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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); ; ; 2 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 Article14 9 - 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 , 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 , Tuning membraneless microbial electrolysis cells operation alters efficiency and anodic microbiome toward scalable hydrogen production from sludge-hydrolysate(Elsevier, 2026-01-21); ; ; ; The practical implementation of microbial electrolysis cells (MECs) is hindered by challenges in optimizing system performance with complex substrates. This study addresses that gap by evaluating MECs fed with hydrolysate, an appealing substrate rich in organic-acids. Through systematic variation of substrate concentration (20–60 %), pH (5–8), and applied anodic potential ( 0.2 to +0.4 V vs standard hydrogen electrode [SHE]), the optimal operational conditions were defined as 40 %-hydrolysate, pH 8, and +0.4 V vs SHE, yielding a mean current density of 3.4 A/m2 and coulombic efficiencies (CE) of 38 % and 96 % based on total organic carbon (TOC) and total volatile fatty acids (VFAs), respectively. Scalability was demonstrated using a 10 L rotating disk bioelectrochemical reactor (RDBER) at 0 and 0.4 V vs SHE, achieving a maximum hydrogen production rate of 30.57 L/m2/d and minimal methane formation at 0.4 V. These findings offer a framework for optimizing MECs under real-feedstock conditions.Publicationtype: Journal Article33 15 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , EBPR process dynamics under variable conditions: interaction between PAOs and the microbial communityThe performance of enhanced biological phosphorus removal (EBPR) is influenced by various process conditions, such as the type of carbon source, temperature, COD:P ratio or pH-value. The activity of polyphosphate accumulating organisms (PAOs) and the composition of biocoenosis are strongly influenced by these process conditions. Nevertheless, critical knowledge gaps remain regarding the relevance of microbial diversity and the correlations between PAO/GAO community composition and EBPR process dynamics under different operational conditions. This study demonstrates that Dechloromonas plays a crucial role in the EBPR process and that the type of carbon source has a more sensitive influence on EBPR dynamics than the COD:P ratio, temperature or pH. Using both a microfluidic model biofilm system (MMBS) and a sequencing batch reactor (SBR) system, we found that the consumption of glucose resulted in maximal PAO activity, whereas EBPR performance was limited when using glycerol, ethanol and amino acids. In both systems, Dechloromonas was the dominant PAO, while in MMBS Zoogloea and in SBR Competibacter/Contendobacter were the dominant GAOs. Tessaracoccus (PAO) and Micropruina (GAO) were relevant in the fermentation of glucose and glycerol. No significant effect on EBPR performance was observed between 12 and 20 °C, and PAO activity peaked at pH 7.5. Our findings highlight that PAO-GAO competition is overestimated. We anticipate that our study provides a deeper understanding of the dynamics in the biocoenosis and emphasizes the relevance of biodiversity in EBPR systems, which would help guide relevant applications.Publicationtype: Journal Article15 11 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Influence of different transposon families on genomic stability of Shewanella Oneidensis MR1Shewanella oneidensis, recognised as an important model organism for exoelectrogenic electron transport, has been extensively studied for its potential applications in bioelectrochemical systems. To date, the activity of transposable elements in this organism has not been conclusively investigated. This study focused on transposases, specifically insertion sequences (IS), which make up approximately 4.7% of the organism's genome, and evaluated their impact on genome stability under stress conditions. Using whole genome sequencing, two IS families, ISSOD1 and ISSOD2, were identified as the most active, both showing similar transposition patterns across all tested stressors. A CRISPR/dCas9 cytosine deaminase system was used to introduce stop codons in the ISSOD2 transposase genes, resulting in a significant reduction of transposition events under stress conditions. Analysis of transposition patterns revealed a high frequency of insertions occurring on the megaplasmid, which predominantly carries non-essential genes. Experiments performed here to delete the megaplasmid resulted in the elimination of approximately 35% of its sequence, including an unexpected complete loss of the ori/repA region. Therefore, it was hypothesised that the megaplasmid either exists in a metastable state, possibly representing a cointegrated intermediate within the ISSOD9 (Tn3 member) transposition mechanism, or consists of two replicons that have been combined in previous assemblies due to long overlapping homologies resulting from the presence of ISSOD9. These findings highlight the dynamics of transposable elements in S. oneidensis and suggest strategies to improve strain stability by inactivating these elements and at least reducing megaplasmid sequences. Such approaches could improve the suitability of the organism for industrial applications.Publicationtype: Journal Article14 13 - 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 17 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Comparative study of bioanodes for microbial electrolysis cells operation in anaerobic digester conditions(Elsevier, 2024-08-01); ; ; Integrating microbial electrolysis cells (MEC) with anaerobic digestion (AD) would offer different synergistic advantages to these technologies. The MEC bioanode could be immersed in the AD reactor, stabilizing the process, or operated as an independent cell, further removing organic matter. However, up to now, bioanodes operated in anaerobic digestion conditions present low current production and tend to deactivate over time. In the present work, we conducted a comparison of six carbon-based and metal-based electrode materials, including novel options such as stainless steel wool (SSW) and carbon nanofibers (ES300), never tested before under these conditions. The electrodes were evaluated using two inoculation procedures, operating simultaneously in the same electrolyte with different feeding media. The bioanodes produced double the current densities when fed with undigested corn silage compared to anaerobic digester effluent, showing the potential for direct integration into anaerobic digesters without pre-fermentation. Unprecedented stable current densities, up to 0.4 mA cm−2, were obtained over 60 days of operation in real anaerobic digestion conditions by Geobacter-dominated bioanodes on SSW and ES300, outperforming state-of-the-art bioanodes and avoiding the dramatic deactivation previously reported. Microbial community analysis of SSW and ES300 elucidated how the microbial composition in the bioanodes was mostly depending on the electrode material, rather than the inoculation procedure. The results achieved with these bioanodes pave the way for scaling up and commercializing integrated AD-MEC systems.Publicationtype: Journal Article12 106 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Electron transfer of extremophiles in bioelectrochemical systems(Springer, 2022-10-12); ; ; ; The interaction of bacteria and archaea with electrodes is a relatively new research field which spans from fundamental to applied research and influences interdisciplinary research in the fields of microbiology, biochemistry, biotechnology as well as process engineering. Although a substantial understanding of electron transfer processes between microbes and anodes and between microbes and cathodes has been achieved in mesophilic organisms, the mechanisms used by microbes under extremophilic conditions are still in the early stages of discovery. Here, we review our current knowledge on the biochemical solutions that evolved for the interaction of extremophilic organisms with electrodes. To this end, the available knowledge on pure cultures of extremophilic microorganisms has been compiled and the study has been extended with the help of bioinformatic analyses on the potential distribution of different electron transfer mechanisms in extremophilic microorganisms.Publicationtype: Review ArticleScopus© Citations 5 60 329