In situ spectroelectrochemical investigation of electrocatalytic microbial biofilms by surface-enhanced resonance Raman spectroscopy

AC Electromagnetic Field Controls the Biofilms on the Glass Surface by Escherichia coli & Staphylococcus epidermidis Inhibition Effect

Biofilms, mainly comprised of bacteria, form on materials' surfaces due to bacterial activity. They are generally composed of water, extracellular polymeric substances (polysaccharides, proteins, nucleic acids, and lipids), and bacteria. Some bacteria that form biofilms cause periodontal disease, corrosion of the metal materials that make up drains, and slippage. Inside of a biofilm is an environment conducive to the growth and propagation of bacteria. Problems with biofilms include the inability of disinfectants and antibiotics to act on them. Therefore, we have investigated the potential application of alternating electromagnetic fields for biofilm control. We obtained exciting results using various materials' specimens and frequency conditions. Through these studies, we gradually understood that the combination of the type of bacteria, the kind of material, and the application of an electromagnetic field with various low frequencies (4 kHz-12 kHz) changes the circumstances of the onset of the biofilm suppression effect. In this study, relatively high frequencies (20 and 30 kHz) were applied to biofilms caused by Escherichia coli (E. coli) and Staphylococcus epidermidis (S. epidermidis), and quantitative evaluation was performed using staining methods. The sample surfaces were analyzed by Raman spectroscopy using a Laser Raman spectrometer to confirm the presence of biofilms on the surface.

Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens'

Anaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by 'Candidatus Methanoperedens nitroreducens', an ANME acclimated to nitrate reduction. Ferrous iron-targeted fluorescent assays, metatranscriptomics, and single-cell imaging suggest that 'Ca. M. nitroreducens' uses surface-localized redox-active cytochromes for metal reduction. Electrochemical and Raman spectroscopic analyses also support the involvement of c-type cytochrome-mediated EET for electrode reduction. Furthermore, several genes encoding menaquinone cytochrome type-c oxidoreductases and extracellular MHCs are differentially expressed when different electron acceptors are used.

Recent advances in enrichment, isolation, and bio-electrochemical activity evaluation of exoelectrogenic microorganisms

Exoelectrogenic microorganisms (EEMs) catalyzed the conversion of chemical energy to electrical energy via extracellular electron transfer (EET) mechanisms, which underlay diverse bio-electrochemical systems (BES) applications in clean energy development, environment and health monitoring, wearable/implantable devices powering, and sustainable chemicals production, thereby attracting increasing attentions from academic and industrial communities in the recent decades. However, knowledge of EEMs is still in its infancy as only ~100 EEMs of bacteria, archaea, and eukaryotes have been identified, motivating the screening and capture of new EEMs. This review presents a systematic summarization on EEM screening technologies in terms of enrichment, isolation, and bio-electrochemical activity evaluation. We first generalize the distribution characteristics of known EEMs, which provide a basis for EEM screening. Then, we summarize EET mechanisms and the principles underlying various technological approaches to the enrichment, isolation, and bio-electrochemical activity of EEMs, in which a comprehensive analysis of the applicability, accuracy, and efficiency of each technology is reviewed. Finally, we provide a future perspective on EEM screening and bio-electrochemical activity evaluation by focusing on (i) novel EET mechanisms for developing the next-generation EEM screening technologies, and (ii) integration of meta-omics approaches and bioinformatics analyses to explore nonculturable EEMs. This review promotes the development of advanced technologies to capture new EEMs.

Label-Free Optical Imaging of the Electron Transfer in Single Live Microbial Cells

Measurement of electron transfer at the single-particle or -cell level is crucial to the in situ study of basic chemical and biological processes. However, it remains challenging to directly probe the microbial extracellular electron transfer process due to the weakness of signals and the lack of techniques. Here, we present a label-free and noninvasive imaging method that is able to measure the electron transfer in microbial cells. We measured the extracellular electron transfer processes by imaging the redox reaction of c-type outer membrane cytochromes in microbial cells using a plasmonic imaging technique, and obtained the electrochemical activity parameters (formal potential and number of electrons transferred) of multiple individual microbial cells, allowing for unveiling ample heterogeneities in electron transfer at the single-cell level. We anticipate that this method will contribute to the study of electron transfer in various biological and chemical processes.

Graphene as Thinnest Coating on Copper Electrodes in Microbial Methanol Fuel Cells

Dehydrogenation of methanol (CH₃OH) into direct current (DC) in fuel cells can be a potential energy conversion technology. However, their development is currently hampered by the high cost of electrocatalysts based on platinum and palladium, slow kinetics, the formation of carbon monoxide intermediates, and the requirement for high temperatures. Here, we report the use of graphene layers (GL) for generating DC electricity from microbially driven methanol dehydrogenation on underlying copper (Cu) surfaces. Genetically tractable Rhodobacter sphaeroides 2.4.1 (Rsp), a nonarchetypical methylotroph, was used for dehydrogenating methanol at the GL-Cu surfaces. We use electrochemical methods, microscopy, and spectroscopy methods to assess the effects of GL on methanol dehydrogenation by Rsp cells. The GL-Cu offers a 5-fold higher power density and 4-fold higher current density compared to bare Cu. The GL lowers charge transfer resistance to methanol dehydrogenation by 4 orders of magnitude by mitigating issues related to pitting corrosion of underlying Cu surfaces. The presented approach for catalyst-free methanol dehydrogenation on copper electrodes can improve the overall sustainability of fuel cell technologies.

Quantitative Analyses of Biofilm by Using Crystal Violet Staining and Optical Reflection

Biofilms have caused many problems, not only in the industrial fields, but also in our daily lives. Therefore, it is important for us to control them by evaluating them properly. There are many instrumental analytical methods available for evaluating formed biofilm qualitatively. These methods include the use of Raman spectroscopy and various microscopes (optical microscopes, confocal laser microscopes, scanning electron microscopes, transmission electron microscopes, atomic force microscopes, etc.). On the other hand, there are some biological methods, such as staining, gene analyses, etc. From the practical viewpoint, staining methods seem to be the best due to various reasons. Therefore, we focused on the staining method that used a crystal violet solution. In the previous study, we devised an evaluation process for biofilms using a color meter to analyze the various staining situations. However, this method was complicated and expensive for practical engineers. For this experiment, we investigated the process of using regular photos that were quantified without any instruments except for digitized cameras. Digitized cameras were used to compare the results. As a result, we confirmed that the absolute values were different for both cases, respectively. However, the tendency of changes was the same. Therefore, we plan to utilize the changes before and after biofilm formation as indicators for the future.

Proposal for Some Affordable Laboratory Biofilm Reactors and Their Critical Evaluations from Practical Viewpoints

Biofilms are a result of bacterial activities and are found everywhere. They often form on metal surfaces and on the surfaces of polymeric compounds. Biofilms are sticky and mostly consist of water. They have a strong resistance to antimicrobial agents and can cause serious problems for modern medicine and industry. Biofilms are composed of extracellular polymeric substances (EPS) such as polysaccharides produced from bacterial cells and are dominated by water at the initial stage. In a series of experiments, using Escherichia coli, we developed three types of laboratory biofilm reactors (LBR) to simulate biofilm formation. For the first trial, we used a rotary type of biofilm reactor for stirring. For the next trial, we tried another rotary type of reactor where the circular plate holding specimens was rotated. Finally, a circular laboratory biofilm reactor was used. Biofilms were evaluated by using a crystal violet staining method and by using Raman spectroscopy. Additionally, they were compared to each other from the practical (industrial) viewpoints. The third type was the best to form biofilms in a short period. However, the first and second were better from the viewpoint of “ease of use”. All of these have their own advantages and disadvantages, respectively. Therefore, they should be properly selected and used for specific and appropriate purposes in the future.

Impedance Characteristics of Monolayer and Bilayer Graphene Films with Biofilm Formation and Growth

Biofilms are the result of bacterial activity. When the number of bacteria (attached to materials’ surfaces) reaches a certain threshold value, then the bacteria simultaneously excrete organic polymers (EPS: extracellular polymeric substances). These sticky polymers encase and protect the bacteria. They are called biofilms and contain about 80% water. Other components of biofilm include polymeric carbon compounds such as polysaccharides and bacteria. It is well-known that biofilms cause various medical and hygiene problems. Therefore, it is important to have a sensor that can detect biofilms to solve such problems. Graphene is a single-atom-thick sheet in which carbon atoms are connected in a hexagonal shape like a honeycomb. Carbon compounds generally bond easily to graphene. Therefore, it is highly possible that graphene could serve as a sensor to monitor biofilm formation and growth. In our previous study, monolayer graphene was prepared on a glass substrate by the chemical vapor deposition (CVD) method. Its biofilm forming ability was compared with that of graphite. As a result, the CVD graphene film had the higher sensitivity for biofilm formation. However, the monolayer graphene has a mechanical disadvantage when used as a biofilm sensor. Therefore, for this new research project, we prepared bilayer graphene with high mechanical strength by using the CVD process on copper substrates. For these specimens, we measured the capacitance component of the specimens’ impedance. In addition, we have included a discussion about the possibility of applying them as future sensors for monitoring biofilm formation and growth.

Pushing the methodological envelope in understanding the photo/electrosynthetic materials-microorganism interface

Biohybrid photo/electrosynthetic systems synergize microbial metabolic pathways and inorganic materials to generate the fuels and chemicals to power our society. They aim to combine the strengths of product selectivity from biological cells and efficient charge generation and light absorption of inorganic materials. However crucial mechanistic questions still remain. In this review we address significant knowledge gaps that must be closed and recent efforts to do so to push biohybrid systems closer to applicability. In particular, we focus on noteworthy advances that have recently been made in applying state-of-the-art analytical spectroscopic, electrochemical, and microelectronic techniques to help pinpoint key complexities of the microbe-materials interface. We discuss the basic function of these techniques, how they have been translated over to study biohybrid systems, and which key insights and implications have been extracted. Finally, we delve into the key advances necessary for the design of next generation biohybrid energy conversion systems.

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.

Understanding active sites in molecular (photo)electrocatalysis through complementary vibrational spectroelectrochemistry

Highlighting vibrational spectroelectrochemistry for the investigation of synthetic molecular (photo) electrocatalysts for key energy conversion reactions.

Improvement of Surface-Enhanced Raman Scattering Method for Single Bacterial Cell Analysis

Surface-enhanced Raman scattering (SERS) is a useful tool for label-free analysis of bacteria at the single cell level. However, low reproducibility limits the use of SERS. In this study, for the sake of sensitive and reproducible Raman spectra, we optimized the methods for preparing silver nanoparticles (AgNPs) and depositing AgNPs onto a cell surface. We found that fast dropwise addition of AgNO₃ into the reductant produced smaller and more stable AgNPs, with an average diameter of 45 ± 4 nm. Compared with that observed after simply mixing the bacterial cells with AgNPs, the SERS signal was significantly improved after centrifugation. To optimize the SERS enhancement method, the centrifugal force, method for preparing AgNPs, concentration of AgNPs, ionic strength of the solution used to suspend the cells, and density of the cells were chosen as impact factors and optimized through orthogonal experiments. Finally, the improved method could generate sensitive and reproducible SERS spectra from single Escherichia coli cells, and the SERS signals primarily arose from the cell envelope. We further verified that this optimal method was feasible for the detection of low to 25% incorporation of ¹³C isotopes by the cells and the discrimination of different bacterial species. Our work provides an improved method for generating sensitive and reproducible SERS spectra.

Disparity of Cytochrome Utilization in Anodic and Cathodic Extracellular Electron Transfer Pathways of Geobacter sulfurreducens Biofilms

Extracellular electron transfer (EET) in microorganisms is prevalent in nature and has been utilized in functional bioelectrochemical systems. EET of Geobacter sulfurreducens has been extensively studied and has been revealed to be facilitated through c-type cytochromes, which mediate charge between the electrode and G. sulfurreducens in anodic mode. However, the EET pathway of cathodic conversion of fumarate to succinate is still under debate. Here, we apply a variety of analytical methods, including electrochemistry, UV-vis absorption and resonance Raman spectroscopy, quartz crystal microbalance with dissipation, and electron microscopy, to understand the involvement of cytochromes and other possible electron-mediating species in the switching between anodic and cathodic reaction modes. By switching the applied bias for a G. sulfurreducens biofilm coupled to investigating the quantity and function of cytochromes, as well as the emergence of Fe-containing particles on the cell membrane, we provide evidence of a diminished role of cytochromes in cathodic EET. This work sheds light on the mechanisms of G. sulfurreducens biofilm growth and suggests the possible existence of a nonheme, iron-involving EET process in cathodic mode.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

On-Line Raman Spectroscopic Study of Cytochromes' Redox State of Biofilms in Microbial Fuel Cells

Bio-electrochemical systems such as microbial fuel cells and microbial electrosynthesis cells depend on efficient electron transfer between the microorganisms and the electrodes. Understanding the mechanisms and dynamics of the electron transfer is important in order to design more efficient reactors, as well as modifying microorganisms for enhanced electricity production. Geobacter are well known for their ability to form thick biofilms and transfer electrons to the surfaces of electrodes. Currently, there are not many “on-line” systems for monitoring the activity of the biofilm and the electron transfer process without harming the biofilm. Raman microscopy was shown to be capable of providing biochemical information, i.e., the redox state of C-type cytochromes, which is integral to external electron transfer, without harming the biofilm. In the current study, a custom 3D printed flow-through cuvette was used in order to analyze the oxidation state of the C-type cytochromes of suspended cultures of three Geobacter sulfurreducens strains (PCA, KN400 and ΔpilA). It was found that the oxidation state is a good indicator of the metabolic state of the cells. Furthermore, an anaerobic fluidic system enabling in situ Raman measurements was designed and applied successfully to monitor and characterize G. sulfurreducens biofilms during electricity generation, for both a wild strain, PCA, and a mutant, ΔS. The cytochrome redox state, monitored by the Raman peak areas, could be modulated by applying different poise voltages to the electrodes. This also correlated with the modulation of current transferred from the cytochromes to the electrode. The Raman peak area changed in a predictable and reversible manner, indicating that the system could be used for analyzing the oxidation state of the proteins responsible for the electron transfer process and the kinetics thereof in-situ.

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.

Interfacing nature's catalytic machinery with synthetic materials for semi-artificial photosynthesis

Semi-artificial photosynthetic systems aim to overcome the limitations of natural and artificial photosynthesis while providing an opportunity to investigate their respective functionality. The progress and studies of these hybrid systems is the focus of this forward-looking perspective. In this Review, we discuss how enzymes have been interfaced with synthetic materials and employed for semi-artificial fuel production. In parallel, we examine how more complex living cellular systems can be recruited for in vivo fuel and chemical production in an approach where inorganic nanostructures are hybridized with photosynthetic and non-photosynthetic microorganisms. Side-by-side comparisons reveal strengths and limitations of enzyme- and microorganism-based hybrid systems, and how lessons extracted from studying enzyme hybrids can be applied to investigations of microorganism-hybrid devices. We conclude by putting semi-artificial photosynthesis in the context of its own ambitions and discuss how it can help address the grand challenges facing artificial systems for the efficient generation of solar fuels and chemicals.

Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N2 Labeling

Nitrogen (N) fixation is the conversion of inert nitrogen gas (N₂) to bioavailable N essential for all forms of life. N₂-fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with ¹⁵N₂ stable isotope probing (SIP) was developed to discern N₂-fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N₂-fixing bacteria), along with a marked ¹⁵N₂-induced Cyt c band shift, generated a highly distinguishable biomarker for N₂ fixation. ¹⁵N₂-induced shift was consistent well with ¹⁵N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N₂-fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus ¹⁵N₂ percentage allowed quantification of N₂ fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.

Smart multifunctional nanoagents for in situ monitoring of small molecules with a switchable affinity towards biomedical targets

The great diversity of nanomaterials provides ample opportunities for constructing effective agents for biomedical applications ranging from biosensing to drug delivery. Multifunctional nanoagents that combine several features in a single particle are of special interest due to capabilities that substantially exceed those of molecular drugs. An ideal theranostic agent should simultaneously be an advanced biosensor to identify a disease and report the diagnosis and a biomedical actuator to treat the disease. While many approaches were developed to load a nanoparticle with various drugs for actuation of the diseased cells (e.g., to kill them), the nanoparticle-based approaches for the localized biosensing with real-time reporting of the marker concentration severely lag behind. Here, we show a smart in situ nanoparticle-based biosensor/actuator system that dynamically and reversibly changes its structural and optical properties in response to a small molecule marker to allow real-time monitoring of the marker concentration and adjustment of the system ability to bind its biomedical target. Using the synergistic combination of signal readout based on the localized surface plasmon resonance and an original method of fabrication of smart ON/OFF-switchable nanoagents, we demonstrate reversible responsiveness of the system to a model small molecule marker (antibiotic chloramphenicol) in a wide concentration range. The proposed approach can be used for the development of advanced multifunctional nanoagents for theranostic applications.

The Planktonic Relationship Between Fluid-Like Electrodes and Bacteria: Wiring in Motion

We have explored a new concept in bacteria-electrode interaction based on the use of fluid-like electrodes and planktonic living cells. We show for the first time that living in a biofilm is not a strict requirement for Geobacter sulfurreducens to exchange electrons with an electrode. The growth of planktonic electroactive G. sulfurreducens could be supported by a fluid-like anode as soluble electron acceptors and with electron transfer rates similar to those reported for electroactive biofilms. This growth was maintained by uncoupling the charge (catabolism) and discharge (extracellular respiration) processes of the cells. Our results reveal a novel method to culture electroactive bacteria in which every single cell in the medium could be instantaneously wired to a fluid-like electrode. Direct extracellular electron transfer is occurring but with a new paradigm behind the bacteria-electrode interaction.

Engineering of Microbial Electrodes

This chapter provides an overview of the current state-of-the-art in the engineering of microbial electrodes for application in microbial electrosynthesis. First, important functional aspects and requirements of basic materials for microbial electrodes are introduced, including the meaningful benchmarking of electrode performance, a comparison of electrode materials, and methods to improve microbe-electrode interaction. Suitable current collectors and composite materials that combine different functionalities are also discussed. Subsequently, the chapter focuses on the design of macroscopic electrode structures. Aspects such as mass transfer and electrode topology are touched upon, and a comparison of the performance of microbial electrodes relevant for practical application is provided. The chapter closes with an overall conclusion and outlook, highlighting the future prospects and challenges for the engineering of microbial electrodes toward practical application in the field of microbial electrosynthesis. Graphical Abstract.

Anodic biofilms as the interphase for electroactive bacterial growth on carbon veil

The structure and activity of electrochemically active biofilms (EABs) are usually investigated on flat electrodes. However, real world applications such as wastewater treatment and bioelectrosynthesis require tridimensional electrodes to increase surface area and facilitate EAB attachment. The structure and activity of thick EABs grown on high surface area electrodes are difficult to characterize with electrochemical and microscopy methods. Here, the authors adopt a stacked electrode configuration to simulate the high surface and the tridimensional structure of an electrode for large-scale EAB applications. Each layer of the stacked electrode is independently characterized using confocal laser scanning microscopy (CLSM) and digital image processing. Shewanella oneidensis MR-1 biofilm on stacked carbon veil electrodes is grown under constant oxidative potentials (0, +200, and +400 mV versus Ag/AgCl) until a stable current output is obtained. The textural, aerial, and volumetric parameters extracted from CLSM images allow tracking of the evolution of morphological properties within the stacked electrodes. The electrode layers facing the bulk liquid show higher biovolumes compared with the inner layer of the stack. The electrochemical performance of S. oneidensis MR-1 is directly linked to the overall biofilm volume as well as connectivity between cell clusters.

In situ monitoring of Shewanella oneidensis MR-1 biofilm growth on gold electrodes by using a Pt microelectrode

Much attention has been focused on electrochemically active bacteria (EAB) in the application of bioelectrochemical systems (BESs). Studying the EAB biofilm growth mechanism as well as electron transfer mechanism provides a route to upgrade BES performance. But an effective bacterial growth monitoring method on the biofilm scale is still absent in this field. In this work, electrode-attached bacterial biofilms formed by Shewanella oneidensis MR-1 were dynamically monitored through a microelectrode method. For S. oneidensis MR-1, a respiratory electron transport chain is associated with the secretion of riboflavin, severing as the cofactor to the outer membrane c-type cytochromes. The biofilm growth was monitored through adopting riboflavin as an electrochemical probe during the approach of the microelectrode to the biofilm external surface. This method allows in vivo and in situ biofilm monitoring at different growth stages without destructive manipulation. Furthermore, the biofilm growth monitoring results have been proved to be relatively accurate through observation under confocal laser scanning microscopy. We further applied this method to investigate the effects of four environmental factors (the concentrations of dissolved oxygen, sodium lactate, riboflavin as well as the electrode potential) on S. oneidensis MR-1 biofilm development.

Analysis of electron transfer dynamics in mixed community electroactive microbial biofilms

Electrochemically active microbial biofilms are capable to produce electric current when grown onto electrodes. This work investigates the dynamics of electron transfer inside the biofilm as well as at the biofilm/electrode interface.

In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy

Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats.

Nature of the Surface-Exposed Cytochrome-Electrode Interactions in Electroactive Biofilms of Desulfuromonas acetoxidans

Metal-respiring bacteria are microorganisms capable of oxidizing organic pollutants present in wastewater and transferring the liberated electrons to an electrode. This ability has led to their application as catalysts in bioelectrochemical systems (BESs), a sustainable technology coupling bioremediation to electricity production. Crucial for the functioning of these BESs is a complex protein architecture consisting of several surface-exposed multiheme proteins, called outer membrane cytochromes, wiring the cell metabolism to the electrode. Although the role of these proteins has been increasingly understood, little is known about the protein-electrode interactions and their impact on the performance of BESs. In this study, we used surface-enhanced resonance Raman spectroscopy in combination with electrochemical techniques to unravel the nature of the protein-electrode interaction for the outer membrane cytochrome OmcB from Desulfuromonas acetoxidans (Dace). Comparing the spectroelectrochemical properties of OmcB bound directly to the electrode surface with those of the same protein embedded inside an electroactive biofilm, we have shown that the surface-exposed cytochromes of Dace biofilms are in direct contact with the electrode surface. Even if direct binding causes protein denaturation, the biofilm possesses the ability to minimize the extent of the damage maximizing the amount of cells in direct electrical communication with the electrode.

A severe reduction in the cytochrome C content of Geobacter sulfurreducens eliminates its capacity for extracellular electron transfer

The ability of Geobacter species to transfer electrons outside the cell enables them to play an important role in a number of biogeochemical and bioenergy processes. Gene deletion studies have implicated periplasmic and outer-surface c-type cytochromes in this extracellular electron transfer. However, even when as many as five c-type cytochrome genes have been deleted, some capacity for extracellular electron transfer remains. In order to evaluate the role of c-type cytochromes in extracellular electron transfer, Geobacter sulfurreducens was grown in a low-iron medium that included the iron chelator (2,2'-bipyridine) to further sequester iron. Haem-staining revealed that the cytochrome content of cells grown in this manner was 15-fold lower than in cells exposed to a standard iron-containing medium. The low cytochrome abundance was confirmed by in situ nanoparticle-enhanced Raman spectroscopy (NERS). The cytochrome-depleted cells reduced fumarate to succinate as well as the cytochrome-replete cells do, but were unable to reduce Fe(III) citrate or to exchange electrons with a graphite electrode. These results demonstrate that c-type cytochromes are essential for extracellular electron transfer by G. sulfurreducens. The strategy for growing cytochrome-depleted G. sulfurreducens will also greatly aid future physiological studies of Geobacter species and other microorganisms capable of extracellular electron transfer.

An Electrochemical Strategy to Measure the Thickness of Electroactive Microbial Biofilms

The study of electroactive microbial biofilms often requires knowledge of the biofilm thickness. Unfortunately, this parameter is, nowadays, only accessible through expensive microscopic techniques. This work overcomes this limitation by presenting a new strategy, exploiting the use of chronoamperometry (CA) alone. A mixed-culture biofilm is exposed to an O₂-saturated solution during anode respiration to suppress its catalytic activity. Assuming that inactivation of the electrocatalytic process is caused by O₂ diffusion through the biofilm, a simple relation allows the use of the time constant extracted from the fitting of the curve of the CA trace during inactivation for the straightforward and quantitative determination of biofilm thickness. The biofilm thickness obtained with this method obeys the expected trend reported for biofilm growth and is in agreement with optical measurements. Contrary to the techniques usually employed to determine biofilm thickness, this new strategy is very rapid, nondisruptive, inexpensive, and may become a convenient alternative with respect to expensive and time-consuming microscopic techniques.

Towards the understanding of the effect of oxygen on the electrocatalytic activity of microbial biofilms: a spectroelectrochemical study

Metal-respiring bacteria oxidize an organic substrate and transfer the liberated electrons to the electrode. Molecular oxygen interrupts the current flow by cutting the electrical circuit wiring the cell metabolism to the electrode.

Close-packed assemblies of discrete tiny silver nanoparticles on triangular gold nanoplates as a high performance SERS probe

An island like array of tiny Ag nanoparticles bounded on triangular Au nanoplates was synthesized as surface-enhanced Raman spectroscopy substrate.

Investigating microbial activities of electrode-associated microorganisms in real-time

Electrode-associated microbial biofilms are essential to the function of bioelectrochemical systems (BESs). These systems exist in a number of different configurations but all rely on electroactive microorganisms utilizing an electrode as either an electron acceptor or an electron donor to catalyze biological processes. Investigations of the structure and function of electrode-associated biofilms are critical to further the understanding of how microbial communities are able to reduce and oxidize electrodes. The community structure of electrode-reducing biofilms is diverse and often dominated by Geobacter spp. whereas electrode-oxidizing biofilms are often dominated by other microorganisms. The application of a wide range of tools, such as high-throughput sequencing and metagenomic data analyses, provide insight into the structure and possible function of microbial communities on electrode surfaces. However, the development and application of techniques that monitor gene expression profiles in real-time are required for a more definite spatial and temporal understanding of the diversity and biological activities of these dynamic communities. This mini review summarizes the key gene expression techniques used in BESs research, which have led to a better understanding of population dynamics, cell–cell communication and molecule-surface interactions in mixed and pure BES communities.

Real-time measurements of the redox states of c-type cytochromes in electroactive biofilms: a confocal resonance Raman Microscopy study

Confocal Resonance Raman Microscopy (CRRM) was used to probe variations of redox state of c-type cytochromes embedded in living mixed-culture electroactive biofilms exposed to different electrode polarizations, under potentiostatic and potentiodynamic conditions. In the absence of the metabolic substrate acetate, the redox state of cytochromes followed the application of reducing and oxidizing electrode potentials. Real-time monitoring of the redox state of cytochromes during cyclic voltammetry (CV) in a potential window where cytochromes reduction occurs, evidenced a measurable time delay between the oxidation of redox cofactors probed by CV at the electrode interface, and oxidation of distal cytochromes probed by CRRM. This delay was used to tentatively estimate the diffusivity of electrons through the biofilm. In the presence of acetate, the resonance Raman spectra of young (10 days, j = 208±49 µA cm⁻²) and mature (57 days, j = 267±73 µA cm⁻²) biofilms show that cytochromes remained oxidized homogeneously even at layers as far as 70 µm from the electrode, implying the existence of slow metabolic kinetics that do not result in the formation of a redox gradient inside the biofilm during anode respiration. However, old biofilms (80 days, j = 190±37 µA cm⁻²) with thickness above 100 µm were characterized by reduced catalytic activity compared to the previous developing stages. The cytochromes in these biofilm were mainly in the reduced redox state, showing that only aged mixed-culture biofilms accumulate electrons during anode respiration. These results differ substantially from recent observations in pure Geobacter sulfurreducens electroactive biofilms, in which accumulation of reduced cytochromes is already observed in thinner biofilms, thus suggesting different bottlenecks in current production for mixed-culture and G. sulfurreducens biofilms.

Spatially resolved confocal resonant Raman microscopic analysis of anode-grown Geobacter sulfurreducens biofilms

When grown on the surface of an anode electrode, Geobacter sulfurreducens forms a multi-cell thick biofilm in which all cells appear to couple the oxidation of acetate with electron transport to the anode, which serves as the terminal metabolic electron acceptor. Just how electrons are transported through such a biofilm from cells to the underlying anode surface over distances that can exceed 20 microns remains unresolved. Current evidence suggests it may occur by electron hopping through a proposed network of redox cofactors composed of immobile outer membrane and/or extracellular multi-heme c-type cytochromes. In the present work, we perform a spatially resolved confocal resonant Raman (CRR) microscopic analysis to investigate anode-grown Geobacter biofilms. The results confirm the presence of an intra-biofilm redox gradient whereby the probability that a heme is in the reduced state increases with increasing distance from the anode surface. Such a gradient is required to drive electron transport toward the anode surface by electron hopping via cytochromes. The results also indicate that at open circuit, when electrons are expected to accumulate in redox cofactors involved in electron transport due to the inability of the anode to accept electrons, nearly all c-type cytochrome hemes detected in the biofilm are oxidized. The same outcome occurs when a comparable potential to that measured at open circuit (-0.30 V vs. SHE) is applied to the anode, whereas nearly all hemes are reduced when an exceedingly negative potential (-0.50 V vs. SHE) is applied to the anode. These results suggest that nearly all c-type cytochrome hemes detected in the biofilm can be electrochemically accessed by the electrode, but most have oxidation potentials too negative to transport electrons originating from acetate metabolism. The results also reveal a lateral heterogeneity (x-y dimensions) in the type of c-type cytochromes within the biofilm that may affect electron transport to the electrode.