new functions, and the development of innovative genetic engineering tools. Here, we present QuickPhage, a rapid, technically accessible, precise, and cost-effective method for engineering Bacillus subtilis phages. Our approach uses CRISPR-Cas9 as a counter-selection system to isolate mutants of the model lytic siphovirus phage, SPP1. Efficient genome editing was achieved using homologous repair patches as short as 40 nucleotides, enabling streamlined patch construction and parallel engineering, resulting in highly accurate genome edits within a day. We applied QuickPhage to delete both essential and nonessential phage genes and to insert reporter genes. Protein production, such as GFP, was synthetically regulated using inducible systems without significantly affecting phage fitness, achieving induction levels of up to 400-fold. Time-series coinfection experiments with fluorescent protein expressing phages also revealed a highly efficient superinfection arrest mechanism that prevents reinfection as early as 13 min after initial infection. These findings highlight the potential of phages for protein production, opening new opportunities for metabolic engineering. This work also lays the foundation for systematic phage genome refactoring workflows and the development of phage-based tools for efficient DNA delivery, thereby expanding the synthetic biology toolbox for B. subtilis.
ano.nymous@ccsd.cnrs.fr.invalid (Arthur Loubat) 10 Jun 2026
https://hal.inrae.fr/hal-05598191v1
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[hal-05648227] Multi-scale characterization of porosity and diffusion in maize STEM internodes
The transition towards sustainable bio-based processes relies on the efficient conversion of lignocellulosic biomass, a renewable and abundant carbon resource. For instance, biotechnological transformation of lignocellulose into chemicals and energy, combining pretreatment, enzymatic hydrolysis and fermentation steps, has been explored for decades and is close to maturity. But underlying mechanisms during hydrolysis remain complex as they depend on many physical and chemical parameters which are deeply impacted by the pretreatment type and severity. In this study, we aim to develop multi-scale approaches to highlight markers of biomass properties and reactivity, focusing on biomass accessibility and porosity. Indeed, enzyme activity and efficiency strongly rely on their diffusion towards their substrate in hydrated plant cell wall substrates. To investigate porosity and molecular transport, our strategy was to combine complementary approaches applied to a reference biomass such as maize stem internodes, considering different genotypes, cell tissues, and pre-treatment conditions. First, the diffusion of water and larger molecular probes such as polyethylene glycols (PEGs) within the biomass global matrix was studied by pulsed-field gradient NMR (PFG-NMR). Then, textural analyses, based on physisorption and pycnometry techniques, provided insights into surface properties, meso and macropore size distribution and overall porosity. Finally, fluorescent PEGs diffusion was followed by Fluorescence recovery after photobleaching (FRAP) to investigate local diffusion, by selecting different cell walls in different tissues. Considering our results, they confirm that pretreated samples enhance molecular probe diffusion, indicating a better surface accessibility. The diffusion behaviour is strongly influenced by pore structure variations across different tissues and samples types. Diffusion is also related to probe size, revealing mesoporosity’s role in enzyme accessibility. Overall, by integrating advanced structural imaging techniques, we aim to refine our understanding of cell wall organization (nanoporosity). The combined use of diffusion-based and textural characterization approaches provides valuable insights into the structural evolution of lignocellulosic biomass, contributing to the optimization of efficient biorefinery processes.
ano.nymous@ccsd.cnrs.fr.invalid (Firat Goc) 08 Jun 2026
https://hal.inrae.fr/hal-05648227v1
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[hal-05638036] Poster, liker, responsabiliser ? Les pratiques des influenceuses engagées dans la mode éthique et durable sur Instagram
Cette recherche explore les pratiques des influenceuses spécialisées dans la mode durable sur Instagram en mobilisant la théorie des pratiques. À travers une analyse netnographique de 220 publications issues de 13 comptes francophones et cinq entretiens semi-directifs, l’étude met en évidence deux registres centraux : la mise en scène vestimentaire (valorisation des tenues éthiques et durables) et la prescription de conseils (achat de seconde main, entretien, tri, sensibilisation aux impacts environnementaux et sociaux). Ces pratiques reposent sur un assemblage de matérialités (vêtements, marques, plateformes numériques), de compétences (savoirs techniques, pédagogiques et créatifs) et de significations (valeurs éthiques, sobriété, transparence). L’analyse révèle une tension entre la promotion d’une consommation responsable et les logiques de renouvellement propres à Instagram, pouvant stimuler le désir de consommer.
ano.nymous@ccsd.cnrs.fr.invalid (Arnaud Lamy) 29 May 2026
https://hal.science/hal-05638036v1
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[hal-05563371] Multi-scale modelling of enzymatic hydrolysis of biomass using numerical homogenization
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ano.nymous@ccsd.cnrs.fr.invalid (Emma Berson) 27 May 2026
https://hal.science/hal-05563371v1
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[hal-05630861] Multi-modal and multi-scale analysis of plant biomass for a better understanding of its degradability
Biomass valorization plays a key role in sustainable development and renewable energy production strategies. It is crucial to better understand biomass structure to identify factors affecting its degradability. While their quantities and proportions can be determined by destructive chemical analysis, the spatial distribution of these components and their interactions at the nanometer scale remain poorly understood. In this poster, we present results obtained using Magnetic Resonance Imaging (MRI), complemented by an original correlative methodological approach that integrates various techniques. These include atomic force microscopy (AFM), which enables topographical and mechanical characterization at the nanometric scale; Raman spectroscopy, which provides information on chemical composition and molecular organization; and mass spectrometry imaging, which enables the identification and localization of specific biomolecules and the detection of local enzymatic activity. We used different types of biomass, such as poplar wood, maize and Brachypodium stem sections.
ano.nymous@ccsd.cnrs.fr.invalid (Oriane Morel) 22 May 2026
https://hal.inrae.fr/hal-05630861v1
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[hal-05625620] Biotechnology for Europe’s agri-food sector and bioeconomy
This May 2026 policy brief by INRAE, B-BEST, and IBISBA argues that Europe's first Biotech Act is too narrowly focused on health, and calls for a broader frame…This May 2026 policy brief by INRAE, B-BEST, and IBISBA argues that Europe's first Biotech Act is too narrowly focused on health, and calls for a broader framework spanning the entire agri-food and bioeconomy sector. While the bio-based market could double by 2032 and cut up to 2.5 Gt CO₂e per year by 2030, Europe is held back by six key obstacles: gaps in fundamental research, a weak lab-to-market transition, fossil-fuel subsidies distorting competition, fragmented R&amp;D funding, poor data interoperability, and low public acceptance of biotechnology. (Contributors by alphabetic order)
ano.nymous@ccsd.cnrs.fr.invalid (Stéphane Aymerich) 18 May 2026
https://hal.inrae.fr/hal-05625620v1
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[hal-05622341] Selective dehydration of isobutanol on H-FER: operando IR, multivariate analysis and kinetic modeling
Introduction Acidic ferrierite (H-FER) is able to dehydrate isobutanol to linear butenes with high selectivity, but the reaction mechanism explaining such selectivity remains elusive.1 This work aims to elucidate the reaction mechanism and provide kinetic rate constants for the main reaction. Results &amp; Discussion The measurements were performed in a custom-made IR cell operating as a closed batch operando reactor and allowing to measure simultaneously the gas phase composition and the species adsorbed on the catalyst. Isobutanol dehydration on HFER was followed along temperature ramps from 40 to 260°C. Intermediates and products were identified and quantified by MCR-ALS analysis of the surface spectra (Figure 1B) and by fitting gas spectra with known references. The high selectivity to linear butenes was confirmed, and 2-butanol was found as an intermediate adsorbed at the HFER surface, suggesting that the key reaction step is the isomerization of the alcohol to the linear isomer. The validity of the proposed mechanism was confirmed by microkinetic modelling of both surface and gas phase concentration profiles, which also showed that the rate limiting step is the alcohol isomerization step. This is the first experimental confirmation of previous computational predictions on a comparable system. Significance This work demonstrates the potential of closed-batch operando IR for identifying reaction intermediates and enabling kinetic modeling of both gas-phase and surface concentrations in catalytic reactions. Applied to the selective dehydration of isobutanol on HFER, it provides the first experimental evidence that the key reaction step is the isomerization of isobutanol to 2-butanol.
ano.nymous@ccsd.cnrs.fr.invalid (Eleonora Vottero) 13 May 2026
https://hal.science/hal-05622341v1
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[hal-05622338] Modulation Excitation Spectroscopy beyond Phase-Sensitive Detection
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ano.nymous@ccsd.cnrs.fr.invalid (Eleonora Vottero) 13 May 2026
https://hal.science/hal-05622338v1
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[hal-05592447] What Makes a Bacterial Model a Good Reservoir Computer? Predicting Performance from Separability and Similarity
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical reservoirs and whether their computational performance can be predicted from dynamical properties linked to separability and similarity. We simulated the growth dynamics of five bacterial species, one yeast species, and 29 Escherichia coli single-gene deletion mutants using dynamic flux balance analysis (dFBA), with glucose and xylose concentrations as inputs and growth curves as reservoir states. Computational performance was assessed on random nonlinear classification tasks using a linear readout, while reservoir properties linked to separability and similarity were characterised through kernel and generalisation ranks computed from growth-curve state matrices. Several microbial models achieved high classification accuracy, showing that bacterial metabolic dynamics can support nonlinear computation. Clear differences were observed between species, with some models converging more rapidly and others reaching higher maximum accuracy, revealing a trade-off between convergence speed and peak performance. In contrast, all E. coli mutants were dominated by the wild-type model, suggesting that gene deletions reduce the dynamical richness required for efficient computation. The difference between kernel and generalisation ranks was generally associated with improved accuracy, but deviations across models and sensitivity at low rank values limited its predictive power in practice. Overall, these results show that bacterial metabolic models constitute promising substrates for reservoir computing and provide a first step towards identifying microbial strains with favourable computational properties for future experimental implementations.
ano.nymous@ccsd.cnrs.fr.invalid (Laura Alonso Bartolomé) 16 Apr 2026
https://hal.science/hal-05592447v1
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[hal-05585455] Unbiased molecular dynamics for the direct determination of catalytic reaction times: Paving the way beyond transition state theory
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ano.nymous@ccsd.cnrs.fr.invalid (Thomas Pigeon) 09 Apr 2026
https://ifp.hal.science/hal-05585455v1
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[hal-05584551] Fluorescence lifetime imaging microscopy of lignocellulosic biomass: principles, applications, and related techniques
Lignocellulosic biomass is a renewable carbon source that could help replacing fossil carbon feedstocks which cause many ecological concerns. However, to improve its bioconversion, the complex microstructure and chemistry of biomass needs thorough characterization. Emerging techniques like Fluorescence Lifetime Imaging Microscopy are particularly promising and this review aims to cover all aspects related to the use of lifetime microscopy for lignocellulosic biomass analysis. First, the mechanisms involved in fluorescence emission and atomistic properties influencing fluorescence lifetime are detailed. Then the three main instrumentations of lifetime microscopy are compared and the decay fitting function of fluorescence lifetime is presented. Numerous examples exposing the relevance of fluorescence lifetime imaging microscopy for biomass analysis are provided. Lifetime microscopy allows for cellulose, hemicelluloses, and lignins differential localization and syringyl / guaiacyl lignin ratio mapping. Fluorescence lifetime imaging microscopy can also provide insights on the effects of pretreatment and hydrolysis on the microstructure and chemistry of lignocellulosic biomass. Additionally, lifetime microscopy can inform on growth conditions like geographical origin or reaction wood formation as a response to gravitropic perturbations. Also, Förster Resonance Energy Transfer, being able to explore lignocellulosic biomass’s interactions with molecular probes, can be based on fluorescence imaging as well. Finally, other fluorescence-lifetime-related techniques having the potential to be implemented on lignocellulosic biomass are discussed.
ano.nymous@ccsd.cnrs.fr.invalid (Noah Remy) 08 Apr 2026
https://hal.science/hal-05584551v1
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[hal-05581048] Multivariate analysis coupled to infrared spectroscopy unravels the diversity of adsorption sites and strengths of a zeolite surface
Quantifying adsorption thermodynamics on heterogeneous catalysts remains challenging because macroscopic techniques yield averaged parameters, while vibrational spectra often contain strongly overlapping contributions from multiple adsorbed species. Here we introduce an infrared (IR)-chemometric framework that extracts site-specific adsorption thermodynamics directly from experimental IR isotherms and we benchmark it against independent microcalorimetry and density functional theory (DFT) calculations. Difference IR spectra recorded for isobutanol adsorption on H-ZSM-5 (MFI) were analysed by principal component analysis and multivariate curve resolution (MCR-ALS) under soft constraints (monotonic concentration profiles, spectral normalisation), and further refined using a hard–soft strategy in which concentration profiles are constrained by an adsorption model. The analysis reveals three adsorption modes associated with bridging Brønsted OH groups, extra-framework Al–OH species, and silanols, providing representative pure-component spectra and site-resolved adsorption isotherms. The thermodynamic trends and site hierarchy obtained from IR–MCR-ALS are consistent with independent microcalorimetry measurements and density functional theory calculations, validating the approach. More broadly, IR–MCR-ALS offers a transferable route to quantitative, site-resolved adsorption thermodynamics in complex catalysts.
ano.nymous@ccsd.cnrs.fr.invalid (Reda Aboulayt) 05 Apr 2026
https://hal.science/hal-05581048v1
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[hal-05496869] D-LIM: A neural network for interpretable gene–gene interactions
<div><p>Recent advances in gene editing can produce large genotype-fitness maps for targeted genes, yet predicting the effects of mutations between genes remains challenging. Indeed, biochemical models require knowledge of underlying parameters and interactions, whereas machine learning methods typically lack interpretability, as they do not link model parameters to biological quantities. We introduce D-LIM, a neural network that infers low-dimensional fitness landscapes directly from mutation-fitness data. The distinctive feature of D-LIM is that it assumes genes act through independent gene-specific molecular phenotypes whose nonlinear interactions determine fitness. When this assumption holds, the model yields accurate predictions and interpretable effective phenotypes. Conversely, failure reveals that a low-dimensional model is insufficient. Applied to deep mutational scanning of metabolic pathways, protein-protein interactions, and yeast environmental adaptation, D-LIM achieves state-ofthe-art predictive accuracy. The inferred phenotype-fitness landscapes reveal whether epistatic interactions can be captured by a low-dimensional continuous model and identify potential trade-offs. Moreover, D-LIM estimates mutational effects on the effective phenotypes, enabling weak extrapolation beyond the training domain. D-LIM demonstrates how simple structure constraints in a neural network can help inference and hypothesis generation in biology.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Shuhui Wang) 26 Mar 2026
https://hal.science/hal-05496869v2
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[hal-05240023] Chemical imaging of lignocellulosic biomass: Mapping plant chemistry
Lignocellulosic biomass (LB), which encompasses various plant samples, requires thorough characterization to optimize its use as a carbon resource. Chemical imaging simultaneously provides chemical and spatial information, offering significant benefits for LB analysis. This review presents an overview of the most advanced techniques for achieving this goal. By combining spectrometry and microscopy, microspectroscopy enables chemical imaging using various irradiation sources (IR, Raman, fluorescence, among others), allowing for the quantitative mapping of key LB components such as lignins, cellulose, and hemicelluloses. Mass Spectrometry Imaging (MSI) generates a mass spectrum for each spot of a sample thereby creating a chemical image pixel-by-pixel. MSI techniques like Matrix-Assisted Laser Desorption/Ionization (MALDI), down to 2–5 μm spatial resolution, and Secondary Ion Mass Spectrometry (SIMS), down to 300 nm for molecular analysis, effectively map small molecules in LB. In contrast, Desorption ElectroSpray Ionization (DESI) has been applied to plant extracts but remains largely unexplored for LB applications. Nuclear Magnetic Resonance (NMR) provides insight into various LB properties too. Solid-state NMR (ssNMR) and Dynamic Nuclear Polarization (DNP) help elucidate the structure of LB, sometimes aided by 3D atomistic modeling, whereas micro–Magnetic Resonance Imaging (micro-MRI) and Time-Domain (TD-NMR) probe the impact of water on LB properties.
ano.nymous@ccsd.cnrs.fr.invalid (Noah Remy) 09 Mar 2026
https://hal.inrae.fr/hal-05240023v1
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[hal-05543880] Unraveling the Mechanism of HMF Oxidation through a Colloidal Nanocatalyst Approach
The work presented here is performed in the context of the PEPR BBEST-FURFUN program, focused on the valorization of bio-sourced furanic derivatives. Our studies aim at developing efficient and sustainable catalytic oxidation of 5-hydroxymethylfurfural (HMF) for producing high-value compounds such as 2,5-furandicarboxylic acid (FDCA) and 2,5-diformylfuran (DFF). Most reported oxidation methods predominantly use efficient heterogeneous noble metal catalysts with soluble bases, but a deep understanding of the catalytic system is still needed to optimize the processes. Quasihomogeneous catalysis, based on stable metallic colloids as nanocatalysts, provides a well-defined environment to identify active sites to study reaction mechanisms, and has been applied for the first time to HMF oxidation under mild conditions. Nanocatalysts in the form of PVP-stabilized Pd nanoparticles (1.86 ± 0.07 nm) were synthesized in water.3 Catalytic oxidation of HMF was carried out under air flow in water (0.5 wt% HMF) with Na2CO3 (1.2 eq./HMF) at 80 °C. Complete HMF conversion was achieved within 48 h, with FDCA selectivity exceeding 80%. The colloidal system allows direct access to the intrinsic behavior of the active metal, free from support effects, enabling detailed mechanistic studies. Kinetic monitoring highlighted the critical role of the soluble base and clarified aspects of the reaction pathway towards selective oxidation. Moreover, the study demonstrates that quasi-homogeneous Pd nanocatalyst combines high efficiency and selectivity with minimal material use, making a promising system for sustainable biosourced chemical production. These findings lay the groundwork for optimization of catalytic processes, offering new perspectives for designing stable and environmentally benign catalysts for HMF valorization.
ano.nymous@ccsd.cnrs.fr.invalid (Lénaïck Hervé) 09 Mar 2026
https://hal.science/hal-05543880v1
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[hal-05523369] From Waste to Wardrobe: Exploring Consumer Acceptance of Biowaste-Dyed Sustainable Fashion
The study explores consumer acceptance of sustainable fashion innovations that use dyes made from biowaste, addressing a significant environmental challenge within the fashion industry. Through in-depth qualitative interviews with 18 participants (comprising both consumers and influencers engaged in sustainable fashion) the research dissects how intuitive judgment heuristics shape acceptance of biowaste-based dyeing. The analysis focuses on three key heuristics: affect (emotional response), trust (credibility and institutional assurance), and the natural-is-better bias (preference for perceived naturalness). Results reveal that while the valorisation of waste and the idea of circularity foster curiosity and positive reactions, acceptance is often limited by perceptions of unfamiliarity, safety concerns, and ambiguity about what is truly “natural.” Trust in regulatory frameworks, scientific validation, and transparent communication emerges as essential but is frequently conditional, requiring tangible proof before consumers feel comfortable. The findings highlight the complexity and ambivalence of consumer attitudes toward biowaste-based dyes, as intuitive heuristics can support both enthusiasm and scepticism, often hinging on how risks and benefits are framed by information sources. . Implications for sustainable innovation diffusion and managerial communication are discussed, alongside limitations and avenues for further research.
ano.nymous@ccsd.cnrs.fr.invalid (Arnaud Lamy) 23 Feb 2026
https://hal.science/hal-05523369v1
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[hal-05515316] RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery
Abstract RetroRules (https://retrorules.org) is an open resource of reaction templates, which are generic reaction representations that describe the atomic transformations underlying biochemical reactions. These templates are key to supporting metabolic pathway discovery, reaction prediction, and enzyme engineering. The 2026 release updates biochemical sources (MetaNetX, Rhea) and newly integrates organic chemistry reactions (USPTO), extending the scope of the database beyond enzymatic systems. The template encoding has been simplified by using implicit hydrogens and minimal atomic descriptors, resulting in faster and more compact representations. Radius range now spans 0–10, allowing finer control of reaction specificity. In addition, mass-imbalanced reactions are included, expanding the coverage of biochemically relevant transformations. Reaction mapping now relies on the transformer-based tool RXNMapper, improving accuracy. RetroRules 2026 comprises 1 174 216 templates derived from 92 698 reactions, covering 5796 fourth-level EC numbers. A redesigned website, updated Online Template Generator, and OpenAPI-defined API enable multi-criteria exploration (dataset, radius, and EC number), visualization, and data export in multiple formats. Sequence annotations from UniProt were refreshed and summarized as a normalized sequence-support score for ranking. Together, these updates establish RetroRules as a cross-domain resource bridging biochemistry and organic chemistry, offering broader coverage, controllable specificity, and enhanced usability for high-throughput pathway design, reaction prediction, and enzyme engineering.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Duigou) 17 Feb 2026
https://hal.science/hal-05515316v1
