¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells

Modeling and experimental investigation of the effect of carbon source on the performance of tubular microbial fuel cell

Microbial fuel cells (MFCs) serve two main purposes: clean energy production and wastewater treatment. This study examines the impact of different carbon sources on MFC performance and develops a mathematical model to replicate the polarization curve. The biological reactor employed three types of carbon sources: glucose as a simple feed, microcrystalline cellulose (MCC), and a slurry of the organic component of municipal solid waste (SOMSW) as complex feeds. The MFCs were operated in both open and closed circuit modes. The maximum open circuit voltages achieved were 695 mV for glucose, 550 mV for MCC, and 520 mV for SOMSW as substrates. The influence of the substrate in closed circuit mode was also investigated, resulting in maximum power densities of 172 mW/m2, 55.5 mW/m2, and 47.9 mW/m2 for glucose, MCC, and SOMSW as substrates, respectively. In the second section, a mathematical model was developed to depict the polarization curve while considering voltage losses, namely activation, ohmic, and concentration loss, with an average relative error (ARE) of less than 10%. The mathematical models demonstrated that the activation loss of voltage increased with the complexity of the substrate and reached its peak value when SOMSW was used as the substrate.

Light-driven ammonium oxidation to dinitrogen gas by self-photosensitized biohybrid anammox systems

The anaerobic ammonium oxidation (anammox) process exerts a very vital role in the global nitrogen cycle (estimated to contribute 30%-50% N₂ production in the oceans) and presents superiority in water/wastewater nitrogen removal performance. Until now, anammox bacteria can convert ammonium (NH₄⁺) to dinitrogen gas (N₂) with nitrite (NO₂^-), nitric oxide (NO), and even electrode (anode) as electron acceptors. However, it is still unclear whether anammox bacteria could utilize photoexcited holes as electron acceptors to directly oxide NH₄⁺ to N₂. Here, we constructed an anammox-cadmium sulfide nanoparticles (CdS NPs) biohybrid system. The photoinduced holes from the CdS NPs could be utilized by anammox bacteria to oxidize NH₄⁺ to N₂. ¹⁵N-isotope labeling experiments demonstrated that NH₂OH instead of NO was the real intermediate. Metatranscriptomics data further proved a similar pathway for NH₄⁺ conversion with anodes as electron acceptors. This study provides a promising and energy-efficient alternative for nitrogen removal from water/wastewater.

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.

Pyrite-Based Autotrophic Denitrifying Microorganisms Derived from Paddy Soils: Effects of Organic Co-Substrate Addition

The presence of organic co-substrate in groundwater and soils is inevitable, and much remains to be learned about the roles of organic co-substrates during pyrite-based denitrification. Herein, an organic co-substrate (acetate) was added to a pyrite-based denitrification system, and the impact of the organic co-substrate on the performance and bacterial community of pyrite-based denitrification processes was evaluated. The addition of organic co-substrate at concentrations higher than 48 mg L^-1 inhibited pyrite-based autotrophic denitrification, as no sulfate was produced in treatments with high organic co-substrate addition. In contrast, both competition and promotion effects on pyrite-based autotrophic denitrification occurred with organic co-substrate addition at concentrations of 24 and 48 mg L^-1. The subsequent validation experiments suggested that competition had a greater influence than promotion when organic co-substrate was added, even at a low concentration. Thiobacillus, a common chemolithoautotrophic sulfur-oxidizing denitrifier, dominated the system with a relative abundance of 13.04% when pyrite served as the sole electron donor. With the addition of organic co-substrate, Pseudomonas became the dominant genus, with 60.82%, 61.34%, 70.37%, 73.44%, and 35.46% abundance at organic matter concentrations of 24, 48, 120, 240, and 480 mg L^-1, respectively. These findings provide an important theoretical basis for the cultivation of pyrite-based autotrophic denitrifying microorganisms for nitrate removal in soils and groundwater.

Interspecific competition by non-exoelectrogenic Citrobacter freundii An1 boosts bioelectricity generation of exoelectrogenic Shewanella oneidensis MR-1

The performance of bioelectrochemical systems (BESs) is significantly influenced by metabolic interactions within a particular microbial community. Although some studies show that interspecific metabolic cooperation benefits BESs performance, the effect of interspecific substrate competition on BESs performance has not yet been discussed. Herein, the impact of interspecific competition is investigated by monitoring the extracellular electron transfer of exoelectrogenic Shewanella oneidensis MR-1 and non-exoelectrogenic Citrobacter freundii An1 alone and simultaneously. The bacterial consortia generate the highest current of 38.4 μA cm^-2, 6 times of that produced by the single strain S. oneidensis MR-1. Though S. oneidensis MR-1 loses out to C. freundii An1 in solution, the competition enhances the metabolic activity of S. oneidensis MR-1 on electrode, which facilitates the biofilm formation and therefore helps S. oneidensis MR-1 to gain an competitive advantage over C. freundii An1. Increased metabolic activity triggers more electrons generation and flavin secretion of S. oneidensis MR-1 which contributes to its excellent exoelectrogenic capacity. The proteomics analysis confirms that the expression of proteins related to lactate metabolism, biofilm formation, and outer membrane c-type cytochromes are significantly upregulated in S. oneidensis MR-1 from bacterial consortia.

Insights into palladium nanoparticles produced by Shewanella oneidensis MR-1: Roles of NADH dehydrogenases and hydrogenases

Biologically synthesized palladium nanoparticles (bio-Pd) have attracted considerable interest as promising green catalysts for environmental remediation. However, the mechanisms by which microorganisms produce bio-Pd remain unclear. In the present study, we investigated the roles of Shewanella oneidensis MR-1 and its NADH dehydrogenases and hydrogenases (HydA and HyaB) in bio-Pd production using formate as the electron donor. The roles of NADH dehydrogenases and hydrogenases were studied by inhibiting NADH dehydrogenases and using hydrogenase mutants (ΔhydA, ΔhyaB, and ΔhydAΔhyaB), respectively. The results showed ~97% reduction of palladium by S. oneidensis MR-1 after 24 h using 250 μM palladium and 500 μM formate. Electron microscopy images showed the presence of bio-Pd on both the outer and cytoplasmic membranes of S. oneidensis MR-1. However, the inhibition of NADH dehydrogenases in S. oneidensis MR-1 resulted in only ~61% reduction of palladium after 24 h, and bio-Pd were not found on the outer membrane. The mutants lacking one or two hydrogenases removed 91-96% of palladium ions after 24 h and showed more cytoplasmic bio-Pd but less periplasmic bio-Pd. To the best of our knowledge, this is the first study to demonstrate the role of NADH dehydrogenases of S. oneidensis MR-1 in the formation of bio-Pd on the outer membrane. It also demonstrates that the hydrogenases (especially HyaB) of S. oneidensis MR-1 contribute to the formation of bio-Pd in the periplasmic space. This study provides mechanistic insights into the production of biogenic metal nanoparticles towards their possible use in industrial and environmental applications.

Effects of bacterial inoculation and nitrogen loading on bacterial-algal consortium composition and functions in an integrated photobioelectrochemical system

An integrated photo-bioelectrochemical system (IPB) for wastewater treatment combines a microbial fuel cell with an algal bioreactor, eliminating requirements for aeration, promoting electricity generation, remediating nutrients and producing algal biomass for conversion into biofuel or other bioproducts. To examine strategies for improving IPB functions of electrochemical output and nutrient removal efficiency, this study tested effects of cathode bacterial inoculation and nitrogen loading on cathode microbial community and IPB performance. IPB cathodes were inoculated with the green alga Chlorella vulgaris, in combination with nitrite-oxidizing bacteria (NOB) Nitrobacter winogradskyi, and/or ammonium-oxidizing bacteria (AOB) Nitrosomonas europaea. IPB performance was examined before and after nitrifying bacteria inoculations and under three ammonium loading concentrations in the wastewater medium. Bacterial communities in the cathode suspension and biofilm were examined by 16S rRNA gene sequence analysis. Relative to the algae only control, cathode inoculation with NOB and/or AOB improved net nutrient removal, but resulted in reduced dissolved oxygen availability, which impaired electricity generation. Higher ammonium loading increased electricity production and nutrient removal, possibly by overcoming algal-bacterial competition. Inoculation with nitrifying bacteria resulted in minor changes to total bacterial composition and AOB or NOB comprised <3% of total sequences after 1 month. Community composition changed more dramatically following increase in ammonium-N concentration from 40 to 80 mg L^-1. Manipulation of N loading could be a useful strategy to improve IPB performance, while inoculation of AOB or NOB may be beneficial for treatment of water with high ammonium loading when N removal is the primary system goal.

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.

Complex Iron Uptake by the Putrebactin-Mediated and Feo Systems in Shewanella oneidensis

Shewanella oneidensis is an extensively studied bacterium capable of respiring minerals, including a variety of iron ores, as terminal electron acceptors (EAs). Although iron plays an essential and special role in iron respiration of S. oneidensis, little has been done to date to investigate the characteristics of iron transport in this bacterium. In this study, we found that all proteins encoded by the pub-putA-putB cluster for putrebactin (S. oneidensis native siderophore) synthesis (PubABC), recognition-transport of Fe³⁺-putrebactin across the outer membrane (PutA), and reduction of ferric putrebactin (PutB) are essential to putrebactin-mediated iron uptake. Although homologs of PutA are many, none can function as its replacement, but some are able to work with other bacterial siderophores. We then showed that Fe²⁺-specific Feo is the other primary iron uptake system, based on the synthetical lethal phenotype resulting from the loss of both iron uptake routes. The role of the Feo system in iron uptake appears to be more critical, as growth is significantly impaired by the absence of the system but not of putrebactin. Furthermore, we demonstrate that hydroxyl acids, especially α-types such as lactate, promote iron uptake in a Feo-dependent manner. Overall, our findings underscore the importance of the ferrous iron uptake system in metal-reducing bacteria, providing an insight into iron homeostasis by linking these two biological processes.IMPORTANCE S. oneidensis is among the first- and the best-studied metal-reducing bacteria, with great potential in bioremediation and biotechnology. However, many questions regarding mechanisms closely associated with those applications, such as iron homeostasis, including iron uptake, export, and regulation, remain to be addressed. Here we show that Feo is a primary player in iron uptake in addition to the siderophore-dependent route. The investigation also resolved a few puzzles regarding the unexpected phenotypes of the putA mutant and lactate-dependent iron uptake. By elucidating the physiological roles of these two important iron uptake systems, this work revealed the breadth of the impacts of iron uptake systems on the biological processes.

Modular Engineering Intracellular NADH Regeneration Boosts Extracellular Electron Transfer of Shewanella oneidensis MR-1

Efficient extracellular electron transfer (EET) of exoelectrogens is essentially for practical applications of versatile bioelectrochemical systems. Intracellular electrons flow from NADH to extracellular electron acceptors via EET pathways. However, it was yet established how the manipulation of intracellular NADH impacted the EET efficiency. Strengthening NADH regeneration from NAD⁺, as a feasible approach for cofactor engineering, has been used in regulating the intracellular NADH pool and the redox state (NADH/NAD⁺ ratio) of cells. Herein, we first adopted a modular metabolic engineering strategy to engineer and drive the metabolic flux toward the enhancement of intracellular NADH regeneration. We systematically studied 16 genes related to the NAD⁺-dependent oxidation reactions for strengthening NADH regeneration in the four metabolic modules of S. oneidensis MR-1, i.e., glycolysis, C1 metabolism, pyruvate fermentation, and tricarboxylic acid cycle. Among them, three endogenous genes mostly responsible for increasing NADH regeneration were identified, namely gapA2 encoding a NAD⁺-dependent glyceraldehyde-3-phosphate dehydrogenase in the glycolysis module, mdh encoding a NAD⁺-dependent malate dehydrogenase in the TCA cycle, and pflB encoding a pyruvate-formate lyase that converted pyruvate to formate in the pyruvate fermentation module. An exogenous gene fdh* from Candida boidinii encoding a NAD⁺-dependent formate dehydrogenase to increase NADH regeneration in the pyruvate fermentation module was further identified. Upon assembling these four genes in S. oneidensis MR-1, ∼4.3-fold increase in NADH/NAD⁺ ratio, and ∼1.2-fold increase in intracellular NADH pool were obtained under anaerobic conditions without discharge, which elicited ∼3.0-fold increase in the maximum power output in microbial fuel cells, from 26.2 ± 2.8 (wild-type) to 105.8 ± 4.1 mW/m² (recombinant S. oneidensis), suggesting a boost in the EET efficiency. This modular engineering method in controlling the intracellular reducing equivalents would be a general approach in tuning the EET efficiency of exoelectrogens.

Temporal Microbial Community Dynamics in Microbial Electrolysis Cells - Influence of Acetate and Propionate Concentration

Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m²), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m²; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m²), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m²; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor's performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its possible role in maintaining functional stability of MECs fed with low and high concentrations of acetate and propionate. Taken together, these results provide new insights on the microbial community dynamics and its correlation to performance in MECs fed with different concentrations of acetate and propionate, which are important volatile fatty acids in wastewater.