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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 Article14 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 15 - 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 Article16 10 - 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 Article70 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 Article29 35 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Tailored enzyme expression modifies Shewanella oneidensis biofilms and increases current density(Elsevier, 2025-06-09); ; ; ; Biofilm formation is the most effective pathway for electron transfer to anodes in bioelectrochemical systems. However, the mechanisms triggering biofilm formation under anoxic conditions, as well as the architectural and compositional factors that positively influence current generation, are not well understood. Recent findings have shown that riboflavin can function similarly to a quorum sensing molecule in the γ-proteobacterium Shewanella oneidensis. Enhanced biofilm formation induced by riboflavin correlates with increased current densities. Only a limited number of candidate proteins were found to have altered concentrations due to this quorum sensing mechanism. This study demonstrates that the catalytic functions of the UDP-N-acetylglucosamine C4 epimerase WbpP and UDP-N-acetyl-D-glucosamine 6-dehydrogenase WbpA affect biofilm formation and lead to increased current density. Using optical coherence tomography, we found that the expression of each protein individually causes specific, quantifiable changes in biofilm architecture, including biovolume, height, and porosity. However, the current density did not significantly differ when these proteins were expressed alone compared to the control. In contrast, co-expression of WbpP and WbpA resulted in a doubling of current density, closely resembling the increases observed with riboflavin-mediated quorum sensing. We hypothesize that riboflavin-based quorum sensing may lead, through several intermediary steps, to the overproduction of WbpA and WbpP, resulting in better attachment to graphite anodes and thus higher current densities.Publicationtype: Journal Article9 18 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , 36 61 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Strategic improvement of Shewanella oneidensis for biocatalysis: approach to media refinement and scalable application in a microbial electrochemical system(Elsevier, 2025-03-25); ; ; ; Microbial electrochemical systems offer a sustainable method for the conversion of chemical energy into electrical energy or hydrogen and the production of valuable compounds, contributing to the development of a bio-based economy. This study aimed to enhance the performance of anodic bioelectrochemical systems by improving the current density of Shewanella oneidensis as a biocatalyst through strain modification and medium refinement. The genetic modification, combining the prophage deletion and overexpression of the speC gene, resulted in a 4.2-fold increase in current density compared to the wild type. Furthermore, medium refinement and incorporating riboflavin, led to an additional 5.7-fold increase in current density. The application of the modified strain and medium in a scalable microbial electrolysis cell resulted in a current density of 1.2 A m-², similar to what was achieved previously with an S. oneidensis and Geobacter sulfurreducens co-culture, substantiating the substantial performance increase for a pure culture of S. oneidensis. Furthermore, S. oneidensis was shown to grow in medium containing up to 500 mM sodium chloride and increasing the salt concentration to 400 mM had a minor influence on growth but significantly lowered the cell voltage of the MEC system.Publicationtype: Journal Article19 10 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Oxygen in the mix: is oxic microbial electrosynthesis a potential alternative for biomass production?Oxic microbial electrosynthesis (oMES) allows the utilization of renewable electricity and industrial gas streams containing CO2 and O2 for biomass production by cultivating aerobic, autotrophic, hydrogen-oxidizing bacteria, commonly known as Knallgas bacteria. oMES is likely not a direct competitor to conventional anoxic microbial electrosynthesis as harnessing aerobic hydrogen-oxidizing bacteria depends on energetically inefficient assimilatory CO2 reduction pathways. However, it might be a complementary approach to classical biomass production from the perspective of limited land use and the availability of cheap renewable energy. The best characterized Knallgas bacterium is Cupriavidus necator. Extensively studied as lithoautotrophic production host, C. necator already offers a broad arsenal of genetic tools. In contrast, mechanistical knowledge about the recently discovered Kyrpidia spormannii is limited, but this species shows remarkable growth when cultivated as cathodic biofilm in bioelectrochemical systems. In addition, first experiments indicate a low energy demand for biomass production, which is in the order of magnitude of gas fermentation with C. necator or heterotrophic and methanotrophic technologies. Still, many aspects of the electrochemical cultivation of K. spormannii need to be better understood and rigorously improved to be a competitive technology in the making, including electron transfer and microbial kinetics, cultivation conditions, mass and energy balances, and reactor design.Publicationtype: Review Article41 62 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Biofilms for production of chemicals and energyThe twenty-first century will be the century of biology. This is not only because of breakthrough advances in molecular biology tools but also because we need to reinvent our economy based on the biological principles of energy efficiency and sustainability. Consequently, new tools for production routines must be developed to help produce platform chemicals and energy sources based on sustainable resources. In this context, biofilm-based processes have the potential to impact future production processes, because they can be carried out continuously and with robust stationary biocatalysts embedded in an extracellular matrix with different properties. We review productive biofilm systems used for heterotrophic and lithoautotrophic production and attempt to identify fundamental reasons why they may be particularly suitable as future production systems.Publicationtype: Review Article7 84