Direct Observation of Electrically Conductive Pili Emanating from Geobacter sulfurreducens

Syntrophic methane production from volatile fatty acids: Focus on interspecies electron transfer

Methane is a renewable biomass energy source produced via anaerobic digestion (AD). Interspecies electron transfer (IET) between methanogens and syntrophic bacteria is crucial for mitigating energy barriers in this process. Understanding IET is essential for enhancing the efficiency of syntrophic methanogenesis in anaerobic digestion. Interspecies electron transfer mechanisms include interspecies H2/formate transfer, direct interspecies electron transfer (DIET), and electron-shuttle-mediated transfer. This review summarizes the mechanisms, developments, and research gaps in IET pathways. Interspecies H2/formate transfer requires strict control of low H2 partial pressure and involves complex enzymatic reactions. In contrast, DIET enhances the electron transfer efficiency and process stability. Conductive materials and key microorganisms can be modulated to stimulate the DIET. Electron shuttles (ES) allow microorganisms to interact with extracellular electron acceptors without direct contact; however, their efficiency depends on various factors. Future studies should elucidate the key functional groups, metabolic pathways, and regulatory mechanisms of IET to guide the optimization of AD processes for efficient renewable energy production.

Lack of physiological evidence for cytochrome filaments functioning as conduits for extracellular electron transfer

Extracellular cytochrome filaments are proposed to serve as conduits for long-range extracellular electron transfer. The primary functional physiological evidence has been the reported inhibition of Geobacter sulfurreducens Fe(III) oxide reduction when the gene for the filament-forming cytochrome OmcS is deleted. Here we report that the OmcS-deficient strain from that original report reduces Fe(III) oxide as well as the wild-type, as does a triple mutant in which the genes for the other known filament-forming cytochromes were also deleted. The triple cytochrome mutant displayed filaments with the same 3 nm diameter morphology and conductance as those produced by Escherichia coli heterologously expressing the G. sulfurreducens PilA pilin gene. Fe(III) oxide reduction was inhibited when the pilin gene in cytochrome-deficient mutants was modified to yield poorly conductive 3 nm diameter filaments. The results are consistent with the concept that 3 nm diameter electrically conductive pili (e-pili) are required for G. sulfurreducens long-range extracellular electron transfer. In contrast, rigorous physiological functional evidence is lacking for cytochrome filaments serving as conduits for long-range electron transport.

IMPORTANCE

Unraveling microbial extracellular electron transfer mechanisms has profound implications for environmental processes and advancing biological applications. This study on Geobacter sulfurreducens challenges prevailing beliefs on cytochrome filaments as crucial components thought to facilitate long-range electron transport. The discovery of an OmcS-deficient strain's unexpected effectiveness in Fe(III) oxide reduction prompted a reevaluation of the key conduits for extracellular electron transfer. By exploring the impact of genetic modifications on G. sulfurreducens' performance, this research sheds light on the importance of 3-nm diameter electrically conductive pili in Fe(III) oxide reduction. Reassessing these mechanisms is essential for uncovering the true drivers of extracellular electron transfer in microbial systems, offering insights that could revolutionize applications across diverse fields.

Beneficial applications of biofilms

Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.

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.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.

Responses of syntrophic microbial communities and their interactions with polystyrene nanoplastics in a microbial electrolysis cell

Microbial electrochemical technologies are promising for simultaneous energy recovery and wastewater treatment. Although the inhibitory effects of emerging pollutants, particularly micro/nanoplastics (MPs/NPs), on conventional wastewater systems have been extensively studied, the current understanding of their impact on microbial electrochemical systems is still quite limited. Microplastics are plastic particles ranging from 1 μm to 5 mm. However, nanoplastics are smaller plastic particles ranging from 1 to 100 nm. Due to their smaller size and greater surface area, they can penetrate deeper into biofilm structures and cell membranes, potentially disrupting their integrity and leading to changes in biofilm composition and function. This study first reports the impact of polystyrene nanoplastics (PsNPs) on syntrophic anode microbial communities in a microbial electrolysis cell. Low concentrations of PsNPs (50 and 250 μg/L) had a minimal impact on current density and hydrogen production. However, 500 μg/L of PsNPs decreased the maximum current density and specific hydrogen production rate by ∼43 % and ∼48 %, respectively. Exposure to PsNPs increased extracellular polymeric substance (EPS) levels, with a higher ratio of carbohydrates to proteins, suggesting a potential defense mechanism through EPS secretion. The downregulation of genes associated with extracellular electron transfer was observed at 500 μg/L of PsNPs. Furthermore, the detrimental impact of 500 μg/L PsNPs on the microbiome was evident from the decrease in 16S rRNA gene copies, microbial diversity, richness, and relative abundances of key electroactive and fermentative bacteria. For the first time, this study presents the inhibitory threshold of any NPs on syntrophic electroactive biofilms within a microbial electrochemical system.

Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism

The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.

Accelerated Microbial Corrosion by Magnetite and Electrically Conductive Pili through Direct Fe0 -to-Microbe Electron Transfer

Electrobiocorrosion, the process in which microbes extract electrons from metallic iron (Fe0 ) through direct Fe0 -microbe electrical connections, is thought to contribute to the costly corrosion of iron-containing metals that impacts many industries. However, electrobiocorrosion mechanisms are poorly understood. We report here that electrically conductive pili (e-pili) and the conductive mineral magnetite play an important role in the electron transfer between Fe0 and Geobacter sulfurreducens, the first microbe in which electrobiocorrosion has been rigorously documented. Genetic modification to express poorly conductive pili substantially diminished corrosive pitting and rates of Fe0 -to-microbe electron flux. Magnetite reduced resistance to electron transfer, increasing corrosion currents and intensifying pitting. Studies with mutants suggested that the magnetite promoted electron transfer in a manner similar to the outer-surface c-type cytochrome OmcS. These findings, and the fact that magnetite is a common product of iron corrosion, suggest a potential positive feedback loop of magnetite produced during corrosion further accelerating electrobiocorrosion. The interactions of e-pili, cytochromes, and magnetite demonstrate mechanistic complexities of electrobiocorrosion, but also provide insights into detecting and possibly mitigating this economically damaging process.

Engineering nanowires in bacteria to elucidate electron transport structural-functional relationships

Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells' bioenergetic programming. Their role is thought to be linked to facilitating electron transfer between cells and the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineered Cupriavidus necator H16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using a Cupriavidus necator chassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.

Microbial nanowires: type IV pili or cytochrome filaments?

A dynamic field of study has emerged involving long-range electron transport by extracellular filaments in anaerobic bacteria, with Geobacter sulfurreducens being used as a model system. The interest in this topic stems from the potential uses of such systems in bioremediation, energy generation, and new bio-based nanotechnology for electronic devices. These conductive extracellular filaments were originally thought, based upon low-resolution observations of dried samples, to be type IV pili (T4P). However, the recently published atomic structure for the T4P from G. sulfurreducens, obtained by cryo-electron microscopy (cryo-EM), is incompatible with the numerous models that have been put forward for electron conduction. As with all high-resolution structures of T4P, the G. sulfurreducens T4P structure shows a partial melting of the α-helix that substantially impacts the aromatic residue positions such that they are incompatible with conductivity. Furthermore, new work using high-resolution cryo-EM shows that conductive filaments thought to be T4P are actually polymerized cytochromes, with stacked heme groups forming a continuous conductive wire, or extracellular DNA. Recent atomic structures of three different cytochrome filaments from G. sulfurreducens suggest that such polymers evolved independently on multiple occasions. The expectation is that such polymerized cytochromes may be found emanating from other anaerobic organisms.

Enhancing electrical outputs of the fuel cells with Geobacter sulferreducens by overexpressing nanowire proteins

Protein nanowires are critical electroactive components for electron transfer of Geobacter sulfurreducens biofilm. To determine the applicability of the nanowire proteins in improving bioelectricity production, their genes including pilA, omcZ, omcS and omcT were overexpressed in G. sulfurreducens. The voltage outputs of the constructed strains were higher than that of the control strain with the empty vector (0.470-0.578 vs. 0.355 V) in microbial fuel cells (MFCs). As a result, the power density of the constructed strains (i.e. 1.39-1.58 W m^-2 ) also increased by 2.62- to 2.97-fold as compared to that of the control strain. Overexpression of nanowire proteins also improved biofilm formation on electrodes with increased protein amount and thickness of biofilms. The normalized power outputs of the constructed strains were 0.18-0.20 W g^-1 that increased by 74% to 93% from that of the control strain. Bioelectrochemical analyses further revealed that the biofilms and MFCs with the constructed strains had stronger electroactivity and smaller internal resistance, respectively. Collectively, these results demonstrate for the first time that overexpression of nanowire proteins increases the biomass and electroactivity of anode-attached microbial biofilms. Moreover, this study provides a new way for enhancing the electrical outputs of MFCs.

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.

Regulation of Bacterial Behavior by Light and Magnetism Mediated by Mesoporous Silica-Coated MnFe2O4@CoFe2O4 Nanoparticles

Unicellular bacterial cells exhibit diverse population behaviors (i.e., aggregation, dispersion, directed assembly, biofilm formation, etc.) to facilitate communication and cooperation. Suitable bacterial behaviors are required for efficient nutrient uptake, cell recycling, and stress response for environmental and industrial application of bacterial populations. However, it remains a great challenge to artificially control bacterial behaviors because of complicated genetic and biochemical mechanisms. In this study, we designed facile mesoporous silica nanoparticle (MSN)-based assemblies to intelligently regulate bacterial behaviors with the help of light and magnetic field. This system was composed of magnetic MSNs, i.e., MnFe₂O₄@CoFe₂O₄@MSN modified by photoactive spiropyran (SP), and the chitosan-based polymers ChiPSP, i.e., chitosan grafted by triphenylphosphine and SP. The assembly strongly bound bacterial cells, inducing reversible bacterial aggregation by visible-light irradiation and dark. Moreover, the formed bacterial aggregates could be further governed by a directed magnetic field (DMF) to form microfibers and by an alternating magnetic field (AMF) to form biofilms. This study realized stimulus-triggered regulation of bacterial behaviors by MSNs and implied the great power of chemical strategies in intelligent control of diverse biological processes for environmental and industrial applications.

Genetic Manipulation of Desulfovibrio ferrophilus and Evaluation of Fe(III) Oxide Reduction Mechanisms

The sulfate-reducing microbe Desulfovibrio ferrophilus is of interest due to its relatively rare ability to also grow with Fe(III) oxide as an electron acceptor and its rapid corrosion of metallic iron. Previous studies have suggested multiple agents for D. ferrophilus extracellular electron exchange including a soluble electron shuttle, electrically conductive pili, and outer surface multiheme c-type cytochromes. However, the previous lack of a strategy for genetic manipulation of D. ferrophilus limited mechanistic investigations. We developed an electroporation-mediated transformation method that enabled replacement of D. ferrophilus genes of interest with an antibiotic resistance gene via double-crossover homologous recombination. Genes were identified that are essential for flagellum-based motility and the expression of the two types of D. ferrophilus pili. Disrupting flagellum-based motility or expression of either of the two pili did not inhibit Fe(III) oxide reduction, nor did deleting genes for multiheme c-type cytochromes predicted to be associated with the outer membrane. Although redundancies in cytochrome or pilus function might explain some of these phenotypes, overall, the results are consistent with D. ferrophilus primarily reducing Fe(III) oxide via an electron shuttle. The finding that D. ferrophilus is genetically tractable not only will aid in elucidating further details of its mechanisms for Fe(III) oxide reduction but also provides a new experimental approach for developing a better understanding of some of its other unique features, such as the ability to corrode metallic iron at high rates and accept electrons from negatively poised electrodes. IMPORTANCE Desulfovibrio ferrophilus is an important pure culture model for Fe(III) oxide reduction and the corrosion of iron-containing metals in anaerobic marine environments. This study demonstrates that D. ferrophilus is genetically tractable, an important advance for elucidating the mechanisms by which it interacts with extracellular electron acceptors and donors. The results demonstrate that there is not one specific outer surface multiheme D. ferrophilus c-type cytochrome that is essential for Fe(III) oxide reduction. This finding, coupled with the lack of apparent porin-cytochrome conduits encoded in the D. ferrophilus genome and the finding that deleting genes for pilus and flagellum expression did not inhibit Fe(III) oxide reduction, suggests that D. ferrophilus has adopted strategies for extracellular electron exchange that are different from those of intensively studied electroactive microbes like Shewanella and Geobacter species. Thus, the ability to genetically manipulate D. ferrophilus is likely to lead to new mechanistic concepts in electromicrobiology.

Electron-pool promotes interfacial electron transfer efficiency between pyrogenic carbon and anodic microbes

Relying on surface functional groups and graphitized structure, pyrogenic carbon (PC) was reported to facilitate microbial extracellular electron transfer (EET), which plays a crucial role in diverse biogeochemical reactions. However, little is known about the role of electrical capacitance on EET between microbes and PCs. Here, PCs were obtained from fermented steam bread after carbonization at different temperatures from 700 °C to 1100 °C. PC-900 exhibited the lowest charge transfer resistance and highest electrical capacitance, ascribed to combined effects of graphitic structure and hierarchical porous structure. The interfacial EET was further investigated by enriching electroactive biofilms on PC surface. Faster interfacial EET was demonstrated in PC-900. Maximum power density was proportional to electrical capacitance rather than conductivity. PC-900 enriched the most Geobacter sp., which was positively correlated with electrical capacitance according to the distance-based redundancy analysis. Electrical capacitance was suggested to act as electron pool to facilitate interfacial EET efficiency.

Different outer membrane c-type cytochromes are involved in direct interspecies electron transfer to Geobacter or Methanosarcina species

Direct interspecies electron transfer (DIET) may be most important in methanogenic environments, but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor. To better understand DIET with methanogens, the transcriptome of Geobacter metallireducens during DIET-based growth with G. sulfurreducens reducing fumarate was compared with G. metallireducens grown in coculture with diverse Methanosarcina. The transcriptome of G. metallireducens cocultured with G. sulfurreducens was significantly different from those with Methanosarcina. Furthermore, the transcriptome of G. metallireducens grown with Methanosarcina barkeri, which lacks outer-surface c-type cytochromes, differed from those of G. metallireducens cocultured with M. acetivorans or M. subterranea, which have an outer-surface c-type cytochrome that serves as an electrical connect for DIET. Differences in G. metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable. Cocultures with c-type cytochrome deletion mutant strains, ∆Gmet_0930, ∆Gmet_0557 and ∆Gmet_2896, never became established with G. sulfurreducens but adapted to grow with all three Methanosarcina. Two porin-cytochrome complexes, PccF and PccG, were important for DIET; however, PccG was more important for growth with Methanosarcina. Unlike cocultures with G. sulfurreducens and M. acetivorans, electrically conductive pili were not needed for growth with M. barkeri. Shewanella oneidensis, another electroactive microbe with abundant outer-surface c-type cytochromes, did not grow via DIET. The results demonstrate that the presence of outer-surface c-type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron-accepting partner on the physiology of the electron-donating DIET partner.

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

Contribution of configurations, electrode and membrane materials, electron transfer mechanisms, and cost of components on the current and future development of microbial fuel cells

Microbial fuel cells (MFCs) are a technology that can be applied to both the wastewater treatment and bioenergy generation. This work discusses the contribution of improvements regarding the configurations, electrode materials, membrane materials, electron transfer mechanisms, and materials cost on the current and future development of MFCs. Analysis of the most recent scientific publications on the field denotes that dual-chamber MFCs configuration offers the greatest potential due to the excellent ability to be adapted to different operating environments. Carbon-based materials show the best performance, biocompatibility of carbon-brush anode favors the formation of the biofilm in a mixed consortium and in wastewater as a substrate resembles the conditions of real scenarios. Carbon-cloth cathode modified with nanotechnology favors the conductive properties of the electrode. Ceramic clay membranes emerge as an interesting low-cost membrane with a proton conductivity of 0.0817 S cm^-1, close to that obtained with the Nafion membrane. The use of nanotechnology in the electrodes also enhances electron transfer in MFCs. It increases the active sites at the anode and improves the interface with microorganisms. At the cathode, it favors its catalytic properties and the oxygen reduction reaction. These features together favor MFCs performance through energy production and substrate degradation with values above 2.0 W m^-2 and 90% respectively. All the recent advances in MFCs are gradually contributing to enable technological alternatives that, in addition to wastewater treatment, generate energy in a sustainable manner. It is important to continue the research efforts worldwide to make MFCs an available and affordable technology for industry and society.

R-based method for quantitative analysis of biofilm thickness by using confocal laser scanning microscopy

Microscopy is mostly the method of choice to analyse biofilms. Due to the high local heterogeneity of biofilms, single and punctual analyses only give an incomplete insight into the local distribution of biofilms. In order to retrieve statistically significant results a quantitative method for biofilm thickness measurements was developed based on confocal laser scanning microscopy and the programming language R. The R-script allows the analysis of large image volumes with little hands-on work and outputs statistical information on homogeneity of surface coverage and overall biofilm thickness. The applicability of the script was shown in microbial fuel cell experiments. It was found that Geobacter sulfurreducens responds differently to poised anodes of different material so that the optimum potential for MFC on poised ITO anodes had to be identified with respect to maximum current density, biofilm thickness and MFC start-up time. Thereby, a positive correlation between current density and biofilm thickness was found, but with no direct link to the applied potential. The optimum potential turned out to be +0.1 V versus SHE. The script proved to be a valuable stand-alone tool to quantify biofilm thickness in a statistically valid manner, which is required in many studies.

Engineering Shewanella carassii, a newly isolated exoelectrogen from activated sludge, to enhance methyl orange degradation and bioelectricity harvest

Electroactive microorganisms (EAMs) play important roles in biogeochemical redox processes and have been of great interest in the fields of energy recovery, waste treatment, and environmental remediation. However, the currently identified EAMs are difficult to be widely used in complex and diverse environments, due to the existence of poor electron transfer capability, weak environmental adaptability, and difficulty with engineering modifications, etc. Therefore, rapid and efficient screening of high performance EAMs from environments is an effective strategy to facilitate applications of microbial fuel cells (MFCs). In this study, to achieve efficient degradation of methyl orange (MO) by MFC and electricity harvest, a more efficient exoelectrogen Shewanella carassii-D₅ that belongs to Shewanella spp. was first isolated from activated sludge by WO₃ nanocluster probe technique. Physiological properties experiments confirmed that S. carassii-D₅ is a Gram-negative strain with rounded colonies and smooth, slightly reddish surface, which could survive in media containing lactate at 30 °C. Moreover, we found that S. carassii-D₅ exhibited remarkable MO degradation ability, which could degrade 66% of MO within 72 h, 1.7 times higher than that of Shewanella oneidensis MR-1. Electrochemical measurements showed that MFCs inoculated with S. carassii-D₅ could generate a maximum power density of 704.6 mW/m², which was 5.6 times higher than that of S. oneidensis MR-1. Further investigation of the extracellular electron transfer (EET) mechanism found that S. carassii-D₅ strain had high level of c-type cytochromes and strong biofilm formation ability compared with S. oneidensis MR-1, thus facilitating direct EET. Therefore, to enhance indirect electron transfer and MO degradation capacity, a synthetic gene cluster ribADEHC encoding riboflavin synthesis pathway from Bacillus subtilis was heterologously expressed in S. carassii-D₅, increasing riboflavin yield from 1.9 to 9.0 mg/g DCW with 1286.3 mW/m² power density output in lactate fed-MFCs. Furthermore, results showed that the high EET rate endowed a faster degradation efficient of MO from 66% to 86% with a maximum power density of 192.3 mW/m², which was 1.3 and 1.6 times higher than that of S. carassii-D₅, respectively. Our research suggests that screening and engineering high-efficient EAMs from sludge is a feasible strategy in treating organic pollutants.

Bioelectricity generation from human urine and simultaneous nutrient recovery: Role of Microbial Fuel Cells

Urine is a 'valuable waste' that can be exploited to generate bioelectricity and recover key nutrients for producing NPK-rich biofertilizers. In recent times, improved and innovative waste management technologies have emerged to manage the rapidly increasing environmental pollution and to accomplish the goal of sustainable development. Microbial fuel cells (MFCs) have attracted the attention of environmentalists worldwide to treat human urine and produce power through bioelectrochemical reactions in presence of electroactive bacteria growing on the anode. The bacteria break down the complex organic matter present in urine into simpler compounds and release the electrons which flow through an external circuit generating current at the cathode. Many other useful products are harvested at the end of the process. So, in this review, an attempt has been made to synthesize the information on MFCs fuelled with urine to generate bioelectricity and recover value-added resources (nutrients), and their modifications to enhance productivity. Moreover, configuration and mode of system operation, and factors enhancing the performance of MFCs have been also presented.

GSU1771 regulates extracellular electron transfer and electroactive biofilm formation in Geobacter sulfurreducens: Genetic and electrochemical characterization

Type IV pili and the >100c-type cytochromes in Geobacter sulfurreducens are essential for extracellular electron transfer (EET) towards metal oxides and electrodes. A previous report about a mutation in the gsu1771 gene indicated an enhanced reduction of insoluble Fe(III) oxides coupled with increased pilA expression. Herein, a marker-free gsu1771-deficient mutant was constructed and characterized to assess the role of this regulator in EET and the formation of electroactive biofilms. Deleting this gene delayed microbial growth in the acetate/fumarate media (electron donor and acceptor, respectively). However, this mutant reduced soluble and insoluble Fe(III) oxides more efficiently. Heme staining, western blot, and RT-qPCR analyses demonstrated that GSU1771 regulates the transcription of several genes (including pilA) and many c-type cytochromes involved in EET, suggesting the broad regulatory role of this protein. DNA-protein binding assays indicated that GSU1771 directly regulates the transcription of pilA, omcE, omcS, and omcZ. Additionally, gsu1771-deficient mutant biofilms are thicker than wild-type strains. Electrochemical studies revealed that the current produced by this biofilm was markedly higher than the wild-type strains (approximately 100-fold). Thus, demonstrating the role of GSU1771 in the EET pathway and establishing a methodology to develop highly electroactive G. sulfurreducens mutants.

Microbial nanowires

In this Quick guide, Derek Lovley introduces microbial nanowires-conductive extracellular appendages made by some bacteria and archaea.

Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations

Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H₂ as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H₂ is actually the electron donor supporting growth has not been rigorously excluded.

Plugging into bacterial nanowires: a comparison of model electrogenic organisms

Extracellular electron transport (EET) is an important metabolic process used by many bacteria to remove excess electrons generated through cellular metabolism. However, there is still limited understanding about how the molecular mechanisms used to export electrons impact cellular metabolism. Here the EET pathways of two of the best-studied electrogenic organisms, Shewanella oneidensis and Geobacter sulferreducens, are described. Both organisms have superficially similar overall EET routes, but differ in the mechanisms used to oxidise menaquinol, transfer electrons across the outer membrane and reduce extracellular substrates. These mechanistic differences substantially impact both substrate choice and bacterial lifestyle.

Biofilm Biology and Engineering of Geobacter and Shewanella spp. for Energy Applications

Geobacter and Shewanella spp. were discovered in late 1980s as dissimilatory metal-reducing microorganisms that can transfer electrons from cytoplasmic respiratory oxidation reactions to external metal-containing minerals. In addition to mineral-based electron acceptors, Geobacter and Shewanella spp. also can transfer electrons to electrodes. The microorganisms that have abilities to transfer electrons to electrodes are known as exoelectrogens. Because of their remarkable abilities of electron transfer, Geobacter and Shewanella spp. have been the two most well studied groups of exoelectrogens. They are widely used in bioelectrochemical systems (BESs) for various biotechnological applications, such as bioelectricity generation via microbial fuel cells. These applications mostly associate with Geobacter and Shewanella biofilms grown on the surfaces of electrodes. Geobacter and Shewanella biofilms are electrically conductive, which is conferred by matrix-associated electroactive components such as c-type cytochromes and electrically conductive nanowires. The thickness and electroactivity of Geobacter and Shewanella biofilms have a significant impact on electron transfer efficiency in BESs. In this review, we first briefly discuss the roles of planktonic and biofilm-forming Geobacter and Shewanella cells in BESs, and then review biofilm biology with the focus on biofilm development, biofilm matrix, heterogeneity in biofilm and signaling regulatory systems mediating formation of Geobacter and Shewanella biofilms. Finally, we discuss strategies of Geobacter and Shewanella biofilm engineering for improving electron transfer efficiency to obtain enhanced BES performance.

Generation of High Current Densities in Geobacter sulfurreducens Lacking the Putative Gene for the PilB Pilus Assembly Motor

Geobacter sulfurreducens is commonly employed as a model for the study of extracellular electron transport mechanisms in the Geobacter species. Deletion of pilB, which is known to encode the pilus assembly motor protein for type IV pili in other bacteria, has been proposed as an effective strategy for evaluating the role of electrically conductive pili (e-pili) in G. sulfurreducens extracellular electron transfer. In those studies, the inhibition of e-pili expression associated with pilB deletion was not demonstrated directly but was inferred from the observation that pilB deletion mutants produced lower current densities than wild-type cells. Here, we report that deleting pilB did not diminish current production. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-type G. sulfurreducens or when e-pili are expressed heterologously from the G. sulfurreducens pilin gene in Escherichia coli. Immunogold labeling demonstrated that a G. sulfurreducens strain expressing a pilin monomer with a His tag continued to express His tag-labeled filaments when pilB was deleted. These results suggest that a reinterpretation of the results of previous studies on G. sulfurreducens pilB deletion strains may be necessary. IMPORTANCE Geobacter sulfurreducens is a model microbe for the study of biogeochemically and technologically significant processes, such as the reduction of Fe(III) oxides in soils and sediments, bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity, direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments, and metal corrosion. Elucidating the phenotypes associated with gene deletions is an important strategy for determining the mechanisms for extracellular electron transfer in G. sulfurreducens. The results reported here demonstrate that we cannot replicate the key phenotype reported for a gene deletion that has been central to the development of models for long-range electron transport in G. sulfurreducens.

Cytochrome OmcS is not essential for extracellular electron transport via conductive pili in Geobacter sulfurreducens strain KN400

The multi-heme c-type cytochrome OmcS is one of the central components for extracellular electron transport in Geobacter sulfurreducens strain DL-1, but its role in other microbes, including other strains of G. sulfurreducens is currently a matter of debate. Therefore, we investigated the function of OmcS in G. sulfurreducens strain KN400, which is even more effective in extracellular electron transfer than strain DL-1. We found that deleting omcS from strain KN400 did not negatively impact the rate of Fe(III) oxide reduction and that the cells expressed conductive filaments. Replacing the wild-type pilin gene with the aro-5 pilin gene eliminated the OmcS-deficient strain's ability for electron transport to insoluble electron acceptors and diminished filament conductivity. These results are consistent with the concept that electrically conductive pili are the primary conduit for long-range electron transfer in G. sulfurreducens and closely related species. These findings, coupled with the lack of OmcS homologs in most other microbes capable of extracellular electron transfer, suggest that OmcS is not a common critical component for extracellular electron transfer. Importance OmcS has been widely studied and noted to be one of the key components for extracellular electron exchange by Geobacter sulfurreducens strain DL-1. However, the true importance of OmcS warrants further investigation as it is well-known that very few bacteria, even within the Geobacteraceae family, contain OmcS homologs, and many bacteria capable of extracellular electron transfer lack an abundance of any type of outer-surface c-type cytochrome. In addition, there is much debate regarding the importance of OmcS filaments in the mechanism of extracellular electron transport to insoluble electron acceptors by G. sulfurreducens. It has been suggested that filaments comprised of OmcS, rather than e-pili, are the predominant conductive filaments expressed by G. sulfurreducens. However, the results presented in this manuscript, along with multiple other lines of evidence, indicate that OmcS filaments cannot be the primary conductive protein nanowires expressed by G. sulfurreducens.

Dissecting the Structural and Conductive Functions of Nanowires in Geobacter sulfurreducens Electroactive Biofilms

Conductive nanowires are thought to contribute to long-range electron transfer (LET) in Geobacter sulfurreducens anode biofilms. Three types of nanowires have been identified: pili, OmcS, and OmcZ. Previous studies highlighted their conductive function in anode biofilms, yet a structural function also has to be considered. We present here a comprehensive analysis of the function of nanowires in LET by inhibiting the expression of each nanowire. Meanwhile, flagella with poor conductivity were expressed to recover the structural function but not the conductive function of nanowires in the corresponding nanowire mutant strain. The results demonstrated that pili played a structural but not a conductive function in supporting biofilm formation. In contrast, the OmcS nanowire played a conductive but not a structural function in facilitating electron transfer in the biofilm. The OmcZ nanowire played both a structural and a conductive function to contribute to current generation. Expression of the poorly conductive flagellum was shown to enhance biofilm formation, subsequently increasing current generation. These data support a model in which multiheme cytochromes facilitate long-distance electron transfer in G. sulfurreducens biofilms. Our findings also suggest that the formation of a thicker biofilm, which contributed to a higher current generation by G. sulfurreducens, was confined by the biofilm formation deficiency, and this has applications in microbial electrochemical systems. IMPORTANCE The low power generation of microbial fuel cells limits their utility. Many factors can affect power generation, including inefficient electron transfer in the anode biofilm. Thus, understanding the mechanism(s) of electron transfer provides a pathway for increasing the power density of microbial fuel cells. Geobacter sulfurreducens was shown to form a thick biofilm on the anode. Cells far away from the anode reduce the anode through long-range electron transfer. Based on their conductive properties, three types of nanowires have been hypothesized to directly facilitate long-range electron transfer: pili, OmcS, and OmcZ nanowires. However, their structural contributions to electron transfer in anode biofilm have not been elucidated. Based on studies of mutants lacking one or more of these facilitators, our results support a cytochrome-mediated electron transfer process in Geobacter biofilms and highlight the structural contribution of nanowires in anode biofilm formation, which contributes to biofilm formation and current generation, thereby providing a strategy to increase current generation.