Measuring conductivity of living Geobacter sulfurreducens biofilms

Long-distance electron transport in multicellular freshwater cable bacteria

Filamentous multicellular cable bacteria perform centimeter-scale electron transport in a process that couples oxidation of an electron donor (sulfide) in deeper sediment to the reduction of an electron acceptor (oxygen or nitrate) near the surface. While this electric metabolism is prevalent in both marine and freshwater sediments, detailed electronic measurements of the conductivity previously focused on the marine cable bacteria (Candidatus Electrothrix), rather than freshwater cable bacteria, which form a separate genus (Candidatus Electronema) and contribute essential geochemical roles in freshwater sediments. Here, we characterize the electron transport characteristics of Ca. Electronema cable bacteria from Southern California freshwater sediments. Current-voltage measurements of intact cable filaments bridging interdigitated electrodes confirmed their persistent conductivity under a controlled atmosphere and the variable sensitivity of this conduction to air exposure. Electrostatic and conductive atomic force microscopies mapped out the characteristics of the cell envelope's nanofiber network, implicating it as the conductive pathway in a manner consistent with previous findings in marine cable bacteria. Four-probe measurements of microelectrodes addressing intact cables demonstrated nanoampere currents up to 200 μm lengths at modest driving voltages, allowing us to quantify the nanofiber conductivity at 0.1 S/cm for freshwater cable bacteria filaments under our measurement conditions. Such a high conductivity can support the remarkable sulfide-to-oxygen electrical currents mediated by cable bacteria in sediments. These measurements expand the knowledgebase of long-distance electron transport to the freshwater niche while shedding light on the underlying conductive network of cable bacteria.

In Situ Biosynthesis of FeS Nanoparticles Boosts Current Generation in Bioelectrochemical Systems Through Efficient Electron Transfer

The utility of electrochemical active biofilm in bioelectrochemical systems has received considerable attention for harvesting energy and chemical products. However, the slow electron transfer between biofilms and electrodes hinders the enhancement of performance and still remains challenging. Here, using Fe3O4 /L-Cys nanoparticles as precursors to induce biomineralization, a facile strategy for the construction of an effective electron transfer pathway through biofilm and biological/inorganic interface is proposed, and the underlying mechanisms are elucidated. Taking advantage of an on-chip interdigitated microelectrode array (IDA), the conductive current of biofilm that is related to the electron transfer process within biofilm is characterized, and a 2.10-fold increase in current output is detected. The modification of Fe3O4/L-Cys on the electrode surface facilitates the electron transfer between the biofilm and the electrode, as the bio/inorganic interface electron transfer resistance is only 16% compared to the control. The in-situ biosynthetic Fe-containing nanoparticles (e.g., FeS) enhance the transmembrane EET and the EET within biofilm, and the peak conductivity increases 3.4-fold compared to the control. The in-situ biosynthesis method upregulates the genes involved in energy metabolism and electron transfer from the transcriptome analysis. This study enriches the insights of biosynthetic nanoparticles on electron transfer process, holding promise in bioenergy conversion.

To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'

Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.

Colony-Based Electrochemistry Reveals Electron Conduction Mechanisms Mediated by Cytochromes and Flavins in Shewanella oneidensis

Bacteria utilize electron conduction in their communities to drive their metabolism, which has led to the development of various environmental technologies, such as electrochemical microbial systems and anaerobic digestion. It is challenging to measure the conductivity among bacterial cells when they hardly form stable biofilms on electrodes. This makes it difficult to identify the biomolecules involved in electron conduction. In the present study, we aimed to identify c-type cytochromes involved in electron conduction in Shewanella oneidensis MR-1 and examine the molecular mechanisms. We established a colony-based bioelectronic system that quantifies bacterial electrical conductivity, without the need for biofilm formation on electrodes. This system enabled the quantification of the conductivity of gene deletion mutants that scarcely form biofilms on electrodes, demonstrating that c-type cytochromes, MtrC and OmcA, are involved in electron conduction. Furthermore, the use of colonies of gene deletion mutants demonstrated that flavins participate in electron conduction by binding to OmcA, providing insight into the electron conduction pathways at the molecular level. Furthermore, phenazine-based electron transfer in Pseudomonas aeruginosa PAO1 and flavin-based electron transfer in Bacillus subtilis 3610 were confirmed, indicating that this colony-based system can be used for various bacteria, including weak electricigens.

Application of dissimilatory iron-reducing bacteria for the remediation of soil and water polluted with chlorinated organic compounds: Progress, mechanisms, and directions

Chlorinated organic compounds are widely used as solvents, but they are pollutants that can have adverse effects on the environment and human health. Dissimilatory iron-reducing bacteria (DIRB) such as Shewanella and Geobacter have been applied to treat a wide range of halogenated organic compounds due to their specific biological properties. Until now, there has been no systematic review on the mechanisms of direct or indirect degradation of halogenated organic compounds by DIRB. This work summarizes the discussion of DIRB's ability to enhance the dechlorination of reaction systems through different pathways, both biological and biochemical. For biological dechlorination, some DIRB have self-dechlorination capabilities that directly dechlorinate by hydrolysis. Adjustment of dechlorination genes through genetic engineering can improve the dechlorination capabilities of DIRB. DIRB can also adjust the capacity for the microbial community to dechlorinate and provide nutrients to enhance the expression of dechlorination genes in other bacteria. In biochemical dechlorination, DIRB bioconverts Fe(III) to Fe(II), which is capable of dichlorination. On this basis, the DIRB-driven Fenton reaction can efficiently degrade chlorinated organics by continuously maintaining anoxic conditions to generate Fe(II) and oxic conditions to generate H2O2. DIRB can drive microbial fuel cells due to their electroactivity and have a good dechlorination capacity at low levels of energy consumption. The contribution of DIRB to the removal of pesticides, antibiotics and POPs is summarized. Then the DIRB electron transfer mechanism is discussed, which is core to their ability to dechlorinate. Finally, the prospect of future work on the removal of chlorine-containing organic pollutants by DIRB is presented, and the main challenges and further research directions are suggested.

Realization of Amyloid-like Aggregation as a Common Cause for Pathogenesis in Diseases

Amyloids were conventionally referred to as extracellular and intracellular accumulation of Aβ42 peptide, which causes the formation of plaques and neurofibrillary tangles inside the brain leading to the pathogenesis in Alzheimer's disease. Subsequently, amyloid-like deposition was found in the etiology of prion diseases, Parkinson's disease, type II diabetes, and cancer, which was attributed to the aggregation of prion protein, α-Synuclein, islet amyloid polypeptide protein, and p53 protein, respectively. Hence, traditionally amyloids were considered aggregates formed exclusively by proteins or peptides. However, since the last decade, it has been discovered that other metabolites, like single amino acids, nucleobases, lipids, glucose derivatives, etc., have a propensity to form amyloid-like toxic assemblies. Several studies suggest direct implications of these metabolite assemblies in the patho-physiology of various inborn errors of metabolisms like phenylketonuria, tyrosinemia, cystinuria, and Gaucher's disease, to name a few. In this review, we present a comprehensive literature overview that suggests amyloid-like structure formation as a common phenomenon for disease progression and pathogenesis in multiple syndromes. The review is devoted to providing readers with a broad knowledge of the structure, mode of formation, propagation, and transmission of different extracellular amyloids and their implications in the pathogenesis of diseases. We strongly believe a review on this topic is urgently required to create awareness about the understanding of the fundamental molecular mechanism behind the origin of diseases from an amyloid perspective and possibly look for a common therapeutic strategy for the treatment of these maladies by designing generic amyloid inhibitors.

Extracellular electron transfer and the conductivity in microbial aggregates during biochemical wastewater treatment: A bottom-up analysis of existing knowledge

Microbial extracellular electron transfer (EET) plays a crucial role in bioenergy production and resource recovery from wastewater. Interdisciplinary efforts have been made to unveil EET processes at various spatial scales, from nanowires to microbial aggregates. Electrical conductivity has been frequently measured as an indicator of EET efficiency. In this review, the conductivity of nanowires, biofilms, and granular sludge was summarized, and factors including subjects, measurement methods, and conducting conditions that affect the conductivity difference were discussed in detail. The high conductivity of nanowires does not necessarily result in efficient EET in microbial aggregates due to the existence of non-conductive substances and contact resistance. Improving the conductivity measurement of microbial aggregates is important because it enables the calculation of an EET flux from conductivity and a comparison of the flux with mass transfer coefficients. This review provides new insight into the significance, characterization, and optimization of EET in microbial aggregates during a wastewater treatment process.

Optimization of biofilm conductance measurement with two-electrode microbial electrochemical cells (MECs)

This study was conducted to develop a standardized and consistent method for biofilm conductance measurement for an improved comprehension of extracellular electron transfer. Biofilm conductance (2.12 ± 0.25 × 10^-4 S) with and without a fixed anode potential did not show significant difference. The conductance showed a sigmoidal relationship with anode potential. The current-voltage profile of the tested biofilm at applied voltage larger than 100 mV showed deviation from Ohm's law. Up to 69% decrease in biofilm conductance and deviation from Ohm's law were observed in the current-voltage profile when the measurement time increased. By choosing the voltage range (0- 100 mV) and step (25 mV), measurement time (100-s at each voltage step), and anode control mode, these operation settings were found more suitable for consistent and accurate biofilm conductance measurement in the 2-Au MEC system. This represents the first study that comprehensively evaluated the environmental and instrumental parameters for biofilm conductance measurement.

Geobacter sulfurreducens' Unique Metabolism Results in Cells with a High Iron and Lipid Content

Geobacter sulfurreducens is a ubiquitous iron-reducing bacterium in soils, and in engineered systems, it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work, we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C, H, O, N, and ash content) showed high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 ± 0.2 μg/g dry weight) and lipids (32 ± 0.5% dry weight/dry weight) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. IMPORTANCE Geobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively "breathing" metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal and, as a ubiquitous iron reducer in soils around the world, G. sulfurreducens has an impact on the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organism's composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria-these observations are important for future microbiologists and biotechnologists working with the organism.

Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire

A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨H_mn⟩), reaction free energies (ΔG_mn), reorganization energies (λ_mn), and activation energies (E_a) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔG_mn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.

Biohydrogen production and purification: Focusing on bioelectrochemical systems

Innovative technologies on green hydrogen production become significant as the hydrogen economy has grown globally. Biohydrogen is one of green hydrogen production methods, and microbial electrochemical cells (MECs) can be key to biohydrogen provision. However, MECs are immature for biohydrogen technology due to several limitations including extracellular electron transfer (EET) engineering. Fundamental understanding of EET also needs more works to accelerate MEC commercialization. Interestingly, studies on biohydrogen gas purification are limited although biohydrogen gas mixture requires complex purification for use. To facilitate an MEC-based biohydrogen technology as the green hydrogen supply this review discussed EET kinetics, engineering of EET and direct interspecies electron transfer associated with hydrogen yield and the application of advanced molecular biology for improving EET kinetics. Finally, this article reviewed biohydrogen purification technologies to better understand purification and use appropriate for biohydrogen, focusing on membrane separation.

Light-Induced Patterning of Electroactive Bacterial Biofilms

Electroactive bacterial biofilms can function as living biomaterials that merge the functionality of living cells with electronic components. However, the development of such advanced living electronics has been challenged by the inability to control the geometry of electroactive biofilms relative to solid-state electrodes. Here, we developed a lithographic strategy to pattern conductive biofilms of Shewanella oneidensis by controlling aggregation protein CdrAB expression with a blue light-induced genetic circuit. This controlled deposition enabled S. oneidensis biofilm patterning on transparent electrode surfaces, and electrochemical measurements allowed us to both demonstrate tunable conduction dependent on pattern size and quantify the intrinsic conductivity of the living biofilms. The intrinsic biofilm conductivity measurements enabled us to experimentally confirm predictions based on simulations of a recently proposed collision-exchange electron transport mechanism. Overall, we developed a facile technique for controlling electroactive biofilm formation on electrodes, with implications for both studying and harnessing bioelectronics.

Single molecule tracking of bacterial cell surface cytochromes reveals dynamics that impact long-distance electron transport

Multiheme cytochromes in Shewanella oneidensis MR-1 transport electrons across the cell wall, in a process called extracellular electron transfer. These electron conduits can also enable electron transport along and between cells. While the underlying mechanism is thought to involve a combination of electron hopping and lateral diffusion of cytochromes along membranes, these diffusive dynamics have never been observed in vivo. Here, we observe the mobility of quantum dot-labeled cytochromes on living cell surfaces and membrane nanowires, quantify their diffusion with single-particle tracking techniques, and simulate the contribution of these dynamics to electron transport. This work reveals the impact of redox molecule dynamics on bacterial electron transport, with implications for understanding and harnessing this process in the environment and bioelectronics.

Using a series of multiheme cytochromes, the metal-reducing bacterium Shewanella oneidensis MR-1 can perform extracellular electron transfer (EET) to respire redox-active surfaces, including minerals and electrodes outside the cell. While the role of multiheme cytochromes in transporting electrons across the cell wall is well established, these cytochromes were also recently found to facilitate long-distance (micrometer-scale) redox conduction along outer membranes and across multiple cells bridging electrodes. Recent studies proposed that long-distance conduction arises from the interplay of electron hopping and cytochrome diffusion, which allows collisions and electron exchange between cytochromes along membranes. However, the diffusive dynamics of the multiheme cytochromes have never been observed or quantified in vivo, making it difficult to assess their hypothesized contribution to the collision-exchange mechanism. Here, we use quantum dot labeling, total internal reflection fluorescence microscopy, and single-particle tracking to quantify the lateral diffusive dynamics of the outer membrane-associated decaheme cytochromes MtrC and OmcA, two key components of EET in S. oneidensis. We observe confined diffusion behavior for both quantum dot-labeled MtrC and OmcA along cell surfaces (diffusion coefficients D_MtrC = 0.0192 ± 0.0018 µm²/s, D_OmcA = 0.0125 ± 0.0024 µm²/s) and the membrane extensions thought to function as bacterial nanowires. We find that these dynamics can trace a path for electron transport via overlap of cytochrome trajectories, consistent with the long-distance conduction mechanism. The measured dynamics inform kinetic Monte Carlo simulations that combine direct electron hopping and redox molecule diffusion, revealing significant electron transport rates along cells and membrane nanowires.

Thickness and roughness of transparent gold-palladium anodes have no impact on growth kinetics and yield coefficients of early-stage Geobacter sulfurreducens biofilms

Geobacter sulfurreducens is the model organism for electroactive microorganisms performing direct extracellular electron transfer and forming thick mature biofilm electrodes. Although numerous physiological properties of mature biofilm electrodes are deciphered, there is an extensive gap of knowledge on the early-stage biofilm formation. We have shown recently that transparent gold-palladium (AuPd) electrodes allow for analysis of early-stage biofilm formation using confocal laser scanning microscopy. Here we analysed the influence of thickness (ranging from 12.5 to 200 nm) and roughness of AuPd electrodes on physiological parameters of G. sulfurreducens early-stage biofilms. We show that when grown potentiostatically at -200 mV vs. Ag/ AgCl sat. KCl neither maximum current density (jmax of ∼ 80-150 µA cm-2) nor lag time (lag t of ∼ 0.2-0.4 days) or single cell yield coefficients (YNe of 1.43 × 1012 cells mole--1) of the biofilms are influenced by the electrode preparation. This confirms the robustness of the experimental approach, which is an inevitable prerequisite for obtaining reliable results in follow-up experiments.

Indicators of water biotoxicity obtained from turn-off microbial electrochemical sensors

The development of biosensors is critical to reducing potential risks associated with contamination accidents. However, the application of microbial electrochemical sensors for water biotoxicity monitoring is hampered by the lack of an indicator with high response magnitudes. In this study, microbial electrochemical sensors were fabricated with interdigitated electrode arrays (IDAs), and indicators from various electrochemical analyses were comprehensively investigated. Only the peak of cyclic voltammetry (CV) was highly linearly correlated with the commonly used current indicator during the enrichment of the electroactive biofilm. The resistance fitted from the electrochemical impedance spectroscopy (EIS) data provided a comparable and even higher inhibition ratio (IR) than the current during toxicity assessments. The differential pulse voltammetry (DPV) did not exhibit a higher sensitivity than the CV peak. However, no clear response was observed in the real-time impedance analysis for use in water biotoxicity monitoring. Most of the microbes were in the propidium iodide (PI)-permeable state after the toxicity assessments, although the current was fully recovered. This study demonstrates the potential to use EIS data as indicators of water biotoxicity using microbial electrochemical sensors.

Engineering Wired Life: Synthetic Biology for Electroactive Bacteria

Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.

Probing peptide nanowire conductivity by THz nanoscopy

Significant efforts have recently been invested in assessing the physical and chemical properties of microbial nanowires for their promising role in developing alternative renewable sources of electricity, bioelectronic materials and implantable sensors. One of their outstanding properties, the ever-desirable conductivity has been the focus of numerous studies. However, the lack of a straightforward and reliable method for measuring it seems to be responsible for the broad variability of the reported data. Routinely employed methods tend to underestimate or overestimate conductivity by several orders of magnitude. In this work, synthetic peptide nanowires conductivity is interrogated employing a non-destructive measurement technique developed on a terahertz scanning near-field microscope to test if peptide aromaticity leads to higher electrical conductivity. Our novel peptide conductivity measurement technique, based on triple standards calibration method, shows that in the case of two biopolymer mimicking peptides, the sample incorporating aromatic residues (W6) is about six times more conductive than the negative control (L6). To the best of our knowledge, this is the first report of a quantitative nano-scale terahertz s-SNOM investigation of peptides. These results prove the suitability of the terahertz radiation-based non-destructive approach in tandem with the designer peptides choice as model test subjects. This approach requires only simple sample preparation, avoids many of the pitfalls of typical contact-based conductivity measurement techniques and could help understanding fundamental aspects of nature's design of electron transfer in biopolymers.

Amyloids as Building Blocks for Macroscopic Functional Materials: Designs, Applications and Challenges

Amyloids are self-assembled protein aggregates that take cross-β fibrillar morphology. Although some amyloid proteins are best known for their association with Alzheimer’s and Parkinson’s disease, many other amyloids are found across diverse organisms, from bacteria to humans, and they play vital functional roles. The rigidity, chemical stability, high aspect ratio, and sequence programmability of amyloid fibrils have made them attractive candidates for functional materials with applications in environmental sciences, material engineering, and translational medicines. This review focuses on recent advances in fabricating various types of macroscopic functional amyloid materials. We discuss different design strategies for the fabrication of amyloid hydrogels, high-strength materials, composite materials, responsive materials, extracellular matrix mimics, conductive materials, and catalytic materials.

Empower C1: Combination of Electrochemistry and Biology to Convert C1 Compounds

The idea to somehow combine electrical current and biological systems is not new. It was subject of research as well as of science fiction literature for decades. Nowadays, in times of limited resources and the need to capture greenhouse gases like CO₂, this combination gains increasing interest, since it might allow to use C1 compounds and highly oxidized compounds as substrate for microbial production by "activating" them with additional electrons. In this chapter, different possibilities to combine electrochemistry and biology to convert C1 compounds into useful products will be discussed. The chapter first shows electrochemical conversion of C1 compounds, allowing the use of the product as substrate for a subsequent biosynthesis in uncoupled systems, further leads to coupled systems of biology and electrochemical conversion, and finally reaches the discipline of bioelectrosynthesis, where electrical current and C1 compounds are directly converted by microorganisms or enzymes. This overview will give an idea about the potentials and challenges of combining electrochemistry and biology to convert C1 molecules.

Evidence of a Streamlined Extracellular Electron Transfer Pathway from Biofilm Structure, Metabolic Stratification, and Long-Range Electron Transfer Parameters

A strain of Geobacter sulfurreducens, an organism capable of respiring solid extracellular substrates, lacking four of five outer membrane cytochrome complexes (extABCD⁺ strain) grows faster and produces greater current density than the wild type grown under identical conditions. To understand cellular and biofilm modifications in the extABCD⁺ strain responsible for this increased performance, biofilms grown using electrodes as terminal electron acceptors were sectioned and imaged using electron microscopy to determine changes in thickness and cell density, while parallel biofilms incubated in the presence of nitrogen and carbon isotopes were analyzed using NanoSIMS (nanoscale secondary ion mass spectrometry) to quantify and localize anabolic activity. Long-distance electron transfer parameters were measured for wild-type and extABCD⁺ biofilms spanning 5-μm gaps. Our results reveal that extABCD⁺ biofilms achieved higher current densities through the additive effects of denser cell packing close to the electrode (based on electron microscopy), combined with higher metabolic rates per cell compared to the wild type (based on increased rates of ¹⁵N incorporation). We also observed an increased rate of electron transfer through extABCD⁺ versus wild-type biofilms, suggesting that denser biofilms resulting from the deletion of unnecessary multiheme cytochromes streamline electron transfer to electrodes. The combination of imaging, physiological, and electrochemical data confirms that engineered electrogenic bacteria are capable of producing more current per cell and, in combination with higher biofilm density and electron diffusion rates, can produce a higher final current density than the wild type.

IMPORTANCE Current-producing biofilms in microbial electrochemical systems could potentially sustain technologies ranging from wastewater treatment to bioproduction of electricity if the maximum current produced could be increased and current production start-up times after inoculation could be reduced. Enhancing the current output of microbial electrochemical systems has been mostly approached by engineering physical components of reactors and electrodes. Here, we show that biofilms formed by a Geobacter sulfurreducens strain producing ∼1.4× higher current than the wild type results from a combination of denser cell packing and higher anabolic activity, enabled by an increased rate of electron diffusion through the biofilms. Our results confirm that it is possible to engineer electrode-specific G. sulfurreducens strains with both faster growth on electrodes and streamlined electron transfer pathways for enhanced current production.

In Situ Spectroelectrochemical Characterization Reveals Cytochrome-Mediated Electric Syntrophy in Geobacter Coculture

Direct interspecies electron transfer (DIET) between microbial species prevails in some key microbial consortia. However, the electron transfer mechanism(s) in these consortia is controversial due to lack of efficient characterization methods. Here, we provide an in situ anaerobic spectroelectrochemical coculture cell (in situ ASCC) to induce the formation of DIET coculture biofilm on the interdigitated microelectrode arrays and characterize the electron transfer directly. Two typical Geobacter DIET cocultures, Geobacter metallireducens and wild-type Geobacter sulfurreducens (G.m&G.s) and G. metallireducens and a G. sulfurreducens strain deficient in citrate synthase (G.m&G.s-ΔgltA), were selected. In situ Raman and electrochemical Fourier transform infrared (FTIR) spectroscopy indicated that cytochromes are abundant in the electric syntrophic coculture. Cyclic voltammetry and potential step experiment revealed a diffusion-controlled electron transfer process and the electrochemical gating measurements further demonstrated a cytochrome-mediated electron transfer in the DIET coculture. Furthermore, the G.m&G.s-ΔgltA coculture displayed a higher redox conductivity than the G.m&G.s coculture, consistent with the existence of an intimate and efficient electrical connection between these two species. Our findings provide the first report of a redox-gradient-driven electron transport facilitated by c-type cytochromes in DIET coculture, supporting the model that DIET is mediated by cytochromes and suggest a platform to explore the other DIET consortia.

High throughput techniques for the rapid identification of electroactive microorganisms

Electroactive microorganisms (EAM), capable of executing extracellular electron transfer (EET) in/out of a cell, are employed in microbial electrochemical technologies (MET) and bioelectronics for harnessing electricity from wastewater, bioremediation and as biosensors. Thus, investigation on EAM is becoming a topic of interest for multidisciplinary areas, such as environmental science, energy and health sectors. Though, EAM are widespread in three domains of life, nevertheless, only a few hundred EAM have been identified so far and hence, the rapid identification of EAM is imperative. In this review, the techniques that are developed for the direct identification of EAM, such as azo dye and WO₃ based techniques, dielectrophoresis, potentiostatic/galvanometric techniques, and other indirect methods, such as spectroscopy and molecular biology techniques, are highlighted with a special focus on time required for the detection of these EAM. The bottlenecks for identifying EAM and the knowledge gaps based on the present investigations are also discussed. Thus, this review is intended to encourage researchers for devolving high-throughput techniques for identifying EAM with more accuracy, while consuming less time.

Engineering Biological Electron Transfer and Redox Pathways for Nanoparticle Synthesis

Many species of bacteria are naturally capable of types of electron transport not observed in eukaryotic cells. Some species live in environments containing heavy metals not typically encountered by cells of multicellular organisms, such as arsenic, cadmium, and mercury, leading to the evolution of enzymes to deal with these environmental toxins. Bacteria also inhabit a variety of extreme environments, and are capable of respiration even in the absence of oxygen as a terminal electron acceptor. Over the years, several of these exotic redox and electron transport pathways have been discovered and characterized in molecular-level detail, and more recently synthetic biology has begun to utilize these pathways to engineer cells capable of detecting and processing a variety of metals and semimetals. One such application is the biologically controlled synthesis of nanoparticles. This review will introduce the basic concepts of bacterial metal reduction, summarize recent work in engineering bacteria for nanoparticle production, and highlight the most cutting-edge work in the characterization and application of bacterial electron transport pathways.

Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials

The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.

Long-distance electron transfer in a filamentous Gram-positive bacterium

Long-distance extracellular electron transfer has been observed in Gram-negative bacteria and plays roles in both natural and engineering processes. The electron transfer can be mediated by conductive protein appendages (in short unicellular bacteria such as Geobacter species) or by conductive cell envelopes (in filamentous multicellular cable bacteria). Here we show that Lysinibacillus varians GY32, a filamentous unicellular Gram-positive bacterium, is capable of bidirectional extracellular electron transfer. In microbial fuel cells, L. varians can form centimetre-range conductive cellular networks and, when grown on graphite electrodes, the cells can reach a remarkable length of 1.08 mm. Atomic force microscopy and microelectrode analyses suggest that the conductivity is linked to pili-like protein appendages. Our results show that long-distance electron transfer is not limited to Gram-negative bacteria.

Endogenous Electric Signaling as a Blueprint for Conductive Materials in Tissue Engineering

Bioelectricity plays an important role in cell behavior and tissue modulation, but is understudied in tissue engineering research. Endogenous electrical signaling arises from the transmembrane potential inherent to all cells and contributes to many cell behaviors, including migration, adhesion, proliferation, and differentiation. Electrical signals are also involved in tissue development and repair. Synthetic and natural conductive materials are under investigation for leveraging endogenous electrical signaling cues in tissue engineering applications due to their ability to direct cell differentiation, aid in maturing electroactive cell types, and promote tissue functionality. In this review, we provide a brief overview of bioelectricity and its impact on cell behavior, report recent literature using conductive materials for tissue engineering, and discuss opportunities within the field to improve experimental design when using conductive substrates.

Pathogens electrogenicity as a tool for in-situ metabolic activity monitoring and drug assessment in biofilms

Concerns regarding increased antibiotic resistance arising from the emergent properties of biofilms have spurred interest in the discovery of novel antibiotic agents and techniques to directly estimate metabolic activity in biofilms. Although a number of methods have been developed to quantify biofilm formation, real-time quantitative assessment of metabolic activity in label-free biofilms remains a challenge. Production of electrical current via extracellular electron transport (EET) has recently been found in pathogens and appears to correlate with their metabolic activity. Accordingly, monitoring the production of electrical currents as an indicator of cellular metabolic activity in biofilms represents a new direction for research aiming to assess and screen the effects of antimicrobials on biofilm activity. In this article, we reviewed EET-capable pathogens and the methods to monitor biofilm activity to discuss advantages of using the capability of pathogens to produce electrical currents and effective combination of these methods. Moreover, we discussed EET mechanisms by pathogenic and environmental bacteria and open questions for the physiological roles of EET in pathogen's biofilm. The present limitations and possible future directions of in situ biofilm metabolic activity assessment for large-scale screening of antimicrobials are also discussed.

Nanoliter scale electrochemistry of natural and engineered electroactive bacteria

Bacterial extracellular electron transfer (EET) is envisioned for use in applied biotechnologies, necessitating electrochemical characterization of natural and engineered electroactive biofilms under conditions similar to the target application, including small-scale biosensing or biosynthesis platforms, which is often distinct from standard 100 mL-scale stirred-batch bioelectrochemical test platforms used in the laboratory. Here, we adapted an eight chamber, nanoliter volume (500 nL) electrochemical flow cell to grow biofilms of both natural (Biocathode MCL community, Marinobacter atlanticus, and Shewanella oneidensis MR1) or genetically modified (S. oneidensis ΔMtr and S. oneidensis ΔMtr + pLB2) electroactive bacteria on electrodes held at a constant potential. Maximum current density achieved by unmodified strains was similar between the nano- and milliliter-scale reactors. However, S. oneidensis biofilms engineered to activate EET upon exposure to 2,4-diacetylphloroglucinol (DAPG) produced current at wild-type levels in the stirred-batch reactor, but not in the nanoliter flow cell. We hypothesize this was due to differences in mass transport of DAPG, naturally-produced soluble redox mediators, and oxygen between the two reactor types. Results presented here demonstrate, for the first time, nanoliter scale chronoamperometry and cyclic voltammetry of a range of electroactive bacteria in a three-electrode reactor system towards development of miniaturized, and potentially high throughput, bioelectrochemical platforms.

How does electron transfer occur in microbial fuel cells?

Microbial fuel cells (MFCs) have emerged as a promising technology for sustainable wastewater treatment coupled with electricity generation. A MFC is a device that uses microbes as catalysts to convert chemical energy present in biomass into electrical energy. Among the various mechanisms that drive the operation of a MFC, extracellular electron transfer (EET) to the anode is one of the most important. Exoelectrogenic bacteria can natively transfer electrons to a conducting surface like the anode. The mechanisms employed for electron transfer can either be direct transfer via conductive pili or nanowires, or mediated transfer that involves either naturally secreted redox mediators like flavins and pyocyanins or artificially added mediators like methylene blue and neutral red. EET is a mechanism wherein microorganisms extract energy for growth and maintenance from their surroundings and transfer the resulting electrons to the anode to generate current. The efficiency of these electron transfer mechanisms is dependent not only on the redox potentials of the species involved, but also on microbial oxidative metabolism that liberates electrons. Attempts at understanding the electron transfer mechanisms will boost efforts in giving rise to practical applications. This article covers the various electron transfer mechanisms involved between microbes and electrodes in microbial fuel cells and their applications.

Direct Extracellular Electron Transfer of the Geobacter sulfurreducens Pili Relevant to Interaromatic Distances

Microorganisms can transfer electrons directly to extracellular acceptors, during which organic compounds are oxidized to carbon dioxide. One of these microbes, Geobacter sulfurreducens, is well known for the "metallic-like" conductivity of its type IV pili. However, there is no consensus on what the mechanism for electron transfer along these conductive pili is. Based on the aromatic distances and orientations of our predicted models, the mechanism of electron transfer in the Geobacter sulfurreducens (GS) pili was explored by quantum chemical calculations with Marcus theory of electron transfer reactions. Three aromatic residues from the N-terminal α-helix of the GS pilin subunit are packed together, resulting in a continuous pi-pi interaction chain. The theoretical conductance (4.69 μS/3.85 μS) of the predicted models is very similar to that in the experiments reported recently (3.40 μS). These findings offer a new concept that the GS pili belongs to a new class of proteins that can transport electrons through pi-pi interaction between aromatic residues and also provide a valuable tool for guiding further researches of these conductive pili, to investigate their roles in biogeochemical cycling, and potential applications in biomaterials, bioelectronics, and bioenergy.

Microbial nanowires and electroactive biofilms

Geobacter bacteria are the only microorganisms known to produce conductive appendages or pili to electronically connect cells to extracellular electron acceptors such as iron oxide minerals and uranium. The conductive pili also promote cell-cell aggregation and the formation of electroactive biofilms. The hallmark of these electroactive biofilms is electronic heterogeneity, mediated by coordinated interactions between the conductive pili and matrix-associated cytochromes. Collectively, the matrix-associated electron carriers discharge respiratory electrons from cells in multilayered biofilms to electron-accepting surfaces such as iron oxide coatings and electrodes poised at a metabolically oxidizable potential. The presence of pilus nanowires in the electroactive biofilms also promotes the immobilization and reduction of soluble metals, even when present at toxic concentrations. This review summarizes current knowledge about the composition of the electroactive biofilm matrix and the mechanisms that allow the wired Geobacter biofilms to generate electrical currents and participate in metal redox transformations.

Thermophiles; or, the Modern Prometheus: The Importance of Extreme Microorganisms for Understanding and Applying Extracellular Electron Transfer

Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures ∼50 - 125°C and do not use molecular oxygen (O2) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteria capable of extracellular electron transfer (EET) are positioned close to the root of the Bacteria kingdom on the tree of life. On the contrary, EET in Gram-negative mesophilic bacteria is a relatively new phenomenon that is evolutionarily distinct from Gram-positive bacteria. This suggests that EET evolved separately in Gram-positive thermophiles and Gram-negative mesophiles, and that EET in these bacterial types is a result of a convergent evolutionary process leading to homoplasy. Thus, the study of dissimilatory metal reducing thermophiles provides a glimpse into some of Earth's earliest forms of respiration. This will provide new insights for understanding biogeochemistry and the development of early Earth in addition to providing unique avenues for exploration and discovery in astrobiology. Lastly, the physiological composition of Gram-positive thermophiles, coupled with the kinetic and thermodynamic consequences of surviving at elevated temperatures, makes them ideal candidates for developing new mathematical models and designing innovative next-generation biotechnologies. KEY CONCEPTS Anaerobe: organism that does not require oxygen for growth. Chemoautotroph: organism that obtains energy by oxidizing inorganic electron donors. Convergent Evolution: process in which organisms which are not closely related independently evolve similar traits due to adapting to similar ecological niches and/or environments. Dissimilatory Metal Reduction: reduction of a metal or metalloid that uses electrons from oxidized organic or inorganic electron donors. Exoelectrogen: microorganism that performs dissimilatory metal reduction via extracellular electron transfer. Extremophiles: organisms that thrive in physical or geochemical conditions that are considered detrimental to most life on Earth. Homoplasy: a character shared by a set of species that is not shared by a common ancestor Non-synonymous Substitutions (K a ): a substitution of a nucleotide that changes a codon sequence resulting in a change in the amino acid sequence of a protein. Synonymous Substitutions (K s ): a substitution of a nucleotide that may change a codon sequence, but results in no change in the amino acid sequence of a protein. Thermophiles: a specific group of extremophiles that survive and operate at temperatures ∼50-125°C.

Programmable and printable Bacillus subtilis biofilms as engineered living materials

Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.

Application of electrochemical surface plasmon resonance (ESPR) to the study of electroactive microbial biofilms

Electrochemical surface plasmon resonance (ESPR) monitors faradaic processes optically by the change in refractive index that occurs with a change in redox state at the electrode surface. Here we apply ESPR to investigate the anode-grown Geobacter sulfurreducens biofilm (GSB), a model system used to study electroactive microbial biofilms (EABFs) which perform electrochemical reactions using electrodes as metabolic electron acceptors or donors. A substantial body of evidence indicates that electron transfer reactions among hemes of c-type cytochromes (c-Cyt) play major roles in the extracellular electron transfer (EET) pathways that connect intracellular metabolic processes of cells in an EABF to the electrode surface. The results reported here reveal that when the potential of the electrode is changed from relatively oxidizing (0.40 V vs. SHE) to reducing (-0.55 V vs. SHE) and then back to oxidizing, 70% of c-Cyt residing closest to the biofilm/electrode (within hundreds of nm from the electrode surface) appear to remain trapped in the reduced state, requiring as long as 12 hours to be re-oxidized. c-Cyt storing electrons cannot contribute to EET, yet turnover current resulting from cellular oxidation of acetate coupled with EET to the electrode surface is unaffected. This suggests that a relatively small fraction of c-Cyt residing closest to the biofilm/electrode interface is involved in EET while the majority store electrons. The results also reveal that biomass density at the biofilm/electrode interface increases rapidly during lag phase, reaching its maximum value at the onset of exponential biofilm growth when turnover current begins to rapidly increase.

Nature's conductors: what can microbial multi-heme cytochromes teach us about electron transport and biological energy conversion?

Microorganisms can acquire energy from the environment by extending their electron transport chains to external solid electron donors or acceptors. This process, known as extracellular electron transfer (EET), is now being heavily pursued for wiring microbes to electrodes in bioelectrochemical renewable energy technologies. Recent studies highlight the crucial role of multi-heme cytochromes in facilitating biotic-abiotic EET both for cellular electron export and uptake. Here we explore progress in understanding the range and function of these biological electron conduits in the context of fuel-to-electricity and electricity-to-bioproduct conversion. We also highlight emerging topics, including the role of multi-heme cytochromes in inter-species electron transfer and in inspiring the design and synthesis of a new generation of protein-based bioelectronic components.

Core/Shell Bacterial Cables: A One-Dimensional Platform for Probing Microbial Electron Transfer

Extracellular electron transfer (EET) from electrochemically active bacteria (EAB) plays a critical role in renewable bioelectricity harvesting through microbial fuel cells (MFC). Comprehensive interpretation and interrogation of EET mechanisms can provide valuable information to enhance MFC performance, which however are still restricted by the intrinsic complexity of natural biofilm. Here, we design core/shell EAB-encapsulating cables as a one-dimensional model system to facilitate EET studies, where the local microenvironments can be rationally controlled to establish structure-function correlations with full biological relevance. In particular, our proof-of-concept studies with Shewanella loihica PV-4 ( S. loihica) encapsulating cables demonstrate the precise modulation of fiber diameters (from 6.9 ± 1.1 to 25.1 ± 2.4 μm) and bacteria interactions, which are found to play important roles in programming the formation of different intercellular structures as revealed by in situ optical and ex situ electron microscopic studies. As-formed bacterial cables exhibit conductivity in the range of 2.5-16.2 mS·cm^-1, which is highly dependent on the bacteria density as well as the nature and number of intercellular interconnections. Under electron-acceptor limited conditions, the closely contacted bacteria promote the development of high density self-assembling nanomaterials at cellular interfaces which can be directly translated to the increase of EET efficiency (16.2 mS·cm^-1) as compared with isolated, remotely connected bacteria samples (6.4 mS·cm^-1). Introducing exceeding concentrations of soluble electron acceptors during cell culture, however, substantially suppresses the formation of cellular interconnections and leads to significantly reduced conductivity (2.5 mS·cm^-1). Frequency-dependent measurements further reveal that EET of EAB networks share similar characteristics to electron hopping in conductive polymer matrix, including dominant direct current-conduction in the low frequency region, and alternating current-induced additional electron hopping when the applied frequency is above the critical frequency (10⁵ Hz). The current work represents a strategically new approach for noninvasively probing EET with rationally defined microenvironment and cellular interactions across a wide range of length scales, which is expected to open up new opportunities for tackling the fundamentals and implications of EET.

Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species

Direct interspecies electron transfer (DIET) may prevail in microbial communities that show methanogenesis and anaerobic methane oxidation and can be an electron source to support anaerobic photosynthesis. Previous mutagenic studies on cocultures of defined Geobacter species indicate that both conductive pili and extracellular cytochromes are essential for DIET. However, the actual functional role of the pili in DIET is uncertain, as the pilus mutation strategy used in these studies affected the extracellular cytochrome profile. Here we repressed the function of pili by deleting the pilus polymerization motor PilB in both Geobacter species. The PilB mutation inhibited the pilus assembly but did not alter the pattern of extracellular cytochromes. We report that the two pilus-free Geobacter species can form aggregates and grow syntrophically with DIET. The results demonstrate that the Gmet_2896 cytochrome of Geobacter metallireducens plays a key role in DIET and that conductive pili are not necessary to facilitate DIET in cocultures of Geobacter species, and they suggest cytochromes by themselves can meditate DIET, deepening the understanding of DIET.

Characterizing Electron Transport through Living Biofilms

Here we demonstrate the method of electrochemical gating used to characterize electrical conductivity of electrode-grown microbial biofilms under physiologically relevant conditions.¹ These measurements are performed on living biofilms in aqueous medium using source and drain electrodes patterned on a glass surface in a specialized configuration referred to as an interdigitated electrode (IDA) array. A biofilm is grown that extends across the gap connecting the source and drain. Potentials are applied to the electrodes (ES and ED) generating a source-drain current (ISD) through the biofilm between the electrodes. The dependency of electrical conductivity on gate potential (the average of the source and drain potentials, EG = [ED + ES]/2) is determined by systematically changing the gate potential and measuring the resulting source-drain current. The dependency of conductivity on gate potential provides mechanistic information about the extracellular electron transport process underlying the electrical conductivity of the specific biofilm under investigation. The electrochemical gating measurement method described here is based directly on that used by M. S. Wrighton^2,3 and colleagues and R. W. Murray^4,5,6 and colleagues in the 1980's to investigate thin film conductive polymers.