Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Effects of Priestia aryabhattai on Phosphorus Fraction and Implications for Ecoremediating Cd-Contaminated Farmland with Plant-Microbe Technology

The application of phosphate-solubilizing bacteria has been widely studied in remediating Cd-contaminated soil, but only a few studies have reported on the interaction of P and Cd as well as the microbiological mechanisms with phosphate-solubilizing bacteria in the soil because the activity of phosphate-solubilizing bacteria is easily inhibited by the toxicity of Cd. This paper investigates the phosphorus solubilization ability of Priestia aryabhattai domesticated under the stress of Cd, which was conducted in a soil experiment with the addition of Cd at different concentrations. The results show that the content of Ca2-P increased by 5.12-19.84%, and the content of labile organic phosphorus (LOP) increased by 3.03-8.42% after the addition of Priestia aryabhattai to the unsterilized soil. The content of available Cd decreased by 3.82% in the soil with heavy Cd contamination. Priestia aryabhattai has a certain resistance to Cd, and its relative abundance increased with the increased Cd concentration. The contents of Ca2-P and LOP in the soil had a strong positive correlation with the content of Olsen-P (p < 0.01), while the content of available Cd was negatively correlated with the contents of Olsen-P, Ca2-P, and LOP (p < 0.05). Priestia aryabhattai inhibits the transport of Cd, facilitates the conversion of low-activity P and insoluble P to Ca2-P and LOP in the soil, and increases the bioavailability and seasonal utilization of P in the soil, showing great potential in ecoremediating Cd-contaminated farmland soil with plant-microbe-combined technology.

Past, present and future trends in the remediation of heavy-metal contaminated soil - Remediation techniques applied in real soil-contamination events

Most worldwide policy frameworks, including the United Nations Sustainable Development Goals, highlight soil as a key non-renewable natural resource which should be rigorously preserved to achieve long-term global sustainability. Although some soil is naturally enriched with heavy metals (HMs), a series of anthropogenic activities are known to contribute to their redistribution, which may entail potentially harmful environmental and/or human health effects if certain concentrations are exceeded. If this occurs, the implementation of rehabilitation strategies is highly recommended. Although there are many publications dealing with the elimination of HMs using different methodologies, most of those works have been done in laboratories and there are not many comprehensive reviews about the results obtained under field conditions. Throughout this review, we examine the different methodologies that have been used in real scenarios and, based on representative case studies, we present the evolution and outcomes of the remediation strategies applied in real soil-contamination events where legacies of past metal mining activities or mine spills have posed a serious threat for soil conservation. So far, the best efficiencies at field-scale have been reported when using combined strategies such as physical containment and assisted-phytoremediation. We have also introduced the emerging problem of the heavy metal contamination of agricultural soils and the different strategies implemented to tackle this problem. Although remediation techniques used in real scenarios have not changed much in the last decades, there are also encouraging facts for the advances in this field. Thus, a growing number of mining companies publicise in their webpages their soil remediation strategies and efforts; moreover, the number of scientific publications about innovative highly-efficient and environmental-friendly methods is also increasing. In any case, better cooperation between scientists and other soil-related stakeholders is still required to improve remediation performance.

Sulfur fertilization and water management ensure phytoremediation coupled with argo-production by mediating rhizosphere microbiota in the Oryza sativa L.-Sedum alfredii Hance rotation system

Sulfur (S) fertilizers, water management and crop rotation are important agronomic practices, related to soil heavy metal bioavailability. However, the mechanisms of microbial interactions remain unclear. Herein, we investigated how S fertilizers (S⁰ and Na₂SO₄) and water management affected plant growth, soil cadmium (Cd) bioavailability, and rhizospheric bacterial communities in the Oryza sativa L. (rice)-Sedum alfredii Hance (S. alfredii) rotation system through 16S rRNA gene sequencing and ICP-MS analysis. During rice cultivation, continuous flooding (CF) was better than alternating wetting and drying (AWD). CF treatment decreased soil Cd bioavailability by the promotion of insoluble metal sulfide production and soil pH, thus lowering Cd accumulation in grains. S application recruited more S-reducing bacteria in the rhizosphere of rice, whilst Pseudomonas promoted metal sulfide production and rice growth. During S. alfredii cultivation, S fertilizer recruited S-oxidizing and metal-activating bacteria in the rhizosphere. Thiobacillus may oxidize metal sulfides and enhance Cd and S absorption into S. alfredii. Notably, S oxidation decreased soil pH and elevated Cd content, thereby promoting S. alfredii growth and Cd absorption. These findings showed rhizosphere bacteria were involved in Cd uptake and accumulation in the rice-S. alfredii rotation system, thus providing useful information for phytoremediation coupled with argo-production.

Soil heavy metal pollution from Pb/Zn smelting regions in China and the remediation potential of biomineralization

Smelting activities pose serious environmental problems due to the local and regional heavy metal pollution in soils they cause. It is therefore important to understand the pollution situation and its source in the contaminated soils. In this paper, data on heavy metal pollution in soils resulting from Pb/Zn smelting (published in the last 10 years) in China was summarized. The heavy metal pollution was analyzed from a macroscopic point of view. The results indicated that Pb, Zn, As and Cd were common contaminants that were present in soils with extremely high concentrations. Because of the extreme carcinogenicity, genotoxicity and neurotoxicity that heavy metals pose, remediation of the soils contaminated by smelting is urgently required. The primary anthropogenic activities contributing to soil pollution in smelting areas and the progressive development of accurate source identification were performed. Due to the advantages of biominerals, the potential of biomineralization for heavy metal contaminated soils was introduced. Furthermore, the prospects of geochemical fraction analysis, combined source identification methods as well as several optimization methods for biomineralization are presented, to provide a reference for pollution investigation and remediation in smelting contaminated soils in the future.

Promoted Sb removal with hydrogen production in microbial electrolysis cell by ZIF-67-derived modified sulfate-reducing bacteria bio-cathode

Bio-cathode Microbial electrolysis cell (MEC) has been widely discovered for heavy metals removal and hydrogen production. However, low electron transfer efficiency and heavy metal toxicity limit MEC treatment efficiency. In this study, ZIF-67 was introduced to modify Sulfate-reducing bacteria (SRB) bio-cathode to enhance the bioreduction of sulfate and Antimony (Sb) with hydrogen production in the MEC. ZIF-67 modified bio-cathode was developed from a bio-anode microbial fuel cell (MFC) by operating with an applied voltage of 0.8 V to reverse the polarity. Cyclic voltammetry, linear sweep voltammetry and electrochemical impedance were done to confirm the performance of the ZIF-67 modified SRB bio-cathode. The synergy reduction of sulfate and Sb was accomplished by sulfide metal precipitation reaction from SRB itself. Maximum sulfate reduction rate approached 93.37 % and Sb removal efficiency could reach 92 %, which relies on the amount of sulfide concentration generated by sulfate reduction reaction, with 0.923 ± 0.04 m³ H₂/m³ of hydrogen before adding Sb and 0.857 m³ H₂/m³ of hydrogen after adding Sb. The hydrogen was mainly produced in this system and the result of gas chromatography (GC) indicated that 73.27 % of hydrogen was produced. Meanwhile the precipitates were analyzed by X-ray diffraction and X-ray photoelectron spectroscopy to confirm Sb₂S₃ was generated from Sb (V).

Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline

This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.

Efficient reduction of antimony by sulfate-reducer enriched bio-cathode with hydrogen production in a microbial electrolysis cell

Bio-cathode Microbial electrolysis cell (MEC) is a promising and eco-friendly technology for concurrent hydrogen production and heavy metal reduction. However, the bioreduction of Antimony (Sb) in a bio-electrochemical system with H₂ production is not explored. In this study, two efficient sulfate-reducing bacterial (SRB) strains were used to investigate the enhanced bioreduction of sulfate and Sb with H₂ production in the MEC. SRB Bio-cathode MEC was developed from the microbial fuel cell (MFC) and operated with an applied voltage of 0.8 V. The performance of the SRB bio-cathode was confirmed by cyclic voltammetry, linear sweep voltammetry and electrochemical impedance spectroscopy. SRB strains of BY7 and SR10 supported the synergy reduction of sulfate and Sb by sulfide metal precipitation reaction. Hydrogen gas was the main product of SRB bio-cathode, with 86.9%, and 83.6% of H₂ is produced by SR10 and BY7, respectively. Sb removal efficiency reached up to 88.2% in BY7 and 96.3% in SR10 with a sulfate reduction rate of 92.3 ± 2.6 and 98.4 ± 1.6 gm^-3d^-1 in BY7 and SR10, respectively. The conversion efficiency of Sb (V) to Sb (III) reached up to 70.1% in BY7 and 89.2% in SR10. It was concluded that the total removal efficiency of Sb relies on the amount of sulfide concentration produced by the sulfate reduction reaction. The hydrogen production rate was increased up to 1.25 ± 0.06 (BY7) and 1.36 ± 0.02 m³ H₂/(m³·d) (SR10) before addition of Sb and produced up to 0.893 ± 0.03 and 0.981 ± 0.02 m³H₂/(m³·d) after addition of Sb. The precipitates were characterized by X-ray diffraction and X-ray photoelectron spectroscopy, which confirmed Sb (V) was reduced to Sb₂S₃.

Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?

FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function of marine species using standard microbiological references. This study, however, has attempted to access the application of FAPROTAX in soil environments. We hypothesized that FAPROTAX was compatible with terrestrial ecosystems. The potential use of FAPROTAX to assign ecological functions of soil bacteria was investigated using meta-analysis and our newly designed experiments. Soil samples from two major terrestrial ecosystems, including agricultural land and forest, were collected. Bacterial taxonomy was analyzed using Illumina sequencing of the 16S rRNA gene and ecological functions of the soil bacteria were assigned by FAPROTAX. The presence of all functionally assigned OTUs (Operation Taxonomic Units) in soil were manually checked using peer-reviewed articles as well as standard microbiology books. Overall, we showed that sample source was not a predominant factor that limited the application of FAPROTAX, but poor taxonomic identification was. The proportion of assigned taxa between aquatic and non-aquatic ecosystems was not significantly different (p > 0.05). There were strong and significant correlations (σ = 0.90–0.95, p < 0.01) between the number of OTUs assigned to genus or order level and the number of functionally assigned OTUs. After manual verification, we found that more than 97% of the FAPROTAX assigned OTUs have previously been detected and potentially performed functions in agricultural and forest soils. We further provided information regarding taxa capable of N-fixation, P and K solubilization, which are three main important elements in soil systems and can be integrated with FAPROTAX to increase the proportion of functionally assigned OTUs. Consequently, we concluded that FAPROTAX can be used for a fast-functional screening or grouping of 16S derived bacterial data from terrestrial ecosystems and its performance could be enhanced through improving the taxonomic and functional reference databases.

Engineering and kinetic aspects of bacterial uranium reduction for the remediation of uranium contaminated environments

Biological reduction of soluble uranium from U(VI) to insoluble U(IV) coupled to the oxidation of an electron donor (hydrogen or organic compounds) is a potentially cost-efficient way to reduce the U concentrations in contaminated waters to below regulatory limits. A variety of microorganisms originating from both U contaminated and non-contaminated environments have demonstrated U(VI) reduction capacity under anaerobic conditions. Bioreduction of U(VI) is considered especially promising for in situ remediation, where the activity of indigenous microorganisms is stimulated by supplying a suitable electron donor to the subsurface to contain U contamination to a specific location in a sparingly soluble form. Less studied microbial biofilm-based bioreactors and bioelectrochemical systems have also shown potential for efficient U(VI) reduction to remove U from contaminated water streams. This review compares the advantages and challenges of U(VI)-reducing in situ remediation processes, bioreactors and bioelectrochemical systems. In addition, the current knowledge of U(VI) bioreduction mechanisms and factors affecting U(VI) reduction kinetics (e.g. pH, temperature, and the chemical composition of the contaminated water) are discussed, as both of these aspects are important in designing efficient remediation processes.

Treatment of acidic sulfate-containing wastewater using revolving algae biofilm reactors: Sulfur removal performance and microbial community characterization

Industries such as mining operations are facing challenges of treating sulfur-containing wastewater such as acid mine drainage (AMD) generated in their plant. The aim of this work is to evaluate the use of a revolving algal biofilm (RAB) reactor to treat AMD with low pH (3.5-4) and high sulfate content (1-4 g/L). The RAB reactors resulted in sulfate removal efficiency up to 46% and removal rate up to 0.56 g/L-day, much higher than those obtained in suspension algal culture. The high-throughput sequencing revealed that the RAB reactor contained diverse cyanobacteria, green algae, diatoms, and acid reducing bacteria that contribute the sulfate removal through various mechanisms. The RAB reactors also showed a superior performance of COD, ammonia and phosphorus removal. Collectively, the study demonstrated that RAB-based process is an effective method to remove sulfate in wastewater with small footprint and can be potentially installed in municipal or industrial wastewater treatment facilities.

Enhanced immobilization of U(VI) on Mucor circinelloides in presence of As(V): Batch and XAFS investigation

The combined pollution of radionuclides and heavy metals has been given rise to widespread concern during uranium mining. The influence of As(V) on U(VI) immobilization by Mucor circinelloides (M. circinelloides) was investigated using batch experiments. The activity of antioxidative enzymes and concentrations of thiol compounds and organic acid in M. circinelloides increased to respond to different U(VI) and As(V) stress. The morphological structure of M. circinelloides changed obviously under U(VI) and As(V) stress by SEM and TEM analysis. The results of XANES and EXAFS analysis showed that U(VI) was mainly reduced to nano-uraninite (nano-UO₂, 30.1%) in U₄₀₀, while only 9.7% of nano-UO₂ was observed in the presence of As(V) in U₄₀₀-As₄₀₀ due to the formation of uranyl arsenate precipitate (Trögerite, 48.6%). These observations will provide the fundamental data for fungal remediation of uranium and heavy metals in uranium-contaminated soils.

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.

The application of iron-based technologies in uranium remediation: A review

Remediating uranium contamination is of worldwide interest because of the increasing release of uranium from mining and processing, nuclear power leaks, depleted uranium components in weapons production and disposal, and phosphate fertilizer in agriculture activities. Iron-based technologies are attractive because they are highly efficient, inexpensive, and readily available. This paper provides an overview of the current literature that addresses the application of iron-based technologies in the remediation of sites with elevated uranium levels. The application of iron-based materials, the current remediation technologies and mechanisms, and the effectiveness and environmental safety considerations of these approaches were discussed. Because uranium can be reduced and reoxidized in the environment, the review also proposes strategies for long-term in situ remediation of uranium. Unfortunately, iron-based materials (nanoscale zerovalent iron and iron oxides) can be toxic to microorganisms. As such, further studies exploring the links among the fates, ecological impacts, and other environmentally relevant factors are needed to better understand the constraints on using iron-based technologies for remediation.

Microbial communities in riparian soils of a settling pond for mine drainage treatment

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage.

Metals other than uranium affected microbial community composition in a historical uranium-mining site

To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

Characterization of pH dependent Mn(II) oxidation strategies and formation of a bixbyite-like phase by Mesorhizobium australicum T-G1

Despite the ubiquity of Mn oxides in natural environments, there are only a few observations of biological Mn(II) oxidation at pH < 6. The lack of low pH Mn-oxidizing bacteria (MOB) isolates limits our understanding of how pH influences biological Mn(II) oxidation in extreme environments. Here, we report that a novel MOB isolate, Mesorhizobium australicum strain T-G1, isolated from an acidic and metalliferous uranium mining area, can oxidize Mn(II) at both acidic and neutral pH using different enzymatic pathways. X-ray diffraction, Raman spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy revealed that T-G1 initiated bixbyite-like Mn oxide formation at pH 5.5 which coincided with multi-copper oxidase expression from early exponential phase to late stationary phase. In contrast, reactive oxygen species (ROS), particularly superoxide, appeared to be more important for T-G1 mediated Mn(II) oxidation at neutral pH. ROS was produced in parallel with the occurrence of Mn(II) oxidation at pH 7.2 from early stationary phase. Solid phase Mn oxides did not precipitate, which is consistent with the presence of a high amount of H2O2 and lower activity of catalase in the liquid culture at pH 7.2. Our results show that M. australicum T-G1, an acid tolerant MOB, can initiate Mn(II) oxidation by varying its oxidation mechanisms depending on the pH and may play an important role in low pH manganese biogeochemical cycling.

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

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

Exploring actinide materials through synchrotron radiation techniques

Synchrotron radiation (SR) based techniques have been utilized with increasing frequency in the past decade to explore the brilliant and challenging sciences of actinide-based materials. This trend is partially driven by the basic needs for multi-scale actinide speciation and bonding information and also the realistic needs for nuclear energy research. In this review, recent research progresses on actinide related materials by means of various SR techniques were selectively highlighted and summarized, with the emphasis on X-ray absorption spectroscopy, X-ray diffraction and scattering spectroscopy, which are powerful tools to characterize actinide materials. In addition, advanced SR techniques for exploring future advanced nuclear fuel cycles dealing with actinides are illustrated as well.

Linkage between community diversity of sulfate-reducing microorganisms and methylmercury concentration in paddy soil

Sulfate-reducing microorganisms (SRM) have been thought to play a key role in mercury (Hg) methylation in anoxic environments. The current study examined the linkage between SRM abundance and diversity and contents of methylmercury (MeHg) in paddy soils collected from a historical Hg mining area in China. Soil profile samples were collected from four sites over a distance gradient downstream the Hg mining operation. Results showed that MeHg content in the soil of each site significantly decreased with the extending distance away from Hg mine. Soil MeHg content was correlated positively with abundance of SRM and the contents of organic matter (OM), NH4(+), SO4(2-), and Hg. The abundances of SRM based on dissimilatory (bi) sulfite reductase (dsrAB) gene at 0-40 cm depths were higher than those at 40-80 cm depth at all sites. The SRM community composition varied in the soils of different sampling sites following terminal restriction fragment length polymorphism (T-RFLP) and phylogenetic analyses, which appeared to be correlated with contents of MeHg, OM, NH4(+), and SO4(2-) through canonical correspondence analysis. The dominant groups of SRM in the soils examined belonged to Deltaproteobacteria and some unknown SRM clusters that could have potential for Hg methylation. These results advance our understanding of the relationship between SRM and methylmercury concentration in paddy soil.

Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations

We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic "Ferrovum myxofaciens" was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and "Ferrovum myxofaciens" revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.

Bacterial diversity and composition of an alkaline uranium mine tailings-water interface

The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine water-tailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.

Mercury mobilization in a flooded soil by incorporation into metallic copper and metal sulfide nanoparticles

Mercury is a highly toxic priority pollutant that can be released from wetlands as a result of biogeochemical redox processes. To investigate the temperature-dependent release of colloidal and dissolved Hg induced by flooding of a contaminated riparian soil, we performed laboratory microcosm experiments at 5, 14, and 23 °C. Our results demonstrate substantial colloidal Hg mobilization concomitant with Cu prior to the main period of sulfate reduction. For Cu, we previously showed that this mobilization was due to biomineralization of metallic Cu nanoparticles associated with suspended bacteria. X-ray absorption spectroscopy at the Hg LIII-edge showed that colloidal Hg corresponded to Hg substituting for Cu in the metallic Cu nanoparticles. Over the course of microbial sulfate reduction, colloidal Hg concentrations decreased but continued to dominate total Hg in the pore water for up to 5 weeks of flooding at all temperatures. Transmission electron microscopy (TEM) suggested that Hg became associated with Cu-rich mixed metal sulfide nanoparticles. The formation of Hg-containing metallic Cu and metal sulfide nanoparticles in contaminated riparian soils may influence the availability of Hg for methylation or volatilization processes and has substantial potential to drive Hg release into adjacent water bodies.

Microbial communities in low permeability, high pH uranium mine tailings: characterization and potential effects

AIMS

To describe the diversity and metabolic potential of microbial communities in uranium mine tailings characterized by high pH, high metal concentration and low permeability.

METHODS AND RESULTS

To assess microbial diversity and their potential to influence the geochemistry of uranium mine tailings using aerobic and anaerobic culture-based methods, in conjunction with next generation sequencing and clone library sequencing targeting two universal bacterial markers (the 16S rRNA and cpn60 genes). Growth assays revealed that 69% of the 59 distinct culturable isolates evaluated were multiple-metal resistant, with 15% exhibiting dual-metal hypertolerance. There was a moderately positive correlation coefficient (R = 0·43, P < 0·05) between multiple-metal resistance of the isolates and their enzyme expression profile. Of the isolates tested, 17 reduced amorphous iron, 22 reduced molybdate and seven oxidized arsenite. Based on next generation sequencing, tailings depth was shown to influence bacterial community composition, with the difference in the microbial diversity of the upper (0-20 m) and middle (20-40 m) tailings zones being highly significant (P < 0·01) from the lower zone (40-60 m) and the difference in diversity of the upper and middle tailings zone being significant (P < 0·05). Phylotypes closely related to well-known sulfate-reducing and iron-reducing bacteria were identified with low abundance, yet relatively high diversity.

CONCLUSIONS

The presence of a population of metabolically-diverse, metal-resistant micro-organisms within the tailings environment, along with their demonstrated capacity for transforming metal elements, suggests that these organisms have the potential to influence the long-term geochemistry of the tailings.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first investigation of the diversity and functional potential of micro-organisms present in low permeability, high pH uranium mine tailings.

Microbial community potentially responsible for acid and metal release from an Ostrobothnian acid sulfate soil

Soils containing an approximately equal mixture of metastable iron sulfides and pyrite occur in the boreal Ostrobothnian coastal region of Finland, termed 'potential acid sulfate soil materials'. If the iron sulfides are exposed to air, oxidation reactions result in acid and metal release to the environment that can cause severe damage. Despite that acidophilic microorganisms catalyze acid and metal release from sulfide minerals, the microbiology of acid sulfate soil (ASS) materials has been neglected. The molecular phylogeny of a depth profile through the plough and oxidized ASS layers identified several known acidophilic microorganisms and environmental clones previously identified from acid- and metal-contaminated environments. In addition, several of the 16S rRNA gene sequences were more similar to sequences previously identified from cold environments. Leaching of the metastable iron sulfides and pyrite with an ASS microbial enrichment culture incubated at low pH accelerated metal release, suggesting microorganisms capable of catalyzing metal sulfide oxidation were present. The 16S rRNA gene analysis showed the presence of species similar to Acidocella sp. and other clones identified from acid mine environments. These data support that acid and metal release from ASSs was catalyzed by indigenous microorganisms adapted to low pH.

Quality and mutagenicity of water and sediment of the streams impacted by the former uranium mine area Olší-Drahonín (Czech Republic)

The water quality research performed in the years 2003-2010 demonstrated an impact of the mine water pumped from the closed Olší uranium mine and discharged from the mine water treatment plant (MWTP) and groundwater from springs in the area on the water quality of the Hadůvka stream. The water ecosystems of the lower part of the Hadůvka stream are impacted mainly by water originated from the springs located in the stream valley and drained syenit subsoil, naturally rich in uranium. Those inflows caused a very high concentration of uranium measured in the water of the stream, which exceeds the given limit value. No negative impact on the water ecosystems of the receiving Bobrůvka River was found. This reduction of impact is caused by five times higher average daily flow rate of the Bobrůvka River in comparison with the Hadůvka stream, which results in a sufficient dilution of pollution from the Hadůvka.

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7

Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.

Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments

Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.

Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp

The determination of the success of in situ bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N(2) gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp., with low levels of other organisms, including methanogens. Four new strains of Pelosinus were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including Desulfovibrio spp., were outcompeted. These results suggest that during times of electron acceptor limitation in situ, organisms such as Pelosinus spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed.

Following the kinetics: iron-oxidizing microbial mats in cold icelandic volcanic habitats and their rock-associated carbonaceous signature

Icelandic streams with mean annual temperatures of less than 5 °C, which receive the cationic products of basaltic rock weathering, were found to host mats of iron-cycling microorganisms. We investigated two representative sites. Iron-oxidizing Gallionella and iron-reducing Geobacter species were present. The mats host a high bacterial diversity as determined by culture-independent methods. β-Proteobacteria, Actinobacteria, α-Proteobacteria, and Bacteroidetes were abundant microbial taxa. The mat contained a high number of phototroph sequences. The carbon compounds in the mat displayed broad G and D bands with Raman spectroscopy. This signature becomes incorporated into the weathered oxidized surface layer of the basaltic rocks and was observed on rocks that no longer host mats. The presence of iron-oxidizing taxa in the stream microbial mats, and the lack of them in previously studied volcanic rocks in Iceland that have intermittently been exposed to surface water flows, can be explained by the kinetic limitations to the extraction of reduced iron from rocks. This type of ecosystem illustrates key factors that control the distribution of chemolithotrophs in cold volcanic environments. The data show that one promising sample type for which the hypothesis of the existence of past life on Mars can be tested is the surface of volcanic rocks that, previously, were situated within channels carved by flowing water. Our results also show that the carbonaceous signatures of life, if life had occurred, could be found in or on these rocks.

Heavy metal tolerance of Fe(III)-reducing microbial communities in contaminated creek bank soils

Fe(III)-reducing soil enrichment cultures can tolerate 100 μM Cu and Cd, 150 μM Co, 600 μM Ni, and 2,500 μM Zn. Metal-tolerant cultures were dominated by Geobacter-related Deltaproteobacteria and Gram-positive Firmicutes spp. (Clostridia and Sedimentibacter). A Cd- and Cu-tolerant Fe(III)-reducing coculture of Desulfosporosinus and Desulfitobacterium indicated the importance of the Firmicutes for Fe(III) reduction in the presence of metals.

Effects of an electric field and zero valent iron on anaerobic treatment of azo dye wastewater and microbial community structures

A zero valent iron (ZVI) bed with a pair of electrodes was packed in an anaerobic reactor aiming at enhancing treatment of azo dye wastewater. The experiments were carried out in three reactors operated in parallel: an electric field enhanced ZVI-anaerobic reactor (R1), a ZVI-anaerobic reactor (R2) and a common anaerobic reactor (R3). R1 presented the highest performance in removal of COD and color. Raising voltage in R1 further improved its performance. Scanning electron microscopy images displayed that the structure of granular sludge from R1 was intact after being fed with the high dye concentration, while that of R3 was broken. Fluorescence in situ hybridization analysis indicated that the abundance of methanogens in R1 was significantly greater than that in the other two reactors. Denaturing gradient gel electrophoresis showed that the coupling of electric field and ZVI increased the diversity of microbial community and especially enhanced bacterial strains responsible for decolorization.