Production scientifique

[hal-05790914] Gas holdup variations driven by porosity changes in a biological aerated filter under field operation

The spatial variability of gas–liquid hydrodynamics in Biological Aerated Filters (BAFs) is critical for improving the accuracy of process models, yet it remains poorly documented under representative full-scale operating conditions. This study presents the first bed-resolved assessment (bottom and top zones) of gas holdup and porosity in a large pilot-scale BAF operated under field conditions. Both parameters were derived from pressure-drop measurements and related to local fouling induced by suspended-solids filtration and biofilm growth. Porosity ranged from 12 to 30% between the operating biofilter and clean-bed reference conditions, with a difference between top and bottom zones under biofiltration: 12–22% in the bottom zone and 16–25% in the top zone. Porosity was negatively correlated with local fouling. Gas holdup varied from 0.8–8.6% depending on fouling, and the superficial velocities of the mobile phases. The gas-to-liquid volume ratio exhibited a non-monotonic trend with porosity, increasing as porosity decreased above 28%, remaining stable between 28 and 15%, and dropping sharply below 15%, reflecting shifts in bubble hydrodynamics driven by porosity changes. Including fouling as an indicator of bed-structure changes greatly improved gas holdup predictions compared with correlations that omit this effect.

ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez Archila) 10 Oct 2026

https://hal.science/hal-05790914v1

[hal-05790982] Microbial functions for nitrogen removal from wastewater: Lessons and challenges

21e congrès national de la Société Française de Microbiologie Du 7 au 9 octobre 2026 Centre des Congrès de Lyon, France Livre des résumés138 Retour sommaire Biotechnologies microbiennesSP19 - Les architectes invisibles des cycles biogéochimiques : dynamiques microbiennes, flux de matière et applications biotechnologiques (en association avec l’AFEM) Communications orales Biotechnologies microbiennes SP19-O.2 Microbial functions for nitrogen removal from wastewater: lessons and challenges Ahlem FILALI (ahlem.filali@inrae.fr) PROSE, INRAE, Antony, France Biological nitrogen removal from wastewater has historically relied on conventional nitrification–denitrification, combining the autotrophic oxidation of ammonium with the heterotrophic reduction of nitrate to nitrogen gas. Decades of research and full-scale implementation have established this conventional pathway as the benchmark process and considerably advanced our understanding of the microorganisms involved and the factors controlling their activity. However, nitrification requires oxygen supplied through aeration, which is one of the largest, if not the largest, energy consumers in wastewater treatment plants [1], while heterotrophic denitrification consumes organic carbon that could otherwise be used for biogas production and energy recovery. These microbial processes can also produce nitrous oxide (N₂O), a potent greenhouse gas that can contribute substantially to the overall carbon footprint of wastewater treatment and, in some cases, even dominate it [2, 3]. The challenges facing wastewater treatment plants now extend beyond pollutant removal alone. As reflected in the recast European Urban Wastewater Treatment Directive (EU) 2024/3019, they are expected to meet more stringent treatment requirements while progressing towards energy neutrality and reducing their carbon footprint. In light of these challenges, the presentation will discuss microbial pathways for nitrogen conversion in wastewater treatment plants, from conventional nitrification–denitrification to alternative pathways supporting more energy- and resource-efficient wastewater treatment, including processes based on anaerobic ammonium oxidation (anammox).

ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 10 Oct 2026

https://hal.inrae.fr/hal-05790982v1

[hal-05744014] From waste to worth: An explorative typology of service- and product-oriented business models for urban biowaste valorization

<div><p>Urban biowaste valorization is a promising pathway for the circular bioeconomy, yet the business models supporting it remain fragile and poorly understood. Research has mainly emphasized product-oriented biomass valorization, while service-based models have received less attention. This paper examines how urban biowaste is integrated into value creation, delivery and capture mechanisms, and whether the product/service distinction captures their diversity. Based on an exploratory qualitative study of ten French initiatives, it identifies three business model families (product-oriented, service-oriented and hybrid) and seven types: value-added product transformation; biowaste trading; product valorization supporting a social mission; core paid waste-management services; ancillary biowaste services; community and non-profit waste services; and integrated product-service approaches. Product-oriented models mainly capture value through marketable outputs, service-oriented models through collection, logistics, regulatory compliance and stakeholder support, and hybrid models through both mechanisms. Across these families, biowaste also creates relational and marketing value through customer engagement and CSR narratives, and social and territorial value through inclusion, education, community building and local resource loops. Environmental value cuts across these mechanisms through waste diversion, resource substitution and reintegration into material, energy or agronomic cycles. The study shows that the product/service distinction is useful but insufficient and contributes a multidimensional typology. It also complements the biomass value pyramid with a business model perspective accounting for product, service, relational, marketing, social and territorial forms of value.</p></div>

ano.nymous@ccsd.cnrs.fr.invalid (Maxime Sebbane) 09 Sep 2026

https://hal.science/hal-05744014v1

[hal-05781695] STAMM: Soft sensor moniToring and mAintenance framework for Machine learning Models

STAMM (Soft sensor moniToring and mAintenance framework for Machine learning Models) is an open source MLOps framework for industrial machine-learning soft sensors. Unlike general-purpose MLOps platforms (MLflow, Kubeflow, Metaflow, ClearML), STAMM targets the regime where ground-truth labels arrive of fline hours or days late, processes exhibit slow non-stationary dynamics, and models are multi-language. The framework comprises five loosely coupled components: a time-series database, workflow orchestrator, language agnostic REST model registry, dashboard with human-in-the-loop labelling, and an extensible drift-detection package. STAMM was validated on an industrial-scale fed-batch penicillin fermentation (IndPenSim) with seven coexisting R and Python soft sensors served through the model registry.

ano.nymous@ccsd.cnrs.fr.invalid (Carlos Suarez) 06 Oct 2026

https://hal.inrae.fr/hal-05781695v1

[hal-05734469] Coupling of stable isotope probing and metagenomics reveals the diversity of viruses infecting formatotrophs during anaerobic digestion process

Background Viruses play a major role in regulating microbial community composition and activity, yet their diversity and host associations in anaerobic digestion (AD)—a complex biotechnological process converting organic waste into biogas—remain poorly characterized. Linking viral sequences to metabolically active hosts in such complex communities is particularly challenging. Here, we applied an integrative approach combining 13C-stable isotope probing (SIP) with shotgun sequencing of viromes and microbiomes to identify and characterize viruses infecting the active formatotrophic guilds in batch AD microcosms. Results Microcosms fed with 13C-labeled formate as sole carbon source selectively enriched two primary formate-consuming guilds: hydrogenotrophic methanogens (Methanobacteriales, predominantly Methanobacterium subterraneum) and acetogenic bacteria (family Natronincolaceae, genus Andreesenella). From cross-assembly of six viromes on the one hand, and six 13C-SIP microbiome fractions on the other, we assembled a catalogue of 2,368 vOTUs, of which 261 were selected for detailed analysis. The striking enrichment of vOTUs associated with methanogenic archaeal hosts, specifically in the heavy (13C-enriched) SIP fractions, contrasted with their near-absence in total viromes—demonstrates that DNA-SIP successfully resolved viruses of active formatotrophs at the viral community level. Novel viruses were identified for both primary guilds, including archaeal viruses of Methanobacteriales (family Anaerodiviridae and a possible novel family) and two Andreesenella viruses carrying diversity-generating retroelements. A provirus predicted to infect Methanothrix—a strictly acetoclastic methanogen—further illustrates the capacity of SIP-viromics to capture viral associations across trophic levels. Analysis of auxiliary viral genes (AVGs) revealed numerous defense-associated genes (dcm, metK, queC) and genuine metabolic AVG candidates, such as cysH (assimilatory sulfate reduction) and, a contiguous cluster including uxe, galU and serB (surface polysaccharide biosynthesis), which may influence on host metabolism. Conclusions This study demonstrates the power of SIP-viromics for resolving virus-host associations in complex anaerobic communities, linking viral diversity directly to metabolically active formatotrophic and methanogenic guilds. The identification of novel viral lineages infecting key AD microorganisms, combined with AVGs with potential consequences for carbon and sulfur cycling, provides a foundation for understanding the functional role of viruses in AD process performance.

ano.nymous@ccsd.cnrs.fr.invalid (Vuong Quoc Hoang Ngo) 01 Sep 2026

https://hal.inrae.fr/hal-05734469v1

[hal-05773377] 8-L bubble column biocathode for low-temperature electromethanogenesis: Start-up dynamics and scale-up prospects

Background: Despite 15 years of MES research, low volumetric production rates, poor energy efficiency, and reactor design that brings high ohmic losses (e.g. H-type cell), limit electromethanogenesis scale-up1. By adopting a cylindrical geometry with a reduced anode/cathode surface area ratio, higher-rate MES for gas production can potentially be achieved2,3. Very few large-scale MES have been presented thus far in literature, notably, among them lies the largest (50 L) and pure culture MES for CH4 production to date2. Here, we present an 8 L modular bench-scale bubble-column biocathode, designed for mixed-culture, low-temperature, high-rate electromethanogenesis, with a view toward biogas upgrading and reduced specific energy demand. Reactor design and methods: A custom-made 8-L (D×H=16×50 cm) MES reactor (Fig.1) was assembled hosting a tubular membrane-electrode assembly (H = 25 cm) in sequence: 1) tubular cathode, 316 SS mesh (667 cm²), 2) tubular anion exchange membrane (6.5cm ID) and 3) graphite rod anode (146 cm²), with 3.15 cm interelectrode distance. Continuously CO2 is provided at 15 mL min−1 and the headspace is recirculated through the liquid phase at 15 – 20 mbar overpressure. We are presenting here start-up phase results, supportive to strategies for overcoming large-scale MES lag phases. Results: The cathodic compartment was inoculated (10% v/v) with a mixed MES cathodic inoculum enriched in Methanobacterium (45% relative abundance) and operation commenced at -0.95 V vs Ag/AgCl with 50 mM formate addition to decrease methanogenesis lag-phase. The latter, was expected to be especially long as the reactor is operated at room temperature, 19 – 21 ℃, usually reported to limit hydrogenotrophic methanogenesis. After a 35-day lag-phase and CH4 sparsely detected (Fig. 2), we additionally observed increased current densities, urging to switch to galvanostatic control (450 mA provided by a power source) due to potentiostat limits. Currently, on day 96 of operation we have achieved 0.05 L L−1 d−1 CH4 production rate (corresponding to 6 L m−2 d−1) at j = 6.75 A m−2, and only 0.4% detected H2 in the headspace. This volumetric production rate is currently 10 times lower than the highest reported with a 20-L MES3, however produced at 18 times lower current density. Outlook: The rates achieved so far, still at preliminary growth phase, signal high-rate, scaled-up electromethanogenesis potential. These startup strategies, including formate addition and step current density increase, unlock low-temperature pilot MES control, filling the critical 1-20L scale gap. Next, we will target modular biogas upgrading with integrated CO2 reduction and simultaneous H2S removal.

ano.nymous@ccsd.cnrs.fr.invalid (Eleftheria Ntagia) 01 Oct 2026

https://hal.inrae.fr/hal-05773377v1

[hal-05773341] BIOELECTROCHEMICAL SULFIDE OXIDATION AT THE MARGINS OF GROWTH: LOOKING FOR ANSWERS IN THE EXTREME

<div><p>Background and objectives: Sulfide-laden streams are generated by various industrial processes and are characterized by extreme pH and high sulfide (HS -) concentration [1] . The microbial sulfur cycle presents vast options for microbial treatment of these streams, especially since sulfureta are often characterized by harsh environmental conditions [2] . The objective was to examine haloalkaliphilic sulfide oxidizing microorganisms enabling removal of sulfide and production of electrons using an anode as e -acceptor in a bioelectrochemical system (BES). Methods: We investigated anoxic haloalkaline HS -oxidation in penicillin bottles with NO3 as e --acceptor and bioelectrochemically with an anode poised at -250 mV vs Ag/AgCl. Triplicate BES inoculated with saline alkaline lake sediment (HUA) and abiotic (A) reactors, were operated in fed-batch at alkaline (pH ≈ 10), mesophilic (22°C) and near-anoxic (O2(g) &lt;3%) conditions (Fig. 1a). After initial adaptation (10 mM [HS -], -300 mV, 70 days) all reactors were operated at 20 mM [HS -]. Sulfide removal, current density (j) and oxidized S species were monitored as performance indicators. Results: During initial operation the inoculated BES (HUA) exhibited lower current densities than the controls. After acclimatization, HUA3 achieved progressively higher j (0.21±0.02 mA/cm²) and eventually surpassed the controls, reaching 0.36±0.06 mA/cm² and 0.11±0.04 mM/day sulfide removal, 1.6-times higher j than the one achieved by the controls (A1 and A2). Sulfide removal and current production was not accompanied by an increase in sulfur oxyanions (SO4 2-, SO3 2-, S2O3 -). Concurrently, a distinct, yellow coloration developed in the electrolyte, suggesting S⁰/polysulfides formation and possible sulfur cycling within the single-chamber reactor. In contrast, HUA2 achieved lower but progressively increasing j, 0.11±0.03 mA/cm², with higher 0.30±0.05 mM/day sulfide removal (Fig. 1b) and production of SO4 2- (Fig. 1c). We are attributing these differences to different sulfur metabolisms developed, possibly triggered by marginal differences in the seed communities as well as in initial S-species formation. Initial 16S-rRNA sequencing of the seed community and the NO3 -enrichments indicated the presence of sulfur cycling and halophilic bacteria e.g., Idiomarinaceae (0.1%), Thioalkalispiraceae (0.1%) and Arcobacteraceae (7.0%) which in the NO3 -growth tests, increased to 16%, 7% and 28% relative abundance, respectively. We will use these results as indicators to compare with future sequencing results of the bioanodic and planktonic communities of BES and attempt further clarification of sulfur oxidation metabolisms in HUA3 versus HUA2.</p></div> <div>Conclusions and outlook:<p>Higher current density in HUA3 and removal of sulfide in HUA2 seem promising results for the application of BES in sulfidic wastewater treatment. The collection of additional molecular and physicochemical data such as elemental sulfur and isotopic fractionation will allow us to understand better the underlying metabolic processes. As a next step, we will also use microbial communities that coupled sulfide oxidation and nitrate reduction and switch from NO3 -to anode as e -acceptor.</p></div>

ano.nymous@ccsd.cnrs.fr.invalid (Gautier Prot) 01 Oct 2026

https://hal.inrae.fr/hal-05773341v1

[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

[hal-05683287] Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion

Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.709 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD systems. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2,760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.

ano.nymous@ccsd.cnrs.fr.invalid (Qihe Tang) 07 Jul 2026

https://hal.science/hal-05683287v1

[hal-05644280] {affiliationExplorer} a Shiny webapp to resolve taxonomy conflicts

Metabarcoding studies in microbial ecology generate taxonomic abundance profiles, with each taxon usually represented by an ASV (Amplicon Sequence Variant). Some taxa may be associated with several, sometimes conflicting, taxonomic affiliations. These ambiguities (or multi-affilia-tions) [1], may be frequent when analysing short sequences and/or when reference databases are incomplete. This complicates ecological interpretation and decreases the reproducibility of results. According to the origin of the samples (e.g. food, fecal, biowaste, etc.) or the conflict source (spelling typo in the reference databases) , manual curation can sometimes resolve these ambigui-ties. Likewise, some inconsistencies can be easily corrected programmatically if a manual curation was performed on a similar dataset and needs to be reapplied. The {affiliationExplorer} R-package provides a user interface dedicated to exploring and resolving these conflicts, and can easily be inserting in BIOM (Biological Observation Matrix) data analysis workflows. Developed in Shiny with the {golem} framework, this package offers a user-friendly interface for ① loading a BIOM file, a multi-affiliation file, and, optionally, one or more expert-verified sequence–taxonomy dictionaries (in FASTA format), ② visualising and ordering multi-affiliated taxa by abundance, ③ automatically resolving conflicts using the provided dictionaries for curated ASV references, ④ performing expert manual curation by selecting the most relevant affiliation among those proposed or specifying it manually, and ⑤ exporting a corrected BIOM file and a sequence–taxonomy dictionary to log the performed curations and for potential reuse in subse-quent curation sessions. The produced BIOM file follows the standards of biom-format.org and is fully compatible with standard metabarcoding workflows. The exported FASTA files can be reused as is in the interface.

ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 12 Jun 2026

https://hal.inrae.fr/hal-05644280v1

[hal-05683273] Antiviral defense systems drive persistence of antimicrobial‐resistant bacteria but limit the transfer of antimicrobial resistance genes in anaerobic digestion

Phage–host interactions critically shape environmental antimicrobial resistance (AMR). Using swine manure anaerobic digestion and multi-omics (metagenomics, meta-transcriptomics, and Hi-C), we mapped the phage–bacteria arms race and its impact on AMR dynamics. We revealed that phage-mediated lysis overwhelmingly dominates transduction, while phages rarely carry antimicrobial resistance genes (ARGs), and phage-borne ARGs showed no expression, challenging the paradigm of phages as primary vectors of ARGs. Crucially, the intense on-going phage–host arms race drives the widespread presence and expression of antiviral defense systems (ADSs) in antimicrobial-resistant bacteria (ARB). These ADSs exhibit a vital ecological dual role: they protect ARBs from phage lysis promoting persistence while simultaneously suppressing horizontal gene transfer (HGT, e.g., conjugation), as validated by in vitro conjugation assays. Our findings elucidate this duality, offering a novel framework to harness phage lytic pressure and ADS-mediated HGT suppression for environmental AMR mitigation.

ano.nymous@ccsd.cnrs.fr.invalid (Junya Zhang) 07 Jul 2026

https://hal.science/hal-05683273v1

[hal-05698089] Création d’un réseau SHINY::ESR

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ano.nymous@ccsd.cnrs.fr.invalid (Élise Maigné) 20 Jul 2026

https://hal.inrae.fr/hal-05698089v1

[hal-05687855] Modelling Nitrification in Densified Activated Sludge Systems requires to consider a dynamic KO2 for granules

Densified activated sludge (DAS) systems enhance conventional activated sludge performance by combining flocculated sludge and granular biomass, improving settleability and treatment capacity. However, oxygen diffusion limitations within granules can impact nitrifier activity and affect system efficiency. This study addresses the challenge of modelling the partitioning of ammonia-oxidizing bacteria (AOB) between flocs and granules in continuous-flow DAS systems. The apparent oxygen half-saturation coefficient of nitrifiers (KO2,NIT) was experimentally determined via respirometry on DAS and granules from three full-scale treatment plants. A positive correlation between granule size and KO2,NIT was established and incorporated into a zero-dimensional plant-wide model with hydrocyclones. Model simulations demonstrated that using a dynamic oxygen diffusion resistance (DRO2,NIT) better predicted the balanced distribution of ammonia-oxidising bacteria (AOB) between flocs and granules compared to a fixed DRO2,NIT. While the later tends to overestimate granule nitrifier fractions and to hinder early AOB growth in granules, a dynamic DRO2,NIT better reflects AOB partitioning during granulation.

ano.nymous@ccsd.cnrs.fr.invalid (Mathilde Lepage) 09 Jul 2026

https://hal.science/hal-05687855v1

[hal-05658485] Mesophilic Anaerobic Digestion of Municipal Sewage Sludge under High Sodium Propionate Concentrations in Semi-continuous Conditions

Anaerobic digestion (AD) treats sewage sludge and agricultural waste, but the accumulation of volatile fatty acids, particularly propionic acid (HPr) or sodium propionate (NaPr), can inhibit performance. This study examined NaPr inhibition in AD using four semi-continuous 5-L reactors operated at 37 °C for 81 days and loaded with increasing NaPr concentrations (0–135.3 mmol L⁻¹). No inhibition occurred at 20.3 mmol L⁻¹, while moderate reductions in methane and biogas production were seen at 81 mmol L⁻¹, and severe inhibition (40%) at 135.3 mmol L⁻¹.Microbial community structure was driven primarily by incubation time and secondarily by NaPr concentration. Higher NaPr levels suppressed methanogens such as Methanothrix and Methanobrevibacter while enriching syntrophic propionate oxidizers, including Pelotomaculum and Cryptanaerobacter, demonstrating the sensitivity and adaptive response of AD microbiomes to propionate stress.

ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 16 Jun 2026

https://hal.science/hal-05658485v1

[hal-05674009] Electromethanogenesis from H2S containing biogas: H2S and cathode potential drive microbial selection and methane yields

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ano.nymous@ccsd.cnrs.fr.invalid (Ankit Rao) 30 Jun 2026

https://hal.inrae.fr/hal-05674009v1

[hal-05674029] Propionic acid-related inhibition during anaerobic digestion: insights into methane production and microbial community responses

Propionic acid (HPr) accumulation is a major indicator of anaerobic digestion (AD) dysfunction, yet the respective contributions of acidity, undissociated HPr and the propionate ion (Pr⁻) to inhibition and microbial community composition remain unclear. Using mesophilic batch microcosms fed with municipal sewage sludge, we compared HPr, sodium propionate (NaPr), NaCl and HCl across two experimental series. Inhibition by HPr was governed by the pH drop rather than by Pr⁻: 20 mM HPr reduced the maximal methane rate by 22%, while 81 mM HPr (pH 5.1) abolished methane production, an effect reproduced by HCl at the same pH. At near-neutral pH, the propionate salt had only a secondary, concentration-dependent effect (81 mM NaPr, -40% on the rate), largely attributable to ionic strength (81 mM NaCl, -23%). 16S rRNA gene amplicon sequencing revealed compound-specific community restructuring: methanogenic archaea fell from 2–3% to &lt;0.2% of relative abundance under 81 mM HPr, and the &gt;100 differentially abundant ASVs were largely shared with HCl reactors, confirming the dominant role of acidity. The number of differentially abundant ASVs was negatively correlated with the methane rate (R² = 0.97). These results clarify the respective roles of pH, undissociated HPr and Pr⁻ in both methane inhibition and microbial community restructuring.

ano.nymous@ccsd.cnrs.fr.invalid (Xiaojun Liu) 07 Oct 2026

https://hal.inrae.fr/hal-05674029v2

[hal-05773363] Enriching for extremophilic, autotrophic sulfide oxidizers growing on nitrate: toward sustainable depollution of sulfidic streams

<div><p>Industrial, sulfide-laden streams are characterized by alkaline pH, high sulfide (HS -) content and elevated salinity. Microbial treatment offers a promising alternative to conventional, energy dense physicochemical treatment. The microbial sulfur cycle provides relevant options, as sulfureta naturally thrive in similar harsh conditions. This study aimed to enrich a haloalkaliphilic, sulfide oxidizing microbial community, capable of autotrophic, anoxic HS - oxidation. Saline, alkaline lake sediment was used as inoculum for microbial incubations under mesophilic (22°C) and near-anoxic (O2(g) &lt;2%) conditions, using nitrate as electron acceptor.</p><p>Sulfide and nitrate were supplied at 10 mM and 20 mM respectively, in DSMZ 925 medium.</p><p>Samples were collected at regular intervals monitoring sulfide, sulfate, nitrate, optical density (for growth (OD600)), yellow colour development (OD400) and microbial diversity with 16S-rRNA sequencing. Upon HS -depletion, concentrations were reset from 1 M stock solutions, initiating a new batch. Sulfide decreased along with nitrate at 0.90 ± 0.12 mmol S/L d and 0.68 ± 0.46 mmol N/L d, this corresponds to a 1:0.75 mol ratio between electron donor and acceptor.</p><p>The sulfide removal rate increased with sulfide additions, from 0.52 mmol S/L d to 1.02 mmol S/L d. In every batch, a yellow colour appeared, coinciding with sulfide removal, suggesting S⁰/polysulfides formation. Coupled with sulfide oxidation and nitrate reduction, the relative abundance of Thioalkalivibrio sp. (known chemolithoautotrophic haloalkaliphilic sulfuroxidizing bacteria) increased from 0.5% to 11%. Moving forward, we will explore the capacity of these enrichments for depollution applications, investigating a less chemical-intensive route for sulfidic stream treatment, specifically in bioelectrochemical systems.</p></div>

ano.nymous@ccsd.cnrs.fr.invalid (Gautier Prot) 01 Oct 2026

https://hal.inrae.fr/hal-05773363v1

[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

[hal-05777090] Scope and objectives of the Astee N₂O sub-working group

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 04 Oct 2026

https://hal.science/hal-05777090v1

[hal-05777096] Emissions from wastewater treatment processes

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Romain Lemaire) 04 Oct 2026

https://hal.science/hal-05777096v1

[hal-05777105] Conclusions and perspectives

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Sperandio Mathieu) 04 Oct 2026

https://hal.science/hal-05777105v1

[hal-05677856] Caractérisation des retours en tête du traitement des boues en vue de leur valorisation

Cet article présente et analyse les principales caractéristiques des flux d’eau interstitielle produits lors du traitement des boues primaires, secondaires ou après digestion et qui sont renvoyés en tête de station d’épuration. L’objectif est de fournir les gammes de valeurs pour les paramètres susceptibles d’influencer le choix et le dimensionnement des procédés de traitement ou de valorisation de ces retours en tête (matières en suspension (MES), matières volatiles en suspension (MVS), demande chimique en oxygène (DCO), N, P, principaux ions). Les résultats bibliographiques couplés à des données acquises sur deux stations françaises montrent une forte variabilité de ces caractéristiques en lien notamment avec les procédés implantés sur les files eau et boues des installations, avec des concentrations en ammonium élevées après digestion anaérobie. La concentration en orthophosphates dépend du type de traitement du phosphore dans la file eau, et des processus de précipitation qui ont lieu dans le digesteur. La mise en place d’un prétraitement thermique avant digestion augmente principalement les concentrations en DCO, en ammonium et l’alcalinité des retours en tête, mais n’a pas d’impact significatif sur la concentration en orthophosphates de ces flux, en lien avec différents précipités qui peuvent se former dans le digesteur.

ano.nymous@ccsd.cnrs.fr.invalid (Devos Perrine) 02 Jul 2026

https://hal.science/hal-05677856v1

[hal-05569770] Digestion anaérobie mésophile des boues d'épuration municipales sous fortes concentrations de propionate de sodium en conditions semicontinues : inhibition et modifications de la communauté microbienne

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 27 Mar 2026

https://hal.science/hal-05569770v1

[hal-05687840] Spatially-Resolved Characterization of Gas Hold-up and Gas-Liquid Mass Transfer in an Operating Large-Scale BAF

This study presents the first quantitative evaluation of gas distribution in a large-scale biological aerated filter (BAF) operated under realistic conditions. A 6.2 m pilot, installed at a WRRF, was continuously fed with real pre-treated wastewater. A key finding is that bed porosity, which evolves with fouling, governs the spatial and temporal dynamics of gas hold-up during biofiltration. Existing correlations based on clean-bed systems failed to capture in-bed gas behavior. New correlations accounting for superficial liquid/gas velocities and fouling significantly improved prediction accuracy, reducing errors from over 50% to around 10%. The results related to oxygen transfer are currently under analysis and will complement the findings presented here on gas hold-up.

ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez-Archila) 09 Jul 2026

https://hal.science/hal-05687840v1

[hal-05502139] Spatial structure: Shaping the ecology and evolution of microbial communities

Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.

ano.nymous@ccsd.cnrs.fr.invalid (Marcel Bäcker) 10 Feb 2026

https://hal.inrae.fr/hal-05502139v1

[hal-05644678] MIFE and MIFD: Minimum information for fermentation experiments and devices

Abstract Background As the technological advancements of the early 21st century are pushing industrial biotechnology (IB) into the realm of Big Data–driven innovation, the requirement for trustworthy data management, annotation, and standardization is emerging as a necessity. Minimum information models (MIMs) have long been used across disciplines as the backbone of good data management practices by providing the scaffold upon which standardized recording of metadata can adequately and succinctly describe an understudied phenomenon. Findings Here we present a minimum set of metadata, named the minimum information for fermentation experiments (MIFE) and devices (MIFD), that has been specifically designed to accommodate the data management and annotation needs of IB-related fermentation experiments. Although the proposed schema is tailored to IB applications, MIFE and MIFD build upon well-established models and community standards to facilitate easier integration with existing infrastructure and easier adoption by the community, as well as aim to integrate Findable, Accessible, Interoperable, and Reproducible (FAIR) principles in the IB field. In addition, the integration with FAIR Data Station (FAIR DS), a tool that offers metadata validation and enables the automated uptake of (meta)data from data management repositories such as FAIRDOM-SEEK, is showcased. The proposed models are accompanied by a Python package that enables their programmatic use by creating a Linked Data Modeling Language (LinkML) schema that can fuel subsequent analyses. Conclusions Through the promotion and simplification of knowledge discovery, we believe that MIFE and MIFD can accelerate the application of state-of-the-art artificial intelligence (AI) methods and the adoption of explainable AI to better understand bioprocesses at scale.

ano.nymous@ccsd.cnrs.fr.invalid (Georgios Georgakilas) 04 Jun 2026

https://hal.science/hal-05644678v1

[hal-05440960] Keystone concept revisited: insights into microbial community dynamics and control

Different definitions of keystone taxa and functions agree that they have an outsized role in maintaining community composition, and thus, the keystone concept continues to attract attention even 50 years after its introduction. In this Perspective, we base our definition of microbial keystones on the original one to explore its implications and limitations. We review different mechanisms behind keystoneness, cover the strengths and weaknesses of current keystone prediction methods and present findings on keystones discovered in recent experiments. In addition, we suggest a new prediction method for keystones based on metabolic modelling. Finally, we discuss the role of keystones in community control strategies. Overall, the development of new prediction methods and the insights from recent experiments illustrate the continued relevance of the keystone concept for microbial communities.

ano.nymous@ccsd.cnrs.fr.invalid (Daniel Rios Garza) 05 Jan 2026

https://hal.science/hal-05440960v1

[hal-05729746] Métabolisme énergétique et azoté d’un méthaniseur coopératif en plaine de grandes cultures végétales : interroger les effets de la méthanisation à l’échelle des territoires agricoles

acteurs des systèmes agricoles et alimentaires sont aujourd’hui soumis à de multiples contraintes (environnementales, réglementaires, économiques et sociétales). Pour y faire face, on observe le déploiement de transitions de plus en plus rapides des territoires agricoles, marquées par l’adoption de pratiques plus ou moins innovantes, aux impacts plus ou moins positifs mais surtout peu évalués, et dont il est aujourd’hui difficile de mesurer la portée globale. L’une de ces transitions est la méthanisation agricole, menée à l’échelle individuelle (au niveau d’exploitations) ou collective (groupes d’exploitations, coopératives agricoles, etc.). Pour les exploitations, la méthanisation constitue une diversification lucrative favorisant la viabilité économique. Elle apporte également des solutions concrètes avec la valorisation rémunératrice des cultures intermédiaires ou des autres coproduits et résidus des filières agricoles et agroalimentaires, ou une plus grande autonomie en fertilisants grâce aux digestats produits. A une échelle plus globale, la méthanisation permettrait une meilleure autonomie énergétique de l’agriculture française, par la production d’énergie non fossile et la substitution des engrais azotés (fortement consommateur d’énergies fossiles pour leur synthèse) par des fertilisants organiques. La production de biogaz agricole participe aussi aux objectifs de durabilité et de souveraineté énergétique de la France. La méthanisation agricole apparaît donc comme un levier pour la transition agroécologique et énergétique des systèmes de production agricole. Le déploiement de la méthanisation à l’échelle des territoires agricoles peut prendre la forme d’accumulation l’accumulation de digesteurs à la ferme ou l’implantation d’unités de grande taille fournies par plusieurs exploitants dans un cadre coopératif et/ou industriel (négociants en matières agricoles, digesteur associé à des industries sucrières, etc.). Le potentiel de transformation induit par le déploiement de la méthanisation est peu étudié à l’échelle, systémique, des territoires agricoles. Les effets peuvent pourtant être délétères pour la résilience du système agricole et sa durabilité (Cadiou et al., 2023), et des études ont notamment indiqué des conséquences négatives telles que l’intensification de concurrence d’accès à certaines biomasses locales qui fragilise des filières (Marty et al., 2021) ; une évolution des emblavements pour intégrer les CIVES qui change les profils de production des territoires (Borros, n.c.) et les impacts et équilibres environnementaux des territoires (Launay et al., 2022). Cette communication vise à contribuer à éclairer cette question sur la base de l’analyse métabolique d’un méthaniseur coopératif situé en plaine de grandes cultures végétales. Afin de déterminer les forces et faiblesses de cette unité de méthanisation, ainsi que ses contributions positives ou négatives au territoire agricole dans lequel elle s’ancre, nous réalisons un bilan transversal des flux d’azote organique et d’énergie mis en jeu par le fonctionnement de cette unité.

ano.nymous@ccsd.cnrs.fr.invalid (Pauline Marty) 28 Aug 2026

https://hal.science/hal-05729746v1

[hal-05612073] From microbes to molecules: Gut microbiota as a prerequisite threshold determinant for cancer immunotherapy efficacy

Cancer immunotherapy, represented by immune checkpoint inhibitors, adoptive cell therapy, and cancer vaccines, has revolutionized the clinical management of multiple malignant tumors, yet profound interindividual heterogeneity in treatment response and widespread primary/acquired resistance remain the most critical bottlenecks restricting its long-term clinical benefits. Accumulating preclinical and clinical evidence has unequivocally established the gut microbiota as a pivotal regulator of host anti-tumor immune responses. However, the vast majority of existing studies and reviews frame the gut microbiota as a mere adjuvant enhancer of immunotherapy efficacy, focusing solely on its role in boosting the upper limit of treatment effects, while neglecting its more fundamental role as a prerequisite for establishing a responsive immune baseline. In this review, we propose a unifying, evidence-based original core hypothesis: the gut microbiota is not merely an enhancer of cancer immunotherapy efficacy, but an indispensable prerequisite condition that sets the minimal baseline threshold for therapeutic responsiveness-a central thesis that distinguishes this review from previous descriptive work. Guided by this hypothesis, we systematically dissect the taxonomic and functional characteristics of threshold-determining gut microbiota, and clarify that microbial metabolites (e.g., short-chain fatty acids, bile acids, tryptophan derivatives) act as core molecular mediators translating microbial signals into host immune activation, which is critical for establishing the baseline efficacy threshold required for effective immunotherapy. We further perform a critical synthesis of clinical data from prospective cohorts, randomized controlled trials, and microbiota intervention studies, validating that threshold-based microbial signatures serve as non-invasive predictive biomarkers for immunotherapy outcomes, and propose mechanism-driven translational strategies targeting the gut microbiota (e.g., fecal microbiota transplantation, probiotic supplementation, dietary modulation) to reset the impaired immunotherapy efficacy threshold. This review provides a novel theoretical framework for understanding the microbiota-immunotherapy axis, which not only deepens the mechanistic insight into microbial metabolite-mediated immune regulation, but also facilitates the development of microbiota-guided personalized cancer immunotherapy and the overcoming of primary treatment resistance.

ano.nymous@ccsd.cnrs.fr.invalid (Xin Su) 07 Jul 2026

https://hal.science/hal-05612073v1

[hal-05668413] Chronic sublethal effects of pulsed versus constant pesticide exposures on the freshwater amphipod Gammarus fossarum: Behavioural and biochemical impairments under field-realistic conditions

After their application to agricultural soils, pesticides frequently reach surface waters, exposing aquatic organisms to fluctuating concentrations influenced by hydrological conditions. However, the influence of exposure dynamics on biological responses remains poorly investigated. In this study, the non-target amphipod Gammarus fossarum was exposed for four weeks in microcosms to environmentally realistic concentrations of three pesticide classes: the insecticide imidacloprid, the fungicide boscalid, and the herbicide bentazone. Two exposure scenarios were compared: (i) repeated short-term pulses mimicking runoff events and (ii) constant low-level exposures, both time-weighted average concentrations. Biochemical biomarkers (enzymes involved in essential functions and stress responses) and behavioural traits (locomotion, respiration, mating and feeding rate) were monitored to assess sublethal effects at cellular and individual levels. Both exposure regimes elicited changes in behaviour of animals and biochemical pathways. Notably, hyperactivity coupled with increased respiration occurred, with pesticide-specific intensity. Unlike repeated pulses, constant exposures to the insecticide and fungicide exerted more persistent inhibitory effects on feeding. Biochemical analyses revealed pesticide-specific disturbances in digestive metabolism, oxidative stress response, and neuronal activity, and suggested trade-offs in energy allocation under chronic chemical stress. Furthermore, these sublethal responses provide evidence of unintended impacts of these chemicals, even at concentrations compliant with environmental quality standards, to which wildlife is naturally exposed under various hydrological conditions. Since such disruptions in physiology and individual performance in this ecosystem engineer may precede population-and ecosystem-level consequences, our results highlight the need to integrate exposure dynamics and multi-level sublethal endpoints in ecotoxicological risk assessment to improve the protection of aquatic wildlife in agriculturally impacted freshwaters.

ano.nymous@ccsd.cnrs.fr.invalid (Jérémie D Lebrun) 24 Jun 2026

https://hal.inrae.fr/hal-05668413v1

[hal-05695906] Host-virus dynamics in anaerobic digesters facing abiotic inhibition

Viruses play a major role in controlling the structure and dynamics of microbial communities in anaerobic digesters, ecosystems sensitive to disturbances that inhibit methane production. Here, we studied the interplay between abiotic disturbances, microbiome and virome composition, and process performance, to assess whether provirus induction can be triggered by abiotic stresses known to inhibit anaerobic digestion (ammonium, phenol and sodium chloride). We monitored viral dynamics in batch mesophilic anaerobic digesters fed with biowaste through shotgun metavirome sequencing. The diversity of both prokaryotes and viruses was high, with Clostridiales dominating the prokaryotic community and Caudoviricetes dominating the viromes. We identified 132 viral contigs and 19 host genera that were differentially abundant under disturbed conditions. No significant impact of the tested abiotic stresses on provirus induction was observed under the current experimental and analytical framework. The results were consistent with viruses exerting steady, background-level predation through a putative combination of kill-the-winner dynamics at the sub-genus level and piggyback-the-winner dynamics, rather than stress-triggered, synchronous lytic bursts. A few auxiliary metabolic genes were detected, potentially targeting carbon, sulfur and cofactor metabolism in anaerobic digestion. Temperate viruses were dominant, representing up to 71% of the viral genomes confirmed as complete across all conditions. Electron microscopy analysis revealed diverse virus-like particles, including head-tailed particles typical of Caudoviricetes, but also spherical, rod-shaped and spindle-shaped particles typical of archaeal viruses. Notably, we present a new virus family, Eurekaviridae, of spindle-shaped viruses associated with methanogenic archaea.

ano.nymous@ccsd.cnrs.fr.invalid (Marion Coves) 12 Aug 2026

https://hal.science/hal-05695906v1

[hal-05777103] Other emission sources

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 04 Oct 2026

https://hal.science/hal-05777103v1

[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

[hal-05442197] Plan de gestion des données de l’unité de recherche PROSE (UR1461 INRAE)

L’unité PROSE mène des recherches sur les biotechnologies environnementales, depuis l’échelle des communautés microbiennes jusqu’à celle des procédés (stations d’épuration, digesteurs anaérobies, procédés bioélectrochimiques pour la bioraffinerie, …), en articulation avec les grands enjeux sociétaux de développement durable, d’économie circulaire et de bioéconomie. Affiliée aux départements TRANSFORM et MICA d’INRAE, l’unité PROSE s’inscrit dans une démarche transdisciplinaire fondée sur l’écologie microbienne, la biogéochimie, le génie des procédés, les mesures physiques et la modélisation. L’unité PROSE est composée d’un pôle de chercheurs et chercheuses porteurs de projets, d’un pôle analytique regroupant un laboratoire de microbiologie moléculaire et un laboratoire de chimie dotés d’équipements de pointe, et d’un pôle expérimentation ayant une capacité à déployer ses compétences à la fois à l’échelle pilote et sur le terrain. Ce plan s’inscrit dans le cadre des activités de recherche de l’unité PROSE et des projets de recherche auxquels elle contribue.

ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 16 Jan 2026

https://hal.inrae.fr/hal-05442197v1

[hal-05653713] Mesophilic Anaerobic Digestion of Municipal Sewage Sludge Under High Sodium Propionate Concentrations in Semi-Continuous Conditions: Inhibition and Microbial Community Shifts

The accumulation of intermediate products, particularly volatile fatty acids (VFAs) like propionic acid (HPr) or its dissociated form, can inhibit biogas production during anaerobic digestion (AD) at low concentrations. Knowledge about the response of microorganisms to VFA inhibition can help control the digesters. In this study, we aimed to determine how sodium propionate (NaPr) inhibits the AD of municipal sewage sludge by identifying shifts in the microbial community. Four 5 L reactors were operated in semi-continuous mode using sewage sludge and then loaded with different levels of NaPr. The reactors operated at 37 °C with two hydraulic retention times. The results show that there was no apparent inhibition of biogas production at NaPr loading up to 20.3 mmol·L−1. However, moderate inhibition was observed at 81 mmol·L−1, corresponding to an approximate 10% decrease in methane production, while a ≈40% decrease in methane production was observed at 135.3 mmol·L−1. Sequencing analysis revealed that the community composition was dominated by Bacillota, Bacteroidota, Proteobacteria, Chloroflexi, and Cloacimonadota, with Halobacterota and Euryarchaeota as the main archaeal groups. PERMANOVA revealed incubation time as the primary driver of community structure, followed by NaPr concentration. Elevated NaPr levels resulted in a decline in Methanothrix and Methanobrevibacter and promoted distinct syntrophic propionate-oxidizing bacteria (SPOB).

ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 11 Jun 2026

https://hal.science/hal-05653713v1

[hal-05393313] Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 02 Dec 2025

https://hal.inrae.fr/hal-05393313v1

[hal-05397464] Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animaux

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ano.nymous@ccsd.cnrs.fr.invalid (Núria Mach) 04 Dec 2025

https://hal.science/hal-05397464v1

[hal-05308646] Spatial distribution of gas–liquid mass transfer in a co-current upflow biological aerated filter

The spatial variability of oxygen transfer in Biological Aerated Filter (BAF) is key to improving model accuracy but remains underexplored. This is the first spatially resolved characterization of gas-liquid transfer parameters in a large-scale pilot BAF under clear-water, biofilm-free conditions. Porosity (ϵ0) and gas hold-up (εG) profiles were measured using pressure and oxygen sensors. Oxygen transfer was quantified using stationary and dynamic methods, with modeling to estimate the transfer coefficient (kLa) across reactor zones. Measured εG and kLa were significantly higher in the bed zone, which comprises 29% of the reactor working volume but accounts for 71.7% of oxygen flux. The bed also showed a stronger dependence of εG on gas velocity, revealing limits of reactor-scale correlations in capturing bed-scale dynamics. Under tested conditions, ϵ0, εG, and kLa were uniform throughout the bed. Correlations developed for εG and kLa in the bed support BAF model refinement.

ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez Archila) 04 Oct 2026

https://hal.inrae.fr/hal-05308646v1

[hal-05308873] Implicit Generalized Predictive Control of a Wastewater Treatment Plant: Application to the SimBio Model

This paper presents an implementation of an implicit Generalized Predictive Control (GPC) strategy applied to a wastewater treatment plant (WWTP) modeled via the SimBio simulator. Without identifying an explicit dynamic model, the control law is derived directly from system input-output behavior. The main goal is to regulate the effluent ammonium (NH<sub>4</sub><sup>+</sup>) concentration by manipulating the aeration rate, while coping with perturbations such as influent flow and ammonium concentration. Several configurations of the control parameters were tested and evaluated using process performance indicators. The obtained results show that the proposed controller allows a good tracking of the desired set-point while presenting a low energy consumption during the considered period of the experiment.

ano.nymous@ccsd.cnrs.fr.invalid (Yasmine Siahmed) 10 Oct 2025

https://hal.inrae.fr/hal-05308873v1

[hal-05400292] COVID-19 and chronic liver disease: results from the 1219 patients French registry

The deleterious impact of Coronavirus SARS CoV-2 related Disease (COVID-19) in patients with chronic liver disease (CLD) has been previously described. We report here data from the largest French “real-life” cohort. Patients with CLD regardless of etiology and liver transplant recipients who developed COVID-19 confirmed by a positive PCR and/or an evocative chest CT scan were included. The primary outcome was 30-days mortality. Prognostic factors were analyzed using both uni- and multivariate models in subgroups of transplanted and non-transplanted patients. Between August, 2020, and December, 2021, 1219 patients were included, mostly men (n = 754), median age 61 years, 477 patients with advanced CLD (decompensated (Child–Pugh B or C) in 164 patients); 366 patients were immunocompromised, including 271 organ transplant recipients. Hospitalization in intensive care unit was required in 11% of cases. The median follow-up was 68 days. The overall 30-days mortality was 13% (159 deaths, 62% related to extra-hepatic causes). Among transplant recipients, age was the only independent prognostic factor. In the non-transplanted population, the independent prognostic factors were advanced liver fibrosis (F3 or F4, HR 2.5), obesity (HR 1.56) and age (HR 1.03), whereas immunosuppression was not. Within the subgroup of patients with advanced CLD, decompensation (Child–Pugh B or C) was an independent predictor of mortality (HR 3.8). In conclusion, our results highlight the increased vulnerability of patients with advanced CLD to COVID-19, particularly those with decompensated disease. Conversely, they confirm the absence of excess mortality related to immunosuppression, particularly in organ transplant recipients. Clinical trial registration: Clinical trial (NCT 04,375,670).

ano.nymous@ccsd.cnrs.fr.invalid (L. Blaise) 23 Apr 2026

https://normandie-univ.hal.science/hal-05400292v1

[hal-05410146] Higher butanol titer and selectivity in electro-fermentation experiments with Clostridium acetobutylicum ATCC 824 are due mainly to methyl viologen rather than electrode polarization

Butanol selectivity is crucial for the development of an industrial process targeting butanol as the main product of acetone-butanol-ethanol (ABE) fermentation by solventogenic Clostridia. This study evaluated electro-fermentation (EF), with an electron carrier, methyl viologen (MV), as a strategy to modify solvent production in Clostridium acetobutylicum ATCC 824 under optimized batch fermentation conditions. Cathodic EF was performed with or without 0.5 mM MV in single-compartment reactors with two-chamber and a negative potential was applied to the cathode. The greatest differences in final products concentrations were observed with the addition of MV compared to the control and EF fermentations. The fermentation with MV only was slowed down and resulted in 11% more butanol (control: 14.2 g.L−1, MV: 15.8 g.L−1) and half as much acetone, increasing the butanol/acetone (B/A) ratio by 137% from 1.93 to 4.57 g C.g C−1. The pH profile was also modified with a final pH 0.5 unit higher. Conversely, EF did not appear to alter product formation significantly, even if slight differences were observed under our conditions. In addition, the reductase activity (RA) was measured by flow cytometry and showed that EF alone affected the intracellular redox state compared to the control fermentation, as did the addition of MV. However, electrode polarization had no effect on the extracellular oxidoreduction potential (ORP) profiles.

ano.nymous@ccsd.cnrs.fr.invalid (Edouard Beudy) 10 Dec 2025

https://ifp.hal.science/hal-05410146v1

[hal-05308832] Dynamiques du transfert gaz-liquide dans un pilote triphasique de biofiltration

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez Archila) 10 Oct 2025

https://hal.science/hal-05308832v1

[hal-05308870] Thermodynamic and Non-thermodynamic Effects on Anodic Electromicrobial Biofilm Growth under Controlled Hydrodynamics

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Elena Roques) 10 Oct 2025

https://hal.science/hal-05308870v1

[hal-05162180] When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM project

Cheese ripening is a crucial step in the production process during which microorganisms such as yeasts, molds, and bacteria transform the curd, developing its flavor, texture, and final characteristics. Like all bacteria, ripening bacteria can be infected by bacteriophages (or phages), viruses that specifically target bacteria. While phages infecting lactic acid bacteria used in milk acidification are well studied — along with the technological issues they cause — very little data exist on the phages of ripening bacteria or their potential involvement in ripening defects, such as altered aromas or textures, unwanted pigmentation, or irregular openings.In this context, the PHAGOFROM project aims to: (i) explore the diversity of phages infecting ripening bacteria, from farms and raw milk to the cheese surface, and identify potential phage reservoirs; (ii) develop innovative, practical, and industry-oriented tools for detecting relevant phages; and (iii) raise awareness and provide practical solutions to stakeholders in the dairy sector, especially those involved in quality-labeled cheese production.The project begins with an awareness phase regarding the issue of phage-related ripening defects, targeting dairy professionals through actions such as webinars and surveys of cheese producers. This step aims at identifying case studies where phages may be linked to ripening defects. Milk and cheese samples will be collected from these cases to study phage diversity and to build bank of characterized phages. In parallel, a metaviromic approach will be used to explore the broader diversity of phage communities. The impact of phages on ripening and on the development of potential defects will be assessed through pilot-scale cheese productions, and transferable detection tools will be developed for use by industry stakeholders.By improving our understanding of ripening defects potentially caused by phages, the PHAGOFROM project will contribute to better control cheese typicity, particularly in quality-labeled products.

ano.nymous@ccsd.cnrs.fr.invalid (Marion Dalmasso) 15 Jul 2025

https://normandie-univ.hal.science/hal-05162180v1

[hal-05308868] Thermodynamic and Non-thermodynamic Effects on Anodic Electromicrobial Biofilm Growth under Controlled Hydrodynamics

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Elena Roques) 10 Oct 2025

https://hal.science/hal-05308868v1

[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

[hal-05721470] Extracting temporal patterns from longitudinal microbiome data through clustering of functional variables

In terms of sequencing, recent technological advances offer the possibility of rapid data acquisition at relatively low cost. These advances naturally pave the way for longitudinal studies to understand not only the composition of a community of microorganisms and their interactions, but also the kinetics of these microbial systems over time. Among the challenges associated with such longitudinal studies, the partitioning of microorganisms according to their evolutionary patterns is of crucial interest to microbiologists [1], in order to reduce the inherent high data dimensionality. To this end, we propose to adapt the clustering of variables CLV, traditionally performed on a matrix or three-way of quantitative variables [2,3], to the case of functional variables in the scope of longitudinal omics. These data can be represented by an matrix whose entry is the function corresponding to the individual . Moreover, it is assumed that all functions are defined on the same compact real interval and take values in . Functional CLV aims at partitioning the set of the functional variables into homogeneous groups, so that each variable is associated as closely as possible with the latent functional variable of the group to which it belongs. We show how to adapt the CLV criterion using the framework of multivariate functional PCA [4], and the associated partitioning algorithm is then detailed. Functional CLV is applied to longitudinal metataxonomic data in the context of the anaerobic digestion bioprocess [5,6]. In particular, the aim is to identify groups of microorganisms based on common longitudinal profiles that also reflect potential differences in their dynamics towards salinity stress.

ano.nymous@ccsd.cnrs.fr.invalid (Véronique Cariou) 19 Aug 2026

https://oniris.hal.science/hal-05721470v1

[hal-05408601] A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.

Abstract Cardiometabolic diseases (CMD) are on the rise globally with one billion people expected to suffer from obesity and 643 million from type 2 diabetes by 2030, of which one-third will likely develop chronic kidney disease and two-thirds will die from cardiovascular disease (CVD). However, the mechanistic and molecular drivers of the transition from health to disease remain elusive. Here, in 275 metabolically healthy individuals recruited to the MetaCardis study, we identify a gut microbiome-kidney-heart axis that is predictive of future cardiovascular events. This axis, as evidenced by the associations between gut microbial metabolism of phenylalanine and tyrosine with variations in both kidney functon(as measured by estimated glomerular filtration rate) and circulating pro-atrial natriuretic peptide concentration, shows a depletion pattern in metabolically unhealthy participants of the MetaCardis study (n = 1,602) indicating a loss of health-sustaining microbiome features with CMD progression. We then validate that microbial compounds from the phenylalanine and tyrosine pathways and their host co-metabolites act as mediators of the gut microbiome-kidney associations. Moreover, Mendelian Randomization analysis adds genetic evidence to suggest that the microbial mediator metabolites regulate host kidney function and vice versa. Finally, we demonstrate that plasma metabolites derived from the microbial metabolism of phenylalanine and tyrosine associate with incident CVD in the Canadian Longitudinal Study on Aging (n = 8,669). Collectively, our results depict the presence of a gut microbiome-kidney-heart axis in metabolically healthy individuals. Major aberrations of the gut microbiome as part of this axis throughout life may increase risk of CVD.

ano.nymous@ccsd.cnrs.fr.invalid (Kanta Chechi) 10 Dec 2025

https://hal.science/hal-05408601v1

[pasteur-05212168] Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Archaeal Viruses Subcommittee, 2025

An erratum of this article has been published full details can be found at 10.1099/jgv.0.002145 The International Committee on Taxonomy of Viruses (ICTV) holds a ratification vote annually following the review of newly proposed taxa by ICTV Study Groups and members of the virology community. This article reports changes to the taxonomy of viruses infecting archaea that were approved and ratified by the ICTV in March 2025. Six new families of head-tailed viruses expanded the order Caudoviricetes (realm Duplodnaviria ); one new family of filamentous viruses was added to the order Ligamenvirales (realm Adnaviria ); one new family of viruses with pleomorphic virions was included within a new phylum, new order and new class in the kingdom Trapavirae (realm Monodnaviria ); finally, three new families were created for spindle-shaped viruses that remain unassigned to higher level taxa. The 25 new species represent viruses infecting a broad range of archaea, including members of the classes Archaeoglobi, Bathyarchaeia, Methanobacteria, Methanomicrobia, Nitrososphaeria and Poseidoniia. Most of these viruses have been discovered by metagenomics in samples derived from diverse environments, including ambient and extreme marine ecosystems, the gastrointestinal tract of humans and animals, anaerobic digesters and terrestrial hot springs. Following this taxonomic update, archaeal viruses are officially classified into a total of 163 virus species in 94 genera within 62 families.

ano.nymous@ccsd.cnrs.fr.invalid (Mart Krupovic) 17 Aug 2025

https://pasteur.hal.science/pasteur-05212168v1

[hal-05073170] Conception d'une ontologie pour la gestion des connaissances en bioraffinerie environnementale, EBO

L'organisation et la structuration des données sont devenues des enjeux majeurs dans le domaine des sciences du vivant et de l'environnement. Face à l'augmentation des volumes de données expérimentales hétérogènes, le besoin d'interopérabilité et de raisonnement automatisé devient crucial. Dans le cadre du développement du système d'information EnviBIS au sein du LBE (INRAE), l'ontologie EBO (Environmental Biorefinery Ontology) a été conçue afin de formaliser et structurer les connaissances relatives aux procédés de bioraffinerie environnementale. En s'appuyant sur la méthode Linked Open Terms (LOT), la construction de l'ontologie repose sur une analyse approfondie du domaine, enrichie par des techniques de traitement appliquées à un corpus scientifique. Implémentée en OWL et alignée avec des standards, EBO est exploitée via RDF4J et Apache Jena. Elle permet d'assurer l'interopérabilité avec d'autres SI. Ce travail s'inscrit dans une dynamique de structuration et de partage des connaissances à l'échelle interinstitutionnelle et nationale.

ano.nymous@ccsd.cnrs.fr.invalid (Emilie Fernandez) 19 May 2025

https://hal.inrae.fr/hal-05073170v1

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Production scientifique

HAL : Dernières publications

[hal-05790914] Gas holdup variations driven by porosity changes in a biological aerated filter under field operation

[hal-05790982] Microbial functions for nitrogen removal from wastewater: Lessons and challenges

[hal-05744014] From waste to worth: An explorative typology of service- and product-oriented business models for urban biowaste valorization

[hal-05781695] STAMM: Soft sensor moniToring and mAintenance framework for Machine learning Models

[hal-05734469] Coupling of stable isotope probing and metagenomics reveals the diversity of viruses infecting formatotrophs during anaerobic digestion process

[hal-05773377] 8-L bubble column biocathode for low-temperature electromethanogenesis: Start-up dynamics and scale-up prospects

[hal-05773341] BIOELECTROCHEMICAL SULFIDE OXIDATION AT THE MARGINS OF GROWTH: LOOKING FOR ANSWERS IN THE EXTREME

[hal-05788702] Time Matters More than Cryoprotectants: Storage Duration Selects for Dormancy-Competent Lineages in Cathodic Microbiomes

[hal-05683287] Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion

[hal-05644280] {affiliationExplorer} a Shiny webapp to resolve taxonomy conflicts

[hal-05683273] Antiviral defense systems drive persistence of antimicrobial‐resistant bacteria but limit the transfer of antimicrobial resistance genes in anaerobic digestion

[hal-05698089] Création d’un réseau SHINY::ESR

[hal-05687855] Modelling Nitrification in Densified Activated Sludge Systems requires to consider a dynamic KO2 for granules

[hal-05658485] Mesophilic Anaerobic Digestion of Municipal Sewage Sludge under High Sodium Propionate Concentrations in Semi-continuous Conditions

[hal-05674009] Electromethanogenesis from H2S containing biogas: H2S and cathode potential drive microbial selection and methane yields

[hal-05674029] Propionic acid-related inhibition during anaerobic digestion: insights into methane production and microbial community responses

[hal-05773363] Enriching for extremophilic, autotrophic sulfide oxidizers growing on nitrate: toward sustainable depollution of sulfidic streams

[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

[hal-05777090] Scope and objectives of the Astee N₂O sub-working group

[hal-05777096] Emissions from wastewater treatment processes

[hal-05777105] Conclusions and perspectives

[hal-05677856] Caractérisation des retours en tête du traitement des boues en vue de leur valorisation

[hal-05569770] Digestion anaérobie mésophile des boues d'épuration municipales sous fortes concentrations de propionate de sodium en conditions semicontinues : inhibition et modifications de la communauté microbienne

[hal-05687840] Spatially-Resolved Characterization of Gas Hold-up and Gas-Liquid Mass Transfer in an Operating Large-Scale BAF

[hal-05502139] Spatial structure: Shaping the ecology and evolution of microbial communities

[hal-05644678] MIFE and MIFD: Minimum information for fermentation experiments and devices

[hal-05440960] Keystone concept revisited: insights into microbial community dynamics and control

[hal-05729746] Métabolisme énergétique et azoté d’un méthaniseur coopératif en plaine de grandes cultures végétales : interroger les effets de la méthanisation à l’échelle des territoires agricoles

[hal-05612073] From microbes to molecules: Gut microbiota as a prerequisite threshold determinant for cancer immunotherapy efficacy

[hal-05668413] Chronic sublethal effects of pulsed versus constant pesticide exposures on the freshwater amphipod Gammarus fossarum: Behavioural and biochemical impairments under field-realistic conditions

[hal-05695906] Host-virus dynamics in anaerobic digesters facing abiotic inhibition

[hal-05777103] Other emission sources

[hal-05693548] Lignocellulose-powered bioelectrochemical systems: microbial communities, controlling factors, and enhancement strategies

[hal-05442197] Plan de gestion des données de l’unité de recherche PROSE (UR1461 INRAE)

[hal-05653713] Mesophilic Anaerobic Digestion of Municipal Sewage Sludge Under High Sodium Propionate Concentrations in Semi-Continuous Conditions: Inhibition and Microbial Community Shifts

[hal-05393313] Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.

[hal-05397464] Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animaux

[hal-05308646] Spatial distribution of gas–liquid mass transfer in a co-current upflow biological aerated filter

[hal-05308873] Implicit Generalized Predictive Control of a Wastewater Treatment Plant: Application to the SimBio Model

[hal-05400292] COVID-19 and chronic liver disease: results from the 1219 patients French registry

[hal-05410146] Higher butanol titer and selectivity in electro-fermentation experiments with Clostridium acetobutylicum ATCC 824 are due mainly to methyl viologen rather than electrode polarization

[hal-05308832] Dynamiques du transfert gaz-liquide dans un pilote triphasique de biofiltration

[hal-05308870] Thermodynamic and Non-thermodynamic Effects on Anodic Electromicrobial Biofilm Growth under Controlled Hydrodynamics

[hal-05162180] When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM project

[hal-05308868] Thermodynamic and Non-thermodynamic Effects on Anodic Electromicrobial Biofilm Growth under Controlled Hydrodynamics

[hal-05788677] Hypersaline microbial electrolyser for the energy efficient production of carboxylates from biowaste

[hal-05721470] Extracting temporal patterns from longitudinal microbiome data through clustering of functional variables

[hal-05408601] A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.

[pasteur-05212168] Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Archaeal Viruses Subcommittee, 2025

[hal-05073170] Conception d'une ontologie pour la gestion des connaissances en bioraffinerie environnementale, EBO

Voir aussi