Modeling reduction of uranium U(VI) under variable sulfate concentrations by sulfate-reducing bacteria

Coupling flow and electric fields to simulate migration and remediation of uranium in groundwater remediated by electroosmosis and a permeable reactive bio-barrier

Combined remediation technologies are increasingly being considered to uranium contaminated groundwater, such as the joint utilize of permeable reactive bio-barrier (Bio-PRB) and electrokinetic remediation (EKR). While the assessment of uranium plume evolution in the combined remediation system (CRS) have often been impeded by insufficient understanding of multi-physical field superposition. Therefore, advanced knowledge in multi-physical field coupling in groundwater flow will be crucial to the practical application of these techniques. A two-dimensional multi-physical field coupling model was constructed for predicting the uranium degradation in CRS. The study demonstrates that the coupling model is able to predict the uranium plume evolution and rapidly evaluate the performance of CRS components. The results show that field electric direction and flow field strength are the key factors that affect the retardation and remediation performance of CRS. The reverse electric field direction significantly affected the contact reaction time of uranium in the system. The uranium residence time in the reverse electric field was 3.8 d, which was significantly greater than the original electric field (2.0 d). Depending on the voltage, the reverse electric field direction was 16%-36% more efficient than the original direction. The strength of the flow field was about two orders of magnitude higher than that of the electric field, so the groundwater flow rate dominated remediation efficiency. Reducing the flow rate by 1/2 could improve the performance of the system by approximately 66%. In addition, the coupling model can be utilized to design standard CRS for real site of uranium contaminated groundwater. To meet the optimal performance, the direction of the electric field should be set opposite to the flow field. This work has successfully used a coupling model to predict uranium contaminant-plume evolution in CRS and estimate the performance of each component.

Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem

A unique environment at Borup Fiord Pass is characterized by a sulfur-enriched glacial ecosystem in the low-temperature Canadian High Arctic. BFP represents one of the best terrestrial analog sites for studying icy, sulfur-rich worlds outside our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Here, we report whole-genome sequencing data that suggest that sulfur cycling metabolisms at BFP are more widely used across bacterial taxa than predicted. From our analyses, the metabolic capability of sulfur oxidation among multiple community members appears likely due to functional redundancy present in their genomes. Functional redundancy, with respect to sulfur-oxidation at the BFP sulfur-ice environment, may indicate that this dynamic ecosystem hosts microorganisms that are able to use multiple sulfur electron donors alongside other metabolic pathways, including those for carbon and nitrogen.

Biological sulfur cycling in polar, low-temperature ecosystems is an understudied phenomenon in part due to difficulty of access and the dynamic nature of glacial environments. One such environment where sulfur cycling is known to play an important role in microbial metabolisms is located at Borup Fiord Pass (BFP) in the Canadian High Arctic. Here, transient springs emerge from ice near the terminus of a glacier, creating a large area of proglacial aufeis (spring-derived ice) that is often covered in bright yellow/white sulfur, sulfate, and carbonate mineral precipitates accompanied by a strong odor of hydrogen sulfide. Metagenomic sequencing of samples from multiple sites and of various sample types across the BFP glacial system produced 31 metagenome-assembled genomes (MAGs) that were queried for sulfur, nitrogen, and carbon cycling/metabolism genes. An abundance of sulfur cycling genes was widespread across the isolated MAGs and sample metagenomes taxonomically associated with the bacterial classes Alphaproteobacteria and Gammaproteobacteria and Campylobacteria (formerly the Epsilonproteobacteria). This corroborates previous research from BFP implicating Campylobacteria as the primary class responsible for sulfur oxidation; however, data reported here suggested putative sulfur oxidation by organisms in both the alphaproteobacterial and gammaproteobacterial classes that was not predicted by previous work. These findings indicate that in low-temperature, sulfur-based environments, functional redundancy may be a key mechanism that microorganisms use to enable coexistence whenever energy is limited and/or focused by redox chemistry.

IMPORTANCE A unique environment at Borup Fiord Pass is characterized by a sulfur-enriched glacial ecosystem in the low-temperature Canadian High Arctic. BFP represents one of the best terrestrial analog sites for studying icy, sulfur-rich worlds outside our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Here, we report whole-genome sequencing data that suggest that sulfur cycling metabolisms at BFP are more widely used across bacterial taxa than predicted. From our analyses, the metabolic capability of sulfur oxidation among multiple community members appears likely due to functional redundancy present in their genomes. Functional redundancy, with respect to sulfur-oxidation at the BFP sulfur-ice environment, may indicate that this dynamic ecosystem hosts microorganisms that are able to use multiple sulfur electron donors alongside other metabolic pathways, including those for carbon and nitrogen.

New approach for the assessment of the contribution of adsorption, biodegradation and self-bioregeneration in the dynamic process of biologically active carbon functioning

This work developed an effective model of the cooperative removal process of organic compounds on biologically active carbon. This model involves the determination of the dynamics of adsorption efficiency and degradation of specific classes of target organic substances but also the dynamics of non-target filling of pores with products of vital microbial activity. It is possible to quantitatively assess the contributions of adsorption, biodegradation and self-bioregeneration in the process of biologically active carbon functioning and the changes in the activated carbon porous properties during the process. The model developed was applied to assess the efficiency of filtration of 2-nitrophenol through a biologically active carbon bed for 38 months. The activated carbon adsorption capacity for removing 2-nitrophenol was preserved after three years of the bed service due to the effective biodegradation that resulted in self-bioregeneration of the sorbent. Nontarget losses of porosity (filling with bioproducts) increased with increasing duration of system operation, and by the end of the experiment, these losses amounted to 61% of the pore volume of the fresh sorbent.

Deciphering Biosignatures in Planetary Contexts

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with "abiosignatures" formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the "right" spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.

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.

pH-dependent speciation and hydrogen (H2 ) control U(VI) respiration by Desulfovibrio vulgaris

In situ bioreduction of soluble hexavalent uranium U(VI) to insoluble U(IV) (as UO₂ ) has been proposed as a means of preventing U migration in the groundwater. This work focuses on the bioreduction of U(VI) and precipitation of U(IV). It uses anaerobic batch reactors with Desulfovibrio vulgaris, a well-known sulfate, iron, and U(VI) reducer, growing on lactate as the electron donor, in the absence of sulfate, and with a 30-mM bicarbonate buffering. In the absence of sulfate, D. vulgaris reduced  >90% of the total soluble U(VI) (1 mM) to form U(IV) solids that were characterized by X-ray diffraction and confirmed to be nano-crystalline uraninite with crystallite size 2.8 ± 0.2 nm. pH values between 6 and 10 had minimal impact on bacterial growth and end-product distribution, supporting that the mono-nuclear, and poly-nuclear forms of U(VI) were equally bioavailable as electron acceptors. Electron balances support that H₂ transiently accumulated, but was ultimately oxidized via U(VI) respiration. Thus, D. vulgaris utilized H₂ as the electron carrier to drive respiration of U(VI). Rapid lactate utilization and biomass growth occurred only when U(VI) respiration began to draw down the sink of H₂ and relieve thermodynamic inhibition of fermentation.

Membrane optode for uranium(vi) preconcentration and colorimetric determination in real samples

A membrane optode formed by physical inclusion of a chromophore 2-(2-benzothiazolylazo)phenol (BTAP) and uranium(vi) anions into a plasticized cellulose triacetate (CTA) matrix was illustrated for preconcentration and colorimetric determination of U(vi) from aqueous samples.

Uranium Bioreduction and Biomineralization

Following the development of nuclear science and technology, uranium contamination has been an ever increasing concern worldwide because of its potential for migration from the waste repositories and long-term contaminated environments. Physical and chemical techniques for uranium pollution are expensive and challenging. An alternative to these technologies is microbially mediated uranium bioremediation in contaminated water and soil environments due to its reduced cost and environmental friendliness. To date, four basic mechanisms of uranium bioremediation-uranium bioreduction, biosorption, biomineralization, and bioaccumulation-have been established, of which uranium bioreduction and biomineralization have been studied extensively. The objective of this review is to provide an understanding of recent developments in these two fields in relation to relevant microorganisms, mechanisms, influential factors, and obstacles.

Bioreduction of U(VI) and stability of immobilized uranium under suboxic conditions

In order to study the bioreduction of U(VI) and stability of immobilized uranium under suboxic conditions, microcosm were amended with ethanol, lactate and glucose, and incubated under suboxic conditions. During the incubation, total dissolved U in amended microcosms decreased from 0.95 mg/L to 0.03 mg/L. Pyrosequencing results showed that, the proportion of anaerobic microorganisms capable of reducing U(VI) under suboxic conditions was small compared with that under anoxic conditions; the proportion of aerobic and facultative anaerobic microorganisms capable of consuming the dissolved oxygen was large; and some of the facultative anaerobic microorganisms could reduce U(VI). These results indicated that different microbial communities were responsible for the bioreduction of U(VI) under suboxic and anoxic conditions. After the electron donors were exhausted, total dissolved U in the amended microcosms remained unchanged, while the U(VI)/U(IV) ratio in the solid phase of sediments increased obviously. This implied that the performance of bioreduction of the U(VI) can be maintained under suboxic condition.

The mechanism of uranium transformation from U(VI) into nano-uramphite by two indigenous Bacillus thuringiensis strains

The mechanism of uranium transformation from U(VI) into nano-uramphite by two indigenous Bacillus thuringiensis strains was investigated in the present work. Our data showed that the bacteria isolated from uranium mine possessed highly accumulation ability to U(VI), and the maximum accumulation capacity was around 400 mg U/g biomass (dry weight). X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FT-IR) analyzes indicated that the U(VI) was adsorbed on the bacterial surface firstly through coordinating with phosphate, CH2 and amide groups, and then needle-like amorphous uranium compounds were formed. With the extension of time, the extracellular crystalline substances were disappeared, but some particles were appeared in the intracellular region, and these particles were characterized as tetragonal-uramphite. Moreover, the disrupted experiment indicated that the cell-free extracts had better uranium-immobilization ability than cell debris. Our findings provided the understanding of the uranium transformation process from amorphous uranium to crystalline uramphite, which would be useful in the regulation of uranium immobilization process.

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site

Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to uranium addition. In this study, uranium amendments were made to groundwater samples from a site of ongoing biostimulation with acetate. The active microbes in the planktonic phase were deduced by monitoring ribosomes production via RT-PCR. The results indicated several microorganisms were synthesizing ribosomes in proportion with uranium amendment up to 2 μM. Concentrations of U (VI) >2 μM were generally found to inhibit ribosome synthesis. Two active bacteria responding to uranium addition in the field were close relatives of Desulfobacter postgateii and Geobacter bemidjiensis. Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites.

Optimization of a bioremediation system of soluble uranium based on the biostimulation of an indigenous bacterial community

High concentrations of uranium(VI) in the Witwatersrand Basin, South Africa from mining leachate is a serious environmental concern. Treatment systems are often ineffective. Therefore, optimization of a bioremediation system that facilitates the bioreduction of U(VI) based on biostimulation of indigenous bacterial communities can be a viable alternative. Tolerance of the indigenous bacteria to high concentrations of U and the amount of citric acid required for U removal was optimized. Two bioreactor studies which showed effective U(VI) removal more than 99 % from low (0.0037 mg L(-1)) and high (10 mg L(-1)) concentrations of U to below the limit allowed by South African National Standards for drinking water (0.0015 mg L(-1)). The second bioreactor was able to successfully adapt even with increasing levels of U(VI) feed water up to 10 mg L(-1), provided that enough electron donor was available. Molecular biology analyses identified Desulfovibrio sp. and Geobacter sp. among known species, which are known to reduce U(VI). The mineralogical analysis determined that part of the uranium precipitated intracellularly, which meant that the remaining U(VI) was precipitated as U(IV) oxides and TEM-EDS also confirmed this analysis. This was predicted with the geochemical model from the chemical data, which demonstrated that the treated drainage was supersaturated with respect to uraninite > U4O9 > U3O8 > UO2(am). Therefore, the tolerance of the indigenous bacterial community could be optimized to remediate up to 10 mg L(-1), and the system can thus be upscaled and employed for remediation of U(VI) impacted sites.

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site

The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.

Uranium bioreduction rates across scales: biogeochemical hot moments and hot spots during a biostimulation experiment at Rifle, Colorado

We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to insoluble U(IV). Bicarbonate was coinjected in half of the domain to mobilize sorbed U(VI). We used reactive transport modeling to integrate hydraulic and geochemical data and to quantify rates at the grid block (0.25 m) and experimental field scale (tens of meters). Although local rates varied by orders of magnitude in conjunction with biostimulation fronts propagating downstream, field-scale rates were dominated by those orders of magnitude higher rates at a few selected hot spots where Fe(III), U(VI), and FeRB were at their maxima in the vicinity of the injection wells. At particular locations, the hot moments with maximum rates negatively corresponded to their distance from the injection wells. Although bicarbonate injection enhanced local rates near the injection wells by a maximum of 39.4%, its effect at the field scale was limited to a maximum of 10.0%. We propose a rate-versus-measurement-length relationship (log R' = -0.63 log L - 2.20, with R' in μmol/mg cell protein/day and L in meters) for orders-of-magnitude estimation of uranium bioreduction rates across scales.

Growth of Desulfovibrio vulgaris when respiring U(VI) and characterization of biogenic uraninite

The capacity of Desulfovibrio vulgaris to reduce U(VI) was studied previously with nongrowth conditions involving a high biomass concentration; thus, bacterial growth through respiration of U(VI) was not proven. In this study, we conducted a series of batch tests on U(VI) reduction by D. vulgaris at a low initial biomass (10 to 20 mg/L of protein) that could reveal biomass growth. D. vulgaris grew with U(VI) respiration alone, as well as with simultaneous sulfate reduction. Patterns of growth kinetics and solids production were affected by sulfate and Fe(2+). Biogenic sulfide nonenzymatically reduced 76% of the U(VI) and greatly enhanced the overall reduction rate in the absence of Fe(2+) but was rapidly scavenged by Fe(2+) to form FeS in the presence of Fe(2+). Biogenic U solids were uraninite (UO2) nanocrystallites associated with 20 mg/g biomass as protein. The crystallite thickness of UO2 was 4 to 5 nm without Fe(2+) but was <1.4 nm in the presence of Fe(2+), indicating poor crystallization inhibited by adsorbed Fe(2+) and other amorphous Fe solids, such as FeS or FeCO3. This work fills critical gaps in understanding the metabolic utilization of U by microorganisms and formation of UO2 solids in bioremediation sites.

U(VI) bioreduction with emulsified vegetable oil as the electron donor--microcosm tests and model development

We conducted microcosm tests and biogeochemical modeling to study U(VI) reduction in contaminated sediments amended with emulsified vegetable oil (EVO). Indigenous microorganisms in the sediments degraded EVO and stimulated Fe(III), U(VI), and sulfate reduction, and methanogenesis. Acetate concentration peaked in 100-120 days in the EVO microcosms versus 10-20 days in the oleate microcosms, suggesting that triglyceride hydrolysis was a rate-limiting step in EVO degradation and subsequent reactions. Acetate persisted 50 days longer in oleate- and EVO- than in ethanol-amended microcosms, indicating that acetate-utilizing methanogenesis was slower in the oleate and EVO than ethanol microcosms. We developed a comprehensive biogeochemical model to couple EVO hydrolysis, production, and oxidation of long-chain fatty acids (LCFA), glycerol, acetate, and hydrogen, reduction of Fe(III), U(VI) and sulfate, and methanogenesis with growth and decay of multiple functional microbial groups. By estimating EVO, LCFA, and glycerol degradation rate coefficients, and introducing a 100 day lag time for acetoclastic methanogenesis for oleate and EVO microcosms, the model approximately matched observed sulfate, U(VI), and acetate concentrations. Our results confirmed that EVO could stimulate U(VI) bioreduction in sediments and the slow EVO hydrolysis and acetate-utilizing methanogens growth could contribute to longer term bioreduction than simple substrates (e.g., ethanol, acetate, etc.) in the subsurface.

Assessment of phosphogypsum impact on the salt-marshes of the Tinto river (SW Spain): role of natural attenuation processes

About 120 Mton of phosphogypsum from the fertiliser industry were stack-piled on the salt-marshes of the Tinto river (Spain). This paper investigates the capacity of salt-marshes to attenuate contamination due to downward leaching from phosphogypsum. Solids and pore-waters were characterized at different depths of the pile to reach the marsh-ground. In superficial zones, metals were highly mobile, and no reduced sulphur was found. However, pollutant concentration decreased in the pore-water in deeper oxygen-restricted zones. Metal removal occurred by precipitation of newly formed sulphides, being this process main responsible for the contamination attenuation. Pyrite-S was the main sulphide component (up to 2528 mg/kg) and occurred as framboids, leading to high degrees of pyritization (up to 97%). The sulphidization reaction is Fe-limited; however, excess of acid-volatile sulphide over other metals cause precipitation of other sulphides, mainly of Cu and As. This decrease in metal mobility significantly minimises the impact of phosphogypsums on the salt-marshes.

Multiple mechanisms of uranium immobilization by Cellulomonas sp. strain ES6

Removal of hexavalent uranium (U(VI)) from aqueous solution was studied using a Gram-positive facultative anaerobe, Cellulomonas sp. strain ES6, under anaerobic, non-growth conditions in bicarbonate and PIPES buffers. Inorganic phosphate was released by cells during the experiments providing ligands for formation of insoluble U(VI) phosphates. Phosphate release was most probably the result of anaerobic hydrolysis of intracellular polyphosphates accumulated by ES6 during aerobic growth. Microbial reduction of U(VI) to U(IV) was also observed. However, the relative magnitudes of U(VI) removal by abiotic (phosphate-based) precipitation and microbial reduction depended on the buffer chemistry. In bicarbonate buffer, X-ray absorption fine structure (XAFS) spectroscopy showed that U in the solid phase was present primarily as a non-uraninite U(IV) phase, whereas in PIPES buffer, U precipitates consisted primarily of U(VI)-phosphate. In both bicarbonate and PIPES buffer, net release of cellular phosphate was measured to be lower than that observed in U-free controls suggesting simultaneous precipitation of U and PO₄³⁻. In PIPES, U(VI) phosphates formed a significant portion of U precipitates and mass balance estimates of U and P along with XAFS data corroborate this hypothesis. High-resolution transmission electron microscopy (HR-TEM) and energy dispersive X-ray spectroscopy (EDS) of samples from PIPES treatments indeed showed both extracellular and intracellular accumulation of U solids with nanometer sized lath structures that contained U and P. In bicarbonate, however, more phosphate was removed than required to stoichiometrically balance the U(VI)/U(IV) fraction determined by XAFS, suggesting that U(IV) precipitated together with phosphate in this system. When anthraquinone-2,6-disulfonate (AQDS), a known electron shuttle, was added to the experimental reactors, the dominant removal mechanism in both buffers was reduction to a non-uraninite U(IV) phase. Uranium immobilization by abiotic precipitation or microbial reduction has been extensively reported; however, the present work suggests that strain ES6 can remove U(VI) from solution simultaneously through precipitation with phosphate ligands and microbial reduction, depending on the environmental conditions. Cellulomonadaceae are environmentally relevant subsurface bacteria and here, for the first time, the presence of multiple U immobilization mechanisms within one organism is reported using Cellulomonas sp. strain ES6.

A bacterial consortium isolated from an Icelandic fumarole displays exceptionally high levels of sulfate reduction and metals resistance

The soils of three fumaroles and one mining site, all with high metal content, were surveyed for the presence of metal-resistant sulfate-reducing bacteria and their potential application in the bioremediation of acid mine drainages. By means of selective soil enrichments a bacterial consortium was isolated from an Icelandic fumarole that displayed very high sulfate reduction in the presence of a mixture of 0.75 g/L of Fe, 0.20 g/L of Zn and 0.080 g/L of Cu. Under these conditions the bacterial consortium reduced 91% of the added 3.9 g/L of sulfate after 28 days, precipitating 100% of the Fe, 96% of the Zn and 97% of the Cu during the same time. Both total bacterial numbers and numbers of culturable sulfate-reducing bacteria remained unchanged when grown in media containing metals, suggesting low or absent inhibitory effects of the metals on the bacterial consortium. PCR-DGGE profiles of the sulfate reducing bacterial communities obtained from the Icelandic fumarole sample showed that bacterial diversity decreased significantly after metal addition: from the original 12 ribotypes only two were detected in the metal-tolerant culture. Phylogenetic analysis of 16S ribosomal RNA gene sequences revealed that these two ribotypes were affiliated with the genera Clostridium and Desulfovibrio, with C. subterminale, C. pascui, C. mesophilum and C. peptidovorans and D. desulfuricans identified as their closest relatives.

Effect of uranium(VI) speciation on simultaneous microbial reduction of uranium(VI) and iron(III)

Uranium is a pollutant of concern to both human and ecosystem health. Uranium's redox state often dictates whether it will reside in the aqueous or solid phase and thus plays an integral role in the mobility of uranium within the environment. In anaerobic environments, the more oxidized and mobile form of uranium (UO2(2+) and associated species) may be reduced, directly or indirectly, by microorganisms to U(IV) with subsequent precipitation of UO. However, various factors within soils and sediments, such as U(VI) speciation and the presence of competitive electron acceptors, may limit biological reduction of U(VI). Here we examine simultaneous dissimilatory reduction of Fe(III) and U(VI) in batch systems containing dissolved uranyl acetate and ferrihydrite-coated sand. Varying amounts of calcium were added to induce changes in aqueous U(VI) speciation. The amount of uranium removed from solution during 100 h of incubation with S. putrefaciens was 77% in absence of Ca or ferrihydrite, but only 24% (with ferrihydrite) and 14% (without ferrihydrite) were removed for systems with 0.8 mM Ca. Dissimilatory reduction of Fe(III) and U(VI) proceed through different enzyme pathways within one type of organism. We quantified the rate coefficients for simultaneous dissimilatory reduction of Fe(III) and U(VI) in systems varying in Ca concecentration (0-0.8 mM). The mathematical construct, implemented with the reactive transport code MIN3P, reveals predominant factors controlling rates and extent of uranium reduction in complex geochemical systems.

Microbial removal of uranyl by sulfate reducing bacteria in the presence of Fe (III) (hydr)oxides

Microbiological reduction of uranyl by sulfate reducing bacteria (SRB) has been proposed as a promising method for removal of radionuclide from groundwater. In this study, we examined the effect of two naturally occurring Fe(III) (hydr)oxides, hematite and goethite, on the bioreduction of U(VI) by a mixed culture of SRB via laboratory batch experiments. The biogenic precipitate from U(VI) bioreduction was determined using X-ray absorption near edge structure (XANES) analysis, showing a typical feature of uraninite (UO(2)). In the presence of either hematite or goethite-containing Fe(III) ranging from 10 to 30 mM, the reduction of U(VI) was retarded by both minerals and the retardatory effect was enhanced with increasing amount of Fe(III) (hydr)oxide. When exposed to a mixture of hematite and goethite with the total Fe(III) kept constant at 20 mM, the retardatory effect on U(VI) reduction by the minerals were directly correlated with the fraction of hematite present. A slow increase in U(VI) concentration was also found in all Fe(III) (hydr)oxide treatments after 10-13 days, accompanied by the release of Fe(II) into the solution. The presence of Fe(III) (hydr)oxide can cause the eventual incomplete bioreduction of U(VI). However, it was not the case for the control without minerals. When mixing biogenic uraninite with hematite or goethite without SRB, Fe(II) was also detected in the solution. These findings suggest that the U(VI) remobilization after 1013 days may be due to reoxidation of the uraninite by the solid-phase Fe(III) (hydr)oxide.

Microbial community changes in response to ethanol or methanol amendments for U(VI) reduction

Microbial community responses to ethanol, methanol, and methanol plus humics amendments in relationship to U(VI) bioreduction were studied in laboratory microcosm experiments using sediments and ground water from a uranium-contaminated site in Oak Ridge, TN. The type of carbon source added, the duration of incubation, and the sampling site influenced the bacterial community structure upon incubation. Analysis of 16S rRNA gene clone libraries indicated that (i) bacterial communities found in ethanol- and methanol-amended samples with U(VI) reduction were similar due to the presence of Deltaproteobacteria and Betaproteobacteria (members of the families Burkholderiaceae, Comamonadaceae, Oxalobacteraceae, and Rhodocyclaceae); (ii) methanol-amended samples without U(VI) reduction exhibited the lowest diversity and the bacterial community contained 69.2 to 92.8% of the family Methylophilaceae; and (iii) the addition of humics resulted in an increase of phylogenetic diversity of Betaproteobacteria (Rodoferax, Polaromonas, Janthinobacterium, Methylophilales, and unclassified) and Firmicutes (Desulfosporosinus and Clostridium).

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 microg l(-1)) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

Can microbially-generated hydrogen sulfide account for the rates of U(VI) reduction by a sulfate-reducing bacterium?

In situ remediation of uranium contaminated soil and groundwater is attractive because a diverse range of microbial and abiotic processes reduce soluble and mobile U(VI) to sparingly soluble and immobile U(IV). Often these processes are linked. Sulfate-reducing bacteria (SRB), for example, enzymatically reduce U(VI) to U(IV), but they also produce hydrogen sulfide that can itself reduce U(VI). This study evaluated the relative importance of these processes for Desulfovibrio aerotolerans, a SRB isolated from a U(VI)-contaminated site. For the conditions evaluated, the observed rate of SRB-mediated U(VI) reduction can be explained by the abiotic reaction of U(VI) with the microbially-generated H(2)S. The presence of trace ferrous iron appeared to enhance the extent of hydrogen sulfide-mediated U(VI) reduction at 5 mM bicarbonate, but had no clear effect at 15 mM. During the hydrogen sulfide-mediated reduction of U(VI), a floc formed containing uranium and sulfur. U(VI) sequestered in the floc was not available for further reduction.

Characterization and remediation of soils contaminated with uranium

Environmental contamination caused by radionuclides, in particular by uranium and its decay products is a serious problem worldwide. The development of nuclear science and technology has led to increasing nuclear waste containing uranium being released and disposed in the environment. The objective of this paper is to develop a better understanding of the techniques for the remediation of soils polluted with radionuclides (uranium in particular), considering: the chemical forms of uranium, including depleted uranium (DU) in soil and other environmental media, their characteristics and concentrations, and some of the effects on environmental and human health; research issues concerning the remediation process, the benefits and results; a better understanding of the range of uses and situations for which each is most appropriate. The paper addresses the main features of the following techniques for uranium remediation: natural attenuation, physical methods, chemical processes (chemical extraction methods from contaminated soils assisted by various suitable chelators (sodium bicarbonate, citric acid, two-stage acid leaching procedure), extraction using supercritical fluids such as solvents, permeable reactive barriers), biological processes (biomineralization and microbial reduction, phytoremediation, biosorption), and electrokinetic methods. In addition, factors affecting uranium removal from soils are furthermore reviewed including soil characteristics, pH and reagent concentration, retention time.

Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide-contaminated subsurface sediments

In order to elucidate the potential mechanisms of U(VI) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. A polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. The addition of ethanol and glucose as supplemental electron donors stimulated microbial nitrate and Fe(III) reduction as the predominant terminal electron-accepting processes (TEAPs). U(VI), Fe(III), and sulfate reduction overlapped in the glucose treatment, whereas U(VI) reduction was concurrent with sulfate reduction but preceded Fe(III) reduction in the ethanol treatments. Phyllosilicate clays were shown to be the major source of Fe(III) for microbial respiration by using variable-temperature Mössbauer spectroscopy. Nitrate- and Fe(III)-reducing bacteria (FeRB) were abundant throughout the shifts in TEAPs observed in biostimulated microcosms and were affiliated with the genera Geobacter, Tolumonas, Clostridium, Arthrobacter, Dechloromonas, and Pseudomonas. Up to two orders of magnitude higher counts of FeRB and enhanced U(VI) removal were observed in ethanol-amended treatments compared to the results in glucose-amended treatments. Quantification of citrate synthase (gltA) levels demonstrated a stimulation of Geobacteraceae activity during metal reduction in carbon-amended microcosms, with the highest expression observed in the glucose treatment. Phylogenetic analysis indicated that the active FeRB share high sequence identity with Geobacteraceae members cultivated from contaminated subsurface environments. Our results show that the functional diversity of populations capable of U(VI) reduction is dependent upon the choice of electron donor.

Growth and cometabolic reduction kinetics of a uranium- and sulfate-reducing Desulfovibrio/Clostridia mixed culture: Temperature effects

Bioremediation of contaminated soils and aquifers is subject to spatial and temporal temperature changes that can alter the kinetics of key microbial processes. This study quantifies temperature effects on the kinetics of an ethanol-fed sulfate-reducing mixed culture derived from a uranium-contaminated aquifer subject to seasonal temperature fluctuations. The mixed culture contains Desulfovibrio sp. and a Clostridia-like organism. Rates of growth, ethanol utilization, decay, and uranium reduction decreased with decreasing temperature. No significant uranium reduction was observed at 10 degrees C. While both Monod saturation kinetics and pseudo second-order kinetics adequately described the rates of growth and utilization of electron donor (ethanol), model parameters for the pseudo second-order expression had smaller uncertainties. Uranium reduction kinetics were best described by pseudo second-order kinetics modified to include a term for inactivation/death of cells.

Inhibition of a U(VI)- and sulfate-reducing consortia by U(VI)

The stimulation of microbial U(VI) reduction is currently being investigated as a means to reduce uranium's mobility in groundwater, but little is known about the concentration at which U(VI) might inhibit microbial activity, or the effect of U(VI) on bacterial community structure. We investigated these questions with an ethanol-fed U(VI)- and sulfate-reducing enrichment developed from sediment from the site of an ongoing field biostimulation experiment at Area 3 of the Oak Ridge Field Research Center (FRC). Sets of triplicate enrichments were spiked with increasing concentrations of U(VI) (from 49 microm to 9.2 mM). As the U(VI) concentration increased to 224 microM, the culture's production of acetate from ethanol slowed, and at or above 1.6 mM U(VI) little acetate was produced over the time frame of the experiment. An uncoupling inhibition model was applied to the data, and the inhibition coefficient for U(VI), Ku, was found to be approximately 100 microM U(VI), or 24 mg/L, indicating the inhibitory effect is relevant at highly contaminated sites. Microbial community structure at the conclusion of the experiment was analyzed with terminal restriction fragment length polymorphism (T-RFLP) analysis. T-RFs associated with Desulfovibrio-like organisms decreased in relative abundance with increasing U(VI) concentration, whereas Clostridia-like T-RFs increased.

Influence of bicarbonate, sulfate, and electron donors on biological reduction of uranium and microbial community composition

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low-bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high-bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and groundwater geochemistry alter microbial communities responsible for U(VI) reduction.

In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen

Groundwater within Area 3 of the U.S. Department of Energy (DOE) Environmental Remediation Sciences Program (ERSP) Field Research Center at Oak Ridge, TN (ORFRC) contains up to 135 microM uranium as U(VI). Through a series of experiments at a pilot scale test facility, we explored the lower limits of groundwater U(VI) that can be achieved by in-situ biostimulation and the effects of dissolved oxygen on immobilized uranium. Weekly 2 day additions of ethanol over a 2-year period stimulated growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria, and immobilization of uranium as U(IV), with dissolved uranium concentrations decreasing to low levels. Following sulfite addition to remove dissolved oxygen, aqueous U(VI) concentrations fell below the U.S. Environmental Protection Agengy maximum contaminant limit (MCL) for drinking water (< 30/microg L(-1) or 0.126 microM). Under anaerobic conditions, these low concentrations were stable, even in the absence of added ethanol. However, when sulfite additions stopped, and dissolved oxygen (4.0-5.5 mg L(-1)) entered the injection well, spatially variable changes in aqueous U(VI) occurred over a 60 day period, with concentrations increasing rapidly from < 0.13 to 2.0 microM at a multilevel sampling (MLS) well located close to the injection well, but changing little at an MLS well located further away. Resumption of ethanol addition restored reduction of Fe(III), sulfate, and U(VI) within 36 h. After 2 years of ethanol addition, X-ray absorption near-edge structure spectroscopy (XANES) analyses indicated that U(IV) comprised 60-80% of the total uranium in sediment samples. Atthe completion of the project (day 1260), U concentrations in MLS wells were less than 0.1 microM. The microbial community at MLS wells with low U(VI) contained bacteria that are known to reduce uranium, including Desulfovibrio spp. and Geobacter spp., in both sediment and groundwater. The dominant Fe(III)-reducing species were Geothrix spp.

Microbial reduction of sulfate injected to gas condensate plumes in cold groundwater

Despite a rapid expansion over the past decade in the reliance on intrinsic bioremediation to remediate petroleum hydrocarbon plumes in groundwater, significant research gaps remain. Although it has been demonstrated that bacterial sulfate reduction can be a key electron accepting process in many petroleum plumes, little is known about the rate of this reduction process in plumes derived from crude oil and gas condensates at cold-climate sites (mean temperature <10 degrees C), and in complex hydrogeological settings such as silt/clay aquitards. In this field study, sulfate was injected into groundwater contaminated by gas condensate plumes at two petroleum sites in Alberta, Canada to enhance in-situ bioremediation. In both cases the groundwater near the water table had low temperature (6-9 degrees C). Monitoring data had provided strong evidence that bacterial sulfate reduction was a key terminal electron accepting process (TEAP) in the natural attenuation of dissolved hydrocarbons at these sites. At each site, water with approximately 2000 mg/L sulfate and a bromide tracer was injected into a low-sulfate zone within a condensate-contaminant plume. Monitoring data collected over several months yielded conservative estimates for sulfate reduction rates based on zero-order kinetics (4-6 mg/L per day) or first-order kinetics (0.003 and 0.01 day(-1)). These results favor the applicability of in-situ bioremediation techniques in this region, under natural conditions or with enhancement via sulfate injection.

Arsenicicoccus bolidensis a novel arsenic reducing actinomycete in contaminated sediments near the Adak mine (northern Sweden): impact on water chemistry

Weathering of mine tailings in Adak results in high As concentrations in surface and ground water, sediments, and soil. In spite of the oxic conditions, As-rich surface and ground water samples indicate As(III) species predominantly (up to 83%). Several microorganisms were isolated from the enrichment cultures that were involved in As cycling. Amongst them was Arsenicicoccus bolidensis - a novel gram-positive, facultatively anaerobic, coccus-shaped actinomycete, which actively reduced As(V) to As(III) in aqueous media. A. bolidensis reduced 0.06-0.20 mM day(-1) As(V). As(V) reduction displays a direct correlation between the initial As(V) concentration, growth rate, and biomass yield.

Modeling in-situ uranium(VI) bioreduction by sulfate-reducing bacteria

We present a travel-time based reactive transport model to simulate an in-situ bioremediation experiment for demonstrating enhanced bioreduction of uranium(VI). The model considers aquatic equilibrium chemistry of uranium and other groundwater constituents, uranium sorption and precipitation, and the microbial reduction of nitrate, sulfate and U(VI). Kinetic sorption/desorption of U(VI) is characterized by mass transfer between stagnant micro-pores and mobile flow zones. The model describes the succession of terminal electron accepting processes and the growth and decay of sulfate-reducing bacteria, concurrent with the enzymatic reduction of aqueous U(VI) species. The effective U(VI) reduction rate and sorption site distributions are determined by fitting the model simulation to an in-situ experiment at Oak Ridge, TN. Results show that (1) the presence of nitrate inhibits U(VI) reduction at the site; (2) the fitted effective rate of in-situ U(VI) reduction is much smaller than the values reported for laboratory experiments; (3) U(VI) sorption/desorption, which affects U(VI) bioavailability at the site, is strongly controlled by kinetics; (4) both pH and bicarbonate concentration significantly influence the sorption/desorption of U(VI), which therefore cannot be characterized by empirical isotherms; and (5) calcium-uranyl-carbonate complexes significantly influence the model performance of U(VI) reduction.

Isolation and characterization of a mesophilic heavy-metals-tolerant sulfate-reducing bacterium Desulfomicrobium sp. from an enrichment culture using phosphogypsum as a sulfate source

A sulfate-reducing bacterium, was isolated from a 6 month trained enrichment culture in an anaerobic media containing phosphogypsum as a sulfate source, and, designated strain SA2. Cells of strain SA2 were rod-shaped, did not form spores and stained Gram-negative. Phylogenetic analysis of the 16S rRNA gene sequence of the isolate revealed that it was related to members of the genus Desulfomicrobium (average sequence similarity of 98%) with Desulfomicrobium baculatum being the most closely related (sequence similarity of 99%). Strain SA2 used thiosulfate, sulfate, sulfite and elemental sulfur as electron acceptors and produced sulfide. Strain SA2 reduced sulfate contained in 1-20g/L phosphogypsum to sulfide with reduction of sulfate contained in 2g/L phosphogypsum being the optimum concentration. Strain SA2 grew with metalloid, halogenated and non-metal ions present in phosphogypsum and with added high concentrations of heavy metals (125ppm Zn and 100ppm Ni, W, Li and Al). The relative order for the inhibitory metal concentrations, based on the IC(50) values, was Cu, Te>Cd>Fe, Co, Mn>F, Se>Ni, Al, Li>Zn.

Uranium Reduction

The dramatic decrease in solubility accompanying the reduction of U(VI) to U(IV), producing the insoluble mineral uraninite, has been viewed as a potential mechanism for sequestration of environmental uranium contamination. In the past 15 years, it has been firmly established that a variety of bacteria exhibit this reductive capacity. To obtain an understanding of the microbial metal metabolism, to develop a practical approach for the acceleration of in situ bioreduction, and to predict the long-term fate of environmental uranium, several aspects of the microbial process have been experimentally explored. This review briefly addresses the research to identify specific uranium reductases and their cellular location, competition between uranium and other electron acceptors, attempts to stimulate in situ reduction, and mechanisms of reoxidation of reduced uranium minerals.

Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of u(VI) and geochemical control of u(VI) bioavailability

In situ microbial reduction of soluble U(VI) to sparingly soluble U(IV) was evaluated at the site of the former S-3 Ponds in Area 3 of the U.S. Department of Energy Natural and Accelerated Bioremediation Research Field Research Center, Oak Ridge, TN. After establishing conditions favorable for bioremediation (Wu, et al. Environ. Sci. Technol. 2006, 40, 3988-3995), intermittent additions of ethanol were initiated within the conditioned inner loop of a nested well recirculation system. These additions initially stimulated denitrification of matrix-entrapped nitrate, but after 2 months, aqueous U levels fell from 5 to approximately 1 microM and sulfate reduction ensued. Continued additions sustained U(VI) reduction over 13 months. X-ray near-edge absorption spectroscopy (XANES) confirmed U(VI) reduction to U(IV) within the inner loop wells, with up to 51%, 35%, and 28% solid-phase U(IV) in sediment samples from the injection well, a monitoring well, and the extraction well, respectively. Microbial analyses confirmed the presence of denitrifying, sulfate-reducing, and iron-reducing bacteria in groundwater and sediments. System pH was generally maintained at less than 6.2 with low bicarbonate level (0.75-1.5 mM) and residual sulfate to suppress methanogenesis and minimize uranium mobilization. The bioavailability of sorbed U(VI) was manipulated by addition of low-level carbonate (< 5 mM) followed by ethanol (1-1.5 mM). Addition of low levels of carbonate increased the concentration of aqueous U, indicating an increased rate of U desorption due to formation of uranyl carbonate complexes. Upon ethanol addition, aqueous U(VI) levels fell, indicating that the rate of microbial reduction exceeded the rate of desorption. Sulfate levels simultaneously decreased, with a corresponding increase in sulfide. When ethanol addition ended but carbonate addition continued, soluble U levels increased, indicating faster desorption than reduction. When bicarbonate addition stopped, aqueous U levels decreased, indicating adsorption to sediments. Changes in the sequence of carbonate and ethanol addition confirmed that carbonate-controlled desorption increased bioavailability of U(VI) for reduction.

Comparative EXAFS investigation of uranium(VI) and -(IV) aquo chloro complexes in solution using a newly developed spectroelectrochemical cell

The coordination of the U(IV) and U(VI) ions as a function of the chloride concentration in aqueous solution has been studied by U L(III)-edge extended X-ray absorption fine structure (EXAFS) spectroscopy. The oxidation state of uranium was changed in situ using a gastight spectroelectrochemical cell, specifically designed for the safe use with radioactive solutions. For U(VI) we observed the complexes UO2(H2O)5(2+), UO2(H2O)4Cl+, UO2(H2O)3Cl2(0), and UO2(H2O)2Cl3- with [Cl-] increasing from 0 to 9 M, and for U(IV) we observed the complexes U(H2O)9(4+), U(H2O)8Cl3+, U(H2O)(6-7)Cl2(2+), and U(H2O)5Cl3+. The distances in the U(VI) coordination sphere are U-Oax = 1.76+/-0.02 A, Oeq = 2.41 +/- 0.02 A, and U-Cl = 2.71 +/- 0.02 A; the distances in the U(IV) coordination sphere are U-O = 2.41 +/- 0.02 A and U-Cl = 2.71 +/- 0.02 A.

Effects of legacy nuclear waste on the compositional diversity and distributions of sulfate-reducing bacteria in a terrestrial subsurface aquifer

The impact of legacy nuclear waste on the compositional diversity and distribution of sulfate-reducing bacteria in a heavily contaminated subsurface aquifer was examined. dsrAB clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis used to evaluate genetic variation between sampling wells. Principal component analysis identified nickel, nitrate, technetium, and organic carbon as the primary variables contributing to well-to-well geochemical variability, although comparative sequence analysis showed the sulfate-reducing bacteria community structure to be consistent throughout contaminated and uncontaminated regions of the aquifer. Only 3% of recovered dsrAB gene sequences showed apparent membership to the Deltaproteobacteria. The remainder of recovered sequences may represent novel, deep-branching lineages that, to our knowledge, do not presently contain any cultivated members; although corresponding phylotypes have recently been reported from several different marine ecosystems. These findings imply resiliency and adaptability of sulfate-reducing bacteria to extremes in environmental conditions, although the possibility for horizontal transfer of dsrAB is also discussed.

Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance

The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused either on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRNA abundance and non-random features in coding sequences (e.g., codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together. Using the AlignACE program, 442 over-represented motifs were identified from the upstream 100bp region of 293 genes located in the known regulons. Regression of mRNA expression data against the measures of coding and non-coding sequence features indicated that 54.1% of the variations in mRNA abundance can be explained by the presence of upstream motifs, while coding sequences alone contribute to 29.7% of the variations in mRNA abundance. Interestingly, most of contribution from coding sequences is overlapping with that from upstream motifs; thereby a total of 60.3% of the variations in mRNA abundance can be explained when coding and non-coding information was included. This result demonstrates that upstream regulatory motifs and coding sequence information contribute to the overall mRNA expression in a combinatorial rather than an additive manner.

Two-Component Signal Transduction Systems of Desulfovibrio vulgaris: Structural and Phylogenetic Analysis and Deduction of Putative Cognate Pairs

A large number of two-component signal transduction systems (TCSTS) including 59 putative sensory histidine kinases (HK) and 55 response regulators (RR) were identified from the Desulfovibrio vulgaris genome. In this study, the structural and phylogenetic analyses of all putative TCSTSs in D. vulgaris were performed. The results showed that D. vulgaris contained 21 hybrid-type HKs, implying that multiple-step phosphorelay may be a common signal transduction mechanism in D. vulgaris. Despite the low sequence similarity that restricted the resolution of the phylogenetic analyses, most TCSTS components of D. vulgaris were found clustered into several subfamilies previously recognized in Escherichia coli and Bacillus subtilis. An attempt was made in this investigation to identify the possible cognate HK-RR pairs not linked on the chromosome in D. vulgaris based on similar expression patterns in response to various environmental and genetic changes. Expression levels of all HK and RR genes were measured using whole-genome microarrays. Five groups of HK-RR genes not linked on the chromosome were identified as possible cognate pairs in D. vulgaris. The results provided a preliminary list of possible cognate HK-RR pairs and constitute a basis for further exploration of interaction and physiological function of TCSTSs in D. vulgaris.

Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI)

A field-scale acetate amendment experiment was performed in a contaminated aquifer at Old Rifle, CO to stimulate in situ microbial reduction of U(VI) in groundwater. To evaluate the microorganisms responsible for microbial uranium reduction during the experiment, 13C-labeled acetate was introduced into well bores via bio-traps containing porous activated carbon beads (Bio-Sep). Incorporation of the 13C from labeled acetate into cellular DNA and phospholipid fatty acid (PLFA) biomarkers was analyzed in parallel with geochemical parameters. An enrichment of active sigma-proteobacteria was demonstrated in downgradient monitoring wells: Geobacter dominated in wells closer to the acetate injection gallery, while various sulfate reducers were prominent in different downgradient wells. These results were consistent with the geochemical evidence of Fe(III), U(VI), and SO(4)2- reduction. PLFA profiling of bio-traps suspended in the monitoring wells also showed the incorporation of 13C into bacterial cellular lipids. Community composition of downgradient monitoring wells based on quinone and PLFA profiling was in general agreement with the 13C-DNA result. The direct application of 13C label to biosystems, coupled with DNA and PLFA analysis,

Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations

Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insights into the metabolic mechanisms underlying complex biological systems. However, because mRNA and protein abundance are affected by many cellular and physical processes, there have been conflicting results on their correlation. Using whole-genome microarray and LC-MS/MS proteomic data collected from Desulfovibrio vulgaris grown under three different conditions, we systematically investigate the relationship between mRNA and protein abundance by a multiple regression approach, in which some of the key covariates that may affect mRNA-protein relationship were included. The results showed that mRNA abundance alone can explain only 20-28% of the total variation of protein abundance, suggesting mRNA-protein correlation can not be determined by mRNA abundance alone. Among various covariates, analytic variation of protein abundance is the major source for the variation of mRNA-protein correlation, which contributes to 34-44% of the total variation of mRNA-protein correlation. The cellular functional category of genes/proteins contributes 10-15% of the total variation of mRNA-protein correlation, with a more pronounced correlation of the two properties was observed for "central intermediary metabolism" and "energy metabolism" categories. In addition, protein stability also contributes 5% of the total variation of mRNA-protein correlation. The study presents the first quantitative analysis of the contributions of various biochemical and physical sources to the correlation of mRNA and protein abundance in D. vulgaris.

Biological and chemical interactions with U(VI) during anaerobic enrichment in the presence of iron oxide coated quartz

Microcosm experiments were performed to understand chemical and biological interactions with hexavalent uranium (U(VI)) in the presence of iron oxide bearing minerals and trichloroethylene (TCE) as a co-contaminant. Interactions of U(VI) and hydrous iron oxide moieties on the mineral oxide surfaces were studied during enrichments for dissimilatory iron reducing (DIRB) and sulfate reducing bacteria (SRB). Microbes enriched from groundwater taken from the Test Area North (TAN) site at the Idaho National Laboratory (INL) were able to reduce the U(VI) in the adsorption medium as well as the iron on quartz surfaces. Early in the experiment disappearance of U(VI) from solution was a function of chemical interactions since no microbial activity was evident. Abiotic removal of U(VI) was enhanced in the presence of carbonate. As the experiment proceeded, further removal of U(VI) from solution was associated with the fermentation of lactate to propionate and acetate. During later phases of the experiment when lactate was depleted from the growth medium in the microcosm containing the DIRB enrichments, U(VI) concentrations in the solution phase increased until additional lactate was added. When additional lactate was added and fermentation proceeded, U(VI) concentrations in the liquid phase again returned to near zero. Similar results were shown for the SRB enrichment but lower uranium concentrations were seen in the liquid phase, while in the enrichment with carbonate a similar increase in uranium concentration was not seen. Chemical and biological interactions appear to be important on the mobilization/immobilization of U(VI) in an iron oxide system when TCE is present as a co-contaminant. Interestingly, TCE present in the microcosm experiments was not dechlorinated which was probably an effect of redox conditions that were unsuitable for reductive dechlorination by the microbial culture tested.

Cadmium accumulation and DNA homology with metal resistance genes in sulfate-reducing bacteria

Cadmium resistance (0.1 to 1.0 mM) was studied in four pure and one mixed culture of sulfate-reducing bacteria (SRB). The growth of the bacteria was monitored with respect to carbon source (lactate) oxidation and sulfate reduction in the presence of various concentrations of cadmium chloride. Two strains Desulfovibrio desulfuricans DSM 1926 and Desulfococcus multivorans DSM 2059 showed the highest resistance to cadmium (0.5 mM). Transmission electron microscopy of the two strains showed intracellular and periplasmic accumulation of cadmium. Dot blot DNA hybridization using the probes for the smtAB, cadAC, and cadD genes indicated the presence of similar genetic determinants of heavy metal resistance in the SRB tested. DNA sequencing of the amplified DNA showed strong nucleotide homology in all the SRB strains with the known smtAB genes encoding synechococcal metallothioneins. Protein homology with the known heavy metal-translocating ATPases was also detected in the cloned amplified DNA of Desulfomicrobium norvegicum I1 and Desulfovibrio desulfuricans DSM 1926, suggesting the presence of multiple genetic mechanisms of metal resistance in the two strains.