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

Review of cathodic electroactive bacteria: Species, properties, applications and electron transfer mechanisms

Cathodic electroactive bacteria (C-EAB) which are capable of accepting electrons from solid electrodes provide fresh avenues for pollutant removal, biosensor design, and electrosynthesis. This review systematically summarized the burgeoning applications of the C-EAB over the past decade, including 1) removal of nitrate, aromatic derivatives, and metal ions; 2) biosensing based on biocathode; 3) electrosynthesis of CH4, H2, organic carbon, NH3, and protein. In addition, the mechanisms of electron transfer by the C-EAB are also classified and summarized. Extracellular electron transfer and interspecies electron transfer have been introduced, and the electron transport mechanism of typical C-EAB, such as Shewanella oneidensis MR-1, has been combed in detail. By bringing to light this cutting-edge area of the C-EAB, this review aims to stimulate more interest and research on not only exploring great potential applications of these electron-accepting bacteria, but also developing steady and scalable processes harnessing biocathodes.

Distinct influence of model electron shuttles on anaerobic mononitrophenols reduction in aquatic environments by Shewanella oneidensis MR-1

The environmental fate and risks of mononitrophenols (mono-NPs), the simplest nitrophenols (NPs) often found in aquatic environments, are profoundly influenced by anaerobic bioreduction and co-existing electron shuttles (ESs), but little is known about the underlying mechanisms. Here, we elucidate the pathways of anaerobic mono-NPs bioreduction by Shewanella oneidensis MR-1 and assess the effect of model ESs on these processes. We found that all three mono-NPs isomers could be readily reduced to their corresponding aminophenols by S. oneidensis MR-1 under anaerobic conditions. CymA, a core component of the Mtr respiratory pathway, performs a dynamic role in these bioreduction, which is highly dependent on the bioreduction kinetics. The exogenous addition of quinones was found to accelerate the mono-NPs bioreduction through interactions with key outer-membrane proteins (e.g., OmcA and MtrC), and all these processes matched well to linear free energy relationships (LFERs). Surprisingly, adding riboflavin did not influence the bioreduction of all three mono-NPs isomers, which may be due to the contribution of OmcA and MtrC to these bioreduction processes and their downregulated expression. This study enhances our understanding of the environmental fate of mono-NPs and their bioconversion processes, providing valuable insights for the bioremediation of nitrophenol-contaminated sites.

Mechanistic insights into sulfadimethoxine degradation via microbially driven Fenton reactions

Biodegradation, while cost-effective, is hindered by the requirement for specialized microorganisms and co-contaminants. Innovative biological technologies like the microbially driven Fenton reaction, hold promise for enhancing degradation efficiency. However, the intricate biochemical processes and essential steps for effective degradation in such systems have remained unclear. In this study, we harnessed the potential of the microbially driven Fenton reaction by employing Shewanella oneidensis MR-1 (MR-1). Our approach showcased remarkable efficacy in degrading a range of contaminants, including sulfadimethoxine (SDM), 4,4'-dibromodiphenyl ether (BDE-15) and atrazine (ATZ). Using SDM as a model contaminant of emergent contaminants (ECs), we unveiled that biodegradation relied on the generation of hydroxyl radicals (•OH) and involvement of oxidoreductases. Transcriptomic analysis shed light on the pivotal components of extracellular electron transfer (EET) during both anaerobic and aerobic periods. The presence of reactive oxidizing species induced cellular damage and impeded DNA repair, thereby affecting the Mtr pathway of EET. Moreover, the formation of vivianite hindered SDM degradation, underscoring the necessity of maintaining iron ions in the solution to ensure sustainable and efficient degradation. Overall, this study offers valuable insights into microbial technique for ECs degradation, providing a comprehensive understanding of degradation mechanisms during aerobic/anaerobic cycling.

The enhancement effect of n-Fe3O4 on methyl orange reduction by nitrogen-fixing bacteria consortium

Although the anaerobic reduction of azo dyes is ecofriendly, high ammonia consumption remains a significant challenge. This work enriched a mixed nitrogen-fixing bacteria consortium (NFBC) using n-Fe3O4 to promote the anaerobic reduction of methyl orange (MO) without exogenous nitrogen. The enriched NFBC was dominated by Klebsiella (80.77 %) and Clostridium (17.16 %), and achieved a 92.7 % reduction of MO with an initial concentration of 25 mg·L-1. Compared with the control, the consortium increased the reduction efficiency of MO, cytochrome c content, and electron transport system (ETS) activity by 11.86 %, 89.86 %, and 58.49 %, respectively. When using 2.5 g·L-1 n-Fe3O4, the extracellular polymeric substances (EPS) of NFBC were present in a concentration of 85.35 mg·g-1. The specific reduction rates of MO by NFBC were 2.26 and 3.30 times faster than those of Fe(II) and Fe(III), respectively, while the enrichment factor of the ribosome pathway in NFBC exceeded 0.75. Transcriptome, carbon consumption, and EPS analyses suggested that n-Fe3O4 stimulated carbon metabolism and secreted protein synthesized by the mixed culture. The latter occurred due to the increased activity of consortium and the content of redox substances. These findings demonstrate that n-Fe3O4 promoted the efficiency of mixed nitrogen-fixing bacteria for removing azo dyes from wastewater. This innovative approach highlights the potential of integrating nanomaterials with biological systems to effectively address complex pollution challenges.

Probiotics Alleviate Microcystin-LR-Induced Developmental Toxicity in Zebrafish Larvae

Microcystin-LR (MCLR) poses a significant threat to aquatic ecosystems and public health. This study investigated the protective effects of the probiotic Lactobacillus rhamnosus against MCLR-induced developmental toxicity in zebrafish larvae. Zebrafish larvae were exposed to various concentrations of MCLR (0, 0.9, 1.8, and 3.6 mg/L) with or without L. rhamnosus from 72 to 168 h post-fertilization (hpf). Probiotic supplementation significantly improved survival, hatching, and growth rates and reduced malformation rates in MCLR-exposed larvae. L. rhamnosus alleviated MCLR-induced oxidative stress by reducing reactive oxygen species (ROS) levels and enhancing glutathione (GSH) content and catalase (CAT) activity. Probiotics also mitigated MCLR-induced lipid metabolism disorders by regulating key metabolites (triglycerides, cholesterol, bile acids, and free fatty acids) and gene expression (ppara, pparb, srebp1, and nr1h4). Moreover, 16S rRNA sequencing revealed that L. rhamnosus modulated the gut microbiome structure and diversity in MCLR-exposed larvae, promoting beneficial genera like Shewanella and Enterobacter and inhibiting potential pathogens like Vibrio. Significant correlations were found between gut microbiota composition and host antioxidant and lipid metabolism parameters. These findings suggest that L. rhamnosus exerts protective effects against MCLR toxicity in zebrafish larvae by alleviating oxidative stress, regulating lipid metabolism, and modulating the gut microbiome, providing insights into probiotic-based strategies for mitigating MCLR toxicity in aquatic organisms.

Combined metabolomics and proteomics to reveal the mechanism of S. oneidensis MR-1 degradation malathion enhanced by FeO/C

Iron oxide @ biochar (FeO/C) promotes bacterial growth and facilitates electron transfer, thereby effectively promoting malathion degradation by Shewanella oneidensis MR-1 (S. oneidensis MR-1). This study elucidated the underlying mechanism of FeO/C-enhanced malathion degradation by S. oneidensis MR-1 through a combination of metabolomics and proteomics analysis. The kinetic fitting results from the degradation experiment indicated that 0.1 g/L FeO/C exerted the most significant enhancement effect on malathion degradation by S. oneidensis MR-1. Observations from Scanning Electron Microscopy and Laser Scanning Confocal Microscopy, along with physiological and biochemical analysis, showed that FeO/C enhanced the growth and oxidative response of S. oneidensis MR-1 under malathion stress. In addition, metabolomics and proteomics analysis revealed an increase in certain electron transfer related metabolites, such as coenzymes, and the upregulation of proteins, including coenzyme A, sdhD, and petC. Overall, spectroscopic analysis suggested that Fe2+, which was reduced from Fe3+ by S. oneidensis MR-1 in FeO/C, promoted electron transfer in S. oneidensis MR-1 to enhance the degradation of malathion. This study offers enhanced strategies for efficient removal of malathion contaminants.

Biotransformation of Chlorpyrifos Shewanella oneidensis MR-1 in the Presence of Goethite: Experimental Optimization and Degradation Products

In this study, the degradation system of Shewanella oneidensis MR-1 and goethite was constructed with chlorpyrifos as the target contaminant. The effects of initial pH, contaminant concentration, and temperature on the removal rate of chlorpyrifos during the degradation process were investigated. The experimental conditions were optimized by response surface methodology with a Box-Behnken design (BBD). The results show that the removal rate of chlorpyrifos is 75.71% at pH = 6.86, an initial concentration of 19.18 mg·L-1, and a temperature of 30.71 °C. LC-MS/MS analyses showed that the degradation products were C4H11O3PS, C7H7Cl3NO4P, C9H11Cl2NO3PS, C7H7Cl3NO3PS, C9H11Cl3NO4P, C4H11O2PS, and C5H2Cl3NO. Presumably, the degradation pathways involved are: enzymatic degradation, hydrolysis, dealkylation, desulfur hydrolysis, and dechlorination. The findings of this study demonstrate the efficacy of the goethite/S. oneidensis MR-1 complex system in the removal of chlorpyrifos from water. Consequently, this research contributes to the establishment of a theoretical framework for the microbial remediation of organophosphorus pesticides in aqueous environments.

Asymmetries among soil fungicide residues, nitrous oxide emissions and microbiomes regulated by nitrification inhibitor at different moistures

Carbendazim residue has been widely concerned, and nitrous oxide (N2O) is one of the dominant greenhouse gases. Microbial metabolisms are fundamental processes of removing organic pollutant and producing N2O. Nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) can change soil abiotic properties and microbial communities and simultaneously affect carbendazim degradation and N2O emission. In this study, the comprehensive linkages among carbendazim residue, N2O emission and microbial community after the DMPP application were quantified under different soil moistures. Under 90% WHC, the DMPP application significantly reduced carbendazim residue by 54.82% and reduced soil N2O emission by 98.68%. The carbendazim residue was negatively related to soil ammonium nitrogen (NH4+-N), urease activity, and ratios of Bacteroidetes, Thaumarchaeota and Nitrospirae under 90% WHC, and the N2O emission was negatively related to NH4+-N content and relative abundance of Acidobacteria under the 60% WHC condition. In the whole (60% and 90% WHC together), the carbendazim residue was negatively related to the abundances of nrfA (correlation coefficient = -0.623) and nrfH (correlation coefficient = -0.468) genes. The hao gene was negatively related to the carbendazim residue but was positively related to the N2O emission rate. The DMPP application had the promising potential to simultaneously reduce ecological risks of fungicide residue and N2O emission via altering soil abiotic properties, microbial activities and communities and functional genes. ENVIRONMENTAL IMPLICATION: Carbendazim was a high-efficiency fungicide that was widely used in agricultural production. Nitrous oxide (N2O) is the third most important greenhouse gas responsible for global warming. The 3, 4-dimethylpyrazole phosphate (DMPP) is an effective nitrification inhibitor widely used in agricultural production. This study indicated that the DMPP application reduced soil carbendazim residues and N2O emission. The asymmetric linkages among the carbendazim residue, N2O emission, microbial community and functional gene abundance were regulated by the DMPP application and soil moisture. The results could broaden our horizons on the utilizations DMPP in decreasing fungicide risks and N2O emission.

Efficient nitrate and Cr(VI) removal by denitrifier: The mechanism of S. oneidensis MR-1 promoting electron production, transportation and consumption

When Cr(VI) and nitrate coexist, the efficiency of both bio-denitrification and Cr(VI) bio-reduction is poor because chromate hinders bacterial normal functions (i.e., electron production, transportation and consumption). Moreover, under anaerobic condition, the method about efficient nitrate and Cr(VI) removal remained unclear. In this paper, the addition of Shewanella oneidensis MR-1 to promote the electron production, transportation and consumption of denitrifier and cause an increase in the removal of nitrate and Cr(VI). The efficiency of nitrate and Cr(VI) removal accomplished by P. denitrificans as a used model denitrifier increased respectively from 51.3% to 96.1% and 34.3% to 99.8% after S. oneidensis MR-1 addition. The mechanism investigations revealed that P. denitrificans provided S. oneidensis MR-1 with lactate, which was utilized to secreted riboflavin and phenazine by S. oneidensis MR-1. The riboflavin served as coenzymes of cellular reductants (i.e., thioredoxin and glutathione) in P. denitrificans, which created favorable intracellular microenvironment conditions for electron generation. Meanwhile, phenazine promoted biofilm formation, which increased the adsorption of Cr(VI) on the cell surface and accelerated the Cr(VI) reduction by membrane bound chromate reductases thereby reducing damage to other enzymes respectively. Overall, this strategy reduced the negative effect of chromate, thus improved the generation, transportation, and consumption of electrons. SYNOPSIS: The presence of S. oneidensis MR-1 facilitated nitrate and Cr(VI) removal by P. denitrificans through decreasing the negative effect of chromate due to the metabolites' secretion.

DIET-like and MIET-like mutualism of S. oneidensis MR-1 and metal-reducing function microflora boosts Cr(VI) reduction

Microbial treatment of Cr(VI) is an environmentally friendly and low-cost approach. However, the mechanism of mutualism and the role of interspecies electron transfer in Cr(VI) reducing microflora are unclear. Herein, we constructed an intersymbiotic microbial association flora to augment interspecies electron transfer via functionalizing electroactive Shewanella oneidensis MR-1 with metal-reducing microflora, and thus the efficiency of Cr(VI) reduction. The findings suggest that the metal-reducing active microflora could converts glucose into lactic acid and riboflavin for S. oneidensis MR-1 to act as a carbon source and electron mediator. Thus, when adding initial 25 mg/L Cr (VI), this microflora exhibited an outstanding Cr (VI) removal efficiency (100%) at 12 h and elevated Cr (III) immobilization efficiency (80%) at 60 h with the assistance of 25 mg/L Cu(II). A series of electrochemical experiments proved this remarkable removal efficiency were ascribed to the improved interspecies electron transfer efficiency through direct interspecies electron transfer and riboflavin through mediated interspecies electron transfer. Furthermore, the metagenomic analysis revealed the expression level of the electron transport pathway was promoted. Intriguing high abundance of genes participating in the bio-reduction and biotransformation of Cr(VI) was also observed in functional microflora. These outcomes give a novel strategy for enhancing the reduction and fixation of harmful heavy metals by coculturing function microflora with electrogenic microorganisms.

Toxic effects of combined exposure to cadmium and diclofenac on freshwater crayfish (Procambarus clarkii): Insights from antioxidant enzyme activity, histopathology, and gut microbiome

In recent years, excessive discharge of pollutants has led to increasing concentrations of cadmium (Cd) and diclofenac (DCF) in water; however, the toxicity mechanism of combined exposure of the two pollutants to aquatic animals has not been fully studied. Procambarus clarkii is an economically important aquatic species that is easily affected by Cd and DCF. This study examined the effects of combined exposure to Cd and DCF on the tissue accumulation, physiology, biochemistry, and gut microflora of P. clarkii. The results showed that Cd and DCF accumulated in tissues in the order of hepatopancreas > gill > intestine > muscle. The hepatopancreas and intestines were subjected to severe oxidative stress, with significantly increased antioxidant enzyme activity. Pathological examination revealed lumen expansion and epithelial vacuolisation in the hepatopancreas and damage to the villous capillaries and wall in the intestine. The co-exposure to Cadmium (Cd) and Diclofenac (DCF) disrupts the Firmicutes/Bacteroidetes (F/B) ratio, impairing the regular functioning of intestinal microbiota in carbon (C) and nitrogen (N) cycling. This disturbance consequently hinders the absorption and utilization of energy and nutrients in Procambarus clarkii. This study offers critical insights into the toxicological mechanisms underlying the combined effects of Cd and DCF, and suggests potential approaches to alleviate their adverse impacts on aquatic ecosystems.

The role of extracellular polymeric substances (EPS) in chemical-degradation of persistent organic pollutants in soil: A review

Persistent organic pollutants (POPs) in soil show high environmental risk due to their high toxicity and low biodegradability. Studies have demonstrated the degradation function of microbial extracellular polymeric substances (EPS) on POPs in various matrices. However, the degradation mechanisms and the factors that influence the process in soil have not been clearly illustrated. In this review, the characteristics of EPS were introduced and the possible mechanisms of EPS on degradation of organic pollutants (e.g., external electron transfer, photodegradation, and enzyme catalysis) were comprehensively discussed. In addition, the environmental conditions (e.g., UV, nutrients, and redox potential) that could influence the production and degradation-related active components of EPS were addressed. Moreover, the current approaches on the application of EPS in biotechnology were summarized. Further, the future perspectives of enhancement on degradation of POPs by regulating EPS were discussed. Overall, this review could provide a new thought on remediation of POPs by widely-existing EPS in soil with low-cost and minimized eco-disturbance.

Nitrogen removal from pharmaceutical wastewater using simultaneous nitrification-denitrification coupled with sulfur denitrification in full-scale system

Fermentation pharmaceutical wastewater (FPW) containing excessive ammonium and low chemical oxygen demand (COD)/nitrogen ratio (C/N ratio) brings serious environmental risks. The stepwise nitrogen removal was achieved in a full-scale anaerobic/aerobic/anoxic treatment system with well-constructed consortia, that enables simultaneous partial nitrification-denitrification coupled with sulfur autotrophic denitrification (SPND-SAD) (∼99 % (NH4+-N) and ∼98 % (TN) removals) at the rate of 0.8-1.2 kg-N/m3/d. Inoculating simultaneous nitrification-denitrification (SND) consortia in O1 tank decreased the consumed ΔCOD and ΔCOD/ΔTN of A1 + O1 tank, resulting in the occurrence of short-cut SND at low C/N ratio. In SAD process (A2 tank), bio-generated polysulfides reacted with HS- to rearrange into shorter polysulfides, enhancing sulfur bioavailability and promoting synergistic SAD removal. PICRUSt2 functional prediction indicated that bioaugmentation increased genes related to Nitrogen/Sulfur/Carbohydrate/Xenobiotics metabolism. Key functional gene analysis highlighted the enrichment of nirS and soxB critical for SPND-SAD system. This work provides new insights into the application of bioaugmentation for FPW treatment.

The roles of Rhodococcus ruber in denitrification with quinoline as the electron donor

Denitrification is an important step in domestic wastewater treatment, but providing bioavailable electron donors is an expense. However, some industrial wastewaters contain organic compounds that could be a no-cost or low-cost electron donor, because they otherwise must be treated separately. In this work, quinoline was used as an electron donor to drive denitrification through bioaugmentation with Rhodococcus ruber, which is able to biodegrade quinoline. When quinoline-acclimated biomass (QAB) was used for denitrification, addition of R. ruber accelerated biodegradation of quinoline and its first mono-oxygenation intermediate (2-hydroxyquinoline). Although R. ruber was not directly active in denitrification, its biodegradation of quinoline and 2-hydroxyquinoline supplied products that other bacteria used to respire nitrate. In contrast, glucose-acclimated biomass (GAB) could not achieve effective denitrification with quinoline, whether or not R. ruber was added. Analysis by high-throughout sequencing showed that genera Ignavibacterium, Ferruginibacter, Limnobacter, and Denitrosoma were important during quinoline biodegradation with denitrification by QAB. In summary, bioaugmented R. ruber and endogenous bacterial strains had complementary roles when biodegrading quinoline to enhance denitrification. The significance of this study is to enable the use of industrial wastewater to provide electron donor to drive denitrification.

Shewanella oneidensis MR-1 and oxalic acid mediated vanadium reduction and redistribution in vanadium-containing tailings

The microbially- and chemically-mediated redox process is critical in controlling the fate of vanadium (V) in tailing environment. Although the microbial reduction of V has been widely studied, the coupled biotic reduction mediated by beneficiation reagents and the underlying mechanism remain unclear. Herein, the reduction and redistribution of V in V-containing tailings and Fe/Mn oxide aggregates mediated by Shewanella oneidensis MR-1 and oxalic acid were explored. The dissolution of Fe-(hydr)oxides by oxalic acid promoted the microbe-mediated V release from solid-phase. After 48-day of reaction, the dissolved V concentrations in the bio-oxalic acid treatment reached maximum values of 1.72 ± 0.36 mg L^-1 and 0.42 ± 0.15 mg L^-1 in the tailing system and the aggregate system, respectively, significantly higher than those in control (0.63 ± 0.14 mg L^-1 and 0.08 ± 0.02 mg L^-1). As the electron donor, oxalic acid enhanced the electron transfer process of S. oneidensis MR-1 for V(V) reduction. The mineralogical characterization of final products indicates that S. oneidensis MR-1 and oxalic acid promoted solid-state conversion from V₂O₅ to NaV₆O₁₅. Collectively, this study demonstrates that microbe-mediated V release and redistribution in solid-phase were promoted by oxalic acid, suggesting that the role of organic agents for the V biogeochemical cycle in natural systems deserves greater attention.

Correction: Enhanced detoxification of Cr6+ by Shewanella oneidensis via adsorption on spherical and flower-like manganese ferrite nanostructures

[This corrects the article DOI: 10.1039/D2NA00691J.].

Modular Engineering Strategy to Redirect Electron Flux into the Electron-Transfer Chain for Enhancing Extracellular Electron Transfer in Shewanella oneidensis

Efficient extracellular electron transfer (EET) of exoelectrogens is critical for practical applications of various bioelectrochemical systems. However, the low efficiency of electron transfer remains a major bottleneck. In this study, a modular engineering strategy, including broadening the sources of the intracellular electron pool, enhancing intracellular nicotinamide adenine dinucleotide (NADH) regeneration, and promoting electron release from electron pools, was developed to redirect electron flux into the electron transfer chain in Shewanella oneidensis MR-1. Among them, four genes include gene SO1522 encoding a lactate transporter for broadening the sources of the intracellular electron pool, gene gapA encoding a glyceraldehyde-3-phosphate dehydrogenase and gene mdh encoding a malate dehydrogenase in the central carbon metabolism for enhancing intracellular NADH regeneration, and gene ndh encoding NADH dehydrogenase on the inner membrane for releasing electrons from intracellular electron pools into the electron-transport chain. Upon assembly of the four genes, electron flux was directly redirected from the electron donor to the electron-transfer chain, achieving 62% increase in intracellular NADH levels, which resulted in a 3.5-fold enhancement in the power density from 59.5 ± 3.2 mW/m² (wild type) to 270.0 ± 12.7 mW/m² (recombinant strain). This study confirmed that redirecting electron flux from the electron donor to the electron-transfer chain is a viable approach to enhance the EET rate of S. oneidensis.