Multistage bioassociation of uranium onto an extremely halophilic archaeon revealed by a unique combination of spectroscopic and microscopic techniques

Bio-adsorption of Fe (II) by dry biomass of metal-tolerant haloarchaeon Haloferax alexandrinus GUSF-1

Mining-associated activities result in iron pollution exceeding the acceptable limit of 0.3 mg L- 1 and are rampant in estuarine soil and water bodies that harbor halophilic microorganisms. Biotechnologies are underway to unveil the concentrations and recover the metals that skip existing physico-chemical methods. Concerning this, the present study describes for the first time the development of a bio-adsorption batch system using dried cells of Haloferax alexandrinus GUSF-1 for Fe (II) from saline water under microaerophilic conditions. A maximum of 99.5% Fe (II) was adsorbed at pH 6.0, 30 ºC in 3 h with 92% efficiency over three adsorption-desorption cycles with saturation and pseudo-second-order kinetics and heterogeneity of Freundlich model having KF of 1.38 mg g- 1 with the n value of 0.96. Adsorbed Fe (II) by the cells was detected by scanning electron microscopy. The involvement of the carboxyl, amino, hydroxyl, and phosphate groups of the cells in interaction with the metal ions was detected by infrared spectroscopy. Conclusively, the study is the first report of whole dried cells mediated metal adsorption by the haloarcheon Haloferax alexandrinus GUSF-1 which acts as promising candidate for metal clean-up strategy and bioremediation in hypersaline ecosystems.

Elimination of uranium pollution from coastal nuclear power plant by marine microorganisms: Capability and mechanism

Uranium is one of the sensitive radionuclides in the wastewater of nuclear powers. Due to the fact that nuclear powers are mainly located in coastal areas, the elimination of uranium (U(VI)) pollution from coastal nuclear power is ultimately rely on marine microorganisms. The fixing of U(VI) on V. alginolyticus surface or converting it into sediments is an effective elimination strategy for U(VI) pollution. In this work, typical marine microorganism V. alginolyticus was used to evaluate the elimination of U(VI) pollution by marine microorganisms. Effects of solution conditions (such as pH, temperature, and bacterium concentrations) on the physicochemical properties and elimination capabilities of V. alginolyticus were studied in detail. FT-IR, XPS and XRD results reveal that COOH, NH2, OH and PO4 on V. alginolyticus were main functional groups for U(VI) elimination and formed (UO2)3(PO4)2·H2O. The elimination of U(VI) by V. alginolyticus includes two stages of adsorption and biomineralization. The theoretical maximum adsorption capacity (Cs,max) of V. alginolyticus for U(VI) can reach up to 133 mg/g at pH 5 and 298 K, and the process reached equilibrium in 3 h. Results show that V. alginolyticus play important role in the elimination of U(VI) pollution in seawater.

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.

Extremophilic microbial metabolism and radioactive waste disposal

Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.

Peptidoglycan as major binding motif for Uranium bioassociation on Magnetospirillum magneticum AMB-1 in contaminated waters

The U(VI) bioassociation on Magnetospirillum magneticum AMB-1 cells was investigated using a multidisciplinary approach combining wet chemistry, microscopy, and spectroscopy methods to provide deeper insight into the interaction of U(VI) with bioligands of Gram-negative bacteria for a better molecular understanding. Our findings suggest that the cell wall plays a prominent role in the bioassociation of U(VI). In time-dependent bioassociation studies, up to 95 % of the initial U(VI) was removed from the suspension and probably bound on the cell wall within the first hours due to the high removal capacity of predominantly alive Magnetospirillum magneticum AMB-1 cells. PARAFAC analysis of TRLFS data highlights that peptidoglycan is the most important ligand involved, showing a stable immobilization of U(VI) over a wide pH range with the formation of three characteristic species. In addition, in-situ ATR FT-IR reveals the predominant strong binding to carboxylic functionalities. At higher pH polynuclear species seem to play an important role. This comprehensive molecular study may initiate in future new remediation strategies on effective immobilization of U(VI). In combination with the magnetic properties of the bacteria, a simple technical water purification process could be realized not only for U(VI), but probably also for other heavy metals.

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.

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.

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO₂²⁺ and Fe³⁺. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.

Microscopic and spectroscopic bioassociation study of uranium(VI) with an archaeal Halobacterium isolate

The safe disposal of high-level radioactive waste in a deep geological repository is a huge social and technical challenge. So far, one of the less considered factors needed for a long-term risk assessment, is the impact of microorganisms occurring in the different host rocks. Even under the harsh conditions of salt formations different bacterial and archaeal species were found, e. g. Halobacterium sp. GP5 1-1, which has been isolated from a German rock salt sample. The interactions of this archaeon with uranium(VI), one of the radionuclides of major concern for the long-term storage of high-level radioactive waste, were investigated. Different spectroscopic techniques, as well as microscopy, were used to examine the occurring mechanisms on a molecular level leading to a more profound process understanding. Batch experiments with different uranium(VI) concentrations showed that the interaction is not only a simple, but a more complex combination of different processes. With the help of in situ attenuated total reflection Fourier-transform infrared spectroscopy the association of uranium(VI) onto carboxylate groups was verified. In addition, time-resolved laser-induced luminescence spectroscopy revealed the formation of phosphate and carboxylate species within the cell pellets as a function of the uranium(VI) concentration and incubation time. The association behavior differs from another very closely related halophilic archaeon, especially with regard to uranium(VI) concentrations. This clearly demonstrates the importance of studying the interactions of different, at first sight very similar, microorganisms with uranium(VI). This work provides new insights into the microbe-uranium(VI) interactions at highly saline conditions relevant to the long-term storage of radioactive waste in rock salt.

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

Biomass and salt-dependent effects of Bacillus spores on radionuclide migration from the Waste Isolation Pilot Plant

Spores of a Bacillus sp., isolated from radioactive waste, were tested for their ability to influence the fate and transport of neodymium (Nd³⁺) under high salt conditions expected at the Waste Isolation Pilot Plant (WIPP) nuclear waste repository. Spores were suspended in neodymium-spiked saline solutions up to 4 M NaCl, and concentrations of Nd and the complexing agent dipicolinic acid (DPA), a component of spores, were monitored along with optical densities and spore numbers. Results support neodymium bioassociation that is dependent upon biomass, with more apparent adsorption occurring at higher spore concentrations. However, probable spore lysis in 2 and 4 M NaCl solutions and possible germination at 0.15 M NaCl appear to drive the release of DPA and subsequent return of Nd to solution. The implications of this work for the WIPP will depend on actual biomass levels and the ionic strength of the repository brines.

Bioassociation of U(VI) and Eu(III) by Plant (Brassica napus) Suspension Cell Cultures-A Spectroscopic Investigation

In this study, we investigated the interaction of U(VI) and Eu(III) with Brassica napus suspension plant cells as a model system. Concentration-dependent (0-200 μM) bioassociation experiments showed that more than 75% of U(VI) and Eu(III) were immobilized by the cells. In addition to this phenomenon, time-dependent studies for 1 to 72 h of exposure showed a multistage bioassociation process for cells that were exposed to 200 μM U(VI), where, after initial immobilization of U(VI) within 1 h of exposure, it was released back into the culture medium starting within 24 h. A remobilization to this extent has not been previously observed. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay was used to correlate the bioassociation behavior of Eu and U with the cell vitality. Speciation studies by spectroscopy and in silico methods highlighted various U and Eu species over the course of exposure. We were able to observe a new U species, which emerged simultaneously with the remobilization of U back into the solution, which we assume to be a U(VI) phosphate species. Thus, the interaction of U(VI) and Eu(III) with released plant metabolites could be concluded.

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.

How to Cope With Heavy Metal Ions: Cellular and Proteome-Level Stress Response to Divalent Copper and Nickel in Halobacterium salinarum R1 Planktonic and Biofilm Cells

Halobacterium salinarum R1 is an extremely halophilic archaeon capable of adhesion and forming biofilms, allowing it to adjust to a range of growth conditions. We have recently shown that living in biofilms facilitates its survival under Cu²⁺ and Ni²⁺ stress, with specific rearrangements of the biofilm architecture observed following exposition. In this study, quantitative analyses were performed by SWATH mass spectrometry to determine the respective proteomes of planktonic and biofilm cells after exposition to Cu²⁺ and Ni²⁺.Quantitative data for 1180 proteins were obtained, corresponding to 46% of the predicted proteome. In planktonic cells, 234 of 1180 proteins showed significant abundance changes after metal ion treatment, of which 47% occurred in Cu²⁺ and Ni²⁺ treated samples. In biofilms, significant changes were detected for 52 proteins. Only three proteins changed under both conditions, suggesting metal-specific stress responses in biofilms. Deletion strains were generated to assess the potential role of selected target genes. Strongest effects were observed for ΔOE5245F and ΔOE2816F strains which exhibited increased and decreased biofilm mass after Ni²⁺ exposure, respectively. Moreover, EPS obviously plays a crucial role in H. salinarum metal ion resistance. Further efforts are required to elucidate the molecular basis and interplay of additional resistance mechanisms.

Impact of uranium exposure on marine yeast, Yarrowia lipolytica: Insights into the yeast strategies to withstand uranium stress

A marine yeast, Yarrowia lipolytica, was evaluated for morphological, physiological and biochemical responses towards uranium (U) exposure at pH 7.5. The yeast revealed biphasic U binding - a rapid biosorption resulting in ∼35% U binding within 15-30 min followed by a slow biomineralization process, binding up to ∼45.5% U by 24 h on exposure to 50 μM of uranyl carbonate. Scanning electron microscopy coupled with Energy Dispersive X-ray spectroscopy analysis of 24 h U challenged cells revealed the deposition of uranyl precipitates due to biomineralization. The loss of intracellular structures together with surface and subcellular localization of uranyl precipitates in 24 h U exposed cells were visualized by transmission electron microscopy. Cells treated with 50 μM U exhibited membrane permeabilization which was higher at 200 μM U. Enhanced reactive oxygen species (ROS) accumulation and lipid peroxidation, transient RNA degradation and protein oxidation were observed in U exposed cells. High superoxide dismutase levels coupled with uranium binding and bioprecipitation possibly helped in counteracting U stress in 50 μM U treated cells. Resistance to U toxicity apparently developed under prolonged uranyl (50 μM) incubations. However, cells could not cope up with toxicity at 200 μM U due to impairment of resistance mechanisms.

Association of Eu(III) and Cm(III) onto an extremely halophilic archaeon

In addition to geological, geochemical, and geophysical aspects, also, microbial aspects have to be taken into account when considering the final storage of high-level radioactive waste in a deep geological repository. Rock salt is a potential host rock formation for such a repository. One indigenous microorganism, that is, common in rock salt, is the halophilic archaeon Halobacterium noricense DSM15987^T, which was used in our study to investigate its interactions with the trivalent actinide curium and its inactive analogue europium as a function of time and concentration. Time-resolved laser-induced fluorescence spectroscopy was applied to characterize formed species in the micromolar europium concentration range. An extended evaluation of the data with parallel factor analysis revealed the association of Eu(III) to a phosphate compound released by the cells (F₂/F₁ ratio, 2.50) and a solid phosphate species (F₂/F₁ ratio, 1.80). The association with an aqueous phosphate species and a solid phosphate species was proven with site-selective TRLFS. Experiments with Cm(III) in the nanomolar concentration range showed a time- and pC_H+-dependent species distribution. These species were characterized by red-shifted emission maxima, 600-602 nm, in comparison to the free Cm(III) aqueous ion, 593.8 nm. After 24 h, 40% of the luminescence intensity was measured on the cells corresponding to 0.18 μg Cm(III)/g_DBM. Our results demonstrate that Halobacterium noricense DSM15987^T interacts with Eu(III) by the formation of phosphate species, whereas for Cm(III), a complexation with carboxylic functional groups was also observed.

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.

Removal and recovery of uranium(VI) by waste digested activated sludge in fed-batch stirred tank reactor

This study demonstrated the removal and recovery of uranium(VI) in a fed-batch stirred tank reactor (STR) using waste digested activated sludge (WDAS). The batch adsorption experiments showed that WDAS can adsorb 200 (±9.0) mg of uranium(VI) per g of WDAS. The maximum adsorption of uranium(VI) was achieved even at an acidic initial pH of 2.7 which increased to a pH of 4.0 in the equilibrium state. Desorption of uranium(VI) from WDAS was successfully demonstrated from the release of more than 95% of uranium(VI) using both acidic (0.5 M HCl) and alkaline (1.0 M Na₂CO₃) eluents. Due to the fast kinetics of uranium(VI) adsorption onto WDAS, the fed-batch STR was successfully operated at a mixing time of 15 min. Twelve consecutive uranium(VI) adsorption steps with an average adsorption efficiency of 91.5% required only two desorption steps to elute more than 95% of uranium(VI) from WDAS. Uranium(VI) was shown to interact predominantly with the phosphoryl and carboxyl groups of the WDAS, as revealed by in situ infrared spectroscopy and time-resolved laser-induced fluorescence spectroscopy studies. This study provides a proof-of-concept of the use of fed-batch STR process based on WDAS for the removal and recovery of uranium(VI).

Diversity and Niche of Archaea in Bioremediation

Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.

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.

Responses exhibited by various microbial groups relevant to uranium exposure

There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.

Comparative analysis of uranium bioassociation with halophilic bacteria and archaea

Rock salt represents a potential host rock formation for the final disposal of radioactive waste. The interactions between indigenous microorganisms and radionuclides, e.g. uranium, need to be investigated to better predict the influence of microorganisms on the safety assessment of the repository. Hence, the association process of uranium with two microorganisms isolated from rock salt was comparatively studied. Brachybacterium sp. G1, which was isolated from the German salt dome Gorleben, and Halobacterium noricense DSM15987T, were selected as examples of a moderately halophilic bacterium and an extremely halophilic archaeon, respectively. The microorganisms exhibited completely different association behaviors with uranium. While a pure biosorption process took place with Brachybacterium sp. G1 cells, a multistage association process occurred with the archaeon. In addition to batch experiments, in situ attenuated total reflection Fourier-transform infrared spectroscopy was applied to characterize the U(VI) interaction process. Biosorption was identified as the dominating process for Brachybacterium sp. G1 with this method. Carboxylic functionalities are the dominant interacting groups for the bacterium, whereas phosphoryl groups are also involved in U(VI) association by the archaeon H. noricense.

Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate

Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria.

BIOLOGICAL SIGNIFICANCE

Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination.