A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium

Long-term tracking of the microbiology of uranium-amended water-saturated bentonite microcosms: A mechanistic characterization of U speciation

Deep geological repositories (DGRs) stand out as one of the optimal options for managing high-level radioactive waste (HLW) such as uranium (U) in the near future. Here, we provide novel insights into microbial behavior in the DGR bentonite barrier, addressing potential worst-case scenarios such as waste leakage (e.g., U) and groundwater infiltration of electron rich donors in the bentonite. After a three-year anaerobic incubation, Illumina sequencing results revealed a bacterial diversity dominated by anaerobic and spore-forming microorganisms mainly from the phylum Firmicutes. Highly U tolerant and viable bacterial isolates from the genera Peribacillus, Bacillus, and some SRB such as Desulfovibrio and Desulfosporosinus, were enriched from U-amended bentonite. The results obtained by XPS and XRD showed that U was present as U(VI) and as U(IV) species. Regarding U(VI), we have identified biogenic U(VI) phosphates, U(UO2)·(PO4)2, located in the inner part of the bacterial cell membranes in addition to U(VI)-adsorbed to clays such as montmorillonite. Biogenic U(IV) species as uraninite may be produced as result of bacterial enzymatic U(VI) reduction. These findings suggest that under electron donor-rich water-saturation conditions, bentonite microbial community can control U speciation, immobilizing it, and thus enhancing future DGR safety if container rupture and waste leakage occurs.

Recent developments and challenges in uranium extraction from seawater through amidoxime-functionalized adsorbents

As per statistical estimations, we have only around 100 years of uranium life in terrestrial ores. In contrast, seawater has viable uranium resources that can secure the future of energy. However, to achieve this, environmental challenges need to be overcome, such as low uranium concentration (3.3 ppb), fouling of adsorbents, uranium speciation, oceanic temperature, and competition between elements for the active site of adsorbent (such as vanadium which has a significant influence on uranium adsorption). Furthermore, the deployability of adsorbent under seawater conditions is a gigantic challenge; hence, leaching-resistant stable adsorbents with good reusability and high elution rates are extremely needed. Powdered (nanostructured) adsorbents available today have limitations in fulfilling these requirements. An increase in the grafting density of functional ligands keeping in view economic sustainability is also a major obstacle but a necessity for high uranium uptake. To cope with these challenges, researchers reported hundreds of adsorbents of different kinds, but amidoxime-based polymeric adsorbents have shown some remarkable advantages and are considered the benchmark in uranium extraction history; they have a high affinity for uranium because of electron donors in their structure, and their amphoteric nature is responsible for effective uranium chelation under a wide range of pH. In this review, we have mainly focused on recent developments in uranium extraction from seawater through amidoxime-based adsorbents, their comparative analysis, and problematic factors that are needed to be considered for future research.

Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF-matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%-40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species-largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.

Biostimulation as a sustainable solution for acid neutralization and uranium immobilization post acidic in-situ recovery

Major uranium (U) deposits worldwide are exploited by acid leaching, known as 'in-situ recovery' (ISR). ISR involves the injection of an acid fluid into ore-bearing aquifers and the pumping of the resulting metal-containing solution through cation exchange columns for the recovery of dissolved U. Rehabilitation of ISR-impacted aquifers could be achieved through natural attenuation, or via biostimulation of autochthonous heterotrophic microorganisms due to the associated acid neutralization and trace metal immobilization. In this study, we analyzed the capacity of pristine aquifer sediments impacted by diluted ISR fluids to buffer pH and immobilize U. The experimental setup consisted of glass columns, filled with sediment from a U ore-bearing aquifer, through which diluted ISR fluids were flowed continuously. The ISR solution was obtained from ISR mining operations at the Muyunkum and Tortkuduk deposits in Kazakhstan. Following this initial phase, columns were biostimulated with a mix of molasses, yeast extract and glycerol to stimulate the growth of autochthonous heterotrophic communities. Experimental results showed that this amendment efficiently promoted the activity of acid-tolerant bacterial guilds, with pH values rising from 4.8 to 6.5-7.0 at the outlet of the stimulated columns. The reduction of sulfate, nitrate, and metals as well as dissimilatory nitrate reduction to ammonia induced the rise in pH values, in agreement with geochemical modelling results. Biostimulation efficiently promoted the complete immobilization of U, with the accumulation of up to 3343 ppm in the first few centimeters of the columns. Synchrotron analysis and SEM-EDS revealed that up to 60% of the injected hexavalent U was immobilized as tetravalent non-crystalline U onto bacterial cell surfaces. 16S rDNA amplicon analysis and qPCR data suggested a predominant role played for members of the Phylum Firmicutes (from the genera Clostridium, Pelosinus and Desulfosporosinus) in biological U reduction and immobilization.

Emerging investigator series: entrapment of uranium-phosphorus nanocrystals inside root cells of Tamarix plants from a mine waste site

We investigated the mechanisms of uranium (U) uptake by Tamarix (salt cedars) growing along the Rio Paguate, which flows throughout the Jackpile mine near Pueblo de Laguna, New Mexico. Tamarix were selected for this study due to the detection of U in the roots and shoots of field collected plants (0.6-58.9 mg kg-1), presenting an average bioconcentration factor greater than 1. Synchrotron-based micro X-ray fluorescence analyses of plant roots collected from the field indicate that the accumulation of U occurs in the cortex of the root. The mechanisms for U accumulation in the roots of Tamarix were further investigated in controlled-laboratory experiments where living roots of field plants were macerated for 24 h or 2 weeks in a solution containing 100 μM U. The U concentration in the solution decreased 36-59% after 24 h, and 49-65% in two weeks. Microscopic and spectroscopic analyses detected U precipitation in the root cell walls near the xylems of the roots, confirming the initial results from the field samples. High-resolution TEM was used to study the U fate inside the root cells, and needle-like U-P nanocrystals, with diameter <7 nm, were found entrapped inside vacuoles in cells. EXAFS shell-by-shell fitting suggest that U is associated with carbon functional groups. The preferable binding of U to the root cell walls may explain the U retention in the roots of Tamarix, followed by U-P crystal precipitation, and pinocytotic active transport and cellular entrapment. This process resulted in a limited translocation of U to the shoots in Tamarix plants. This study contributes to better understanding of the physicochemical mechanisms affecting the U uptake and accumulation by plants growing near contaminated sites.

Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018

The carriage of both, heavy metal and antibiotic resistance appears to be a common trait in bacterial communities native to long-term contaminated habitats, including the Savannah River Site (SRS). There is widespread soil contamination at the SRS; a United States Department of Energy (DOE) facility with long-term contamination from past industrial and nuclear weapons production activities. To further evaluate the genomic and metabolic traits that underpin metal and antibiotic resistance, a robust mercury (Hg) and uranium (U)-resistant strain- SRS-8-S-2018, was isolated. Minimum inhibitory concentration of this strain revealed resistance to Hg (10 μg/ml) and U (5 mM), the two main heavy metal contaminants at the SRS. Metabolic assessment of strain SRS-8-S-2018 using Biolog metabolic fingerprinting analysis revealed preference for carbohydrate utilization followed by polymers, amino acids, carboxy acids, and esters; this physiological activity diminished when Hg stress was provided at 1 and 3 μg/ml and completely ceased at 5 μg/ml Hg, indicating that continued release of Hg will have negative metabolic impacts to even those microorganisms that possess high resistance ability. Development of antibiotic resistance in strain SRS-8-S-2018 was evaluated at a functional level using phenomics, which confirmed broad resistance against 70.8% of the 48 antibiotics tested. Evolutionary and adaptive traits of strain SRS-8-S-2018 were further assessed using genomics, which revealed the strain to taxonomically affiliate with Serratia marcescens species, possessing a genome size of 5,323,630 bp, 5,261 proteins (CDS), 55 genes for transfer RNA (tRNA), and an average G + C content of 59.48. Comparative genomics with closest taxonomic relatives revealed 360 distinct genes in SRS-8-S-2018, with multiple functions related to both, antibiotic and heavy metal resistance, which likely facilitates the strain’s survival in a metalliferous soil habitat. Comparisons drawn between the environmentally isolated Serratia SRS-8-S-2018 with 31 other strains revealed a closer functional association with medically relevant isolates suggesting that propensity of environmental Serratia isolates in acquiring virulence traits, as a function of long-term exposure to heavy metals, which is facilitating development, recruitment and proliferation of not only metal resistant genes (MRGs) but antibiotic resistant genes (ARGs), which can potentially trigger future bacterial pathogen outbreaks emanating from contaminated environmental habitats.

Bioprospecting potential of microbial communities in solid waste landfills for novel enzymes through metagenomic approach

Landfills are repository for complex microbial diversity responsible for bio-degradation of solid waste. To elucidate this complexity, samples from three different landfill sites of North India (sample V: Bhalswa near Karnal byepass road, New Delhi, India; sample T: Chandigarh, India and sample S3: Una, H.P., India) were analyzed using metagenomic approach. Selected landfill sites had different geographical location, varied in waste composition, size of landfill and climate zone. For comparison, one sample from high altitude (sample J) having less human interference was taken in this study. The aim of this study was to explore microbial diversity of communities responsible for degradation of landfill. Samples were characterized by 16S rRNA gene sequencing. Data from three landfill sites showed abundance of phylum Proteobacteria while less contaminated sample from high altitude showed abundance of phylum Cholroflexi followed by phylum Proteobacteria. The most abundant genus was unknown suggesting that these landfills could be repository for various novel bacterial communities. Sample T was relatively more active in terms of microbial activity. It was relatively abundant in enzymes responsible for dioxin degradation, styrene degradation, steroid degradation, streptomycin biosynthesis, carbapenem biosynthesis, monobactam biosynthesis, furfural degradation pathways while sample J was predicted to be enriched in plant cell wall degrading enzymes. Co-occurrence analysis revealed presence of complex interaction networks between microbial assemblages responsible for bio-degradation of hydrocarbons. The data provides insights about synergetic interactions and functional interplay between bacterial communities in different landfill sites which could be further exploited to develop an effective bioremediation process.

Ultrafast Recovery of Uranium from Seawater by Bacillus velezensis Strain UUS-1 with Innate Anti-Biofouling Activity

Highly-efficient recovery of uranium from seawater is of great concern in the growing demand for nuclear energy. Bacteria are thought to be potential alternatives for uranium recovery. Herein, a Bacillus velezensis strain, UUS-1, with highly-efficient uranium immobilization capacity is isolated and is used in the recovery of uranium from seawater. The strain exhibits time-dependent uranium recovery capacity and only immobilizes uranium after growing for 12 h. The carboxyl group together with the amino group inside the bacterial cells, but not previously identified phosphate group, are essential for uranium immobilization. UUS-1 shows broad-spectrum antimicrobial activity by producing diverse antimicrobial metabolites, which endows the strain with innate resistance to the biofouling of marine microorganisms. Based on the dry weight of the initially used bacterial cultures, UUS-1 concentrates uranium by 6.26 × 105 times and reaches the high immobilization capacity of 9.46 ± 0.39 mg U g-1 bacterial cultures in real seawater within 48 h, which is the fastest uranium immobilization capacity observed from real seawater. Overall considering the ultrafast and highly-efficient uranium recovery capacity and the innate anti-biofouling activity, UUS-1 is a promising alternative for uranium recovery from seawater.

Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome

BACKGROUND

Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O₂).

METHODS

We repeatedly exposed anoxic (4% H₂:96% N₂) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 10², 1.05 × 10³, and 1.05 × 10⁴ mmol O₂ kg^-1 soil h^-1 during pulsed oxygenation treatments. Metatranscriptomic analysis and ⁵⁷Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively.

RESULTS

Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO₂ to CH₄ and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation.

CONCLUSIONS

This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O₂ influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments.

Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment

The capability of microorganisms to alter metal speciation offers potential for the development of new strategies for immobilization of toxic metals in the environment. A metal-reducing microbe, "Pelosinus lilae" strain UFO1, was isolated under strictly anaerobic conditions from an Fe(III)-reducing enrichment established with uncontaminated soil from the Department of Energy Oak Ridge Field Research Center, Tennessee. "P. lilae" UFO1 is a rod-shaped, spore-forming, and Gram-variable anaerobe with a fermentative metabolism. It is capable of reducing the humic acid analog anthraquinone-2,6-disulfonate (AQDS) using a variety of fermentable substrates and H2. Reduction of Fe(III)-nitrilotriacetic acid occurred in the presence of lactate as carbon and electron donor. Ferrihydrite was not reduced in the absence of AQDS. Nearly complete reduction of 1, 3, and 5 ppm Cr(VI) occurred within 24 h in suspensions containing 108 cells mL-1 when provided with 10 mM lactate; when 1 mM AQDS was added, 3 and 5 ppm Cr(VI) were reduced to 0.1 ppm within 2 h. Strain UFO1 is a novel species within the bacterial genus Pelosinus, having 98.16% 16S rRNA gene sequence similarity with the most closely related described species, Pelosinus fermentans R7T. The G+C content of the genomic DNA was 38 mol%, and DNA-DNA hybridization of "P. lilae" UFO1 against P. fermentans R7T indicated an average 16.8% DNA-DNA similarity. The unique phylogenetic, physiologic, and metal-transforming characteristics of "P. lilae" UFO1 reveal it is a novel isolate of the described genus Pelosinus.

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.

Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions

Chromium and uranium are highly toxic metals that contaminate many natural environments. We investigated their mechanisms of toxicity under anaerobic conditions using nitrate-reducing Pseudomonas stutzeri RCH2, which was originally isolated from a chromium-contaminated aquifer. A random barcode transposon site sequencing library of RCH2 was grown in the presence of the chromate oxyanion (Cr[VI]O42−) or uranyl oxycation (U[VI]O22+). Strains lacking genes required for a functional nitrate reductase had decreased fitness as both metals interacted with heme-containing enzymes required for the later steps in the denitrification pathway after nitrate is reduced to nitrite. Cr[VI]-resistance also required genes in the homologous recombination and nucleotide excision DNA repair pathways, showing that DNA is a target of Cr[VI] even under anaerobic conditions. The reduced thiol pool was also identified as a target of Cr[VI] toxicity and psest_2088, a gene of previously unknown function, was shown to have a role in the reduction of sulfite to sulfide. U[VI] resistance mechanisms involved exopolysaccharide synthesis and the universal stress protein UspA. As the first genome-wide fitness analysis of Cr[VI] and U[VI] toxicity under anaerobic conditions, this study provides new insight into the impact of Cr[VI] and U[VI] on an environmental isolate from a chromium contaminated site, as well as into the role of a ubiquitous protein, Psest_2088.