Metatranscriptomics Supports the Mechanism for Biocathode Electroautotrophy by "Candidatus Tenderia electrophaga"

SeqCode facilitates naming of South African rhizobia left in limbo

South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.

Performance of a combined electrotrophic and electrogenic biofilm operated under long-term, continuous cycling

OBJECTIVES

Evaluate electrochemically active biofilms as high energy density rechargeable microbial batteries toward providing persistent power in applications where traditional battery technology is limiting (, remote monitoring applications).

RESULTS

Here we demonstrated that an electrochemically active biofilm was able to store and release electrical charge for alternating charge/discharge cycles of up to 24 h periodicity (50% duty cycle) with no significant decrease in average current density (0.16 ± 0.04 A/m2) for over 600 days. However, operation at 24 h periodicity for > 50 days resulted in a sharp decrease in the current to nearly zero. This current crash was recoverable by decreasing the periodicity. Overall, the coulombic efficiency remained near unity within experimental error (102 ± 3%) for all of the tested cycling periods. Electrochemical characterization here suggests that electron transfer occurs through multiple routes, likely a mixture of direct and mediated mechanisms.

CONCLUSIONS

These results indicate that bidirectional electrogenic/electrotrophic biofilms are capable of efficient charge storage/release over a wide range of cycling frequency and may eventually enable development of sustainable, high energy density rechargeable batteries.

The impact of alloying element Cu on corrosion and biofilms of 316L stainless steel exposed to seawater

Copper-containing stainless steel (SS) has been reported to mitigate biofilms in industrial and clinical environments. However, the impact of copper released from copper-containing SS in natural seawater on biofilms and corrosion is still unclear. In this study, three kinds of 316L SS were immersed in natural seawater for 6 months, and the pitting depth decreased in the order: 316L-Cu SS (annealed) > 316L SS > 316L-Cu SS (aged). The biofilm thickness and number of sessile cells on the surface of 316L-Cu SS (annealed) and 316L SS were similar but notably greater than those of 316L-Cu SS (aged). Furthermore, the results of the community analysis indicated that the addition of copper in 316L-Cu SS (aged) reduced the diversity and richness of the microbial community, resulting in a significant reduction in the number of genera constituting the biofilms. Copper ions exhibit a broad-spectrum bactericidal effect, effectively reducing the abundance of dominant populations and microbial genera in the biofilms, thereby mitigating pitting corrosion induced by microorganisms. In addition, the PCoA scatter plot showed that time also played an important role in the regulation of microbial community structure.

Marine Biofilm Engineered to Produce Current in Response to Small Molecules

Engineered electroactive bacteria have potential applications ranging from sensing to biosynthesis. In order to advance the use of engineered electroactive bacteria, it is important to demonstrate functional expression of electron transfer modules in chassis adapted to operationally relevant conditions, such as non-freshwater environments. Here, we use the Shewanella oneidensis electron transfer pathway to induce current production in a marine bacterium, Marinobacter atlanticus, during biofilm growth in artificial seawater. Genetically encoded sensors optimized for use in Escherichia coli were used to control protein expression in planktonic and biofilm attached cells. Significant current production required the addition of menaquinone, which M. atlanticus does not produce, for electron transfer from the inner membrane to the expressed electron transfer pathway. Current through the S. oneidensis pathway in M. atlanticus was observed when inducing molecules were present during biofilm formation. Electron transfer was also reversible, indicating that electron transfer into M. atlanticus could be controlled. These results show that an operationally relevant marine bacterium can be genetically engineered for environmental sensing and response using an electrical signal.

NADH dehydrogenases drive inward electron transfer in Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a promising chassis organism for microbial electrosynthesis because it has a well-defined biochemical pathway (the Mtr pathway) that can connect extracellular electrodes to respiratory electron carriers inside the cell. We previously found that the Mtr pathway can be used to transfer electrons from a cathode to intracellular electron carriers and drive reduction reactions. In this work, we hypothesized that native NADH dehydrogenases form an essential link between the Mtr pathway and NADH in the cytoplasm. To test this hypothesis, we compared the ability of various mutant strains to accept electrons from a cathode and transfer them to an NADH-dependent reaction in the cytoplasm, reduction of acetoin to 2,3-butanediol. We found that deletion of genes encoding NADH dehydrogenases from the genome blocked electron transfer from a cathode to NADH in the cytoplasm, preventing the conversion of acetoin to 2,3-butanediol. However, electron transfer to fumarate was not blocked by the gene deletions, indicating that NADH dehydrogenase deletion specifically impacted NADH generation and did not cause a general defect in extracellular electron transfer. Proton motive force (PMF) is linked to the function of the NADH dehydrogenases. We added a protonophore to collapse PMF and observed that it blocked inward electron transfer to acetoin but not fumarate. Together these results indicate a link between the Mtr pathway and intracellular NADH. Future work to optimize microbial electrosynthesis in S. oneidensis MR-1 should focus on optimizing flux through NADH dehydrogenases.

In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent

Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.

Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge

The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.

Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb₃ oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO₂ fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.

"Electroactive biofilms: how microbial electron transfer enables bioelectrochemical applications"

Microbial biofilms are ubiquitous. In marine and freshwater ecosystems, microbe–mineral interactions sustain biogeochemical cycles, while biofilms found on plants and animals can range from pathogens to commensals. Moreover, biofouling and biocorrosion represent significant challenges to industry. Bioprocessing is an opportunity to take advantage of biofilms and harness their utility as a chassis for biocommodity production. Electrochemical bioreactors have numerous potential applications, including wastewater treatment and commodity production. The literature examining these applications has demonstrated that the cell–surface interface is vital to facilitating these processes. Therefore, it is necessary to understand the state of knowledge regarding biofilms’ role in bioprocessing. This mini-review discusses bacterial biofilm formation, cell–surface redox interactions, and the role of microbial electron transfer in bioprocesses. It also highlights some current goals and challenges with respect to microbe-mediated bioprocessing and future perspectives.

Engineering Wired Life: Synthetic Biology for Electroactive Bacteria

Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.

Microbial survival and growth on non-corrodible conductive materials

Biofilms growing aerobically on conductive substrates are often correlated with a positive, sustained shift in their redox potential. This phenomenon has a beneficial impact on microbial fuel cells by increasing their overall power output but can be detrimental when occurring on stainless steel by enhancing corrosion. The biological mechanism behind this potential shift is unresolved and a metabolic benefit to cells has not been demonstrated. Here, biofilms containing the electroautotroph 'Candidatus Tenderia electrophaga' catalysed a shift in the open circuit potential of graphite and indium tin oxide electrodes by >100 mV. Biofilms on open circuit electrodes had increased biomass and a significantly higher proportion of 'Ca. Tenderia electrophaga' compared to those on plain glass. Addition of metabolic inhibitors showed that living cells were required to maintain the more positive potential. We propose a model to describe these observations, in which 'Ca. Tenderia electrophaga' drives the shift in open circuit potential through electron uptake for oxygen reduction and CO₂ fixation. We further propose that the electrode is continuously recharged by oxidation of trace redox-active molecules in the medium at the more positive potential. A similar phenomenon is possible on natural conductive substrates in the environment.

Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle

Marinobacter spp. are opportunitrophs with a broad metabolic range including interactions with metals and electrodes. Marinobacter atlanticus strain CP1 was previously isolated from a cathode biofilm microbial community enriched from a sediment microbial fuel cell. Like other Marinobacter spp., M. atlanticus generates small amounts of electrical current when grown as a biofilm on an electrode, which is enhanced by the addition of redox mediators. However, the molecular mechanism resulting in extracellular electron transfer is unknown. Here, RNA-sequencing was used to determine changes in gene expression in electrode-attached and planktonic cells of M. atlanticus when grown at electrode potentials that enable current production (310 and 510 mV vs. SHE) compared to a potential that enables electron uptake (160 mV). Cells grown at current-producing potentials had increased expression of genes for molybdate transport, regardless of planktonic or attached lifestyle. Electrode-attached cells at current-producing potentials showed increased expression of the major export protein for the type VI secretion system. Growth at 160 mV resulted in an increase in expression of genes related to stress response and DNA repair including both RecBCD and the LexA/RecA regulatory network, as well as genes for copper homeostasis. Changes in expression of proteins with PEP C-terminal extracellular export motifs suggests that M. atlanticus is remodeling the biofilm matrix in response to electrode potential. These results improve our understanding of the physiological adaptations required for M. atlanticus growth on electrodes, and suggest a role for metal acquisition, either as a requirement for metal cofactors of redox proteins or as a possible electron shuttling mechanism.

Catalysis of the electrochemical oxygen reduction reaction (ORR) by animal and human cells

Animal cells from the Vero lineage and MRC5 human cells were checked for their capacity to catalyse the electrochemical oxygen reduction reaction (ORR). The Vero cells needed 72 hours’ incubation to induce ORR catalysis. The cyclic voltammetry curves were clearly modified by the presence of the cells with a shift of ORR of 50 mV towards positive potentials and the appearance of a limiting current (59 μA.cm^-2). The MRC5 cells induced considerable ORR catalysis after only 4 h of incubation with a potential shift of 110 mV but with large experimental deviation. A longer incubation time, of 24 h, made the results more reproducible with a potential shift of 90 mV. The presence of carbon nanotubes on the electrode surface or pre-treatment with foetal bovine serum or poly-D-lysine did not change the results. These data are the first demonstrations of the capability of animal and human cells to catalyse electrochemical ORR. The discussion of the possible mechanisms suggests that these pioneering observations could pave the way for electrochemical biosensors able to characterize the protective system of cells against oxidative stress and its sensitivity to external agents.

Microbial fuel cell-upflow biofilter coupling system for deep denitrification and power recovery: Efficiencies, bacterial succession and interactions

The excess organic carbon is often added to meet denitrification requirements during municipal wastewater treatment, resulting in the carbon waste and increased risk of secondary pollution. In this study, microbial fuel cell (MFC) was coupled with an up-flow denitrification biofilter (BF), and the long-term performances of denitrification and power output were investigated under the different carbon source concentration. With sodium acetate (NaAc) of 600 mg/L and 300 mg/L, the favorable denitrification efficiencies were obtained (98.60%) and the stable current output was maintained (0.44 mÃ0.48 mA). By supplying NaAc of 150 mg/L, the high denitrification efficiency remained in a high range (89.31%) and the current output maintained at 0.12 mA, while, the denitrification efficiency dropped to 71.34% without coupling MFC. Electron balance analysis indicated that both nitrate removal and electron recovery efficiencies were higher in MFC-BF than that in BF, verifying the improved denitrification and carbon utilization performance. Coupling MFC significantly altered the bacterial community structure and composition, and while, the diversified abundance and distribution of bacterial genera were observed at the different locations. Compared with BF, the more exoelectrogenic genera (Desulfobacterium, Trichococcus) and genera holding both denitrifying and electrogenic functions (Dechloromonas, Geobacter) were found dominated in MFC-BF. Instead, the dominating genera in BF were Dechloromonas, Desulfomicrobium, Acidovorax and etc. By coupling MFC, the more complex and diversified network and the closer interaction relationships between the dominant potential functional genera were found. The study provides a feasible approach to effectively improve the denitrification efficiency and organic carbon recovery for deep denitrification process.

Analysis of a Methanogen and an Actinobacterium Dominating the Thermophilic Microbial Community of an Electromethanogenic Biocathode

Electromethanogenesis refers to the bioelectrochemical synthesis of methane from CO₂ by biocathodes. In an electromethanogenic system using thermophilic microorganisms, metagenomic analysis along with quantitative real-time polymerase chain reaction and fluorescence in situ hybridization revealed that the biocathode microbiota was dominated by the methanogen Methanothermobacter sp. strain EMTCatA1 and the actinobacterium Coriobacteriaceae sp. strain EMTCatB1. RNA sequencing was used to compare the transcriptome profiles of each strain at the methane-producing biocathodes with those in an open circuit and with the methanogenesis inhibitor 2-bromoethanesulfonate (BrES). For the methanogen, genes related to hydrogenotrophic methanogenesis were highly expressed in a manner similar to those observed under H₂-limited conditions. For the actinobacterium, the expression profiles of genes encoding multiheme c-type cytochromes and membrane-bound oxidoreductases suggested that the actinobacterium directly takes up electrons from the electrode. In both strains, various stress-related genes were commonly induced in the open-circuit biocathodes and biocathodes with BrES. This study provides a molecular inventory of the dominant species of an electromethanogenic biocathode with functional insights and therefore represents the first multiomics characterization of an electromethanogenic biocathode.

Long-term operation of bio-catalyzed cathodes within continuous flow membrane-less microbial fuel cells

Microorganisms were observed to facilitate cathodic oxygen reduction and enhance cathode performance of microbial fuel cells (MFCs). However, the long-term activity and stability of bio-catalyzed cathode needs to be explored. This study evaluated the long-term performance of bio-catalyzed cathode and iron(II) phthalocyanine (FePc)-catalyzed cathode MFCs through effluent water quality, electricity production and electrochemical impedance spectroscopy (EIS) analysis under different scenarios, including conventional wastewater treatment and energy harvesting using a power management system (PMS). During the continuous operation, both systems demonstrated high chemical oxygen demand and ammonium removal, but bio-catalyzed cathode MFCs could achieve significantly better total nitrogen removal than FePc-catalyzed cathode MFCs. The FePc-coated cathode showed constant cathode potential during the entire operation period, but the biocathode showed varied but step-wise increased cathode potential to achieve more than 500 mV versus the standard hydrogen electrode, likely due to the gradual enrichment of biocathode biofilm. EIS analysis revealed that biocathode had higher ohmic resistance than bare carbon felt cathode but the microbial biofilm could largely decrease polarization resistance of cathode material. Microbial community analysis has shown the presence of nitrifying and denitrifying bacteria in the bio-catalyzed cathode biofilm. When connecting PMS, both bio-catalyzed cathode and FePc-catalyzed cathode MFCs successfully charged a capacitor, but the bio-catalyzed cathode MFC voltage significantly dropped to less than 100 mV after charging for 91 h, and gradually recovered when disconnecting PMS. This study has demonstrated the potential application of oxygen reduction bio-catalyzed cathode MFCs for continuous wastewater treatment and energy harvesting for long period of time.

Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria

Some bacteria and archaea have evolved the means to use extracellular electron donors and acceptors for energy metabolism, a phenomenon broadly known as extracellular electron transfer (EET). One such EET mechanism is the transmembrane electron conduit MtrCAB, which has been shown to transfer electrons derived from metabolic substrates to electron acceptors, like Fe(III) and Mn(IV) oxides, outside the cell. Although most studies of MtrCAB-mediated EET have been conducted in Shewanella oneidensis MR-1, recent investigations in Vibrio and Aeromonas species have revealed that the electron-donating proteins that support MtrCAB in Shewanella are not as representative as previously thought. This begs the question of how widespread the capacity for MtrCAB-mediated EET is, the changes it has accrued in different lineages, and where these lineages persist today. Here, we employed a phylogenetic and comparative genomics approach to identify the MtrCAB system across all domains of life. We found mtrCAB in the genomes of numerous diverse Bacteria from a wide range of environments, and the patterns therein strongly suggest that mtrCAB was distributed through both horizontal and subsequent vertical transmission, and with some cases indicating downstream modular diversification of both its core and accessory components. Our data point to an emerging evolutionary story about metal-oxidizing and -reducing metabolism, demonstrates that this capacity for EET has broad relevance to a diversity of taxa and the biogeochemical cycles they drive, and lays the foundation for further studies to shed light on how this mechanism may have coevolved with Earth's redox landscape. IMPORTANCE While many metabolisms make use of soluble, cell-permeable substrates like oxygen or hydrogen, there are other substrates, like iron or manganese, that cannot be brought into the cell. Some bacteria and archaea have evolved the means to directly "plug in" to such environmental electron reservoirs in a process known as extracellular electron transfer (EET), making them powerful agents of biogeochemical change and promising vehicles for bioremediation and alternative energy. Yet the diversity, distribution, and evolution of EET mechanisms are poorly constrained. Here, we present findings showing that the genes encoding one such EET system (mtrCAB) are present in a broad diversity of bacteria found in a wide range of environments, emphasizing the ubiquity and potential impact of EET in our biosphere. Our results suggest that these genes have been disseminated largely through horizontal transfer, and the changes they have accrued in these lineages potentially reflect adaptations to changing environments.

Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities

The mechanisms of extracellular electron transfer and the microbial taxa associated with the observed electroactivity are fundamental to oxygen-reducing microbial cathodes. Here we confirmed the apparent 'electroautotrophic' behavior of electroactive biofilms (EABs) grown on carbon electrodes at + 0.20V vs. Ag/AgCl under air. The EABs catalyzed O₂ electroreduction into water ─ as demonstrated by a rotating ring disc experiment ─ and performed quasi-reversible heterogeneous electron transfer (HET). By using electrodes of low surface capacitance, we report for the first time nonturnover redox peaks that are very likely intrinsic to the redox protein(s) performing the HET. Because the formal potential of redox proteins is pH-dependent, we investigated the evolution of characteristic potentials of the EABs with the solution pH: (i) open circuit potential, (ii) half-wave potential, and (iii) averaged peak potential of nonturnover cyclic voltammograms, which is presumably the formal potential of the primary electron acceptor(s) for the community. In addition to describing the redox thermodynamics behind HET, we suggest that the corresponding data provides an electrochemical fingerprint that could help in comparing the electroactivity of diverse microbial communities. The taxon with the highest relative abundance in our EABs was an unclassified member of the Gammaproteobacteria that was phylogenetically closely related to most other abundant unclassified Gammaproteobacteria commonly reported in EABs reducing O₂ at high potentials, further suggesting that those taxa are responsible for the bioelectroactivity. Phylogenetic and electrochemical similarities between reported EABs jointly support the hypothesis that similar biomolecular mechanisms may be responsible for this highly probable electroautotrophic metabolism.

Oxygen-reducing microbial cathodes in hypersaline electrolyte

Hypersaline electrolytes offer a way to boost the development of microbial fuel cells by overcoming the issue due to the low conductivity of the usual media. Efficient halotolerant bioanodes have already been designed but O₂-reducing cathodes remain a strong bottleneck. Here, O₂-reducing biocathodes were designed by using salt marsh sediment as the inoculum and a hypersaline media (45 g/L NaCl) of high conductivity (10.4 S m^-1). Current density up to 2.2 A m^-2 was reached from potential of +0.2 V/SCE. The efficiency of the biocathodes was correlated to the presence of Gammaproteobacteria strain(s) related to Thiohalobacter thiocyanaticus, which were considerably enriched in the best performing biocathodes. This work opens up new perspectives to overcome the O₂ reduction issue in hypersaline MFCs by designing efficient halotolerant microbial cathodes and pointing out the strains that should now be focused to improve them.

Large-scale switchable potentiostatically controlled/microbial fuel cell bioelectrochemical wastewater treatment system

The treatment of municipal wastewater is an energy-intensive process, with the delivery of oxygen as an electron acceptor accounting for a significant share of the total energy consumption. Microbial communities growing on polarized electrodes can facilitate wastewater treatment processes by exchanging electrons with the electrodes. As a new approach, we combined the use of polarized electrodes with microbial fuel cells (MFCs) to develop a switchable dual-mode bioelectrochemical wastewater treatment system. In this system, we first enriched microbial communities on polarized anodes and cathodes. After enrichment, the system was switched to either a self-powered MFC (SP-MFC) mode or a potentiostatically controlled (PC) mode. The system was evaluated at the laboratory scale (260 L, 4 anode and cathode pairs) and the pilot scale (1200 L, 16 anode and cathode pairs). PC and SP-MFC systems showed improved COD removal relative to control (41.6 ± 3.5 and 38.4 ± 3.1 vs 28.8 ± 2.1 mg L^-1 d^-1, respectively). The laboratory-scale system was operated without biological or electrical interruption for one year. Finally, specific enrichment of active microbial communities was observed on PC anodes in comparison to mixed-operation and non-polarized control anodes. The combined PC and SP-MFC systems allowed us to develop a sustainable and failure-free bioelectrochemical wastewater treatment system.

Nanoliter scale electrochemistry of natural and engineered electroactive bacteria

Bacterial extracellular electron transfer (EET) is envisioned for use in applied biotechnologies, necessitating electrochemical characterization of natural and engineered electroactive biofilms under conditions similar to the target application, including small-scale biosensing or biosynthesis platforms, which is often distinct from standard 100 mL-scale stirred-batch bioelectrochemical test platforms used in the laboratory. Here, we adapted an eight chamber, nanoliter volume (500 nL) electrochemical flow cell to grow biofilms of both natural (Biocathode MCL community, Marinobacter atlanticus, and Shewanella oneidensis MR1) or genetically modified (S. oneidensis ΔMtr and S. oneidensis ΔMtr + pLB2) electroactive bacteria on electrodes held at a constant potential. Maximum current density achieved by unmodified strains was similar between the nano- and milliliter-scale reactors. However, S. oneidensis biofilms engineered to activate EET upon exposure to 2,4-diacetylphloroglucinol (DAPG) produced current at wild-type levels in the stirred-batch reactor, but not in the nanoliter flow cell. We hypothesize this was due to differences in mass transport of DAPG, naturally-produced soluble redox mediators, and oxygen between the two reactor types. Results presented here demonstrate, for the first time, nanoliter scale chronoamperometry and cyclic voltammetry of a range of electroactive bacteria in a three-electrode reactor system towards development of miniaturized, and potentially high throughput, bioelectrochemical platforms.

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

BACKGROUND

Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

RESULTS

Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.

CONCLUSIONS

This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.

Electrochemical Bacterial Enrichment from Natural Seawater and Its Implications in Biocorrosion of Stainless-Steel Electrodes

Microbial electrochemical technologies have revealed the opportunity of electrochemical enrichment for specific bacterial groups that are able to catalyze reactions of interest. However, there are unsolved challenges towards their application under aggressive environmental conditions, such as in the sea. This study demonstrates the impact of surface electrochemical potential on community composition and its corrosivity. Electrochemical bacterial enrichment was successfully carried out in natural seawater without nutrient amendments. Experiments were carried out for ten days of exposure in a closed-flow system over 316L stainless steel electrodes under three different poised potentials (−150 mV, +100 mV, and +310 mV vs. Ag/AgCl). Weight loss and atomic force microscopy showed a significant difference in corrosion when +310 mV (vs. Ag/AgCl) was applied in comparison to that produced under the other tested potentials (and an unpoised control). Bacterial community analysis conducted using 16S rRNA gene profiles showed that poised potentials are more positive as +310 mV (vs. Ag/AgCl) resulted in strong enrichment for Rhodobacteraceae and Sulfitobacter. Hence, even though significant enrichment of the known electrochemically active bacteria from the Rhodobacteraceae family was accomplished, the resultant bacterial community could accelerate pitting corrosion in 316 L stainless steel, thereby compromising the durability of the electrodes and the microbial electrochemical technologies.

From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst

Coupling microbial electrosynthesis to renewable energy sources can provide a promising future technology for carbon dioxide conversion. However, this technology suffers from a limited number of suitable biocatalysts, resulting in a narrow product range. Here, we present the characterization of the first thermoacidophilic electroautotrophic community using chronoamperometric, metagenomic, and ¹³C-labeling analyses. The cathodic biofilm showed current consumption of up to -80 µA cm^-2 over a period of 90 days (-350 mV vs. SHE). Metagenomic analyses identified members of the genera Moorella, Desulfofundulus, Thermodesulfitimonas, Sulfolobus, and Acidianus as potential primary producers of the biofilm, potentially thriving via an interspecies sulfur cycle. Hydrogenases seem to be key for cathodic electron uptake. An isolation campaign led to a pure culture of a Knallgas bacterium from this community. Growth of this organism on cathodes led to increasing reductive currents over time. Transcriptomic analyses revealed a distinct gene expression profile of cells grown at a cathode. Moreover, pressurizable flow cells combined with optical coherence tomography allowed an in situ observation of cathodic biofilm growth. Autotrophic growth was confirmed via isotope analysis. As a natural polyhydroxybutyrate (PHB) producer, this novel species, Kyrpidia spormannii, coupled the production of PHB to CO₂ fixation on cathode surfaces.

Strategies for improving the electroactivity and specific metabolic functionality of microorganisms for various microbial electrochemical technologies

Electroactive microorganisms, which possess extracellular electron transfer (EET) capabilities, are the basis of microbial electrochemical technologies (METs) such as microbial fuel and electrolysis cells. These are considered for several applications ranging from the energy-efficient treatment of waste streams to the production of value-added chemicals and fuels, bioremediation, and biosensing. Various aspects related to the microorganisms, electrodes, separators, reactor design, and operational or process parameters influence the overall functioning of METs. The most fundamental and critical performance-determining factor is, however, the microorganism-electrode interactions. Modification of the electrode surfaces and microorganisms for optimizing their interactions has therefore been the major MET research focus area over the last decade. In the case of microorganisms, primarily their EET mechanisms and efficiencies along with the biofilm formation capabilities, collectively considered as microbial electroactivity, affect their interactions with the electrodes. In addition to electroactivity, the specific metabolic or biochemical functionality of microorganisms is equally crucial to the target MET application. In this article, we present the major strategies that are used to enhance the electroactivity and specific functionality of microorganisms pertaining to both anodic and cathodic processes of METs. These include simple physical methods based on the use of heat and magnetic field along with chemical, electrochemical, and growth media amendment approaches to the complex procedure-based microbial bioaugmentation, co-culture, and cell immobilization or entrapment, and advanced toolkit-based biofilm engineering, genetic modifications, and synthetic biology strategies. We further discuss the applicability and limitations of these strategies and possible future research directions for advancing the highly promising microbial electrochemistry-driven biotechnology.

Towards sustainable bioplastic production using the photoautotrophic bacterium Rhodopseudomonas palustris TIE-1

Bacterial synthesis of polyhydroxybutyrates (PHBs) is a potential approach for producing biodegradable plastics. This study assessed the ability of Rhodopseudomonas palustris TIE-1 to produce PHBs under various conditions. We focused on photoautotrophy using a poised electrode (photoelectroautotrophy) or ferrous iron (photoferroautotrophy) as electron donors. Growth conditions were tested with either ammonium chloride or dinitrogen gas as the nitrogen source. Although TIE-1's capacity to produce PHBs varied fairly under different conditions, photoelectroautotrophy and photoferroautotrophy showed the highest PHB electron yield and the highest specific PHB productivity, respectively. Gene expression analysis showed that there was no differential expression in PHB biosynthesis genes. This suggests that the variations in PHB accumulation might be post-transcriptionally regulated. This is the first study to systematically quantify the amount of PHB produced by a microbe via photoelectroautotrophy and photoferroautotrophy. This work could lead to sustainable bioproduction using abundant resources such as light, electricity, iron, and carbon dioxide.

Thermophiles; or, the Modern Prometheus: The Importance of Extreme Microorganisms for Understanding and Applying Extracellular Electron Transfer

Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures ∼50 – 125°C and do not use molecular oxygen (O₂) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteria capable of extracellular electron transfer (EET) are positioned close to the root of the Bacteria kingdom on the tree of life. On the contrary, EET in Gram-negative mesophilic bacteria is a relatively new phenomenon that is evolutionarily distinct from Gram-positive bacteria. This suggests that EET evolved separately in Gram-positive thermophiles and Gram-negative mesophiles, and that EET in these bacterial types is a result of a convergent evolutionary process leading to homoplasy. Thus, the study of dissimilatory metal reducing thermophiles provides a glimpse into some of Earth’s earliest forms of respiration. This will provide new insights for understanding biogeochemistry and the development of early Earth in addition to providing unique avenues for exploration and discovery in astrobiology. Lastly, the physiological composition of Gram-positive thermophiles, coupled with the kinetic and thermodynamic consequences of surviving at elevated temperatures, makes them ideal candidates for developing new mathematical models and designing innovative next-generation biotechnologies.

KEY CONCEPTS

Anaerobe: organism that does not require oxygen for growth.

Chemoautotroph: organism that obtains energy by oxidizing inorganic electron donors.

Convergent Evolution: process in which organisms which are not closely related independently evolve similar traits due to adapting to similar ecological niches and/or environments.

Dissimilatory Metal Reduction: reduction of a metal or metalloid that uses electrons from oxidized organic or inorganic electron donors.

Exoelectrogen: microorganism that performs dissimilatory metal reduction via extracellular electron transfer.

Extremophiles: organisms that thrive in physical or geochemical conditions that are considered detrimental to most life on Earth.

Homoplasy: a character shared by a set of species that is not shared by a common ancestor

Non-synonymous Substitutions (K_a): a substitution of a nucleotide that changes a codon sequence resulting in a change in the amino acid sequence of a protein.

Synonymous Substitutions (K_s): a substitution of a nucleotide that may change a codon sequence, but results in no change in the amino acid sequence of a protein.

Thermophiles: a specific group of extremophiles that survive and operate at temperatures ∼50–125°C.

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater

Microorganisms can increase the open-circuit potential of stainless steel immersed in seawater of several hundred millivolts in a phenomenon called ennoblement. It raises the chance of corrosion as the open-circuit potential may go over the pitting corrosion potential. Despite the large impact of the ennoblement, no unifying mechanisms have been described as responsible for the phenomenon. Here we show that the strict electrotroph bacterium "Candidatus Tenderia electrophaga" is detected as an ennoblement biomarker and is only present at temperatures at which we observe ennoblement. This bacterium was previously enriched in biocathode systems. Our results suggest that "Candidatus Tenderia electrophaga," and its previously described extracellular electron transfer metabolism coupled to oxygen reduction activity, could play a central role in modulating stainless steel open-circuit potential and consequently mediating ennoblement.

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal‐sulfides are wide‐spread in marine benthic habitats. At deep‐sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene‐based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate‐reducing Nitrospirae and sulfide‐oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr‐clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide‐oxidizers potentially facilitating metal‐sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.

Metagenomic insights into the ecology and physiology of microbes in bioelectrochemical systems

In bioelectrochemical systems (BESs), electrons are transferred between electrochemically active microbes (EAMs) and conductive materials, such as electrodes, via extracellular electron transfer (EET) pathways, and electrons thus transferred stimulate intracellular catabolic reactions. Catabolic and EET pathways have extensively been studied for several model EAMs, such as Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA, whereas it is also important to understand the ecophysiology of EAMs in naturally occurring microbiomes, such as those in anode biofilms in microbial fuel cells treating wastewater. Recent studies have exploited metagenomics and metatranscriptomics (meta-omics) approaches to characterize EAMs in BES-associated microbiomes. Here we review recent BES studies that used meta-omics approaches and show that these studies have discovered unexpected features of EAMs and deepened our understanding of functions and behaviors of microbes in BESs. It is desired that more studies will employ meta-omics approaches for advancing our knowledge on microbes in BESs.

Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community

Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture‐independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO₂ fixation to extracellular electron transfer and O₂ reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady‐state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing ‘Ca. Tenderia electrophaga’ was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.