Diffusion-Based Recycling of Flavins Allows Shewanella oneidensis MR-1 To Yield Energy from Metal Reduction Across Physical Separations

Improvement of biotic nitrate reduction in constructed photoautotrophic biofilm-soil microbial fuel cells

The biotic nitrate reduction rate in freshwater ecosystems is typically constrained by the scarcity of carbon sources. In this study, 'two-chambers' - 'two-electrodes' photoautotrophic biofilm-soil microbial fuel cells (P-SMFC) was developed to accelerate nitrate reduction by activating in situ electron donors that originated from the soil organic carbon (SOC). The nitrate reduction rate of P-SMFC (0.1341 d-1) improved by ∼ 1.6 times on the 28th day compared to the control photoautotrophic biofilm. The relative abundance of electroactive bacterium increased in the P-SMFC and this bacterium contributed to obtain electrons from SOC. Biochar amendment decreased the resistivity of P-SMFC, increased the electron transferring efficiency, and mitigated anodic acidification, which continuously facilitated the thriving of putative electroactive bacterium and promoted current generation. The results from physiological and ecological tests revealed that the cathodic photoautotrophic biofilm produced more extracellular protein, increased the relative abundance of Lachnospiraceae, Magnetospirillaceae, Pseudomonadaceae, and Sphingomonadaceae, and improved the activity of nitrate reductase and ATPase. Correspondingly, P-SMFC in the presence of biochar achieved the highest reaction rate constant for nitrate reduction (kobs) (0.2092 d-1) which was 2.4 times higher than the control photoautotrophic biofilm. This study provided a new strategy to vitalize in situ carbon sources in paddy soil for nitrate reduction by the construction of P-SMFC.

Mediating the performance of anaerobic granular sludge by exogenous flavin supplementation: Flavin binding capacity and behavior, interspecies electron transfer, and methane production

Although flavins are known as effective electron mediators, the binding capacity of exogenous flavins by anaerobic granular sludge (AGS) and their role in interspecies electron transfer (IET) remains unknown. In this study, AGS was mediated by using three exogenous flavins of riboflavin (RF), flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD). Results showed that the total amounts of flavins associated with extracellular polymeric substance (EPS) of AGS increased by 2.03-2.42 and 3.83-4.94 folds, after exposure to 50 and 200 μM of exogenous flavins, respectively. A large portion of FMN and FAD was transformed into RF by AGS. Exogenous flavin mediation also stimulated the production of EPS and cytochrome c (c-Cyts) as well as cytochrome-bound flavins. The increased abundance of these electron mediators led to a reduced electrochemical impedance of EPS and improved extracellular electron transfer capacity. The methane production of AGS after mediation with exogenous RF, FMN, and FAD increased by 19.03-31.71%, 22.86-26.04%, and 28.51-33.44%, respectively. This study sheds new light on the role of exogenous flavins in promoting the IET process of a complex microbial aggregate of AGS.

Pyrogenic Black Carbon Suppresses Microbial Methane Production by Serving as a Terminal Electron Acceptor

Methane (CH4) is the second most important greenhouse gas, 27 times as potent as CO2 and responsible for >30% of the current anthropogenic warming. Globally, more than half of CH4 is produced microbially through methanogenesis. Pyrogenic black carbon possesses a considerable electron storage capacity (ESC) and can be an electron donor or acceptor for abiotic and microbial redox transformation. Using wood-derived biochar as a model black carbon, we demonstrated that air-oxidized black carbon served as an electron acceptor to support anaerobic oxidation of organic substrates, thereby suppressing CH4 production. Black carbon-respiring bacteria were immediately active and outcompeted methanogens. Significant CH4 did not form until the bioavailable electron-accepting capacity of the biochar was exhausted. An experiment with labeled acetate (13CH3COO-) yielded 1:1 13CH4 and 12CO2 without biochar and predominantly 13CO2 with biochar, indicating that biochar enabled anaerobic acetate oxidation at the expense of methanogenesis. Methanogens were enriched following acetate fermentation but only in the absence of biochar. The electron balance shows that approximately half (∼2.4 mmol/g) of biochar's ESC was utilized by the culture, corresponding to the portion of the ESC > +0.173 V (vs SHE). These results provide a mechanistic basis for quantifying the climate impact of black carbon and developing ESC-based applications to reduce CH4 emissions from biogenic sources.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

Kinetics of Hydroxyl Radical Production from Oxygenation of Reduced Iron Minerals and Their Reactivity with Trichloroethene: Effects of Iron Amounts, Iron Species, and Sulfate Reducing Bacteria

Reactive oxygen species generated during the oxygenation of different ferrous species have been documented at groundwater field sites, but their effect on pollutant destruction remains an open question. To address this knowledge gap, a kinetic model was developed to probe mechanisms of •OH production and reactivity with trichloroethene (TCE) and competing species in the presence of reduced iron minerals (RIM) and oxygen in batch experiments. RIM slurries were formed by combining different amounts of Fe(II) and sulfide (with Fe(II):S ratios from 1:1 to 50:1) or Fe(II) and sulfate with sulfate reducing bacteria (SRB) added. Extents of TCE oxidation and •OH production were both greater with RIM prepared under more reducing conditions (more added Fe(II)) and then amended with O₂. Kinetic rate constants from modeling indicate that •OH production from free Fe(II) dominates •OH production from solid Fe(II) and that TCE competes for •OH with Fe(II) and organic matter (OM). Competition with OM only occurs in experiments with SRB, which include cells and their exudates. Experimental results indicate that cells and/or exudates also provide electron equivalents to reform Fe(II) from oxidized RIM. Our work provides new insights into mechanisms and environmental significance of TCE oxidation by •OH produced from oxygenation of RIM. However, further work is necessary to confirm the relative importance of reaction pathways identified here and to probe potentially unaccounted for mechanisms that affect abiotic TCE oxidation in natural systems.

Cysteine-Mediated Extracellular Electron Transfer of Lysinibacillus varians GY32

Microbial extracellular electron transfer (EET) is essential in many natural and engineering processes. Compared with the versatile EET pathways of Gram-negative bacteria, the EET of Gram-positive bacteria has been studied much less and is mainly limited to the flavin-mediated pathway. Here, we investigate the EET pathway of a Gram-positive filamentous bacterium Lysinibacillus varians GY32. Strain GY32 has a wide electron donor spectrum (including lactate, acetate, formate, and some amino acids) in electrode respiration. Transcriptomic, proteomic, and electrochemical analyses show that the electrode respiration of GY32 mainly depends on electron mediators, and c-type cytochromes may be involved in its respiration. Fluorescent sensor and electrochemical analyses demonstrate that strain GY32 can secrete cysteine and flavins. Cysteine added shortly after inoculation into microbial fuel cells accelerated EET, showing cysteine is a new endogenous electron mediator of Gram-positive bacteria, which provides novel information to understand the EET networks in natural environments. IMPORTANCE Extracellular electron transport (EET) is a key driving force in biogeochemical element cycles and microbial chemical-electrical-optical energy conversion on the Earth. Gram-positive bacteria are ubiquitous and even dominant in EET-enriched environments. However, attention and knowledge of their EET pathways are largely lacking. Gram-positive bacterium Lysinibacillus varians GY32 has extremely long cells (>1 mm) and conductive nanowires, promising a unique and enormous role in the microenvironments where it lives. Its capability to secrete cysteine renders it not only an EET pathway to respire and survive, but also an electrochemical strategy to connect and shape the ambient microbial community at a millimeter scale. Moreover, its incapability of using flavins as an electron mediator suggests that the common electron mediator is species-dependent. Therefore, our results are important to understanding the EET networks in natural and engineering processes.

Versatile mechanisms and enhanced strategies of pollutants removal mediated by Shewanella oneidensis: A review

The removal of environmental pollutants is important for a sustainable ecosystem and human health. Shewanella oneidensis (S. oneidensis) has diverse electron transfer pathways and can use a variety of contaminants as electron acceptors or electron donors. This paper reviews S. oneidensis's function in removing environmental pollutants, including heavy metals, inorganic non-metallic ions (INMIs), and toxic organic pollutants. S. oneidensis can mineralize o-xylene (OX), phenanthrene (PHE), and pyridine (Py) as electron donors, and also reduce azo dyes, nitro aromatic compounds (NACs), heavy metals, and iodate by extracellular electron transfer (EET). For azo dyes, NACs, Cr(VI), nitrite, nitrate, thiosulfate, and sulfite that can cross the membrane, S. oneidensis transfers electrons to intracellular reductases to catalyze their reduction. However, most organic pollutants cannot be directly degraded by S. oneidensis, but S. oneidensis can remove these pollutants by self-synthesizing catalysts or photocatalysts, constructing bio-photocatalytic systems, driving Fenton reactions, forming microbial consortia, and genetic engineering. However, the industrial-scale application of S. oneidensis is insufficient. Future research on the metabolism of S. oneidensis and interfacial reactions with other materials needs to be deepened, and large-scale reactors should be developed that can be used for practical engineering applications.

Investigating the interaction between Shewanella oneidensis and phenazine 1-carboxylic acid in the microbial electrochemical processes

Many exoelectrogens utilize small redox mediators for extracellular electron transfer (EET). Notable examples include Shewanella species, which synthesize flavins, and Pseudomonas species, which produce phenazines. In natural and engineered environments, redox-active metabolites from different organisms coexist. The interaction between Shewanella oneidensis and phenazine 1-carboxylic acid (PCA, a representative phenazine compound) was investigated to demonstrate exoelectrogens utilizing metabolites secreted by other organisms as redox mediators. After 24 h in a reactor with and without added PCA (1 μM), the anodic current generated by Shewanella was 235 ± 11 and 51.7 ± 2.8 μA, respectively. Shewanella produced oxidative current approximately three times as high with medium containing PCA as with medium containing the same concentration of riboflavin. PCA also stimulated inward EET in Shewanella. The strong effect of PCA on EET was attributed to its enrichment at the biofilm/electrode interface. The PCA voltammetric peak heights with a Shewanella bioanode were 25-30 times higher than under abiotic conditions. The electrochemical properties of PCA were also altered by the transition from two-electron to single-electron electrochemistry, which suggests PCA was bound between the electrode and cell surface redox proteins. This behavior would benefit electroactive bacteria, which usually dwell in open systems where mediators are present in low concentrations. Like flavins, PCA can be immobilized under both bioanode and biocathode conditions but not under metabolically inactive conditions. Shewanella rapidly transfers electrons to PCA via its Mtr pathway. Compared with wild-type Shewanella, the PCA reduction ability was decreased in gene knockout mutants lacking Mtr pathway cytochromes, especially in the mutants with severely undermined electrode-reduction capacities. These strains also lost the ability to immobilize PCA, even under current-generating conditions.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

Thermodynamic controls on rates of iron oxide reduction by extracellular electron shuttles

Anaerobic microbial respiration in suboxic and anoxic environments often involves particulate ferric iron (oxyhydr-)oxides as terminal electron acceptors. To ensure efficient respiration, a widespread strategy among iron-reducing microorganisms is the use of extracellular electron shuttles (EES) that transfer two electrons from the microbial cell to the iron oxide surface. Yet, a fundamental understanding of how EES-oxide redox thermodynamics affect rates of iron oxide reduction remains elusive. Attempts to rationalize these rates for different EES, solution pH, and iron oxides on the basis of the underlying reaction free energy of the two-electron transfer were unsuccessful. Here, we demonstrate that broadly varying reduction rates determined in this work for different iron oxides and EES at varying solution chemistry as well as previously published data can be reconciled when these rates are instead related to the free energy of the less exergonic (or even endergonic) first of the two electron transfers from the fully, two-electron reduced EES to ferric iron oxide. We show how free energy relationships aid in identifying controls on microbial iron oxide reduction by EES, thereby advancing a more fundamental understanding of anaerobic respiration using iron oxides.

Nanomaterials Facilitating Microbial Extracellular Electron Transfer at Interfaces

Electrochemically active bacteria can transport their metabolically generated electrons to anodes, or accept electrons from cathodes to synthesize high-value chemicals and fuels, via a process known as extracellular electron transfer (EET). Harnessing of this microbial EET process has led to the development of microbial bio-electrochemical systems (BESs), which can achieve the interconversion of electrical and chemical energy and enable electricity generation, hydrogen production, electrosynthesis, wastewater treatment, desalination, water and soil remediation, and sensing. Here, the focus is on the current understanding of the microbial EET process occurring at both the bacteria-electrode interface and the biotic interface, as well as some attempts to improve the EET by using various nanomaterials. The behavior of nanomaterials in different EET routes and their influence on the performance of BESs are described. The inherent mechanisms will guide rational design of EET-related materials and lead to a better understanding of EET mechanisms.

Oxidation of Fe(II) by Flavins under Anoxic Conditions

Flavin-mediated electron transfer is an important pathway for Fe(III) reduction by dissimilatory iron-reducing bacteria. Although the mechanisms and kinetics of Fe(III) reduction by reduced flavins have been widely studied, the reaction between Fe(II) and oxidized flavins is rarely investigated. Results of this study show that under anoxic conditions, Fe(II) can be oxidized by the oxidized forms of riboflavin (RBF) and flavin mononucleotide (FMN) at pH 7-9. For instance, at pH 9, 73% of 17.8 μM Fe(II) was oxidized by 10 μM RBF within 20 min. Both the rate and extent of oxidation increased with increasing concentrations of oxidized flavins and increasing solution pH. Thermodynamic calculations and kinetic analyses implied that the oxidation of Fe(II) proceeded predominantly via the autodecomposition of Fe²⁺-RBF^- and Fe²⁺-FMN^- complexes, along with minor contributions from direct oxidation of Fe(II) by flavins and flavin radicals. Our findings suggest that the reoxidation of Fe(II) by oxidized flavins may be a rate-controlling factor in microbial Fe(III) reduction via flavin-mediated electron transfer.

Extracellular Electron Shuttling Mediated by Soluble c-Type Cytochromes Produced by Shewanella oneidensis MR-1

How metal-reducing bacteria transfer electrons during dissimilatory energy generation under electron acceptor-limited conditions is poorly understood. Here, we incubated the iron and manganese-reducing bacterium Shewanella oneidensis MR-1 without electron acceptors. Removal of soluble extracellular organic compounds (EOCs) dramatically retarded transfer of electrons to an experimental electron acceptor, Cr(VI), by MR-1. However, the return of either high MW (>3000 Da) or low MW (<3000 Da) soluble EOCs produced by MR-1 to washed cells restored Cr(VI) reduction though Cr(VI) reduction was fastest when both size fractions were added together. Spectral and electrochemical characterization of EOCs indicated the presence of flavins and c-type cytochromes (c-Cyts). A model of the kinetics of individual elementary reactions between cells, flavins, released c-Cyts, and Cr(VI), including the direct reduction of flavins, released c-Cyts, and Cr(VI) by cells and the indirect reduction of Cr(VI) by reduced forms of flavins and released c-Cyts, was developed. Model results suggest that released c-Cyts could act as electron mediators to accelerate electron transfer from cells to Cr(VI), and the relative contribution of this pathway was higher than that mediated by flavins. Hence, extracellular c-Cyts produced by MR-1 likely play a role in extracellular electron transfer under electron acceptor-limited conditions. These findings provide new insights into extracellular electron shuttling and the metabolic strategy of metal-reducing bacteria under electron acceptor-limited conditions.

Visualizing electron storage capacity distribution in biochar through silver tagging

Electron storage capacity (ESC) is the capacity of a black carbon to store and reversibly donate and accept electrons in redox processes. Electrochemical and chemical analyses have shown the ESC of black carbon (e.g., plant-based biochars) was on the order of a few mmol/g. However, it remains unknown where ESC is located. The spatial distribution of ESC is important because it controls the bioaccessibility of ESC and the rates of biochar redox reactions. Here we used silver to tag the ESC of a wood-derived biochar. Ag⁺ was allowed to diffuse into the pores of reduced biochar at a constant pH. Up to 2.49 mmol Ag⁺/g biochar (corresponding to 62% of its ESC) was reduced to Ag^o nanoparticles (nAg), which served as an ESC marker and was visualized by electron microscopy. Abundant and dense nAg were observed on the biochar surface. In addition, microtomed samples showed ubiquitous and well-dispersed nAg in the interior of biochar, which explains pore diffusion-limited redox reactions and the partial bioaccessibility of its ESC. In addition to probing ESC distribution in black carbon, this method represents a new, ESC-based approach to incorporate large quantities of Ag and other redox-active elements into carbon media for potential environmental applications.

AQDS and Redox-Active NOM Enables Microbial Fe(III)-Mineral Reduction at cm-Scales

Redox-active organic molecules such as anthraquinone-2,6-disulfonate (AQDS) and natural organic matter (NOM) can act as electron shuttles thus facilitating electron transfer from Fe(III)-reducing bacteria (FeRB) to terminal electron acceptors such as Fe(III) minerals. In this research, we examined the length scale over which this electron shuttling can occur. We present results from agar-solidified experimental incubations, containing either AQDS or NOM, where FeRB were physically separated from ferrihydrite or goethite by 2 cm. Iron speciation and concentration measurements coupled to a diffusion-reaction model highlighted clearly Fe(III) reduction in the presence of electron shuttles, independent of the type of FeRB. Based on our fitted model, the rate of ferrihydrite reduction increased from 0.07 to 0.19 μmol d^-1 with a 10-fold increase in the AQDS concentration, highlighting a dependence of the reduction rate on the electron-shuttle concentration. To capture the kinetics of Fe(II) production, the effective AQDS diffusion coefficient had to be increased by a factor of 9.4. Thus, we postulate that the 2 cm electron transfer was enabled by a combination of AQDS molecular diffusion and an electron hopping contribution from reduced to oxidized AQDS molecules. Our results demonstrate that AQDS and NOM can drive microbial Fe(III) reduction across 2 cm distances and shed light on the electron transfer process in natural anoxic environments.

Carbon dots-fed Shewanella oneidensis MR-1 for bioelectricity enhancement

Bioelectricity generation, by Shewanella oneidensis (S. oneidensis) MR-1, has become particularly alluring, thanks to its extraordinary prospects for energy production, pollution treatment, and biosynthesis. Attempts to improve its technological output by modification of S. oneidensis MR-1 remains complicated, expensive and inefficient. Herein, we report on the augmentation of S. oneidensis MR-1 with carbon dots (CDs). The CDs-fed cells show accelerated extracellular electron transfer and metabolic rate, with increased intracellular charge, higher adenosine triphosphate level, quicker substrate consumption and more abundant extracellular secretion. Meanwhile, the CDs promote cellular adhesion, electronegativity, and biofilm formation. In bioelectrical systems the CDs-fed cells increase the maximum current value, 7.34 fold, and power output, 6.46 fold. The enhancement efficacy is found to be strongly dependent on the surface charge of the CDs. This work demonstrates a simple, cost-effective and efficient route to improve bioelectricity generation of S. oneidensis MR-1, holding promise in all relevant technologies.

Bacterial fuel cells have generated attention with the prospect of green energy production; current research is focused on optimising the system to improve efficiency. Here, the authors report on the feeding of carbon dots to S. oneidensis MR-1 to enhance metabolic activity and bioelectric generation.

Phenazine-1-Carboxylic Acid-Producing Bacteria Enhance the Reactivity of Iron Minerals in Dryland and Irrigated Wheat Rhizospheres

Phenazine-1-carboxylic acid (PCA) is a broad-spectrum antibiotic produced by rhizobacteria in the dryland wheat fields of the Columbia Plateau. PCA and other phenazines reductively dissolve Fe and Mn oxyhydroxides in bacterial culture systems, but the impact of PCA upon Fe and Mn cycling in the rhizosphere is unknown. Here, concentrations of dithionite-extractable and poorly crystalline Fe were approximately 10% and 30-40% higher, respectively, in dryland and irrigated rhizospheres inoculated with the PCA-producing (PCA⁺) strain Pseudomonas synxantha 2-79 than in rhizospheres inoculated with a PCA-deficient mutant. However, rhizosphere concentrations of Fe(II) and Mn did not differ significantly, indicating that PCA-mediated redox transformations of Fe and Mn were transient or were masked by competing processes. Total Fe and Mn uptake into wheat biomass also did not differ significantly, but the PCA⁺ strain significantly altered Fe translocation into shoots. X-ray absorption near edge spectroscopy revealed an abundance of Fe-bearing oxyhydroxides and phyllosilicates in all rhizospheres. These results indicate that the PCA⁺ strain enhanced the reactivity and mobility of Fe derived from soil minerals without producing parallel changes in plant Fe uptake. This is the first report that directly links significant alterations of Fe-bearing minerals in the rhizosphere to a single bacterial trait.