Interaction mechanisms of bacterial strains isolated from extreme habitats with uranium

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.

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.

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.

Uranium sequestration abilities of Bacillus bacterium isolated from an alkaline mining region

The present study elaborates uranium sequestration by bacteria from alkaline wastewaters. In the investigation, a few bacterial strains were isolated from alkaline uranium mine water and were tested for uranium sequestration properties 16S rRNA analysis assigned the 10 bacterial isolates to 4 genera of Actinobacteria and Firmicutes. Among all the isolates tested, the strain Bacillus aryabhattai (TP03) has shown superior sequestration capacity at 5 and 10 mg/L U in 1 mM carbonate-bicarbonate buffer at pH 9.2. At low uranium concentrations (5 mg/L as uranyl carbonate), the strain could sequester ~70% of the uranium in 6 h with a loading capacity of 4.3 mg U/g dry bacterial biomass. Increase in carbonate-bicarbonate buffer concentrations and pH reduced the sequestration capacity. Scanning electron microscopy and energy dispersive X-ray fluorescence spectroscopy studies indicated the presence of uranium with the bacterial biomass. Fourier transform infra-red spectroscopy results confirmed the uranium sequestration by cell membrane phosphate, amide, and carboxyl functional groups. Transmission electron microscopy study showed uranium presence within the cell cytoplasm, thus supporting the hypothesis on active metabolism-dependent bioaccumulation of uranium. The kinetics study of uranium sequestration was well fitted to the pseudo-second-order model. Overall, this study infers that the isolated alkaliphilic bacteria from the mine waters have significant sequestration property for treating uranium-containing alkaline wastewaters.

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.

Soil uranium concentration at Ranger Uranium Mine Land Application Areas drives changes in the bacterial community

Soil microorganisms may respond to metal stress by a shift in the microbial community from metal sensitive to metal resistant microorganisms. We assessed the bacterial community from low (2-20 mg kg^-1), medium (200-400 mg kg^-1), high (500-900 mg kg^-1) and very high (>900 mg kg^-1) uranium soils at Ranger Uranium Mine in northern Australia through pyrosequencing. Proteobacteria (28.85%) was the most abundant phylum at these sites, followed by Actinobacteria (9.31%), Acidobacteria (7.33%), Verrucomicrobia (2.11%), Firmicutes (2.02%), Chloroflexi (1.11%), Cyanobacteria (0.93%), Planctomycetes (0.82%), Bacteroidetes (0.46%) and Candidate_division_WS3 (Latescibacteria) (0.21%). However, 46.79% of bacteria were unclassified. Bacteria at low U soils differed from soils with elevated uranium. Bacterial OTUs closely related to Kitasatospora spp., Sphingobacteria spp. and Rhodobium spp. were only present at higher uranium concentrations and the bacterial community also changed with seasonal and temporal changes in soil uranium and physicochemical variables. This study using next generation sequencing in association with environmental variables at a uranium mine has laid a foundation for further studies of soil-microbe-metal interactions which may be useful for developing sustainable management and rehabilitation strategies. Furthermore, bacterial species associated with higher uranium may serve as useful indicators of uranium contamination in the wet-dry tropics.

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.

Multidisciplinary characterization of U(VI) sequestration by Acidovorax facilis for bioremediation purposes

The contamination of the environment by U may affect plant life and consequently may have an impact on animal and human health. The present work describes U(VI) sequestration by Acidovorax facilis using a multidisciplinary approach combining wet chemistry, transmission electron microscopy, and spectroscopy methods (e.g. cryo-time resolved laser-induced fluorescence spectroscopy, extended X-ray absorption fine structure spectroscopy, and in-situ attenuated total reflection Fourier transform infrared spectroscopy). This bacterial strain is widely distributed in nature including U-contaminated sites. In kinetic batch experiments cells of A. facilis were contacted for 5 min to 48 h with 0.1 mM U(VI). The results show that the local coordination of U species associated with the cells depends upon time contact. U is bound mainly to phosphate groups of lipopolysaccharide (LPS) at the outer membrane within the first hour. And, that both, phosphoryl and carboxyl functionality groups of LPS and peptidoglycan of A. facilis cells may effectuate the removal of high U amounts from solution at 24-48 h of incubation. It is clearly demonstrated that A. facilis may play an important role in predicting the transport behaviour of U in the environment and that the results will contribute to the improvement of bioremediation methods of U-contaminated sites.

Unusual Versatility of the Filamentous, Diazotrophic Cyanobacterium Anabaena torulosa Revealed for Its Survival during Prolonged Uranium Exposure

Reports on interactions between cyanobacteria and uranyl carbonate are rare. Here, we present an interesting succession of the metabolic responses employed by a marine, filamentous, diazotrophic cyanobacterium, Anabaena torulosa for its survival following prolonged exposure to uranyl carbonate extending up to 384 h at pH 7.8 under phosphate-limited conditions. The cells sequestered uranium (U) within polyphosphates on initial exposure to 100 μM uranyl carbonate for 24 to 28 h. Further incubation until 120 h resulted in (i) significant degradation of cellular polyphosphates causing extensive chlorosis and cell lysis, (ii) akinete differentiation followed by (iii) extracellular uranyl precipitation. X-ray diffraction (XRD) analysis, fluorescence spectroscopy, X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) spectroscopy established the identity of the bioprecipitated uranium as a U(VI) autunite-type mineral, which settled at the bottom of the vessel. Surprisingly, A. torulosa cells resurfaced as small green flakes typical of actively growing colonies on top of the test solutions within 192 to 240 h of U exposure. A consolidated investigation using kinetics, microscopy, and physiological and biochemical analyses suggested a role of inducible alkaline phosphatase activity of cell aggregates/akinetes in facilitating the germination of akinetes leading to substantial regeneration of A. torulosa by 384 h of uranyl incubation. The biomineralized uranium appeared to be stable following cell regeneration. Altogether, our results reveal novel insights into the survival mechanism adopted by A. torulosa to resist sustained uranium toxicity under phosphate-limited oxic conditions.IMPORTANCE Long-term effects of uranyl exposure in cyanobacteria under oxic phosphate-limited conditions have been inadequately explored. We conducted a comprehensive examination of the metabolic responses displayed by a marine cyanobacterium, Anabaena torulosa, to cope with prolonged exposure to uranyl carbonate at pH 7.8 under phosphate limitation. Our results highlight distinct adaptive mechanisms harbored by this cyanobacterium that enabled its natural regeneration following extensive cell lysis and uranium biomineralization under sustained uranium exposure. Such complex interactions between environmental microbes such as Anabaena torulosa and uranium over a broader time range advance our understanding on the impact of microbial processes on uranium biogeochemistry.

Screening of bacterial strains isolated from uranium mill tailings porewaters for bioremediation purposes

The present work characterizes at different levels a number of bacterial strains isolated from porewaters sampled in the vicinity of two French uranium tailing repositories. The 16S rRNA gene from 33 bacterial isolates, corresponding to the different morphotypes recovered, was almost fully sequenced. The resulting sequences belonged to 13 bacterial genera comprised in the phyla Firmicutes, Actinobacteria and Proteobacteria. Further characterization at physiological level and metals/metalloid tolerance provided evidences for an appropriate selection of bacterial strains potentially useful for immobilization of uranium and other common contaminants. By using High Resolution Transmission Electron Microscope (HRTEM), this potential ability to immobilize uranium as U phosphate mineral phases was confirmed for the bacterial strains Br3 and Br5 corresponding to Arthrobacter sp. and Microbacterium oxydans, respectively. Scanning Transmission Electron Microscope- High-Angle Annular Dark-Field (STEM-HAADF) analysis showed U accumulates on the surface and within bacterial cytoplasm, in addition to the extracellular space. Energy Dispersive X-ray (EDX) element-distribution maps demonstrated the presence of U and P within these accumulates. These results indicate the potential of certain bacterial strains isolated from porewaters of U mill tailings for immobilizing uranium, likely as uranium phosphates. Some of these bacterial isolates might be considered as promising candidates in the design of uranium bioremediation strategies.

Combined use of flow cytometry and microscopy to study the interactions between the gram-negative betaproteobacterium Acidovorax facilis and uranium(VI)

The former uranium mine Königstein (Saxony, Germany) is currently in the process of remediation by means of controlled underground flooding. Nevertheless, the flooding water has to be cleaned up by a conventional wastewater treatment plant. In this study, the uranium(VI) removal and tolerance mechanisms of the gram-negative betaproteobacterium Acidovorax facilis were investigated by a multidisciplinary approach combining wet chemistry, flow cytometry, and microscopy. The kinetics of uranium removal and the corresponding mechanisms were investigated. The results showed a biphasic process of uranium removal characterized by a first phase where 95% of uranium was removed within the first 8h followed by a second phase that reached equilibrium after 24h. The bacterial cells displayed a total uranium removal capacity of 130mgU/g dry biomass. The removal of uranium was also temperature-dependent, indicating that metabolic activity heavily influenced bacterial interactions with uranium. TEM analyses showed biosorption on the cell surface and intracellular accumulation of uranium. Uranium tolerance tests showed that A. facilis was able to withstand concentrations up to 0.1mM. This work demonstrates that A. facilis is a suitable candidate for in situ bioremediation of flooding water in Königstein as well as for other contaminated waste waters.

Bioaccumulation characterization of uranium by a novel Streptomyces sporoverrucosus dwc-3

The biosorption mechanisms of uranium on an aerobic bacterial strain Streptomyces sporoverrucosus dwc-3, isolated from a potential disposal site for (ultra-)low uraniferous radioactive waste in Southwest China, were evaluated by using transmission electron microscopy (TEM), energy dispersive X-ray (EDX) analysis, Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), proton induced X-ray emission (PIXE) and enhanced proton backscattering spectrometry (EPBS). Approximately 60% of total uranium at an initial concentration of 10mg/L uranium nitrate solution could be absorbed on 100mg S. sporoverrucosus dwc-3 with an adsorption capacity of more than 3.0mg/g (wet weight) after 12hr at room temperature at pH3.0. The dynamic biosorption process of S. sporoverrucosus dwc-3 for uranyl ions was well described by a pseudo second-order model. S. sporoverrucosus dwc-3 could accumulate uranium on cell walls and within the cell, as revealed by SEM and TEM analysis as well as EDX spectra. XPS and FT-IR analysis further suggested that the absorbed uranium was bound to amino, phosphate and carboxyl groups of the cells. Additionally, PIXE and EPBS results confirmed that ion exchange also contributed to the adsorption process of uranium.

Mechanism of Uranium Reduction and Immobilization in Desulfovibrio vulgaris Biofilms

The prevalent formation of noncrystalline U(IV) species in the subsurface and their enhanced susceptibility to reoxidation and remobilization, as compared to crystalline uraninite, raise concerns about the long-term sustainability of the bioremediation of U-contaminated sites. The main goal of this study was to resolve the remaining uncertainty concerning the formation mechanism of noncrystalline U(IV) in the environment. Controlled laboratory biofilm systems (biotic, abiotic, and mixed biotic-abiotic) were probed using a combination of U isotope fractionation and X-ray absorption spectroscopy (XAS). Regardless of the mechanism of U reduction, the presence of a biofilm resulted in the formation of noncrystalline U(IV). Our results also show that biotic U reduction is the most effective way to immobilize and reduce U. However, the mixed biotic-abiotic system resembled more closely an abiotic system: (i) the U(IV) solid phase lacked a typically biotic isotope signature and (ii) elemental sulfur was detected, which indicates the oxidation of sulfide coupled to U(VI) reduction. The predominance of abiotic U reduction in our systems is due to the lack of available aqueous U(VI) species for direct enzymatic reduction. In contrast, in cases where bicarbonate is present at a higher concentration, aqueous U(VI) species dominate, allowing biotic U reduction to outcompete the abiotic processes.

Uranium Binding Mechanisms of the Acid-Tolerant Fungus Coniochaeta fodinicola

The uptake and binding of uranium [as (UO2)(2+)] by a moderately acidophilic fungus, Coniochaeta fodinicola, recently isolated from a uranium mine site, is examined in this work in order to better understand the potential impact of organisms such as this on uranium sequestration in hydrometallurgical systems. Our results show that the viability of the fungal biomass is critical to their capacity to remove uranium from solution. Indeed, live biomass (viable cells based on vital staining) were capable of removing ∼16 mg U/g dry weight in contrast with dead biomass (autoclaved) which removed ∼45 mg U/g dry weight after 2 h. Furthermore, the uranium binds with different strength, with a fraction ranging from ∼20-50% being easily leached from the exposed biomass by a 10 min acid wash. Results from X-ray absorption spectroscopy measurements show that the strength of uranium binding is strongly influenced by cell viability, with live cells showing a more well-ordered uranium bonding environment, while the distance to carbon or phosphorus second neighbors is similar in all samples. When coupled with time-resolved laser fluorescence and Fourier transformed infrared measurements, the importance of organic acids, phosphates, and polysaccharides, likely released with fungal cell death, appear to be the primary determinants of uranium binding in this system. These results provide an important progression to our understanding with regard to uranium sequestration in hydrometallurgical applications with implications to the unwanted retention of uranium in biofilms and/or its mobility in a remediation context.

Use of combined microscopic and spectroscopic techniques to reveal interactions between uranium and Microbacterium sp. A9, a strain isolated from the Chernobyl exclusion zone

Although uranium (U) is naturally found in the environment, soil remediation programs will become increasingly important in light of certain human activities. This work aimed to identify U(VI) detoxification mechanisms employed by a bacteria strain isolated from a Chernobyl soil sample, and to distinguish its active from passive mechanisms of interaction. The ability of the Microbacterium sp. A9 strain to remove U(VI) from aqueous solutions at 4 °C and 25 °C was evaluated, as well as its survival capacity upon U(VI) exposure. The subcellular localisation of U was determined by TEM/EDX microscopy, while functional groups involved in the interaction with U were further evaluated by FTIR; finally, the speciation of U was analysed by TRLFS. We have revealed, for the first time, an active mechanism promoting metal efflux from the cells, during the early steps following U(VI) exposure at 25 °C. The Microbacterium sp. A9 strain also stores U intracellularly, as needle-like structures that have been identified as an autunite group mineral. Taken together, our results demonstrate that this strain exhibits a high U(VI) tolerance based on multiple detoxification mechanisms. These findings support the potential role of the genus Microbacterium in the remediation of aqueous environments contaminated with U(VI) under aerobic conditions.

A spectroscopic study on U(VI) biomineralization in cultivated Pseudomonas fluorescens biofilms isolated from granitic aquifers

The interaction between the Pseudomonas fluorescens biofilm and U(VI) were studied using extended X-ray absorption fine structure spectroscopy (EXAFS), and time-resolved laser fluorescence spectroscopy (TRLFS). In EXAFS studies, the formation of a stable uranyl phosphate mineral, similar to autunite (Ca[UO2]2[PO4]2•2-6H2O) or meta-autunite (Ca[UO2]2[PO4]2•10-12H2O) was observed. This is the first time such a biomineralization process has been observed in P. fluorescens. Biomineralization occurs due to phosphate release from the cellular polyphosphate, likely as a cell's response to the added uranium. It differs significantly from the biosorption process occurring in the planktonic cells of the same strain. TRLFS studies of the uranium-contaminated nutrient medium identified aqueous Ca2UO2(CO3)3 and UO2(CO3)3 (4-) species, which in contrast to the biomineralization in the P. fluorescens biofilm, may contribute to the transport and migration of U(VI). The obtained results reveal that biofilms of P. fluorescens may play an important role in predicting the transport behavior of uranium in the environment. They will also contribute to the improvement of remediation methods in uranium-contaminated sites.

Biosorption of uranium on Bacillus sp. dwc-2: preliminary investigation on mechanism

In this paper, the biosorption mechanisms of uranium on an aerobic Bacillus sp. dwc-2, isolated from a potential disposal site for (ultra-) low uraniferous radioactive waste in Southwest China, was explored by transmission electron microscopy (TEM), energy dispersive X-ray (EDX) analysis, FT-IR spectroscopy, proton induced X-ray emission (PIXE) and enhanced proton backscattering spectrometry (EPBS). The biosorption experiments for uranium were carried out at a low pH (pH 3.0), where the uranium solution speciation is dominated by highly mobile uranyl ions. The bioaccumulation was found to be the potential mechanism involved in uranium biosorption by Bacillus sp. dwc-2, and the bioaccumulated uranium was deposited in the cell interior as needle shaped particles at pH 3.0, as revealed by TEM analysis as well as EDX spectra. FTIR analysis further suggested that the absorbed uranium was bound to amino, phosphate and carboxyl groups of bacterial cells. Additionally, PIXE and EPBS results confirmed that ion-exchange also contributed to the adsorption process of uranium. All the results implied that the biosorption mechanism of uranium on Bacillus sp. is complicated and at least involves bioaccumulation, ion exchange and complexation process.

Biosorption and Biomineralization of U(VI) by the marine bacterium Idiomarina loihiensis MAH1: effect of background electrolyte and pH

The main goal of this study is to compare the effects of pH, uranium concentration, and background electrolyte (seawater and NaClO₄ solution) on the speciation of uranium(VI) associated with the marine bacterium Idiomarina loihiensis MAH1. This was done at the molecular level using a multidisciplinary approach combining X-ray Absorption Spectroscopy (XAS), Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS), and High Resolution Transmission Electron Microscopy (HRTEM). We showed that the U(VI)/bacterium interaction mechanism is highly dependent upon pH but also the nature of the used background electrolyte played a role. At neutral conditions and a U concentration ranging from 5·10⁻⁴ to 10⁻⁵ M (environmentally relevant concentrations), XAS analysis revealed that uranyl phosphate mineral phases, structurally resembling meta-autunite [Ca(UO₂)₂(PO₄)₂ 2–6H₂O] are precipitated at the cell surfaces of the strain MAH1. The formation of this mineral phase is independent of the background solution but U(VI) luminescence lifetime analyses demonstrated that the U(VI) speciation in seawater samples is more intricate, i.e., different complexes were formed under natural conditions. At acidic conditions, pH 2, 3 and 4.3 ([U] = 5·10⁻⁴ M, background electrolyte  = 0.1 M NaClO₄), the removal of U from solution was due to biosorption to Extracellular Polysaccharides (EPS) and cell wall components as evident from TEM analysis. The L_III-edge XAS and TRLFS studies showed that the biosorption process observed is dependent of pH. The bacterial cell forms a complex with U through organic phosphate groups at pH 2 and via phosphate and carboxyl groups at pH 3 and 4.3, respectively. The differences in the complexes formed between uranium and bacteria on seawater compared to NaClO₄ solution demonstrates that the actinide/microbe interactions are influenced by the three studied factors, i.e., the pH, the uranium concentration and the chemical composition of the solution.

Insights into the interactions of cyanobacteria with uranium

Due to various activities associated with nuclear industry, uranium is migrated to aquatic environments like groundwater, ponds or oceans. Uranium forms stable carbonate complexes in the oxic waters of pH 7-10 which results in a high degree of uranium mobility. Microorganisms employ various mechanisms which significantly influence the mobility and the speciation of uranium in aquatic environments. Uranyl bioremediation studies, this far, have generally focussed on low pH conditions and related to adsorption of positively charged UO2 (2+) onto negatively charged microbial surfaces. Sequestration of anionic uranium species, i.e. [UO2(CO3) 2 (2-) ] and [UO2(CO3) 3 (4-) ] onto microbial surfaces has received only scant attention. Marine cyanobacteria are effective metal adsorbents and represent an important sink for metals in aquatic environment. This article addresses the cyanobacterial interactions with toxic metals in general while stressing on uranium. It focusses on the possible mechanisms employed by cyanobacteria to sequester uranium from aqueous solutions above circumneutral pH where negatively charged uranyl carbonate complexes dominate aqueous uranium speciation. The mechanisms demonstrated by cyanobacteria are important components of biogeochemical cycle of uranium and are useful for the development of appropriate strategies, either to recover or remediate uranium from the aquatic environments.

Bio-precipitation of uranium by two bacterial isolates recovered from extreme environments as estimated by potentiometric titration, TEM and X-ray absorption spectroscopic analyses

This work describes the mechanisms of uranium biomineralization at acidic conditions by Bacillus sphaericus JG-7B and Sphingomonas sp. S15-S1 both recovered from extreme environments. The U-bacterial interaction experiments were performed at low pH values (2.0-4.5) where the uranium aqueous speciation is dominated by highly mobile uranyl ions. X-ray absorption spectroscopy (XAS) showed that the cells of the studied strains precipitated uranium at pH 3.0 and 4.5 as a uranium phosphate mineral phase belonging to the meta-autunite group. Transmission electron microscopic (TEM) analyses showed strain-specific localization of the uranium precipitates. In the case of B. sphaericus JG-7B, the U(VI) precipitate was bound to the cell wall. Whereas for Sphingomonas sp. S15-S1, the U(VI) precipitates were observed both on the cell surface and intracellularly. The observed U(VI) biomineralization was associated with the activity of indigenous acid phosphatase detected at these pH values in the absence of an organic phosphate substrate. The biomineralization of uranium was not observed at pH 2.0, and U(VI) formed complexes with organophosphate ligands from the cells. This study increases the number of bacterial strains that have been demonstrated to precipitate uranium phosphates at acidic conditions via the activity of acid phosphatase.

Influence of uranium on bacterial communities: a comparison of natural uranium-rich soils with controls

This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil.

Coordination of uranium(VI) with functional groups of bacterial lipopolysaccharide studied by EXAFS and FT-IR spectroscopy

The complexation of uranyl ions with lipopolysaccharide (LPS), the main component of the cell wall of Gram-negative bacteria, was investigated on a molecular level with U L(III)-edge extended X-ray absorption fine structure (EXAFS) and attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectroscopy over a wide pH range (2.6 to 7.0). For the first time, structural determinations of uranyl complexes with cell wall compounds were extended from acidic up to neutral pH. The main functionalities responsible for uranyl binding are phosphoryl and carboxyl groups. At an excess of LPS, related to environmental conditions, the uranyl ion is mainly complexed by phosphoryl groups four-fold monodentately coordinated in the equatorial plane of the uranyl dioxo cation UO(2)(2+) showing great homologies to the uranyl mineral phase meta-autunite in the EXAFS spectra. At equimolar ratios of uranyl and functional groups of LPS, according to a slight deficit of phosphoryl groups, additional carboxyl coordination in a bidentate manner becomes important as it is shown by IR spectroscopy. From the vibrational spectra, a mixed coordination of UO(2)(2+) with both phosphoryl and carboxyl groups is derived. The coordination of uranyl ions to the LPS molecule is obviously mainly controlled by the U/LPS concentration ratio, and the influence of pH is only of minor significance at the investigated range.

Bioaccumulation of U(VI) by Sulfolobus acidocaldarius under moderate acidic conditions

U(VI) accumulation by the acidothermophilic archaeon Sulfolobus acidocaldarius at a moderate acidic pH of 4.5 was investigated. This pH value is relevant for some heavy metal and uranium polluted environments where populations of S. acidocaldarius were found to persist. We demonstrate that U(VI) is rapidly complexed by the archaeal cells. A combination of X-ray absorption spectroscopy and time-resolved laser-induced fluorescence spectroscopy revealed that at pH 4.5 organic phosphate and carboxylic groups are involved in the U(VI) complexation. These results are in contrast to those published for most bacteria which at this pH precipitate U(VI) mainly in inorganic uranyl phosphate phases. As demonstrated by TEM only a limited part of the added U(VI) was biomineralized extracellularly in the case of the studied archaeon. Most of the U(VI) accumulates were localized in a form of intracellular deposits which were associated with the inner side of the cytoplasma membrane. Observed differences in U(VI) bioaccumulation between the studied archaeon and bacteria can be explained by the significant differences in their cell wall structures as well as by their different physiological characteristics.

Uranium biomineralization by a metal resistant Pseudomonas aeruginosa strain isolated from contaminated mine waste

Uranium biomineralization by a metal-resistant Pseudomonas aeruginosa strain isolated from uranium mine waste was characterized for its potential in bioremediation. Uranium resistance, its cellular localization and chemical nature of uranium-bacteria interaction were elucidated. Survival and uranium biomineralization from mine water were investigated using microcosm experiments. The selected bacterium showed U resistance and accumulation (maximum of 275 mg U g(-1)cell dry wt.) following incubation in 100 mg U L(-1), pH 4.0, for 6 h. Transmission electron microscopy and X-ray diffraction analyses revealed that bioaccumulated uranium was deposited within the cell envelope as needle shaped U-phosphate compounds that attain crystallinity only at pH 4.0. A synergistic involvement of deprotonated phosphate and carboxyl moieties in facilitating bioprecipitation of uranium was evident from FTIR analysis. Based on these findings we attribute the localized U sequestration by this bacterium as innocuous complex to its possible mechanism of uranium resistance. Microcosm data confirmed that the strain can remove soluble uranium (99%) and sequester it as U oxide and phosphate minerals while maintaining its viability. The study showed that indigenous bacteria from contaminated site that can survive uranium and other heavy metal toxicity and sequester soluble uranium as biominerals could play important role in uranium bioremediation.

Isolation and physiology of bacteria from contaminated subsurface sediments

The majority of environmental microorganisms cannot be grown by traditional techniques. Here we employed, and contrasted with conventional plating, an alternative approach based on cultivation of microorganisms inside diffusion chambers incubated within natural samples, followed by subculturing in petri dishes. Using this approach, we isolated microorganisms from subsurface sediments from the Field Research Center (FRC) in Oak Ridge, TN. The sediments were acidic and highly contaminated with uranium, heavy metals, nitrate, and organic pollutants. Phylogenetic analysis of 16S rRNA gene sequences revealed clear differences between diversity of isolates obtained by the diffusion chamber approach and those obtained by conventional plating. The latter approach led to isolation of members of the Alpha- and Gammaproteobacteria, Actinobacteria, and Verrucomicrobia. Isolates obtained via the diffusion chamber approach represented the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Notably, one-third of the isolates obtained by the new method were closely related to species known from previous molecular surveys conducted in the FRC area. Since the initial growth of microorganisms inside diffusion chambers occurred in the presence of the environmental stress factors, we expected the isolates we obtained to be tolerant of these factors. We investigated the physiologies of selected isolates and discovered that the majority were indeed capable of growth under low pH and/or high concentrations of heavy metals and nitrate. This indicated that in contrast to conventional isolation, the diffusion chamber-based approach leads to isolation of species that are novel, exhibit tolerance to extant environmental conditions, and match some of the species previously discovered by molecular methods.

Bacterial biomineralization: new insights from Myxococcus-induced mineral precipitation

Bacteria have contributed to the formation of minerals since the advent of life on Earth. Bacterial biomineralization plays a critical role on biogeochemical cycles and has important technological and environmental applications. Despite the numerous efforts to better understand how bacteria induce/mediate or control mineralization, our current knowledge is far from complete. Considering that the number of recent publications on bacterial biomineralization has been overwhelming, here we attempt to show the importance of bacteria–mineral interactions by focusing in a single bacterial genus, Myxococcus, which displays an unusual capacity of producing minerals of varying compositions and morphologies. First, an overview of the recent history of bacterial mineralization, the most common bacteriogenic minerals and current models on bacterial biomineralization is presented. Afterwards a description of myxobacteria is presented, followed by a section where Myxococcus-induced precipitation of a number of phosphates, carbonates, sulphates, chlorides, oxalates and silicates is described and discussed in lieu of the information presented in the first part. As concluding remarks, implications of bacterial mineralization and perspectives for future research are outlined. This review strives to show that the mechanisms which control bacterial biomineralization are not mineral- or bacterial-specific. On the contrary, they appear to be universal and depend on the environment in which bacteria dwell.

Interactions of Sulfolobus acidocaldarius with uranium

Interactions of the acidothermophilic archaeon Sulfolobus acidocaldarius DSM 639 with U(VI) were studied by using a combination of batch experiments, X-ray absorption spectroscopy (XAS), and time-resolved laser-induced fluorescence spectroscopy (TRLFS). We demonstrated that at pH 2 this archaeal strain possesses a low tolerance to U(VI) and that its growth is limited to a uranium concentration below 1.1 mM. At similarly high acidic conditions (pH 1.5 and 3.0), covering the physiological pH growth optimum of S. acidocaldarius, at which U(VI) is soluble and highly toxic, rapid accumulation of the radionuclide by the cells of the strain occurred. About half of the uranium binding capacity was reached by the strain after an incubation of five minutes and nearly total saturation of the binding sites was achieved after 30 min. Both, EXAFS- and TRLF-spectroscopic analyses showed that the accumulated U(VI) was complexed mainly through organic phosphate groups. The EXAFS measurements revealed that U(VI) is coordinated to the organic phosphate ligands of the archaeal cells in a monodentate binding mode with an average U–P bond distance of 3.60±0.02 Å.

U(VI) sequestration in hydroxyapatite produced by microbial glycerol 3-phosphate metabolism

Previous studies have demonstrated the potential for removal of U(VI) from solution via precipitation of U(VI)-bearing calcium-phosphate (Ca-P) minerals coupled to microbial hydrolysis of glycerol phosphate compounds. We evaluated this process in circumneutral-pH groundwater from Area 2 of the U.S. Department of Energy Field Research Center at Oak Ridge National Laboratory. Area 2 groundwater contains high concentrations of dissolved calcium (ca. 4 mM), and thus, release of phosphate during glycerol phosphate metabolism has the potential to create conditions favorable for U(VI) sequestration in Ca-P minerals. Microbial enumeration and isolation studies verified the presence of aerobic and nitrate-reducing glycerol 3-phosphate (G3P)-metabolizing microorganisms in Area 2 sediments. Coprecipitation of U(VI) with Ca-P minerals coupled to microbial G3P hydrolysis was demonstrated in artificial groundwater under aerobic and nitrate-reducing conditions. Transmission electron microscopy analysis and mineral-washing experiments demonstrated that U(VI) was incorporated into the structure of the insoluble Ca-P mineral hydroxyapatite [Ca5(PO4)3OH]. Our results support the idea that U(VI) can be effectively removed from solution in contaminated aquifers through stimulation of microbial organophosphate metabolism.

Biogeochemical changes induced in uranium mining waste pile samples by uranyl nitrate treatments under anaerobic conditions

Response of the subsurface soil bacterial community of a uranium mining waste pile to treatments with uranyl nitrate over different periods of time was studied under anaerobic conditions. The fate of the added U(VI) without supplementation with electron donors was investigated as well. By using 16S rRNA gene retrieval, we demonstrated that incubation with uranyl nitrate for 4 weeks resulted in a strong reduction in and even disappearance of some of the most predominant bacterial groups of the original sample. Instead, a strong proliferation of denitrifying and uranium-resistant populations of Rahnella spp. from Gammaproteobacteria and of Firmicutes occurred. After longer incubations for 14 weeks with uranyl nitrate, bacterial diversity increased and populations intrinsic to the untreated samples such as Bacteroidetes and Deltaproteobacteria propagated and replaced the above-mentioned uranium-resistant groups. This indicated that U(VI) was immobilized. Mössbauer spectroscopic analysis revealed an increased Fe(III) reduction by increasing the incubation time from four to 14 weeks. This result signified that Fe(III) was used as an electron acceptor by the bacterial community established at the later stages of the treatment. X-ray absorption spectroscopic analysis demonstrated that no detectable amounts of U(VI) were reduced to U(IV) in the time frames of the performed experiments. The reason for this observation is possibly due to the low level of electron donors in the studied oligotrophic environment. Time-resolved laser-induced fluorescence spectroscopic analysis demonstrated that most of the added U(VI) was bound by organic or inorganic phosphate phases both of biotic origin.

Complexation of uranium(VI) with peptidoglycan

We investigated the interaction of UO(2)(2+) with peptidoglycan (PG), the main part of the outer membrane of Gram-positive bacteria, by potentiometric titration and time-resolved laser-induced fluorescence spectroscopy (TRLFS) over a wide pH (2.0 to 9.0) and concentration range (10(-5) to 10(-4) M U(vi), 0.01 to 0.2 g L(-1) PG). With potentiometry two different dissociation constants for the carboxyl sites of glutamic acid and diaminopimelic acid (pK(a) = 4.55 +/- 0.02 and 6.31 +/- 0.01), and one averaged pK(a) for hydroxyl and amino groups (which are not distinguishable) (9.56 +/- 0.03) and the site densities could be identified. With potentiometry three different uranyl PG complexes were ascertained: two 1 : 1 uranyl carboxyl complexes R-COO-UO(2)(+), one with the glutamic acid carboxyl group (log beta(110) = 4.02 +/- 0.03), which has a very small formation ratio, and one with the diaminopimelic acid carboxyl group (log beta(110) = 7.28 +/- 0.03), and a mixed 1 : 1 : 1 complex with additional hydroxyl or amino coordination, R-COO-UO(2)((+))-A(i)-R (A(i) = NH(2) or O(-)) (log beta(1110) = 14.95 +/- 0.02). With TRLFS, also three, but different, species could be identified: a 1 : 1 uranyl carboxyl complex R-COO-UO(2)(+) (log beta(110) = 6.9 +/- 0.2), additionally a 1 : 2 uranyl carboxyl complex (R-COO)(2)-UO(2) (log beta(120) = 12.1 +/- 0.2), both with diaminopimelic acid carboxyl groups, and the mixed species R-COO-UO(2)((+))-A(i)-R (A(i) = NH(2) or O(-)) (log beta(1110) = 14.5 +/- 0.1). The results are in accordance within the errors of determination.

Engineering a uranyl-specific binding protein from NikR

A new pick-up line: The first uranyl-selective DNA-binding protein is designed using the E. coli nickel(II)-responsive protein NikR as the template. The resulting NikR' protein binds uranyl (see picture) with a dissociation constant K(d) = 53 nM and selectively binds to DNA in the presence of uranyl.

Bacterial interactions with uranium: an environmental perspective

The presence of actinides in radioactive wastes is of major concern because of their potential for migration from the waste repositories and long-term contamination of the environment. Studies have been and are being made on inorganic processes affecting the migration of radionuclides from these repositories to the environment but it is becoming increasingly evident that microbial processes are of importance as well. Bacteria interact with uranium through different mechanisms including, biosorption at the cell surface, intracellular accumulation, precipitation, and redox transformations (oxidation/reduction). The present study is intended to give a brief overview of the key processes responsible for the interaction of actinides e.g. uranium with bacterial strains isolated from different extreme environments relevant to radioactive repositories. Fundamental understanding of the interaction of these bacteria with U will be useful for developing appropriate radioactive waste treatments, remediation and long-term management strategies as well as for predicting the microbial impacts on the performance of the radioactive waste repositories.

Supramolecular structure of 5-aminosalycilic acid/halloysite composites

This paper assesses the supramolecular structure of nanocomposites prepared by including the anti-inflammatory drug 5-aminosalycilic acid in halloysite nanotubes. Halloysite tubes have sub-micron individual lengths with outer diameters ∼0.1 µm, as observed by FESEM. The mercury intrusion plots showed bimodal profiles with pore dimensions ∼10 and 0.06 µm. X-ray diffraction and thermogravimetric results revealed changes in the hydration form of the clay after the interaction. The groups associated to the interaction were studied by FTIR. The location of the drug in the composites was determined after uranium staining of its amino groups by X-EDS microanalysis coupled with HREM. The drug was located both inside and on the surface of the halloysite nanotubes. These results confirm the occurrence of two concomitant interaction mechanisms: rapid adsorption of 5-ASA at the external halloysite surface followed by slow adsorption of the drug inside the tubes.

Interaction of uranium(VI) with lipopolysaccharide

Bacteria have a great influence on the migration behaviour of heavy metals in the environment. Lipopolysaccharides form the main part of the outer membrane of Gram-negative bacteria. We investigated the interaction of the uranyl cation (UO2(2+)) with lipopolysaccharide (LPS) from Pseudomonas aeruginosa by using potentiometric titration and time-resolved laser-induced fluorescence spectroscopy (TRLFS) over a wide pH and concentration range. Generally, LPS consists of a high density of different functionalities for metal binding such as carboxyl, phosphoryl, amino and hydroxyl groups. The dissociation constants and corresponding site densities of these functional groups were determined using potentiometric titration. The combination of both methods, potentiometry and TRLFS, show that at an excess of LPS uranyl phosphoryl coordination dominates, whereas at a slight deficit on LPS compared to uranyl, carboxyl groups also become important for uranyl coordination. The stability constants of one uranyl carboxyl complex and three different uranyl phosphoryl complexes and the luminescence properties of the phosphoryl complexes are reported.

Uranium(VI) complexes with phospholipid model compounds--a laser spectroscopic study

We present the complex formation of the uranyl ion (UO(2)(2+)) in the aqueous system with phosphocholine, O-phosphoethanolamine and O-phosphoserine. These phosphonates (R-O-PO(3)(2-)) represent the hydrophilic head groups of phospholipids. The complexation was investigated by time-resolved laser-induced fluorescence spectroscopy (TRLFS) at pH=2-6. An increase of the fluorescence intensity, connected with a strong red-shift of about 8 nm compared to the free uranyl ion, indicates a complex formation between UO(2)(2+) and the phosphonates already at pH=2. Even at pH=6 these complexes prevail over the uranyl hydroxide and carbonate species, which are generated naturally at this pH. At pH=4 and higher a 1:2 complex between uranyl and O-phosphoserine was found. Complexes with a metal-to-ligand ratio of 1:1 were observed for all other ligands. Fluorescence lifetimes, emission maxima and complex stability constants at T=22+/-1 degrees C are reported. The TRLFS spectra of uranyl complexes with two phosphatidic acids (1,2-dimyristoyl-sn-glycero-3-phosphate and 1,2-dipalmitoyl-sn-glycero-3-phosphate), which represent the apolaric site of phospholipids, show in each case two different species.