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

A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer

Microbial extracellular electron transfer (EET) drives various globally important environmental phenomena and has biotechnology applications. Diverse prokaryotes have been proposed to perform EET via surface-displayed "nanowires" composed of multi-heme cytochromes. However, the mechanism that enables only a few cytochromes to polymerize into nanowires is unclear. Here, we identify a highly conserved omcS-companion (osc) cluster that drives the formation of cytochrome OmcS nanowires in Geobacter sulfurreducens. Through a combination of genetic, biochemical, and biophysical methods, we establish that prolyl isomerase-containing chaperon OscH, channel-like OscEFG, and β-propeller-like OscD are involved in the folding, secretion, and morphology maintenance of OmcS nanowires, respectively. OscH and OscG can interact with OmcS. Furthermore, overexpression of oscG accelerates EET by overproducing nanowires in an ATP-dependent manner. Heme loading splits OscD; ΔoscD accelerates cell growth, bundles nanowires into cables. Our findings establish the mechanism and prevalence of a specialized and modular assembly system for nanowires across phylogenetically diverse species and environments.

Visualization of Syntrophic Benzene-Fermenting Desulfobacterota ORM2 in a Methanogenic Enrichment Culture Using Fluorescence In Situ Hybridization

Benzene degradation under anoxic conditions was first reported more than 25 years ago; however, the activation mechanism in the absence of oxygen remains elusive. Progress has been hindered by the difficulty in cultivating anaerobic benzene-degrading enrichment cultures. Our laboratory has sustained a methanogenic enrichment culture harboring Desulfobacterota ORM2, a benzene fermenter distinct from any known genus but related to other known or predicted benzene degraders. ORM2's slow doubling time (∼30 days) and extended lag phase after inoculation complicate its study. We developed a fluorescent in situ hybridization (FISH) probe for ORM2, revealing rod-shaped cells of variable length that tend to cluster with other organisms, particularly methanogens. Microscopy and genomic evidence suggest that ORM2 may produce extracellular polymeric substances, facilitating cell aggregation and possibly consuming energy that contributes to the lag phase. Interestingly, higher benzene concentrations (90-120 mg/L) appeared to reduce cell aggregation. This study visualized the cells of Desulfobacterota ORM2 within a methanogenic community, offering insights into spatial organization and potential strategies to enhance its growth rate.

Key active mercury methylating microorganisms and their synergistic effects on methylmercury production in paddy soils

Rice contamination with neurotoxic methylmercury (MeHg) from paddy soils is an escalating global concern. Identifying the microorganisms responsible for mercury (Hg) methylation in these soils is essential for controlling Hg contamination in the food chain and mitigating health impacts. Current research often focuses on total Hg-methylating microorganisms, overlooking the contributions of active ones, which can lead to either overestimating or neglecting the specific roles of microorganisms in Hg methylation within paddy soils. In this study, active Hg-methylating microorganisms in paddy soils were identified using a combination of DNA-SIP, Hg isotope labelling, and Hg methylation gene sequencing techniques. Our findings revealed that Geobacter and Anaerolinea are pivotal active Hg-methylating microorganisms across a contamination gradient in paddy soils. Transcriptomic analysis of soils from major rice-producing provinces in China confirmed the widespread and synergistic involvement of these microorganisms. Microbial incubation further validated their interaction significantly enhances Hg methylation, with Me198Hg concentrations increasing 2.8-fold compared to Geobacter alone and 5.2-fold compared to Anaerolinea alone. These findings enhance our understanding of microbial Hg methylation in paddy soils, providing critical insights for accurately predicting soil MeHg load, rice grain MeHg contamination, and human MeHg exposure risks.

Correlation between intracellular electron transfer and gene expression for electrically conductive pili in electroactive bacteria during anaerobic digestion with ethanol

Ethanol feeding has been widely documented as an economical and effective strategy for establishing direct interspecies electron transfer (DIET) during anaerobic digestion. However, the mechanisms involved are still unclear, especially on correlation between intracellular electron transfer in electroactive bacteria and their gene expression for electrically conductive pili (e-pili), the most essential electrical connection component for DIET. Upon cooling from room temperature, the conductivity of digester aggregates with ethanol exponentially increased by an order of magnitude (from 45.5 to 125.4 μS/cm), whereas which with its metabolites (acetaldehyde [from 40.5 to 54.4 μS/cm] or acetate [from 32.1 to 50.4 μS/cm]) did not increase significantly. In addition, the digester aggregates only with ethanol were observed with a strong dependence of conductivity on pH. Metagenomic and metatranscriptomic analysis showed that Desulfovibrio desulfuricans was the most dominant and metabolically active bacterium that contained and highly expressed the genes for e-pili. Abundance of genes encoding the total type IV pilus assembly proteins (6.72E-04 vs 1.24E-03, P < 0.05), PilA that determined the conductive properties (2.22E-04 vs 2.44E-04, P > 0.05), and PilB that proceeded the polymerization of pilin (1.56E-04 vs 3.52E-03, P < 0.05) with ethanol was lower than that with acetaldehyde. However, transcript abundance of these genes with ethanol was generally higher than that with acetaldehyde. In comparison to acetaldehyde, ethanol increased the transcript abundance of genes encoding the key enzymes involved in NADH/NAD+ transformation on complex I and ATP synthesis on complex V in intracellular electron transport chain. The improvement of intracellular electron transfer in D. desulfuricans suggested that electrons were intracellularly energized with high energy to activate e-pili during DIET.

A biocompatible electrode/exoelectrogens interface augments bidirectional electron transfer and bioelectrochemical reactions

Bidirectional electron transfer is about that exoelectrogens produce bioelectricity via extracellular electron transfer at anode and drive cytoplasmic biochemical reactions via extracellular electron uptake at cathode. The key factor to determine above bioelectrochemical performances is the electron transfer efficiency under biocompatible abiotic/biotic interface. Here, a graphene/polyaniline (GO/PANI) nanocomposite electrode specially interfacing exoelectrogens (Shewanella loihica) and augmenting bidirectional electron transfer was conducted by in-situ electrochemical modification on carbon paper (CP). Impressively, the GO/PANI@CP electrode tremendously improved the performance of exoelectrogens at anode for wastewater treatment and bioelectricity generation (about 54 folds increase of power density compared to blank CP electrode). The bacteria on electrode surface not only showed fast electron release but also exhibited high electricity density of extracellular electron uptake through the proposed direct electron transfer pathway. Thus, the cathode applications of microbial electrosynthesis and bio-denitrification were developed via GO/PANI@CP electrode, which assisted the close contact between microbial outer-membrane cytochromes and nanocomposite electrode for efficient nitrate removal (0.333 mM/h). Overall, nanocomposite modified electrode with biocompatible interfaces has great potential to enhance bioelectrochemical reactions with exoelectrogens.

Enhanced Microbial Protein Production from CO2 and Air by a MoS2 Catalyzed Bioelectrochemical System

Carbon dioxide can be relatively easily reduced to organic matter in a bioelectrochemical system (BES). However, due to insufficient reduction force from in-situ hydrogen evolution, it is difficult for nitrogen reduction. In this study, MoS2 was firstly used as an electrocatalyst for the simultaneous reduction of CO2 and N2 to produce microbial protein (MP) in a BES. Cell dry weight (CDW) could reach 0.81±0.04 g/L after 14 d operation at -0.7 V (vs. RHE), which was 108±3 % higher than that from non-catalyst control group (0.39±0.01 g/L). The produced protein had a better amino acid profile in the BES than that in a direct hydrogen system (DHS), particularly for proline (Pro). Besides, MoS2 promoted the growth of bacterial cell on an electrode and improved the biofilm extracellular electron transfer (EET) by microscopic observation and electrochemical characterization of MoS2 biocathode. The composition of the microbial community and the relative abundance of functional enzymes revealed that MoS2 as an electrocatalyst was beneficial for enriching Xanthobacter and enhancing CO2 and N2 reduction by electrical energy. These results demonstrated that an efficient strategy to improve MP production of BES is to use MoS2 as an electrocatalyst to shift amino acid profile and microbial community.

Unnatural Direct Interspecies Electron Transfer Enabled by Living Cell-Cell Click Chemistry

Direct interspecies electron transfer (DIET) is essential for maintaining the function and stability of anaerobic microbial consortia. However, only limited natural DIET modes have been identified and DIET engineering remains highly challenging. In this study, an unnatural DIET between Shewanella oneidensis MR-1 (SO, electron donating partner) and Rhodopseudomonas palustris (RP, electron accepting partner) was artificially established by a facile living cell-cell click chemistry strategy. By introducing alkyne- or azide-modified monosaccharides onto the cell outer surface of the target species, precise covalent connections between different species in high proximity were realized through a fast click chemistry reaction. Remarkably, upon covalent connection, outer cell surface C-type cytochromes mediated DIET between SO and RP was achieved and identified, although this was never realized naturally. Moreover, this connection directly shifted the natural H2 mediated interspecies electron transfer (MIET) to DIET between SO and RP, which delivered superior interspecies electron exchange efficiency. Therefore, this work demonstrated a naturally unachievable DIET and an unprecedented MIET shift to DIET accomplished by cell-cell distance engineering, offering an efficient and versatile solution for DIET engineering, which extends our understanding of DIET and opens up new avenues for DIET exploration and applications.

Elucidating the development of cooperative anode-biofilm-structures

Microbial electrochemical systems are a highly versatile platform technology with a particular focus on the interplay of chemical and electrical energy conversion and offer immense potential for a sustainable bioeconomy. The industrial realization of this potential requires a critical focus on biofilm optimization if performance is to be controlled over a long period of time. Moreover, the aspect and influence of cooperativity has to be addressed as many applied anodic bioelectrochemical systems will most likely be operated with a diversity of interacting microbial species. Hence, the aim of this study was to analyze how interspecies dependence and cooperativity of a model community influence the development of anodic biofilms. To investigate biofilm activity in a spatially resolved manner, a microfluidic bioelectrochemical flow cell was developed that can be equipped with user-defined electrode materials and operates under laminar flow conditions. With this infrastructure, the development of single and co-culture biofilms of the two model organisms Shewanella oneidensis and Geobacter sulfurreducens on graphite electrodes was monitored by optical coherence tomography analysis. The interdependence in the co-culture biofilm was achieved by feeding the community with lactate, which is converted by S. oneidensis into acetate, which in turn serves as substrate for G. sulfurreducens. The results show that co-cultivation resulted in the formation of denser biofilms than in single culture. Moreover, we hypothesize that S. oneidensis in return utilizes the conductive biofilm matrix build by G. sulfurreducens for direct interspecies electron transfer (DIET) to the anode. FISH analysis revealed that the biofilms consisted of approximately two-thirds G. sulfurreducens cells, which most likely formed a conductive 3D network throughout the biofilm matrix, in which evenly distributed tubular S. oneidensis colonies were embedded without direct contact to the anode surface. Live/dead staining shows that the outermost biofilm contained almost exclusively dead cells (98 %), layers near the anode contained 45-56 % and the entire biofilm contained 82 % live cells. Our results exemplify how the architecture of the exoelectrogenic biofilm dynamically adapts to the respective process conditions.

Significance of a minor pilin PilV in biofilm cohesion of Geobacter sulfurreducens

Bacterial adhesion plays a vital role in forming and shaping the structure of electroactive biofilms that are essential for the performance of bioelectrochemical systems (BESs). Type IV pili are known to mediate cell adhesion in many Gram-negative bacteria, but the mechanism of pili-mediated cell adhesion of Geobacter species on anode surface remains unclear. Herein, a minor pilin PilV2 was found to be essential for cell adhesion ability of Geobacter sulfurreducens since the lack of pilV2 gene depressed the cell adhesion capability by 81.2% in microplate and the anodic biofilm density by 23.1 % at -0.1 V and 37.7 % at -0.3 V in BESs. The less cohesiveness of mutant biofilms increased the charge transfer resistance and biofilm resistance, which correspondingly lowered current generation of the pilV2-deficient strain by up to 63.2 % compared with that of the wild-type strain in BESs. The deletion of pilV2 posed an insignificant effect on the production of extracellular polysaccharides, pili, extracellular cytochromes and electron shuttles that are involved in biofilm formation or extracellular electron transfer (EET) process. This study demonstrated the significance of pilV2 gene in cell adhesion and biofilm formation of G. sulfurreducens, as well as the importance of pili-mediated adhesion for EET of electroactive biofilm.

Exploring nature's filters: Peat-mineral mix for low and high-strength oilfield produced water reclamation

Nature-based solutions are encouraged for treating oilfield produced water from oil and gas extraction, a crucial undertaking that aligns with the Canadian oil sands industry's ambitious goal of zero waste, and the globally recognized Sustainable Development Goals (SDGs) pertaining to water conservation and ecosystem preservation. This study explored the use of peat-mineral mix (PMM), a leftover of inevitable oil sands mining, for treating low and high-strength wastewaters during biofiltration, which contained large molecular weight (44.3 kDa), which include alcohols, aliphatics, aromatics, and ketones, and can impart high toxicity to both fauna and flora (MicroTox: 99 %). The breakthrough curve indicated an effective initial adsorption phase driven by advection within the column dynamics. For complete organics removal and mechanistic insights, the wastewater was re-circulated in a continuous mode for up to 42 days. Here, we found that chemical oxygen demand was reduced from ∼85,000 mg/L to ∼965 mg/L). Kinetics investigations along with physicochemical characterization of PMM and wastewater suggested that chemisorption and anaerobic digestion contributed to the overall removal of contaminants. Chemisorption, led by hydrogen bonding and hydrophobic interactions, was the dominant mechanism, with a limited contribution from physical adsorption (surface area: 2.85 m2/g). The microbial community within the PMM bed was rich/diverse (Shannon > 6.0; Chao1 > 600), with ∼ 50 % unclassified phylotypes representing 'microbial dark matter'. High electric conductivity (332.1 μS cm-1) of PMM and the presence of Geobacter, syntrophs, and Methanosaeta suggest that direct interspecies electron transfer was likely occurring during anaerobic digestion. Both low and high-strength wastewaters showed effective removal of dissolved organics (e.g., naphthenic acids, acid extractable fraction, oil and grease content), nutrients, and potentially toxic metals. The successful use of PMM in treating oilfield produced water offers promising avenues for embracing nature-based remediation solutions at oil refining sites.

Electron Transfer in the Biogeochemical Sulfur Cycle

Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability to perform extracellular electron transfer. A growing body of research has highlighted their extensive phylogenetic and metabolic diversity, revealing their crucial roles in ecological processes. In this review, we delve into the electron transfer process between sulfate-reducing bacteria and anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, we review the phenomenon of long-distance electron transfer and potential extracellular electron transfer in multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with their vast application prospects and ecological significance, play a pivotal role in various ecological processes. Subsequently, we discuss the important role of the pili/cytochrome for electron transfer and presented cutting-edge approaches for exploring and studying electroactive microorganisms. This review provides a comprehensive overview of electroactive microorganisms participating in the biogeochemical sulfur cycle. By examining their electron transfer mechanisms, and the potential ecological and applied implications, we offer novel insights into microbial sulfur metabolism, thereby advancing applications in the development of sustainable bioelectronics materials and bioremediation technologies.

Metagenomic insights into phenanthrene biodegradation in electrical field-governed biofilms for groundwater bioremediation

Electrical fields (EFs)-assisted in-situ bioremediation of petroleum-contaminated groundwater, such as polycyclic aromatic hydrocarbons, has drawn increasing attention. However, the long-term stability, the EFs influence, and metabolic pathways are still poorly understood, hindering the further development of robust technology design. Herein, a series of EFs was applied to the phenanthrene-contaminated groundwater, and the corresponding system performance was investigated. The highest removal capacity of phenanthrene (phe) (7.63 g/(m3·d)) was achieved with EF_0.8 V biofilm at a hydrolytic retention time of 0.5 d. All the biofilms with four EFs exhibited a high removal efficiency of phe over 80% during a 100-d continuous-flow operation. Intermediates analysis revealed the main pathways of phe degradation: phthalate and salicylate via hydroxylation, methylation, carboxylation, and ring cleavage steps. Synergistic effects between phe-degraders (Dechloromonas), fermentative bacteria (Delftia), and electroactive microorganisms (Geobacter) were the main contributors to the complete phe mineralization. Genes encoding various proteins of methyl-accepting (mcp), response regulator (cheABDRY), and type IV pilus (pilABCMQV) were dominant, revealing the importance of cell motility and extracellular electron transfer. Metagenomics analysis unveiled phe-degrading genes, including ring reduction enzymes (bamBCDE), carboxylase of aromatics (ubiD), and methyltransferase protein (ubiE, pcm). These findings offered a molecular understanding of refractory organics' decompositions in EFs-governed biotechnology.

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.

Magnetic biochar accelerates microbial succession and enhances assimilatory nitrate reduction during pig manure composting

Biochar promotes microbial metabolic activities and reduces N2O on aerobic composting. However, the effects of magnetic biochar (MBC) on the microbial succession and N2O emissions during pig manure composting remain unclear. Herein, a 42-day composting experiment was conducted with five treatment regimes: pig manure without biochar (CK), 5 % pig manure-based biochar (5 % PBC), 2 % MBC (2 % MBC), 5 % MBC (5 % MBC) and 7.5 % MBC (7.5 % MBC)), to clarify the variation in functional microorganisms and genes associated with nitrogen and direct interspecies electron transfer via metagenomics. Fourier-transform infrared spectroscopy showed that MBC possessed more stable aromatic structures than pig manure-based biochar (PBC), indicating its greater potential for nitrous oxide reduction. MBC treatments were more effective in composting organic matter and improving the carbon/nitrogen ratio than PBC. The microbial composition during composting varied significantly, with the dominant phyla shifting from Firmicutes to Proteobacteria, Actinobacteria, and Bacteroidota. Network and hierarchical clustering analyses showed that the MBC treatment enhanced the interactions of dominant microbes (Proteobacteria and Bacteroidota) and accelerated the composting process. The biochar addition accelerated assimilatory nitrate reduction and slowed dissimilatory nitrate reduction and denitrification. The Mantel test demonstrated that magnetic biochar potentially helped regulate composting nutrients and affected functional nitrogen genes. These findings shed light on the role of MBC in mitigating greenhouse gas emissions during aerobic composting.

The survival strategy of direct interspecies electron transfer-capable coculture under electron donor-limited environments

Direct interspecies electron transfer (DIET) has been considered as an effective mechanism for interspecies electron exchange in microbial syntrophy. Understanding DIET-capable syntrophic associations under energy-limited environments is important because these conditions more closely approximate those found in natural subsurface environments than in the batch cultures in the laboratory. This study, investigated the metabolic dynamics and electron transfer mechanisms in DIET-capable syntrophic coculture of Geobacter metallireducens and Geobacter sulfurreducens under electron donor-limited condition. The wild-coculture and the mutant-coculture with a citrate synthase-deficient G. sulfurreducens exhibited similar rates of syntrophic metabolism under ethanol-limited and ethanol-replete conditions. Transcriptomic analyses revealed that, in the mutant-coculture in which interspecies electron exchange was the sole electron source for G. sulfurreducens, the transcription of genes associated with uptake hydrogenase in G. sulfurreducens were significantly repressed and thus DIET tended to be the preferred mode of interspecies electron exchange under electron donor-limited condition. To overcome electron donor limitation, c-type cytochromes in the coculture actively moved from outer membrane to extracellular environment, potentially via increased secretion of outer-membrane vesicles. These results suggested a preferred electron transfer mechanism for DIET-capable syntrophic communities' survival in the electron donor-limited environments, providing valuable insights into the biogeochemical processes mediated by DIET in natural and engineered environments.

Nonelectroactive clostridium obtains extracellular electron transfer-capability after forming chimera with Geobacter

Extracellular electron transfer (EET) of microorganisms is a major driver of the microbial growth and metabolism, including reactions involved in the cycling of C, N, and Fe in anaerobic environments such as soils and sediments. Understanding the mechanisms of EET, as well as knowing which organisms are EET-capable (or can become so) is fundamental to electromicrobiology and geomicrobiology. In general, Gram-positive bacteria very seldomly perform EET due to their thick non-conductive cell wall. Here, we report that a Gram-positive Clostridium intestinale (C.i) attained EET-capability for ethanol metabolism only after forming chimera with electroactive Geobacter sulfurreducens (G.s). Mechanism analyses demonstrated that the EET was possible after the cell fusion of the two species was achieved. Under these conditions, the ethanol metabolism pathway of C.i was integrated by the EET pathway of G.s, by which achieved the oxidation of ethanol for the subsequent reduction of extracellular electron acceptors in the coculture. Our study displays a new approach to perform EET for Gram-positive bacteria via recruiting the EET pathway of an electroactive bacterium, which suggests a previously unanticipated prevalence of EET in the microbial world. These findings also provide new perspectives to understand the energetic coupling between bacterial species and the ecology of interspecies mutualisms.

Microbial electron flow promotes naphthalene degradation in anaerobic digestion in the presence of nitrate electron acceptor: Focus on electron flow regulation and microbial interaction succession

Microbial electron flow (MEF) is produced from microbial degradation of organic compounds. Regulating MEF to promote organic pollutants biodegradation such as naphthalene (Nap) is a potential way but remains a lack of theoretical basis. Here, we regulated MEF by adding electron acceptor NO3- to achieve 2.6 times increase of Nap biodegradation with cyclodextrin as co-metabolism carbon source. With the NO3- addition, the genes inhibited by Nap of electron generation significantly up-regulated. Especially, key genes ubiD and nahD for anaerobic Nap degradation significantly up-regulated respectively 3.7 times and 6.7 times. Moreover, the ability of electron transfer in MEF was also improved consistent with 7.2 times increase of electron transfer system (ETS) activity. Furthermore, total 60 metagenome-assembled genomes (MAGs) were reconstructed through the metagenomic sequencing data with assembly and binning strategies. Interestingly, it was also first found that the Klebsiella MAG. SDU (Shandong University) 14 had the ability of simultaneous Nap biodegradation and denitrification. Our results firstly offered an effective method of regulating MEF to promote polycyclic aromatic hydrocarbons (PAHs) degradation and simultaneous methanogenesis.

Facilitating direct interspecies electron transfer in anaerobic digestion via speeding up transmembrane transport of electrons and CO2 reduction in methanogens by Na+ adjustment

The possibility of facilitating direct interspecies electron transfer (DIET) in anaerobic digestion with different concentrations of NaCl was explored. Additional NaCl at 2 or 4 g/L strengthened anaerobic digestion to resist the high-organic loading rate impacts, whereas the higher concentrations of NaCl (6 or 8 g/L) suppressed methanogenesis. Additional MgCl2 with the same ion strength as NaCl at 2 g/L had no effect on performances. Additional NaCl at 2 or 4 g/L dramatically increased the abundance of Methanosarcina species (20.7%/23.4% vs 8.6%) and stimulated the growth of Sphaerochaeta and Petrimonas species that could transfer electrons to the soluble Fe(III) or elemental sulfur. Electrochemical evidences showed that, additional NaCl at 2 or 4 g/L increased capacitances and decreased charge transfer resistances of Methanosarcina-dominant communities. Metagenomic evidences showed that, additional NaCl at 2 or 4 g/L increased the abundance of genes that encoded the type IV pilus assembly proteins (1.98E-04/1.87E-04 vs 1.85E-04) and cytochrome c-like proteins (5.51E-04/5.60E-04 vs 5.31E-04). In addition, additional NaCl at 2 or 4 g/L increased the abundance of genes for methanophenazine (MP)/MPH2 transformation (1.04E-05/1.24E-05 vs 8.06E-06) and CO2 reduction (1.64E-03/1.86E-03 vs 1.06E-03), suggesting a rapid transmembrane transport of electrons and CO2 reduction in methanogens. Both processes were closely associated with F420/F420H2 transformation that required ATP. Additional NaCl at 2 or 4 g/L increased the yield of ATP (256.0/249.3 vs 231.8 nmol/L) that might promote F420/F420H2 transformation in methanogens, which overcame the thermodynamic limitations of combining electrons with protons for the reduction of CO2 to methane and facilitated DIET.

Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest

Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.

Biophotoelectrochemical process co-driven by dead microalgae and live bacteria

Anaerobic reduction processes in natural waters can be promoted by dead microalgae that have been attributed to nutrient substances provided by the decomposition of dead microalgae for other microorganisms. However, previous reports have not considered that dead microalgae may also serve as photosensitizers to drive microbial reduction processes. Here we demonstrate a photoelectric synergistic linkage between dead microalgae and bacteria capable of extracellular electron transfer (EET). Illumination of dead Raphidocelis subcapitata resulted in two-fold increase in the rate of anaerobic bioreduction by pure Geobacter sulfurreducens, suggesting that photoelectrons generated from the illuminated dead microalgae were transferred to the EET-capable microorganisms. Similar phenomena were observed in NO3- reduction driven by irradiated dead Chlorella vulgaris and living Shewanella oneidensis, and Cr(VI) reduction driven by irradiated dead Raphidocelis subcapitata and living Bacillus subtilis. Enhancement of bioreduction was also seen when the killed microalgae were illuminated in mixed-culture lake water, suggesting that EET-capable bacteria were naturally present and this phenomenon is common in post-bloom systems. The intracellular ferredoxin-NADP+-reductase is inactivated in the dead microalgae, allowing the production and extracellular transfer of photoelectrons. The use of mutant strains confirmed that the electron transport pathway requires multiheme cytochromes. Taken together, these results suggest a heretofore overlooked biophotoelectrochemical process jointly mediated by illumination of dead microalgae and live EET-capable bacteria in natural ecosystems, which may add an important component in the energetics of bioreduction phenomena particularly in microalgae-enriched environments.

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.

Conductive Materials on Biocathodes Altered the Electron-Transfer Paths and Modulated γ-HCH Dechlorination and CH4 Production in Microbial Electrochemical Systems

Adding conductive materials to the cathode of a microbial electrochemical system (MES) can alter the route of interspecies electron transfer and the kinetics of reduction reactions. We tested reductive dechlorination of γ-hexachlorocyclohexane (γ-HCH), along with CH₄ production, in MES systems whose cathodes were coated with conductive magnetite nanoparticles (NaFe), biochar (BC), magnetic biochar (FeBC), or anti-conductive silica biochar (SiBC). Coating with NaFe enriched electroactive microorganisms, boosted electro-bioreduction, and accelerated γ-HCH dechlorination and CH₄ production. In contrast, BC only accelerated dechlorination, while FeBC only accelerated methanogenesis, because of their assemblies of functional taxa that selectively transferred electrons to those electron sinks. SiBC, which decreased electro-bioreduction, yielded the highest CH₄ production and increased methanogens and the mcrA gene. This study provides a strategy to selectively control the distribution of electrons between reductive dechlorination and methanogenesis by adding conductive or anti-conductive materials to the MES's cathode. If the goal is to maximize dechlorination and minimize methane generation, then BC is the optimal conductive material. If the goal is to accelerate electro-bioreduction, then the best addition is NaFe. If the goal is to increase the rate of methanogenesis, adding anti-conductive SiBC is the best.

Biochar Facilitated Direct Interspecies Electron Transfer in Anaerobic Digestion to Alleviate Antibiotics Inhibition and Enhance Methanogenesis: A Review

Efficient conversion of organic waste into low-carbon biofuels such as methane through anaerobic digestion (AD) is a promising technology to alleviate energy shortages. However, issues such as inefficient methane production and poor system stability remain for AD technology. Biochar-facilitated direct interspecies electron transfer (DIET) has recently been recognized as an important strategy to improve AD performance. Nonetheless, the underlying mechanisms of biochar-facilitated DIET are still largely unknown. For this reason, this review evaluated the role of biochar-facilitated DIET mechanism in enhancing AD performance. First, the evolution of DIET was introduced. Then, applications of biochar-facilitated DIET for alleviating antibiotic inhibition and enhancing methanogenesis were summarized. Next, the electrochemical mechanism of biochar-facilitated DIET including electrical conductivity, redox-active characteristics, and electron transfer system activity was discussed. It can be concluded that biochar increased the abundance of potential DIET microorganisms, facilitated microbial aggregation, and regulated DIET-associated gene expression as a microbial mechanism. Finally, we also discussed the challenges of biochar in practical application. This review elucidated the role of DIET facilitated by biochar in the AD system, which would advance our understanding of the DIET mechanism underpinning the interaction of biochar and anaerobic microorganisms. However, direct evidence for the occurrence of biochar-facilitated DIET still requires further investigation.

Conductive materials as fantastic toolkits to stimulate direct interspecies electron transfer in anaerobic digestion: new insights into methanogenesis contribution, characterization technology, and downstream treatment

Direct interspecies electron transfer (DIET) stimulated by conductive materials (CMs) enables intercellular metabolic coupling that can address the unfavorable thermodynamical dilemma inherent in anaerobic digestion (AD). Although the DIET mechanism and stimulation have been extensively summarized, the methanogenesis contribution, characterization techniques, and downstream processes of CMs-led DIET in AD are surprisingly under-reviewed. Therefore, this review aimed to address these gaps. First, the contribution of CMs-led DIET to methanogenesis was re-evaluated by comparing the effect of various factors, including volatile fatty acids, free ammonia, and functional enzymes. It was revealed that AD systems are usually intricate and cannot allow the methanogenesis stimulation to be singularly attributed to the establishment of DIET. Additionally, considerable attention has been attached to the characterization of DIET occurrence, involving species identification, gene expression, electrical properties, cellular features, and syntrophic metabolism, suggesting the significance of accurate characterization methods for identifying the syntrophic metabolism interactions. Moreover, the type of CMs has a significant impact on AD downstream processes involving biogas purity, sludge dewaterability, and biosolids management. Finally, the central bottleneck consists in building a mathematical model of DIET to explain the mechanism of DIET in a deeper level from kinetics and thermodynamics.

Light-independent anaerobic microbial oxidation of manganese driven by an electrosyntrophic coculture

Anaerobic microbial manganese oxidation (AMMO) has been considered an ancient biological metabolism for Mn element cycling on Archaean Earth before the presence of oxygen. A light-dependent AMMO was recently observed under strictly anoxic conditions, providing a new proxy for the interpretation of the evolution of oxygenic photosynthesis. However, the feasibility of biotic Mn(II) oxidation in dark geological habitats that must have been abundant remains unknown. Therefore, we discovered that it would be possible to achieve AMMO in a light-independent electrosyntrophic coculture between Rhodopseudomonas palustris and Geobacter metallireducens. Transmission electron microscopy analysis revealed insoluble particle formation in the coculture with Mn(II) addition. X-ray diffraction and X-ray photoelectron spectroscopy analysis verified that these particles were a mixture of MnO2 and Mn3O4. The absence of Mn oxides in either of the monocultures indicated that the Mn(II)-oxidizing activity was induced via electrosyntrophic interactions. Radical quenching and isotopic experiments demonstrated that hydroxyl radicals (•OH) produced from H2O dissociation by R. palustris in the coculture contributed to Mn(II) oxidation. All these findings suggest a new, symbiosis-dependent and light-independent AMMO route, with potential importance to the evolution of oxygenic photosynthesis and the biogeochemical cycling of manganese on Archaean and modern Earth.

Enhanced performance and electron transfer of sulfur-mediated biological process under polyethylene terephthalate microplastics exposure

Microplastics are ubiquitous in estuaries, coasts, sewage and wastewater treatment plants (WWTPs), which could arouse unexpected effects on critical microbial processes in wastewater treatment. In this study, polyethylene terephthalate microplastics (PET-MPs) were selected to investigate the mechanism of its influence on the performance of sulfur-mediated biological process from the perspective of microbial metabolic activity, electron transfer capacity and microbial community. The results indicated that the exposure of 50 particles/L PET-MPs improved the chemical oxygen demand (COD) and sulfate removal efficiencies by 6.6 ± 0.5% and 4.5 ± 0.3%, respectively, due to the stimulation of microbial metabolic activity and the enrichment of sulfate-reducing bacteria (SRB) species, such as Desulfobacter. In addition, we found that the PET-MPs promoted Cytochrome C (Cyt C) production and improved the direct electron transfer (DET) capacity mediated by Cyt C. The long-term presence of PET-MPs stimulated the secretion of extracellular polymeric substance (EPS), especially the proteins and humic substances, which have been verified to be electroactive polymers to act as electron shuttles to promote the interspecies electron transfer pathway in sulfur-mediated biological process. Meanwhile, the transformation products (bis-(2-hydroxyethyl) terephthalate (BHET) and Mono (2-hydroxyethyl) terephthalic acid (MHET) of PET-MPs were detected in sulfur-mediated biological process. These findings indicate that the sulfur-mediated biological process has good adaptability to the toxicity of PET-MPs, which strengthens a deeper understanding of the dual function of microplastics in WWTPs.

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.

Effect of magnetite addition on transcriptional profiles of syntrophic Bacteria and Archaea during anaerobic digestion of propionate in wastewater sludge

Anaerobic digestion (AD) is an important technology for the effective conversion of waste and wastewater to methane. Here, syntrophic bacteria transfer molecular hydrogen (H₂ ), formate, or directly supply electrons (direct interspecies electron transfer, DIET) to the methanogens. Evidence is accumulating that the methanation of short-chain fatty acids can be enhanced by the addition of conductive material to the anaerobic digester, which has often been attributed to the stimulation of DIET. Since little is known about the transcriptional response of a complex AD microbial community to the addition of conductive material, we added magnetite to propionate-fed laboratory-scale reactors that were inoculated with wastewater sludge. Compared to the control reactors, the magnetite-amended reactors showed improved methanation of propionate. A genome-centric metatranscriptomics approach identified the active SCFA-oxidizing bacteria that affiliated with Firmicutes, Desulfobacterota and Cloacimonadota. The transcriptional profiles revealed that the syntrophic bacteria transferred acetate, H₂ and formate to acetoclastic and hydrogenotrophic methanogens, whereas transcription of potential determinants for DIET such as conductive pili and outer-membrane cytochromes did not significantly change with magnetite addition. Overall, changes in the transcriptional profiles of syntrophic Bacteria and Archaea in propionate-fed lab-scale reactors amended with magnetite refute a major role of DIET in the studied system.

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.

Fumarate disproportionation by Geobacter sulfurreducens and its involvement in biocorrosion and interspecies electron transfer

The model electroactive bacterium Geobacter sulfurreducens can acquire electrons directly from solid donors including metals and other species. Reports on this physiology concluding that solid donors are the only electron sources were conducted with fumarate believed to serve exclusively as the terminal electron acceptor (TEA). Here, G. sulfurreducens was repeatedly transferred for adaptation within a growth medium containing only fumarate and no other solid or soluble substrate. The resulting evolved strain grew efficiently with either the C4-dicarboxylate fumarate or malate acting simultaneously as electron donor, carbon source, and electron acceptor via disproportionation. Whole-genome sequencing identified 38 mutations including one in the regulator PilR known to repress the expression of the C4-dicarboxylate antiporter DcuB essential to G. sulfurreducens when growing with fumarate. Futhermore, the PilR mutation was identical to the sole mutation previously reported in an evolved G. sulfurreducens grown in a co-culture assumed to derive energy solely from direct interspecies electron transfer, but cultivated with fumarate as the TEA. When cultivating the fumarate-adapted strain in the presence of stainless steel and fumarate, biocorrosion was observed and bacterial growth was accelerated 2.3 times. These results suggest that G. sulfurreducens can conserve energy concomitantly from C4-dicarboxylate disproportionation and the oxidation of a solid electron donor. This co-metabolic capacity confers an advantage to Geobacter for survival and colonization and explains in part why these microbes are omnipresent in different anaerobic ecosystems.

The Role of Exopolysaccharides in Direct Interspecies Electron Transfer

Direct interspecies electron transfer (DIET) is an effective mechanism for microbial species to exchange electrons cooperatively during syntrophic metabolism. It is generally accepted that DIET is mainly mediated by electrically conductive pili and outer surface c-type cytochromes (c-Cyts). However, as an extracellular matrix is ubiquitous and abundant on the surface of microorganisms, the effect and mechanism of exopolysaccharides on DIET are still unclear. This study constructed a co-culture of exopolysaccharides-deficient Geobacter sulfurreducens with Geobacter metallireducens to explore the role of exopolysaccharides in DIET. Results revealed that the deficiency of exopolysaccharides extended the metabolic period of the co-culture by 44.4% and changed the proportions of each species in the co-culture. The exopolysaccharides-deficient co-culture failed to form large, tight spherical aggregates and the expression of c-Cyts and pili was decreased. The addition of magnetite and granular activated carbon (GAC), respectively, might compensate for the functions of c-Cyts and pili in the first generation of co-culture, but the stimulatory effect on the metabolic stable period co-culture was fairly limited. These findings demonstrate that non-conductive exopolysaccharides are an important component of DIET aggregates and an extracellular matrix for DIET-required c-Cyts.

Glycol/glycerol-fed electrically conductive aggregates suggest a mechanism of stimulating direct interspecies electron transfer in methanogenic digesters

The possibility of stimulating direct interspecies electron transfer (DIET) within aggregates of methanogenic digesters respectively with ethanol, glycol, and glycerol as a primary substrate was investigated to better understand the mechanisms of alcohol compounds stimulating DIET. Aggregates fed with ethanol, glycol, and glycerol were electrically conductive (10.4-19.4 uS/cm), with a temperature dependence of metallic-like conductivity. Close examination of transmission electron microscope images observed the potential interspecies connected networks assembled by filaments within these aggregates. Further investigations via metatranscriptomics found that, genes for electrically conductive pili (e-pili) (Log₂FPKM, 9.39-10.96) and c-type cytochromes (8.90-9.64) were highly expressed within aggregates. Glycerol-fed aggregates exhibited the highest gene expression for e-pili, while glycol-fed aggregates exhibited the highest gene expression for c-type cytochromes. Methanothrix species were dominant and metabolically active within aggregates. Genes encoding the enzymes involved in carbon dioxide reduction were highly expressed in Methanothrix species, suggesting that they participated in DIET. In addition, transcript abundance of genes encoding alcohol dehydrogenase and NADH-quinone oxidoreductase in alcohol dehydrogenation closely associated with NADH/NAD⁺ transformation within glycol- and glycerol-fed aggregates was generally higher than that within ethanol-fed aggregates. These results, and the fact that NADH/NAD⁺ transformation was very linked to the ATP synthesis complex that further supported the formation of extracellular electrical connection components, e-pili and membrane-bound multi-heme c-type cytochromes (MHCs), provided a possibility that alcohol compounds comprised of hydroxy groups could stimulate DIET and more hydroxy groups comprised were better for this stimulation.

Two key Geobacter species of wastewater-enriched electroactive biofilm respond differently to electric field

Electroactive biofilms have attracted increasing attention due to their unique ability to exchange electrons with electrodes. Geobacter spp. are widely found to be dominant in biofilms in acetate-rich environments when an appropriate voltage is applied, but it is still largely unknown how these bacteria are selectively enriched. Herein, two key Geobacter spp. that have been demonstrated predominant in wastewater-enriched electroactive biofilm after long-term operation, G. sulfurreducens and G. anodireducens, responded to electric field (EF) differently, leading to a higher abundance of EF-sensitive G. anodireducens in the strong EF region after cocultivation with G. sulfurreducens. Transcriptome analysis indicated that two-component systems containing sensor histidine kinases and response regulators were the key for EF sensing in G. anodireducens rather than in G. sulfurreducens, which are closely connected to chemotaxis, c-di-GMP, fatty acid metabolism, pilus, oxidative phosphorylation and transcription, resulting in an increase in extracellular polymeric substance secretion and rapid cell proliferation. Our data reveal the mechanism by which EF select specific Geobacter spp. over time, providing new insights into Geobacter biofilm formation regulated by electricity.

Improving electroautotrophic ammonium production from nitrogen gas by simultaneous carbon dioxide fixation in a dual-chamber microbial electrolysis cell

Microbial electrosynthesis is a promising technology for high-value added products generation from organic and inorganic waste. In this work, autotrophic dual-chamber microbial electrolysis cells (MECs) were set up for N2 fixation at -0.9 V vs Ag/AgCl (sat. KCl) cathodic potential under ambient conditions. Higher NH4+ production yield (average value of 0.35 µmol h-1 cm-2, normalized to cathode surface area) and higher faradaic efficiency (FE, 20.25%) were obtained with intermittent addition of N2 and CO2, while the yield and FE were only 0.018 µmol h-1 cm-2 and 4.21% in the absence of CO2. Furthermore, cyclic voltammograms (CV) explained the bioelectrochemical behavior of N2 reduction was coupled with CO2 reduction in the autotrophic MECs. Microbial community analysis and functional prediction in the cathodic chamber revealed that Xanthobacter and Hydrogenophaga played as producers for N2 and CO2 fixation and Pannonibacter acting as a decomposer for converting organic nitrogen to ammonium. This work not only provided an optional bioelectrocatalytic method for N2 fixation with negative CO2-emissions but also revealed the mechanism of simultaneous fixation of N2 and CO2 via Calvin cycle in autotrophic MECs.

Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil

A strictly anaerobic bacterial strain, designated Jerry-YXT, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YXT was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YXT was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C16 : 0 and C16 : 1  ω7c/C16 : 1  ω6c (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus Geobacter , being most closely related to Geobacter metallireducens (98.2 % similarity), Geobacter hydrogenophilus (98.1 %) and Geobacter grbiciae (98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YXT and G. metallireducens GS-15T were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YXT from its closest species, which suggested that strain Jerry-YXT represents a novel species of the genus Geobacter . The name for the proposed new species is Geobacter benzoatilyticus sp. nov. The type strain is Jerry-YXT (=MCCC 1K05659T=JCM 39190T).

Exopolysaccharides matrix affects the process of extracellular electron transfer in electroactive biofilm

The applications of bioelectrochemical systems (BESs) in the field of environment and energy are achieved through the bioelectrocatalytic process of electroactive biofilms. As a primary component of biofilm, the role of exopolysaccharides in electroactive biofilm in BESs is poorly understood. This study constructed an exopolysaccharides-deficient Geobacter sulfurreducens-based BES to explore the role of exopolysaccharides in electroactive biofilm. Compared with the wild type, the mutant biofilm expressing less exopolysaccharides decreased the capacity of current generation. In the mutant biofilm, the content of exopolysaccharides decreased significantly, resulting in a thinner biofilm and lower cell viability compared with the wild-type biofilm. However, the mutant with overexpressed pili developed a mature biofilm with extended time, which indicating the importance of exopolysaccharides for early biofilm formation and the compensatory role of pili in biofilm formation. The mutant biofilm had less content of c-type cytochromes (c-Cyts) and lower electrochemical activity of extracellular polymeric substances than the wild-type biofilm, suggesting a function of exopolysaccharides anchoring extracellular c-Cyts that essential to extracellular electron transfer (EET) in electroactive biofilms. Our findings demonstrated the essential role of exopolysaccharides in the process of EET in electroactive biofilm, which contributed to a better understanding and optimization of the performance of BESs.

Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture

The direct conversion of CO₂ to value-added chemical commodities, thereby storing solar energy, offers a promising option for alleviating both the current energy crisis and global warming. Semiconductor-biological hybrid systems are novel approaches. However, the inherent defects of photocorrosion, photodegradation, and the toxicity of the semiconductor limit the application of these biohybrid systems. We report here that Rhodopseudomonas palustris was able to directly act as a living photosensitizer to drive CO₂ to CH₄ conversion by Methanosarcina barkeri under illumination after coculturing. Specifically, R. palustris formed a direct electric syntrophic coculture with M. barkeri. Here, R. palustris harvested solar energy, performed anoxygenic photosynthesis using sodium thiosulfate as an electron donor, and transferred electrons extracellularly to M. barkeri to drive methane generation. The methanogenesis of M. barkeri in coculture was a light-dependent process with a production rate of 4.73 ± 0.23 μM/h under light, which is slightly higher than that of typical semiconductor-biohybrid systems (approximately 4.36 μM/h). Mechanistic and transcriptomic analyses showed that electrons were transferred either directly or indirectly (via electron shuttles), subsequently driving CH₄ production. Our study suggests that R. palustris acts as a natural photosensitizer that, in coculture with M. barkeri, results in a new way to harvest solar energy that could potentially replace semiconductors in biohybrid systems.

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.

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.

Anaerobic oxidation of methane mediated by microbial extracellular respiration

Anaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane-oxidizing archaea transfer electrons to external electron acceptors or to interdependent microbial species, which are mechanistically dependent on versatile extracellular electron transfer (EET) pathways. This review compiles recent progress in the research of electromicrobiology of AOM based on the catalogue of different electron acceptors. Naturally distributed and artificially constructed EET-mediated AOM is summarized, with the discussion of their environmental importance and application potentials. The diversity of responsible microorganisms involved in EET-mediated AOM is discussed with both methane-oxidizing archaea and their putative bacterial partners. More importantly, the review highlights progress and deficiencies in our understanding of EET pathways in EET-mediated AOM, raising open research questions for future research.

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.

Long-Term Succession Shows Interspecies Competition of Geobacter in Exoelectrogenic Biofilms

Geobacter spp. are well-known exoelectrogenic microorganisms that often predominate acetate-fed biofilms in microbial fuel cells (MFCs) and other bioelectrochemical systems (BESs). By using an amplicon sequence variance analysis (at one nucleotide resolution), we observed a succession between two closely related species (98% similarity in 16S RNA), Geobacter sulfurreducens and Geobacter anodireducens, in the long-term studies (20 months) of MFC biofilms. Geobacter spp. predominated in the near-electrode portion of the biofilm, while the outer layer contained an abundance of aerobes, which may have helped to consume oxygen but reduced the relative abundance of Geobacter. Removal of the outer aerobes by norspermidine washing of biofilms revealed a transition from G. sulfurreducens to G. anodireducens. This succession was also found to occur rapidly in co-cultures in BES tests even in the absence of oxygen, suggesting that oxygen was not a critical factor. G. sulfurreducens likely dominated in early biofilms by its relatively larger cell size and production of extracellular polymeric substances (individual advantages), while G. anodireducens later predominated due to greater cell numbers (quantitative advantage). Our findings revealed the interspecies competition in the long-term evolution of Geobacter genus, providing microscopic insights into Geobacter's niche and competitiveness in complex electroactive microbial consortia.

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.

The role of conductive nanoparticles in anaerobic digestion: Mechanism, current status and future perspectives

In the current scenario, alternative energy sources are the need of the hour. Organic wastes having a larger fraction of biodegradable constituents present a sustainable bioenergy source. It has been reported that the calorific value of biogas generated by anaerobic digestion (AD) is 21-25 MJ/m³ with the treatment which makes it an excellent replacement of natural gas and fossil fuels and can reduce more than 80% greenhouse gas emission to the surroundings. However, there are some limitations associated with the AD process for instance ammonia build-up at the first stage reduces the rate of hydrolysis of biomass, whereas, in the last stage it interferes with methane formation. Owing to special physicochemical properties such as high activity, high reactive surface area, and high specificity, tailor-made conductive nanoparticles can improve the performance of the AD process. In the AD process, H₂ is used as an electron carrier, referred as mediated interspecies electron transfer (MIET). Due to the diffusion limitation of these electron carriers, the MIET efficiency is relatively low that limits the methanogenesis. Direct interspecies electron transfer (DIET), which enables direct cell-to-cell electron transport between bacteria and methanogen, has been considered an alternative efficient approach to MIET that creates metabolically favorable conditions and results in faster conversion of organic acids and alcohols into methane. This paper discusses in detail the application of conductive nanoparticles to enhance the AD process efficiency. Interaction between microbes in anaerobic conditions for electron transfer with the help of CNPs is discussed. Application of a variety of conductive nanomaterials as an additive is discussed with their potential biogas production and treatment enhancement in the anaerobic digestion process.

Structure of Geobacter pili reveals secretory rather than nanowire behaviour

Extracellular electron transfer by Geobacter species through surface appendages known as microbial nanowires¹ is important in a range of globally important environmental phenomena², as well as for applications in bio-remediation, bioenergy, biofuels and bioelectronics. Since 2005, these nanowires have been thought to be type 4 pili composed solely of the PilA-N protein¹. However, previous structural analyses have demonstrated that, during extracellular electron transfer, cells do not produce pili but rather nanowires made up of the cytochromes OmcS^2,3 and OmcZ⁴. Here we show that Geobacter sulfurreducens binds PilA-N to PilA-C to assemble heterodimeric pili, which remain periplasmic under nanowire-producing conditions that require extracellular electron transfer⁵. Cryo-electron microscopy revealed that C-terminal residues of PilA-N stabilize its copolymerization with PilA-C (to form PilA-N-C) through electrostatic and hydrophobic interactions that position PilA-C along the outer surface of the filament. PilA-N-C filaments lack π-stacking of aromatic side chains and show a conductivity that is 20,000-fold lower than that of OmcZ nanowires. In contrast with surface-displayed type 4 pili, PilA-N-C filaments show structure, function and localization akin to those of type 2 secretion pseudopili⁶. The secretion of OmcS and OmcZ nanowires is lost when pilA-N is deleted and restored when PilA-N-C filaments are reconstituted. The substitution of pilA-N with the type 4 pili of other microorganisms also causes a loss of secretion of OmcZ nanowires. As all major phyla of prokaryotes use systems similar to type 4 pili, this nanowire translocation machinery may have a widespread effect in identifying the evolution and prevalence of diverse electron-transferring microorganisms and in determining nanowire assembly architecture for designing synthetic protein nanowires.