Influence of uranium on bacterial communities: a comparison of natural uranium-rich soils with controls

Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.

Ultraviolet Resistance of Microorganisms Isolated from Uranium-Rich Minerals from Perus, Brazil

The district of Perus, located in the city of São Paulo, Brazil, is renowned for its weathered granitic-pegmatitic masses, which harbor a significant number of uraniferous minerals that contribute to ionizing radiation levels up to 20 times higher than the background levels. In this study, aseptically collected mineral samples from the area were utilized to isolate 15 microorganisms, which were subjected to pre-screening tests involving UV-C and UV-B radiation. The microorganisms that exhibited the highest resistance to ultraviolet (UV) radiation were selected for the construction of survival curves for UV-C, broad-band UV-B, and solar simulation resistance testing. Subsequently, the four strains that demonstrated superior survival capabilities under UV radiation exposure were chosen for 16S rRNA gene sequencing. Among these, Nocardioides sp. O4R and Nocardioides sp. MA2R demonstrated the most promising outcomes in the UV radiation resistance assessments, showcasing comparable performance to the well-established radioresistant model organism Deinococcus radiodurans. These findings underscore the potential of naturally occurring high-radiation environments as valuable resources for the investigation of UV-resistant microorganisms.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

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

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

Impact of ionizing radiation on the environmental microbiomes of Chornobyl wetlands

Radioactive contamination has the potential to cause damage to DNA and other biomolecules. Anthropogenic sources of radioactive contamination include accidents in nuclear power plants, such as the one in Chornobyl in 1986 which caused long-term radioactive pollution. Studies on animals within radioactive zones have provided us with a greater understanding of how wildlife can persevere despite chronic radiation exposure. However, we still know very little about the effects of radiation on the microbial communities in the environment. We examined the impact of ionizing radiation and other environmental factors on the diversity and composition of environmental microbiomes in the wetlands of Chornobyl. We combined detailed field sampling along a gradient of radiation together with 16 S rRNA high-throughput metabarcoding. While radiation did not affect the alpha diversity of the microbiomes in sediment, soil, or water, it had a significant effect on the beta diversity in all environment types, indicating that the microbial composition was affected by ionizing radiation. Specifically, we detected several microbial taxa that were more abundant in areas with high radiation levels within the Chornobyl Exclusion Zone, including bacteria and archaea known to be radioresistant. Our results reveal the existence of rich and diverse microbiomes in Chornobyl wetlands, with multiple taxonomic groups that are able to thrive despite the radioactive contamination. These results, together with additional field and laboratory-based approaches examining how microbes cope with ionizing radiation will help to forecast the functionality and re-naturalization dynamics of radiocontaminated environments.

Response of soil microbial communities to natural radionuclides along specific-activity gradients

Understanding the response of soil microbial community to abnormal natural radionuclides is important to maintain soil ecological function, but the underlying mechanism of tolerance and survival of microbes is poorly studied. The effects of natural radionuclides on the topsoil microbial communities in anomalous natural radiation area were investigated in this work, and it was found that microbial community composition was significantly influenced by the specific-activities of natural radionuclides. The results revealed that relative abundances of 10 major microbial phyla and genera displayed different patterns along specific-activity gradients, including decreasing, increasing, hump-shaped, U-shaped, and similar sinusoidal or cosine wave trends, which indicated that the natural radionuclides were the predominant driver for change of microbial community structure. At the phylum and genus level, microbial communities were divided into two special groups according to the tolerance to natural radionuclides, such as ²³⁸U and ²³²Th, including tolerant and sensitive groups. Taken together, our findings suggest that the high specific-activities of natural radionuclides can obviously drive changes in microbial communities, providing a possibility for future studies on the microbial tolerance genes and bioremediation strains.

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

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

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

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

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.

Biogenic Sulfidation of U(VI) and Ferrihydrite Mediated by Sulfate-Reducing Bacteria at Elevated pH

Globally, the need for radioactive waste disposal and contaminated land management is clear. Here, gaining an improved understanding of how biogeochemical processes, such as Fe(III) and sulfate reduction, may control the environmental mobility of radionuclides is important. Uranium (U), typically the most abundant radionuclide by mass in radioactive wastes and contaminated land scenarios, may have its environmental mobility impacted by biogeochemical processes within the subsurface. This study investigated the fate of U(VI) in an alkaline (pH ∼9.6) sulfate-reducing enrichment culture obtained from a high-pH environment. To explore the mobility of U(VI) under alkaline conditions where iron minerals are ubiquitous, a range of conditions were tested, including high (30 mM) and low (1 mM) carbonate concentrations and the presence and absence of Fe(III). At high carbonate concentrations, the pH was buffered to approximately pH 9.6, which delayed the onset of sulfate reduction and meant that the reduction of U(VI)_(aq) to poorly soluble U(IV)_(s) was slowed. Low carbonate conditions allowed microbial sulfate reduction to proceed and caused the pH to fall to ∼7.5. This drop in pH was likely due to the presence of volatile fatty acids from the microbial respiration of gluconate. Here, aqueous sulfide accumulated and U was removed from solution as a mixture of U(IV) and U(VI) phosphate species. In addition, sulfate-reducing bacteria, such as Desulfosporosinus species, were enriched during development of sulfate-reducing conditions. Results highlight the impact of carbonate concentrations on U speciation and solubility in alkaline conditions, informing intermediate-level radioactive waste disposal and radioactively contaminated land management.

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

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

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.

Complete Genome Sequences of Four Microbacterium Strains Isolated from Metal- and Radionuclide-Rich Soils

Here, we present the genome sequences of four Microbacterium strains, which were isolated at different locations in Europe from metal- or radionuclide-rich soils. High-quality complete genome sequences were obtained with PacBio and Illumina data sets with an original two-step procedure.

Microbial communities in a former pilot-scale uranium mine in Eastern Finland - Association with radium immobilization

The bacterial, fungal and archaeal communities were characterized in 17 top soil organic and mineral layer samples and in top sediment samples of the Paukkajanvaara area, a former pilot-scale uranium mine, located in Eno, Eastern Finland, using amplicon sequencing and qPCR. Soil and sediment samples were in addition analyzed for radium (²²⁶Ra), sulfate (SO₄^2-), nitrate (NO₃^-) and phosphate (PO₄^3-) concentrations. New bacterial strains, representing Pseudomonas spp., were isolated from the mine and reference area and used in laboratory experiments on uptake and leaching of radium (Ra). The effect of these strains on the sulfate leaching from the soil samples was also tested in vitro. Between 6 × 10⁶ and 5 × 10⁸ copies g^-1 DW (dry weight) of bacterial 16S rRNA genes, 5 × 10⁵-1 × 10⁸ copies g^-1 DW archaeal 16S rRNA genes and 1 × 10⁵-1 × 10⁸ copies g^-1 DW fungal 5.8S rRNA genes were detected in the samples. A total of 814, 54 and 167 bacterial, archaeal and fungal genera, respectively, were identified. Proteobacteria, Euryarchaeota and Mortiriella were the dominant bacterial, archaeal and fungal phyla, respectively. All tested Pseudomonas spp. strains isolates from Paukkajanvaara removed Ra from the solution, but the amount of removed Ra depended on incubation conditions (temperature, time and nutrient broth). The highest removal of Ra (5320 L/kg DW) was observed by the Pseudomonas sp. strain T5-6-I at 37 °C. All Pseudomonas spp. strains decreased the release of Ra from soil with an average of 23% while simultaneously increasing the concentration of SO₄^2- in the solution by 11%. As Pseudomonas spp. were frequent in both the sequence data and the cultures, these bacteria may play an important role in the immobilization of Ra in the Paukkajanvaara mine area.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.

Speciation Distribution of Heavy Metals in Uranium Mining Impacted Soils and Impact on Bacterial Community Revealed by High-Throughput Sequencing

This study investigated the influence of heavy metals on bacterial community structure in a uranium mine. Soils from three differently polluted ditches (Yangchang ditch, Zhongchang ditch, and Sulimutang ditche) were collected from Zoige County, Sichuan province, China. Soil physicochemical properties and heavy metal concentrations were measured. Differences between bacterial communities were investigated using the high-throughput sequencing of the 16S rRNA genes. The obtained results demonstrated that bacterial richness index (Chao and Ace) were similar among three ditches, while the highest bacterial diversity index was detected in the severely contaminated soils. The compositions of bacterial communities varied among three examined sites, but Proteobacteria and Acidobacteria were abundant in all samples. Redundancy analysis revealed that soil organic matter, Cr and pH were the three major factors altering the bacterial community structure. Pearson correlation analysis indicated that the most significant correlations were observed between the contents of non-residual Cr and the abundances of bacterial genera, including Thiobacillus, Nitrospira, and other 10 genera. Among them, the abundances of Sphingomonas and Pseudomonas were significant and positively correlated with the concentrations of non-residual U and As. The results highlighted the factors influencing the bacterial community in uranium mines and contributed a better understanding of the effects of heavy metals on bacterial community structure by considering the fraction of heavy metals.

Effect of depleted uranium on a soil microcosm fungal community and influence of a plant-ectomycorrhizal association

Fungi are one of the most biogeochemically active components of the soil microbiome, becoming particularly important in metal polluted terrestrial environments. There is scant information on the mycobiota of uranium (U) polluted sites and the effect of metallic depleted uranium (DU) stress on fungal communities in soil has not been reported. The present study aimed to establish the effect of DU contamination on a fungal community in soil using a culture-independent approach, fungal ribosomal intergenic spacer analysis (F-RISA). Experimental soil microcosms also included variants with plants (Pinus silvestris) and P. silvestris/Rhizopogon rubescens ectomycorrhizal associations. Soil contamination with DU resulted in the appearance of RISA bands of the ITS fragments of fungal metagenomic DNA that were characteristic of the genus Mortierella (Mortierellomycotina: Mucoromycota) in pine-free microcosms and for ectomycorrhizal fungi of the genus Scleroderma (Basidiomycota) in microcosms with mycorrhizal pines. The precise taxonomic affinity of the ITS fragments from the band appearing for non-mycorrhizal pines combined with DU remained uncertain, the most likely being related to the subphylum Zoopagomycotina. Thus, soil contamination by thermodynamically unstable metallic depleted uranium can cause a significant change in a soil fungal community under experimental conditions. These changes were also strongly affected by the presence of pine seedlings and their mycorrhizal status which impacted on DU biocorrosion and the release of bioavailable uranium species.

Uranium biomineralization induced by a metal tolerant Serratia strain under acid, alkaline and irradiated conditions

It has become increasingly apparent that the environmental microorganisms residing in uranium (U) enriched sites offer the possibility of understanding the biological mechanisms catalyzing the processes important for uranium bioremediation. Here, we present the results of uranium biomineralization over a wide pH range by a metal tolerant Serratia sp. strain OT II 7 isolated from the subsurface soil of a U ore deposit at Domiasiat in India. The Serratia cells actively expressed acid and alkaline phosphatase enzymes which hydrolyzed differential amounts of phosphate from an organophosphate substrate in the presence of uranium between pH 5 to 9. These cells precipitated ∼91% uranium from aqueous solutions supplemented with 1 mM uranyl nitrate at pH 5 within 120 h. More rapid precipitation was observed at pH 7 and 9 wherein the cells removed ∼93-94% of uranium from solutions containing 1 mM uranyl carbonate within 24 h. The aqueous uranyl speciation prevalent under the studied pH conditions influenced the localization of crystalline uranyl phosphate precipitates, which in turn, impacted the cell viability to a great extent. Furthermore, the cells tolerated up to ∼1.6 kGy 60Co gamma radiation and their uranium precipitation abilities at pH 5, 7 and 9 were uncompromised even after exposure to a high dose of ionizing radiation. Overall, this study establishes the ecological adaptation of a natural strain like Serratia in a uranium enriched environment and corroborates its contribution towards uranium immobilization in contaminated subsurfaces through the formation of stable uranyl phosphate minerals over a wide pH range.

Microbial nanowires and electroactive biofilms

Geobacter bacteria are the only microorganisms known to produce conductive appendages or pili to electronically connect cells to extracellular electron acceptors such as iron oxide minerals and uranium. The conductive pili also promote cell-cell aggregation and the formation of electroactive biofilms. The hallmark of these electroactive biofilms is electronic heterogeneity, mediated by coordinated interactions between the conductive pili and matrix-associated cytochromes. Collectively, the matrix-associated electron carriers discharge respiratory electrons from cells in multilayered biofilms to electron-accepting surfaces such as iron oxide coatings and electrodes poised at a metabolically oxidizable potential. The presence of pilus nanowires in the electroactive biofilms also promotes the immobilization and reduction of soluble metals, even when present at toxic concentrations. This review summarizes current knowledge about the composition of the electroactive biofilm matrix and the mechanisms that allow the wired Geobacter biofilms to generate electrical currents and participate in metal redox transformations.

Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA

Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.

Rahnella sp. LRP3 induces phosphate precipitation of Cu (II) and its role in copper-contaminated soil remediation

Microbially induced phosphate precipitation (MIPP) is an advanced bioremediation technology to immobilize heavy metals in soil. In this study, an indigenous bacterial strain LRP3, identified as Rahnella sp., was isolated from Cu-contaminated dark brown soil in the mining area. Strain LRP3 could produce phytase and alkaline phosphatase to degrade phytic acid, which released soluble phosphate to the bacterial culture. Due to the metabolism of bacterial growth, the pH value of bacterial culture was increased. The minimum inhibitory concentration of Cu (II) to bacterial growth in solution was up to 130 mg/L. The bacterial culture could rapidly precipitate Cu (II) in solution through MIPP. The analysis results of Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transform-Infrared Spectrometer (FTIR), and X-ray Diffraction (XRD) revealed that the precipitate form by bacterial culture was rod-shaped Cu₃(OH)₃PO₄ crystal with a diameter of 10 μm. The bacterial culture decreased the content of DTPA-Cu of 83 mg/kg soil in the soil by 58.2%, 61.5% and 75.8% after 5, 10 and 30 days of incubation, respectively, at the temperature of 25 °C. The results indicate that MIPP-based bioremediation by Rahnella sp. LRP3 is a practical, environmental friendly technology for the cleaning-up of copper-contaminated soil.

Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions

Surface layers (S-layers) are components of the cell walls throughout the Bacteria and the Archaea that provide protection for microorganisms against diverse environmental stresses, including metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in an archaeon for which the S-layer represents the only cell wall component. Here, we test the hypothesis originally proposed in cyanobacteria that a “shedding” mechanism exists for replacing S-layers that have become mineral-encrusted, using Lysinibacillus sp. TchIII 20n38, metallotolerant gram-positive bacterium, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, depending on physiological state of the cells and metal exposure times, leading to the encrustation of the S-layer and changes in the cell morphology as observed by scanning electron microscopy. Using Nanoscale Secondary Ion Mass Spectrometry, we show that mineral-encrusted S-layers are shed by the bacterial cells after a period of latency (2 days under the conditions tested) in a heterogeneous fashion likely reflecting natural variations in metal stress resistance. The emerging cells regenerate new S-layers as part of their cell wall structure. Given the wide diversity of S-layer bearing prokaryotes, S-layer shedding may represent an important mechanism for microbial survival in metal-contaminated environments.

Soil uranium concentration at Ranger Uranium Mine Land Application Areas drives changes in the bacterial community

Soil microorganisms may respond to metal stress by a shift in the microbial community from metal sensitive to metal resistant microorganisms. We assessed the bacterial community from low (2-20 mg kg^-1), medium (200-400 mg kg^-1), high (500-900 mg kg^-1) and very high (>900 mg kg^-1) uranium soils at Ranger Uranium Mine in northern Australia through pyrosequencing. Proteobacteria (28.85%) was the most abundant phylum at these sites, followed by Actinobacteria (9.31%), Acidobacteria (7.33%), Verrucomicrobia (2.11%), Firmicutes (2.02%), Chloroflexi (1.11%), Cyanobacteria (0.93%), Planctomycetes (0.82%), Bacteroidetes (0.46%) and Candidate_division_WS3 (Latescibacteria) (0.21%). However, 46.79% of bacteria were unclassified. Bacteria at low U soils differed from soils with elevated uranium. Bacterial OTUs closely related to Kitasatospora spp., Sphingobacteria spp. and Rhodobium spp. were only present at higher uranium concentrations and the bacterial community also changed with seasonal and temporal changes in soil uranium and physicochemical variables. This study using next generation sequencing in association with environmental variables at a uranium mine has laid a foundation for further studies of soil-microbe-metal interactions which may be useful for developing sustainable management and rehabilitation strategies. Furthermore, bacterial species associated with higher uranium may serve as useful indicators of uranium contamination in the wet-dry tropics.

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.

Comprehensive Evaluation of Soil Near Uranium Tailings, Beishan City, China

To evaluate the impact of uranium tailings on soil composition and soil microbial, six soil samples at different distance from the uranium tailings (Beishan City, China) were collected for further analysis. Concentrations of radionuclides (²³⁸U and ²³²Th), heavy metals (Mn, Cd, Cr, Ni, Zn, and Pb) and organochlorine pesticide were determined by ICP-MS and GC, they were significantly higher than those of the control. And the Average Well Color Development as well as the Shannon, the Evenness, and the Simpson index were calculated to evaluate the soil microbial diversity. The carbon utilization model of soil microbial community was also analyzed by Biolog-eco. All results indicated that uranium tailings leaded to excessive radionuclides and heavy metals, and decreased the diversity of the soil microbial community. Our study will provide a valuable basis for soil quality evaluation around uranium tailing repositories and lay a foundation for the management and recovery of uranium tailings.

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments

Elevated uranium dose (4 g kg^-1) causes a shift in billabong sediment communities that result in the enrichment of five bacterial species. These taxa include Geobacter, Geothrix and Dyella species, as well as a novel-potentially predatory-Bacteroidetes species, and a new member of class Anaerolineae (Chloroflexi). Additionally, a population of methanogenic Methanocella species was also identified. Genomic reconstruction and metabolic examination of these taxa reveal a host of divergent life strategies and putative niche partitioning. Resistance-nodulation-division heavy metal efflux (RND-HME) transporters are implicated as potential uranium tolerance strategies among the bacterial taxa. Potential interactions, uranium tolerance and ecologically relevant catabolism are presented in a conceptual model of life in this environment.

In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis

Microbial phosphatase activity can trigger the precipitation of metal-phosphate minerals, a process called phosphatogenesis with global geochemical and environmental implications. An increasing diversity of phosphatases expressed by diverse microorganisms has been evidenced in various environments. However, it is challenging to link the functional properties of genomic repertoires of phosphatases with the phosphatogenesis capabilities of microorganisms. Here, we studied the betaproteobacterium Ramlibacter tataouinensis (Rta), known to biomineralize Ca-phosphates in the environment and the laboratory. We investigated the functional repertoire of this biomineralization process at the cell, genome and molecular level. Based on a mineralization assay, Rta is shown to hydrolyse the phosphoester bonds of a wide range of organic P molecules. Accordingly, its genome has an unusually high diversity of phosphatases: five genes belonging to two non-homologous families, phoD and phoX, were detected. These genes showed diverse predicted cis-regulatory elements. Moreover, they encoded proteins with diverse structural properties according to molecular models. Heterologously expressed PhoD and PhoX in Escherichia coli had different profiles of substrate hydrolysis. As evidenced for Rta cells, recombinant E. coli cells induced the precipitation of Ca-phosphate mineral phases, identified as poorly crystalline hydroxyapatite. The phosphatase genomic repertoire of Rta (containing phosphatases of both the PhoD and PhoX families) was previously evidenced as prevalent in marine oligotrophic environments. Interestingly, the Tataouine sand from which Rta was isolated showed similar P-depleted, but Ca-rich conditions. Overall, the diversity of phosphatases in Rta allows the hydrolysis of a broad range of organic P substrates and therefore the release of orthophosphates (inorganic phosphate) under diverse trophic conditions. Since the release of orthophosphates is key to the achievement of high saturation levels with respect to hydroxyapatite and the induction of phosphatogenesis, Rta appears as a particularly efficient driver of this process as shown experimentally.

Intestinal Bacterial Communities of Trypanosome-Infected and Uninfected Glossina palpalis palpalis from Three Human African Trypanomiasis Foci in Cameroon

Glossina sp. the tsetse fly that transmits trypanosomes causing the Human or the Animal African Trypanosomiasis (HAT or AAT) can harbor symbiotic bacteria that are known to play a crucial role in the fly's vector competence. We hypothesized that other bacteria could be present, and that some of them could also influence the fly's vector competence. In this context the objectives of our work were: (a) to characterize the bacteria that compose the G. palpalis palpalis midgut bacteriome, (b) to evidence possible bacterial community differences between trypanosome-infected and non-infected fly individuals from a given AAT and HAT focus or from different foci using barcoded Illumina sequencing of the hypervariable V3-V4 region of the 16S rRNA gene. Forty G. p. palpalis flies, either infected by Trypanosoma congolense or uninfected were sampled from three trypanosomiasis foci in Cameroon. A total of 143 OTUs were detected in the midgut samples. Most taxa were identified at the genus level, nearly 50% at the species level; they belonged to 83 genera principally within the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Prominent representatives included Wigglesworthia (the fly's obligate symbiont), Serratia, and Enterobacter hormaechei. Wolbachia was identified for the first time in G. p. palpalis. The average number of bacterial species per tsetse sample was not significantly different regarding the fly infection status, and the hierarchical analysis based on the differences in bacterial community structure did not provide a clear clustering between infected and non-infected flies. Finally, the most important result was the evidence of the overall very large diversity of intestinal bacteria which, except for Wigglesworthia, were unevenly distributed over the sampled flies regardless of their geographic origin and their trypanosome infection status.

Screening of bacterial strains isolated from uranium mill tailings porewaters for bioremediation purposes

The present work characterizes at different levels a number of bacterial strains isolated from porewaters sampled in the vicinity of two French uranium tailing repositories. The 16S rRNA gene from 33 bacterial isolates, corresponding to the different morphotypes recovered, was almost fully sequenced. The resulting sequences belonged to 13 bacterial genera comprised in the phyla Firmicutes, Actinobacteria and Proteobacteria. Further characterization at physiological level and metals/metalloid tolerance provided evidences for an appropriate selection of bacterial strains potentially useful for immobilization of uranium and other common contaminants. By using High Resolution Transmission Electron Microscope (HRTEM), this potential ability to immobilize uranium as U phosphate mineral phases was confirmed for the bacterial strains Br3 and Br5 corresponding to Arthrobacter sp. and Microbacterium oxydans, respectively. Scanning Transmission Electron Microscope- High-Angle Annular Dark-Field (STEM-HAADF) analysis showed U accumulates on the surface and within bacterial cytoplasm, in addition to the extracellular space. Energy Dispersive X-ray (EDX) element-distribution maps demonstrated the presence of U and P within these accumulates. These results indicate the potential of certain bacterial strains isolated from porewaters of U mill tailings for immobilizing uranium, likely as uranium phosphates. Some of these bacterial isolates might be considered as promising candidates in the design of uranium bioremediation strategies.

Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River

Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.

Uranium(VI) Scavenging by Amorphous Iron Phosphate Encrusting Sphaerotilus natans Filaments

U(VI) sorption to iron oxyhydroxides, precipitation of phosphate minerals, as well as biosorption on bacterial biomass are among the most reported processes able to scavenge U(VI) under oxidizing conditions. Although phosphates significantly influence bacterially mediated as well as iron oxyhydroxide mediated scavenging of uranium, the sorption or coprecipitation of U(VI) with poorly crystalline nanosized iron phosphates has been scarcely documented, especially in the presence of microorganisms. Here we show that dissolved U(VI) can be bound to amorphous iron phosphate during their deposition on Sphaerotilus natans filamentous bacteria. Uranium LIII-edge EXAFS analysis reveals that the adsorbed uranyl ions share an equatorial oxygen atom with a phosphate tetrahedron of the amorphous iron phosphate, with a characteristic U-P distance of 3.6 Å. In addition, the uranyl ions are connected to FeO6 octahedra with U-Fe distances at ~3.4 Å and at ~4.0 Å. The shortest U-Fe distance corresponds to a bidentate edge-sharing complex often reported for uranyl adsorption onto iron oxyhydroxides, whereas the longest U-Fe and U-P distances can be interpreted as a bidentate corner-sharing complex, in which two adjacent equatorial oxygen atoms are shared with the vertices of a FeO6 octahedron and of a phosphate tetrahedron. Furthermore, based on these sorption reactions, we demonstrate the ability of an attached S. natans biofilm to remove uranium from solution without any filtration step.

Metagenomic analysis of microbial community in uranium-contaminated soil

Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

Use of combined microscopic and spectroscopic techniques to reveal interactions between uranium and Microbacterium sp. A9, a strain isolated from the Chernobyl exclusion zone

Although uranium (U) is naturally found in the environment, soil remediation programs will become increasingly important in light of certain human activities. This work aimed to identify U(VI) detoxification mechanisms employed by a bacteria strain isolated from a Chernobyl soil sample, and to distinguish its active from passive mechanisms of interaction. The ability of the Microbacterium sp. A9 strain to remove U(VI) from aqueous solutions at 4 °C and 25 °C was evaluated, as well as its survival capacity upon U(VI) exposure. The subcellular localisation of U was determined by TEM/EDX microscopy, while functional groups involved in the interaction with U were further evaluated by FTIR; finally, the speciation of U was analysed by TRLFS. We have revealed, for the first time, an active mechanism promoting metal efflux from the cells, during the early steps following U(VI) exposure at 25 °C. The Microbacterium sp. A9 strain also stores U intracellularly, as needle-like structures that have been identified as an autunite group mineral. Taken together, our results demonstrate that this strain exhibits a high U(VI) tolerance based on multiple detoxification mechanisms. These findings support the potential role of the genus Microbacterium in the remediation of aqueous environments contaminated with U(VI) under aerobic conditions.

Radionuclides distribution, properties, and microbial diversity of soils in uranium mill tailings from southeastern China

OBJECTIVE

To collect the radioactive contamination data for environmental rehabilitation in uranium mill tailings in southeastern China.

METHOD

The sample areas were divided into high, moderate and low concentration areas, according to the uranium concentration. For every area, 3 soil samples were collected at 0-15 cm, 15-30 cm and 30-45 cm depth respectively, with 5 repetitions for each. Total 45 (3 × 5 × 3) soil samples were collected. Physicochemical properties and enzyme activities of soils were determined as described by references. The concentrations of the radionuclides (238)U, (232)Th, (226)Ra and (40)K in soils were determined by using HPGe gamma-ray spectrometer. Soil microbial diversity was analyzed via denaturing gradient gel electrophoresis (DGGE).

RESULTS

Soil samples were all acidic. Physicochemical properties, like pH, content of total/available N, P and K, as well as enzyme activities were all increased along with decreased uranium concentration. The (232)Th concentration was increased with the decreased uranium concentration and was not influenced by the depth of sample sites. However, uranium concentration and depth of sample showed no significant influence on the concentrations of (226)Ra and (40)K. The concentration of (232)Th was significantly correlated with that of (226)Ra and (40)K, while the concentrations of (226)Ra and (40)K were significantly correlated. However, Pearson correlation coefficients between (238)U and other radionuclides were not significant. The microbial population in different concentration areas was different with four domain strains in low area, and two for both moderate and high areas. Furthermore, in each sample site, Proteobacteria was the most dominant flora, while environmental samples were the second according to GenBank database. Moreover, Serratia sp. of Proteobacteria was the dominant strain.

CONCLUSION

Radionuclides distribution in the uranium mill tailing showed a profound influence on soil properties and microbial diversity. This primarily study might provide valuable data for further research towards a better understanding of the radioactive contamination in uranium mill tailings in southeast China.

Escherichia coli response to uranyl exposure at low pH and associated protein regulations

Better understanding of uranyl toxicity in bacteria is necessary to optimize strains for bioremediation purposes or for using bacteria as biodetectors for bioavailable uranyl. In this study, after different steps of optimization, Escherichia colicells were exposed to uranyl at low pH to minimize uranyl precipitation and to increase its bioavailability. Bacteria were adapted to mid acidic pH before exposure to 50 or 80 µM uranyl acetate for two hours at pH≈3. To evaluate the impact of uranium, growth in these conditions were compared and the same rates of cells survival were observed in control and uranyl exposed cultures. Additionally, this impact was analyzedby two-dimensional differential gel electrophoresis proteomics to discover protein actors specifically present or accumulated in contact with uranium.Exposure to uranium resulted in differential accumulation of proteins associated with oxidative stress and in the accumulation of the NADH/quinone oxidoreductase WrbA. This FMN dependent protein performs obligate two-electron reduction of quinones, and may be involved in cells response to oxidative stress. Interestingly, this WrbA protein presents similarities with the chromate reductase from E. coli, which was shown to reduce uranyl in vitro.

Microbial communities in uranium mine tailings and mine water sediment from Jaduguda U mine, India: A culture independent analysis

Microbial diversity within uranium mine tailings and mine water sediment from the Jaduguda uranium mine, India was characterized by metagenome-derived 16S rRNA gene clone libraries. Samples from fresh tailings (JFT244), abandoned (vegetated) tailings (JOT245) and mine water sediment (J1-5) having wide ranges of pH (5.7 to 10.4), nitrogen, phosphorus and organic carbon [150-5700 ppm, 800-9100 ppm and 0.18-6.5% (w/w)] and elevated metals (Ni, Cu, Zn and U) were used to explore the inhabitant bacterial and archaeal community structures. Consistent to the sample's physicochemical properties, up to four orders of magnitude variation in bacterial CFU counts was observed. The data showed that with increasing metal and decreasing nutrient (organic C, N, P, etc.) contents, microbial diversity indices decrease within the samples. Culture-independent analyses revealed predominance of phyla Proteobacteria and/or Acidobacteria within the samples along with members of Actinobacteria, Cyanobacteria, Chloroflexi, Genera incertae sedis OP10, Firmicutes and Planctomycete as relatively minor groups. Abundance of Crenarchaeota in tailings samples and Euryachaeota in mine water sediment was noted. Diversity of dissimilatory sulfate reductase gene (dsr) was studied. Putative metabolic properties as derived from taxonomy and phylogenetic lineages indicated presence of chemolithotrophic and heteotrophic aerobic and anaerobic organisms capable of nitrogen fixation, nitrate reduction and biogeochemical cycling of metals, sulfur and methane. The data indicated that indigenous microbial populations are capable of maintaining self-sustenance in these highly hazardous environments and possess catalytic potential for their use in in situ bioremediation.

Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus Microbacterium , for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).

Ascomycota members dominate fungal communities during straw residue decomposition in arable soil

This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested.

Uranium interaction with two multi-resistant environmental bacteria: Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris

Depending on speciation, U environmental contamination may be spread through the environment or inversely restrained to a limited area. Induction of U precipitation via biogenic or non-biogenic processes would reduce the dissemination of U contamination. To this aim U oxidation/reduction processes triggered by bacteria are presently intensively studied. Using X-ray absorption analysis, we describe in the present article the ability of Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris, highly resistant to a variety of metals and metalloids or to organic pollutants, to withstand high concentrations of U and to immobilize it either through biosorption or through reduction to non-uraninite U(IV)-phosphate or U(IV)-carboxylate compounds. These bacterial strains are thus good candidates for U bioremediation strategies, particularly in the context of multi-pollutant or mixed-waste contaminations.

Electron transfer at the cell–uranium interface in Geobacter spp

The in situ stimulation of Fe(III) oxide reduction in the subsurface stimulates the growth of Geobacter spp. and the precipitation of U(VI) from groundwater. As with Fe(III) oxide reduction, the reduction of uranium by Geobacter spp. requires the expression of their conductive pili. The pili bind the soluble uranium and catalyse its extracellular reductive precipitation along the pili filaments as a mononuclear U(IV) complexed by carbon-containing ligands. Although most of the uranium is immobilized by the pili, some uranium deposits are also observed in discreet regions of the outer membrane, consistent with the participation of redox-active foci, presumably c-type cytochromes, in the extracellular reduction of uranium. It is unlikely that cytochromes released from the outer membrane could associate with the pili and contribute to the catalysis, because scanning tunnelling microscopy spectroscopy did not reveal any haem-specific electronic features in the pili, but, rather, showed topographic and electronic features intrinsic to the pilus shaft. Pili not only enhance the rate and extent of uranium reduction per cell, but also prevent the uranium from traversing the outer membrane and mineralizing the cell envelope. As a result, pili expression preserves the essential respiratory activities of the cell envelope and the cell's viability. Hence the results support a model in which the conductive pili function as the primary mechanism for the reduction of uranium and cellular protection in Geobacter spp.

Dynamic alteration of the colonic microbiota in intestinal ischemia-reperfusion injury

Background

Intestinal ischemia-reperfusion (I/R) plays an important role in critical illnesses. Gut flora participate in the pathogenesis of the injury. This study is aimed at unraveling colonic microbiota alteration pattern and identifying specific bacterial species that differ significantly as well as observing colonic epithelium change in the same injury model during the reperfusion time course.

Methodology/Principal Findings

Denaturing gradient gel electrophoresis (DGGE) was used to monitor the colonic microbiota of control rats and experimental rats that underwent 0.5 hour ischemia and 1, 3, 6, 12, 24, and 72 hours following reperfusion respectively. The microbiota similarity, bacterial diversity and species that characterized the dysbiosis were estimated based on the DGGE profiles using a combination of statistical approaches. The interested bacterial species in the gel were cut and sequenced and were subsequently quantified and confirmed with real-time PCR. Meanwhile, the epithelial barrier was checked by microscopy and D-lactate analysis. Colonic flora changed early and differed significantly at 6 hours after reperfusion and then started to recover. The shifts were characterized by the increase of Escherichia coli and Prevotella oralis, and Lactobacilli proliferation together with epithelia healing.

Conclusion/Significance

This study shows for the first time that intestinal ischemia-reperfusion results in colonic flora dysbiosis that follows epithelia damage, and identifies the bacterial species that contribute most.