Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii

Advances in mechanisms and engineering of electroactive biofilms

Electroactive biofilms (EABs) are electroactive microorganisms (EAMs) encased in conductive polymers that are secreted by EAMs and formed by the accumulation and cross-linking of extracellular polysaccharides, proteins, nucleic acids, lipids, and other components. EABs are present in the form of multicellular aggregates and play a crucial role in bioelectrochemical systems (BESs) for diverse applications, including biosensors, microbial fuel cells for renewable bioelectricity production and remediation of wastewaters, and microbial electrosynthesis of valuable chemicals. However, naturally occurred EABs are severely limited owing to their low electrical conductivity that seriously restrict the electron transfer efficiency and practical applications. In the recent decade, synthetic biology strategies have been adopted to elucidate the regulatory mechanisms of EABs, and to enhance the formation and electrical conductivity of EABs. Based on the formation of EABs and extracellular electron transfer (EET) mechanisms, the synthetic biology-based engineering strategies of EABs are summarized and reviewed as follows: (i) Engineering the structural components of EABs, including strengthening the synthesis and secretion of structural elements such as polysaccharides, eDNA, and structural proteins, to improve the formation of biofilms; (ii) Enhancing the electron transfer efficiency of EAMs, including optimizing the distribution of c-type cytochromes and conducting nanowire assembly to promote contact-based EET, and enhancing electron shuttles' biosynthesis and secretion to promote shuttle-mediated EET; (iii) Incorporating intracellular signaling molecules in EAMs, including quorum sensing systems, secondary messenger systems, and global regulatory systems, to increase the electron transfer flux in EABs. This review lays a foundation for the design and construction of EABs for diverse BES applications.

A critical review on biochar-assisted free radicals mediated redox reactions influencing transformation of potentially toxic metals: Occurrence, formation, and environmental applications

Potentially toxic metals have become a viable threat to the ecosystem due to their carcinogenic nature. Biochar has gained substantial interest due to its redox-mediated processes and redox-active metals. Biochar has the capacity to directly adsorb the pollutants from contaminated environments through several mechanisms such as coprecipitation, complexation, ion exchange, and electrostatic interaction. Biochar's electron-mediating potential may be influenced by the cyclic transition of surface moieties and conjugated carbon structures. Thus, pyrolysis configuration, biomass material, retention time, oxygen flow, and heating time also affect biochar's redox properties. Generally, reactive oxygen species (ROS) exist as free radicals (FRs) in radical and non-radical forms, i.e., hydroxyl radical, superoxide, nitric oxide, hydrogen peroxide, and singlet oxygen. Heavy metals are involved in the production of FRs during redox-mediated reactions, which may contribute to ROS formation. This review aims to critically evaluate the redox-mediated characteristics of biochar produced from various biomass feedstocks under different pyrolysis conditions. In addition, we assessed the impact of biochar-assisted FRs redox-mediated processes on heavy metal immobilization and mobility. We also revealed new insights into the function of FRs in biochar and its potential uses for environment-friendly remediation and reducing the dependency on fossil-based materials, utilizing local residual biomass as a raw material in terms of sustainability.

Electrochemically Initiated Synthesis of Polyacrylamide Microgels and Core-shell Particles

Herein, we developed a simple procedure for synthesizing micrometer-sized microgel particles as a suspension in an aqueous solution and thin films deposited as shells on different inorganic cores. A sufficiently high constant potential was applied to the working electrode to commence the initiator decomposition that resulted in gelation. Under hydrodynamic conditions, this initiation allowed preparing different morphology microgels at room temperature. Importantly, neither heating nor UV-light illumination was needed to initiate the polymerization. Moreover, thin films of the cross-linked gel were anchored on different core substrates, including silica and magnetic nanoparticles. Scanning electron microscopy and transmission electron microscopy imaging confirmed the microgel particles' and films' irregular shape and porous structure. Energy-dispersive X-ray spectroscopy indicated that the core coating with the microgel film was successful. Dynamic light scattering measured the micrometer size of gel particles with different combinations of acrylic monomers. Thermogravimetric analysis and the first-derivative thermogravimetric analysis revealed that the microgels' thermal stability of different compositions was different. Fourier-transform infrared and 13C NMR spectroscopy showed successful copolymerization of the main, functional, and cross-linking monomers.

Experimental Methods for Investigating Uptake 2 Processes In Vivo

Neuromodulators are critical regulators of the brain's signaling processes, and thus they are popular pharmacological targets for psychoactive therapies. It is clear that monoamine uptake mechanisms are complicated and subject to multiple uptake mechanisms. Uptake 1 describes uptake of the monoamine via its designated transporter (SERT for serotonin, NET for norepinephrine, and DAT for dopamine), whereas Uptake 2 details multiple transporter types on neurons and glia taking up different types of modulators, not necessarily specific to the monoamine. While Uptake 1 processes have been well-studied over the past few decades, Uptake 2 mechanisms have remained more difficult to study because of the limitations in methods that have the sensitivity and spatiotemporal resolution to look at the subtleties in uptake profiles. In this chapter we review the different experimental approaches that have yielded important information about Uptake 2 mechanisms in vivo. The techniques (scintillation microspectrophotometry, microdialysis, chronoamperometry, and voltammetry) are described in detail, and pivotal studies associated with each method are highlighted. It is clear from these reviewed works that Uptake 2 processes are critical to consider to advance our understanding of the brain and develop effective neuropsychiatric therapies.

Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities

The mechanisms of extracellular electron transfer and the microbial taxa associated with the observed electroactivity are fundamental to oxygen-reducing microbial cathodes. Here we confirmed the apparent 'electroautotrophic' behavior of electroactive biofilms (EABs) grown on carbon electrodes at + 0.20V vs. Ag/AgCl under air. The EABs catalyzed O₂ electroreduction into water ─ as demonstrated by a rotating ring disc experiment ─ and performed quasi-reversible heterogeneous electron transfer (HET). By using electrodes of low surface capacitance, we report for the first time nonturnover redox peaks that are very likely intrinsic to the redox protein(s) performing the HET. Because the formal potential of redox proteins is pH-dependent, we investigated the evolution of characteristic potentials of the EABs with the solution pH: (i) open circuit potential, (ii) half-wave potential, and (iii) averaged peak potential of nonturnover cyclic voltammograms, which is presumably the formal potential of the primary electron acceptor(s) for the community. In addition to describing the redox thermodynamics behind HET, we suggest that the corresponding data provides an electrochemical fingerprint that could help in comparing the electroactivity of diverse microbial communities. The taxon with the highest relative abundance in our EABs was an unclassified member of the Gammaproteobacteria that was phylogenetically closely related to most other abundant unclassified Gammaproteobacteria commonly reported in EABs reducing O₂ at high potentials, further suggesting that those taxa are responsible for the bioelectroactivity. Phylogenetic and electrochemical similarities between reported EABs jointly support the hypothesis that similar biomolecular mechanisms may be responsible for this highly probable electroautotrophic metabolism.

Electroactivity across the cell wall of Gram-positive bacteria

The growing interest on sustainable biotechnological processes for the production of energy and industrial relevant organic compounds have increased the discovery of electroactive organisms (i.e. organisms that are able to exchange electrons with an electrode) and the characterization of their extracellular electron transfer mechanisms. While most of the knowledge on extracellular electron transfer processes came from studies on Gram-negative bacteria, less is known about the processes performed by Gram-positive bacteria. In contrast to Gram-negative bacteria, Gram-positive bacteria lack an outer-membrane and contain a thick cell wall, which were thought to prevent extracellular electron transfer. However, in the last decade, an increased number of Gram-positive bacteria have been found to perform extracellular electron transfer, and exchange electrons with an electrode. In this mini-review the current knowledge on the extracellular electron transfer processes performed by Gram-positive bacteria is introduced, emphasising their electroactive role in bioelectrochemical systems. Also, the existent information of the molecular processes by which these bacteria exchange electrons with an electrode is highlighted. This understanding is fundamental to advance the implementation of these organisms in sustainable biotechnological processes, either through modification of the systems or through genetic engineering, where the organisms can be optimized to become better catalysts.

Convenient non-invasive electrochemical techniques to monitor microbial processes: current state and perspectives

Real-time electrochemical monitoring in bioprocesses is an improvement over existing systems because it is versatile and provides more information to the user than periodic measurements of cell density or metabolic activity. Real-time electrochemical monitoring provides the ability to monitor the physiological status of actively growing cells related to electron transfer activity and potential changes in the proton gradient of the cells. Voltammetric and amperometric techniques offer opportunities to monitor electron transfer reactions when electrogenic microbes are used in microbial fuel cells or bioelectrochemical synthesis. Impedance techniques provide the ability to monitor the physiological status of a wide range of microorganisms in conventional bioprocesses. Impedance techniques involve scanning a range of frequencies to define physiological activity in terms of equivalent electrical circuits, thereby enabling the use of computer modeling to evaluate specific growth parameters. Electrochemical monitoring of microbial activity has applications throughout the biotechnology industry for generating real-time data and offers the potential for automated process controls for specific bioprocesses.

Identification of Clostridium cochlearium as an electroactive microorganism from the mouse gut microbiome

Microbial electroactivity, the metabolically relevant transfer of electrons between microorganisms and solid conductors, was first discovered for now well characterized model organisms from hypoxic or anaerobic water or sediment samples. Recent findings indicate that the metabolic trait of electroactivity might as well be important within the microbiome of the mammalian gut. Based on a pre-selection from the mouse intestinal bacterial collection five microorganisms originating from diverse parts of the gut were screened for electroactivity. As there is no marker gene for electroactivity, the ability to synthesize cytochromes and metabolize redox-mediators was studied in-silico. Clostridium cochlearium showed highest electroactivity and Lactobacillus reuteri as well as Staphylococcus xylosus show putative electroactivity, as well. The maximum current density of C. cochlearium of 0.53 ± 0.02 mA cm^-2 after only 5.2 h of incubation was clearly linked to growth and glucose consumption. Cyclic voltammetric analysis on C. cochlearium revealed a formal potential of the extracellular electron transfer (EET) site of +0.22 ± 0.05 V versus Ag/AgCl sat. KCl (and + 0.42 V versus SHE) and indicates that EET is not based on biofilm formation, but the involvement of either redox-active molecules or planktonic cells. The potential of the gut as habitat for electroactives and their physiological role are discussed.

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified with a mechanistic model how well tri-culture dynamics was predicted from mono-culture data. With the model as reference, we demonstrated that strains grown in co-culture behaved differently than those in mono-culture and confirmed their altered behavior at the transcriptional level. In addition, we showed with replicate tri-cultures and simulations that dominance in tri-culture sensitively depends on the initial conditions. Our work has important implications for gut microbial community modeling as well as for ecological interaction detection from batch cultures.

Our gut is home to trillions of microorganisms, most of them bacteria, which have an important impact on our body. During healthy periods, these microorganisms help our digestion, protect our cells, and compete against disease-causing bacteria. But specific communities of gut bacteria are linked to many diseases.

We already have a good knowledge of the bacterial composition present in a wide range of human guts, but how the different bacterial species within such communities affect each other, has so far been unclear. Future disease treatments may be able to steer ‘bad’ communities to healthier mixtures. For this to happen we need to know how species interact and how these interactions change the behavior of the whole community.

To investigate this further, D'hoe, Vet, Faust et al. studied three common species of gut bacteria under controlled conditions in the laboratory. The different species were either grown alone, in pairs or together, and the number of bacteria and the concentration of nutrients were measured over time. The results showed that when grown alone or together, their behavior changed.

D'hoe et al. then used a mathematical model to estimate the rates at which species multiplied and consumed nutrients. This model was able to predict the dynamics of each of the species grown alone. However, the data from bacteria grown in pairs was needed to predict the dynamics of bacteria grown as a group of three. Next, D'hoe et al. compared the activity of genes between bacteria grown alone or together, and discovered several differences.

This suggests that bacterial species affect each other greatly, and community behavior cannot be predicted from knowledge of its members alone. Therefore, studying bacteria in isolation is not enough to understand the complex environments of our guts, which are inhabited not by three but hundreds of bacterial species. In future, interactions between bacteria will need to be studied to ultimately be able to shift the gut community into better shapes.

The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

BACKGROUND

Gut bacteria are closely associated with host. Chrysomya megacephala, as a vector and resource insect, can transmit various pathogenic bacteria and consume manure to produce biofertilizer and larva biomass. However, the gut bacteria composition and abundance of C. megacephala remain unclear.

RESULTS

Illumina MiSeq platform was used to compare composition of gut bacterial community in eggs, 1-day-old larvae, 5-day-old larvae, pupae, adult females and males by sequencing with variation in V4 region of 16S ribosomal DNA gene. In total, 928 operational taxonomic units (OTUs) were obtained. These OTUs were annotated into 19 phyla, 42 classes, 77 orders, 153 families and 289 genera. More than 0.5% abundance of 32 OTU core genera were found across all life stages. At class level, Alphaproteobacteria, Bacilli, Bacteroidia, Betaproteobacteria, Flavobacteriia and Gammaproteobacteria were the most abundant in C. megacephala. Eight species were identified to have significantly different abundance between 1-d-larvae and 5-day-larvae and took 28.95% of shared species between these two groups. Sex-specific bacterial species were identified that Faecalibacterium prausnitzii was merely present in females, while Rhodococcus fascians was merely present in males.

CONCLUSION

Gut bacteria of C. megacephala varied across life stages. The composition and community structure of the bacterial community differed from young larvae to mature larvae, while that were similar in adult females and males. These data will provide an overall view of bacterial community across life stages in C. megacephala with attention on manure associated and pathogenic bacteria.

A Novel Shewanella Isolate Enhances Corrosion by Using Metallic Iron as the Electron Donor with Fumarate as the Electron Acceptor

The involvement of Shewanella spp. in biocorrosion is often attributed to their Fe(III)-reducing properties, but they could also affect corrosion by using metallic iron as an electron donor. Previously, we isolated Shewanella strain 4t3-1-2LB from an acetogenic community enriched with Fe(0) as the sole electron donor. Here, we investigated its use of Fe(0) as an electron donor with fumarate as an electron acceptor and explored its corrosion-enhancing mechanism. Without Fe(0), strain 4t3-1-2LB fermented fumarate to succinate and CO₂, as was shown by the reaction stoichiometry and pH. With Fe(0), strain 4t3-1-2LB completely reduced fumarate to succinate and increased the Fe(0) corrosion rate (7.0 ± 0.6)-fold in comparison to that of abiotic controls (based on the succinate-versus-abiotic hydrogen formation rate). Fumarate reduction by strain 4t3-1-2LB was, at least in part, supported by chemical hydrogen formation on Fe(0). Filter-sterilized spent medium increased the hydrogen generation rate only 1.5-fold, and thus extracellular hydrogenase enzymes appear to be insufficient to explain the enhanced corrosion rate. Electrochemical measurements suggested that strain 4t3-1-2LB did not excrete dissolved redox mediators. Exchanging the medium and scanning electron microscopy (SEM) imaging indicated that cells were attached to Fe(0). It is possible that strain 4t3-1-2LB used a direct mechanism to withdraw electrons from Fe(0) or favored chemical hydrogen formation on Fe(0) through maintaining low hydrogen concentrations. In coculture with an Acetobacterium strain, strain 4t3-1-2LB did not enhance acetogenesis from Fe(0). This work describes a strong corrosion enhancement by a Shewanella strain through its use of Fe(0) as an electron donor and provides insights into its corrosion-enhancing mechanism.IMPORTANCE Shewanella spp. are frequently found on corroded metal structures. Their role in microbial influenced corrosion has been attributed mainly to their Fe(III)-reducing properties and, therefore, has been studied with the addition of an electron donor (lactate). Shewanella spp., however, can also use solid electron donors, such as cathodes and potentially Fe(0). In this work, we show that the electron acceptor fumarate supported the use of Fe(0) as the electron donor by Shewanella strain 4t3-1-2LB, which caused a (7.0 ± 0.6)-fold increase of the corrosion rate. The corrosion-enhancing mechanism likely involved cell surface-associated components in direct contact with the Fe(0) surface or maintenance of low hydrogen levels by attached cells, thereby favoring chemical hydrogen formation by Fe(0). This work sheds new light on the role of Shewanella spp. in biocorrosion, while the insights into the corrosion-enhancing mechanism contribute to the understanding of extracellular electron uptake processes.

A novel high-throughput method for kinetic characterisation of anaerobic bioproduction strains, applied to Clostridium kluyveri

Hexanoic acid (HA), also called caproic acid, can be used as an antimicrobial agent and as a precursor to various chemicals, such as fuels, solvents and fragrances. HA can be produced from ethanol and acetate by the mesophilic anaerobic bacterium Clostridium kluyveri, via two successive elongation steps over butyrate. A high-throughput anaerobic growth curve technique was coupled to a data analysis framework to assess growth kinetics for a range of substrate and product concentrations. Using this method, growth rates and several kinetic parameters were determined for C. kluyveri. A maximum growth rate (µ_max) of 0.24 ± 0.01 h^-1 was found, with a half-saturation index for acetic acid (K_S,AA) of 3.8 ± 0.9 mM. Inhibition by butyric acid occurred at of 124.7 ± 5.7 mM (K_I,BA), while the final product, HA, linearly inhibited growth with complete inhibition above 91.3 ± 10.8 mM (K_HA of 10.9*10^-3 ± 1.3*10^-3 mM^-1) at pH = 7, indicating that the hexanoate anion also exerts toxicity. These parameters were used to create a dynamic mass-balance model for bioproduction of HA. By coupling data collection and analysis to this modelling framework, we have produced a powerful tool to assess the kinetics of anaerobic micro-organisms, demonstrated here with C. kluyveri, in order further explore the potential of micro-organisms for chemicals production.

Applications of biochar in redox-mediated reactions

Biochar is chemically more reduced and reactive than the original feedstock biomass. Graphite regions, functional groups, and redox-active metals in biochar contribute to its redox characteristics. While the functional groups such as phenolic species in biochar are the main electron donating moieties (i.e., reducers), the quinones and polycondensed aromatic functional groups are the components accepting electrons (oxidants). The redox capacity of biochar depends on feedstock properties and pyrolysis conditions. This paper aims to review and summarize the various synthesis techniques for biochars and the methods for probing their redox characteristics. We review the abiotic and microbial applications of biochars as electron donors, electron acceptors, or electron shuttles for pollutant degradation, metal(loid)s (im)mobilization, nutrient transformation, and discuss the underlying mechanisms. Furthermore, knowledge gaps that exist in the exploration and differentiation of the electron transfer mechanisms involving biochars are also identified.

Electroactive Biofilms for Sensing: Reflections and Perspectives

Microbial electrochemistry has from the onset been recognized for its sensing potential due to the microbial ability to enhance signals through metabolic cascades, its relative selectivity toward substrates, and the higher stability conferred by the microbial ability to self-replicate. The greatest challenge has been to achieve stable and efficient transduction between a microorganism and an electrode surface. Over the past decades, a new kind of microbial architecture has been observed to spontaneously develop on polarized electrodes: the electroactive biofilm (EAB). The EAB conducts electrons over long distances and performs quasi-reversible electron transfer on conventional electrode surfaces. It also possesses self-regenerative properties. In only a few years, EABs have inspired considerable research interest for use as biosensors for environmental or bioprocess monitoring. Multiple challenges still need to be overcome before implementation at larger scale of this new kind of biosensors can be realized. This perspective first introduces the specific characteristics of the EAB with respect to other electrochemical biosensors. It summarizes the sensing applications currently proposed for EABs, stresses their limitations, and suggests strategies toward potential solutions. Conceptual prospects to engineer EABs for sensing purposes are also discussed.

Electrobioremediation of oil spills

Annually, thousands of oil spills occur across the globe. As a result, petroleum substances and petrochemical compounds are widespread contaminants causing concern due to their toxicity and recalcitrance. Many remediation strategies have been developed using both physicochemical and biological approaches. Biological strategies are most benign, aiming to enhance microbial metabolic activities by supplying limiting inorganic nutrients, electron acceptors or donors, thus stimulating oxidation or reduction of contaminants. A key issue is controlling the supply of electron donors/acceptors. Bioelectrochemical systems (BES) have emerged, in which an electrical current serves as either electron donor or acceptor for oil spill bioremediation. BES are highly controllable and can possibly also serve as biosensors for real time monitoring of the degradation process. Despite being promising, multiple aspects need to be considered to make BES suitable for field applications including system design, electrode materials, operational parameters, mode of action and radius of influence. The microbiological processes, involved in bioelectrochemical contaminant degradation, are currently not fully understood, particularly in relation to electron transfer mechanisms. Especially in sulfate rich environments, the sulfur cycle appears pivotal during hydrocarbon oxidation. This review provides a comprehensive analysis of the research on bioelectrochemical remediation of oil spills and of the key parameters involved in the process.

The electron donating capacity of biochar is dramatically underestimated

Biochars have gathered considerable interest for agronomic and engineering applications. In addition to their high sorption ability, biochars have been shown to accept or donate considerable amounts of electrons to/from their environment via abiotic or microbial processes. Here, we measured the electron accepting (EAC) and electron donating (EDC) capacities of wood-based biochars pyrolyzed at three different highest treatment temperatures (HTTs: 400, 500, 600 °C) via hydrodynamic electrochemical techniques using a rotating disc electrode. EACs and EDCs varied with HTT in accordance with a previous report with a maximal EAC at 500 °C (0.4 mmol(e(-)).gchar(-1)) and a large decrease of EDC with HTT. However, while we monitored similar EAC values than in the preceding study, we show that the EDCs have been underestimated by at least 1 order of magnitude, up to 7 mmol(e(-)).gchar(-1) for a HTT of 400 °C. We attribute this existing underestimation to unnoticed slow kinetics of electron transfer from biochars to the dissolved redox mediators used in the monitoring. The EDC of other soil organic constituents such as humic substances may also have been underestimated. These results imply that the redox properties of biochars may have a much bigger impact on soil biogeochemical processes than previously conjectured.

Electrochemical imaging for microfluidics: a full-system approach

Electrochemistry is developed as a new chemical imaging modality for microfluidics. The technique is based on multipoint voltammetry using an embedded 20 × 10 miniature electrode array implemented on a customized printed circuit board. Electrode durability was enhanced by chemical modification of the electrode surfaces, which enabled continuous, stable use for over 2 months. A system-level approach enables automatic calibration, data acquisition and data processing through a graphical user interface. Following data processing, redox currents and peak positions are extracted from location-specific voltammograms and converted into pixels of an "electrochemical image". The system is validated by imaging steady-state and dynamic laminar flow patterns of flow-confined solutions of the redox pairs Fe(CN)6(3-/4-) or multi-redox environments that include coflowing Ru(NH3)6(2+/3+) solutions. The images obtained are compared with flow simulations and optical images for validation. A strategy to achieve measurements with spatial resolution smaller than the individual electrodes is also demonstrated as an avenue to enhance image spatial resolution. It is expected that this new approach to chemical imaging will expand the applicability of microfluidics in certain areas of chemistry and biology without requiring expertise in electrochemistry.