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Item type:Publication, Access status: with files , Selective bioelectrochemical purification of propionate from food waste hydrolysate(Elsevier, 2026-12-21); ; Dark fermentation enables hydrogen production while generating propionate-rich streams from food waste. However, efficient separation of propionate from short-chain fatty acid (SCFA) mixtures remains challenging and costly in the downstream processes. Therefore, strategies enabling selective purification of propionate prior to separation from the fermentation broth are highly desirable. In this study, a bioelectrochemically assisted bench-scale process was developed as a proof-of-concept pretreatment to enhance selective purification of propionate prior to downstream processing. A single-chamber rotating disc bioelectrochemical reactor (RDBER) was used to selectively purify the hydrolysate via enhancing the consumption of butyrate by an electroactive biofilm of a recently published butyrate-oxidizing microbial consortium. In the RDBER, different hydraulic retention times (HRTs) without and with pH control were evaluated to investigate their effects on propionate fraction among SCFAs and process stability. The results show that with a pH of 7.0–7.3 and an HRT of 8 days, a propionate fraction of up to 95.5% can be achieved, with its concentration doubling compared to the feed. These results demonstrate the potential of this process as a pretreatment step prior to downstream separation, with the aim of reducing separation complexity and enhancing propionate recovery.Publicationtype: Journal Article15 7 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Limits of Knallgas bacteria for autotrophic CO₂ conversion: physiology, H₂ kinetics and reactor constraintsAerobic hydrogen-oxidizing bacteria, commonly referred to as Knallgas bacteria, are chemoautotrophic microorganisms that oxidize molecular hydrogen (H₂) while fixing carbon dioxide (CO₂) into cellular material. Historically studied as model systems for lithoautotrophic metabolism, these organisms have regained attention due to their potential for renewable H₂ utilization, land-independent biomass production, and electrochemically coupled CO₂ conversion. Among them, Cupriavidus necator has emerged as a promising industrial platform, while thermophilic and high-affinity H₂-oxidizers such as Kyrpidia spormannii are increasingly explored in bioelectrochemical systems. Despite growing interest, substantial gaps remain between laboratory demonstrations and scalable industrial performance. This review analyzes the physiological characteristics of Knallgas bacteria, including growth kinetics and H₂ oxidation parameters, and evaluates their translation into gas fermentation and oxic microbial electrosynthesis systems. Particular emphasis is placed on key engineering limitations, including H₂ mass transfer, electron partitioning during aerobic metabolism, reactor safety constraints, and electrochemical surface scaling.Publicationtype: Review Article10 2 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Grammar-guided symbolic regression as tool for model development of enzymatic reactions(Elsevier, 2026-09-23); ; ; The transition of the chemical industry toward renewable biocatalysis requires robust kinetic models to scale and optimize enzymatic processes. However, deriving these models typically relies on manual, trial-and-error fitting of predefined equations, while data-driven machine learning approaches often produce accurate but physically meaningless “black-box” models. Here, we present an adaptive kinetic model evaluation framework that automates the discovery of enzymatic rate laws directly from batch progress curves. By employing Grammar-Guided Symbolic Regression (GGSR) the algorithm autonomously constructs rate equations using only physically permissible kinetic building blocks. The framework’s reliability was first validated against 13 synthetic kinetic mechanisms, confirming structural and parametric identifiability. The pipeline was then applied to a real experimental case study of glucose-fructose isomerization using Streptomyces murinus isomerase. The algorithm successfully recovered a reversible kinetic equation featuring an apparent uncompetitive-type interaction term providing specific activities and Michaelis constants that align well with literature. This work demonstrates that GGSR can bridge the gap between data-driven automation and mechanistically interpretable biochemical engineering.Publicationtype: Journal Article16 14 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Synthetic polymers promote cell aggregation and accelerate cathode-associated layer formation in Kyrpidia spormannii EA-1(Elsevier, 2026-09-15); ; ; 4 4 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Identification of genetic determinants that promote biofilm growth under heterotrophic conditions in Cupriavidus necator using transposon enrichment(Elsevier, 2026-09-01); ; ; Cupriavidus necator is a metabolically versatile β-proteobacterium of growing interest for auto- and heterotrophic bioprocesses, yet the genetic determinants governing its biofilm formation remain largely uncharacterized, particularly under process-relevant heterotrophic conditions. Here, we applied a forward-genetics transposon-enrichment approach to identify loci which promote surface-associated growth. A high-density mini-Tn5 mutant library (26,185 insertion clones, exceeding the >17,000 required for genome-wide coverage) was cultivated as a biofilm in a microfluidic flow-cell system on fructose for 168 h, and the surface-associated community was characterized by deep sequencing. Twelve genes showed significantly elevated insertion frequencies, several with documented links to biofilm formation in other bacteria, including the ferrous-iron uptake system (feoA/feoB), galU, and a GSDEF/EAL dual-domain protein. The gene B2043 (E6A55_RS29530), encoding this c-di-GMP-metabolizing protein, was selected for validation by markerless deletion. Under static conditions, the ΔB2043 mutant showed a 1.69 ± 0.06-fold increase in biofilm-associated biomass (p = 5.16 × 10<sup>−15</sup>). Under flow-through conditions, the mutant attached faster, entered exponential growth ∼10 h earlier, reached its biovolume plateau ∼16 h earlier than the wild-type, and formed distinct tower-like structures. These results identify B2043 as a negative regulator of biofilm formation acting predominantly during attachment, provide the first experimental evidence for c-di-GMP-dependent biofilm regulation in C. necator H16, and establish a functional-genomics framework — together with eleven further candidate loci — for engineering productive biofilms in this organism.Publicationtype: Journal Article15 10 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Living electronics: coupling S. oneidensis MtrC-SpyTag cells to SpyCatcher-functionalized electrodes for direct electron transfer(Elsevier, 2026-08-15); ; ; ; This work set out to establish an easily applicable system to improve a broad range of bioelectronic devices using the SpyTag-SpyCatcher crosslinking system together with one of the model organisms for extracellular electron transport, Shewanella oneidensis . Therefore, the surface-displayed c -type cytochrome MtrC was equipped with an accessible SpyTag and coupled to SpyCatcher-functionalized surfaces. A transposon screen followed by nanopore sequencing was conducted in order to identify integration positions which facilitate MtrC functionality while the SpyTag is surface accessible. Three integration positions (W314, Y417, T603) were chosen for further characterization. Expression of the MtrC-SpyTag constructs in a S. oneidensis strain lacking all outer membrane cytochromes restored the ability to reduce an extracellular electron acceptor. Two of the three strains reached reduction rates at the wildtype MtrC level proving that the integrated SpyTag does not hamper extracellular electron transfer. In vivo, all three constructs showed significantly better binding properties to SpyCatcher functionalized magnetic beads than the wildtype MtrC control. The two most promising candidates were coupled to conductive, magnetic gold nanoparticles and directed towards a screen-printed electrode showcasing how MtrC-SpyTag expression can improve bioelectronic devices. A significantly higher charge transfer compared to the wildtype control was reached in linear sweep voltammetry and chronoamperometry experiments. Moreover, a shift towards direct electron transfer was observed which reduces the problem of redox shuttle washout in flowthrough systems. Direct binding of the cells to SpyCatcher functionalized electrodes enabled robust current production even after thorough washing of the electrodes while control cells failed to produce current under these conditions. The versatile SpyCatcher toolbox can be used together with the here reported strains to eliminate bottlenecks in bioelectronics like poor biofilm formation or the production of an insulating extracellular polymer matrix.Publicationtype: Journal Article47 11 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Aerographite vs Graphite: Investigating the role of electrode architecture in H2-mediated electroautotrophic biofilms(American Chemical Society (ACS), 2026-08-07); ; ; ; Oxic microbial electrosynthesis using aerobic hydrogenotrophic bacteria requires productive cathodic biofilm formation, yet reactive oxygen species (ROS) generated at the electrode surface present a critical barrier to initial colonization. This study investigates biofilm development by Cupriavidus necator H16 on Aerographite, an ultralow-density carbon foam (3–12 mg cm–3, porosity > 99%) with a hierarchical tetrapodal pore network, as a cathode material in microfluidic bioelectrochemical systems and compares it to graphite (a composite material consisting of graphite and polypropylene (PPG86)). A biphasic cultivation strategy, in which heterotrophic biofilm establishment preceded a switch to electroautotrophic conditions at −45.45 μA cm–2, successfully overcame the ROS barrier on both electrode materials. Noninvasive optical coherence tomography revealed a final biovolume of 0.086 mm3 mm–2 on graphite after 14 days, representing the first continuous kinetic characterization of C. necator cathode biofilm formation under defined flow conditions. Despite lower absolute biovolume per projected area, Aerographite supported higher biomass per unit electrode mass, reflecting its 585-fold higher mass-specific electroactive surface area relative to graphite. Scanning electron microscopy confirmed C. necator colonization of internal pore regions up to 500 μm below the electrode surface under laminar flow-over conditions. The macropore dimensions substantially exceed documented self-limiting biofilm thicknesses, indicating that pore occlusion is unlikely even at full biofilm development, and positioning Aerographite as a structurally enabling electrode material for smart, scalable, flow-through CO2 valorization systems.Publicationtype: Journal Article66 25 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Oxygen-dependent redox control enables growth-decoupled biotransformations in Cupriavidus necatorGenetic instability and environmental heterogeneity present persistent challenges to the stable microbial production of reduced, value-added chemicals. This work shows that limiting oxygen availability redirects electrons from respiration toward targeted reductive pathways in Cupriavidus necator, steering growth-decoupled biotransformations — exemplified by the conversion of acetoin to 2,3-butanediol and of glycerol to 1,3-propanediol. In cell suspension assays under a hydrogen-containing atmosphere, anoxic conditions stabilised near-stoichiometric acetoin-to-2,3-butanediol conversion (93% molar efficiency) despite minimal fructose consumption, indicating that the reductive pathway served as the primary sink for reducing equivalents. Under oxic conditions, rapid product re-oxidation lowered the final 2,3-butanediol titre to 2.6 mM. The same principle extended to 1,3-propanediol formation in a glycerol-kinase-deficient strain: anoxic incubation yielded 6.6 mM 1,3-propanediol, whereas aerobic conditions suppressed accumulation despite rapid substrate uptake. Viability assays showed that Cupriavidus necator retained above 84% viable cells under electron-acceptor exclusion for 144 h, declining to about 68% at 312 h and below 30% by 696 h, with cell aggregation from 48 h onward. This defined operational window, together with the lithoautotrophic capability of the organism, distinguishes the approach. By providing a metabolic configuration in which loss of production would be expected to be selectively disfavored, oxygen-controlled redox steering offers a route toward more robust reductive biotransformations. Oxygen availability thus acts as a single, tunable lever determining whether reducing equivalents flow into reduced products or into respiration.Publicationtype: Journal Article28 32 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Flow-driven structural and transcriptomic responses in syntrophic electroactive biofilms(Elsevier, 2026-07-07); ; ; ; Bioelectrochemical systems (BES) are versatile platforms for energy and resource recovery, where electroactive biofilms serve as the key biocatalyst. While performance depends on flow dynamics, the interplay between hydrodynamic conditions, biofilm architecture, and gene-regulation in syntrophic communities remains poorly understood. We investigated defined surface flow velocities (0.2 and 0.8 mm/s) on the structure and electroactivity of Shewanella oneidensis–Geobacter sulfurreducens coculture biofilms. Higher flow produced more compact biofilms with lower biovolume and porosity, yielding higher current densities. Flow transitions induced persistent structural and electrochemical shifts, indicating an adaptive, gene-regulated response to shear. Since G. sulfurreducens monoculture biofilms were flow-insensitive, regulation appears to originate from S. oneidensis. Transcriptomics showed strong shear response, including 10.7-fold upregulation of bpfD. Its deletion reduced current density and increased porosity despite comparable biovolume. Three-dimensional fluorescence in situ hybridization imaging revealed a porous, loosely organized structure within the mutant biofilm. This was consistent with the structural and electrochemical differences observed. These findings reveal that community-level electrochemical performance can be governed by a minor transcriptional contributor rather than by the dominant current-producing species.Publicationtype: Journal Article15 6 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Design approach and performance of a scalable granular packed bed biofilter for electro-fermentationBioelectrochemical systems (BES) represent a promising technology for the production of energy, energy carriers, and chemicals; however, their implementation in industrial applications faces significant challenges related to scalability. In this study, we introduce a novel, scalable, single-chamber BES in which the working electrode is realised as a packed bed of electrically conductive equal-sized spheres made from a graphite-polymer composite. The reactor has a total volume of 3.56 L and a packed bed volume of 1.66 L with an electrode surface area of 1.06 m². A model microbial electrolysis / electro-fermentation of lactate to acetate was catalysed by the exoelectrogenic bacterium Shewanella oneidensis , achieving a maximum current density of 430 mA m<sup>-2</sup> at an anode potential of 300 mV relative to the standard hydrogen electrode.Publicationtype: Journal Article19 6