Bacterial interactions with uranium: an environmental perspective

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.

Mitigation of uranium toxicity in rice by Sphingopyxis sp. YF1: Evidence from growth, ultrastructure, subcellular distribution, and physiological characteristics

Uranium (U) contamination of rice is an urgent ecological and agricultural problem whose effective alleviation is in great demand. Sphingopyxis genus has been shown to remediate heavy metal-contaminated soils. Rare research delves into the mitigation of uranium (U) toxicity to rice by Sphingopyxis genus. In this study, we exposed rice seedlings for 7 days at U concentrations of 0, 10, 20, 40, and 80 mg L-1 with or without the Sphingopyxis sp. YF1 in the rice nutrient solution. Here, we firstly found YF1 colonized on the root of rice seedlings, significantly mitigated the growth inhibition, and counteracted the chlorophyll content reduction in leaves induced by U. When treated with 1.1 × 107 CFU mL-1 YF1 with the amendment of 10 mg L-1 U, the decrease of U accumulation in rice seedling roots and shoots was the largest among all treatments; reduced by 39.3% and 32.1%, respectively. This was associated with the redistribution of the U proportions in different organelle parts, leading to the alleviation of the U damage to the morphology and structure of rice root. Interestingly, we found YF1 significantly weakens the expression of antioxidant enzymes genes (CuZnSOD,CATA,POD), promotes the up-regulation of metal-transporters genes (OsHMA3 and OsHMA2), and reduces the lipid peroxidation damage induced by U in rice seedlings. In summary, YF1 is a plant-probiotic with potential applications for U-contaminated rice, benefiting producers and consumers.

The effect of bacteria on uranium sequestration stability by different forms of phosphorus

Immobilisation of uranium (U (VI)) by direct precipitation of uranyl phosphate (U-P) exhibits a great potential application in the remediation of U (VI)-contaminated environments. However, phosphorus, vital element of bacteria's decomposition, absorption and transformationmay affect the stability of U (VI) with ageing time. The main purpose of this work is to study the effect of bacteria on uranium sequestration mechanism and stability by different forms of phosphorus in a water sedimentary system. The results showed that phosphate effectively enhanced the removal of U (VI), with 99.84%. X-Ray Diffraction (XRD), Scanning Electron Microscopy and Energy Dispersive Spectrometer (SEM-EDS), and X-ray Photoelectron Spectroscopy (XPS) analyses imply that U (VI) and U (IV) co-exist on the surface of the samples. Combined with BCR results, it demonstrated that bacteria and phosphorus have a synergistic effect on the removal of U (VI), realising the immobilisation of U (VI) from a transferable phase to a stable phase. However, from a long-term perspective, the redissolution and release of uranium immobilisation of U (VI) by pure bacteria with ageing time are worthy of attention, especially in uranium mining environments rich in sensitive substances. This observation implies that the stability of the uranium may be impacted by the prevailing environmental conditions. The novel findings could provide theoretical evidence for U (VI) bio-immobilisation in U (VI)-contaminated environments.

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

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

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

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

Microbial features with uranium pollution in artificial reservoir sediments at different depths under drought stress

The uranium (U) containing leachate from uranium tailings dam into the natural settings, may greatly affect the downstream environment. To reveal such relationship between uranium contamination and microbial communities in the most affected downstream environment under drought stress, a 180 cm downstream artificial reservoir depth sediment profile was collected, and the microbial communities and related genes were analyzed by 16S rDNA and metagenomics. Besides, the sequential extraction scheme was employed to shed light on the distinct role of U geochemical speciations in shaping microbial community structures. The results showed that U content ranged from 28.1 to 70.1 mg/kg, with an average content of 44.9 mg/kg, significantly exceeding the value of background sediments. Further, U in all the studied sediments was related to remarkably high portions of mobile fractions, and U was likely deposited layer by layer depending on the discharge/leachate inputs from uranium-involving anthoropogenic facilities/activities upstream. The nexus between U speciation, physico-chemical indicators and microbial composition showed that Fe, S, and N metabolism played a vital role in microbial adaptation to U-enriched environment; meanwhile, the fraction of Ureducible and the Fe and S contents had the most significant effects on microbial community composition in the sediments under drought stress.

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

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

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.

U mobilization and associated U isotope fractionation by sulfur-oxidizing bacteria

Uranium (U) contamination of the environment causes high risk to health, demanding for effective and sustainable remediation. Bioremediation via microbial reduction of soluble U(VI) is generating high fractions (>50%) of insoluble non-crystalline U(IV) which, however, might be remobilized by sulfur-oxidizing bacteria. In this study, the efficacy of Acidithiobacillus (At.) ferrooxidans and Thiobacillus (T.) denitrificans to mobilize non-crystalline U(IV) and associated U isotope fractionation were investigated. At. ferrooxidans mobilized between 74 and 91% U after 1 week, and U mobilization was observed for both, living and inactive cells. Contrary to previous observations, no mobilization by T. denitrificans could be observed. Uranium mobilization by At. ferrooxidans did not cause U isotope fractionation suggesting that U isotope ratio determination is unsuitable as a direct proxy for bacterial U remobilization. The similar mobilization capability of active and inactive At. ferrooxidans cells suggests that the mobilization is based on the reaction with the cell biomass. This study raises doubts about the long-term sustainability of in-situ bioremediation measures at U-contaminated sites, especially with regard to non-crystalline U(IV) being the main component of U bioremediation.

Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia's Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.

Influence of microorganisms on uranium release from mining-impacted lake sediments under various oxygenation conditions

Microbial processes can be involved in the remobilization of uranium (U) from reduced sediments under O₂ reoxidation events such as water table fluctuations. Such reactions could be typically encountered after U-bearing sediment dredging operations. Solid U(IV) species may thus reoxidize into U(VI) that can be released in pore waters in the form of aqueous complexes with organic and inorganic ligands. Non-uraninite U(IV) species may be especially sensitive to reoxidation and remobilization processes. Nevertheless, little is known regarding the effect of microbially mediated processes on the behaviour of U under these conditions.

Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar

Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.

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.

Stabilization and mechanism of uranium sequestration by a mixed culture consortia of sulfate-reducing and phosphate-solubilizing bacteria

In this study, a highly efficient phosphate-solubilizing bacteria (PSB) (Pantoea sp. grinm-12) was screened out from uranium (U) tailings, and the carbon and nitrogen sources of mixed culture with sulfate-reducing bacteria (SRB) were optimized. Results showed that the functional expression of SRB-PSB could be promoted effectively when glucose + sodium lactate was used as carbon source and ammonium nitrate + ammonium sulfate as nitrogen source. The concentration of PO₄^3- in the culture system could reach 107.27 mg·L^-1, and the sulfate reduction rate was 81.72%. In the process of biological stabilization of U tailings by mixed SRB-PSB culture system, the chemical form of U in the remediation group was found to transfer to stable state with the extension of remediation time, which revealed the effectiveness of bioremediation on the harmless treatment of U tailings. XRD, FT-IR, SEM-EDS, high-throughput sequencing, and metagenomics were also used to assist in revealing the microstructure and composition changes during the biological stabilization process, and explore the microbial community/functional gene response. Finally, the stabilization mechanism of U was proposed. In conclusion, the stabilization of U in U tailings was realized through the synergistic effect of bio-reduction, bio-precipitation, and bio-adsorption.

Review of Clay-Based Nanocomposites as Adsorbents for the Removal of Heavy Metals

Due to rapid industrialization, urbanization, and surge in modern human activities, water contamination is a major threat to humanity globally. Contaminants ranging from organic compounds, dyes, to inorganic heavy metals have been of major concern in recent years. This necessitates the development of affordable water remediation technologies to improve water quality. There is a growing interest in nanotechnology recently because of its application in eco-friendly, cost-effective, and durable material production. This study presents a review of recent nanocomposite technologies based on clay, applied in the removal of heavy metals from wastewater, and highlights the shortcomings of existing methods. Recently published reports, articles, and papers on clay-based nanocomposites for the removal of heavy metals have been reviewed. Currently, the most common methods utilized in the removal of heavy metals are reverse osmosis, electrodialysis, ion exchange, and activated carbon. These methods, however, suffer major shortcomings such as inefficiency when trace amounts of contaminant are involved, uneconomical costs of operation and maintenance, and production of contaminated sludge. The abundance of clay on the Earth’s surface and the ease of modification to improve adsorption capabilities have made it a viable candidate for the synthesis of nanocomposites. Organoclay nanocomposites such as polyacrylamide-bentonite, polyaniline-montmorillonite, and β-cyclodextrin-bentonite have been synthesized for the selective removal of various heavy metals such as Cu2+, Co2+, among others. Bacterial clay nanocomposites such as E. coli kaolinite nanocomposites have also been successfully synthesized and applied in the removal of heavy metals. Low-cost nanocomposites of clay using biopolymers like chitosan and cellulose are especially in demand due to the cumulative abundance of these materials in the environment. A comparative analysis of different synthetic processes to efficiently remove heavy metal contaminants with clay-based nanocomposite adsorbents is made.

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.

A critical review on the occurrence and distribution of the uranium- and thorium-decay nuclides and their effect on the quality of groundwater

This critical review presents the key factors that control the occurrence of natural elements from the uranium- and thorium-decay series, also known as naturally occurring radioactive materials (NORM), including uranium, radium, radon, lead, polonium, and their isotopes in groundwater resources. Given their toxicity and radiation, elevated levels of these nuclides in drinking water pose human health risks, and therefore understanding the occurrence, sources, and factors that control the mobilization of these nuclides from aquifer rocks is critical for better groundwater management and human health protection. The concentrations of these nuclides in groundwater are a function of the groundwater residence time relative to the decay rates of the nuclides, as well as the net balance between nuclides mobilization (dissolution, desorption, recoil) and retention (adsorption, precipitation). This paper explores the factors that control this balance, including the relationships between the elemental chemistry (e.g., solubility and speciation), lithological and hydrogeological factors, groundwater geochemistry (e.g., redox state, pH, ionic strength, ion-pairs availability), and their combined effects and interactions. The various chemical properties of each of the nuclides results in different likelihoods for co-occurrence. For example, the primordial ²³⁸U, ²²²Rn, and, in cases of high colloid concentrations also ²¹⁰Po, are all more likely to be found in oxic groundwater. In contrast, in reducing aquifers, Ra nuclides, ²¹⁰Pb, and in absence of high colloid concentrations, ²¹⁰Po, are more mobile and frequently occur in groundwater. In highly permeable sandstone aquifers that lack sufficient adsorption sites, Ra is often enriched, even in low salinity and oxic groundwater. This paper also highlights the isotope distributions, including those of relatively long-lived nuclides (²³⁸U/²³⁵U) with abundances that depend on geochemical conditions (e.g., fractionation induced from redox processes), as well as shorter-lived nuclides (²³⁴U/²³⁸U, ²²⁸Ra/²²⁶Ra, ²²⁴Ra/²²⁸Ra, ²¹⁰Pb/²²²Rn, ²¹⁰Po/²¹⁰Pb) that are strongly influenced by physical (recoil), lithological, and geochemical factors. Special attention is paid in evaluating the ability to use these isotope variations to elucidate the sources of these nuclides in groundwater, mechanisms of their mobilization from the rock matrix (e.g., recoil, ion-exchange), and retention into secondary mineral phases and ion-exchange sites.

Radioactive waste treatment technology: a review

Radioactive waste is generated from activities that utilize nuclear materials such as nuclear medicine or power plants. Depending on their half-life, they emit radiation continuously, ranging from seconds to millions of years. Exposure to ionizing radiation can cause serious harm to humans and the environment. Therefore, special attention is paid to the management of radioactive waste in order to deal with its large quantity and dangerous levels. Current treatment technologies are still being developed to improve efficiency in reducing the hazard level and waste volume, to minimize the impact on living organisms. Thus, the aim of this study was to provide an overview of the global radioactive waste treatment technologies that have been released in 2019–2021.

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

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

From individual response to population ecology: Environmental factors restricting survival of vegetative bacteria at solid-air interfaces

Combating microbial survival on dry surfaces contributes to improving public health in indoor environments (clinical and industrial settings) and extends to the natural environment. For vegetative bacteria at solid-air interfaces, lack of water impacts cellular response, and acclimation depends on community support in response to ecological processes. Gaining insights about important ecological processes leading to inhibition of microbial survival under extreme conditions, such as vicinity of highly radioactive nuclear waste, is key for improving engineering designs. Canada plans to store used nuclear fuel and radioactive waste in a deep geological repository (DGR) with a multiple-barrier system constructed at an approximate depth of 500 m. Microorganisms in highly compacted bentonite surrounding used fuel containers will be challenged by high pressure, temperature, and radiation, as well as limited water and nutrients. Thus, it is difficult to estimate microbial activities, given that the prime concern for a microbial community is survival, and energy expenditure is regulated. To enable preventive measures and for risk evaluation, a deeper understanding of community-based survival strategies of bacterial cells exposed to air (gaseous phase) during prolonged periods of desiccation is required. An in-depth review of collective studies that assess microbial survival and persistence during desiccation is presented here to augment and direct our prior knowledge about tactics used by bacteria for survival at interfaces in hostile natural environments including and similar to a DGR.

Microbial interaction with and tolerance of radionuclides: underlying mechanisms and biotechnological applications

Radionuclides (RNs) generated by nuclear and civil industries are released in natural ecosystems and may have a hazardous impact on human health and the environment. RN-polluted environments harbour different microbial species that become highly tolerant of these elements through mechanisms including biosorption, biotransformation, biomineralization and intracellular accumulation. Such microbial-RN interaction processes hold biotechnological potential for the design of bioremediation strategies to deal with several contamination problems. This paper, with its multidisciplinary approach, provides a state-of-the-art review of most research endeavours aimed to elucidate how microbes deal with radionuclides and how they tolerate ionizing radiations. In addition, the most recent findings related to new biotechnological applications of microbes in the bioremediation of radionuclides and in the long-term disposal of nuclear wastes are described and discussed.

Kinetic modelling of the uranium biosorption by Deinococcus radiodurans biofilm

Increasing number of reports on uranium contamination in groundwater bodies is a growing concern. Deinococcus radiodurans biofilm-based U(VI) bioremediation has great potential to provide solution. This study focuses on the kinetic modelling of uranium biosorption by D. radiodurans biofilm biomass and identification of the functional groups involved in the sequestration process. The effect of temperature, pH and amount of biofilm dry mass were studied using two uranyl ion concentrations (100 and 1000 mg/L). D. radiodurans dry biomass showed good affinity for uranyl ion adsorption. The kinetic experiments revealed that the biosorption process was spontaneous and exothermic in nature. The modelling of kinetic adsorption data revealed that U(VI) sorption by D. radiodurans biofilm biomass follows a pseudo-second-order reaction. Mechanism of U(VI) sorption was suggested to follow an intra-particle diffusion model, which includes covalent bonding between U(VI) and functional groups present on the surface of biofilm biomass, and diffusional barrier acts as a rate limiting step. External mass transfer was the rate-limiting step as evident from Boyd and Elovich plot. Chemical modifications in surface functional groups of biofilm biomass, confirmed the involvement of carboxyl, phosphate, and hydroxyl groups in uranium binding as a significant loss in U(VI) sorption capacity was recorded in these chemically modified biomasses. XRD data indicated the formation of metal deposits, predominantly as uranyl phosphates.

Transcriptome Response of the Tropical Marine Yeast Yarrowia lipolytica on Exposure to Uranium

In our earlier investigation, we reported the consequences of uranium (U)-induced oxidative stress and cellular defense mechanisms alleviating uranium toxicity in the marine yeast Yarrowia lipolytica NCIM 3589. However, there is lack of information on stress response towards uranium toxicity at molecular level in this organism. To gain an insight on this, transcriptional response of Y. lipolytica after exposure to 50 µM uranium was investigated by RNA sequencing at the global level in this study. The de novo transcriptome analysis (in triplicates) revealed 56 differentially expressed genes with significant up-regulation and down-regulation of 33 and 23 transcripts, respectively, in U-exposed yeast cells as compared to the control, U-unexposed cells. Highly up-regulated genes under U-treated condition were identified to be primarily involved in transport, DNA damage repair and oxidative stress. The major reaction of Y. lipolytica to uranium exposure was the activation of oxidative stress response mechanisms to protect the important biomolecules of the cells. On the other hand, genes involved in cell wall and cell cycle regulation were significantly down-regulated. Overall, the transcriptional profiling by RNA sequencing to stress-inducing concentration of uranium sheds light on the various responses of Y. lipolytica for coping with uranium toxicity, providing a foundation for understanding the molecular interactions between uranium and this marine yeast.

The Emerging Trend of Bio-Engineering Approaches for Microbial Nanomaterial Synthesis and Its Applications

Micro-organisms colonized the world before the multi-cellular organisms evolved. With the advent of microscopy, their existence became evident to the mankind and also the vast processes they regulate, that are in direct interest of the human beings. One such process that intrigued the researchers is the ability to grow in presence of toxic metals. The process seemed to be simple with the metal ions being sequestrated into the inclusion bodies or cell surfaces enabling the conversion into nontoxic nanostructures. However, the discovery of genome sequencing techniques highlighted the genetic makeup of these microbes as a quintessential aspect of these phenomena. The findings of metal resistance genes (MRG) in these microbes showed a rather complex regulation of these processes. Since most of these MRGs are plasmid encoded they can be transferred horizontally. With the discovery of nanoparticles and their many applications from polymer chemistry to drug delivery, the demand for innovative techniques of nanoparticle synthesis increased dramatically. It is now established that microbial synthesis of nanoparticles provides numerous advantages over the existing chemical methods. However, it is the explicit use of biotechnology, molecular biology, metabolic engineering, synthetic biology, and genetic engineering tools that revolutionized the world of microbial nanotechnology. Detailed study of the micro and even nanolevel assembly of microbial life also intrigued biologists and engineers to generate molecular motors that mimic bacterial flagellar motor. In this review, we highlight the importance and tremendous hidden potential of bio-engineering tools in exploiting the area of microbial nanoparticle synthesis. We also highlight the application oriented specific modulations that can be done in the stages involved in the synthesis of these nanoparticles. Finally, the role of these nanoparticles in the natural ecosystem is also addressed.

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

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

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

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

The importance of the bacterial cell wall in uranium(VI) biosorption

The bacterial cell envelope, in particular the cell wall, is considered the main controlling factor in the biosorption of aqueous uranium(vi) by microorganisms. However, the specific roles of the cell wall, associated biomolecules, and other components of the cell envelope are not well defined. Here we report findings on the biosorption of uranium by isolated cell envelope components and associated biomolecules, with P. putida 33015 and B. subtilis 168 investigated as representative strains for the differences in Gram-negative and Gram-positive cell envelope architecture, respectively. The cell wall and cell surface membrane were isolated from intact cells and characterised by X-ray Photoelectron Spectroscopy (XPS) and Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FT-IR) spectroscopy; revealing variations in the abundance of functional moieties and biomolecules associated with components of the cell envelope. Uranium biosorption was investigated as a function of cell envelope component and pH, comparing with intact cells. The isolated cell wall from both strains exhibited the greatest uranium biosorption capacity. Deprotonation of favourable functional groups on the biomass as the pH increased from 3 to 5.5 increased their uranium biosorption capacity by approximately 3 fold. The results from ATR-FT-IR indicated that uranium(vi) biosorption was mediated by phosphate and carboxyl groups associated with proteins and phosphorylated biopolymers of the cell envelope. This includes outer membrane phospholipids and LPS of Gram-negative bacteria and teichoic acids, surface proteins and peptidoglycan from Gram-positive bacteria. As a result, the biosorption process of uranium(vi) to microorganisms is controlled by surface interactions, resulting in higher accumulation of uranium in the cell envelope. This demonstrates the importance of bacterial cell wall as the key mediator of uranium biosorption with microorganisms.

Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site

The use of nuclear power has been a significant part of the United Kingdom’s energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 10⁴–10⁶ mL^–1 were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.

Removal of uranium by immobilized biomass of a tropical marine yeast Yarrowia lipolytica

A marine yeast, Yarrowia lipolytica isolated from an oil polluted sea water and shown earlier to sequester dissolved uranium (U) at pH 7.5, was utilized in the present study for developing an immobilized-cell process for U removal from aqueous solutions under batch and continuous flow through systems. In batch system, optimum biosorption conditions for U removal were assessed by investigating the effects of biomass dose, initial U concentration, contact time and pH of solution using Y. lipolytica cells immobilized in calcium alginate beads. Appreciable uranium-binding capabilities over a wide pH range (3-9) were observed with the alginate beads bearing yeast cells. Out of Langmuir and Freundlich models employed for describing the sorption equilibrium data under batch mode, uranyl adsorption followed Langmuir approach with satisfactory correlation coefficient higher than 0.9. Uranyl adsorption kinetics by Y. lipolytica entrapped in alginate beads was best described by the pseudo-second-order model. While the environmental scanning electron microscopy established the immobilization and the uniform distribution of Y. lipolytica cells in the alginate beads, the Energy Dispersive X-ray spectroscopy analysis confirmed the deposition of U in the beads following their exposure to uranyl solution. Fixed bed flow-through column comprising of Y. lipolytica biomass immobilized in polyacrylamide matrix displayed high efficacy for continuous removal of uranium at pH 7.5 up to five adsorption-desorption cycles. Adsorbed U by immobilized cells could be significantly desorbed using 0.1 N HCl. Overall, our results present the superior efficiency of immobilized Y. lipolytica biomass for U removal using batch and regenerative approaches.

Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides

Lanthanides and actinides are elements of ever-increasing technological importance in the modern world. However, the similar chemical and physical properties within these groups make purification of individual elements a challenge. Current industrial standards for the extraction, separation, and purification of these metals from natural sources, recycled materials, and industrial waste are inefficient, relying upon harsh conditions, repetitive steps, and ligands with only modest selectivity. Biological, biomolecular, and bio-inspired strategies towards improving these separations and making them more environmentally sustainable have been researched for many years; however, these methods often have insufficient selectivity for practical application. Recent developments in the understanding of how lanthanides are selectively acquired and used by certain bacteria offer the opportunity for a newer, more efficient take on these designs, as well as the possibility for fundamentally new designs and strategies. Herein, we review current cell-based and biomolecular (primarily small-molecule and protein-based) methods for detection, extraction, and separations of f-block elements. We discuss how the increasing knowledge regarding the selective recognition, uptake, trafficking, and storage of these elements in biological systems has informed and will continue to promote development of novel approaches to achieve these ends.

The impact of cell structure, metabolism and group behavior for the survival of bacteria under stress conditions

Microbes from diverse types of habitats are continuously exposed to external challenges, which may include acidic, alkaline, and toxic metabolites stress as well as nutrient deficiencies. To promote their own survival, bacteria have to rapidly adapt to external perturbations by inducing particular stress responses that typically involve genetic and/or cellular changes. In addition, pathogenic bacteria need to sense and withstand these environmental stresses within a host to establish and maintain infection. These responses can be, in principle, induced by changes in bacterial cell structure, metabolism and group behavior. Bacterial nucleic acids may serve as the core part of the stress response, and the cell envelope and ribosomes protect genetic structures from damage. Cellular metabolism and group behavior, such as quorum sensing system, can play a more important role in resisting stress than we have now found. Since bacteria survival can be only appreciated if we better understand the mechanisms behind bacterial stress response, here we review how morphological and physiological features may lead to bacterial resistance upon exposure to particular stress-inducing factors.

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.

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

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

Uranium Isotope Fractionation (238U/235U) during U(VI) Uptake by Freshwater Plankton

Uranium contamination in the environment is a serious public health concern. Biotic U(VI) reduction and nonreductive U(VI) uptake by microorganisms (e.g., U(VI) biosorption by cyanobacteria) are effective U remediation techniques. Variations of ²³⁸U/²³⁵U have been extensively explored to track biotic U(VI) reduction in laboratory experiments and field applications. However, U isotope fractionation during nonreductive U(VI) uptake by microorganisms is poorly constrained. To investigate U isotope fractionation in this process, we cultured freshwater plankton in the presence of U(VI) and measured ²³⁸U/²³⁵U in the culture media and biomass. We found that nonreductive U(VI) uptake by freshwater plankton fractionated U isotopes in the opposite direction compared to biotic U(VI) reduction. δ²³⁸U values in freshwater plankton were consistently ∼0.23 ± 0.06‰ lighter than those in dissolved U in the culture medium at various fractions of U removal (12-30%), consistent with equilibrium isotope fractionation in a closed system. The equilibrium isotope fractionation observed in our experiments possibly results from changes in coordination geometry between dissolved U(VI) in the culture media and adsorbed U(VI) on cell surfaces. Our experimental results highlight the need to consider U isotope fractionation during nonredox U(VI) uptake by microorganisms and organic matter when applying variations of ²³⁸U/²³⁵U to track biogeochemical processes and evaluate U remediation.

The role of bacterial cell envelope structures in acid stress resistance in E. coli

Acid resistance (AR) is an indispensable mechanism for the survival of neutralophilic bacteria, such as Escherichia coli (E. coli) strains that survive in the gastrointestinal tract. E. coli acid tolerance has been extensively studied during past decades, with most studies focused on gene regulation and mechanisms. However, the role of cell membrane structure in the context of acid stress resistance has not been discussed in depth. Here, we provide a comprehensive review of the roles and mechanisms of the E. coli cell envelope from different membrane components, such as membrane proteins, fatty acids, chaperones, and proton-consuming systems, and particularly focus on the innovative effects revealed by recent studies. We hope that the information guides us to understand the bacterial survival strategies under acid stress and to further explore the AR regulatory mechanisms to prevent or treat E. coli and other related Gram-negative bacteria infection, or to enhance the AR of engineering E. coli.

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.

Shifts in bentonite bacterial community and mineralogy in response to uranium and glycerol-2-phosphate exposure

The multi-barrier deep geological repository system is currently considered as one of the safest option for the disposal of high-level radioactive wastes. Indigenous microorganisms of bentonites may affect the structure and stability of these clays through Fe-containing minerals biotransformation and radionuclides mobilization. The present work aimed to investigate the behavior of bentonite and its bacterial community in the case of a uranium leakage from the waste containers. Hence, bentonite microcosms were amended with uranyl nitrate (U) and glycerol-2-phosphate (G2P) and incubated aerobically for 6 months. Next generation 16S rRNA gene sequencing revealed that the bacterial populations of all treated microcosms were dominated by Actinobacteria and Proteobacteria, accounting for >50% of the community. Additionally, G2P and nitrate had a remarkable effect on the bacterial diversity of bentonites by the enrichment of bacteria involved in the nitrogen and carbon biogeochemical cycles (e.g. Azotobacter). A significant presence of sulfate-reducing bacteria such as Desulfonauticus and Desulfomicrobium were detected in the U-treated microcosms. The actinobacteria Amycolatopsis was enriched in G2P‑uranium amended bentonites. High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy analyses showed the capacity of Amycolatopsis and a bentonite consortium formed by Bradyrhizobium-Rhizobium and Pseudomonas to precipitate U as U phosphate mineral phases, probably due to the phosphatase activity. The different amendments did not affect the mineralogy of the bentonite pointing to a high structural stability. These results would help to predict the impact of microbial processes on the biogeochemical cycles of elements (N and U) within the bentonite barrier under repository relevant conditions and to determine the changes in the microbial community induced by a uranium release.

Role of extracellular polymeric substances in biofilm formation by Pseudomonas stutzeri strain XL-2

Pseudomonas stutzeri strain XL-2 exhibited significant performance on biofilm formation. Extracellular polymeric substances (EPS) secreted by strain XL-2 were characterized by colorimetry and Fourier transform infrared (FT-IR) spectroscopy. The biofilm growth showed a strong positive correlation (r_P=0.96, P<0.01) to extracellular protein content, but no correlation to exopolysaccharide content. Hydrolyzing the biofilm with proteinase K caused a significant decrease in biofilm growth (t=3.7, P<0.05), whereas the changes in biofilm growth were not significant when the biofilm was hydrolyzed by α-amylase and β-amylase, implying that proteins rather than polysaccharides played the dominant role in biofilm formation. More specifically, confocal laser scanning microscopy (CLSM) revealed that the extracellular proteins were tightly bound to the cells, resulting in the cells with EPS presenting more biofilm promotion protein secondary structures, such as three-turn helices, β-sheet, and α-helices, than cells without EPS. Both bio-assays and quantitative analysis demonstrated that strain XL-2 produced signal molecules of N-acylhomoserine lactones (AHLs) during biofilm formation process. The concentrations of C₆-HLS and C₆-oxo-HLS were both significantly positively correlated with protein contents (P<0.05). Dosing exogenous C₆-HLS and C₆-oxo-HLS also resulted in the increase in protein content. Therefore, it was speculated that C₆-HLS and C₆-oxo-HLS released by strain XL-2 could up-regulate the secretion of proteins in EPS, and thus promote the formation of biofilm.

Uranium Uptake in Paracentrotus lividus Sea Urchin, Accumulation and Speciation

Uranium speciation and bioaccumulation were investigated in the sea urchin Paracentrotus lividus. Through accumulation experiments in a well-controlled aquarium followed by ICP-OES analysis, the quantification of uranium in the different compartments of the sea urchin was performed. Uranium is mainly distributed in the test (skeletal components), as it is the major constituent of the sea urchin, but in terms of quantity of uranium per gram of compartment, the following rating: intestinal tract > gonads ≫ test, was obtained. Combining both extended X-ray Absorption Spectroscopy and time-resolved laser-induced fluorescence spectroscopic analysis, it was possible to identify two different forms of uranium in the sea urchin, one in the test, as a carbonato-calcium complex, and the second one in the gonads and intestinal tract, as a protein complex. Toposome is a major calcium-binding transferrin-like protein contained within the sea urchin. EXAFS data fitting of both contaminated organs in vivo and the uranium-toposome complex from protein purified out of the gonads revealed that it is suspected to complex uranium in gonads and intestinal tract. This hypothesis is also supported by the results from two imaging techniques, i.e., Transmission Electron Microscopy and Scanning Transmission X-ray Microscopy. This thorough investigation of uranium uptake in sea urchin is one of the few attempts to assess the speciation in a living marine organism in vivo.

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.

Mechanisms of strontium's adsorption by Saccharomyces cerevisiae: Contribution of surface and intracellular uptakes

The objective of this work was to explore the mechanisms participating in strontium sorption by living Saccharomyces cerevisiae (S. cerevisiae). The location of strontium adsorbed by S. cerevisiae was studied by our plasmolysis treatment. The contribution of physical and chemical mechanisms was determined quantitatively by desorption and blockage of functional groups. Moreover, our results indicated that bioaccumulation also played a major role in biosorption by living cells. Thus, supplementary methods including 2-DE (two-dimensional electrophoresis) and Matrix-Assisted Laser Desorption/Ionization Tandem Time of Flight Mass Spectrometry (MALDI-TOF-TOF) were employed to analyze the different proteins. The subsequent desorption % of Sr²⁺ by Distilled Water (DW), NH₄NO₃ and EDTA-Na₂ from Sr²⁺ loaded sorbents indicated a minor role for physical adsorption, while ion exchange and complexation were responsible for approximately 20% and 40%. Specific blockage of functional groups revealed that carboxyl and amine groups played an important role in Sr²⁺ binding to the living S. cerevisiae. From our MALDI-TOF-TOF results, we concluded that 38 proteins showed up-regulated expression profiles and 11 proteins showed down-regulated after biosorption. Moreover, proteins belong to: phagocytic function (Act1p); ion channel (S-adenosylmethionine synthase); glycolysis (Tubulin) may directly involve in strontium bioaccumulation. In conclusion, the present work indicates that the strontium sorption mechanism by living S. cerevisiae is complicated including ion-exchange along with complexation as the main mechanism, whereas the other mechanisms such as physical adsorption play a minor contribution. Metabolically-dependent proteins may play an important role in bioaccumulation.