Genes required for alleviation of uranium toxicity in sulfate reducing bacterium Desulfovibrio alaskensis G20 [corrected]

A review of remediation technologies for uranium-contaminated water

Uranium is a naturally existing radioactive element present in the Earth's crust. It exhibits lithophilic characteristics, indicating its tendency to be located near the surface of the Earth and tightly bound to oxygen. It is ecotoxic, hence the need for its removal from the aqueous environment. This paper focuses on the variety of water treatment processes for the removal of uranium from water and this includes physical (membrane separation, adsorption and electrocoagulation), chemical (ion exchange, photocatalysis and persulfate reduction), and biological (bio-reduction and biosorption) approaches. It was observed that membrane filtration and ion exchange are the most popular and promising processes for this application. Membrane processes have high throughput but with the challenge of high power requirements and fouling. Besides high pH sensitivity, ion exchange does not have any major challenges related to its application. Several other unique observations were derived from this review. Chitosan/Chlorella pyrenoidosa composite adsorbent bearing phosphate ligand, hydroxyapatite aerogel and MXene/graphene oxide composite has shown super-adsorbent performance (>1000 mg/g uptake capacity) for uranium. Ultrafiltration (UF) membranes, reverse osmosis (RO) membranes and electrocoagulation have been observed not to go below 97% uranium removal/conversion efficiency for most cases reported in the literature. Heat persulfate reduction has been explored quite recently and shown to achieve as high as 86% uranium reduction efficiency. We anticipate that future studies would explore hybrid processes (which are any combinations of multiple conventional techniques) to solve various aspects of the process design and performance challenges.

Enhanced indigenous consortia for the remediation of uranium-contaminated groundwater by bioaugmentation: Reducing and phosphate-solubilizing consortia

To investigate the strengthening effects and mechanisms of bioaugmentation on the microbial remediation of uranium-contaminated groundwater via bioreduction coupled to biomineralization, two exogenous microbial consortia with reducing and phosphate-solubilizing functions were screened and added to uranium-contaminated groundwater as the experimental groups (group B, reducing consortium added; group C, phosphate-solubilizing consortium added). β-glycerophosphate (GP) was selected to stimulate the microbial community as the sole electron donor and phosphorus source. The results showed that bioaugmentation accelerated the consumption of GP and the proliferation of key functional microbes in groups B and C. In group B, Dysgonomonas, Clostridium_sensu_stricto_11 and Clostridium_sensu_stricto_13 were the main reducing bacteria, and Paenibacillus was the main phosphate-solubilizing bacteria. In group C, the microorganisms that solubilized phosphate were mainly unclassified_f_Enterobacteriaceae. Additionally, bioaugmentation promoted the formation of unattached precipitates and alleviated the inhibitory effect of cell surface precipitation on microbial metabolism. As a result, the formation rate of U-phosphate precipitates and the removal rates of aqueous U(VI) in both groups B and C were elevated significantly after bioaugmentation. The U(VI) removal rate was poor in the control group (group A, with only an indigenous consortium). Propionispora, Sporomusa and Clostridium_sensu_stricto_11 may have played an important role in the removal of uranium in group A. Furthermore, the addition of a reducing consortium promoted the reduction of U(VI) to U(IV), and immobilized uranium existed in the form of U(IV)-phosphate and U(VI)-phosphate precipitates in group B. In contrast, U was present mainly as U(VI)-phosphate precipitates in groups A and C. Overall, bioaugmentation with an exogenous consortium resulted in the rapid removal of uranium from groundwater and the formation of U-phosphate minerals and served as an effective strategy for improving the treatment of uranium-contaminated groundwater in situ.

Weak electro-stimulation promotes microbial uranium removal: Efficacy and mechanisms

Removal and recovery of uranium from uranium-mine wastewater is beneficial to environmental protection and resource preservation. Reduction of soluble hexavalent U (U(VI)) to insoluble tetravalent uranium (U(IV)) by microbes is a plausible approach for this purpose, but its practical implementation has long been restricted by its intrinsic drawbacks. The electro-stimulated microbial process offers promise in overcoming these drawbacks. However, its applicability in real wastewater has not been evaluated yet, and its U(VI) removal mechanisms remain poorly understood. Herein, we report that introducing a weak electro-stimulation considerably boosted microbial U(VI) removal activities in both synthetic and real wastewater. The U(VI) removal has proceeded via U(VI)-to-U(IV) reduction in the biocathode, and the electrochemical characterization demonstrates the crucial role of the electroactive biofilm. Microbial community analysis shows that the broad biodiversity of the cathode biofilm is capable of U(VI) reduction, and the molecular ecological network indicates that synthetic metabolisms among electroactive and metal-reducing bacteria play major roles in electro-microbial-mediated uranium removal. Metagenomic sequencing elucidates that the electro-stimulated U(VI) bioreduction may proceed via e-pili, extracellular electron shuttles, periplasmic and outer membrane cytochrome, and thioredoxin pathways. These findings reveal the potential and mechanism of the electro-stimulated U(VI) bioreduction system for the treatment of U-bearing wastewater.

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.

Uranium bioremediation with U(VI)-reducing bacteria

Uranium (U) pollution is an environmental hazard caused by the development of the nuclear industry. Microbial reduction of hexavalent uranium (U(VI)) to tetravalent uranium (U(IV)) reduces U solubility and mobility and has been proposed as an effective method to remediate uranium contamination. In this review, U(VI) remediation with respect to U(VI)-reducing bacteria, mechanisms, influencing factors, products, and reoxidation are systematically summarized. Reportedly, some metal- and sulfate-reducing bacteria possess excellent U(VI) reduction capability through mechanisms involving c-type cytochromes, extracellular pili, electron shuttle, or thioredoxin reduction. In situ remediation has been demonstrated as an ideal strategy for large-scale degradation of uranium contaminants than ex situ. However, U(VI) reduction efficiency can be affected by various factors, including pH, temperature, bicarbonate, electron donors, and coexisting metal ions. Furthermore, it is noteworthy that the reduction products could be reoxidized when exposed to oxygen and nitrate, inevitably compromising the remediation effects, especially for non-crystalline U(IV) with weak stability.

OrpR is a σ54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough

Enhancer binding proteins (EBPs) are key players of σ⁵⁴ -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ⁵⁴ -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]²⁺ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ⁵⁴ -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.

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.

Transposon Mutagenesis Paired with Deep Sequencing of Caulobacter crescentus under Uranium Stress Reveals Genes Essential for Detoxification and Stress Tolerance

The ubiquitous aquatic bacterium Caulobacter crescentus is highly resistant to uranium (U) and facilitates U biomineralization and thus holds promise as an agent of U bioremediation. To gain an understanding of how C. crescentus tolerates U, we employed transposon (Tn) mutagenesis paired with deep sequencing (Tn-seq) in a global screen for genomic elements required for U resistance. Of the 3,879 annotated genes in the C. crescentus genome, 37 were found to be specifically associated with fitness under U stress, 15 of which were subsequently tested through mutational analysis. Systematic deletion analysis revealed that mutants lacking outer membrane transporters (rsaFa and rsaFb), a stress-responsive transcription factor (cztR), or a ppGpp synthetase/hydrolase (spoT) exhibited a significantly lower survival rate under U stress. RsaFa and RsaFb, which are homologues of TolC in Escherichia coli, have previously been shown to mediate S-layer export. Transcriptional analysis revealed upregulation of rsaFa and rsaFb by 4- and 10-fold, respectively, in the presence of U. We additionally show that rsaFa mutants accumulated higher levels of U than the wild type, with no significant increase in oxidative stress levels. Our results suggest a function for RsaFa and RsaFb in U efflux and/or maintenance of membrane integrity during U stress. In addition, we present data implicating CztR and SpoT in resistance to U stress. Together, our findings reveal novel gene targets that are key to understanding the molecular mechanisms of U resistance in C. crescentus.

IMPORTANCE

Caulobacter crescentus is an aerobic bacterium that is highly resistant to uranium (U) and has great potential to be used in U bioremediation, but its mechanisms of U resistance are poorly understood. We conducted a Tn-seq screen to identify genes specifically required for U resistance in C. crescentus. The genes that we identified have previously remained elusive using other omics approaches and thus provide significant insight into the mechanisms of U resistance by C. crescentus. In particular, we show that outer membrane transporters RsaFa and RsaFb, previously known as part of the S-layer export machinery, may confer U resistance by U efflux and/or by maintaining membrane integrity during U stress.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Global transcriptome analysis of hexavalent chromium stress responses in Staphylococcus aureus LZ-01

Staphylococcus aureus strain LZ-01, isolated from the Lanzhou reaches of the Yellow River, is capable of reducing Cr(VI) to Cr(III) aerobically. We employed transcriptome sequencing analysis to identify genes involved in Cr(VI) stress responses in S. aureus LZ-01. Our results showed that 512 of the 2,370 predicted genes displayed up-regulation (>2-fold), and 49 genes were down-regulated (<50 %) after Cr(VI) exposure. Among up-regulated genes, 128 genes were annotated to encode proteins involved in cellular processes; 68 were categorized to transport and binding proteins; 26 were involved in DNA repair and 32 were associated with regulatory functions. To further elucidate the Cr(VI) resistance and reduction mechanism, we carried out physiological tests and quantitative PCR analysis. Both RNA-seq and qRT-PCR data showed genes encoding a thioredoxin reductase and main subunits of cytochrome c oxidase complex were up-regulated upon Cr(VI) treatment. Either cadmium or NaN3 treatment could inhibit Cr(VI) reduction which indicates that thioredoxin and cytochrome are involved in Cr(VI) reduction strain LZ-01. 29 ABC-type metal/multidrug transporters and efflux pumps were up-regulated, suggesting that they are involved in Cr(VI) resistance by pumping chromium ions out of cells. The up-regulation of 26 DNA repair genes demonstrate that Cr(VI) is toxic to DNA and those DNA protection proteins need to be responded for Cr(VI) stress. Based on these results, the mechanism of strain LZ-01 resists and reduces Cr(VI) is revealed.