Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling

Investigation of acetate uptake kinetics of mature Geobacter sulfurreducens biofilms in continuous bioelectrochemical systems reveals unexpected challenges

Mature Geobacter sulfurreducens biofilms cultivated at two distinct anode potentials, representing unlimited and limited electron acceptor availability, were subjected to different acetate concentrations in a continuous reactor system. The Nernst-Michaelis-Menten equation, being modified to consider the conditions of a continuous stirred-tank reactor, was applied to analyze the acetate uptake kinetics. For the first time, the kinetics of pure G. sulfurreducens biofilms based on quantification of the acetate consumption were determined. Acetate uptake parameters (KM,Ac = 1.41 ± 0.42 mM, vmax,Ac = 1.10 ± 0.12 mmolAc- h-1 gDW-1, n = 4) obtained from cultivation at 0.4 V (vs. SHE), showed significant differences compared to an approach that derived acetate uptake parameters from the current production. This deviation is likely related to the coulombic efficiency, which exhibited a dependence on the acetate concentration. The coulombic efficiency was 30-50 % for acetate concentrations <1 mM, and saturated at 78.6 ± 4.0 % for more than 2 mM acetate. Despite the Nernst-Michaelis-Menten equation being developed to cover limiting terminal electron acceptor conditions, its application to biofilms cultivated at -0.1 V yielded contradictory results indicating application limits. Considering the complexity and plasticity of acetate uptake kinetics together with the complex extracellular electron transfer machinery, Geobacter sulfurreducens biofilms are a model system that is shown to provide unexpected challenges and demanding highly controlled experimental conditions.

Cytochrome "nanowires" are physically limited to sub-picoamp currents that suffice for cellular respiration

Mineral-respiring microorganisms from hydrothermal vents to terrestrial soils express filaments that electrically connect intracellular respiration to extracellular geochemistry. Filaments dubbed "cytochrome nanowires" (CNs) have been resolved by CryoEM, but whether they are the two-decades-long sought-after physiological "nanowires" remains unproven. To assess their functional competence, we analyzed biological redox conduction in all CNs by computing driving forces in the presence of redox anti-cooperativities, reorganization energies with electronic polarizability, and Marcus rates for diffusive and protein-limited flux models. The chain of heme cofactors in any CN must be densely packed to realize weak (≤0.01 eV) electronic coupling for electron transfer, as evidenced by a single Soret band produced from coincidental absorptions on multiple hemes. Dense packing, in turn, has three consequences: (1) limited driving forces (≤|0.3| eV) due to shared electrostatic microenvironments, (2) strong (≤0.12 eV) redox anti-cooperativities that would accentuate the free energy landscape if the linear heme arrangement did not dictate a contra-thermodynamic oxidation order, and (3) an entropic penalty that is offset by thioether 'tethers' of the hemes to the protein backbone. These linkages physically necessitate the rate-throttling T-stacked motif (10-fold slower than the other highly conserved slip-stacked motif). If the sequence of slip- and T-stacked hemes in the CNs had the fastest known nanosecond rates at every step, a micron-long filament would carry a diffusive 0.02 pA current at a physiological 0.1 V, or a protein-limited current of 0.2 pA. Actual CNs have sub-optimal (≤102-fold lower), but sufficient conductivities for cellular respiration, with at most thousands of filaments needed for total cellular metabolic flux. Reported conductivities once used to argue for metallic-like pili against the cytochrome hypothesis and now attributed to CNs remain inconsistent by 102-105-fold with the physical constraints on biological redox conduction through multiheme architectures.

Electrogenic Staphylococcus epidermidis Diminishes the Ultraviolet B-Induced Labile Irons in Mouse Skin

The tremendous abundance of Staphylococcus epidermidis (S. epidermidis) on the skin surface have been found electrogenic. However, the role of electrogenic S. epidermidis in biological activities remains elusive. Addition of S. epidermidis plus glycerol reinstated the reduction of electric currents of vancomycin-treated human skin bacteria collected by skin swabs. In the presence of glycerol, an endogenous molecule in human skin, S. epidermidis exerted the electrogenicity measured by the changes in voltages and currents as well as ferrozine assays. A substantial increase in iron contents in skin was detected when mouse skin was exposed to ultraviolet B (UV-B). Topical application of S. epidermidis plus glycerol onto mouse skin mitigated the UV-B-induced production of labile ferrous iron, demonstrating that S. epidermidis electricity acted as a regulator of the redox cycling of irons in skin. Low expression of cyclophilin A, an electron mediator, in S. epidermidis caused the loss of bacterial activities to reduce the UV-B-induced labile ferrous iron. Cumulatively, skin electrogenic S. epidermidis may mediate cyclophilin A to combat the UV-B-induced iron imbalance in skin.

Comparing the performance of microbial electrochemical assisted and aerated treatment wetlands in pilot-scale: Removal of major pollutants and organic micropollutants

The combination of treatment wetlands (TWs) with microbial electrochemical technologies (MET) is often studied in the lab to improve the performance and decrease the footprint of TWs. In this article we evaluated the long-term performance of four pilot-scale vertical sub-surface flow TWs for major pollutants' and organic micropollutants' removal from domestic wastewater. Three of them were filled with electroconductive material and operated under saturated (MET SAT), unsaturated (MET UNSAT) and unsaturated-saturated (MET HYBRID) conditions while the fourth one was a saturated intensified aerated system (AEW) filled with gravel. The MET-TWs achieved significant removals of COD (>78 %) with no clogging issues at the maximum applied OLR (249 g COD m-3 d-1) while under these loading conditions TSS removal exceeded 84 %. Among all electroactive TWs, UNSAT could remove 25 g NH4-N m-3 d-1 through nitrification when peak ammonium loading rate was applied; however this removal was significantly lower than AEW (35 g NH4-N m-3d-1). No important removal of P was observed in all systems with the exception of MET-SAT were precipitation reactions of P with iron occurred when anaerobic pretreated wastewater was used. The removal of the sum of studied organic micropollutants ranged between 70 ± 18 % (MET UNSAT) to 91 ± 4 % (AEW) and improved with feeding pulses increase. Moderate to high removal of specific microcontaminants was observed depending on the target compound, the studied system and the operational conditions. AEW and MET HYBRID systems complied with the limits set by EU for wastewater discharge to non-sensitive water bodies and for Class B water reuse. Scale-up calculations for a settlement of 500 PE showed that these systems require much less area per PE (0.51 m2 PE-1) comparing to conventional TWs while the operational cost was calculated to 0.07 € m-3 for the AEW and 0.02 € m-3 for the MET HYBRID.

Syntrophic propionate degradation in anaerobic digestion facilitated by hydrochar: Microbial insights as revealed by genome-centric metatranscriptomics

Propionate is a model substrate for studying energy-limited syntrophic communities in anaerobic digestion, and syntrophic bacteria usually catalyze its degradation in syntrophy with methanogens. In the present study, metagenomics and metatranscriptomics were used to study the effect of the supportive material (e.g., hydrochar) on the key members of propionate degradation and their cooperation mechanism. The results showed that hydrochar increased the methane production rate (up to 57.1%) from propionate. The general transcriptional behavior of the microbiome showed that both interspecies H2 transfer (IHT) and direct interspecies electron transfer (DIET) played essential roles in the hydrochar-mediated methanation of propionate. Five highly active syntrophic propionate-oxidizing bacteria were identified by genome-centric metatranscriptomics. H85pel, a member of the family Pelotomaculaceae, was specifically enriched by hydrochar. Hydrochar enhanced the expression of the flagellum subunit, which interacted with methanogens and hydrogenases in H85pel, indicating that IHT was one of the essential factors promoting propionate degradation. Hydrochar also enriched H162tha belonging to the genus of Thauera. Hydrochar induced the expression of genes related to the complete propionate oxidation pathway, which did not produce acetate. Hydrochar and e-pili-mediated DIET were enhanced, which was another factor promoting propionate degradation. These findings improved the understanding of metabolic traits and cooperation between syntrophic propionate oxidizing bacteria (SPOB) and co-metabolizing partners and provided comprehensive transcriptional insights on function in propionate methanogenic systems.

Transcriptomic insights unveil the crucial roles of cytochromes, NADH, and pili in Ag(I) reduction by Geobacter sulfurreducens

Silver (Ag) is a pivotal transition metal with applications in multiple industries, necessitating efficient recovery techniques. Despite various proposed methods for silver recovery from wastewaters, challenges persist especially for low concentrations. In this context, bioreduction by bacteria like Geobacter sulfurreducens, offers a promising approach by converting Ag(I) to Ag nanoparticles. To reveal the mechanisms driving microbial Ag(I) reduction, we conducted transcriptional profiling of G. sulfurreducens under Ag(I)-reducing condition. Integrated transcriptomic and protein-protein interaction network analyses identified significant transcriptional shifts, predominantly linked to c-type cytochromes, NADH, and pili. When compared to a pilus-deficient strain, the wild-type strain exhibited distinct cytochrome gene expressions, implying specialized functional roles. Additionally, despite a down-regulation in NADH dehydrogenase genes, we observed up-regulation of specific downstream cytochrome genes, highlighting NADH's potential role as an electron donor in the Ag(I) reduction process. Intriguingly, our findings also highlight the significant influence of pili on the morphology of the resulting Ag nanoparticles. The presence of pili led to the formation of smaller and more crystallized Ag nanoparticles. Overall, our findings underscore the intricate interplay of cytochromes, NADH, and pili in Ag(I) reduction. Such insights suggest potential strategies for further enhancing microbial Ag(I) reduction.

Quantifying Geobacter sulfurreducens growth: A mathematical model based on acetate concentration as an oxidizing substrate

We developed a mathematical model to simulate dynamics associated with the proliferation of Geobacter and ultimately optimize cellular operation by analyzing the interaction of its components. The model comprises two segments: an initial part comprising a logistic form and a subsequent segment that incorporates acetate oxidation as a saturation term for the microbial nutrient medium. Given that four parameters can be obtained by minimizing the square root of the mean square error between experimental Geobacter growth and the mathematical model, the model underscores the importance of incorporating nonlinear terms. The determined parameter values closely align with experimental data, providing insights into the mechanisms that govern Geobacter proliferation. Furthermore, the model has been transformed into a scaleless equation with only two parameters to simplify the exploration of qualitative properties. This allowed us to conduct stability analysis of the fixed point and construct a co-dimension two bifurcation diagram.

Influence of fumarate on interspecies electron transfer and the metabolic shift induced in Clostridium pasteurianum by Geobacter sulfurreducens

AIMS

In previous studies, it was demonstrated that co-culturing Clostridium pasteurianum and Geobacter sulfurreducens triggers a metabolic shift in the former during glycerol fermentation. This shift, attributed to interspecies electron transfer and the exchange of other molecules, enhances the production of 1,3-propanediol at the expense of the butanol pathway. The aim of this investigation is to examine the impact of fumarate, a soluble compound usually used as an electron acceptor for G. sulfurreducens, in the metabolic shift previously described in C. pasteurianum.

METHODS AND RESULTS

Experiments were conducted by adding along with glycerol, acetate, and different quantities of fumarate in co-cultures of G. sulfurreducens and C. pasteurianum. A metabolic shift was exhibited in all the co-culture conditions. This shift was more pronounced at higher fumarate concentrations. Additionally, we observed G. sulfurreducens growing even in the absence of fumarate and utilizing small amounts of this compound as an electron donor rather than an electron acceptor in the co-cultures with high fumarate addition.

CONCLUSIONS

This study provided evidence that interspecies electron transfer continues to occur in the presence of a soluble electron acceptor, and the metabolic shift can be enhanced by promoting the growth of G. sulfurreducens.

Spatially-assembled binary carbon anode synergizing directional electron transfer and enriched microbe accommodation for wastewater treatment and energy conversion: From simulation to experiments

Bioelectrochemical systems (BESs) hold prospects in wastewater energy and resource recovery. Anode optimization is important for simultaneous enhancement of wastewater energy conversion and effluent quality in BESs. In this study, a multi-physics model coupling fluid flow, organic degradation and electrochemical process was constructed to guide the design and optimization of BES anodes. Based on the multi-physics simulation, spatially-assembled binary carbon anodes composed of three-dimensional carbon mesh skeleton and granular activated carbon were proposed and established. The granular activated carbon conducive to microbe accommodation played a vital role in improving effluent water quality, while the carbon mesh skeleton favoring electron collection and transfer could enhance the bioelectricity output. With an average chemical oxygen demand (COD) removal rate of 0.442 kg m-3 d-1, a maximum power density of 20.6 W m-3 was achieved in the optimized composite anode BES, which was 25% and 154% higher than carbon mesh skeleton BES and granular activated carbon BES. Electroactive bacteria were enriched in composite anodes and performed important functions related to microbial metabolism and energy production. The spatially-assembled binary carbon anode with low carbon mesh packing density was more cost-effective with a daily energy output per anode cost of 221 J d-1 RMB-1. This study not only provides a cost-efficient alternative anode to simultaneously improve organic degradation and power generation performance, but also demonstrates the potential of multi-physics simulation in offering theoretical support and prediction for BES configuration design as well as optimization.

An investigation of the environmental implications of bioplastics: Recent advancements on the development of environmentally friendly bioplastics solutions

The production and utilization of plastics may prove beneficial, but the environmental impact suggests the opposite. The single-use plastics (SUP) and conventional plastics are harmful to the environment and need prompt disposal. Bioplastics are increasingly being considered as a viable alternative to conventional plastics due to their potential to alleviate environmental concerns such as greenhouse gas emissions and pollution. However, the previous reviews revealed a lack of consistency in the methodologies used in the Life Cycle Assessments (LCAs), making it difficult to compare the results across studies. The current study provides a systematic review of LCAs that assess the environmental impact of bioplastics. The different mechanical characteristics of bio plastics, like tensile strength, Young's modulus, flexural modulus, and elongation at break are reviewed which suggest that bio plastics are comparatively much better than synthetic plastics. Bioplastics have more efficient mechanical properties compared to synthetic plastics which signifies that bioplastics are more sustainable and reliable than synthetic plastics. The key challenges in bioplastic adoption and production include competition with food production for feedstock, high production costs, uncertainty in end-of-life management, limited biodegradability, lack of standardization, and technical performance limitations. Addressing these challenges requires collaboration among stakeholders to drive innovation, reduce costs, improve end-of-life management, and promote awareness and education. Overall, the study suggests that while bioplastics have the potential to reduce environmental impact, further research is needed to better understand their life cycle and optimize their end-of-life (EoL) management and production to maximize their environmental benefits.

Biochemical characterization and mercury methylation capacity of Geobacter sulfurreducens biofilms grown in media containing iron hydroxide or fumarate

Geobacter species are common in iron-rich environments and can contribute to formation of methylmercury (MeHg), a neurotoxic compound with high bioaccumulation potential formed as a result of bacterial and archaeal physiological activity. Geobacter sulfurreducens can utilize various electron acceptors for growth including iron hydroxides or fumarate. However, it remains poorly understood how the growth on these compounds affects physiological properties of bacterial cells in biofilms, including the capacity to produce MeHg. The purpose of this study was to determine changes in the biochemical composition of G. sulfurreducens during biofilm cultivation in media containing iron hydroxide or fumarate, and to quantify mercury (Hg) methylation capacity of the formed biofilms. Biofilms were characterized by Fourier-transform infrared spectroscopy in the attenuated total reflection mode (ATR-FTIR), Resonance Raman spectroscopy and confocal laser scanning microscopy. MeHg formation was quantified by mass spectrometry after incubation of biofilms with 100 nM Hg. The results of ATR-FTIR experiments showed that in presence of fumarate, G. sulfurreducens biofilm formation was accompanied by variation in content of the energy-reserve polymer glycogen over time, which could be cancelled by the addition of supplementary nutrients (yeast extract). In contrast, biofilms cultivated on Fe(III) hydroxide did not accumulate glycogen. The ATR-FTIR results further suggested that Fe(III) hydroxide surfaces bind cells via phosphate and carboxylate groups of bacteria that form complexes with iron. Furthermore, biofilms grown on Fe(III) hydroxide had higher fraction of oxidized cytochromes and produced two to three times less biomass compared to conditions with fumarate. Normalized to biofilm volume, the content of MeHg was similar in assays with biofilms grown on Fe(III) hydroxide and on fumarate (with yeast extract and without). These results suggest that G. sulfurreducens biofilms produce MeHg irrespectively from glycogen content and cytochrome redox state in the cells, and warrant further investigation of the mechanisms controlling this process.

Comparing theoretical and practical biomass yields calls for revisiting thermodynamic growth models for electroactive microorganisms

Research on electroactive microorganisms (EAM) often focuses either on their physiology and the underlying mechanisms of extracellular electron transfer or on their application in microbial electrochemical technologies (MET). Thermodynamic understanding of energy conversions related to growth and activity of EAM has received only a little attention. In this study, we aimed to prove the hypothesized restricted energy harvest of EAM by determining biomass yields by monitoring growth of acetate-fed biofilms presumably enriched in Geobacter, using optical coherence tomography, at three anode potentials and four acetate concentrations. Experiments were concurrently simulated using a refined thermodynamic model for EAM. Neither clear correlations were observed between biomass yield and anode potential nor acetate concentration, albeit the statistical significances are limited, mainly due to the observed experimental variances. The experimental biomass yield based on acetate consumption (YX/ac = 37 ± 9 mgCODbiomass gCODac-1) was higher than estimated by modeling, indicating limitations of existing growth models to predict yields of EAM. In contrast, the modeled biomass yield based on catabolic energy harvest was higher than the biomass yield from experimental data (YX/cat = 25.9 ± 6.8 mgCODbiomass kJ-1), supporting restricted energy harvest of EAM and indicating a role of not considered energy sinks. This calls for an adjusted growth model for EAM, including, e.g., the microbial electrochemical Peltier heat to improve the understanding and modeling of their energy metabolism. Furthermore, the reported biomass yields are important parameters to design strategies for influencing the interactions between EAM and other microorganisms and allowing more realistic feasibility assessments of MET.

Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil

An anaerobic, Gram-staining-negative, rod-shaped, Fe(III)-reducing strain, designated SG189^T, was isolated from paddy soil in Fujian Province, China. Growth occurred at 20-35 ℃ (optimum 30 ℃), pH 6.5-8.0 (optimum 7.0) and 0-0.2% (w/v) NaCl (optimum 0%). The strain SG189^T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix fermentans DSM 14018^T (98.9%), "Geothrix terrae" SG184^T (99.0%) and "Geothrix alkalitolerans" SG263^T (99.3%). ANI and dDDH values between strain SG189^T and the most closely related Geothrix species were 86.5-87.1% and 31.5-32.9%, which lower than the cut-off values (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Further, genome-based phylogenomic trees constructed using 81 core genes (UBCG2) and 120 conserved genes (GTDB) showed that strain SG189^T formed a clade with members of the genus Geothrix. The menaquinone was shown to be MK-8, and the major fatty acids were iso-C_15:0 and iso-C_13:0 3OH. The genomic DNA G + C content was 68.2%. Additionally, we found that strain SG189^T possessed ability to reduce ferric iron, and strain SG189^T could reduce 10 mM of ferric citrate in 10 days with lactate as the sole electron donor. Based on the observed physiological and biochemical properties, chemotaxonomic characteristics, ANI and dDDH values, SG189^T represents a novel species of the genus Geothrix, for which the name Geothrix oryzisoli sp. nov. is proposed. The type strain is SG189^T (= GDMCC 1.3408^T = JCM 39324^T).

Anaerobic bioreduction of elemental sulfur improves bioavailability of Fe (III) oxides for bioremediation

Fe(III) oxides are ubiquitous electron acceptors for anaerobic bioremediation, although their bioavailability was limited due to the passivation of secondary mineralization products. Here we found the solid S⁰ can be added to improve their bioavailability. Using lepidocrocite (γ-FeOOH), acetate and Geobacter sulfurreducens PCA as representatives of Fe(III) oxides, intermediate of pollutant degradation and microbes, a 6 times higher amount of FeOOH reduction in the presence of S⁰ was observed with a time needed for S⁰ reduction shortened by half. The bioreduction of S⁰ activated the reduction of FeOOH, while the product (conductive FeS) may have bridged electron transfer across the cell membrane and periplasm. The proportion of excessive Fe(II) produced from Fe(III) was quantified as a direct bioreduction (26 %), with an abiotic FeOOH reduction to FeS (20 %) and an FeS-conducted FeOOH bioreduction (54 %), which highlight the key role of gradually formed FeS from S⁰ in the bioreduction of FeOOH. Our results showed that S⁰ can be an effective additive for the bioremediation of environments with abundant Fe(III) oxides, which has broader implications for elemental biogeochemical cycling.

Metabolic turnover of cysteine-related thiol compounds at environmentally relevant concentrations by Geobacter sulfurreducens

Low-molecular-mass (LMM) thiol compounds are known to be important for many biological processes in various organisms but LMM thiols are understudied in anaerobic bacteria. In this work, we examined the production and turnover of nanomolar concentrations of LMM thiols with a chemical structure related to cysteine by the model iron-reducing bacterium Geobacter sulfurreducens. Our results show that G. sulfurreducens tightly controls the production, excretion and intracellular concentration of thiols depending on cellular growth state and external conditions. The production and cellular export of endogenous cysteine was coupled to the extracellular supply of Fe(II), suggesting that cysteine excretion may play a role in cellular trafficking to iron proteins. Addition of excess exogenous cysteine resulted in a rapid and extensive conversion of cysteine to penicillamine by the cells. Experiments with added isotopically labeled cysteine confirmed that penicillamine was formed by a dimethylation of the C-3 atom of cysteine and not via indirect metabolic responses to cysteine exposure. This is the first report of de novo metabolic synthesis of this compound. Penicillamine formation increased with external exposure to cysteine but the compound did not accumulate intracellularly, which may suggest that it is part of G. sulfurreducens' metabolic strategy to maintain cysteine homeostasis. Our findings highlight and expand on processes mediating homeostasis of cysteine-like LMM thiols in strict anaerobic bacteria. The formation of penicillamine is particularly noteworthy and this compound warrants more attention in microbial metabolism studies.

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

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

Physiological Benefits of Oxygen-Terminating Extracellular Electron Transfer

Extracellular electron transfer (EET) is a process via which certain microorganisms, such as bacteria, exchange electrons with extracellular materials by creating an electrical link across their membranes. EET has been studied for the reactions on solid materials such as minerals and electrodes with implication in geobiology and biotechnology. EET-capable bacteria exhibit broad phylogenetic diversity, and some are found in environments with various types of electron acceptors/donors not limited to electrodes or minerals. Oxygen has also been shown to serve as the terminal electron acceptor for EET of Pseudomonas aeruginosa and Faecalibacterium prausnitzii. However, the physiological significance of such oxygen-terminating EETs, as well as the mechanisms underlying them, remain unclear. In order to understand the physiological advantage of oxygen-terminating EET and its link with energy metabolism, in this review, we compared oxygen-terminating EET with aerobic respiration, fermentation, and electrode-terminating EET. We also summarized benefits and limitations of oxygen-terminating EET in a biofilm setting, which indicate that EET capability enables bacteria to create a niche in the anoxic zone of aerobic biofilms, thereby remodeling bacterial metabolic activities in biofilms.

How different nitrogen fertilizers affect arsenic mobility in paddy soil after straw incorporation?

In straw return fields, nitrogen-fertilizers are added to mitigate microbial competition for nitrogen with plants. However, in arsenic (As)-contaminated paddy fields, the specific effects of different nitrogen fertilizers on As mobility after straw incorporation and the interactions among iron(Fe)/carbon(C)/nitrogen(N)/As are not well understood. In the reported microcosm experiment we monitored As-mobility as a function of different dosages of KNO₃, NH₄Cl and rice straw incorporation. Addition of both KNO₃ and NH₄Cl significantly inhibited the As mobilization induced by straw incorporation. Following the KNO₃ addition, the As concentration in porewater dropped by 51-66% after 2 days of the incubation by restraining Fe reduction and enhancing Fe oxidation. High-dose NH₄Cl addition reduced As in porewater by 22-43% throughout the incubation by decreasing porewater pH. High-throughput sequencing results demonstrated that KNO₃ addition enriches both the denitrifying and Fe-oxidizing bacteria, while diminishing Fe-reducing bacteria; NH₄Cl addition has the opposite effect on Fe-reducing bacteria. Network analysis revealed that As and Fe concentrations in porewater were positively correlated with the abundance of denitrifying and Fe-reducing bacteria. This study broadens our insight into the As biogeochemistry associated with the N/C/Fe balance in soil, which are of great significance for agronomic management and mitigation the risk of As-contaminated paddy fields.

Construction of a new type of three-dimensional honeycomb-structure anode in microbial electrochemical systems for energy harvesting and pollutant removal

Electrode materials occupy most of the construction cost of the microbial electrochemical system (MES), and the low mechanical strength and poor electrochemical performance of the commonly used traditional carbon-based materials restrict the promotion and application of this technology. In this study, polymer-based three-dimensional (3D) honeycomb-structure (HS) materials with good mechanical properties were used as supporting materials. Graphene (GR), carbon nanotube (CNT), and polypyrrole (PPy) was separately chosen as a surface conductivity coating layer for preparing MES anodes. The introduction of GR, CNT, and PPy on HS increased surface roughness, hydrophilicity, O and N content, electrochemically active surface area, and decreased charge transfer internal resistance, which promoted the adhesion of microorganisms on their surface and enhanced the extracellular electron transfer process at the electrode/microbe interface. The CNT-HS anode system got the better maximal power density (1700.7 ± 149.0 mW/m²) of the three modified anode systems and 3.60 times that of MES using CC (471.8 ± 27.2 mW/m²) as the anode. The accelerated reactions of the redox species in the outer cell membrane, the promoted electron shuttle secretion, and the enhanced abundance of the tricarboxylic acid cycle-related functional genes in biofilm led to better performance of the CNT-HS anode system. The CNT-HS anode system also exhibited long-term operational stability (>6 months) and a good chemical oxygen demand degradation effect. Furthermore, CNT-HS material exhibited its cost advantage, and its projected cost is estimated to be about $1.8/m², much lower than the currently used MES anodes ($8.2-548.2/m²). Considering the good mechanical properties, simple preparation process, low manufacturing cost, long-term stability, excellent bio-electrochemical performance, and good pollutant removal ability, HS-based anode has promising potential for high-performance MES in applications.

Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.

In situ COD monitoring with use of a hybrid of constructed wetland-microbial fuel cell

The hybrid system of constructed wetland and microbial fuel cell (CW-MFC) used as a biosensor is becoming a new research focus with the advantage of resisting the shock loading and enriching more electricigens. In this study, a structural parameter S integrating the size, the position and the spacing of the anode and the cathode was proposed. And the electrogenesis and biosensing performances of the vertical flow CW-MFC biosensors were evaluated at different S values. The results showed that all the three biosensors could achieve good monitoring for COD (R² > 0.97). And the coulombic yield was more suitable for the response signal than output voltage. But different biosensing properties including detection signal, detection range, detection time, correlation fitting degree and sensitivity were also displayed. Further, in order to optimize the biosensing performance, the coulombic yield in stable voltage stage (Qs) was proposed which can shorten the detection time by 70% at most. On the anodes, abundant nitrogen-transforming bacteria (NTB) were enriched as well as electrochemically active bacteria (EAB). The competition of NTB for substrates and electrons with EAB disturbed the output voltage signal but not affect the stability of coulombic yield signal. Moreover, the significant linear correlation between the S values and the ratios of EAB to NTB colonized both on anodes and on cathodes indicated the differences of the electricity generation and biosensing performance at the different structural parameters.

Application of pyritic sludge with an anaerobic granule consortium for nitrate removal in low carbon systems

Granules recovered from a highly reduced anaerobic digester were capable of active nitrogen removal in the absence of exogenous electron donors, averaging 0.25 mg mgNO3--N /gVSS/d over 546 days of operation. Electron mass balance indicated that about half the influent nitrate was converted to ammonia via DNRA and another half denitrified. This capacity was associated with an onion-like structure of multiple layers enriched in reduced iron and sulfur, and a complex microbial community shown by metagenomic sequencing to consist of multiple physiological groups and associated activities, including methanogenesis, denitrification, dissimilatory nitrate reduction to ammonia (DNRA), iron oxidation and reduction, and sulfur reduction and oxidation. Nitrate reduction was supported by both entrained organic material and reduced iron and sulfur species, corresponding to 2.13 mg COD/gVSS/d. Batch incubations showed that approximately 15% of denitrified nitrate was coupled to the oxidation of sulfur derived from both sulfate respiration and granular material enriched in iron-sulfide. Inhibition of sulfate reduction resulted in redirection of electron flow to methanogenesis and, in combination with other batch tests, showed that these granules supported a complex microbial community in which cryptic redox cycles linked carbon, sulfur, and iron oxidation with nitrate, sulfate, iron, and carbon dioxide reduction. This system shows promise for treatment of nitrate contaminated ground water without addition of an external organic carbon source as well as wastewater treatment in combination with (granular) sludge elimination leading in a net reduction of solid treatment costs.

Anode respiration-dependent biological nitrogen fixation by Geobacter sulfurreducens

The present nitrogen fixation industry is usually energy-intensive and environmentally detrimental. Therefore, it is appealing to find alternatives. Here, we achieved both a synchronized biological nitrogen fixation and electric energy production by using Geobacter sulfurreducens in a microbial electrochemical system. The results showed that G. sulfurreducens was able to fix nitrogen depending on anode respiration, producing a maximum current density of 0.17 ± 0.015 mA cm^-2 and a nitrogen-fixing activity of ca. 0.78 μmol C₂H₄ mg protein^-1 h^-1, thereby achieving a net total nitrogen-fixing rate of ca. 5.6 mg L^-1 day^-1. Specifically, nitrogen fixation did not impair coulombic efficiency. Transcriptomic and metabolic analyses demonstrated that anode respiration provided sufficient energy to drive nitrogen fixation, and in turn nitrogen fixation promoted anode respiration of the cell by increasing acetate catabolism but reducing acetate anabolism. Furthermore, we showed that G. sulfurreducens could be supplied in a bioelectrochemical system for N-deficient wastewater treatment to relieve N-deficiency stress contributing to the formation of an electroactive biofilm, thereby simultaneously achieving nitrogen fixation, current generation and dissoluble organic carbon removal. Our study revealed a synergistic effect between biological nitrogen fixation and current generation by G. sulfurreducens, providing a green nitrogen fixation alternative through shifting the nitrogen fixation field from energy consumption to energy production and having implications for N-deficient wastewater treatment.

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.

Making protons tag along with electrons

Every living cell needs to get rid of leftover electrons when metabolism extracts energy through the oxidation of nutrients. Common soil microbes such as Geobacter sulfurreducens live in harsh environments that do not afford the luxury of soluble, ingestible electron acceptors like oxygen. Instead of resorting to fermentation, which requires the export of reduced compounds (e.g. ethanol or lactate derived from pyruvate) from the cell, these organisms have evolved a means to anaerobically respire by using nanowires to export electrons to extracellular acceptors in a process called extracellular electron transfer (EET) [ 1]. Since 2005, these nanowires were thought to be pili filaments [ 2]. But recent studies have revealed that nanowires are composed of multiheme cytochromes OmcS [ 3, 4] and OmcZ [ 5] whereas pili remain inside the cell during EET and are required for the secretion of nanowires [ 6]. However, how electrons are passed to these nanowires remains a mystery ( Figure 1A). Periplasmic cytochromes (Ppc) called PpcA-E could be doing the job, but only two of them (PpcA and PpcD) can couple electron/proton transfer - a necessary condition for energy generation. In a recent study, Salgueiro and co-workers selectively replaced an aromatic with an aliphatic residue to couple electron/proton transfer in PpcB and PpcE (Biochem. J. 2021, 478 (14): 2871-2887). This significant in vitro success of their protein engineering strategy may enable the optimization of bioenergetic machinery for bioenergy, biofuels, and bioelectronics applications.

Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality

Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.

Proteomic Analysis of a Syntrophic Coculture of Syntrophobacter fumaroxidans MPOBT and Geobacter sulfurreducens PCAT

We established a syntrophic coculture of Syntrophobacter fumaroxidans MPOBT (SF) and Geobacter sulfurreducens PCAT (GS) growing on propionate and Fe(III). Neither of the bacteria was capable of growth on propionate and Fe(III) in pure culture. Propionate degradation by SF provides acetate, hydrogen, and/or formate that can be used as electron donors by GS with Fe(III) citrate as electron acceptor. Proteomic analyses of the SF-GS coculture revealed propionate conversion via the methylmalonyl-CoA (MMC) pathway by SF. The possibility of interspecies electron transfer (IET) via direct (DIET) and/or hydrogen/formate transfer (HFIT) was investigated by comparing the differential abundance of associated proteins in SF-GS coculture against (i) SF coculture with Methanospirillum hungatei (SF-MH), which relies on HFIT, (ii) GS pure culture growing on acetate, formate, hydrogen as propionate products, and Fe(III). We noted some evidence for DIET in the SF-GS coculture, i.e., GS in the coculture showed significantly lower abundance of uptake hydrogenase (43-fold) and formate dehydrogenase (45-fold) and significantly higher abundance of proteins related to acetate metabolism (i.e., GltA; 62-fold) compared to GS pure culture. Moreover, SF in the SF-GS coculture showed significantly lower abundance of IET-related formate dehydrogenases, Fdh3 (51-fold) and Fdh5 (29-fold), and the rate of propionate conversion in SF-GS was 8-fold lower than in the SF-MH coculture. In contrast, compared to GS pure culture, we found lower abundance of pilus-associated cytochrome OmcS (2-fold) and piliA (5-fold) in the SF-GS coculture that is suggested to be necessary for DIET. Furthermore, neither visible aggregates formed in the SF-GS coculture, nor the pili-E of SF (suggested as e-pili) were detected. These findings suggest that the IET mechanism is complex in the SF-GS coculture and can be mediated by several mechanisms rather than one discrete pathway. Our study can be further useful in understanding syntrophic propionate degradation in bioelectrochemical and anaerobic digestion systems.

Evaluation of NOx removal from flue gas and Fe(II)EDTA regeneration using a novel BTF-ABR integrated system

A promising process is under development for the removal of NOx and regeneration of Fe(II)EDTA in a novel biotrickling filter-anaerobic baffled reactor (BTF-ABR) integrated system at 50 ± 0.5 ℃. In this work, we investigated the NOx removal capacity of a BTF under different O₂ concentrations (7.0 vol%, 5.25 vol% and 3.5 vol%), and tested the effect of an ABR on NOx removal and regeneration of Fe(II)EDTA. The results showed that the NOx removal capacity was significantly increased with the O₂ concentration reduced from 7.0% to 3.5%. The microoxygen environment produced by the BTF-ABR integrated system was more conducive to the removal of NOx and regeneration of Fe(II)EDTA compared with that in the BTF. Real-time polymerase chain reaction (PCR) analysis showed that the coordinated expression of denitrification genes was the major reason for no N₂O emission, along with no nitrate and nitrite accumulation. The 16S rRNA gene amplicon sequencing analysis showed that the cooperation of denitrifying bacteria (Klebsiella, Petrimonas, Rhodococcus and Ochrobactium) and iron-reducing bacteria (Klebsiella, Geobacter and Petrimonas) in the system was the key to the stable and efficient removal of NOx and the regeneration of Fe(II)EDTA simultaneously.

Rational design of electron/proton transfer mechanisms in the exoelectrogenic bacteria Geobacter sulfurreducens

The redox potential values of cytochromes can be modulated by the protonation/deprotonation of neighbor groups (redox-Bohr effect), a mechanism that permits the proteins to couple electron/proton transfer. In the respiratory chains, this effect is particularly relevant if observed in the physiological pH range, as it may contribute to the electrochemical gradient for ATP synthesis. A constitutively produced family of five triheme cytochromes (PpcA-E) from the bacterium Geobacter sulfurreducens plays a crucial role in extracellular electron transfer, a hallmark that permits this bacterium to be explored for several biotechnological applications. Two members of this family (PpcA and PpcD) couple electron/proton transfer in the physiological pH range, a feature not shared with PpcB and PpcE. That ability is crucial for G. sulfurreducens' growth in Fe(III)-reducing habitats since extra contributors to the electrochemical gradient are needed. It was postulated that the redox-Bohr effect is determined by the nature of residue 6, a leucine in PpcA/PpcD and a phenylalanine in PpcB/PpcE. To confirm this hypothesis, Phe6 was replaced by leucine in PpcB and PpcE. The functional properties of these mutants were investigated by NMR and UV-visible spectroscopy to assess their capability to couple electron/proton transfer in the physiological pH range. The results obtained showed that the mutants have an increased redox-Bohr effect and are now capable of coupling electron/proton transfer. This confirms the determinant role of the nature of residue 6 in the modulation of the redox-Bohr effect in this family of cytochromes, opening routes to engineer Geobacter cells with improved biomass production.

Assessing METland® Design and Performance Through LCA: Techno-Environmental Study With Multifunctional Unit Perspective

Conventional wastewater treatment technologies are costly and energy demanding; such issues are especially remarkable when small communities have to clean up their pollutants. In response to these requirements, a new variety of nature-based solution, so-called METland®, has been recently develop by using concepts from Microbial Electrochemical Technologies (MET) to outperform classical constructed wetland regarding wastewater treatment. Thus, the current study evaluates two operation modes (aerobic and aerobic-anoxic) of a full-scale METland®, including a Life Cycle Assessment (LCA) conducted under a Net Environmental Balance perspective. Moreover, a combined technical and environmental analysis using a Net Eutrophication Balance (NEuB) focus concluded that the downflow (aerobic) mode achieved the highest removal rates for both organic pollutant and nitrogen, and it was revealed as the most environmentally friendly design. Actually, aerobic configuration outperformed anaero/aero-mixed mode in a fold-range from 9 to 30%. LCA was indeed recalculated under diverse Functional Units (FU) to determine the influence of each FU in the impacts. Furthermore, in comparison with constructed wetland, METland® showed a remarkable increase in wastewater treatment capacity per surface area (0.6 m2/pe) without using external energy. Specifically, these results suggest that aerobic-anoxic configuration could be more environmentally friendly under specific situations where high N removal is required. The removal rates achieved demonstrated a robust adaptation to influent variations, revealing a removal average of 92% of Biology Oxygen Demand (BOD), 90% of Total Suspended Solids (TSS), 40% of total nitrogen (TN), and 30% of total phosphorus (TP). Moreover, regarding the global warming category, the overall impact was 75% lower compared to other conventional treatments like activated sludge. In conclusion, the LCA revealed that METland® appears as ideal solution for rural areas, considering the low energy requirements and high efficiency to remove organic pollutants, nitrogen, and phosphates from urban wastewater.

Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria

Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.

Selenite and selenate removal in a permeable flow-through bioelectrochemical barrier

This study demonstrated the removal of selenite and selenate in flow-through permeable bioelectrochemical barriers (microbial electrolysis cells, MECs). The bioelectrochemical barriers consisted of cathode and anode electrode compartments filled with granular carbon or metallurgical coke. A voltage of 1.4 V was applied to the electrodes to enable the bioelectrochemical removal of selenium species. For comparison, a similarly designed permeable anaerobic biobarrier filled with granular carbon was operated without voltage. All biobarrier setups were fed with water containing up to 5,000 µg L^-1 of either selenite or selenate and 70 mg L^-1 of acetate as a source of organic carbon. Significant removal of selenite and selenate was observed in MEC experimental setups, reaching 99.5-99.8% over the course of the experiment, while in the anaerobic biobarrier the removal efficiency did not exceed 88%. By simultaneously operating several setups and changing operating parameters (selenium species, influent Se and acetate concentrations, etc.) we demonstrated enhanced removal of Se species under bioelectrochemical conditions.

A CMOS Multi-Modal Electrochemical and Impedance Cellular Sensing Array for Massively Paralleled Exoelectrogen Screening

The paper presents a 256-pixel CMOS sensor array with in-pixel dual electrochemical and impedance detection modalities for rapid, multi-dimensional characterization of exoelectrogens. The CMOS IC has 16 parallel readout channels, allowing it to perform multiple measurements with a high throughput and enable the chip to handle different samples simultaneously. The chip contains a total of 2 × 256 working electrodes of size 44 μm × 52 μm, along with 16 reference electrodes of dimensions 56 μm × 399 μm and 32 counter electrodes of dimensions 399 μm × 106 μm, which together facilitate the high resolution screening of the test samples. The chip was fabricated in a standard 130nm BiCMOS process. The on-chip electrodes are subjected to additional fabrication processes, including a critical Al-etch step that ensures the excellent biocompatibility and long-term reliability of the CMOS sensor array in bio-environment. The electrochemical sensing modality is verified by detecting the electroactive analyte NaFeEDTA and the exoelectrogenic Shewanella oneidensis MR-1 bacteria, illustrating the chip's ability to quantify the generated electrochemical current and distinguish between different analyte concentrations. The impedance measurements with the HEK-293 cancer cells cultured on-chip successfully capture the cell-to-surface adhesion information between the electrodes and the cancer cells. The reported CMOS sensor array outperforms the conventional discrete setups for exoelectrogen characterization in terms of spatial resolution and speed, which demonstrates the chip's potential to radically accelerate synthetic biology engineering.

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.

Comparative proteomics of Geobacter sulfurreducens PCAT in response to acetate, formate and/or hydrogen as electron donor

Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO₂ fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO₂ , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.

Extracellular electron transfer leading to the biological mediated production of reduced graphene oxide

To explore a green, low-cost, and efficient strategy to synthesis reduced graphene oxide (RGO), the process and mechanism of the graphene oxide (GO) reduction by a model electrochemically active bacteria (EAB), Geobacter sulfurreducens PCA, were studied. In this work, up to 1.0 mg mL^-1 of GO was reduced by G. sulfurreducens within 0.5-8 days. I_D/I_G ratio in reduced product was similar to chemically RGO. After microbial reduction, the peak which corresponded to the reflection of graphene oxide (001) disappeared, while another peak considered as graphite spacing (002) appeared. The peak intensity of typical oxygen function groups, such as carboxyl C-O and >O (epoxide) groups, diminished in bacterially induced RGO comparing to initial GO. Besides, we observed the doping of nitrogen and phosphorus elements in bacterially induced RGO. In a good agreement with that, better electrochemical performance was noticed after GO reduction. As confirmed with differential pulse voltammetry (DPV) and cyclic voltammetry (CV) analysis, the maximum value of peak currents of bacterially induced RGO were significantly higher than those of GO. Our results showed the electron transfer at microbial cell/GO interface promoted the GO reduction, suggesting a broader application of EAB in biological mediated production of RGO.

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

In this study we analyze the growth-phase dependent metabolic states of Bdellovibrio bacteriovorus by constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide computational evidences supporting potential axenic growth of B. bacteriovorus's in a rich medium based on its encoded metabolic capabilities. Our systems-level analysis confirms the presence of "energy-saving" mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacteria's metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications.

Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism’s phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as bio-stimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation.

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities

Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at −0.2 to −0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.

The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate

Multiple Fe(III)-reducing Geobacter species including the model Geobacter sulfurreducens are thought to be incapable of carbon dioxide fixation. The discovery of the reversed oxidative tricarboxylic acid cycle (roTCA) for CO₂ reduction with citrate synthase as key enzyme raises the possibility that G. sulfurreducens harbors the metabolic potential for chemolithoautotrophic growth. We investigate this hypothesis by transferring G. sulfurreducens PCA serially with Fe(III) as electron acceptor and formate as electron donor and carbon source. The evolved strain T17-3 grew chemolithoautotrophically with a 2.7-fold population increase over 48 h and a Fe(III) reduction rate of 417.5 μM h^-1. T17-3 also grew with CO₂ as carbon source. Mutations in T17-3 and enzymatic assays point to an adaptation process where the succinyl-CoA synthetase, which is inactive in the wild-type, became active to complete the roTCA cycle. Deletion of the genes coding for the succinyl-CoA synthetase in T17-3 prevented growth with formate as substrate. Enzymatic assays also showed that the citrate synthase can perform the necessary cleavage of citrate for the functional roTCA cycle. These results demonstrate that G. sulfurreducens after adaptation reduced CO₂ via the roTCA cycle. This previously hidden metabolism can be harnessed for biotechnological applications and suggests hidden ecological functions for Geobacter.

Progress and Prospects of Bioelectrochemical Systems: Electron Transfer and Its Applications in the Microbial Metabolism

Bioelectrochemical systems are revolutionary new bioengineering technologies which integrate microorganisms or enzymes with the electrochemical method to improve the reducing or oxidizing metabolism. Generally, the bioelectrochemical systems show the processes referring to electrical power generation or achieving the reducing reaction with a certain potential poised by means of electron transfer between the electron acceptor and electron donor. Researchers have focused on the selection and optimization of the electrode materials, design of electrochemical device, and screening of electrochemically active or inactive model microorganisms. Notably, all these means and studies are related to electron transfer: efflux and consumption. Thus, here we introduce the basic concepts of bioelectrochemical systems, and elaborate on the extracellular and intracellular electron transfer, and the hypothetical electron transfer mechanism. Also, intracellular energy generation and coenzyme metabolism along with electron transfer are analyzed. Finally, the applications of bioelectrochemical systems and the prospect of microbial electrochemical technologies are discussed.

Quantification of microaerobic growth of Geobacter sulfurreducens

Geobacter sulfurreducens was originally considered a strict anaerobe. However, this bacterium was later shown to not only tolerate exposure to oxygen but also to use it as terminal electron acceptor. Research performed has so far only revealed the general ability of G. sulfurreducens to reduce oxygen, but the oxygen uptake rate has not been quantified yet, nor has evidence been provided as to how the bacterium achieves oxygen reduction. Therefore, microaerobic growth of G. sulfurreducens was investigated here with better defined operating conditions as previously performed and a transcriptome analysis was performed to elucidate possible metabolic mechanisms important for oxygen reduction in G. sulfurreducens. The investigations revealed that cell growth with oxygen is possible to the same extent as with fumarate if the maximum specific oxygen uptake rate (sOUR) of 95 mg_O2 g_CDW^-1 h^-1 is not surpassed. Hereby, the entire amount of introduced oxygen is reduced. When oxygen concentrations are too high, cell growth is completely inhibited and there is no partial oxygen consumption. Transcriptome analysis suggests a menaquinol oxidase to be the enzyme responsible for oxygen reduction. Transcriptome analysis has further revealed three different survival strategies, depending on the oxygen concentration present. When prompted with small amounts of oxygen, G. sulfurreducens will try to escape the microaerobic area; if oxygen concentrations are higher, cells will focus on rapid and complete oxygen reduction coupled to cell growth; and ultimately cells will form protective layers if a complete reduction becomes impossible. The results presented here have important implications for understanding how G. sulfurreducens survives exposure to oxygen.

Effect of anaerobic sludge on the bioelectricity generation enhancement of bufferless single-chamber microbial fuel cells

Enhancing the self-buffering capacity is critical in the operation of bufferless microbial fuel cells (BLMFCs). Inorganic carbon (IC) is an ideal endogenous buffer, but its spontaneously accumulated concentration is insufficient to adjust anolyte pH. In this study, BLMFCs were operated with anaerobic sludge to enhance IC accumulation and increase anolyte pH. The accumulated IC concentration during a single running cycle was elevated from 8.3 mM to 12.5 mM, and anolyte pH remained above 7.5. The electric power output was significantly promoted from 332.2 mW·m^-2 to 628.1 mW·m^-2, and the coulombic efficiency (CE) slightly increased from 16.4% to 19.5%. Geobacter was the electro-active genus in the anode biofilms of the MFCs, and its relative abundance in the KCl-S anode biofilm increased from 0.2% to 5.75%. After continuous operation, the predominant genus of the anaerobic sludge had changed from Flavobacterium to Fusibacter.

Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1

The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 μM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.

Spotlight on the Energy Harvest of Electroactive Microorganisms: The Impact of the Applied Anode Potential

Electroactive microorganisms (EAM) harvest energy by reducing insoluble terminal electron acceptors (TEA) including electrodes via extracellular electron transfer (EET). Therefore, compared to microorganisms respiring soluble TEA, an adapted approach is required for thermodynamic analyses. In EAM, the thermodynamic frame (i.e., maximum available energy) is restricted as only a share of the energy difference between electron donor and TEA is exploited via the electron-transport chain to generate proton-motive force being subsequently utilized for ATP synthesis. However, according to a common misconception, the anode potential is suggested to co-determine the thermodynamic frame of EAM. By comparing the model organism Geobacter spp. and microorganisms respiring soluble TEA, we reason that a considerable part of the electron-transport chain of EAM performing direct EET does not contribute to the build-up of proton-motive force and thus, the anode potential does not co-determine the thermodynamic frame. Furthermore, using a modeling platform demonstrates that the influence of anode potential on energy harvest is solely a kinetic effect. When facing low anode potentials, NADH is accumulating due to a slow direct EET rate leading to a restricted exploitation of the thermodynamic frame. For anode potentials ≥ 0.2 V (vs. SHE), EET kinetics, NAD⁺/NADH ratio as well as exploitation of the thermodynamic frame are maximized, and a further potential increase does not result in higher energy harvest. Considering the limited influence of the anode potential on energy harvest of EAM is a prerequisite to improve thermodynamic analyses, microbial resource mining, and to transfer microbial electrochemical technologies (MET) into practice.

The electrifying physiology of Geobacter bacteria, 30 years on

The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.