Effect of NAD+-dependent formate dehydrogenase on anaerobic respiration of Shewanella oneidensis MR-1

An expression plasmid was constructed in order to carry out heterologous expression of the gene of the NAD⁺-dependent formate dehydrogenase (FDH) from methylotrophic bacterium Moraxella sp. in the cells of Shewanella oneidensis MR-1 under aerobic and anaerobic conditions. In both modes of cell cultivation, recombinant FDH activity was revealed in the cell lysate of the transformants. In the medium with la? tate as a carbon source, the rate of anaerobic respiration determined as the rate of conversion of fumarate (the electron acceptor) to succinate was higher in the transformant with recombinant FDH. Anaerobic cultivation of the FDH-containing transformant of S. oneidensis MR-1 in a microbial fuel cell (MFC) revealed increased current density.     

Mutants of an electrogenic bacterium <Emphasis Type="Italic">Shewanella oneidensis</Emphasis> MR-1 with increased reducing activity

The mutants of Shewanella oneidensis MR-1 resistant to fosfomycin, a toxic analogue of phosphoenolpyruvate, were obtained. The mutants exhibited increased reducing activity and higher rates of lactate utilization. A correlation was shown between the rates of metabolism of oxidized substrates and the rate of reduction of methylene blue, a mediator of electron transport. The mutants of S. oneidensis MR-1 may be used in microbial fuel cells for intensification of energy production from organic compounds.     

Current Production and Metal Oxide Reduction by Shewanella oneidensis MR-1 Wild Type and Mutants

Shewanella oneidensis MR-1 is a gram-negative facultative anaerobe capable of utilizing a broad range of electron acceptors, including several solid substrates. S. oneidensis MR-1 can reduce Mn(IV) and Fe(III) oxides and can produce current in microbial fuel cells. The mechanisms that are employed by S. oneidensis MR-1 to execute these processes have not yet been fully elucidated. Several different S. oneidensis MR-1 deletion mutants were generated and tested for current production and metal oxide reduction. The results showed that a few key cytochromes play a role in all of the processes but that their degrees of participation in each process are very different. Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1.     

Microfabricated Microbial Fuel Cell Arrays Reveal Electrochemically Active Microbes

Microbial fuel cells (MFCs) are remarkable “green energy” devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated.     

Glycerol-fed microbial fuel cell with a co-culture of <Emphasis Type="Italic">Shewanella oneidensis</Emphasis> MR-1 and <Emphasis Type="Italic">Klebsiella pneumonae</Emphasis> J2B

Glycerol is an attractive feedstock for bioenergy and bioconversion processes but its use in microbial fuel cells (MFCs) for electrical energy recovery has not been investigated extensively. This study compared the glycerol uptake and electricity generation of a co-culture of Shewanella oneidensis MR-1 and Klebsiella pneumonia J2B in a MFC with that of a single species inoculated counterpart. Glycerol was metabolized successfully in the co-culture MFC (MFC-J&M) with simultaneous electricity production but it was not utilized in the MR-1 only MFC (MFC-M). A current density of 10 mA/m² was obtained while acidic byproducts (lactate and acetate) were consumed in the co-culture MFC, whereas they are accumulated in the J2B-only MFC (MFC-J). MR-1 was distributed mainly on the electrode in MFC-J&M, whereas most of the J2B was observed in the suspension in the MFC-J reactor, indicating that the co-culture of both strains provides an ecological driving force for glycerol utilization using the electrode as an electron acceptor. This suggests that a co-culture MFC can be applied to electrical energy recovery from glycerol, which was previously known as a refractory substrate in a bioelectrochemical system.     

Uridine phosphorylase from Shewanella oneidensis MR-1: Heterological expression, regulation, transcription, and properties

A DNA fragment containing a promoter-operator and structural parts of the uridine phosphorylase gene from Shewanella oneidensis MR-1 was cloned. Cross-heterological expression of the udp genes from Sh. oneidensis MR-1 and Escherichia coli under the control of authentic regulatory regions is shown. The UDP protein accumulates in an active form in the cytoplasmic fraction of cells. The recombinant UDP protein from Sh. oneidensis MR-1 obtained by heterological expression was isolated and characterized. E. coli udp gene promoter activity was observed during heterological expression in Sh. oneidensis MR-1 cells under both aerobic and anaerobic conditions.     

A microfluidic microbial fuel cell fabricated by soft lithography

Here we report a new microfluidic microbial fuel cell (MFC) platform built by soft-lithography techniques. The MFC design includes a unique sub-5 μL polydimethylsiloxane soft chamber featuring carbon cloth electrodes and microfluidic delivery of electrolytes. Bioelectricity was generated using Shewanella oneidensis MR-1 cultivated on either complex organic substrates or lactate-based minimal medium. These micro-MFCs exhibited fast start-ups, reproducible current generation, and enhanced power densities up to 62.5 W m⁻³ that represents the best result for sub-100 μL MFCs. Systematic comparisons of custom-made MFC reactors having different chamber sizes indicate volumetric power density is inversely correlated with chamber size in our systems: i.e., the smaller the chamber, the higher the power density is achieved.     

The role of riboflavin in decolourisation of Congo red and bioelectricity production using <Emphasis Type="Italic">Shewanella oneidensis</Emphasis>-MR1 under MFC and non-MFC conditions

Dissimilatory metal reducing bacteria can exchange electrons extracellularly and hold great promise for their use in simultaneous wastewater treatment and electricity production. This study investigated the role of riboflavin, an electron carrier, in the decolourisation of Congo red in microbial fuel cells (MFCs) using Shewanella oneidensis MR-1 as a model organism. The contribution of the membrane-bound protein MtrC to the decolourisation process was also investigated. Within the range of riboflavin concentrations tested, 20 µM was found to be the best with >95% of the dye (initial concentration 200 mg/L) decolourised in MFCs within 50 h compared to 90% in the case where no riboflavin was added. The corresponding maximum power density was 45 mW/m². There was no significant difference in the overall decolourisation efficiencies of Shewanela oneidensis MR-1 ΔMtrC mutants compared to the wild type. However, in terms of power production the mutant produced more power (P_max 76 mW/m²) compared to the wild type (P_max 46 mW/m²) which was attributed to higher levels of riboflavin secreted in solution. Decolourisation efficiencies in non-MFC systems (anaerobic bottles) were similar to those under MFC systems indicating that electricity generation in MFCs does not impair dye decolourisation efficiencies. The results suggest that riboflavin enhances both decolourisation of dyes and simultaneous electricity production in MFCs.     

The utility of Shewanella japonica for microbial fuel cells

Shewanella-containing microbial fuel cells (MFCs) typically use the fresh water wild-type strain Shewanella oneidensis MR-1 due to its metabolic diversity and facultative oxidant tolerance. However, S. oneidensis MR-1 is not capable of metabolizing polysaccharides for extracellular electron transfer. The applicability of Shewanella japonica (an agar-lytic Shewanella strain) for power applications was analyzed using a diverse array of carbon sources for current generation from MFCs, cellular physiological responses at an electrode surface, biofilm formation, and the presence of soluble extracellular mediators for electron transfer to carbon electrodes. Critically, air-exposed S. japonica utilizes biosynthesized extracellular mediators for electron transfer to carbon electrodes with sucrose as the sole carbon source.     

Promotion of Iron Oxide Reduction and Extracellular Electron Transfer in Shewanella oneidensis by DMSO

The dissimilatory metal reducing bacterium Shewanella oneidensis MR-1, known for its capacity of reducing iron and manganese oxides, has great environmental impacts. The iron oxides reducing process is affected by the coexistence of alternative electron acceptors in the environment, while investigation into it is limited so far. In this work, the impact of dimethyl sulphoxide (DMSO), a ubiquitous chemical in marine environment, on the reduction of hydrous ferric oxide (HFO) by S. oneidensis MR-1 was investigated. Results show that DMSO promoted HFO reduction by both wild type and ΔdmsE, but had no effect on the HFO reduction by ΔdmsB, indicating that such a promotion was dependent on the DMSO respiration. With the DMSO dosing, the levels of extracellular flavins and omcA expression were significantly increased in WT and further increased in ΔdmsE. Bioelectrochemical analysis show that DMSO also promoted the extracellular electron transfer of WT and ΔdmsE. These results demonstrate that DMSO could stimulate the HFO reduction through metabolic and genetic regulation in S. oneidensis MR-1, rather than compete for electrons with HFO. This may provide a potential respiratory pathway to enhance the microbial electron flows for environmental and engineering applications.     

Developing a base-editing system to expand the carbon source utilization spectra of Shewanella oneidensis MR-1 for enhanced pollutant degradation

Shewanella oneidensis MR-1, a model strain of exoelectrogenic bacteria (EEB), plays a key role in environmental bioremediation and bioelectrochemical systems because of its unique respiration capacity. However, only a narrow range of substrates can be utilized by S. oneidensis MR-1 as carbon sources, resulting in its limited applications. In this study, a rapid, highly efficient, and easily manipulated base-editing system pCBEso was developed by fusing a Cas9 nickase (Cas9n (D10A)) with the cytidine deaminase rAPOBEC1 in S. oneidensis MR-1. The C-to-T conversion of suitable C within the base-editing window could be readily and efficiently achieved by the pCBEso system without requiring double-strand break or repair templates. Moreover, double-locus simultaneous editing was successfully accomplished with an efficiency of 87.5%. With this tool, the key genes involving in N-acetylglucosamine (GlcNAc) or glucose metabolism in S. oneidensis MR-1 were identified. Furthermore, an engineered strain with expanded carbon source utilization spectra was constructed and exhibited a higher degradation rate for multiple organic pollutants (i.e., azo dyes and organoarsenic compounds) than the wild-type when glucose or GlcNAc was used as the sole carbon source. Such a base-editing system could be readily applied to other EEB. This study not only enhances the substrate utilization and pollutant degradation capacities of S. oneidensis MR-1 but also accelerates the robust construction of engineered strains for environmental bioremediation.     

A derivative of the menaquinone precursor 1,4-dihydroxy-2-naphthoate is involved in the reductive transformation of carbon tetrachloride by aerobically grown<Emphasis Type="Italic"> Shewanella oneidensis</Emphasis> MR-1

Transformation of carbon tetrachloride (CT) by Shewanella oneidensis MR-1 has been proposed to involve the anaerobic respiratory-chain component menaquinone. To investigate this hypothesis a series of menaquinone mutants were constructed. The menF mutant is blocked at the start of the menaquinone biosynthetic pathway. The menB, menA and menG mutants are all blocked towards the end of the pathway, being unable to produce 1,4-dihydroxy-2-naphthoic acid (DHNA), demethyl-menaquinone and menaquinone , respectively. Aerobically grown mutants unable to produce the menaquinone precursor DHNA (menF and menB mutants) showed a distinctly different CT transformation profile than mutants able to produce DHNA but unable to produce menaquinone (menA and menG mutants). While DHNA did not reduce CT in an abiotic assay, the addition of DHNA to the menF and menB mutants restored normal CT transformation activity. We conclude that a derivative of DHNA, that is distinct from menaquinone, is involved in the reduction of CT by aerobically grown S. oneidensis MR-1. When cells were grown anaerobically with trimethylamine-N-oxide as the terminal electron acceptor, all the menaquinone mutants showed wild-type levels of CT reduction. We conclude that S. oneidensis MR-1 produces two different factors capable of dehalogenating CT. The factor produced under anaerobic growth conditions is not a product of the menaquinone biosynthetic pathway.     

Decolorization and detoxification of a sulfonated triphenylmethane dye aniline blue by Shewanella oneidensis MR-1 under anaerobic conditions

In this work, the extracellular decolorization of aniline blue, a sulfonated triphenylmethane dye, by Shewanella oneidensis MR-1 was confirmed. S. oneidensis MR-1 showed a high capacity for decolorizing aniline blue even at a concentration of up to 1,000 mg/l under anaerobic conditions. Maximum decolorization efficiency appeared at pH?7.0 and 30 °C. Lactate was a better candidate of electron donor for the decolorization of aniline blue. The addition of nitrate, hydrous ferric oxide, or trimethylamine N-oxide all could cause a significant decline of decolorization efficiency. The Mtr respiratory pathway was found to be involved into the decolorization of aniline blue by S. oneidensis MR-1. The toxicity evaluation through phytotoxicity and genotoxicity showed that S. oneidensis MR-1 could decrease the toxicity of aniline blue during the decolorization process. Thus, this work may facilitate a better understanding on the degradation mechanisms of the triphenylmethane dyes by Shewanella and is beneficial to their application in bioremediation.     

Shewanella oneidensis MR-1 Msh pilin proteins are involved in extracellular electron transfer in microbial fuel cells

Shewanella is a microbial genus that can oxidize lactate for the reduction of insoluble electron acceptors. This reduction is possible by either direct (cell-surface interaction, nanowires) or indirect (soluble redox mediators) mechanisms. However, the actual molecular identification of a nanowire has not been determined. Through mutational studies, Shewanella oneidensis MR-1 was analyzed for its ability to transfer electrons to an electrode after deletion of the structural pilin genes (ΔmshA-D) or the entire biosynthetic expression system (ΔmshH-Q) of one of its pilin complexes (Msh type IV pilus gene locus). The complete removal of the Msh complex (ΔmshH-Q) significantly decreased the current generated from a fuel cell compared to MR-1. However, the mutant with only extracellular Msh structural proteins removed (ΔmshA-D) was able to generate 80% of the current compared to MR-1. Thus, the intracellular and membrane bound Msh biogenesis complex is a pathway for extracellular electron transfer in S. oneidensis MR-1.     

Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1

We performed whole-genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine its possible role in regulating gene expression and other cellular processes. Single-molecule real-time (SMRT) sequencing revealed extensive methylation of adenine (N6mA) throughout the genome. These methylated bases were located in five sequence motifs, including three novel targets for type I restriction/modification enzymes. The sequence motifs targeted by putative methyltranferases were determined via SMRT sequencing of gene knockout mutants. In addition, we found that S. oneidensis MR-1 cultures grown under various culture conditions displayed different DNA methylation patterns. However, the small number of differentially methylated sites could not be directly linked to the much larger number of differentially expressed genes under these conditions, suggesting that DNA methylation is not a major regulator of gene expression in S. oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of replication indicates that DNA methylation may regulate genome replication in a manner similar to that seen in Escherichia coli. Furthermore, comparative analyses suggest that many Gammaproteobacteria, including all members of the Shewanellaceae family, may also utilize DNA methylation to regulate genome replication.     

Analyses of Current-Generating Mechanisms of Shewanella loihica PV-4 and Shewanella oneidensis MR-1 in Microbial Fuel Cells

Although members of the genus Shewanella have common features (e.g., the presence of decaheme c-type cytochromes [c-cyts]), they are widely variable in genetic and physiological features. The present study compared the current-generating ability of S. loihica PV-4 in microbial fuel cells (MFCs) with that of well-characterized S. oneidensis MR-1 and examined the roles of c-cyts in extracellular electron transfer. We found that strains PV-4 and MR-1 exhibited notable differences in current-generating mechanisms. While the MR-1 MFCs maintained a constant current density over time, the PV-4 MFCs continued to increase in current density and finally surpassed the MR-1 MFCs. Coulombic efficiencies reached 26% in the PV-4 MFC but 16% in the MR-1 MFCs. Although both organisms produced quinone-like compounds, anode exchange experiments showed that anode-attached cells of PV-4 produced sevenfold more current than planktonic cells in the same chamber, while planktonic cells of MR-1 produced twice the current of the anode-attached cells. Examination of the genome sequence indicated that PV-4 has more c-cyt genes in the metal reductase-containing locus than MR-1. Mutational analysis revealed that PV-4 relied predominantly on a homologue of the decaheme c-cyt MtrC in MR-1 for current generation, even though it also possesses two homologues of the decaheme c-cyt OmcA in MR-1. These results suggest that current generation in a PV-4 MFC is in large part accomplished by anode-attached cells, in which the MtrC homologue constitutes the main path of electrons toward the anode.Some species of dissimilatory metal-reducing bacteria (DMRB) are able to reduce solid metal oxides as terminal electron acceptors and generate currents in microbial fuel cells (MFCs) (2, 11, 14, 30, 46). Although mixed cultures are often used in MFC experiments (13), studies seeking a mechanistic understanding of electron transfer to electrode surfaces typically target pure cultures of such DMRB, due to the complexity in microbial communities. Presently, two model DMRB, Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA (2, 3, 12, 18, 31), are used in most investigations.S. oneidensis MR-1 is a metabolically diverse DMRB that has been studied extensively for its potential use in bioremediation applications. For this reason, MR-1 was the first Shewanella species to have its genome completely sequenced and annotated (10). In addition, since the first report in 1999 when this microorganism was shown to have the ability to transfer electrons to the electrode without an exogenously added mediator (14), it has also become one of the model organisms for the study of electron transfer mechanisms in MFCs.Although the molecular mechanisms for extracellular electron transfer have not yet been elucidated fully, c-type cytochromes (c-cyts) appear to be the key cellular components involved in this process (38). In S. oneidensis MR-1, OmcA and MtrC are outer membrane (OM), decaheme c-cyts that are considered to be involved in the direct (directly attached) electron transfer to solid metal oxides and anodes of MFCs (9, 20, 22, 23, 47). Several pieces of evidence suggest that OmcA and MtrC form a complex and act in a cooperative manner (33, 37, 42), and these results correlate with the fact that the genes encoding these proteins constitute an operon-like cluster in the chromosome (1). It has also been shown that MtrC and OmcA have overlapping functions as terminal reductases of metal oxides (25, 38). OmcA and MtrC are also present on the surface of nanowires and may be involved in the long-range transfer of electrons (8). In addition to direct electron transfer, MR-1 has the ability to produce water-soluble electron-shuttle compounds (quinones and flavins) that are involved in the mediated electron transfer from cells to distant solid electron acceptors (metal oxides or MFC anodes) (21, 27, 44).Recently, the genome sequences of nearly 20 Shewanella strains have been completed and annotated, opening the door to study the diversity of their extracellular electron transfer mechanisms. A comparison of their genomes has shown that although they have some consensus OM c-cyt genes, variations exist in the number and order of these genes in their metal reductase-containing loci (6). One such species is S. loihica strain PV-4, which was recently isolated from an iron-rich microbial mat near a deep-sea hydrothermal vent located on the Loihi Seamount in Hawaii (7, 32). The phenotypic and phylogenetic characteristics of PV-4 were determined, with a subsequent study focusing on the metal reduction and iron biomineralization capabilities of this bacterium (32). Initial experiments performed in our laboratory revealed that PV-4 developed a c-cyt-dependent deep red color that was much more striking than that of strain MR-1 when grown anaerobically with iron oxide as the terminal electron acceptor (26). This allowed us to assume that PV-4 could have a high extracellular electron transfer ability. Accordingly, the present study evaluated the current-producing ability of strain PV-4 in MFCs and examined the roles of some c-cyts in extracellular electron transfer. Special attention was paid to the comparison of PV-4 with MR-1 to reveal differences in mechanisms for extracellular electron transfer. We report herein differences between these strains in the roles of OM c-cyts for extracellular electron transfer, the behaviors and metabolic patterns of MFC, and the resultant MFC performances.     

Aerated Shewanella oneidensis in continuously fed bioelectrochemical systems for power and hydrogen production

We studied the effects of aeration of Shewanella oneidensis on potentiostatic current production, hydrogen production in a microbial electrolysis cell, and electric power generation in a microbial fuel cell (MFC). The potentiostatic performance of aerated S. oneidensis was considerably enhanced to a maximum current density of 0.45 A/m² or 80.3 A/m³ (mean: 0.34 A/m², 57.2 A/m³) compared to anaerobically grown cultures. Biocatalyzed hydrogen production rates with aerated S. oneidensis were studied within the applied potential range of 0.3–0.9 V and were highest at 0.9 V with 0.3 m³ H₂/m³ day, which has been reported for mixed cultures, but is ～10 times higher than reported for an anaerobic culture of S. oneidensis. Aerated MFC experiments produced a maximum power density of 3.56 W/m³ at a 200‐Ω external resistor. The main reasons for enhanced electrochemical performance are higher levels of active biomass and more efficient substrate utilization under aerobic conditions. Coulombic efficiencies, however, were greatly reduced due to losses of reducing equivalents to aerobic respiration in the anode chamber. The next challenge will be to optimize the aeration rate of the bacterial culture to balance between maximization of bacterial activation and minimization of aerobic respiration in the culture. Biotechnol. Bioeng. 2010;105: 880–888. © 2009 Wiley Periodicals, Inc.     

Expression of a Tetraheme Protein, Desulfovibrio vulgaris Miyazaki F Cytochrome c3, in Shewanella oneidensis MR-1

Cytochrome c₃ from Desulfovibrio vulgaris Miyazaki F was successfully expressed in the facultative aerobe Shewanella oneidensis MR-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. A derivative of the broad-host-range plasmid pRK415 containing the cytochrome c₃ gene from D. vulgaris Miyazaki F was used for transformation of S. oneidensis MR-1, resulting in the production of protein product that was indistinguishable from that produced by D. vulgaris Miyazaki F, except for the presence of one extra alanine residue at the N terminus.     

Simultaneous analysis of physiological and electrical output changes in an operating microbial fuel cell with Shewanella oneidensis

Changes in metabolism and cellular physiology of facultative anaerobes during oxygen exposure can be substantial, but little is known about how these changes connect with electrical current output from an operating microbial fuel cell (MFC). A high‐throughput voltage based screening assay (VBSA) was used to correlate current output from a MFC containing Shewanella oneidensis MR‐1 to carbon source (glucose or lactate) utilization, culture conditions, and biofilm coverage over 250 h. Lactate induced an immediate current response from S. oneidensis MR‐1, with both air‐exposed and anaerobic anodes throughout the duration of the experiments. Glucose was initially utilized for current output by MR‐1 when cultured and maintained in the presence of air. However, after repeated additions of glucose, the current output from the MFC decreased substantially while viable planktonic cell counts and biofilm coverage remained constant suggesting that extracellular electron transfer pathways were being inhibited. Shewanella maintained under an anaerobic atmosphere did not utilize glucose consistent with literature precedents. Operation of the VBSA permitted data collection from nine simultaneous S. oneidensis MR‐1 MFC experiments in which each experiment was able to demonstrate organic carbon source utilization and oxygen dependent biofilm formation on a carbon electrode. These data provide the first direct evidence of complex cellular responses to electron donor and oxygen tension by Shewanella in an operating MFC at select time points. Biotechnol. Bioeng. 2009;103: 524–531. Published 2009 Wiley Periodicals, Inc.