Uranium extremophily is an adaptive, rather than intrinsic, feature for extremely thermoacidophilic Metallosphaera species

Improved protocol for metabolite extraction and identification of respiratory quinones in extremophilic Archaea grown on mineral materials

We investigated the metabolome of the iron- and sulfur-oxidizing, extremely thermoacidophilic archaeon Metallosphaera sedula grown on mineral pyrite (FeS2). The extraction of organic materials from these microorganisms is a major challenge because of the tight contact and interaction between cells and mineral materials. Therefore, we applied an improved protocol to break the microbial cells and separate their organic constituents from the mineral surface, to extract lipophilic compounds through liquid-liquid extraction, and performed metabolomics analyses using MALDI-TOF MS and UHPLC-UHR-Q/TOF. Using this approach, we identified several molecules involved in central carbon metabolism and in the modified Entner-Doudoroff pathway found in Archaea, sulfur metabolism-related compounds, and molecules involved in the adaptation of M. sedula to extreme environments, such as metal tolerance and acid resistance. Furthermore, we identified molecules involved in microbial interactions, i.e., cell surface interactions through biofilm formation and cell-cell interactions through quorum sensing, which relies on messenger molecules for microbial communication. Moreover, we successfully extracted and identified different saturated thiophene-bearing quinones using software for advanced compound identification (MetaboScape). These quinones are respiratory chain electron carriers in M. sedula, with biomarker potential for life detection in extreme environmental conditions.

Overview of radon gas in groundwater around the world: Health effects and treatment technologies

The natural radioactive decay of uranium in rocks and soils gives rise to the presence of radon in groundwater. The existence of radon in groundwater at activity levels way higher than the reference limits set by US-EPA and WHO was widely covered in literature. The exposure to elevated levels of radon in ground and drinking water have been reported in literature to cause adverse health impacts. The aim of the present paper is to give an overview of radon gas in groundwater followed by the safe limits suggested by international organizations and agencies such as US-EPA and WHO. The paper also discusses the health effects associated with the exposure to radon levels and the estimation of the annual effective dose through ingestion and inhalation. This is followed by the radon levels around the world as well as the corresponding annual effective doses reported in literature. The determination techniques of radon levels in water covered in literature such as liquid scintillation counting, gamma-ray spectrometry and emanometry were also discussed and reviewed in the present work. Next, the paper sheds light on the most frequently used treatment techniques such as aeration, adsorption, filtration as well as biological techniques and evaluates their efficiency in mitigating radon levels in water. The paper also highlights the main precautions and future mitigation plans for radon in groundwater as well as delved onto future research perspectives of radon. It was found out that the type of rock played a key role in determining the radon levels. For instance, granitic rock types were reported to contribute to the elevation in the groundwater radon levels due to their characteristic permeability as a result of the formed fractures as well as their natural incorporation of high levels of uranium. Some of the reported radon levels in groundwater in literature were way higher than the guidelines set by the World Health Organization (WHO) for drinking water and US-EPA alternative higher maximum contaminant level. This review paper could be of importance to researchers working on the evaluation as well as the treatment of radon gas in water as it will provide a critical and state of the art review on radon gas in groundwater.

Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation

Factors that contribute to optimal chalcopyrite bioleaching by extremely thermoacidophilic archaea were examined for ten species belonging to the order Sulfolobales from the genera Acidianus (A. brierleyi), Metallosphaera (M. hakonensis, M. sedula, M. prunae), Sulfuracidifex (S. metallicus, S. tepriarius), Sulfolobus (S. acidocaldarius), Saccharlobus (S. solfataricus) and Sulfurisphaera (S. ohwakuensis, S. tokodaii). Only A. brierleyi, M. sedula, S. metallicus, S. tepriarius, S. ohwakuensis, and S. tokodai exhibited significant amounts of bioleaching and were investigated further. At 70-75 °C, Chalcopyrite loadings of 10 g/l were leached for 21 days during which pH, redox potential, planktonic cell density, iron concentrations and sulfate levels were monitored, in addition to copper mobilization. S. ohwakuensis proved to be the most prolific bioleacher. This was attributed to balanced iron and sulfur oxidation, thereby reducing by-product (e.g., jarosites) formation and minimizing surface passivation. Comparative genomics suggest markers for bioleaching potential, but the results here point to the need for experimental verification.

Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?

Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.

Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea

Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSPs) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as type II toxin-antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologues in other Sulfolobales, as well as in other archaea (e.g. Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea.

Manesh MJ, Sivabalasarma S, Albers SV, Kelly RM. Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin

A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.

"Freezing" Thermophiles: From One Temperature Extreme to Another

New detections of thermophiles in psychrobiotic (i.e., bearing cold-tolerant life forms) marine and terrestrial habitats including Arctic marine sediments, Antarctic accretion ice, permafrost, and elsewhere are continually being reported. These microorganisms present great opportunities for microbial ecologists to examine biogeographical processes for spore-formers and non-spore-formers alike, including dispersal histories connecting warm and cold biospheres. In this review, we examine different examples of thermophiles in cryobiotic locations, and highlight exploration of thermophiles at cold temperatures under laboratory conditions. The survival of thermophiles in psychrobiotic environments provokes novel considerations of physiological and molecular mechanisms underlying natural cryopreservation of microorganisms. Cultures of thermophiles maintained at low temperature may serve as a non-sporulating laboratory model for further exploration of metabolic potential of thermophiles at psychrobiotic temperatures, as well as for elucidating molecular mechanisms behind natural preservation and adaptation to psychrobiotic environments. These investigations are highly relevant for the search for life on other cold and icy planets in the Solar System, such as Mars, Europa and Enceladus.

A systematic review on groundwater radon distribution with human health consequences and probable mitigation strategy

Groundwater radon contamination is a serious global concern for its eco-toxicological effects. The major health hazard occurs due to toxic indoor air inhalation and consumption of contaminated drinking water supplied from different distribution systems, especially groundwater. There are fragmented reports on the measurement of radon contamination and their health consequences with physical radon removal strategies as well as characterization of inhabitant microbial communities. As it concerned with human health, collective information is much essential on their groundwater distribution, their physicochemical properties and possible mitigation strategies, not done so far. In such prospect, this review summarizes the physicochemical properties of radon, their sources, global as well as Indian groundwater radon contamination scenario, health effects and inhabitant microbes along with their survival strategies. It also summarizes the physical radon removal techniques and especially emphasizes the microbes based bioremediation process as well as a combination of both as a future effective radon remediation process.

Remediation of cadmium contaminated soil by composite spent mushroom substrate organic amendment under high nitrogen level

Cadmium (Cd) contamination in soil poses a serious threat to ecological environment and crop quality, especially under high nitrogen level. Here, the efficiency of composite organic amendment (spent mushroom substrate and its biochar) on remediation of Cd contaminated soil under high nitrogen level has been studied through a 42 days' soil incubation experiment. The results showed: (i) the application of composite organic amendment minimized the repercussions of high nitrogen and significantly reduced the exchangeable Cd proportion by 28.3%-29.5%, especially for Ca(NO₃)₂ treatment; (ii) the application of composite organic amendment improved the physicochemical properties of soil, such as pH, CEC and organic matter content increased by 0.63-0.99 unit, 39.69%-45.00% and 7.77%-11.47%, and EC decreased by 16.21%-44.47% compared with non-amendment Cd-contaminated soil, respectively; (iii) the application of composite organic amendment significantly increased the soil enzyme activities and microbial biomass, among which urease activity was increased most by 12.06-16.42 mg·g^-1·d^-1, and the copy number of AOA was decreased by 30.6%- 92.0%, and the copy number of AOB was increased most by about 45 times. In brief, the composite organic amendment can alleviate the adverse effects of Cd and nitrogen on the soil, but its long-term efficacy needs to be verified in further field study.

Thermoacidophilic Bioleaching of Industrial Metallic Steel Waste Product

The continuous deposition of hazardous metalliferous wastes derived from industrial steelmaking processes will lead to space shortages while valuable raw metals are being depleted. Currently, these landfilled waste products pose a rich resource for microbial thermoacidophilic bioleaching processes. Six thermoacidophilic archaea (Sulfolobus metallicus, Sulfolobus acidocaldarius, Metallosphaera hakonensis, Metallosphaera sedula, Acidianus brierleyi, and Acidianus manzaensis) were cultivated on metal waste product derived from a steelmaking process to assess microbial proliferation and bioleaching potential. While all six strains were capable of growth and bioleaching of different elements, A. manzaensis outperformed other strains and its bioleaching potential was further studied in detail. The ability of A. manzaensis cells to break down and solubilize the mineral matrix of the metal waste product was observed via scanning and transmission electron microscopy. Refinement of bioleaching operation parameters shows that changes in pH influence the solubilization of certain elements, which might be considered for element-specific solubilization processes. Slight temperature shifts did not influence the release of metals from the metal waste product, but an increase in dust load in the bioreactors leads to increased element solubilization. The formation of gypsum crystals in course of A. manzaensis cultivation on dust was observed and clarified using single-crystal X-ray diffraction analysis. The results obtained from this study highlight the importance of thermoacidophilic archaea for future small-scale as well as large-scale bioleaching operations and metal recycling processes in regard to circular economies and waste management. A thorough understanding of the bioleaching performance of thermoacidophilic archaea facilitates further environmental biotechnological advancements.

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO₂²⁺ and Fe³⁺. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.

Fox Cluster determinants for iron biooxidation in the extremely thermoacidophilic Sulfolobaceae

Within the extremely thermoacidophilic Sulfolobaceae, the capacity to oxidize iron varies considerably. While some species are prolific iron oxidizers (e.g. Metallosphaera sedula), other species do not oxidize iron at all (e.g. Sulfolobus acidocaldarius). Iron oxidation capacity maps to a genomic locus, referred to previously as the 'Fox Cluster', that encodes putative proteins that are mostly unique to the Sulfolobaceae. The role of putative proteins in the Fox Cluster has not been confirmed, but proteomic analysis here of iron-oxidizing membranes from M. sedula indicates that FoxA2 and FoxB (both cytochrome c oxidase-like subunits) and FoxC (CbsA/cytochrome b domain-containing) are essential. Furthermore, comparative genomics (locus organization and gene disruptions) and transcriptomics (polarity effects and differential expression) connect these genomic determinants with disparate iron biooxidation and respiration measurements among Sulfolobaceae species. While numerous homologous proteins can be identified for FoxA in genome databases (COX-like domains are prevalent across all domains of life), few homologues exist for FoxC or for most other Fox Cluster proteins. Phylogenetic reconstructions suggest this locus may have existed in early Sulfolobaceae, while the only other close homologues to the locus appear in the recently discovered candidate phylum Marsarchaota.

The biology of thermoacidophilic archaea from the order Sulfolobales

Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.

Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales

The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.

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.

Nitrogen combined with biochar changed the feedback mechanism between soil nitrification and Cd availability in an acidic soil

Inorganic nitrogen (N) inputs increase soil nitrification, acidification and trace metal toxicity e.g. cadmium (Cd). Biochar (B) has been widely used for metal immobilization. However, little is known about how the combination of N fertilizers with biochar (N-B) changes soil Cd availability through altering nitrification process. Here, (NH₄)₂SO₄ or CO(NH₂)₂ was applied in combination with biochar to an acidic, artificially enriched Cd contaminated soil. Not as we expected, available Cd did not increase following (NH₄)₂SO₄ or CO(NH₂)₂ addition. Nitrification and acidification of Cd contaminated soils were greatly inhibited, accompanied by elimination of ammonia-oxidizing bacteria (AOB). Exchangeable H⁺ of Cd contaminated soils was significantly lower than that of uncontaminated soils, thus inhibiting Cd itself from mobilization. N-B addition nearly halved soil available Cd and significantly increased nitrification by promoting AOB recovery. However, the restored nitrification did not cause soil acidification, due to the high buffering and slow liming effects of biochar. Available Cd continuously decreased with decreasing soil acidity and exchangeable Al. This study firstly demonstrated a feedback between soil nitrification and Cd after N application, and how biochar modified the feedback. Biochar, therefore, provides a feasible strategy for eliminating potential Cd toxicity on both soil biological and chemical processes.

Genomic and functional insights into the adaptation and survival of Chryseobacterium sp. strain PMSZPI in uranium enriched environment

Metal enriched areas represent important and dynamic microbiological ecosystems. In this study, the draft genome of a uranium (U) tolerant bacterium, Chryseobacterium sp. strain PMSZPI, isolated from the subsurface soil of Domiasiat uranium ore deposit in Northeast India, was analyzed. The strain revealed a genome size of 3.8 Mb comprising of 3346 predicted protein-coding genes. The analysis indicated high abundance of genes associated with metal resistance and efflux, transporters, phosphatases, antibiotic resistance, polysaccharide synthesis, motility, protein secretion systems, oxidoreductases and DNA repair. Comparative genomics with other closely related Chryseobacterium strains led to the identification of unique inventory of genes which were of adaptive significance in PMSZPI. Consistent with the genome analysis, PMSZPI showed superior tolerance to uranium and other heavy metals. The metal exposed cells exhibited transcriptional induction of metal translocating P_IB ATPases suggestive of their involvement in metal resistance. Efficient U binding (~90% of 100 μM U) and U bioprecipitation (~93-94% of 1 mM U at pH 5, 7 and 9) could be attributed as uranium tolerance strategies in PMSZPI. The strain demonstrated resistance to a large number of antibiotics which was in agreement with in silico prediction. Reduced gliding motility in the presence of cadmium and uranium, enhanced biofilm formation on uranium exposure and tolerance to 1.5 kGy of ⁶⁰Co gamma radiation were perceived as adaptive responses in PMSZPI. Overall, the positive correlation observed between uranium/metal tolerance abilities predicted using genome analysis and the functional characterization reinforced the multifaceted adaptation strategies employed by PMSZPI for its survival in the soil of uranium ore deposit comprising of high concentrations of uranium and other heavy metals.

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.

Exploring the microbial biotransformation of extraterrestrial material on nanometer scale

Exploration of microbial-meteorite redox interactions highlights the possibility of bioprocessing of extraterrestrial metal resources and reveals specific microbial fingerprints left on extraterrestrial material. In the present study, we provide our observations on a microbial-meteorite nanoscale interface of the metal respiring thermoacidophile Metallosphaera sedula. M. sedula colonizes the stony meteorite Northwest Africa 1172 (NWA 1172; an H5 ordinary chondrite) and releases free soluble metals, with Ni ions as the most solubilized. We show the redox route of Ni ions, originating from the metallic Ni° of the meteorite grains and leading to released soluble Ni²⁺. Nanoscale resolution ultrastructural studies of meteorite grown M. sedula coupled to electron energy loss spectroscopy (EELS) points to the redox processing of Fe-bearing meteorite material. Our investigations validate the ability of M. sedula to perform the biotransformation of meteorite minerals, unravel microbial fingerprints left on meteorite material, and provide the next step towards an understanding of meteorite biogeochemistry. Our findings will serve in defining mineralogical and morphological criteria for the identification of metal-containing microfossils.

Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response

The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.

Biotransformation of Scheelite CaWO4 by the Extreme Thermoacidophile Metallosphaera sedula: Tungsten-Microbial Interface

The tungsten-microbial interactions and microbial bioprocessing of tungsten ores, which are still underexplored, are the focus of the current study. Here we show that the biotransformation of tungsten mineral scheelite performed by the extreme thermoacidophile Metallosphaera sedula leads to the breakage of scheelite structure and subsequent tungsten solubilization. Total soluble tungsten is significantly higher in cultures containing M. sedula grown on scheelite than the abiotic control, indicating active bioleaching. Advanced analytical electron microscopy was used in order to achieve nanoscale resolution ultrastructural studies of M. sedula grown on tungsten bearing scheelite. In particular, we describe that M. sedula mediated the biotransformation of scheelite, which was accompanied by the release of tungsten into solution and tungsten biomineralization of the cell surface. Furthermore, we observed intracellular incorporation of redox heterogenous Mn- and Fe-containing nano-clusters. Our results highlight unique metallophilic life in hostile environments extending the knowledge of tungsten biogeochemistry. Based on these findings biohydrometallurgical processing of tungsten ores can be further explored. Importantly, biogenic tungsten carbide-like nanolayers described herein are potential targets for developing nanomaterial biotechnology.

Nanoscale Tungsten-Microbial Interface of the Metal Immobilizing Thermoacidophilic Archaeon Metallosphaera sedula Cultivated With Tungsten Polyoxometalate

Inorganic systems based upon polyoxometalate (POM) clusters provide an experimental approach to develop artificial life. These artificial symmetric anionic macromolecules with oxidometalate polyhedra as building blocks were shown to be well suited as inorganic frameworks for complex self-assembling and organizing systems with emergent properties. Analogously to mineral cells based on iron sulfides, POMs are considered as inorganic cells in facilitating prelife chemical processes and displaying "life-like" characteristics. However, the relevance of POMs to life-sustaining processes (e.g., microbial respiration) has not yet been addressed, while iron sulfides are very well known as ubiquitous mineral precursors and energy sources for chemolithotrophic metabolism. Metallosphaera sedula is an extreme metallophilic and thermoacidophilic archaeon, which flourishes in hot acid and respires by metal oxidation. In the present study we provide our observations on M. sedula cultivated on tungsten polyoxometalate (W-POM). The decomposition of W-POM macromolecular clusters and the appearance of low molecular weight W species (e.g., WO) in the presence of M. sedula have been detected by electrospray ionization mass spectrometry (ESI-MS) analysis. Here, we document the presence of metalloorganic assemblages at the interface between M. sedula and W-POM resolved down to the nanometer scale using scanning and transmission electron microscopy (SEM and TEM) coupled to electron energy loss spectroscopy (EELS). High-resolution TEM (HR-TEM) and selected-area electron diffraction (SAED) patterns indicated the deposition of redox heterogeneous tungsten species on the S-layer of M. sedula along with the accumulation of intracellular tungsten-bearing nanoparticles, i.e., clusters of tungsten atoms. These results reveal the effectiveness of the analytical spectroscopy coupled to the wet chemistry approach as a tool in the analysis of metal-microbial interactions and microbial cultivation on supramolecular self-assemblages based on inorganic metal clusters. We discuss the possible mechanism of W-POM decomposition by M. sedula in light of unique electrochemical properties of POMs. The findings presented herein highlight unique metallophilicity in hostile environments, extending our knowledge of the relevance of POMs to life-sustaining processes, understanding of the transition of POMs as inorganic prebiotic model to life-sustainable material precursors and revealing biogenic signatures obtained after the decomposition of an artificial inorganic compound, which previously was not associated with any living matter.

Increased chalcopyrite bioleaching capabilities of extremely thermoacidophilic Metallosphaera sedula inocula by mixotrophic propagation

Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales, such as Metallosphaera sedula, are metabolically versatile and of great relevance in bioleaching. However, the impacts of extreme thermoacidophiles propagated with different energy substrates on subsequent bioleaching of refractory chalcopyrite remain unknown. Transcriptional responses underlying their different bioleaching potentials are still elusive. Here, it was first showed that M. sedula inocula propagated with typical energy substrates have different chalcopyrite bioleaching capabilities. Inoculum propagated heterotrophically with yeast extract was deficient in bioleaching; however, inoculum propagated mixotrophically with chalcopyrite, pyrite or sulfur recovered 79%, 78% and 62% copper, respectively, in 12 days. Compared with heterotrophically propagated inoculum, 937, 859 and 683 differentially expressed genes (DEGs) were identified in inoculum cultured with chalcopyrite, pyrite or sulfur, respectively, including upregulation of genes involved in bioleaching-associated metabolism, e.g., Fe²⁺ and sulfur oxidation, CO₂ fixation. Inoculum propagated with pyrite or sulfur, respectively, shared 480 and 411 DEGs with chalcopyrite-cultured inoculum. Discrepancies on repertories of DEGs that involved in Fe²⁺ and sulfur oxidation in inocula greatly affected subsequent chalcopyrite bioleaching rates. Novel genes (e.g., Msed_1156, Msed_0549) probably involved in sulfur oxidation were first identified. This study highlights that mixotrophically propagated extreme thermoacidophiles especially with chalcopyrite should be inoculated into chalcopyrite heaps at industrial scale.

Extremely Thermoacidophilic Metallosphaera Species Mediate Mobilization and Oxidation of Vanadium and Molybdenum Oxides

Certain species from the extremely thermoacidophilic genus Metallosphaera directly oxidize Fe(II) to Fe(III), which in turn catalyzes abiotic solubilization of copper from chalcopyrite to facilitate recovery of this valuable metal. In this process, the redox status of copper does not change as it is mobilized. Metallosphaera species can also catalyze the release of metals from ores with a change in the metal's redox state. For example, Metallosphae ra sedula catalyzes the mobilization of uranium from the solid oxide U₃O₈, concomitant with the generation of soluble U(VI). Here, the mobilization of metals from solid oxides (V₂O₃, Cu₂O, FeO, MnO, CoO, SnO, MoO₂, Cr₂O₃, Ti₂O₃, and Rh₂O₃) was examined for M. sedula and M. prunae at 70°C and pH 2.0. Of these oxides, only V and Mo were solubilized, a process accelerated in the presence of FeCl₃ However, it was not clear whether the solubilization and oxidation of these metals could be attributed entirely to an Fe-mediated indirect mechanism. Transcriptomic analysis for growth on molybdenum and vanadium oxides revealed transcriptional patterns not previously observed for growth on other energetic substrates (i.e., iron, chalcopyrite, organic compounds, reduced sulfur compounds, and molecular hydrogen). Of particular interest was the upregulation of Msed_1191, which encodes a Rieske cytochrome b ₆ fusion protein (Rcbf, referred to here as V/MoxA) that was not transcriptomically responsive during iron biooxidation. These results suggest that direct oxidation of V and Mo occurs, in addition to Fe-mediated oxidation, such that both direct and indirect mechanisms are involved in the mobilization of redox-active metals by Metallosphaera species.IMPORTANCE In order to effectively leverage extremely thermoacidophilic archaea for the microbially based solubilization of solid-phase metal substrates (e.g., sulfides and oxides), understanding the mechanisms by which these archaea solubilize metals is important. Physiological analysis of Metallosphaera species growth in the presence of molybdenum and vanadium oxides revealed an indirect mode of metal mobilization, catalyzed by iron cycling. However, since the mobilized metals exist in more than one oxidation state, they could potentially serve directly as energetic substrates. Transcriptomic response to molybdenum and vanadium oxides provided evidence for new biomolecules participating in direct metal biooxidation. The findings expand the knowledge on the physiological versatility of these extremely thermoacidophilic archaea.

Impact of Haloarchaea on Speciation of Uranium-A Multispectroscopic Approach

Haloarchaea represent a predominant part of the microbial community in rock salt, which can serve as host rock for the disposal of high level radioactive waste. However, knowledge is missing about how Haloarchaea interact with radionuclides. Here, we used a combination of spectroscopic and microscopic methods to study the interactions of an extremely halophilic archaeon with uranium, one of the major radionuclides in high level radioactive waste, on a molecular level. The obtained results show that Halobacterium noricense DSM 15987^T influences uranium speciation as a function of uranium concentration and incubation time. X-ray absorption spectroscopy reveals the formation of U(VI) phosphate minerals, such as meta-autunite, as the major species at a lower uranium concentration of 30 μM, while U(VI) is mostly associated with carboxylate groups of the cell wall and extracellular polymeric substances at a higher uranium concentration of 85 μM. For the first time, we identified uranium biomineralization in the presence of Halobacterium noricense DSM 15987^T cells. These findings highlight the potential importance of Archaea in geochemical cycling of uranium and their role in biomineralization in hypersaline environments, offering new insights into the microbe-actinide interactions in highly saline conditions relevant to the disposal of high-level radioactive waste as well as bioremediation.

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.

Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation

Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose. However, the natural physiological plasticity of such extremophilic microfactories can be further explored to nourish different hallmarks of M&R bioremediation, which are scantly approached in the literature and were never integrated. Therefore, this review not only briefly describes major valuable extremophilic pathways for M&R bioremediation, as it highlights the advances, challenges and gaps from the interplay of ‘omics’ and biological engineering to improve extremophilic microfactories performance for M&R clean-up. Microfactories’ potentialities are also envisaged to close the M&R bioremediation processes and shift the classical idea of never ‘getting rid’ of M&Rs into making them ‘the belle of the ball’ through bio-recycling and bio-recovering techniques.

Enhancement of Metallosphaera sedula Bioleaching by Targeted Recombination and Adaptive Laboratory Evolution

Thermophilic and lithoautotrophic archaea such as Metallosphaera sedula occupy acidic, metal-rich environments and are used in biomining processes. Biotechnological approaches could accelerate these processes and improve metal recovery by biomining organisms, but systems for genetic manipulation in these organisms are currently lacking. To gain a better understanding of the interplay between metal resistance, autotrophy, and lithotrophic metabolism, a genetic system was developed for M. sedula and used to evaluate parameters governing the efficiency of copper bioleaching. Additionally, adaptive laboratory evolution was used to select for naturally evolved M. sedula cell lines with desirable phenotypes for biomining, and these adapted cell lines were shown to have increased bioleaching capacity and efficiency. Genomic methods were used to analyze mutations that led to resistance in the experimentally evolved cell lines, while transcriptomics was used to examine changes in stress-inducible gene expression specific to the environmental conditions.

Metal-tolerant thermophiles: metals as electron donors and acceptors, toxicity, tolerance and industrial applications

Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously. Metals are essential for biological systems, as they participate in biochemistries that cannot be achieved only by organic molecules. However, the excess concentration of metals can disrupt natural biogeochemical processes and can impose toxicity. Thermophiles counteract metal toxicity via their unique cell wall, metabolic factors and enzymes that carry out metal-based redox transformations, metal sequestration by metallothioneins and metallochaperones as well as metal efflux. Thermophilic metal resistance is heterogeneous at both genetic and physiology levels and may be chromosomally, plasmid or transposon encoded with one or more genes being involved. These effective response mechanisms either individually or synergistically make proliferation of thermophiles in metal-rich habitats possibly. This article presents the state of the art and future perspectives of responses of thermophiles to metals at genetic as well as physiological levels.

Vertical distribution of archaeal communities associated with anaerobic degradation of pentabromodiphenyl ether (BDE-99) in river-based groundwater recharge with reclaimed water

When groundwater is recharged with reclaimed water, the presence of trace amounts of biorefractory pentabromodiphenyl ether (PBDE, specifically BDE-99) might cause potential groundwater pollution. A laboratory-scale column was designed to investigate the distribution of the community of archaea in this scenario and the associated anaerobic degradation of BDE-99. The concentration of BDE-99 decreased significantly as soil depth increased, and fluorescence in situ hybridization (FISH) analysis suggested that archaea exerted significant effects on the biodegradation of PBDE. Through 454 pyrosequencing of 16s rRNA genes, we found that the distribution and structure of the archaeal community associated with anaerobic degradation of BDE-99 in the river-based aquifer media changed significantly between different soil depths. The primary debrominated metabolites varied with changes in the vertically distributed archaeal community. The archaea in the surface layer were dominated by Methanomethylovorans, and the middle layer was mainly composed of Nitrososphaera. Nitrosopumilus and Nitrososphaera were equally abundant in the bottom layer. In addition, Methanomethylovorans abundance depended on the depth of soil, and the relative abundance of Nitrosopumilus increased with increasing depth, which was associated with the oxidation-reduction potential and the content of intermediate metabolites. We propose that Nitrososphaera and Nitrosopumilus might be the key archaeal taxa mediating the biodegradation of BDE-99.

Exploring Fingerprints of the Extreme Thermoacidophile Metallosphaera sedula Grown on Synthetic Martian Regolith Materials as the Sole Energy Sources

The biology of metal transforming microorganisms is of a fundamental and applied importance for our understanding of past and present biogeochemical processes on Earth and in the Universe. The extreme thermoacidophile Metallosphaera sedula is a metal mobilizing archaeon, which thrives in hot acid environments (optimal growth at 74°C and pH 2.0) and utilizes energy from the oxidation of reduced metal inorganic sources. These characteristics of M. sedula make it an ideal organism to further our knowledge of the biogeochemical processes of possible life on extraterrestrial planetary bodies. Exploring the viability and metal extraction capacity of M. sedula living on and interacting with synthetic extraterrestrial minerals, we show that M. sedula utilizes metals trapped in the Martian regolith simulants (JSC Mars 1A; P-MRS; S-MRS; MRS07/52) as the sole energy sources. The obtained set of microbiological and mineralogical data suggests that M. sedula actively colonizes synthetic Martian regolith materials and releases free soluble metals. The surface of bioprocessed Martian regolith simulants is analyzed for specific mineralogical fingerprints left upon M. sedula growth. The obtained results provide insights of biomining of extraterrestrial material as well as of the detection of biosignatures implementing in life search missions.

VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae

When abruptly exposed to toxic levels of hexavalent uranium, the extremely thermoacidophilic archaeon Metallosphaera prunae, originally isolated from an abandoned uranium mine, ceased to grow, and concomitantly exhibited heightened levels of cytosolic ribonuclease activity that corresponded to substantial degradation of cellular RNA. The M. prunae transcriptome during 'uranium-shock' implicated VapC toxins as possible causative agents of the observed RNA degradation. Identifiable VapC toxins and PIN-domain proteins encoded in the M. prunae genome were produced and characterized, three of which (VapC4, VapC7, VapC8) substantially degraded M. prunae rRNA in vitro. RNA cleavage specificity for these VapCs mapped to motifs within M. prunae rRNA. Furthermore, based on frequency of cleavage sequences, putative target mRNAs for these VapCs were identified; these were closely associated with translation, transcription, and replication. It is interesting to note that Metallosphaera sedula, a member of the same genus and which has a nearly identical genome sequence but not isolated from a uranium-rich biotope, showed no evidence of dormancy when exposed to this metal. M. prunae utilizes VapC toxins for post-transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation.

Increased acid resistance of the archaeon, Metallosphaera sedula by adaptive laboratory evolution

Extremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78 % more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions. These unique genomic and transcriptomic features support a model for increased acid resistance arising from enhanced control over cytoplasmic pH.

Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal "Shock" Reveal Generic and Specific Metal Responses

The extremely thermoacidophilic archaeon Metallosphaera sedula mobilizes metals by novel membrane-associated oxidase clusters and, consequently, requires metal resistance strategies. This issue was examined by "shocking" M. sedula with representative metals (Co(2+), Cu(2+), Ni(2+), UO2 (2+), Zn(2+)) at inhibitory and subinhibitory levels. Collectively, one-quarter of the genome (554 open reading frames [ORFs]) responded to inhibitory levels, and two-thirds (354) of the ORFs were responsive to a single metal. Cu(2+) (259 ORFs, 106 Cu(2+)-specific ORFs) and Zn(2+) (262 ORFs, 131 Zn(2+)-specific ORFs) triggered the largest responses, followed by UO2 (2+) (187 ORFs, 91 UO2 (2+)-specific ORFs), Ni(2+) (93 ORFs, 25 Ni(2+)-specific ORFs), and Co(2+) (61 ORFs, 1 Co(2+)-specific ORF). While one-third of the metal-responsive ORFs are annotated as encoding hypothetical proteins, metal challenge also impacted ORFs responsible for identifiable processes related to the cell cycle, DNA repair, and oxidative stress. Surprisingly, there were only 30 ORFs that responded to at least four metals, and 10 of these responded to all five metals. This core transcriptome indicated induction of Fe-S cluster assembly (Msed_1656-Msed_1657), tungsten/molybdenum transport (Msed_1780-Msed_1781), and decreased central metabolism. Not surprisingly, a metal-translocating P-type ATPase (Msed_0490) associated with a copper resistance system (Cop) was upregulated in response to Cu(2+) (6-fold) but also in response to UO2 (2+) (4-fold) and Zn(2+) (9-fold). Cu(2+) challenge uniquely induced assimilatory sulfur metabolism for cysteine biosynthesis, suggesting a role for this amino acid in Cu(2+) resistance or issues in sulfur metabolism. The results indicate that M. sedula employs a range of physiological and biochemical responses to metal challenge, many of which are specific to a single metal and involve proteins with yet unassigned or definitive functions.

IMPORTANCE

The mechanisms by which extremely thermoacidophilic archaea resist and are negatively impacted by metals encountered in their natural environments are important to understand so that technologies such as bioleaching, which leverage microbially based conversion of insoluble metal sulfides to soluble species, can be improved. Transcriptomic analysis of the cellular response to metal challenge provided both global and specific insights into how these novel microorganisms negotiate metal toxicity in natural and technological settings. As genetics tools are further developed and implemented for extreme thermoacidophiles, information about metal toxicity and resistance can be leveraged to create metabolically engineered strains with improved bioleaching characteristics.

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.

Modulation of medium pH by Caulobacter crescentus facilitates recovery from uranium-induced growth arrest

The oxidized form of uranium [U(VI)] predominates in oxic environments and poses a major threat to ecosystems. Due to its ability to mineralize U(VI), the oligotroph Caulobacter crescentus is an attractive candidate for U(VI) bioremediation. However, the physiological basis for U(VI) tolerance is unclear. Here we demonstrated that U(VI) caused a temporary growth arrest in C. crescentus and three other bacterial species, although the duration of growth arrest was significantly shorter for C. crescentus. During the majority of the growth arrest period, cell morphology was unaltered and DNA replication initiation was inhibited. However, during the transition from growth arrest to exponential phase, cells with shorter stalks were observed, suggesting a decoupling between stalk development and the cell cycle. Upon recovery from growth arrest, C. crescentus proliferated with a growth rate comparable to that of a control without U(VI), although a fraction of these cells appeared filamentous with multiple replication start sites. Normal cell morphology was restored by the end of exponential phase. Cells did not accumulate U(VI) resistance mutations during the prolonged growth arrest, but rather, a reduction in U(VI) toxicity occurred concomitantly with an increase in medium pH. Together, these data suggest that C. crescentus recovers from U(VI)-induced growth arrest by reducing U(VI) toxicity through pH modulation. Our finding represents a unique U(VI) detoxification strategy and provides insight into how microbes cope with U(VI) under nongrowing conditions, a metabolic state that is prevalent in natural environments.

Insights into the interactions of cyanobacteria with uranium

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