Uranium biomineralization as a result of bacterial phosphatase activity: insights from bacterial isolates from a contaminated subsurface

Long-term tracking of the microbiology of uranium-amended water-saturated bentonite microcosms: A mechanistic characterization of U speciation

Deep geological repositories (DGRs) stand out as one of the optimal options for managing high-level radioactive waste (HLW) such as uranium (U) in the near future. Here, we provide novel insights into microbial behavior in the DGR bentonite barrier, addressing potential worst-case scenarios such as waste leakage (e.g., U) and groundwater infiltration of electron rich donors in the bentonite. After a three-year anaerobic incubation, Illumina sequencing results revealed a bacterial diversity dominated by anaerobic and spore-forming microorganisms mainly from the phylum Firmicutes. Highly U tolerant and viable bacterial isolates from the genera Peribacillus, Bacillus, and some SRB such as Desulfovibrio and Desulfosporosinus, were enriched from U-amended bentonite. The results obtained by XPS and XRD showed that U was present as U(VI) and as U(IV) species. Regarding U(VI), we have identified biogenic U(VI) phosphates, U(UO2)·(PO4)2, located in the inner part of the bacterial cell membranes in addition to U(VI)-adsorbed to clays such as montmorillonite. Biogenic U(IV) species as uraninite may be produced as result of bacterial enzymatic U(VI) reduction. These findings suggest that under electron donor-rich water-saturation conditions, bentonite microbial community can control U speciation, immobilizing it, and thus enhancing future DGR safety if container rupture and waste leakage occurs.

Microbial consortium involved in ferromanganese and francolite biomineralization in an anchialine environment (Zinzulùsa Cave, Castro, Italy)

Tidally-influenced subterranean settings represent natural geomicrobiological laboratories, relatively unexplored, that facilitate the investigation of new biomineralization processes. The unusual water chemistry of Zinzulùsa Cave and its oligotrophic and aphotic conditions have allowed the development of a unique ecosystem in which complex bacterial activities induce rare biomineralization processes. A diversified microbial community develops on centimeter-thick crusts that form in the submerged part of the cave. The crusts are formed of Ca-phosphate minerals, mostly carbonate-fluoroapatite (francolite), covered by a black crust, few microns in thickness, composed of ferromanganiferous oxides (hematite and vernadite). Diffuse coccoidal and filamentous bacteria and amorphous organic matter are mixed with the minerals. The micromorphologies and comparative 16S rRNA gene-based metabarcoding analyses identify a "core microbiota" also common to other natural environments characterized by FeMn and Ca-phosphate mineralization. The microbiota is characterized by nitrifying, sulfide/sulfur/thiosulfate-oxidizing and sulfate/thiosulfate/sulfur-reducing bacteria. In addition, manganese-oxidizing bacteria include the recently described "Ca. Manganitrophus noduliformans" and an abundance of bacteria belonging to the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum, as well as Haliangiales (fruiting body-forming bacteria) and Hyphomicrobiales (stalked and budding bacteria) that are known to produce extracellular polymers that trap iron and manganese oxides. 16S rRNA gene metabarcoding analysis showed the presence of bacteria able to utilize many organic P substrates, including Ramlibacter, and SEM images revealed traces of fossilized microorganisms resembling "cable bacteria", which may play a role in Ca-phosphate biomineralization. Overall, the data indicate biomineralization processes induced by microbial metabolic activities for both ferromanganiferous oxide and francolite components of these crusts.

Acidovorax bellezanensis sp. nov., a novel bacterium from uranium mill tailings repository sites with selenium bioremediation capabilities

A Gram-stain-negative bacterial strain designated Be4T, belonging to the genus Acidovorax, was isolated from mining porewaters sampled in uranium mill tailings repository sites, located in Bellezane, near Bessines-sur-Gartempe (Limousin, France). Cells were facultative anaerobic, rod-shaped, non-endospore-forming and motile with flagella. The mean cell size was 1.25-1.31 μm long and 0.70-0.73 μm wide. Colonies were light yellow, opaque, circular, convex with smooth margins, and 1-2 mm in diameter. Growth occurs at 4-37 °C and between pH 5.5-9.0. It differed from its phylogenetically related strains by phenotypic and physiological characteristics such as growth at 4 °C, presence of acid phosphatase, naphthol-AS-BI-phosphohydrolase and β-glucosidase enzymatic activities, and fermentation of l-xylose and esculin. The major fatty acids were C16:0, C16:1 ω7c/C16:1 ω6c, C17:0 cyclo and C18:1 ω7c. Phylogenetic analysis based on 16S rRNA and 938 core genes, confirmed its placement within the genus Acidovorax as a novel species. Strain Be4T showed highest 16S rRNA sequence similarity to Acidovorax antarcticus (98.2 %), Acidovorax radicis (97.9 %), Acidovorax temperans (97.8 %) and Acidovorax facilis (97.7 %). The genome of strain Be4T is 5,041,667 bp size with a DNA G + C content of 65.15 %. By automatic annotation numerous sequences involved in the interaction with metals/metalloids including some genes related to Se uptake and selenite resistance were detected in its genome. The average nucleotide identity (ANI) values calculated from whole genome sequences between strain Be4T and the most closely related strains A. radicis and A. facilis were below the threshold value of 95 %. Thus, the data from the phylogenetic, physiological, biochemical, and genomic analyses clearly indicates that strain Be4T represents a novel species with the suggested name Acidovorax bellezanensis sp. nov. The type strain is Acidovorax bellezanensis Be4T (=DSM116209T = CECT30865T). This novel species, due to its unique isolation source, genomic analysis, and preliminary laboratory tests where it was able to reduce toxic Se(IV) to less harmful Se(0) in the form of nanoparticles, holds great potential for further investigation in bioremediation, particularly concerning Se.

Comprehensive bioremediation effect of phosphorus-mineralized bacterium Enterobacter sp. PMB-5 on cadmium contaminated soil-crop system

Phosphate-mineralizing bacteria (PMBs) have been widely studied by inducing phosphate heavy metal precipitation, but current researches neglect to study their effects on soil-microbe-crop systems on cadmium (Cd) contaminated. Based on this, a strain PMB, Enterobacter sp. PMB-5, was inoculated into Cd contaminated pots to detect soil characteristics, Cd occurrence forms, soil biological activities, plant physiological and biochemical indicators. The results showed that the inoculation of strain PMB-5 significantly increased the available phosphorus content (85.97%-138.64%), Cd-residual fraction (11.04%-29.73%), soil enzyme activities (31.94%-304.63%), plant biomass (6.10%-59.81%), while decreased the state of Cd-HOAc (11.50%-31.17%) and plant bioconcentration factor (23.76%-44.24%). These findings indicated that strain PMB-5 could perform the function of phosphorus solubilization to realize the immobilization of Cd in the complex soil environment. Moreover, SEM-EDS, FTIR, XPS, and XRD analysis revealed that strain PMB-5 does not significantly alter the soil morphology, structure, elemental distribution, and chemical composition, which suggested that remediation of Cd contamination using strain PMB-5 would not further burden the soil. This research implies that PMB-5 could be a safe and effective bioinoculant for remediating Cd-contaminated soils, contributing to the sustainable management of soil health in contaminated environments.

Isolation and identification of a high-efficiency hexavalent uranium adsorption strain and preliminary study of the influencing factors and adsorption mechanism

In this study, a bacterial strain Chryseobacterium bernardetii WK-3 was isolated from the rhizosphere soil of a uranium tailings in Southern China. It can efficiently adsorb hexavalent uranium with an adsorption ratio of 92.3%. The influence of different environmental conditions on the adsorption ratio of Chryseobacterium bernardetii strain WK-3 was investigated, and the adsorption mechanism was preliminarily discussed by scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS). The results showed that the optimal adsorption conditions for U(VI) by Chryseobacterium bernardetii strain WK-3 were pH = 5, temperature 30 ℃, NaCl concentration 1%, and inoculation volume 10%. When the initial concentration of U was 50 ~ 150 mg/L, the adsorption capacity of Chryseobacterium bernardetii strain WK-3 to U(VI) reached the maximum and maintained the equilibrium at 44 h. SEM-EDS results showed that phosphorus in cells participates in the interaction of uranyl ions, which may indicate that phosphate was produced during cell metabolism and was further combined to form U(VI)-phosphate minerals. In summary, Chryseobacterium bernardetii strain WK-3 would be a promising alternative for environmental uranium contamination remediation.

Assessing the chronic effect of the bioavailable fractions of radionuclides and heavy metals on stream microbial communities: A case study at the Rophin mining site

This study aimed to assess the potential impact of long-term chronic exposure (69 years) to naturally-occurring radionuclides (RNs) and heavy metals on microbial communities in sediment from a stream flowing through a watershed impacted by an ancient mining site (Rophin, France). Four sediment samples were collected along a radioactivity gradient (for 238U368 to 1710 Bq.Kg-1) characterized for the presence of the bioavailable fractions of radionuclides (226Ra, 210Po), and trace metal elements (Th, U, As, Pb, Cu, Zn, Fe). Results revealed that the available fraction of contaminants was significant although it varied considerably from one element to another (0 % for As and Th, 5-59 % for U). Nonetheless, microbial communities appeared significantly affected by such chronic exposure to (radio)toxicities. Several microbial functions carried by bacteria and related with carbon and nitrogen cycling have been impaired. The high values of fungal diversity and richness observed with increasing downstream contamination (H' = 4.4 and Chao1 = 863) suggest that the community had likely shifted toward a more adapted/tolerant one as evidenced, for example, by the presence of the species Thelephora sp. and Tomentella sp. The bacterial composition was also affected by the contaminants with enrichment in Myxococcales, Acidovorax or Nostocales at the most contaminated points. Changes in microbial composition and functional structure were directly related to radionuclide and heavy metal contaminations, but also to organic matter which also significantly affected, directly or indirectly, bacterial and fungal compositions. Although it was not possible to distinguish the specific effects of RNs from heavy metals on microbial communities, it is essential to continue studies considering the available fraction of elements, which is the only one able to interact with microorganisms.

Bibliometric insights into the evolution of uranium contamination reduction research topics: Focus on microbial reduction of uranium

Confronting the threat of environment uranium pollution, decades of research have yielded advanced and significant findings in uranium bioremediation, resulting in the accumulation of tremendous amount of high-quality literature. In this study, we analyzed over 10,000 uranium reduction-related papers published from 1990 to the present in the Web of Science based on bibliometrics, and revealed some critical information on knowledge structure, thematic evolution and additional attention. Methods including contribution comparison, co-occurrence and temporal evolution analysis are applied. The results of the distribution and impact analysis of authors, sources, and journals indicated that the United States is a leader in this field of research and China is on the rise. The top keywords remained stable, primarily focused on chemicals (uranium, iron, plutonium, nitrat, carbon), characters (divers, surfac, speciat), and microbiology (microbial commun, cytochrome, extracellular polymeric subst). Keywords related to new strains, reduction mechanisms and product characteristics demonstrated the strongest uptrend, while some keywords related to mechanism and performance were clearly emerging in the past 5 years. Furthermore, the evolution of the thematic progression can be categorized into three stages, commencing with the discovery of the enzymatic reduction of hexavalent uranium to tetravalent uranium, developing in the groundwater remediation process at uranium-contaminated sites, and delving into the research on microbial reduction mechanisms of uranium. For future research, enhancing the understanding of mechanisms, improving uranium removal performance, and exploring practical applications can be considered. This study provides unique insights into microbial uranium reduction research, providing valuable references for related studies in this field.

Uranium biomineralization by immobilized Chryseobacterium sp. strain PMSZPI cells for efficient uranium removal

Uranium (U) contamination is hazardous to human health and the environment owing to its radiotoxicity and chemical toxicity and needs immediate attention. In this study, the immobilized biomass of Chryseobacterium sp. strain PMSZPI isolated from U enriched site, was investigated for U(VI) biomineralization in batch and column set-up. Under batch mode, the fresh or lyophilized cells successfully entrapped in calcium alginate beads demonstrated effectual U precipitation under acid and alkaline conditions. The maximum removal was detected at pH 7 wherein ∼98-99% of uranium was precipitated from 1 mM uranyl carbonate solution loading ∼350 mg U/g of biomass within 24 h in the presence of organic phosphate substrate. The resulting uranyl phosphate precipitates within immobilized biomass loaded beads were observed by SEM-EDX and TEM while the formation of U biomineral was confirmed by FTIR and XRD. Retention of phosphatase activity without any loss of uranium precipitation ability was observed for alginate beads with lyophilized biomass stored for 90 d at 4 °C. Continuous flow through experiment with PMSZPI biomass immobilized in polyacrylamide gel exhibited U loading of 0.8 g U/g of biomass at pH 7 using 1 l of 1 mM uranyl solution. This investigation established the feasibility for the application of immobilized PMSZPI biomass for field studies. ENVIRONMENTAL IMPLICATION: Uranium contamination is currently a serious environmental concern owing to anthropogenic activities and needs immediate attention. We have developed here a biotechnological method for successful uranium removal using immobilized cells of a uranium tolerant environmental bacterium, Chryseobacterium sp. strain PMSZPI isolated from U ore deposit via phosphatase enzyme mediated uranium precipitation. The ability of immobilized PMSZPI cells to precipitate U(VI) as long-term stable U phosphates under environmental conditions relevant for contaminated waters containing high concentrations of U that exerts toxicity for biological systems is explored here. The long term stability of the immobilized biomass without compromising its U removal capacity shows the relevance of the bioremediation strategy for uranium contamination proposed in this work.

Periodic trends in trivalent actinide halides, phosphates, and arsenates

Due to the limited abundance of the actinide elements, computational methods, for now, remain an exclusive avenue to investigate the periodic trends across the actinide series. As every actinide element can exhibit a +3-oxidation state, we have explored model systems of gas-phase actinide trihalides, phosphates, and arsenates across the series to capture the periodic trends. By doing so, we were able to capture the periodic trends down the halogen series as well, and for the first time we are reporting a study on actinide astatides. Using scalar and spin-orbit relativistic Density Functional Theory (DFT) calculations, we have explored the variations in bond lengths, bond angles, and the charges on actinides (An). Despite the use of different sets of ligands, the trends remain similar. The properties of trivalent Pa, U, Np, and Pu are nearly identical; similar ionic radii could be the reason. The actinide elements show a tendency to exhibit a pre-Pu and a post-Cm behaviour, with Am acting as a switch. This could be due to the change in the behaviour from d-f-type to f-filling/d-type at around Pu-Cm in the actinides as already proposed in the previous literature. Bond lengths in the AnX3 increase down the halide series, and the atomic charges decrease on the actinide elements.

Phosphate (Bio)mineralization Remediation of 90Sr-Contaminated Groundwaters

Historical operations at nuclear mega-facilities such as Hanford, USA, and Sellafield, UK have led to a legacy of radioactivity-contaminated land. Calcium phosphate phases (e.g., hydroxyapatite) can adsorb and/or incorporate radionuclides, including 90Sr. Past work has shown that aqueous injection of Ca-phosphate-generating solutions into the contaminated ground on both laboratory and field scales can reduce the amount of aqueous 90Sr in the systems. Here, two microbially mediated phosphate amendment techniques which precipitated Ca-phosphate, (i) Ca-citrate/Na-phosphate and (ii) glycerol phosphate, were tested in batch experiments alongside an abiotic treatment ((iii) polyphosphate), using stable Sr and site relevant groundwaters and sediments. All three amendments led to enhanced Sr removal from the solution compared to the sediment-only control. The Ca-citrate/Na-phosphate treatment removed 97%, glycerol phosphate 60%, and polyphosphate 55% of the initial Sr. At experimental end points, scanning electron microscopy showed that Sr-containing, Ca-phosphate phases were deposited on sediment grains, and XAS analyses of the sediments amended with Ca-citrate/Na-phosphate and glycerol phosphate confirmed Sr incorporation into Ca-phosphates occurred. Overall, Ca-phosphate-generating treatments have the potential to be applied in a range of nuclear sites and are a key option within the toolkit for 90Sr groundwater remediation.

Concurrent reductive decontamination of chromium (VI) and uranium (VI) in groundwater by Fe(0)-based autotrophic bioprocess

The co-presence of chromium (VI) [Cr(VI)] and uranium (VI) [U(VI)] is widely found in groundwater, imposing severe risks on human health. Although zerovalent iron [Fe(0)] supports superb performance for bioreduction of Cr(VI) and U(VI) individually, the biogeochemical process involving their concurrent removal with Fe(0) as electron donor remains unexplored. In the 6-d batch study, 86.1% ± 0.7% of Cr(VI) was preferentially eliminated, while 78.4% ± 0.5% of U(VI) removal was achieved simultaneously. Efficient removal of Cr(VI) (100%) and U(VI) (51.2% ∼ 100%) was also obtained in a continuous 160-d column experiment. As a result, Cr(VI) and U(VI) were reduced to less mobile Cr(III) and insoluble U(IV), respectively. 16 S rRNA sequencing was performed to investigate the dynamics of microbial community. Delftia, Acinetobacter, Pseudomonas and Desulfomicrobium were the major contributors mediating the bioreduction process. The initial Cr(VI) and hydraulic retention time (HRT) incurred pronounced effects on community diversity, which in turn altered the reactor's performance. The enrichment of Cr(VI) resistance (chrA), U(VI) reduction (dsrA) and Fe(II) oxidation (mtrA) genes were observed by reverse transcription qPCR. Cytochrome c, glutathione and NADH as well as VFAs and gas metabolites also involved in the bioprocess. This study demonstrated a promising approach for removing the combined contaminants of Cr(VI) and U(VI) in groundwater.

Impact of microbial processes on the safety of deep geological repositories for radioactive waste

To date, the increasing production of radioactive waste due to the extensive use of nuclear power is becoming a global environmental concern for society. For this reason, many countries have been considering the use of deep geological repositories (DGRs) for the safe disposal of this waste in the near future. Several DGR designs have been chemically, physically, and geologically well characterized. However, less is known about the influence of microbial processes for the safety of these disposal systems. The existence of microorganisms in many materials selected for their use as barriers for DGRs, including clay, cementitious materials, or crystalline rocks (e.g., granites), has previously been reported. The role that microbial processes could play in the metal corrosion of canisters containing radioactive waste, the transformation of clay minerals, gas production, and the mobility of the radionuclides characteristic of such residues is well known. Among the radionuclides present in radioactive waste, selenium (Se), uranium (U), and curium (Cm) are of great interest. Se and Cm are common components of the spent nuclear fuel residues, mainly as 79Se isotope (half-life 3.27 × 105 years), 247Cm (half-life: 1.6 × 107 years) and 248Cm (half-life: 3.5 × 106 years) isotopes, respectively. This review presents an up-to-date overview about how microbes occurring in the surroundings of a DGR may influence their safety, with a particular focus on the radionuclide-microbial interactions. Consequently, this paper will provide an exhaustive understanding about the influence of microorganisms in the safety of planned radioactive waste repositories, which in turn might improve their implementation and efficiency.

PrsQ2, a small periplasmic protein involved in increased uranium resistance in the bacterium Cupriavidus metallidurans

Uranium contamination is a widespread problem caused by natural and anthropogenic activities. Although microorganisms thrive in uranium-contaminated environments, little is known about the actual molecular mechanisms mediating uranium resistance. Here, we investigated the resistance mechanisms driving the adaptation of Cupriavidus metallidurans NA4 to toxic uranium concentrations. We selected a spontaneous mutant able to grow in the presence of 1 mM uranyl nitrate compared to 250 µM for the parental strain. The increased uranium resistance was acquired via the formation of periplasmic uranium-phosphate precipitates facilitated by the increased expression of a genus-specific small periplasmic protein, PrsQ₂, regulated as non-cognate target of the CzcS₂-CzcR₂ two-component system. This study shows that bacteria can adapt to toxic uranium concentrations and explicates the complete genetic circuit behind the adaptation.

Effect of different phosphate sources on uranium biomineralization by the Microbacterium sp. Be9 strain: A multidisciplinary approach study

Introduction

Industrial activities related with the uranium industry are known to generate hazardous waste which must be managed adequately. Amongst the remediation activities available, eco-friendly strategies based on microbial activity have been investigated in depth in the last decades and biomineralization-based methods, mediated by microbial enzymes (e.g., phosphatase), have been proposed as a promising approach. However, the presence of different forms of phosphates in these environments plays a complicated role which must be thoroughly unraveled to optimize results when applying this remediation process.

Methods

In this study, we have looked at the effect of different phosphate sources on the uranium (U) biomineralization process mediated by Microbacterium sp. Be9, a bacterial strain previously isolated from U mill tailings. We applied a multidisciplinary approach (cell surface characterization, phosphatase activity, inorganic phosphate release, cell viability, microscopy, etc.).

Results and Discussion

It was clear that the U removal ability and related U interaction mechanisms by the strain depend on the type of phosphate substrate. In the absence of exogenous phosphate substrate, the cells interact with U through U phosphate biomineralization with a 98% removal of U within the first 48 h. However, the U solubilization process was the main U interaction mechanism of the cells in the presence of inorganic phosphate, demonstrating the phosphate solubilizing potential of the strain. These findings show the biotechnological use of this strain in the bioremediation of U as a function of phosphate substrate: U biomineralization (in a phosphate free system) and indirectly through the solubilization of orthophosphate from phosphate (P) containing waste products needed for U precipitation.

Surface biomineralization of uranium onto Shewanella putrefaciens with or without extracellular polymeric substances

The influence of extracellular polymeric substances (EPS) on the interaction between uranium [U(VI)] and Shewanella putrefaciens (S. putrefaciens), especially the U(VI) biomineralization process occurring on whole cells and cell components of S. putrefaciens was investigated in this study. The removal efficiency of U(VI) by S. putrefaciens was decreased by 22% after extraction of EPS. Proteins were identified as the main components of EPS by EEM analysis and were determined to play a major role in the biosorption of uranium. SEM-EDS results showed that U(VI) was distributed around the whole cell as 500-nanometer schistose structures, which consisted primarily of U and P. However, similar uranium lamellar crystal were wrapped only on the surface of EPS-free S. putrefaciens cells. FTIR and XPS analysis indicated that phosphorus- and nitrogen-containing groups played important roles in complexing U (VI). XRD and U L_III-edge EXAFS analyses demonstrated that the schistose structure consisted of hydrogen uranyl phosphate [H₂(UO₂)₂(PO₄)₂•8H₂O]. Our study provides new insight into the mechanisms of induced uranium crystallization by EPS and cell wall membranes of living bacterial cells under aerobic conditions.

The dynamic behavior and mechanism of uranium (VI) biomineralization in Enterobacter sp. X57

The important role of microbes in the biomineralization and migration behavior of uranium in the field of environmental chemistry has been well emphasized in previous work. However, limited work on mineralization processes of indigenous microorganism has prevented us from a deeper understanding of the process and mechanisms of uranium biomineralization. In this work, the dynamic process and mechanism of uranium biomineralization in Enterobacter sp. X57, a novel uranium-tolerant microorganism separated from uranium contaminated soil, were systematically investigated. Enterobacter sp. X57 can induce intracellular mineralization of U (VI) to Uramphite (NH₄UO₂PO₄·3H₂O) under neutral conditions by alkaline phosphatase. In this biomineralization process, soluble U (VI) first bonded with the amino and phosphate groups on the plasma membrane, providing initial nucleation site for the formation of U (VI) biominerals. Then the impairment of cell barrier function and the enhancement of alkaline phosphatase metabolism occurred with the accumulation of uranium in cells, creating a possible pathway for soluble U (VI) to diffuse into the cell and be further mineralized into U (VI)-phosphate minerals. All the results revealed that the intracellular biomineralization of uranium by Enterobacter sp. X57 was a combined result of biosorption, intracellular accumulation and phosphatase metabolism. These findings may contribute to a better understanding of uranium biomineralization behavior and mechanism of microorganisms, as well as possible in-situ bioremediation strategies for uranium by indigenous microorganisms.

Risk of colloidal and pseudo-colloidal transport of actinides in nitrate contaminated groundwater near a radioactive waste repository after bioremediation

The possible role of biogeochemical processes in the transport of colloidal and pseudo-colloidal U, Np, and Pu during bioremediation of radionuclide- and nitrate-contaminated groundwater was investigated. In two laboratory experiments with water samples taken from contaminated aquifers before and post bioremediation, we found that microbial processes could cause clayed, ferruginous, and actinide colloids to coagulate. The main mechanisms are biogenic insoluble ferrous iron species formations (goethite, pyrrhotite, siderite, troilite, and ferrihydrite), the aggregation of clay particles by microbial metabolites, and the immobilization of actinides in the bacterial cells, large polymers, and iron and clayed sediments. This process decreases the risk of colloidal and pseudo-colloidal transport of actinides.

Molecular Mechanisms Underlying Bacterial Uranium Resistance

Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.

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.

Effect of Temperature and Cell Viability on Uranium Biomineralization by the Uranium Mine Isolate Penicillium simplicissimum

The remediation of heavy-metal-contaminated sites represents a serious environmental problem worldwide. Currently, cost- and time-intensive chemical treatments are usually performed. Bioremediation by heavy-metal-tolerant microorganisms is considered a more eco-friendly and comparatively cheap alternative. The fungus Penicillium simplicissimum KS1, isolated from the flooding water of a former uranium (U) mine in Germany, shows promising U bioremediation potential mainly through biomineralization. The adaption of P. simplicissimum KS1 to heavy-metal-contaminated sites is indicated by an increased U removal capacity of up to 550 mg U per g dry biomass, compared to the non-heavy-metal-exposed P. simplicissimum reference strain DSM 62867 (200 mg U per g dry biomass). In addition, the effect of temperature and cell viability of P. simplicissimum KS1 on U biomineralization was investigated. While viable cells at 30°C removed U mainly extracellularly via metabolism-dependent biomineralization, a decrease in temperature to 4°C or use of dead-autoclaved cells at 30°C revealed increased occurrence of passive biosorption and bioaccumulation, as confirmed by scanning transmission electron microscopy. The precipitated U species were assigned to uranyl phosphates with a structure similar to that of autunite, via cryo-time-resolved laser fluorescence spectroscopy. The major involvement of phosphates in U precipitation by P. simplicissimum KS1 was additionally supported by the observation of increased phosphatase activity for viable cells at 30°C. Furthermore, viable cells actively secreted small molecules, most likely phosphorylated amino acids, which interacted with U in the supernatant and were not detected in experiments with dead-autoclaved cells. Our study provides new insights into the influence of temperature and cell viability on U phosphate biomineralization by fungi, and furthermore highlight the potential use of P. simplicissimum KS1 particularly for U bioremediation purposes.

Graphical Abstract

Mechanism of recombinant bacteria adsorb UO22+ under culture condition

Research on the ability and mechanism of genetically recombinant E. coli DH5α containing DSR A gene to enrich uranium under culture conditions provides a theoretical basis for the application of the bacteria in the treatment of uranium pollution. By exploring the influence of factors such as the initial concentration of uranium, culture time, and inoculation amount on the characteristics of uranium enrichment in genetically recombinant E. coli, using FTIR, SEM-EDS, XPS and XRD explore the mechanism of uranium-enriched bacteria. The results showed that when initial UO₂²⁺ concentration reach 600 mg/L, E. Coli D1 could not survived, indicated that the maximum tolerance concentration is lower than 600 mg/L. While concentration between 0∼500 mg/L, strains D1 can grow normally and has the ability to enrich uranium. In the prime stage, strains D1 resist toxics through release inorganic phosphates to precipitate UO₂²⁺ on cell wall, after 96 h, most UO₂²⁺ were transferred into cytoplasm and metabolized into U(IV) which is less toxic. In the metabolize process, all groups involved in metabolizing UO₂²⁺, especially protein contain groups like hydroxyl, amine and carboxyl paly a huge role. It shows that within a certain concentration rage, strains D1 has a good enrichment effect on uranium under culture conditions.

Uranium removal from complex mining waters by alginate beads doped with cells of Stenotrophomonas sp. Br8: Novel perspectives for metal bioremediation

Uranium-containing effluents generated by nuclear energy industry must be efficiently remediated before release to the environment. Currently, numerous microbial-based strategies are being developed for this purpose. In particular, the bacterial strain Stenotrophomonas sp. Br8, isolated from U mill tailings porewaters, has been already shown to efficiently precipitate U(VI) as stable U phosphates mediated by phosphatase activity. However, the upscaling of this strategy should overcome some constraints regarding cell exposure to harsh environmental conditions. In the present study, the immobilization of Br8 biomass in an inorganic matrix was optimized to provide protection to the cells as well as to make the process more convenient for real-scale utilization. The use of biocompatible, highly porous alginate beads for Br8 cells immobilization resulted the best alternative when investigating by a multidisciplinary approach (High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy (HAADF-STEM), Environmental Scanning Electron Microscopy (ESEM), Fourier Transform Infrared Spectroscopy with Attenuated Total Reflectance, etc.) several consolidated entrapment methods. This biomaterial was applied to complex real U mining porewaters (containing 47 mg/L U) in presence of an organic phosphate source (glycerol-2-phosphate) to produce reactive free orthophosphates through Br8 phosphatase activity. Uranium immobilization rates around 98 % were observed after one cycle of 72 h. In terms of U removal ability as a function of biomass, Br8-doped alginate beads were determined to remove up to 1199.5 mg U/g dry biomass over two treatment cycles. Additionally, optimized conditions for storing Br8-doped beads and for a correct application were assessed. Results for U accumulation kinetics and HAADF-STEM/ESEM analyses revealed that U removal by the immobilized cells is a biphasic process combining a first passive U sorption onto bead and/or cell surfaces and a second slow active biomineralization. This work provides new practical insights into the biological and physico-chemical parameters governing a high-efficient U bioremediation process based on the phosphatase activity of immobilized bacterial cells when applied to complex mining waters under laboratory conditions.

Multisystem combined uranium resistance mechanisms and bioremediation potential of Stenotrophomonas bentonitica BII-R7: Transcriptomics and microscopic study

The potential use of microorganisms in the bioremediation of U pollution has been extensively described. However, a lack of knowledge on molecular resistance mechanisms has become a challenge for the use of these technologies. We reported on the transcriptomic and microscopic response of Stenotrophomonas bentonitica BII-R7 exposed to 100 and 250 μM of U. Results showed that exposure to 100 μM displayed up-regulation of 185 and 148 genes during the lag and exponential phases, respectively, whereas 143 and 194 were down-regulated, out of 3786 genes (>1.5-fold change). Exposure to 250 μM of U showed up-regulation of 68 genes and down-regulation of 290 during the lag phase. Genes involved in cell wall and membrane protein synthesis, efflux systems and phosphatases were up-regulated under all conditions tested. Microscopic observations evidenced the formation of U-phosphate minerals at membrane and extracellular levels. Thus, a biphasic process is likely to occur: the increased cell wall would promote the biosorption of U to the cell surface and its precipitation as U-phosphate minerals enhanced by phosphatases. Transport systems would prevent U accumulation in the cytoplasm. These findings contribute to an understanding of how microbes cope with U toxicity, thus allowing for the development of efficient bioremediation strategies.

Influence of Uranium Concentration and pH on U-Phosphate Biomineralization by Caulobacter OR37

Uranium contamination of soils and groundwater in the United States represents a significant health risk and will require multiple remediation approaches. Microbial phosphatase activity coupled to the addition of an organic P source has recently been studied as a remediation strategy that provides an extended release of inorganic P (Pi) into U-contaminated sites, resulting in the precipitation of meta-autunite minerals. Previous laboratory- and field-based biomineralization studies have investigated environments with relatively high U concentrations (>20 μM). However, most contaminated sites have much lower U concentrations (<2 μM). The Environmental Protection Agency (EPA) limit for U in drinking water is 0.126 μM. Reaching this regulatory limit becomes challenging as U concentrations approach autunite solubility. We studied the precipitation of U(VI)-phosphate minerals by an environmental isolate of Caulobacter sp. (strain OR37) from an Oak Ridge, Tennessee, U-contaminated site. Abiotic U(VI) solubility experiments reveal that U(VI)-phosphate minerals do not form in the presence of excess Pi (500 μM) when U(VI) concentrations are <1 μM and pH is <5. When OR37 cells are reacted under the same conditions with Pi or glycerol-2-phosphate, U(VI)-phosphate mineral formation was observed, along with the formation of intracellular polyphosphate granules. These results show that bacteria provide supersaturated microenvironments needed for U(VI)-phosphate mineralization while hydrolyzing organic P sources. This provides a pathway to lower U concentrations to below EPA limits for drinking water.

Advances in microbial remediation for heavy metal treatment: a mini review

Abstract

In recent years, microbiological treatment to remediate contamination by heavy metals has aroused public attention as such pollution has seriously threatens ecosystems and human health and impedes sustainable development. However, the aspect of actual industrial wastewater and solid waste remediation by microorganisms is not explored sufficiently. And what we focus on is technical field of microbial remediation. Therefore, in this review, we discuss and summarize heavy metal treatment via microbiological approaches in different media, including wastewater, solid waste from industrial factories and polluted sites. We also clarify the technical applicability from the perspective of biosorption, bioleaching, biominerization, etc. In particular, the exploration of the combination of microbiological approaches with chemical methods or phytoextraction are scrutinized in this review relative to real waste heavy metal remediation. Furthermore, we highlight the importance of hyperaccumulator endophytes.

Graphical abstract

High-efficient microbial immobilization of solved U(VI) by the Stenotrophomonas strain Br8

The environmental impact of uranium released during nuclear power production and related mining activity is an issue of great concern. Innovative environmental-friendly water remediation strategies, like those based on U biomineralization through phosphatase activity, are desirable. Here, we report the great U biomineralization potential of Stenotrophomonas sp. Br8 CECT 9810 over a wide range of physicochemical and biological conditions. Br8 cells exhibited high phosphatase activity which mediated the release of orthophosphate in the presence of glycerol-2-phosphate around pH 6.3. Mobile uranyl ions were bioprecipitated as needle-like fibrils at the cell surface and in the extracellular space, as observed by Scanning Transmission Electron Microscopy (STEM). Extended X-Ray Absorption Fine Structure (EXAFS) and X-Ray Diffraction (XRD) analyses showed the local structure of biogenic U precipitates to be similar to that of meta-autunite. In addition to the active U phosphate biomineralization process, the cells interact with this radionuclide through passive biosorption, removing up to 373 mg of U per g of bacterial dry biomass. The high U biomineralization capacity of the studied strain was also observed under different conditions of pH, temperature, etc. Results presented in this work will help to design efficient U bioremediation strategies for real polluted waters.

Redox mechanism and stability of uranyl phosphites at mineral surfaces: Cooperative proton/electron transfer and high efficacy for Uranium(VI) reduction

Uranium phosphites have recently emerged as promising materials to remediate radioactive contamination. In this study, the redox mechanisms of uranyl phosphites at mineral surfaces have been addressed by periodic DFT calculations with dispersion corrections. Different from other ligands, the phosphite anions (H₂PO₃^-, HPO₃^2-) are efficient reducing agents for uranyl reduction, and the redox reactions are divided into three steps, as isomerization between two phosphite anion isomers (Step 1), conformational transition (Step 2) and dissociation of the water molecule (Step 3). A second water molecule is critical to lower the activation barriers of Step 1, and all activation barriers are moderate so that the redox reactions occur favorably under normal conditions, which are further dramatically accelerated by the highly exergonic Step 3. Accordingly, formation of uranyl phosphites becomes an effective approach to manage uranium pollution. Moreover, the lower activation barriers for H₂PO₃^- rather than HPO₃^2- rationalize the superior reduction activities of uranyl phosphites and the enhanced stability of U(IV) products at lower pH conditions. Owing to the cooperative proton/electron transfer, the U(VI) reduction to U(IV) and P(III) oxidation to P(V) are completed within one step, with transition states being featured by the U(V) and P(IV) species.

Profiling native aquifer bacteria in a uranium roll-front deposit and their role in biogeochemical cycle dynamics: Insights regarding in situ recovery mining

A uranium-mineralized sandy aquifer, planned for mining by means of uranium in situ recovery (U ISR), harbors a reservoir of bacterial life that may influence the biogeochemical cycles surrounding uranium roll-front deposits. Since microorganisms play an important role at all stages of U ISR, a better knowledge of the resident bacteria before any ISR actuations is essential to face environmental quality assessment. The focus here was on the characterization of bacteria residing in an aquifer surrounding a uranium roll-front deposit that forms part of an ISR facility project at Zoovch Ovoo (Mongolia). Water samples were collected following the natural redox zonation inherited in the native aquifer, including the mineralized orebody, as well as compartments located both upstream (oxidized waters) and downstream (reduced waters) of this area. An imposed chemical zonation for all sensitive redox elements through the roll-front system was observed. In addition, high-throughput sequencing data showed that the bacterial community structure was shaped by the redox gradient and oxygen availability. Several interesting bacteria were identified, including sulphate-reducing (e.g. Desulfovibrio, Nitrospira), iron-reducing (e.g. Gallionella, Sideroxydans), iron-oxidizing (e.g. Rhodobacter, Albidiferax, Ferribacterium), and nitrate-reducing bacteria (e.g. Pseudomonas, Aquabacterium), which may also be involved in metal reduction (e.g. Desulfovibrio, Ferribacterium, Pseudomonas, Albidiferax, Caulobacter, Zooglea). Canonical correspondence analysis (CCA) and co-occurrence patterns confirmed strong correlations among the bacterial genera, suggesting either shared/preferred environmental conditions or the performance of similar/complementary functions. As a whole, the bacterial community residing in each aquifer compartment would appear to define an ecologically functional ecosystem, containing suitable microorganisms (e.g. acidophilic bacteria) prone to promote the remediation of the acidified aquifer by natural attenuation. Assessing the composition and structure of the aquifer's native bacteria is a prerequisite for understanding natural attenuation and predicting the role of bacterial input in improving ISR efficiency.

Effect of Leifsonia sp. on retardation of uranium in natural soil and its potential mechanisms

Uranium mining and milling activities for many years resulted in release of uranium into the adjoining soil in varying degrees. Bioremediation approaches (i.e., immobilization via the action of bacteria) resulting in uranium bearing solid is supposed as an economic and clean in-situ approach for the treatment of uranium contaminated sites. This study purposes to determine the immobilization efficiency of uranium in soil by Leifsonia sp. The results demonstrated that cells have a good proliferation ability under the stress of uranium and play a role in retaining uranium in soil. Residual uranium in active Leifsonia-medium group (66%) was higher than that in the controls, which was 31% in the deionised water control, 46% in the Leifsonia group, and 47% in the medium group, respectively. This indicated that Leifsonia sp. facilitates the immobilization efficiency of uranium in soil by converting part of the reducible and oxidizable fraction of uranium into the residual fraction. X-ray photoelectron fitting results showed that tetravalent states uranium existed in the soil samples, which indicated that the hexavalent uranium was converted into tetravalent by cells. This is the first report of effect of Leifsonia sp. on uranium immobilization in soil. The findings implied that Leifsonia sp. could, to some extent, prevent the migration and diffusion of uranium in soil by changing the chemical states into less toxicity and less risky forms.

The utilization of biomineralization technique based on microbial induced phosphate precipitation in remediation of potentially toxic ions contaminated soil: A mini review

In recent years, many studies have been devoted to investigate the application of microbial induced phosphate precipitation (MIPP) process for potentially toxic element polluted soil remediation. MIPP biomineralization technique exhibits a great potential to efficiently remediate polluted soil considering its low cost, green and ecofriendly process, and simple in operation. This paper represented a review on the state of the art of polluted soil remediation based on MIPP technique. Briefly, certain defined criteria on targeted microbe selection was discussed; an overall review on the utilization of MIPP process for toxic ions biomineralization in soil was provided; influencing factors reported in the literature, such as pH, temperature, humic substances, coexisting ions, effective microbial population, and enzyme activity, were then comprehensively reviewed; finally; a special emphasis was given to enhance MIPP remediation performance in soil in future research.

Uranium bioremediation by acid phosphatase activity of Staphylococcus aureus biofilms: Can a foe turn a friend?

In this study, Staphylococcus aureus biofilms, which are considered a foe for being pathogenic, were tested for their uranium bioremediation capacity to find out if they can turn out to be a friend. Acid phosphatase activity, which is speculated to aid in bio-precipitation of U(VI) from uranyl nitrate solution, was assayed in biofilms of seven different S. aureus strains. The presence of acid phosphatase enzyme was detected in the biofilms of all S. aureus strains (in the range of 3.1 ± 0.21 to 26.90 ± 2.32 μi.u./g), and found to be higher when compared to that of their planktonic phenotypes. Among all, S. aureus V329 biofilm showed highest biofilm formation ability along with maximum phosphatase activity (26.9 ± 2.32 μi.u./g of biomass). Addition of phosphate enhanced the U(VI) remediation when treated with uranyl nitrate solution. S. aureus V329 biofilm showed significant U tolerance with only a 3-log reduction when exposed to 10 ppm U(VI) for 1 h. When treated in batch mode, V329 biofilm successfully remediated up to 47% of the 10 ppm U(VI). This new approach using the acid phosphatase from the S. aureus V329 biofilm presents an alternative method for the remediation of uranium contamination.

Abiotic reduction of uranium(VI) with humic acid at mineral surfaces: Competing mechanisms, ligand and substituent effects, and electronic structure and vibrational properties

Abiotic reduction represents an attractive technology to control U(VI) contamination. In this work, an abiotic route of U(VI) reduction with humic acid at mineral surfaces is proposed and reaction mechanisms are addressed by periodic density functional theory calculations. Different influencing factors such as ligand effect, content of CO₃^2- ligands and substituent effect are inspected. The coordination chemistry of uranyl(VI) surface complexes relies strongly on substrates and ligands, and the calculated results are in good agreements with experimental observations available. For the OH^- ligand, two competitive mechanisms co-exist that respectively produce the U(IV) and U(V) species, and the former is significantly preferred because of lower energy barriers. Instead, the NO₃^- ligand leads to the formation of U(V) while for the Cl^- ligand, the U(VI) surface complex remains very stable and is not likely to be reduced because of very high energy barriers. The U(V) and U(IV) complexes are the predominant products for low and high CO₃^2- contents, respectively. Accordingly, the abiotic reduction processes with humic acid are efficient to manage U(VI) contamination and become preferred under basic conditions or at higher CO₃^2- contents. The U(VI) reduction is further promoted by introduction of electron-donating rather than electron-withdrawing substituents to humic acid. Electronic structure analyses and vibrational frequency assignments are calculated for the various uranium surface complexes of the reduction processes, serving as a guide for future experimental and engineered studies. The molecular-level understanding given in this work offers an abiotic route for efficient reduction of U(VI) and remediation of U(VI)-contaminated sites at ambient conditions.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.

Speciation Distribution of Heavy Metals in Uranium Mining Impacted Soils and Impact on Bacterial Community Revealed by High-Throughput Sequencing

This study investigated the influence of heavy metals on bacterial community structure in a uranium mine. Soils from three differently polluted ditches (Yangchang ditch, Zhongchang ditch, and Sulimutang ditche) were collected from Zoige County, Sichuan province, China. Soil physicochemical properties and heavy metal concentrations were measured. Differences between bacterial communities were investigated using the high-throughput sequencing of the 16S rRNA genes. The obtained results demonstrated that bacterial richness index (Chao and Ace) were similar among three ditches, while the highest bacterial diversity index was detected in the severely contaminated soils. The compositions of bacterial communities varied among three examined sites, but Proteobacteria and Acidobacteria were abundant in all samples. Redundancy analysis revealed that soil organic matter, Cr and pH were the three major factors altering the bacterial community structure. Pearson correlation analysis indicated that the most significant correlations were observed between the contents of non-residual Cr and the abundances of bacterial genera, including Thiobacillus, Nitrospira, and other 10 genera. Among them, the abundances of Sphingomonas and Pseudomonas were significant and positively correlated with the concentrations of non-residual U and As. The results highlighted the factors influencing the bacterial community in uranium mines and contributed a better understanding of the effects of heavy metals on bacterial community structure by considering the fraction of heavy metals.

Uranium biomineralization induced by a metal tolerant Serratia strain under acid, alkaline and irradiated conditions

It has become increasingly apparent that the environmental microorganisms residing in uranium (U) enriched sites offer the possibility of understanding the biological mechanisms catalyzing the processes important for uranium bioremediation. Here, we present the results of uranium biomineralization over a wide pH range by a metal tolerant Serratia sp. strain OT II 7 isolated from the subsurface soil of a U ore deposit at Domiasiat in India. The Serratia cells actively expressed acid and alkaline phosphatase enzymes which hydrolyzed differential amounts of phosphate from an organophosphate substrate in the presence of uranium between pH 5 to 9. These cells precipitated ∼91% uranium from aqueous solutions supplemented with 1 mM uranyl nitrate at pH 5 within 120 h. More rapid precipitation was observed at pH 7 and 9 wherein the cells removed ∼93-94% of uranium from solutions containing 1 mM uranyl carbonate within 24 h. The aqueous uranyl speciation prevalent under the studied pH conditions influenced the localization of crystalline uranyl phosphate precipitates, which in turn, impacted the cell viability to a great extent. Furthermore, the cells tolerated up to ∼1.6 kGy 60Co gamma radiation and their uranium precipitation abilities at pH 5, 7 and 9 were uncompromised even after exposure to a high dose of ionizing radiation. Overall, this study establishes the ecological adaptation of a natural strain like Serratia in a uranium enriched environment and corroborates its contribution towards uranium immobilization in contaminated subsurfaces through the formation of stable uranyl phosphate minerals over a wide pH range.

Kinetic and equilibrium of U(VI) biosorption onto the resistant bacterium Bacillus amyloliquefaciens

This study evaluated U(VI) biosorption properties by the resistant bacterium, Bacillus amyloliquefaciens, which was isolated from the soils with residual radionuclides. The effect of biosorption factors (uptake time, pH, ionic concentration, biosorbent dosage and temperature) on U(VI) removal was determined by batch experiments. The uptake processes were characterized by using SEM, FTIR, and XPS. The experimental data of U(VI) biosorption were fitted by the pseudo-second-order. The maximum uptake capacity was 179.5 mg/g at pH 6.0 by Langmuir model. The thermodynamic results: ΔG^о, ΔH^о and ΔS^о for uptake processes were calculated as -6.359 kJ/mol, 14.20 kJ/mol and 67.19 J/mol/K, respectively. The results showed that the biosorption of Bacillus amyloliquefaciens will be an ideal method to remove radionuclides.

Bacterial-facilitated uranium transport in the presence of phytate at Savannah River Site

At the Department of Energy (DOE) managed Savannah River Site (SRS), uranium and other heavy metals continue to pose threats to the ecosystem health and processes. In the oxic soil of this site, uranium is present primarily as soluble salts of the uranyl ion (i.e., U(VI) or UO₂²⁺). Although UO₂²⁺ has a strong sorption to the soil, the mobile indigenous bacteria may facilitate its transport. On the contrary, precipitation of UO₂²⁺ with phosphate has been found to be an alternative remediation strategy. This research investigated the effects of mobile bacteria and phytate on UO₂²⁺ transport at SRS in column experiments. It was discovered that UO₂²⁺ can barely be mobilized by de-ionized water but can be significantly transported with the aid of mobile indigenous bacteria. UO₂²⁺ had the most facilitated transport observation when it reached equilibrium with the bacteria before the transport. When UO₂²⁺ and bacterial were introduced to the soil at the same time or UO₂²⁺ was pre-deposited in the soil, the facilitated transport was less pronounced. In the presence of phytate, bacterial-facilitated UO₂²⁺ transport was hindered. pH was found to play the key role for UO₂²⁺ immobilization in the presence of phytate. The immobilization of UO₂²⁺ with the addition of phytate increased with the increase of pH within the pH range of this study because of the impact of pH on the solubility of UO₂(OH)₂. Phytate promoted UO₂^--PO₄^3- complex and/or [Ca(UO₂)₂(PO₄)₂] formation, leading to enhanced UO₂²⁺ immobilization in the SRS soil.

Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA

Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.

Effect of Staphylococcus epidermidis on U(VI) sequestration by Al-goethite

Effect of Staphylococcus epidermidis (S. epidermidis) on U(VI) sequestration by Al-goethite were conducted under different geologic conditions. The batch experiments showed that S. epidermidis significantly enhanced the adsorption rates of U(VI) at pH < 9.0 due to the additional metal binding sites. The maximum adsorption capacities of U(VI) on Al-goethite and Al-goethite +S. epidermidis at pH 4.0 and 310 K were calculated from Langmuir equation to be 13.16 and 47.86 mg/g, respectively. The decreased adsorption of U(VI) on Al-goethite+ S. epidermidis at high carbonate and pH conditions were primarily driven by the electrostatic repulsion between negatively charged U(VI)-carbonate complexes and the negatively charged adsorbents. According to XPS analysis, the adsorbed U(VI) can be reduced to U(IV) by S. epidermidis, whereas inhibited reduction of U(VI) on Al-goethite + S. epidermidis at high pH could be attributed to the complexation of structural Fe(III) with the oxygen-containing functional groups of S. epidermidis. FT-IR analysis further demonstrated that the bonding of structural Fe(III) with functional groups (e.g., carboxyl and phosphate groups) of S. epidermidis. These results herein are important to understand the fate and transport of U(VI) on the mineral-bacteria ternary systems in the near-surface environment.

The influence of humic substances on uranium biomineralization induced by Bacillus sp. dwc-2

In this paper, the influence of humic acid (HA) and fulvic acid (FA) on biomineralization behaviour was evaluated. The results showed HA and FA did not obviously inhabit or promote the precipitation of U-phosphate minerals. The data from molecular dynamic simulation indicated that the free energy for the dissociation of uranyl the PO₄^3- -uranyl was 202.49 kJ/mol, which was much larger than that form HA-uranyl (88.3 kJ/mol). These simulated results revealed the less competitiveness of HA and FA with PO₄^3- for uranyl and explained why HA and FA had less impacted on the formation of U-phosphate minerals. However, the influence of HA/FA on the morphology was obvious, the microstructure of the bio-minerals changed from small particles to lamellar stacking structure with the addition of HA or FA. The findings of this study are helpful for us to gain a better understanding natural U-phosphate biomineralization behaviour.

Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress

Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.

Accumulation of U(VI) on the Pantoea sp. TW18 isolated from radionuclide-contaminated soils

Pantoea sp. TW18 isolated from radionuclide-contaminated soils was used for the bioremediation of radionuclides pollution. Accumulation mechanism of U(VI) on Pantoea sp. TW18 was investigated by batch experiments and characterization techniques. The batch experiments revealed that Pantoea sp. TW18 rapidly reached accumulation equilibrium at approximately 4 h with a high accumulation capacity (79.87 mg g^-1 at pH 4.1 and T = 310 K) for U(VI). The accumulation data of U(VI) onto Pantoea sp. TW18 can be satisfactorily fitted by pseudo-second-order model. The accumulation of U(VI) on Pantoea sp. TW18 was affected by pH levels, not independent of ionic strength. Analysis of the FT-IR and XPS spectra demonstrated that accumulated U(VI) ions were primarily bound to nitrogen- and oxygen-containing functional groups (i.e., carboxyl, amide and phosphoryl groups) on the Pantoea sp. TW18 surface. This study showed that Pantoea sp. TW18 can be considered as a promising sorbent for remediation of radionuclides in environmental cleanup.

Impact of Haloarchaea on Speciation of Uranium-A Multispectroscopic Approach

Haloarchaea represent a predominant part of the microbial community in rock salt, which can serve as host rock for the disposal of high level radioactive waste. However, knowledge is missing about how Haloarchaea interact with radionuclides. Here, we used a combination of spectroscopic and microscopic methods to study the interactions of an extremely halophilic archaeon with uranium, one of the major radionuclides in high level radioactive waste, on a molecular level. The obtained results show that Halobacterium noricense DSM 15987^T influences uranium speciation as a function of uranium concentration and incubation time. X-ray absorption spectroscopy reveals the formation of U(VI) phosphate minerals, such as meta-autunite, as the major species at a lower uranium concentration of 30 μM, while U(VI) is mostly associated with carboxylate groups of the cell wall and extracellular polymeric substances at a higher uranium concentration of 85 μM. For the first time, we identified uranium biomineralization in the presence of Halobacterium noricense DSM 15987^T cells. These findings highlight the potential importance of Archaea in geochemical cycling of uranium and their role in biomineralization in hypersaline environments, offering new insights into the microbe-actinide interactions in highly saline conditions relevant to the disposal of high-level radioactive waste as well as bioremediation.

Co-expression of YieF and PhoN in Deinococcus radiodurans R1 improves uranium bioprecipitation by reducing chromium interference

Overexpression of the enzyme phosphatase (PhoN/PhoK) in the radiation-resistant bacterium Deinococcus radiodurans could be an efficient strategy for uranium remediation. However, the presence of other metals in nuclear wastes often interferes with uranium bioprecipitation. In our study, the uranium-precipitating ability of the PhoN-expressing D. radiodurans strain (Deino-phoN) significantly decreased by 45.4% in 13 h in the presence of chromium (VI); however, it was partially recovered after supplementation with chromium (III). Therefore, the reduction of chromium (VI) to chromium (III) was obtained by the co-expression of the YieF protein and PhoN in D. radiodurans (Deino-phoN-yieF). As a result, an increase in the chromium (VI) reduction (25.1%) rate was observed in 24 h. Furthermore, uranium precipitation also increased by 28.0%. For the decontamination of groundwater, we immobilized Deino-phoN-yieF cells using Polyvinyl alcohol (PVA)-sodium alginate (SA) beads, followed by incubation in a bioreactor. Approximately 99% of chromium (VI) and uranium (VI) was removed after 4 continuous cycles operated for a period of over 20 days at room temperature (25 °C). Therefore, Deino-phoN-yieF could be used as a potential biological agent for mixed radioactive nuclear waste remediation.

Uranium adsorption and subsequent re-oxidation under aerobic conditions by Leifsonia sp. - Coated biochar as green trapping agent

It has generally been assumed that the immobilization of U(VI) via polyphosphate accumulating microorganisms may present a sink for uranium, but the potential mechanisms of the process and the stability of precipitated uranium under aerobic conditions remain elusive. This study seeks to explore the mechanism, capacity, and stability of uranium precipitation under aerobic conditions by a purified indigenous bacteria isolated from acidic tailings (pH 6.5) in China. The results show that over the treatment ranges investigated, maximum removal of U(VI) from aqueous solution was 99.82% when the initial concentration of U(VI) was 42 μM, pH was 3.5, and the temperature was with 30 °C much higher than that of other reported microorganisms. The adsorption mechanism was elucidated via the use of SEM-EDS, XPS and FTIR. SEM-EDS showed two peaks of uranium on the surface. A plausible explanation for this, supported by FTIR, is that uranium precipitated on the biosorbent surfaces. XPS measurements indicated that the uranium product is most likely a mixture of 13% U(VI) and 87% U(IV). Notably, the reoxidation experiment found that the uranium precipitates were stable in the presence of Ca²⁺ and Mg²⁺, however, U(IV) is oxidized to U(VI) in the presence of NO₃^- and Na⁺ ions, resulting in rapid dissolution. It implies that the synthesized Leifsonia sp. coated biochar could be utilized as a green and effective biosorbent. However, it may not a good choice for in-situ remediation due to the subsequent re-oxidation under aerobic conditions. These observations can be of some guiding significance to the application of the bioremediation technology in surface environments.

Biomineralization mechanism of U(VI) induced by Bacillus cereus 12-2: The role of functional groups and enzymes

Current studies reveal that the biomineralization of U(VI) by anaerobes normally produces nano-sized U(IV) minerals that can easily re-migrate/re-oxidize, while the biomineralization of U(VI) by aerobes has been constrained because the general mechanism has not yet been fully characterized. The biomineralization of U(VI) by Bacillus cereus 12-2 was investigated in this work. The maximum biosorption capability of intact cells was 448.68 mg U/g biomass (dry weight) at pH 5, while a decrease over 60% was induced when phosphate, amino, and especially carboxyl groups were shielded. X-ray diffraction, electron microscopy, and tracing the concentration of soluble intracellular U(VI) demonstrated that extracellular amorphous uranium particles can directly enter cells as solid, and about 10 nm-sized (NH₄)(UO₂)PO₄·3H₂O was formed subsequently. It was also revealed that the biosorption capability was not affected by a high uranium concentration, while biomineralization was inhibited, suggesting that a high concentration of heavy metals may inhibit the enzyme activity involved in biomineralization. Besides, U(VI) could trigger the overexpression of proteins with a molecular weight of 22 kD, including various phosphatases, kinases, and other enzymes that are related to metabolism and stimulus response, which may contribute to the intracellular transformation of U(VI) compounds from amorphous to crystalline phase. Taken together, the immobilization of U(VI) by B. cereus 12-2 contains two major steps: (1) fast immobilization of U(VI) on the cell surface as amorphous compounds, in which the carboxyl groups served as the predominant coordination functional groups and (2) transport of amorphous particles to cells directly and enzyme-related formation of uramphite.