Evaluation of mtr cluster expression in Shewanella RCRI7 during uranium removal

Bioremediation Performance of Recombinant Shewanella azerbaijanica; Considering Uranium Removal in the Presence of Nitrate

Genetic engineering in microorganisms has emerged as a promising approach for pollutant removal from industrial wastewater. Shewanella azerbaijanica has the ability to reduce uranium. This study examined the impact of high-nitrate concentrations on uranium bioreduction in both native and recombinant bacterial strains. Bacterial performance was evaluated in terms of uranium bioreduction (measured via ICP-AES method), and survival in anaerobic conditions (measured via Neubauer chamber counting) in the presence of uranium and nitrate over various time intervals (24 h, 1 week, 4 weeks, 4 months, and 9 months). Although the recombinant strain showed a lower cell population than the wild-type strain, it achieved 20% higher uranium reduction after 24 h of incubation in uranium and nitrate-containing conditions. This suggests that the genetic modifications enhanced extracellular electron transfer (EET). The improved bioremediation efficiency may be attributed to the cloned mtrC gene, which promotes more effective electron transfer in Shewanella bacteria. Additionally, uranium removal may have been further enhancedby the inactivation of the napB gene using the SDM method. This high-performance trends was consistent across all time intervals. In wild-type S. azerbaijanica uranium removal rates were74%, 54%, 96 and 99% after 1 week, 4 weeks, 4 months, and 9 months, respectively. Inrecombinant bacteria, these rates increased to 91%, 78%, 96%, and 100% at the same time points. The bioreduction mechanism was further confirmed by X-ray diffraction (XRD) analysis, which verified the ability of S. azerbaijanica to reduce uranium in the presence of nitrate. Overall, this study identifies the recombinant bacterium as promising candidate for future metal bioreduction research.

Extracellular electron transfer-dependent bioremediation of uranium-contaminated groundwater: Advancements and challenges

Efficient and sustainable remediation of uranium-contaminated groundwater is critical for groundwater safety and the sustainable development of nuclear energy, particularly in the context of global carbon neutrality goals. This review explores the potential of microbial reduction processes that utilize extracellular electron transfer (EET) to convert soluble uranium (U(VI)) into its insoluble form (U(IV)), presenting a promising approach to groundwater remediation. The review first outlines the key processes and factors influencing the effectiveness of dissimilatory metal-reducing bacteria (DMRB), such as Geobacter and Shewanella, during uranium bioremediation and recovery. The cutting-edge progress on the molecular mechanism of EET-driven U(VI) reduction mediated by c-type cytochromes, conductive pili, and electron mediators, is critically reviewed. Additionally, advanced strategies such as optimizing electron transfer, leveraging synthetic biology approach, and integration with machine learning are discussed to enhance the efficiency of EET-driven processes. The review also considers the integration of EET processes into practical engineering applications, highlighting the need for optimization and innovation in bioremediation technologies. By providing a comprehensive overview of current progress and challenges, this review aims to inspire novel research and practical advancements in the field of uranium-contaminated groundwater remediation.

Optimizing the Metal Bioreduction Process in Recombinant Shewanella azerbaijanica Bacteria: A Novel Approach via mtrC Gene Cloning and Nitrate-Reducing Pathway Destruction

Environmental pollution is growing every day in terms of the increase in population, industrialization, and urbanization. Shewanella azerbaijanica is introduced as a highly potent bacterium in metal bioremediation. The mtrC gene was selected as a cloning target to improve electron flux chains in the EET (extracellular electron transfer) pathway. Using the SDM (site-directed mutagenesis) technique, the unique gene assembly featured the mtrC gene sandwiched between two napD/B genes to disrupt the nitrate reduction pathway, which serves as the primary metal reduction competitor. Shew-mtrC gene construction was transferred to expression plasmid pET28a (+) in the expression host bacteria (E. coli BL21 and S. azerbaijanica), in pUC57, cloning plasmid, which was transferred to the cloning host bacteria E. coli Top10 and S. azerbaijanica. All cloning procedures (i.e., synthesis, insertion, transformation, cloning, and protein expression) were verified and confirmed by precise tests. ATR-FTIR analysis, CD, western blotting, affinity chromatography, SDS-PAGE, and other techniques were used to confirm the expression and structure of the MtrC protein. The genome sequence and primers were designed according to the submitted Shewanella oneidensis MR-1 genome, the most similar bacteria to this native species. The performance of recombinant S. azerbaijanica bacterium in metal bioremediation, as sustainable strategy, has to be verified by more research.

Biomineralization of uranium by Desulfovibrio desulfuricans A3-21ZLL under various hydrochemical conditions

Uranium pollution in groundwater environment has become an important issue of global concern. In this study, a strain of Desulfovibrio desulfuricans was isolated from the tailings of acid heap leaching, and was shown to be able to remove uranium from water via biosorption, bio-reduction, passive biomineralization under uranium stress, and active metabolically dependent bioaccumulation. This research explored the effects of nutrients, pH, initial uranium and sulfate concentration on the functional groups, uranium valence, and crystal size and morphology of uranium immobilization products. Results showed that tetravalent and hexavalent phosphorus-containing uranium minerals was both formed. In sulfate-containing water where Desulfovibrio desulfuricans A3-21ZLL can grow, the sequestration of uranium by bio-reduction was significantly enhanced compared to that with no sulfate loading or no growth. Ungrown Desulfovibrio desulfuricans A3-21ZLL or dead ones released inorganic phosphate group in response to the stress of uranium, which associated with soluble uranyl ion to form insoluble uranium-containing precipitates. This study revealed the influence of hydrochemical conditions on the mineralogy characteristics and spatial distribution of microbial uranium immobilization products. This study is conducive to the long-term and stable bioremediation of groundwater in decommissioned uranium mining area.

Bacterial exopolysaccharides as emerging bioactive macromolecules: from fundamentals to applications

Microbial exopolysaccharides (EPS) are extracellular carbohydrate polymers forming capsules or slimy coating around the cells. EPS can be secreted by various bacterial genera that can help bacterial cells in attachment, environmental adaptation, stress tolerance and are an integral part of microbial biofilms. Several gut commensals (e.g., Lactobacillus, Bifidobacterium) produce EPS that possess diverse bioactivities. Bacterial EPS also has extensive commercial applications in the pharmaceutical and food industries. Owing to the structural and functional diversity, genetic and metabolic engineering strategies are currently employed to increase EPS production. Therefore, the current review provides a comprehensive overview of the fundamentals of bacterial exopolysaccharides, including their classification, source, biosynthetic pathways, and functions in the microbial community. The review also provides an overview of the diverse bioactivities of microbial EPS, including immunomodulatory, anti-diabetic, anti-obesity, and anti-cancer properties. Since several gut microbes are EPS producers and gut microbiota helps maintain a functional gut barrier, emphasis has been given to the intestinal-level bioactivities of the gut microbial EPS. Collectively, the review provides a comprehensive overview of microbial bioactive exopolysaccharides.

Moving towards the enhancement of extracellular electron transfer in electrogens

Electrogens are very common in nature and becoming a contemporary theme for research as they can be exploited for extracellular electron transfer. Extracellular electron transfer is the key mechanism behind bioelectricity generation and bioremediation of pollutants via microbes. Extracellular electron transfer mechanisms for electrogens other than Shewanella and Geobacter are less explored. An efficient extracellular electron transfer system is crucial for the sustainable future of bioelectrochemical systems. At present, the poor extracellular electron transfer efficiency remains a decisive factor in limiting the development of efficient bioelectrochemical systems. In this review article, the EET mechanisms in different electrogens (bacteria and yeast) have been focused. Apart from the well-known electron transfer mechanisms of Shewanella oneidensis and Geobacter metallireducens, a brief introduction of the EET pathway in Rhodopseudomonas palustris TIE-1, Sideroxydans lithotrophicus ES-1, Thermincola potens JR, Lysinibacillus varians GY32, Carboxydothermus ferrireducens, Enterococcus faecalis and Saccharomyces cerevisiae have been included. In addition to this, the article discusses the several approaches to anode modification and genetic engineering that may be used in order to increase the rate of extracellular electron transfer. In the side lines, this review includes the engagement of the electrogens for different applications followed by the future perspective of efficient extracellular electron transfer.

The effect of not-anaerobicization and discolored bacteria on uranium reduction by Shewanella sp. RCRI7

Shewanella sp. RCRI7 is a native strain capable of reducing uranium in anaerobic conditions. In order to employ this bacterium for the bioremediation, the mutual effects of uranium and the bacteria are studied in two different approaches. The optimal settings for the bacterial proliferation capacity and uranium reduction without anaerobicization of the environment, as well as the related effects of bioremediation and bacterial color under uranium-reducing conditions, have been investigated in this study. Uranium reduction procedure was analyzed using XRD, spectrophotometry and ICP-AES. In addition, the uranium's effect on the population of the first-generation of the bacteria as well as the color and growth of the second-generation were investigated using neobar lam and CFU (Colony Forming Unit), respectively. Uranium toxicity reduced the population of non-anaerobicized bacteria more than the anaerobicized bacteria after one day of incubation, while the amount of uranium extracted by the bacteria was almost the same. In both situations, the bacteria were able to reduce uranium after two weeks of incubation. In addition to the cell counts, uranium toxicity disrupts the growth and development of healthy second-generation anaerobicized bacteria, as created creamy-colored colonies grow slower than red-colored colonies. Furthermore, due to malfunctioning cytochromes, unlike red bacteria, creamy-colored bacteria were unable to extract the optimum amount of uranium. This study reveals that reduced uranium can be produced in a deprived environment without anaerobicization. Creamy-colored Shewanella can remove soluble uranium, however the most effective bacteria have red cytochromes. These findings represent a big step forward in the industrialization of uranium bioremediation.

Effects of UV stress on Shewanella azerbaijanica bioremediation response

Shewanella azerbaijanica roles as a live electrode, passing electrons from electron donors to electron acceptors, to gain energy from the extracellular electron transfer (EET) pathway. The present study, considered the quantitative expressions of the major EET reductase genes (mtr cluster), together with uranium removal, live-cell counting, and spectrophotometry in UV-C treated bacteria (0, 60, 120 and 180 s). The simultaneous decline in the uranium removal and cell counting, along with major mtr gene expression patterns (mtrABDEF), approved the negative effects of UV-C radiation on uranium bioreduction in S. azerbaijanica. Uranium removal and cell counting decreased to 25.49% and 0.45 × 109 cells/mL in the 180s UV-C treated sample, respectively at 2 mM uranium concentration, while no decline trend found in 0.5 mM for the counted cells and uranium removal tests. No considerable expression of omcA and omcB (mtrC) genes were traced due to spontaneous mutagenesis during the in vitro serial passages, proposing a novel alternative EET pathway in S. azerbaijanica during uranium bioreduction process. The results could pave the way for further researches to modify the bioremediation process through genetic manipulation.

Growth and genome-based insights of Fe(III) reduction of the high-temperature and NaCl-tolerant Shewanella xiamenensis from Changqing oilfield of China

Introduction

A facultative anaerobe bacterium Shewanella xiamenensis CQ-Y1 was isolated from the wastewater of Changqing oilfield in Shaanxi Province of China. Shewanella is the important dissimilatory metal-reducing bacteria. It exhibited a well potential application in biodegradation and bioremediation.

Methods

Genome sequencing, assembling and functional annotation were conducted to explore the genome information of CQ-Y1. The effect of temperatures and NaCl concentrations on the CQ-Y1 growth and Fe(III) reduction were investigated by UV visible spectrophotometry, SEM and XRD.

Results

Genomic analysis revealed its complete genome was a circular chromosome of 4,710,887 bp with a GC content of 46.50% and 4,110 CDSs genes, 86 tRNAs and 26 rRNAs. It contains genes encoding for Na⁺/H⁺ antiporter, K⁺/Cl^- transporter, heat shock protein associated with NaCl and high-temperature resistance. The presence of genes related to flavin, Cytochrome c, siderophore, and other related proteins supported Fe(III) reduction. In addition, CQ-Y1 could survive at 10% NaCl (w/v) and 45°C, and temperature showed more pronounced effects than NaCl concentration on the bacterial growth. The maximum Fe(III) reduction ratio of CQ-Y1 reached 70.1% at 30°C without NaCl, and the reduction reaction remained active at 40°C with 3% NaCl (w/v). NaCl concentration was more effective than temperature on microbial Fe(III) reduction. And the reduction products under high temperature and high NaCl conditions were characterized as Fe₃(PO₄)₂, FeCl₂ and Fe(OH)₂.

Discussion

Accordingly, a Fe(III) reduction mechanism of CQ-Y1 mediated by Cytochrome c and flavin was hypothesised. These findings could provide information for a better understanding of the origin and evolution of genomic and metabolic diversity of S. xiamenensis.

Shewanella azerbaijanica sp. nov. a novel aquatic species with high bioremediation abilities

A novel Gram-negative, facultative anaerobic, rod-shaped, and non-motile bacterium with bio-degradation potential of polycyclic aromatic hydrocarbons (PAHs) and uranium bio-reduction, designated as RCRI7^T, was isolated from Qurugöl Lake water near Tabriz city. Strain RCRI7^T can grow in the absence of NaCl and tolerates up to 3% NaCl (optimum, 0-0.5%), at the temperature range of 4-45 °C (optimum, 30 °C) and a pH range of 6-9 (optimum, pH 7 ± 0.5). Results of phylogenetic analysis based on 16S rRNA gene sequence indicated that strain RCRI7^T is affiliated with the genus Shewanella, most closely related to Shewanella xiamenensis S4^T (99.1%) and Shewanella putrefaciens JCM 20190^T (98.9%). The genomic DNA G+C content of strain RCRI7^T is 41 mol%. The major fatty acids are C_16:1ω9c, C_18:1ω9c and iso-C_17:1ω5c. The OrthoANI and ANIb values between RCRI7^T and Shewanella xiamenensis S4^T were 87.4% and 87.7%, and between RCRI7^T and Shewanella putrefaciens JCM 20190^T were 79.5% and 79.7%, respectively. Strain RCRI7^T displayed dDDH values of 30.2% and 39.8% to Shewanella xiamenensis S4^T and Shewanella putrefaciens JCM 20190^T, respectively. The major polar lipids include phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The respiratory quinone is Q8. Based on the polyphasic evidence presented in this paper, strain RCRI7^T is considered to represent a novel species, with bioremediation potential, in the genus Shewanella, for which the name Shewanella azerbaijanica sp. nov. is proposed. The type strain is RCRI7^T (= JCM 17276^T) (= KCTC 62476^T).

Cupriavidus metallidurans NA4 actively forms polyhydroxybutyrate-associated uranium-phosphate precipitates

Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans NA4. Strain NA4 actively captured 98 ± 1% of the uranium in its biomass after growing 24 h in the presence of 100 µM uranyl nitrate. TEM HAADF-EDX microscopy confirmed intracellular uranium-phosphate precipitates that were mainly associated with polyhydroxybutyrate. Furthermore, whole transcriptome sequencing indicated a complex transcriptional response with upregulation of genes encoding general stress-related proteins and several genes involved in metal resistance. More in particular, gene clusters known to be involved in copper and silver resistance were differentially expressed. This study provides further insights into bacterial interactions with and their response to uranium. Our results could be promising for uranium bioremediation purposes with the multi-metal resistant bacterium C. metallidurans NA4.

U (VI) tolerance affects Shewanella sp. RCRI7 biological responses: growth, morphology and bioreduction ability

Native Shewanella sp. RCRI7 is recently counted as an operative bacterium in the uranium bio-reduction. The aim of this study was to investigate the effects of uranium tolerance on the morphology and population of RCRI7, following its potential removal capacity in different time intervals. In this research, the bacterial growth and uranium removal kinetic were evaluated in aerobic TSB medium, uranium-reducing condition (URC), aerobic uranium-containing (AUC) and anaerobic uranium-free (AUF) solution, following evaluations of omcAB gene expressions. In addition, spectrophotometry analyses were performed in URC confirming the bio-reduction mechanism. It was found that the bacteria can grow efficiently in the presence of 0.5 mM uranium anaerobically, unlike AUC and AUF solutions. Since the bacterium's adsorption capacity is quickly saturated, it can be deduced that uranium reduction should be dominant as incubation times proceed up to 84 h in URC. In 92 h incubation, the adsorbed uranium containing unreduced and reduced (U (IV) monomeric), was released to the solution due to either increased pH or bacterial death. In AUC and AUF, improper conditions lead to the reduced bacterial size (coccus-shape formation) and increased bacterial aggregations; however, membrane vesicles produced by the bacteria avoid the uranium incrustation in AUC. In overall, this study implies that Shewanella sp. RCRI7 are well tolerated by uranium under anaerobic conditions and the amount of regenerated uranium increases over time in the reduced form.