Necessity of electrically conductive pili for methanogenesis with magnetite stimulation

Magnetite Alters the Metabolic Interaction between Methanogens and Sulfate-Reducing Bacteria

It is known that the presence of sulfate decreases the methane yield in the anaerobic digestion systems. Sulfate-reducing bacteria can convert sulfate to hydrogen sulfide competing with methanogens for substrates such as H2 and acetate. The present work aims to elucidate the microbial interactions in biogas production and assess the effectiveness of electron-conductive materials in restoring methane production after exposure to high sulfate concentrations. The addition of magnetite led to a higher methane content in the biogas and a sharp decrease in the level of hydrogen sulfide, indicating its beneficial effects. Furthermore, the rate of volatile fatty acid consumption increased, especially for butyrate, propionate, and acetate. Genome-centric metagenomics was performed to explore the main microbial interactions. The interaction between methanogens and sulfate-reducing bacteria was found to be both competitive and cooperative, depending on the methanogenic class. Microbial species assigned to the Methanosarcina genus increased in relative abundance after magnetite addition together with the butyrate oxidizing syntrophic partners, in particular belonging to the Syntrophomonas genus. Additionally, Ruminococcus sp. DTU98 and other species assigned to the Chloroflexi phylum were positively correlated to the presence of sulfate-reducing bacteria, suggesting DIET-based interactions. In conclusion, this study provides new insights into the application of magnetite to enhance the anaerobic digestion performance by removing hydrogen sulfide, fostering DIET-based syntrophic microbial interactions, and unraveling the intricate interplay of competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, influenced by the specific methanogenic group.

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.

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.

Graphene: An Antibacterial Agent or a Promoter of Bacterial Proliferation?

Graphene materials (GMs) are being investigated for multiple microbiological applications because of their unique physicochemical characteristics including high electrical conductivity, large specific surface area, and robust mechanical strength. In the last decade, studies on the interaction of GMs with bacterial cells appear conflicting. On one side, GMs have been developed to promote the proliferation of electroactive bacteria on the surface of electrodes in bioelectrochemical systems or to accelerate interspecies electron transfer during anaerobic digestion. On the other side, GMs with antibacterial properties have been synthesized to prevent biofilm formation on membranes for water treatment, on medical equipment, and on tissue engineering scaffolds. In this review, we discuss the mechanisms and factors determining the positive or negative impact of GMs on bacteria. Furthermore, we examine the bacterial growth-promoting and antibacterial applications of GMs and debate their practicability.

Sparking Anaerobic Digestion: Promoting Direct Interspecies Electron Transfer to Enhance Methane Production

Anaerobic digestion was one of the first bioenergy strategies developed, yet the interactions of the microbial community that is responsible for the production of methane are still poorly understood. For example, it has only recently been recognized that the bacteria that oxidize organic waste components can forge electrical connections with methane-producing microbes through biologically produced, protein-based, conductive circuits. This direct interspecies electron transfer (DIET) is faster than interspecies electron exchange via diffusive electron carriers, such as H2. DIET is also more resilient to perturbations such as increases in organic load inputs or toxic compounds. However, with current digester practices DIET rarely predominates. Improvements in anaerobic digestion associated with the addition of electrically conductive materials have been attributed to increased DIET, but experimental verification has been lacking. This deficiency may soon be overcome with improved understanding of the diversity of microbes capable of DIET, which is leading to molecular tools for determining the extent of DIET. Here we review the microbiology of DIET, suggest molecular strategies for monitoring DIET in anaerobic digesters, and propose approaches for re-engineering digester design and practices to encourage DIET.

Graphene: An Antibacterial Agent or a Promoter of Bacterial Proliferation?

Graphene materials (GMs) are being investigated for multiple microbiological applications because of their unique physicochemical characteristics including high electrical conductivity, large specific surface area, and robust mechanical strength. In the last decade, studies on the interaction of GMs with bacterial cells appear conflicting. On one side, GMs have been developed to promote the proliferation of electroactive bacteria on the surface of electrodes in bioelectrochemical systems or to accelerate interspecies electron transfer during anaerobic digestion. On the other side, GMs with antibacterial properties have been synthesized to prevent biofilm formation on membranes for water treatment, on medical equipment, and on tissue engineering scaffolds. In this review, we discuss the mechanisms and factors determining the positive or negative impact of GMs on bacteria. Furthermore, we examine the bacterial growth-promoting and antibacterial applications of GMs and debate their practicability.

In Vivo Molecular Insights into Syntrophic Geobacter Aggregates

Direct interspecies electron transfer (DIET) has been considered as a novel and highly efficient strategy in both natural anaerobic environments and artificial microbial fuel cells. A syntrophic model consisting of Geobacter metallireducens and Geobacter sulfurreducens was studied in this work. We conducted in vivo molecular mapping of the outer surface of the syntrophic community as the interface of nutrients and energy exchange. System for Analysis at the Liquid Vacuum Interface combined with time-of-flight secondary ion mass spectrometry was employed to capture the molecular distribution of syntrophic Geobacter communities in the living and hydrated state. Principal component analysis with selected peaks revealed that syntrophic Geobacter aggregates were well differentiated from other control samples, including syntrophic planktonic cells, pure cultured planktonic cells, and single population biofilms. Our in vivo imaging indicated that a unique molecular surface was formed. Specifically, aromatic amino acids, phosphatidylethanolamine components, and large water clusters were identified as key components that favored the DIET of syntrophic Geobacter aggregates. Moreover, the molecular changes in depths of the Geobacter aggregates were captured using dynamic depth profiling. Our findings shed new light on the interface components supporting electron transfer in syntrophic communities based on in vivo molecular imaging.

Baltic Sea methanogens compete with acetogens for electrons from metallic iron

Microbially induced corrosion of metallic iron (Fe⁰)-containing structures is an environmental and economic hazard. Methanogens are abundant in low-sulfide environments and yet their specific role in Fe⁰ corrosion is poorly understood. In this study, Sporomusa and Methanosarcina dominated enrichments from Baltic Sea methanogenic sediments that were established with Fe⁰ as the sole electron donor and CO₂ as the electron acceptor. The Baltic-Sporomusa was phylogenetically affiliated to the electroactive acetogen S. silvacetica. Baltic-Sporomusa adjusted rapidly to growth on H₂. On Fe⁰, spent filtrate enhanced growth of this acetogen suggesting that it was using endogenous enzymes to retrieve electrons and produce acetate. Previous studies have proposed that acetate produced by acetogens can feed commensal acetoclastic methanogens such as Methanosarcina. However, Baltic-methanogens could not generate methane from acetate, plus the decrease or absence of acetogens stimulated their growth. The decrease in numbers of Sporomusa was concurrent with an upsurge in Methanosarcina and increased methane production, suggesting that methanogens compete with acetogens for electrons from Fe⁰. Furthermore, Baltic-methanogens were unable to use H₂ (1.5 atm) for methanogenesis and were inhibited by spent filtrate additions, indicating that enzymatically produced H₂ is not a favorable electron donor. We hypothesize that Baltic-methanogens retrieve electrons from Fe⁰ via a yet enigmatic direct electron uptake mechanism.

Stimulation of Smithella-dominating propionate oxidation in a sediment enrichment by magnetite and carbon nanotubes

Recent studies have shown that application of conductive materials including magnetite and carbon nanotubes (CNTs) can promote the methanogenic decomposition of short-chain fatty acids and even more complex organic matter in anaerobic digesters and natural habitats. The linkage to microbial identity and the mechanisms, however, remain poorly understood. Here, we evaluate the effects of nanoscale magnetite (nanoFe₃ O₄ ) and multiwalled CNTs on the syntrophic oxidation of propionate in an enrichment obtained from lake sediment. The microbial populations were composed mainly of Smithella, Syntrophomonas, Methanosaeta, Methanosarcina and Methanoregula. In addition to acetate, butyrate was transiently accumulated indicating that propionate was oxidized by Smithella via the dismutation pathway and part of the leaked butyrate was oxidized by Syntrophomonas. Propionate oxidation and CH₄ production were significantly accelerated in the presence of nanoFe₃ O₄ and CNTs. While propionate oxidation was suppressed upon H₂ application and suspended completely upon formate application in the control, this suppressive effect was substantially compromised in the presence of nanoFe₃ O₄ and CNTs. The tests on hydrogenotrophic methanogenesis of a pure culture methanogen and of the enrichment culture without propionate showed negative effect by both materials. The positive effect of nanoFe₃ O₄ disappeared when it was insulated by surface-coating with silica. Observations made with fluorescence in situ hybridization and scanning electron microscope indicated the extensive formation of microbial cell-conductive material mixture aggregates. Our results suggest that direct interspecies electron transfer is likely activated by the conductive materials and operates in concert with H₂ /formate-dependent electron transfer for syntrophic propionate oxidation in the sediment enrichment.

Anaerobic Bacterial Immobilization and Removal of Toxic Sb(III) Coupled With Fe(II)/Sb(III) Oxidation and Denitrification

Antimony (Sb) pollution is a worldwide problem. In some anoxic sites, such as Sb mine drainage and groundwater sediment, the Sb concentration is extremely elevated. Therefore, effective Sb remediation strategies are urgently needed. In contrast to microbial aerobic antimonite [Sb(III)] oxidation, the mechanism of microbial anaerobic Sb(III) oxidation and the effects of nitrate and Fe(II) on the fate of Sb remain unknown. In this study, we discovered the mechanism of anaerobic Sb(III) oxidation coupled with Fe(II) oxidation and denitrification in the facultative anaerobic Sb(III) oxidizer Sinorhizobium sp. GW3. We observed the following: (1) under anoxic conditions with nitrate as the electron acceptor, strain GW3 was able to oxidize both Fe(II) and Sb(III) during cultivation; (2) in the presence of Fe(II), nitrate and Sb(III), the anaerobic Sb(III) oxidation rate was remarkably enhanced, and Fe(III)-containing minerals were produced during Fe(II) and Sb(III) oxidation; (3) qRT-PCR, gene knock-out and complementation analyses indicated that the arsenite oxidase gene product AioA plays an important role in anaerobic Sb(III) oxidation, in contrast to aerobic Sb(III) oxidation; and (4) energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and powder X-ray diffraction (XRD) analyses revealed that the microbially produced Fe(III) minerals were an effective chemical oxidant responsible for abiotic anaerobic Sb(III) oxidation, and the generated Sb(V) was adsorbed or coprecipitated on the Fe(III) minerals. This process included biotic and abiotic factors, which efficiently immobilize and remove soluble Sb(III) under anoxic conditions. The findings revealed a significantly novel development for understanding the biogeochemical Sb cycle. Microbial Sb(III) and Fe(II) oxidation coupled with denitrification has great potential for bioremediation in anoxic Sb-contaminated environments.

Geobacter Strains Expressing Poorly Conductive Pili Reveal Constraints on Direct Interspecies Electron Transfer Mechanisms

Cytochrome-to-cytochrome electron transfer and electron transfer along conduits of multiple extracellular magnetite grains are often proposed as strategies for direct interspecies electron transfer (DIET) that do not require electrically conductive pili (e-pili). However, physical evidence for these proposed DIET mechanisms has been lacking. To investigate these possibilities further, we constructed Geobacter metallireducens strain Aro-5, in which the wild-type pilin gene was replaced with the aro-5 pilin gene that was previously shown to yield poorly conductive pili in Geobacter sulfurreducens strain Aro-5. G. metallireducens strain Aro-5 did not reduce Fe(III) oxide and produced only low current densities, phenotypes consistent with expression of poorly conductive pili. Like G. sulfurreducens strain Aro-5, G. metallireducens strain Aro-5 displayed abundant outer surface cytochromes. Cocultures initiated with wild-type G. metallireducens as the electron-donating strain and G. sulfurreducens strain Aro-5 as the electron-accepting strain grew via DIET. However, G. metallireducens Aro-5/G. sulfurreducens wild-type cocultures did not. Cocultures initiated with the Aro-5 strains of both species grew only when amended with granular activated carbon (GAC), a conductive material known to be a conduit for DIET. Magnetite could not substitute for GAC. The inability of the two Aro-5 strains to adapt for DIET in the absence of GAC suggests that there are physical constraints on establishing DIET solely through cytochrome-to-cytochrome electron transfer or along chains of magnetite. The finding that DIET is possible with electron-accepting partners that lack highly conductive pili greatly expands the range of potential electron-accepting partners that might participate in DIET.IMPORTANCE DIET is thought to be an important mechanism for interspecies electron exchange in natural anaerobic soils and sediments in which methane is either produced or consumed, as well as in some photosynthetic mats and anaerobic digesters converting organic wastes to methane. Understanding the potential mechanisms for DIET will not only aid in modeling carbon and electron flow in these geochemically significant environments but will also be helpful for interpreting meta-omic data from as-yet-uncultured microbes in DIET-based communities and for designing strategies to promote DIET in anaerobic digesters. The results demonstrate the need to develop a better understanding of the diversity of types of e-pili in the microbial world to identify potential electron-donating partners for DIET. Novel methods for recovering as-yet-uncultivated microorganisms capable of DIET in culture will be needed to further evaluate whether DIET is possible without e-pili in the absence of conductive materials such as GAC.