Microbial uranium immobilization independent of nitrate reduction

Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment

Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.

Potential of indigenous bacteria driven U(VI) reduction under relevant deep geological repository (DGR) conditions

Understanding the biogeochemical U redox processes is crucial for controlling U mobility and toxicity under conditions relevant to deep geological repositories (DGRs). In this study, we examined the microbial reduction of aqueous hexavalent uranium U(VI) [U(VI)aq] by indigenous bacteria in U-contaminated groundwater. Three indigenous bacteria obtained from granitic groundwater at depths of 44-60 m (S1), 92-116 m (S2), and 234-244 m (S3) were used in U(VI)aq bioreduction experiments. The concentration of U(VI)aq was monitored to evaluate its removal efficiency for 24 weeks under anaerobic conditions with the addition of 20 mM sodium acetate. During the anaerobic reaction, U(VI)aq was precipitated in the form of U(IV)-silicate with a particle size >100 nm. The final U(VI)aq removal efficiencies were 37.7%, 43.1%, and 57.8% in S1, S2, and S3 sample, respectively. Incomplete U(VI)aq removal was attributed to the presence of a thermodynamically stable calcium uranyl carbonate complex in the U-contaminated groundwater. High-throughput 16S rRNA gene sequencing analysis revealed the differences in indigenous bacterial communities in response to the depth, which affected to the U(VI)aq removal efficiency. Pseudomonas peli was found to be a common bacterium related to U(VI)aq bioreduction in S1 and S2 samples, while two SRB species, Thermodesulfovibrio yellowstonii and Desulfatirhabdium butyrativorans, played key roles in the bioreduction of U(VI)aq in S3 sample. These results indicate that remediation of U(VI)aq is possible by stimulating the activity of indigenous bacteria in the DGR environment.

Remediation techniques for uranium removal from polluted environment - Review on methods, mechanism and toxicology

Uranium, a radionuclide, is a predominant element utilized for speciality requirements in industrial applications, as fuels and catalyst. The radioactive properties and chemical toxicity of uranium causes a major threat to the ecosystem. The hazards associated with Uranium pollution includes the cancer in bones, liver, and lungs. The toxicological properties of Uranium are discussed in detail. Although there are many methods to eliminate those hazards, this research work is aimed to describe the application of bioremediation methods. Bioremediation methods involve elimination of the hazards of uranium, by transforming into low oxidation form using natural microbes and plants. This study deeply elucidates the methods as bioleaching, biosorption, bioreduction and phytoremediation. Bioleaching process involves bio-oxidation of tetravalent uranium when it gets in contact with acidophilic metal bacterial complex to obtain leach liquor. In biosorption, chitin/chitosan derived sorbents act as chelators and binds with uranium by electrostatic attraction. Bio reduction employs a bacterial transformation into enzymes which immobilize and reduce uranium. Phytoremediation includes phytoextraction and phytotranslocation of uranium through xylems from soil to roots and shoots of plants. The highest uranium removal and uptake reported using the different methods are listed as follows: bioleaching (100% uranium recovery), biosorption (167 g kg^-1 uranium uptake), bioreduction (98.9% uranium recovery), and phytoremediation (49,639 mg kg^-1 uranium uptake). Among all the techniques mentioned above, bioleaching has been proved to be the most efficient for uranium remediation.

Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico

The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.

Engineering and kinetic aspects of bacterial uranium reduction for the remediation of uranium contaminated environments

Biological reduction of soluble uranium from U(VI) to insoluble U(IV) coupled to the oxidation of an electron donor (hydrogen or organic compounds) is a potentially cost-efficient way to reduce the U concentrations in contaminated waters to below regulatory limits. A variety of microorganisms originating from both U contaminated and non-contaminated environments have demonstrated U(VI) reduction capacity under anaerobic conditions. Bioreduction of U(VI) is considered especially promising for in situ remediation, where the activity of indigenous microorganisms is stimulated by supplying a suitable electron donor to the subsurface to contain U contamination to a specific location in a sparingly soluble form. Less studied microbial biofilm-based bioreactors and bioelectrochemical systems have also shown potential for efficient U(VI) reduction to remove U from contaminated water streams. This review compares the advantages and challenges of U(VI)-reducing in situ remediation processes, bioreactors and bioelectrochemical systems. In addition, the current knowledge of U(VI) bioreduction mechanisms and factors affecting U(VI) reduction kinetics (e.g. pH, temperature, and the chemical composition of the contaminated water) are discussed, as both of these aspects are important in designing efficient remediation processes.

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.

Microbial reduction of uranium (VI) by Bacillus sp. dwc-2: A macroscopic and spectroscopic study

The microbial reduction of U(VI) by Bacillus sp. dwc-2, isolated from soil in Southwest China, was explored using transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge spectroscopy (XANES). Our studies indicated that approximately 16.0% of U(VI) at an initial concentration of 100mg/L uranium nitrate could be reduced by Bacillus sp. dwc-2 at pH8.2 under anaerobic conditions at room temperature. Additionally, natural organic matter (NOM) played an important role in enhancing the bioreduction of U(VI) by Bacillus sp. dwc-2. XPS results demonstrated that the uranium presented mixed valence states (U(VI) and U(IV)) after bioreduction, which was subsequently confirmed by XANES. Furthermore, the TEM and high resolution transmission electron microscopy (HRTEM) analysis suggested that the reduced uranium was bioaccumulated mainly within the cell and as a crystalline structure on the cell wall. These observations implied that the reduction of uranium may have a significant effect on its fate in the soil environment in which these bacterial strains occur.

Biogeochemical behaviour and bioremediation of uranium in waters of abandoned mines

The discharges of uranium and associated radionuclides as well as heavy metals and metalloids from waste and tailing dumps in abandoned uranium mining and processing sites pose contamination risks to surface and groundwater. Although many more are being planned for nuclear energy purposes, most of the abandoned uranium mines are a legacy of uranium production that fuelled arms race during the cold war of the last century. Since the end of cold war, there have been efforts to rehabilitate the mining sites, initially, using classical remediation techniques based on high chemical and civil engineering. Recently, bioremediation technology has been sought as alternatives to the classical approach due to reasons, which include: (a) high demand of sites requiring remediation; (b) the economic implication of running and maintaining the facilities due to high energy and work force demand; and (c) the pattern and characteristics of contaminant discharges in most of the former uranium mining and processing sites prevents the use of classical methods. This review discusses risks of uranium contamination from abandoned uranium mines from the biogeochemical point of view and the potential and limitation of uranium bioremediation technique as alternative to classical approach in abandoned uranium mining and processing sites.

Fermentation and hydrogen metabolism affect uranium reduction by clostridia

Previously, it has been shown that not only is uranium reduction under fermentation condition common among clostridia species, but also the strains differed in the extent of their capability and the pH of the culture significantly affected uranium(VI) reduction. In this study, using HPLC and GC techniques, metabolic properties of those clostridial strains active in uranium reduction under fermentation conditions have been characterized and their effects on capability variance of uranium reduction discussed. Then, the relationship between hydrogen metabolism and uranium reduction has been further explored and the important role played by hydrogenase in uranium(VI) and iron(III) reduction by clostridia demonstrated. When hydrogen was provided as the headspace gas, uranium(VI) reduction occurred in the presence of whole cells of clostridia. This is in contrast to that of nitrogen as the headspace gas. Without clostridia cells, hydrogen alone could not result in uranium(VI) reduction. In alignment with this observation, it was also found that either copper(II) addition or iron depletion in the medium could compromise uranium reduction by clostridia. In the end, a comprehensive model was proposed to explain uranium reduction by clostridia and its relationship to the overall metabolism especially hydrogen (H2) production.

The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1

Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H(2) -evolving and H(2) -consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H(2) cycling in the bacterium. The mechanism of metal reduction remains unknown.

Biological reduction of uranium--from the laboratory to the field

The chemical and biological processes underlying in situ bioremediation of uranium-contaminated groundwater have been studied in the laboratory and in the field. This article focuses on the long-term stability of uraninite (UO(2)) in the underground. A large tailings pond, 'Dänkritz 1' in Germany, was selected for this investigation. A single-pass flow-through experiment was run in a 100-liter column: bioremediation for 1year followed by infiltration of tap water (2.5years) saturated with oxygen, sufficient to oxidize the precipitated uraninite in two months. Instead, only 1wt.% uraninite was released over 2.4years at concentrations typically less than 20μg/L. Uraninite was protected against oxidation by the mineral mackinawite (FeS(0.9)), a considerable amount of which had formed, together with uraninite. A confined field test was conducted adjacent to the tailings pond, which after bio-stimulation showed similarly encouraging results as in the laboratory. Taking Dänkritz 1 as an example we show that in situ bioremediation can be a viable option for long-term site remediation, if the process is designed based on sufficient laboratory and field data. The boundary conditions for the site in Germany are discussed.

Microbial community changes in response to ethanol or methanol amendments for U(VI) reduction

Microbial community responses to ethanol, methanol, and methanol plus humics amendments in relationship to U(VI) bioreduction were studied in laboratory microcosm experiments using sediments and ground water from a uranium-contaminated site in Oak Ridge, TN. The type of carbon source added, the duration of incubation, and the sampling site influenced the bacterial community structure upon incubation. Analysis of 16S rRNA gene clone libraries indicated that (i) bacterial communities found in ethanol- and methanol-amended samples with U(VI) reduction were similar due to the presence of Deltaproteobacteria and Betaproteobacteria (members of the families Burkholderiaceae, Comamonadaceae, Oxalobacteraceae, and Rhodocyclaceae); (ii) methanol-amended samples without U(VI) reduction exhibited the lowest diversity and the bacterial community contained 69.2 to 92.8% of the family Methylophilaceae; and (iii) the addition of humics resulted in an increase of phylogenetic diversity of Betaproteobacteria (Rodoferax, Polaromonas, Janthinobacterium, Methylophilales, and unclassified) and Firmicutes (Desulfosporosinus and Clostridium).

Uranium reduction and resistance to reoxidation under iron-reducing and sulfate-reducing conditions

Oxidation and mobilization of microbially-generated U(IV) is of great concern for in situ uranium bioremediation. This study investigated the reoxidation of uranium by oxygen and nitrate in a sulfate-reducing enrichment and an iron-reducing enrichment derived from sediment and groundwater from the Field Research Center in Oak Ridge, Tennessee. Both enrichments were capable of reducing U(VI) rapidly. 16S rRNA gene clone libraries of the two enrichments revealed that Desulfovibrio spp. are dominant in the sulfate-reducing enrichment, and Clostridium spp. are dominant in the iron-reducing enrichment. In both the sulfate-reducing enrichment and the iron-reducing enrichment, oxygen reoxidized the previously reduced uranium but to a lesser extent in the iron-reducing enrichment. Moreover, in the iron-reducing enrichment, the reoxidized U(VI) was eventually re-reduced to its previous level. In both, the sulfate-reducing enrichment and the iron-reducing enrichment, uranium reoxidation did not occur in the presence of nitrate. The results indicate that the Clostridium-dominated iron-reducing communities created conditions that were more favorable for uranium stability with respect to reoxidation despite the fact that fewer electron equivalents were added to these systems. The likely reason is that more of the added electrons are present in a form that can reduce oxygen to water and U(VI) back to U(IV).

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.

Donor-dependent extent of uranium reduction for bioremediation of contaminated sediment microcosms

Bioremediation of uranium was investigated in microcosm experiments containing contaminated sediments from Oak Ridge, Tennessee to explore the importance of electron donor selection for uranium reduction rate and extent. In these experiments, all of the electron donors, including ethanol, glucose, methanol, and methanol with added humic acids, stimulated the reduction and immobilization of aqueous uranium by the indigenous microbial community. Uranium loss from solution began after the completion of nitrate reduction but essentially concurrent with sulfate reduction. When electron donor concentrations were normalized for their equivalent electron donor potential yield, the rates of uranium reduction were nearly equivalent for all treatments (0.55-0.95 micromol L(-1) d(-1)). Uranium reduction with methanol proceeded after a 15-d longer lag time relative to that of ethanol or glucose. Significant differences were not found with the inclusion of humic acids. The extent of U reduction in sediment slurries measured by XANES at various time periods after the start of the experiment increased in the order of ethanol (5-7% reduced at 77 and 153 d), glucose (49% reduced at 53 d), and methanol (93% reduced at 90 d). The microbial diversity of ethanol- and methanol-amended microcosms in their late stage of U reduction was analyzed with 16S rRNA gene amplification. Members of the Geobacteraceae were found in all microcosms as well as other potential uranium-reducing organisms, such as Clostridium and Desulfosporosinus. The effectiveness of methanol relative to ethanol at reducing aqueous and sediment-hosted uranium suggests that bioremediation strategies that encourage fermentative poising of the subsurface to a lower redox potential may be more effective for long-term uranium immobilization as compared with selecting an electron donor that is efficiently metabolized by known uranium-reducing microorganisms.

Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths

Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5-year period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate and ethanol were strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate reducers and metal reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared with the population variation through canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bioreduction; however, the two biostimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.

Reduction of uranium(VI) to uranium(IV) by clostridia

Several different species of clostridia reduced U(VI) to U(IV) to various degrees. The optimal pH for U(VI) reduction is 5 to 6 in most cases; a Clostridium sp. showed the highest rate at pH 4. Nitrate did not affect U(VI) reduction, indicating that this process in clostridia is nitrate independent.