Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA: expression in Escherichia coli confers the ability to reduce soluble Fe(III) chelates

Globally distributed marine Gemmatimonadota have unique genomic potentials

BACKGROUND

Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.

RESULTS

Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.

CONCLUSIONS

This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.

Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation

Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.

Automated in vivo enzyme engineering accelerates biocatalyst optimization

Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.

Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils

In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.

Metabolic regulation of Shewanella oneidensis for microbial electrosynthesis: From extracellular to intracellular

Shewanella oneidensis MR-1 (S. oneidensis MR-1) has been shown to benefit from microbial electrosynthesis (MES) due to its exceptional electron transfer efficiency. In this study, genes involved in both extracellular electron uptake (EEU) and intracellular CO2 conversion processes were examined and regulated to enhance MES performance. The key genes identified for MES in the EEU process were mtrB, mtrC, mtrD, mtrE, omcA and cctA. Overexpression of these genes resulted in 1.5-2.1 times higher formate productivity than that of the wild-type strains (0.63 mmol/(L·μg protein)), as 0.94-1.61 mmol/(L·μg protein). In the intracellular CO2 conversion process, overexpression of the nadE, nadD, nadR, nadV, pncC and petC genes increased formate productivity 1.3-fold-3.4-fold. Moreover, overexpression of the formate dehydrogenase genes fdhA1, fdhB1 and fdhX1 in modified strains led to a 2.3-fold-3.1-fold increase in formate productivity compared to wild-type strains. The co-overexpression of cctA, fdhA1 and nadV in the mutant strain resulted in 5.59 times (3.50 mmol/(L·μg protein)) higher formate productivity than that of the wild-type strains. These findings revealed that electrons of MES derived from the electrode were utilized in the energy module for synthesizing ATP and NADH, followed by the synthesis of formate in formate dehydrogenase by the combinatorial effects of ATP, NADH, electrons and CO2. The results provide new insights into the mechanism of MES in S. oneidensis MR-1 and pave the way for genetic improvements that could facilitate the further application of MES.

Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

BACKGROUND

Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.

RESULTS

Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.

CONCLUSIONS

This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.

Protein Interactions in Rhodopseudomonas palustris TIE-1 Reveal the Molecular Basis for Resilient Photoferrotrophic Iron Oxidation

Rhodopseudomonas palustris is an alphaproteobacterium with impressive metabolic versatility, capable of oxidizing ferrous iron to fix carbon dioxide using light energy. Photoferrotrophic iron oxidation is one of the most ancient metabolisms, sustained by the pio operon coding for three proteins: PioB and PioA, which form an outer-membrane porin-cytochrome complex that oxidizes iron outside of the cell and transfers the electrons to the periplasmic high potential iron-sulfur protein (HIPIP) PioC, which delivers them to the light-harvesting reaction center (LH-RC). Previous studies have shown that PioA deletion is the most detrimental for iron oxidation, while, the deletion of PioC resulted in only a partial loss. The expression of another periplasmic HiPIP, designated Rpal_4085, is strongly upregulated in photoferrotrophic conditions, making it a strong candidate for a PioC substitute. However, it is unable to reduce the LH-RC. In this work we used NMR spectroscopy to map the interactions between PioC, PioA, and the LH-RC, identifying the key amino acid residues involved. We also observed that PioA directly reduces the LH-RC, and this is the most likely substitute upon PioC deletion. By contrast, Rpal_4085 demontrated significant electronic and structural differences from PioC. These differences likely explain its inability to reduce the LH-RC and highlight its distinct functional role. Overall, this work reveals the functional resilience of the pio operon pathway and further highlights the use of paramagnetic NMR for understanding key biological processes.

Effects of carbon source on electricity generation and PAH removal in aquaculture sediment microbial fuel cells

Sediment microbial fuel cells (SMFCs) have been used for treating pollutants in sediment or overlying water. This study investigated the feasibility of constructing SMFCs under aquaculture conditions by employing indigenous carbohydrates as substrates to enhance the removal efficiency of polycyclic aromatic hydrocarbons (PAHs) in sediment, as well as the correlation between PAHs removal and electricity generation in SMFCs. The results showed that adding glucose could allow SMFCs to generate more electrical power and increase the removal efficiency of PAHs (by 57.2% for naphthalene, 41.3% for acenaphthene, and 36.5% for pyrene). In addition, starch enhanced PAHs removal by 49.9%, 35.8%, and 31.2%, respectively, whereas cellulose enhanced removal by 44.3%, 29.3%, and 26.9%, respectively. Pearson correlation coefficients between the level of electrical power generated and the removal masses of the three PAHs were 0.485, 0.830**, and 0.851**. Thus, the use of SMFCs could be an effective approach for PAH treatment in aquaculture, and the electrical power generated could be used as an in-situ indicator for the biodegradation rate of SMFCs.

Release of Pb adsorbed on graphene oxide surfaces under conditions of Shewanella putrefaciens metabolism

In this study, Pb(II) was used as a target heavy metal pollutant, and the metabolism of Shewanella putrefaciens (S. putrefaciens) was applied to achieve reducing conditions to study the effect of microbial reduction on lead that was preadsorbed on graphene oxide (GO) surfaces. The results showed that GO was transformed to its reduced form (r-GO) by bacteria, and this process induced the release of Pb(II) adsorbed on the GO surfaces. After 72 hr of exposure in an S. putrefaciens system, 5.76% of the total adsorbed Pb(II) was stably dispersed in solution in the form of a Pb(II)-extracellular polymer substance (EPS) complex, while another portion of Pb(II) released from GO-Pb(II) was observed as lead phosphate hydroxide (Pb₁₀(PO₄)₆(OH)₂) precipitates or adsorbed species on the surface of the cell. Additionally, increasing pH induced the stripping of oxidative debris (OD) and elevated the content of dispersible Pb(II) in aqueous solution under the conditions of S. putrefaciens metabolism. These research results provide valuable information regarding the migration of heavy metals adsorbed on GO under reducing conditions due to microbial metabolism.

Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion

The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate the binding of MtrA to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). The EET efficiency was found to be inversely correlated with the proximity of the insertion to the heme prosthetic groups. Mutants with decreased EET efficiencies also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular cytochrome MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET efficiencies. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III) respiration conditions correlated with anode reduction. The peptide insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for the regulation of EET.

Significance of Shewanella Species for the Phytoavailability and Toxicity of Arsenic-A Review

Simple Summary

The availability of some toxic heavy metals, such as arsenic (As), is related to increased human and natural activities. This type of metal availability in the environment is associated with various health and environmental issues. Such problems may arise due to direct contact with or consumption of plant products containing this metal in some of their parts. A microbial approach that employs a group of bacteria (Shewanella species) is proposed to reduce the negative consequences of the availability of this metal (As) in the environment. This innovative strategy can reduce As mobility, its spread, and uptake by plants in the environment. The benefits of this approach include its low cost and the possibility of not exposing other components of the environment to unfavourable consequences.

Abstract

The distribution of arsenic continues due to natural and anthropogenic activities, with varying degrees of impact on plants, animals, and the entire ecosystem. Interactions between iron (Fe) oxides, bacteria, and arsenic are significantly linked to changes in the mobility, toxicity, and availability of arsenic species in aquatic and terrestrial habitats. As a result of these changes, toxic As species become available, posing a range of threats to the entire ecosystem. This review elaborates on arsenic toxicity, the mechanisms of its bioavailability, and selected remediation strategies. The article further describes how the detoxification and methylation mechanisms used by Shewanella species could serve as a potential tool for decreasing phytoavailable As and lessening its contamination in the environment. If taken into account, this approach will provide a globally sustainable and cost-effective strategy for As remediation and more information to the literature on the unique role of this bacterial species in As remediation as opposed to conventional perception of its role as a mobiliser of As.

Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation

Denitrifying Betaproteobacteria play a key role in the anaerobic degradation of monoaromatic hydrocarbons. We performed a multi-omics study to better understand the metabolism of the representative organism Georgfuchsia toluolica strain G5G6 known as a strict anaerobe coupling toluene oxidation with dissimilatory nitrate and Fe(III) reduction. Despite the genomic potential for degradation of different carbon sources, we did not find sugar or organic acid transporters, in line with the inability of strain G5G6 to use these substrates. Using a proteomics analysis, we detected proteins of fumarate-dependent toluene activation, membrane-bound nitrate reductase, and key components of the metal-reducing (Mtr) pathway under both nitrate- and Fe(III)-reducing conditions. High abundance of the multiheme cytochrome MtrC implied that a porin-cytochrome complex was used for respiratory Fe(III) reduction. Remarkably, strain G5G6 contains a full set of genes for aerobic toluene degradation, and we detected enzymes of aerobic toluene degradation under both nitrate- and Fe(III)-reducing conditions. We further detected an ATP-dependent benzoyl-CoA reductase, reactive oxygen species detoxification proteins, and cytochrome c oxidase indicating a facultative anaerobic lifestyle of strain G5G6. Correspondingly, we found diffusion through the septa a substantial source of oxygen in the cultures enabling concurrent aerobic and anaerobic toluene degradation by strain G5G6.

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

Novel Microbial Groups Drive Productivity in an Archean Iron Formation

Deep subsurface environments are decoupled from Earth's surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C1-C4. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H2/CO2 or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.

A Hybrid Extracellular Electron Transfer Pathway Enhances the Survival of Vibrio natriegens

Vibrio natriegens is the fastest-growing microorganism discovered to date, making it a useful model for biotechnology and basic research. While it is recognized for its rapid aerobic metabolism, less is known about anaerobic adaptations in V. natriegens or how the organism survives when oxygen is limited. Here, we describe and characterize extracellular electron transfer (EET) in V. natriegens, a metabolism that requires movement of electrons across protective cellular barriers to reach the extracellular space. V. natriegens performs extracellular electron transfer under fermentative conditions with gluconate, glucosamine, and pyruvate. We characterized a pathway in V. natriegens that requires CymA, PdsA, and MtrCAB for Fe(III) citrate and Fe(III) oxide reduction, which represents a hybrid of strategies previously discovered in Shewanella and Aeromonas Expression of these V. natriegens genes functionally complemented Shewanella oneidensis mutants. Phylogenetic analysis of the inner membrane quinol dehydrogenases CymA and NapC in gammaproteobacteria suggests that CymA from Shewanella diverged from Vibrionaceae CymA and NapC. Analysis of sequenced Vibrionaceae revealed that the genetic potential to perform EET is conserved in some members of the Harveyi and Vulnificus clades but is more variable in other clades. We provide evidence that EET enhances anaerobic survival of V. natriegens, which may be the primary physiological function for EET in Vibrionaceae IMPORTANCE Bacteria from the genus Vibrio occupy a variety of marine and brackish niches with fluctuating nutrient and energy sources. When oxygen is limited, fermentation or alternative respiration pathways must be used to conserve energy. In sedimentary environments, insoluble oxide minerals (primarily iron and manganese) are able to serve as electron acceptors for anaerobic respiration by microorganisms capable of extracellular electron transfer, a metabolism that enables the use of these insoluble substrates. Here, we identify the mechanism for extracellular electron transfer in Vibrio natriegens, which uses a combination of strategies previously identified in Shewanella and Aeromonas We show that extracellular electron transfer enhanced survival of V. natriegens under fermentative conditions, which may be a generalized strategy among Vibrio spp. predicted to have this metabolism.

Mitigation effects of the microbial fuel cells on heavy metal accumulation in rice (Oryza sativa L.)

The increase in toxic heavy metal pollutants in rice paddies threatens food safety. There is an urgent need for lnow-cost remediation technology for immobilizing these trace metals. In this study, we showed that the application of the soil microbial fuel cell (sMFC) can greatly reduce the accumulation of Cd, Cu, Cr, and Ni in the rice plant tissue. In the sMFC treatment, the accumulation of Cd, Cu, Cr, and Ni in rice grains was 35.1%, 32.8%, 56.9% and 21.3% lower than the control, respectively. The reduction of these elements in the rice grain was due to their limited mobility in the soil porewater of soils employing the sMFC. The restriction in Cd, Cu, Cr, and Ni bioavailability was ascribed to the sMFC ability to immobilize trace metals through both biotic and abiotic means. The results suggest that the sMFC may be used as a promising technique to limit toxic trace metal bioavailability and translocation in the rice plants.

Microbial fuel cell system: a promising technology for pollutant removal and environmental remediation

The microbial fuel cell (MFC) system is a promising environmental remediation technology due to its simple compact design, low cost, and renewable energy producing. MFCs can convert chemical energy from waste matters to electrical energy, which provides a sustainable and environmentally friendly solution for pollutant degradations. In this review, we attempt to gather research progress of MFC technology in pollutant removal and environmental remediation. The main configurations and pollutant removal mechanism by MFCs are introduced. The research progress of MFC systems in pollutant removal and environmental remediation, including wastewater treatment, soil remediation, natural water and groundwater remediation, sludge and solid waste treatment, and greenhouse gas emission control, as well as the application of MFCs in environmental monitoring have been reviewed. Subsequently, the application of MFCs in environmental monitoring and the combination of MFCs with other technologies are described. Finally, the current limitations and potential future research has been demonstrated in this review.

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.

Soluble versions of outer membrane cytochromes function as exporters for heterologously produced cargo proteins

This study reveals that it is possible to secrete truncated versions of outer membrane cytochromes into the culture supernatant and that these proteins can provide a basis for the export of heterologously produced proteins. Different soluble and truncated versions of the outer membrane cytochrome MtrF were analyzed for their suitability to be secreted. A protein version with a very short truncation of the N-terminus to remove the recognition sequence for the addition of a lipid anchor is secreted efficiently to the culture supernatant, and moreover this protein could be further truncated by a deletion of 160 amino acid and still is detectable in the supernatant. By coupling a cellulase to this soluble outer membrane cytochrome, the export efficiency was measured by means of relative cellulase activity. We conclude that outer membrane cytochromes of S. oneidensis can be applied as transporters for the export of target proteins into the medium using the type II secretion pathway.

Kinetics of Intracellular Electron Generation in Shewanella oneidensis MR-1

Efficient utilization of bacterial bioresources requires quantitative evaluation of metabolic activity in living bacterial cells. Shewanella oneidensis MR-1 transfers electrons generated within the cell to the extracellular environment via the cytochrome complex in the inner/outer membranes and is one of the most useful bacteria for the recovery of metals, treatment of wastewater, and preparation of microbial fuel cells. Here, we performed a quantitative evaluation of electron generation based on individual enzyme reactions in S. oneidensis MR-1. By using potentiometric measurements, we have examined intracellular electron generation in bacterial suspensions of S. oneidensis supplemented with different carbon sources (formate, lactate, pyruvate, or acetyl coenzyme A) or ferricyanide, which was almost completely reduced to ferrocyanide during the incubation without affecting bacterial cell viability. The amount of electron generation strongly depended on the nature of the carbon source. Analysis of the obtained kinetic parameters of intracellular electron generation demonstrated that formate was the most effective carbon source, as it enabled 2.5-fold faster electron generation rate than other sources. We established that the respective contributions of lactate dehydrogenase, pyruvate dehydrogenase/pyruvate-formate-lyase, and tricarboxylic acid cycle to lactate metabolism were 62%, 31%, and 7.4%, correspondingly. Furthermore, we clarified that electrons may be generated at 1.6 × 10^-12 A s^-1 by ideal metabolism in a single living cell. These findings establish the basis for biological strategies of electron production and facilitate the utilization of S. oneidensis as a bioresource in practical applications, including energy production, environmental purification, and recovery of useful materials.

Biofabrication of Lysinibacillus sphaericus-reduced graphene oxide in three-dimensional polyacrylamide/carbon nanocomposite hydrogels for skin tissue engineering

The biological synthesis of reduced graphene oxide (rGO) from graphene oxide (GO) is an emerging phenomenon for developing biocompatible nanomaterials for its potential applications in nanomedicine. In this study, we demonstrated a simple, green, and non-toxic method for graphene synthesis using the live biomass of Lysinibacillus sphaericus as the reducing and stabilizing agent under ambient conditions. Ultraviolet-visible spectroscopic analysis confirmed the formation of graphene from GO suspension. X-ray diffraction studies showed the disappearance of the GO peak and the appearance of characteristic graphene broad peak at 2θ = 22.8°. Infrared analysis showed the decrease/disappearance of peaks corresponding to the oxygen-containing functionalities, and appearance of a peak at 1620 cm^-1 from unoxidized graphitic domains. Scanning electron microscopic images showed that L. sphaericus-reduced graphene oxide (L-rGO) contains aggregated graphene nanoflakes. Evaluation of the in vitro cytotoxicity of L-rGO nanosheets on human skin fibroblasts using the WST-1 assay did not show any significant effects after 24 h of exposure, which is indicative of biocompatibility. Polyacrylamide hydrogels with L-rGO were synthesized and used as scaffolds to support the growth and proliferation of skin fibroblasts. Cell viability assays and DAPI staining showed proliferation of fibroblasts and exhibited 83% of cell viability even after 28 days. Biofilm formation by Pseudomonas aeruginosa and Staphylococcus aureus was enhanced in nanocomposite hydrogels in the presence of 0.25 mg/mL GO and L-rGO in 48 h. Overall, this study showed that microbially-synthesized L-rGO can be used as a dopant in polymeric scaffolds for tissue engineering and highlighted their role in biofilm formation.

Microbial Electrosynthesis I: Pure and Defined Mixed Culture Engineering

In the past 6 years, microbial bioelectrochemistry has strongly increased in attraction and audience when expanding from mainly environmental technology applications to biotechnology. In particular, the promise to combine electrosynthesis with microbial catalysis opens attractive approaches for new sustainable redox-cofactor recycling, redox-balancing, or even biosynthesis processes. Much of this promise is still not fulfilled, but it has opened and fueled entirely new research areas in this discipline. Activities in designing, tailoring, and applying specific microbial catalysts as pure or defined co-cultures for defined target bioproductions are greatly accelerating. This chapter gives an overview of the current progress as well as the emerging trends in molecular and ecological engineering of defined microbial biocatalysts to prepare them for evolving microbial electrosynthesis processes. In addition, the multitude of microbial electrosynthetic processes with complex undefined mixed cultures is covered by ter Heijne et al. (Adv Biochem Eng Biotechnol. https://doi.org/10.1007/10_2017_15 , 2017). Graphical Abstract.

Polarity and Molecular Weight of Compost-Derived Humic Acids Impact Bio-dechlorination of Pentachlorophenol

Compost-derived humic acids (HAs) as cheap soil conditioners have potential to facilitate pentachlorophenol (PCP) bio-dechlorination but lack proof and studies. To clarify this, PCP bio-dechlorination mediated by compost-derived HAs under Fe(III) reduction conditions was investigated. Reverse phase high-performance liquid chromatography and high-performance size exclusion chromatography were employed to identify the functional components within compost-derived HAs. Our results showed that compost-derived HAs facilitated the bio-dechlorination of PCP under Fe(III) reduction conditions, and four kinds of byproducts were detected during the process. The relatively hydrophilic and high molecular weight (MW) components within compost-derived HAs presented significant associations with the concentration of byproducts from bio-dechlorination of PCP in Fe₂O₃ reduction conditions. In contrast, the hydrophobic and low MW components were the main functional components for PCP bio-dechlorination in Fe₃O₄ reduction environment. These findings clarified the effects of polarity and MW of compost-derived HAs on PCP bio-dechlorination, giving clues to optimize composting technology to utilize compost products for in situ contamination remediation of paddy soil.

Improvement of the electron transfer rate in Shewanella oneidensis MR-1 using a tailored periplasmic protein composition

Periplasmic c-type cytochromes are essential for the electron transport between the cytoplasmic membrane bound menquinol oxidase CymA and the terminal ferric iron reductase MtrABC in the outer membrane of Shewanella oneidensis cells. Either STC or FccA are necessary for periplasmic electron transfer. We followed the hypothesis that the elimination of potential competing reactions in the periplasm and the simultaneous overexpression of STC (cctA) could lead to an accelerated electron transfer to the cell surface. The genes nrfA, ccpA, napB and napA were replaced by cctA. This led to a 1.7-fold increased ferric iron reduction rate and a 23% higher current generation in a bioelectrochemical system. Moreover, the quadruple mutant had a higher periplasmic flavin content. Further deletion of fccA and its replacement by cctA resulted in a strain with ferric iron reduction rates similar to the wild type and a lower concentration of periplasmic flavin compared to the quadruple mutant. A transcriptomic analysis revealed that the quadruple mutant had a 3.7-fold higher cctA expression which could not be further increased by the replacement of fccA. This work indicates that a synthetic adaptation of Shewanella towards extracellular respiration holds potential for increased respiratory rates and consequently higher current densities.

Engineering an electroactive Escherichia coli for the microbial electrosynthesis of succinate from glucose and CO2

BACKGROUND

Electrochemical energy is a key factor of biosynthesis, and is necessary for the reduction or assimilation of substrates such as CO₂. Previous microbial electrosynthesis (MES) research mainly utilized naturally electroactive microbes to generate non-specific products.

RESULTS

In this research, an electroactive succinate-producing cell factory was engineered in E. coli T110(pMtrABC, pFccA-CymA) by expressing mtrABC, fccA and cymA from Shewanella oneidensis MR-1, which can utilize electricity to reduce fumarate. The electroactive T110 strain was further improved by incorporating a carbon concentration mechanism (CCM). This strain was fermented in an MES system with neutral red as the electron carrier and supplemented with HCO₃⁺, which produced a succinate yield of 1.10 mol/mol glucose-a 1.6-fold improvement over the parent strain T110.

CONCLUSIONS

The strain T110(pMtrABC, pFccA-CymA, pBTCA) is to our best knowledge the first electroactive microbial cell factory engineered to directly utilize electricity for the production of a specific product. Due to the versatility of the E. coli platform, this pioneering research opens the possibility of engineering various other cell factories to utilize electricity for bioproduction.

A brief survey of the "cytochromome"

Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.

Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili

Biosensors detect signals using biological sensing components such as redox enzymes and biological cells. Although cellular versatility can be beneficial for different applications, limited stability and efficiency in signal transduction at electrode surfaces represent a challenge. Recent studies have shown that the Mtr electron conduit from Shewanella oneidensis MR-1 can be produced in Escherichia coli to generate an exoelectrogenic model system with well-characterized genetic tools. However, means to specifically immobilize this organism at solid substrates as electroactive biofilms have not been tested previously. Here, we show that mannose-binding Fim pili can be produced in exoelectrogenic E. coli and can be used to selectively attach cells to a mannose-coated material. Importantly, cells expressing fim genes retained current production by the heterologous Mtr electron conduit. Our results demonstrate the versatility of the exoelectrogenic E. coli system and motivate future work that aims to produce patterned biofilms for bioelectronic devices that can respond to various biochemical signals.

Bacterial response to graphene oxide and reduced graphene oxide integrated in agar plates

There are contradictory reports in the literature regarding the anti-bacterial activity of graphene, graphene oxide (GO) and reduced graphene oxide (rGO). This controversy is mostly due to variations in key parameters of the reported experiments, like: type of substrate, form of graphene, number of layers, type of solvent and most importantly, type of bacteria. Here, we present experimental data related to bacterial response to GO and rGO integrated in solid agar-based nutrient plates-a standard set-up for bacterial growth that is widely used by microbiologists. Bacillus subtilis and Pseudomonas aeruginosa strains were used for testing bacterial growth. We observed that plate-integrated rGO showed strong anti-bacterial activity against both bacterial species. By contrast, plate-integrated GO was harmless to both bacteria. These results reinforce the notion that the response of bacteria depends critically on the type of graphene material used and can vary dramatically from one bacterial strain to another, depending on bacterial physiology.

Microbial Mineralization of Montmorillonite in Low-Permeability Oil Reservoirs for Microbial Enhanced Oil Recovery

Microbial mineralization (corrosion, decomposition, and weathering) has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of biomineralization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe(III)-reducing microbial strains under anaerobic growth conditions on Ca-montmorillonite. The mineralogical characterization of Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy, and energy-dispersive spectrometry. Results showed that the microbial strains could efficiently reduce Fe(III) at an optimal rate of 71%, alter the crystal lattice structure of the lamella to promote interlayer cation exchange, and efficiently inhibit Ca-montmorillonite swelling at a rate of 48.9%.IMPORTANCE Microbial mineralization is ubiquitous in the natural environment. Microbes in low-permeability reservoirs are able to facilitate alteration of the structure and phase of the Fe-poor minerals by reducing Fe(III) and inhibiting clay swelling, which is still poorly studied. This study aimed to reveal the interaction mechanism between Fe(III)-reducing bacterial strains and Ca-montmorillonite under anaerobic conditions and to investigate the extent and rates of Fe(III) reduction and phase changes with their activities. Application of Fe(III)-reducing bacteria will provide a new way to inhibit clay swelling, to elevate reservoir permeability, and to reduce pore throat resistance after water flooding for enhanced oil recovery in low-permeability reservoirs.

Electrochemical Study on the Extracellular Electron Transfer Pathway from Shewanella Strain Hac319 to Electrodes

Shewanella can transfer electrons to various extracellular electron acceptors. We electrochemically investigated the pathway of extracellular electron transfer from Shewanella strain Hac319 to electrodes. A resting cell suspension of Shewanella strain Hac319 containing lactate produced a steady-state sigmoidal wave in the presence of flavin mononucleotide (FMN) in cyclic voltammetry, but not in the absence of FMN. A harvested cell suspension without cell-washing also produced a similar catalytic wave without any external addition of free FMN. The midpoint potentials of the two sigmoidal waves were identical to the redox potential of free FMN. The data indicate that FMN secreted from the Shewanella strain Hac319 works as an electron-transfer mediator from the cell to electrodes. An addition of cyanide to a resting cell suspension of Shewanella strain Hac319 increased the rate of the FMN reduction in the presence of lactate, while it decreased the respiration rate. By considering the fact that cyanide is coordinated to the heme moiety of hemoproteins and shifts the redox potential to the negative potential side, the data indicate that the electron derived from lactate is predominantly transferred in a down-hill mode from an electron donor with a redox potential more negative than that of FMN without going through outer membrane cytochromes c molecules.

A Hierarchically Modified Graphite Cathode with Au Nanoislands, Cysteamine, and Au Nanocolloids for Increased Electricity-Assisted Production of Isobutanol by Engineered Shewanella oneidensis MR-1

It is necessary to understand the surface structural effects of electrodes on the bioalcohol productivity of Shewanella oneidensis MR-1, but this research area has not been deeply explored. Here, we report that the electricity-assisted isobutanol productivity of Shewanella oneidensis MR-1::pJL23 can be enhanced by sequentially modifying a graphite felt (GF) surface with Au nanoislands (Au), cysteamine (NH₂), and Au nanoparticles (Au NPs). After bacteria were incubated for 50 h with the unmodified GF under various electrode potentials (vs Ag/AgCl), the bacterial isobutanol concentrations increased from 2.9 ± 1 mg/L under no electricity supply to a maximum of 5.9 ± 1 mg/L at -0.6 V. At this optimum electrode potential, the concentrations continued increasing to 9.1 ± 1, 14 ± 2, and 27 ± 2 mg/L when the GF electrodes were modified with Au, NH₂-Au, and Au NP-NH₂-Au, respectively. We further studied how each surface structure affected the bacterial adsorptions, current profiles, and biofilms' electrochemical performances. In particular, these modifications induced the adsorption of elongated bacteria, with the amount dependent on the electrode structure. In the presence of electric supply, the amount of elongated bacteria further increased. We also found that the NH₂-Au-GF and Au NP-NH₂-Au-GF electrodes themselves could increase the concentrations to 11 ± 0.3 and 12 ± 2 mg/L, respectively, upon the bacterial incubation without electricity. Among the electrodes tested, the contribution of electricity to the bacterial isobutanol production was the greatest with the Au NP-NH₂-Au-GF electrode. After 96 h of incubation, the concentration increased to 72 ± 2 mg/L, which was 4.7 and 3.7 times the previously reported values obtained without and with electricity, respectively.

Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering

More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering.

Observation of dielectric universalities in albumin, cytochrome C and Shewanella oneidensis MR-1 extracellular matrix

The electrodynamics of metals is well understood within the Drude conductivity model; properties of insulators and semiconductors are governed by a gap in the electronic states. But there is a great variety of disordered materials that do not fall in these categories and still respond to external field in an amazingly uniform manner. At radiofrequencies delocalized charges yield a frequency-independent conductivity σ 1(ν) whose magnitude exponentially decreases while cooling. With increasing frequency, dispersionless conductivity starts to reveal a power-law dependence σ 1(ν)∝ν s with s < 1 caused by hopping charge carriers. At low temperatures, such Universal Dielectric Response can cross over to another universal regime with nearly constant loss ε″∝σ1/ν = const. The powerful research potential based on such universalities is widely used in condensed matter physics. Here we study the broad-band (1-1012 Hz) dielectric response of Shewanella oneidensis MR-1 extracellular matrix, cytochrome C and serum albumin. Applying concepts of condensed matter physics, we identify transport mechanisms and a number of energy, time, frequency, spatial and temperature scales in these biological objects, which can provide us with deeper insight into the protein dynamics.

Microbial fuel cell-photoelectrocatalytic cell combined system for the removal of azo dye wastewater

In this study, a novel parallel circuit microbial fuel cell-photoelectrocatalytic cell (MFC-PEC) combined system was established to enhance azo dye removal. Results showed that this system had synergistic effects compared with the MFC alone. In the MFC part, a 56% decrease in chemical oxygen demand (COD) and 85% decolorization were achieved, and further reduced by 25% and 12% in the PEC part where titania nanotube functioned as the photoelectrode. For one thing, the PEC raised the maximum current of the MFC by 14.2%, which facilitated COD removal and decolorization in the MFC and promoted adenosine triphosphate (ATP) level of anode microorganisms, for another, this system significantly increased the dye removal in the PEC. Besides, cyclic voltammograms illustrated intermediate products degradation in this system. Hence, the system achieved marked deep decolorization and rapid toxic intermediate products degradation of high concentration azo dyes.

Deep-Sea Bacterium Shewanella piezotolerans WP3 Has Two Dimethyl Sulfoxide Reductases in Distinct Subcellular Locations

Dimethyl sulfoxide (DMSO) acts as a substantial sink for dimethyl sulfide (DMS) in deep waters and is therefore considered a potential electron acceptor supporting abyssal ecosystems. Shewanella piezotolerans WP3 was isolated from west Pacific deep-sea sediments, and two functional DMSO respiratory subsystems are essential for maximum growth of WP3 under in situ conditions (4°C/20 MPa). However, the relationship between these two subsystems and the electron transport pathway underlying DMSO reduction by WP3 remain unknown. In this study, both DMSO reductases (type I and type VI) in WP3 were found to be functionally independent despite their close evolutionary relationship. Moreover, immunogold labeling of DMSO reductase subunits revealed that the type I DMSO reductase was localized on the outer leaflet of the outer membrane, whereas the type VI DMSO reductase was located within the periplasmic space. CymA, a cytoplasmic membrane-bound tetraheme c-type cytochrome, served as a preferential electron transport protein for the type I and type VI DMSO reductases, in which type VI accepted electrons from CymA in a DmsE- and DmsF-independent manner. Based on these results, we proposed a core electron transport model of DMSO reduction in the deep-sea bacterium S. piezotolerans WP3. These results collectively suggest that the possession of two sets of DMSO reductases with distinct subcellular localizations may be an adaptive strategy for WP3 to achieve maximum DMSO utilization in deep-sea environments.IMPORTANCE As the dominant methylated sulfur compound in deep oceanic water, dimethyl sulfoxide (DMSO) has been suggested to play an important role in the marine biogeochemical cycle of the volatile anti-greenhouse gas dimethyl sulfide (DMS). Two sets of DMSO respiratory systems in the deep-sea bacterium Shewanella piezotolerans WP3 have previously been identified to mediate DMSO reduction under in situ conditions (4°C/20 MPa). Here, we report that the two DMSO reductases (type I and type VI) in WP3 have distinct subcellular localizations, in which type I DMSO reductase is localized to the exterior surface of the outer membrane and type VI DMSO reductase resides in the periplasmic space. A core electron transport model of DMSO reduction in WP3 was constructed based on genetic and physiological data. These results will contribute to a comprehensive understanding of the adaptation mechanisms of anaerobic respiratory systems in benthic microorganisms.

Engineering a Native Inducible Expression System in Shewanella oneidensis to Control Extracellular Electron Transfer

Shewanella oneidensis MR-1 is a model organism for understanding extracellular electron transport, in which cells transfer intracellular electrons to an extracellular terminal electron acceptor such as insoluble minerals or poised electrodes. Biotechnological applications exploiting the respiratory capabilities of Shewanella species have led to their proposed use in wastewater treatment, bioremediation, and remote sensors. Transcriptional regulation tools can be used to rationally engineer S. oneidensis, optimizing performance in biotechnological applications, introducing new capabilities, or investigating physiology. Engineered gene expression in S. oneidensis has primarily involved the use of foreign regulatory systems from Escherichia coli. Here we characterize a native S. oneidensis pathway that can be used to induce gene expression with trimethylamine N-oxide, then engineer strains in which extracellular electron transfer is controlled by this compound. The ability to induce this pathway was assessed by measuring iron reduction over time and by analyzing anodic current produced by cells grown in bioreactors.

Remediation of PAH polluted soils using a soil microbial fuel cell: Influence of electrode interval and role of microbial community

The soil microbial fuel cells (SMFCs) were constructed to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs). With a maximum power density of 12.1mWm^-2 and an internal resistance of 470Ω, a closed SMFC showed electricity generation comparable to that by an open SMFC after 175days of operation and meanwhile increased the removal rates of anthracene, phenanthrene, and pyrene to 54.2±2.7%, 42.6±1.9% and 27.0±2.1% from 20.8±1.1%, 17.3±1.2% and 11.7±0.9%, respectively, by the open SMFC. Both the electricity generation and the removal of PAHs increased with the decreased electrode interval. When the electrode interval ranged between 4cm and 10cm, the more closely the electrodes were positioned, the more efficient the electricity generation and removal of PAHs became. Dominated by the genus of Geobacter, the SMFC was enriched in electrogenic bacteria at the anode surface, and the growth of certain microbes other than electrogenic bacteria in the soil was improved by electrical stimulation. This finding reveals the critical mechanism underlying electricity generation and improved the removal of PAHs.

A Synthetic Biology Approach to Engineering Living Photovoltaics

The ability to electronically interface living cells with electron accepting scaffolds is crucial for the development of next-generation biophotovoltaic technologies. Although recent studies have focused on engineering synthetic interfaces that can maximize electronic communication between the cell and scaffold, the efficiency of such devices is limited by the low conductivity of the cell membrane. This review provides a materials science perspective on applying a complementary, synthetic biology approach to engineering membrane-electrode interfaces. It focuses on the technical challenges behind the introduction of foreign extracellular electron transfer pathways in bacterial host cells and the past and future efforts to engineer photosynthetic organisms with artificial electron-export capabilities for biophotovoltaic applications. The article highlights advances in engineering protein-based, electron-exporting conduits in a model host organism, E. coli, before reviewing state-of-the-art biophotovoltaic technologies that use both unmodified and bioengineered photosynthetic bacteria with improved electron transport capabilities. A thermodynamic analysis is used to propose an energetically feasible pathway for extracellular electron transport in engineered cyanobacteria and identify metabolic bottlenecks amenable to protein engineering techniques. Based on this analysis, an engineered photosynthetic organism expressing a foreign, protein-based electron conduit yields a maximum theoretical solar conversion efficiency of 6-10% without accounting for additional bioengineering optimizations for light-harvesting.

Denitrification and Nitrate-Dependent Fe(II) Oxidation in Various Pseudogulbenkiania Strains

Pseudogulbenkiania is a relatively recently characterized genus within the order Neisseriales, class Betaproteobacteria. This genus contains several strains that are capable of anaerobic, nitrate-dependent Fe(II) oxidation (NDFO), a geochemically important reaction for nitrogen and iron cycles. In the present study, we examined denitrification functional gene diversities within this genus, and clarified whether other Pseudogulbenkiania sp. strains perform denitrification and NDFO. Seventy strains were analyzed, including two type strains, a well-characterized NDFO strain, and 67 denitrifying strains isolated from various rice paddy fields and rice-soybean rotation fields in Japan. We also attempted to identify the genes responsible for NDFO by mutagenesis. Our comprehensive analysis showed that all Pseudogulbenkiania strains tested performed denitrification and NDFO; however, we were unable to obtain NDFO-deficient denitrifying mutants in our mutagenesis experiment. This result suggests that Fe(II) oxidation in these strains is not enzymatic, but is caused by reactive N-species that are formed during nitrate reduction. Based on the results of the comparative genome analysis among Pseudogulbenkiania sp. strains, we identified low sequence similarity within the nos gene as well as different gene arrangements within the nos gene cluster, suggesting that nos genes were horizontally transferred. Since Pseudogulbenkiania sp. strains have been isolated from various locations around the world, their denitrification and NDFO abilities may contribute significantly to nitrogen and iron biogeochemical cycles.

Hardwiring microbes via direct interspecies electron transfer: mechanisms and applications

Multicellular microbial communities are important catalysts in engineered systems designed to treat wastewater, remediate contaminated sediments, and produce energy from biomass. Understanding the interspecies interactions within them is therefore essential to design effective processes. The flow of electrons within these communities is especially important in the determination of reaction possibilities (thermodynamics) and rates (kinetics). Conventional models of electron transfer incorporate the diffusion of metabolites generated by one organism and consumed by a second, frequently referred to as mediated interspecies electron transfer (MIET). Evidence has emerged in the last decade that another method, called direct interspecies electron transfer (DIET), may occur between organisms or in conjunction with electrically conductive materials. Recent research has suggested that DIET can be stimulated in engineered systems to improve desired treatment goals and energy recovery in systems such as anaerobic digesters and microbial electrochemical technologies. In this review, we summarize the latest understanding of DIET mechanisms, the associated microorganisms, and the underlying thermodynamics. We also critically examine approaches to stimulate DIET in engineered systems and assess their effectiveness. We find that in most cases attempts to promote DIET in mixed culture systems do not yield the improvements expected based on defined culture studies. Uncertainties of other processes that may be co-occurring in real systems, such as contaminant sorption and biofilm promotion, need to be further investigated. We conclude by identifying areas of future research related to DIET and its application in biological treatment processes.

CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli

Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. Here we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits, the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe2O3 (s) reducing conditions. Overall, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.

Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei

A facultative anaerobic bacterium, designated as strain SCS5, was isolated from the anodic biofilm of a mediator-less microbial fuel cell using acetate as the electron donor and α-FeOOH as the electron acceptor. The isolate was Gram-negative, motile, and shaped as short rods (0.9-1.3 μm in length and 0.4-0.5 μm in width). A phylogenetic analysis of the 16S rRNA, gyrB, and rpoD genes suggested that strain SCS5 belonged to the Aeromonas genus in the Aeromonadaceae family and exhibited the highest 16S rRNA gene sequence similarity (99.45%) with Aeromonas jandaei ATCC 49568. However, phenotypic, cellular fatty acid profile, and DNA G+C content analyses revealed that there were some distinctions between strain SCS5 and the type strain A. jandaei ATCC 49568. The optimum growth temperature, pH, and NaCl (%) for strain SCS5 were 35°C, 7.0, and 0.5% respectively. The DNA G+C content of strain SCS5 was 59.18%. The isolate SCS5 was capable of reducing insoluble iron oxide (α-FeOOH) and transferring electrons to extracellular material (the carbon electrode). The electrochemical activity of strain SCS5 was corroborated by cyclic voltammetry and a Raman spectroscopic analysis. The cyclic voltammogram of strain SCS5 revealed two pairs of oxidation-reduction peaks under anaerobic and aerobic conditions. In contrast, no redox pair was observed for A. jandaei ATCC 49568. Thus, isolated strain SCS5 is a novel exoelectrogenic bacterium phylogenetically related to A. jandaei, but shows distinct electrochemical activity from its close relative A. jandaei ATCC 49568.