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.

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.

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.

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).

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.

New insights into the role of calcium in the bioreduction of uranium(VI) under varying pH conditions

The effect of calcium in the uranium-contaminated groundwater on U(VI)_aq bioreduction remains uncertain. Some studies indicated that the presence of calcium may inhibit the bioreduction. However, our calculations show the negative standard molar Gibbs free energy of reduction. The bioreduction of the ternary uranyl-carbonate-calcium complexes seems thermodynamically favorable at specific pH. Sorption and reduction experiments were conducted to gain new insights of calcium into the bioreduction. The results show that the complexes were greatly reduced by Shewanella putrefaciens in the slightly acidic pH ~6.0 and alkaline pH ~7.9 solutions with the relatively high CaCl₂ (1.0-6.0 mmol/L) although the reduction was difficult at the nearly neutral pH ~6.9. At pH ~6.9, the removal percentage of U(VI)_aq decreased from 97.0% to 24.4% with increasing CaCl₂ from 0 to 6.0 mmol/L, in contrast to the increasing percentage from 50.9% to 89.7% at pH ~7.9. The obvious removal of U(VI)_aq was ascribed to the bioreduction instead of the biosorption, as evidenced by XPS, HRTEM and UV-vis spectra. The calculations such as [Formula: see text] and [Formula: see text] partially accounted for the reduction mechanisms. Accordingly, the U(VI)_aq bioreduction is a promising method to remediate the groundwater even rich in calcium and carbonate.

pH-dependent microbial reduction of uranium(VI) in carbonate-free solutions: UV-vis, XPS, TEM, and thermodynamic studies

U(VI)_aq bioreduction has an important effect on the fate and transport of uranium isotopes in groundwater at nuclear test sites. In this study, we focus on the pH-dependent bioreduction of U(VI)_aq in carbonate-free solutions and give mechanistic insight into the removal kinetics of U(VI)_aq. An enhancement in the removal of U(VI)_aq with increasing pH was observed within 5 h, e.g., from 19.4% at pH 4.52 to 99.7% at pH 8.30. The removal of U(VI)_aq at pH 4.52 was due to the biosorption of U(VI)_aq onto the living cells of Shewanella putrefaciens, as evidenced by the almost constant UV-vis absorption intensity of U(VI)_aq immediately after contact with S. putrefaciens. Instead, the removal observed at pH 5.97 to 8.30 resulted from the bioreduction of U(VI)_aq. The end product of U(VI)_aq bioreduction was analyzed using XPS and HRTEM and identified as nanosized UO₂. An increasing trend in the biosorption of U(VI)_aq onto heat-killed cells was also observed, e.g., ~ 80% at pH 8.38. Evidently, the U(VI)_aq that sorbed onto the living cells at pH > 4.52 was further reduced to UO₂, although biosorption made a large contribution to the initial removal of U(VI)_aq. These results may reveal the removal mechanism, in which the U(VI)_aq that was sorbed onto cells rather than the U(VI)_aq complexed in solution was reduced. The decreases in the redox potentials of the main complex species of U(VI)_aq (e.g., [Formula: see text] and [Formula: see text]) with increasing pH support the proposed removal mechanism.

Humic acids facilitated microbial reduction of polymeric Pu(IV) under anaerobic conditions

Flavins and humic substances have been extensively studied with emphasis on their ability to transfer extracellular electrons to insoluble metal oxides. Nevertheless, whether the low-solubility Pu(IV) polymers are microbially reduced to aqueous Pu(III) remains uncertain. Experiments were conducted under anaerobic and slightly alkaline conditions to study the difference between humic acids and flavins to transport extracellular electrons to Pu(IV) polymers. Our study demonstrates that Shewanella putrefaciens was unable to directly reduce polymeric Pu(IV) with a notably low reduction rate (3.4×10^-12mol/L Pu(III)_aq within 144h). The relatively high redox potential of flavins reveals the thermodynamically unfavorable reduction: E_h(PuO₂(am)/Pu³⁺)<E_h^o'(FMN/FMNH₂)≈E_h^o'(RBF/RBFH₂)≈-220mV at pH7.2. The microbially reduced humic acids facilitated the extracellular electron transfer to the polymers and reduced polymeric Pu(IV) (2.1×10^-10mol/L Pu(III)_aq) 62 times more rapidly than the flavins. The driving force for electron transfer explains the observed reduction: E_h(HA_ox/HA_red)<E_h(PuO₂(am)/Pu³⁺) when S. putrefaciens oxidized lactate and respired on the humic acids. In contrast, flavins were able to substantially reduce aqueous Pu(IV)-EDTA (1.9×10^-9mol/L Pu(III)_aq) because of the available driving force for electron transfer: Δ_rG_m=-F[E_h(PuL₂^4-/PuL₂^5-)-E_h^o'(FMN/FMNH₂)]=-33.5kJ/mol is a result of E_h(PuL₂^4-/PuL₂^5-)≫E_h(PuO₂(am)/Pu³⁺), where L is the EDTA ligand. In the presence of humic acids, the reduction of Pu(IV)-EDTA exhibited the most rapid rate (2.2×10^-9mol/L Pu(III)_aq). This result further demonstrates that humic acids facilitated the extracellular electron transfer to polymeric and aqueous Pu(IV). Reductive solubilization of the polymers may enhance Pu mobility in the geosphere and hence increases risks to human health.