Biogeochemical processes in ethanol stimulated uranium-contaminated subsurface sediments

Bibliometric insights into the evolution of uranium contamination reduction research topics: Focus on microbial reduction of uranium

Confronting the threat of environment uranium pollution, decades of research have yielded advanced and significant findings in uranium bioremediation, resulting in the accumulation of tremendous amount of high-quality literature. In this study, we analyzed over 10,000 uranium reduction-related papers published from 1990 to the present in the Web of Science based on bibliometrics, and revealed some critical information on knowledge structure, thematic evolution and additional attention. Methods including contribution comparison, co-occurrence and temporal evolution analysis are applied. The results of the distribution and impact analysis of authors, sources, and journals indicated that the United States is a leader in this field of research and China is on the rise. The top keywords remained stable, primarily focused on chemicals (uranium, iron, plutonium, nitrat, carbon), characters (divers, surfac, speciat), and microbiology (microbial commun, cytochrome, extracellular polymeric subst). Keywords related to new strains, reduction mechanisms and product characteristics demonstrated the strongest uptrend, while some keywords related to mechanism and performance were clearly emerging in the past 5 years. Furthermore, the evolution of the thematic progression can be categorized into three stages, commencing with the discovery of the enzymatic reduction of hexavalent uranium to tetravalent uranium, developing in the groundwater remediation process at uranium-contaminated sites, and delving into the research on microbial reduction mechanisms of uranium. For future research, enhancing the understanding of mechanisms, improving uranium removal performance, and exploring practical applications can be considered. This study provides unique insights into microbial uranium reduction research, providing valuable references for related studies in this field.

Towards sulfide removal and sulfate reducing bacteria inhibition: Function of biosurfactants produced by indigenous isolated nitrate reducing bacteria

The effectiveness of nitrate-mediated souring control highly depends on the interactions of sulfate reducing bacteria (SRB) and nitrate reducing bacteria (NRB). Biosurfactants produced by natural NRB are promising bio-agents for enhancing NRB competence towards SRB. However, the function of NRB-produced biosurfactants in NRB-SRB interactions remains unexplored due to the rarely successful isolation of natural biosurfactant-producing NRB. Hereby, biosurfactant-aided inhibitory control of SRB strain Desulfomicrobium escambiense ATCC 51164 by biosurfactant-producing NRB strain Pseudomonas stutzeri CX3, reported in our previous work, was investigated. Under non-sour conditions, insufficient nitrate injection resulted in limited SRB inhibition. Phospholipid fatty acid (PLFA) biomarkers traced the overall bacterial responses. Compositional PLFA patterns revealed biosurfactant addition benefitted both SRB and NRB towards stressful conditions. Under sour conditions, nitrite oxidation of sulfide proved to be the primary mechanism for sulfide removal. The subsequent elevation of redox potential and pH inhibited SRB activities. NRB-produced biosurfactants significantly enhanced SRB inhibition by NRB through more efficient sulfide removal and effective duration of nitrate in the microcosms. Biosurfactants specially produced by the NRB strain are for the first time reported to significantly strengthen SRB inhibition by NRB via reduced nitrate usage and prolonged effective duration of nitrate, which has encouraging potential in nitrate-dependent souring control.

Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation

Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.

Phospholipid fatty acid (PLFA) analysis for profiling microbial communities in offshore produced water

A method based on phospholipid fatty acid (PLFA) analysis for profiling microbial communities in offshore produced water was optimized. The operation parameters affecting final PLFA profiling performance from the solid phase extraction (SPE) purification and fatty acid methyl esters (FAMEs) yielding process were investigated. Under the selected conditions, 92.9%, 96.3% and 92.8% of the spiked phospholipid standards C16:1 (cis-9) PC, C18:1 (cis-9) PC, and C19:0 PC were recovered, respectively, using 10mL methanol as elution solvent on a non-commercial SPE column. Over 90% of spiked C19:0 PC was recovered before sample transesterification. Four parameters including alkaline reagent, volume of acid for neutralization, time and temperature for FAMEs derivatization were examined. Gas Chromatography-Mass Spectrometry (GC-MS) was used to analyze FAMEs and the method linearities, recoveries of 29 FAMEs during transesterification, detection limits, relative standard deviations were presented. The results provided valuable information for biological reservoir souring control.

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.

In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions

Reoxidation and mobilization of previously reduced and immobilized uranium by dissolved-phase oxidants poses a significant challenge for remediating uranium-contaminated groundwater. Preferential oxidation of reduced sulfur-bearing species, as opposed to reduced uranium-bearing species, has been demonstrated to limit the mobility of uranium at the laboratory scale yet field-scale investigations are lacking. In this study, the mobility of uranium in the presence of nitrate oxidant was investigated in a shallow groundwater system after establishing conditions conducive to uranium reduction and the formation of reduced sulfur-bearing species. A series of three injections of groundwater (200 L) containing U(VI) (5 μM) and amended with ethanol (40 mM) and sulfate (20 mM) were conducted in ten test wells in order to stimulate microbial-mediated reduction of uranium and the formation of reduced sulfur-bearing species. Simultaneous push-pull tests were then conducted in triplicate well clusters to investigate the mobility of U(VI) under three conditions: 1) high nitrate (120 mM), 2) high nitrate (120 mM) with ethanol (30 mM), and 3) low nitrate (2 mM) with ethanol (30 mM). Dilution-adjusted breakthrough curves of ethanol, nitrate, nitrite, sulfate, and U(VI) suggested that nitrate reduction was predominantly coupled to the oxidation of reduced-sulfur bearing species, as opposed to the reoxidation of U(IV), under all three conditions for the duration of the 36-day tests. The amount of sulfate, but not U(VI), recovered during the push-pull tests was substantially more than injected, relative to bromide tracer, under all three conditions and further suggested that reduced sulfur-bearing species were preferentially oxidized under nitrate-reducing conditions. However, some reoxidation of U(IV) was observed under nitrate-reducing conditions and in the absence of detectable nitrate and/or nitrite. This suggested that reduced sulfur-bearing species may not be fully effective at limiting the mobility of uranium in the presence of dissolved and/or solid-phase oxidants. The results of this field study confirmed those of previous laboratory studies which suggested that reoxidation of uranium under nitrate-reducing conditions can be substantially limited by preferential oxidation of reduced sulfur-bearing species.

Potential for microbial oxidation of ferrous iron in basaltic glass

Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and utilization of dissolved Fe(II) as an energy source is not likely to take place.

Effects of supplemental organic carbon on long-term reduction and reoxidation of uranium

Higher concentration of ethanol supported more extensive sulfate reduction to sulfide, which protected biogenic UO₂from oxidants reoxidation.

Fe-phyllosilicate redox cycling organisms from a redox transition zone in Hanford 300 Area sediments

Microorganisms capable of reducing or oxidizing structural iron (Fe) in Fe-bearing phyllosilicate minerals were enriched and isolated from a subsurface redox transition zone at the Hanford 300 Area site in eastern Washington, USA. Both conventional and in situ “i-chip” enrichment strategies were employed. One Fe(III)-reducing Geobacter (G. bremensis strain R1, Deltaproteobacteria) and six Fe(II) phyllosilicate-oxidizing isolates from the Alphaproteobacteria (Bradyrhizobium japonicum strains 22, is5, and in8p8), Betaproteobacteria (Cupriavidus necator strain A5-1, Dechloromonas agitata strain is5), and Actinobacteria (Nocardioides sp. strain in31) were recovered. The G. bremensis isolate grew by oxidizing acetate with the oxidized form of NAu-2 smectite as the electron acceptor. The Fe(II)-oxidizers grew by oxidation of chemically reduced smectite as the energy source with nitrate as the electron acceptor. The Bradyrhizobium isolates could also carry out aerobic oxidation of biotite. This is the first report of the recovery of a Fe(II)-oxidizing Nocardioides, and to date only one other Fe(II)-oxidizing Bradyrhizobium is known. The 16S rRNA gene sequences of the isolates were similar to ones found in clone libraries from Hanford 300 sediments and groundwater, suggesting that such organisms may be present and active in situ. Whole genome sequencing of the isolates is underway, the results of which will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with microbial phyllosilicate Fe redox cycling in sediments.

U(VI) reduction in sulfate-reducing subsurface sediments amended with ethanol or acetate

An experiment was conducted with subsurface sediments from Oak Ridge National Laboratory to determine the potential for reduction of U(VI) under sulfate-reducing conditions with either ethanol or acetate as the electron donor. The results showed extensive U(VI) reduction in sediments supplied with either electron donor, where geochemical and microbiological analyses demonstrated active sulfate reduction.

Isolation and microbial reduction of Fe(III) phyllosilicates from subsurface sediments

Fe(III)-bearing phyllosilicates can be important sources of Fe(III) for dissimilatory microbial iron reduction in clay-rich anoxic soils and sediments. The goal of this research was to isolate Fe(III) phyllosilicate phases, and if possible, Fe(III) oxide phases, from a weathered shale saprolite sediment in order to permit experimentation with each phase in isolation. Physical partitioning by density gradient centrifugation did not separate phyllosilicate and Fe(III) oxide phases (primarily nanoparticulate goethite). Hence we examined the ability of chemical extraction methods to remove Fe(III) oxides without significantly altering the properties of the phyllosilicates. XRD analysis showed that extraction with acid ammonium oxalate (AAO) or AAO in the presence of added Fe(II) altered the structure of Fe-bearing phyllosilicates in the saprolite. In contrast, citrate-dithionite-bicarbonate (CDB) extraction at room temperature or 80 °C led to minimal alteration of phyllosilicate structures. Reoxidation of CDB-extracted sediment with H(2)O(2) restored phyllosilicate mineral d-spacing and Fe redox speciation to conditions similar to that in the pristine sediment. The extent of microbial (Geobacter sulfurreducens) reduction of Fe(III) phyllosilicates isolated by CDB extraction and H(2)O(2) reoxidation (16 ± 3% reduction) was comparable to what took place in pristine sediments as determined by Mossbauer spectroscopy (20 ± 11% reduction). These results suggest that materials isolated by CDB extraction and H(2)O(2) reoxidation are appropriate targets for detailed studies of natural soil/sediment Fe(III) phyllosilicate reduction.

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.

Redox behavior of uranium at the nanoporous aluminum oxide-water interface: implications for uranium remediation

Sorption-desorption experiments show that the majority (ca. 80-90%) of U(VI) presorbed to mesoporous and nanoporous alumina could not be released by extended (2 week) extraction with 50 mM NaHCO(3) in contrast with non-nanoporous α alumina. The extent of reduction of U(VI) presorbed to aluminum oxides was semiquantitatively estimated by comparing the percentages of uranium desorbed by anoxic sodium bicarbonate between AH(2)DS-reacted and unreacted control samples. X-ray absorption spectroscopy confirmed that U(VI) presorbed to non-nanoporous alumina was rapidly and completely reduced to nanoparticulate uraninite by AH(2)DS, whereas reduction of U(VI) presorbed to nanoporous alumina was slow and incomplete (<5% reduction after 1 week). The observed nanopore size-dependent redox behavior of U has important implications in developing efficient remediation techniques for the subsurface uranium contamination because the efficiency of in situ bioremediation depends on how effectively and rapidly U(VI) bound to sediment or soil can be converted to an immobile phase.

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

This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil.

Linking specific heterotrophic bacterial populations to bioreduction of uranium and nitrate in contaminated subsurface sediments by using stable isotope probing

Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [¹³C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H(2), hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

16S rRNA gene microarray analysis of microbial communities in ethanol-stimulated subsurface sediment

A high-density 16S rRNA gene microarray was used to analyze microbial communities in a slurry of ethanol-amended, uranium-contaminated subsurface sediment. Of specific interest was the extent to which the microarray could detect temporal patterns in the relative abundance of major metabolic groups (nitrate-reducing, metal-reducing, sulfate-reducing, and methanogenic taxa) that were stimulated by ethanol addition. The results show that the microarray, when used in conjunction with geochemical data and knowledge of the physiological properties of relevant taxa, provided accurate assessment of the response of key functional groups to biostimulation.

Geobacter: the microbe electric's physiology, ecology, and practical applications

Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.

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).

Microbial reduction of uranium under iron- and sulfate-reducing conditions: Effect of amended goethite on microbial community composition and dynamics

There is a growing need for a better understanding of the biogeochemical dynamics involved in microbial U(VI) reduction due to an increasing interest in using biostimulation via electron donor addition as a means to remediate uranium contaminated sites. U(VI) reduction has been observed to be maximized during iron-reducing conditions and to decrease upon commencement of sulfate-reducing conditions. There are many unknowns regarding the impact of iron/sulfate biogeochemistry on U(VI) reduction. This includes Fe(III) availability as well as the microbial community changes, including the activity of iron-reducers during the uranium biostimulation period even after sulfate reduction becomes dominant. Column experiments were conducted with Old Rifle site sediments containing Fe-oxides, Fe-clays, and sulfate rich groundwater. Half of the columns had sediment that was augmented with small amounts of Fe(III) in the form of (57)Fe-goethite, allowing for a detailed tracking of minute changes of this added phase to study the effects of increased Fe(III) levels on the overall biostimulation dynamics. Mössbauer spectroscopy showed that the added (57)Fe-goethite was bioreduced only during the first thirty days of biostimultuion, after which it remained constant. Augmentation with Fe(III) had a significant effect on the total flux of electrons towards different electron acceptors; it suppressed the degree of sulfate reduction, had no significant impact on Geobacter-type bacterial numbers but decreased the bacterial numbers of sulfate reducers and affected the overall microbial community composition. The addition of Fe(III) had no noticeable effect on the total uranium reduction.

A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction

'Bioimmobilization' of redox-sensitive heavy metals and radionuclides is being investigated as a way to remediate contaminated groundwater and sediments. In one approach, growth-limiting substrates are added to the subsurface to stimulate the activity of targeted groups of indigenous microorganisms and create conditions favorable for the microbially-mediated reductive precipitation ('bioreduction') of targeted contaminants. We present a theoretical framework for modeling this process that modifies conventional geochemical reaction path modeling to include thermodynamic descriptions for microbial growth and may be called biogeochemical reaction path modeling. In this approach, the actual microbial community is represented by a synthetic microbial community consisting of a collection of microbial groups; each with a unique growth equation that couples a specific pair of energy yielding redox reactions. The growth equations and their computed standard-state free energy yields are appended to the thermodynamic database used in conventional geochemical reaction path modeling, providing a direct coupling between chemical species participating in both microbial growth and geochemical reactions. To compute the biogeochemical reaction paths, growth substrates are reacted incrementally with the defined geochemical environment and the coupled equations are solved simultaneously to predict reaction paths that display changing microbial biomass, community composition (i.e. the fraction of total biomass in each microbial group), and the aqueous and mineral composition of the system, including aqueous speciation and oxidation state of the targeted contaminants. The approach, with growth equations derived from the literature using well-known bioenergetics principles, was used to predict the results of a laboratory microcosm experiment and an in situ field experiment that investigated the bioreduction of uranium. Predicted effects of ethanol or acetate addition on uranium concentration and speciation, major ion geochemistry, mineralogy, microbial biomass and community composition were in qualitative agreement with experimental observations although the available data precluded rigorous model testing. While originally developed for use in better understanding of bioimmobilization of heavy metals and radionuclides, the modeling approach is potentially useful for exploring the coupling of microbial growth and geochemical reactions in a variety of other basic and applied biotechnology research settings.

Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library

Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.

Uranium transformations in static microcosms

Elucidation of complex biogeochemical processes and their effects on speciation of U in the subsurface is critical for developing remediation strategies with an understanding of stability. We have developed static microcosms that are similar to bioreduction process studies in situ under laminar flow conditions or in sediment pores. Uranium L(3)-edge X-ray absorption near-edge spectroscopy analysis with depth in the microcosms indicated that transformation of U(VI) to U(IV) occurred by at least two distinct processes. Extended X-ray absorption fine structure (EXAFS) analysis indicated that initial U(VI) species associated with C- and P-containing ligands were transformed to U(IV) in the form of uraninite and U associated with Fe-bound ligands. Microbial community analysis identified putative Fe(III) and sulfate reducers at two different depths in the microcosms. The slow reduction of U(VI) to U(IV) may contribute the stability of U(IV) within microcosms at 11 months after a decrease in bioreducing conditions due to limited electron donors.

Impact of biostimulated redox processes on metal dynamics in an iron-rich creek soil of a former uranium mining area

Understanding the dynamics of metals and radionuclides in soil environments is necessary for evaluating risks to pristine sites. An iron-rich creek soil of a former uranium-mining district (Ronneburg, Germany) showed high porewater concentrations of heavy metals and radionuclides. Thus, this study aims to (i) evaluate metal dynamics during terminal electron accepting processes (TEAPs) and (ii) characterize active microbial populations in biostimulated soil microcosms using a stable isotope probing (SIP) approach. In biostimulated soil slurries, concentrations of soluble Co, Ni, Zn, As, and unexpectedly U increased during Fe(III)-reduction. This suggests that there was a release of sorbed metals and As during reductive dissolution of Fe(III)-oxides. Subsequent sulfate-reduction was concurrent with a decrease of U, Co, Ni, and Zn concentrations. The relative contribution of U(IV) in the solid phase changed from 18.5 to 88.7% after incubation. The active Fe(III)-reducing population was dominated by delta-Proteobacteria (Geobacter) in (13)C-ethanol amended microcosms. A more diverse community was present in (13)C-lactate amended microcosms including taxa related to Acidobacteria, Firmicutes, delta-Proteobacteria, and beta-Proteobacteria. Our results suggested that biostimulated Fe(III)-reducing communities facilitated the release of metals including U to groundwater which is in contrast to other studies.

Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation

The increasing availability of the genome sequences of microorganisms involved in important bioremediation processes makes it feasible to consider developing genome-scale models that can aid in predicting the likely outcome of potential subsurface bioremediation strategies. Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction. Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation. In order to simplify the modelling, the influence of only three growth factors was considered: acetate, the electron donor added to stimulate U(VI) reduction; Fe(III), the electron acceptor primarily supporting growth of Geobacter; and ammonium, a key nutrient. The constraint-based model predicted that growth yields of Geobacter varied significantly based on the availability of these three growth factors and that there are minimum thresholds of acetate and Fe(III) below which growth and activity are not possible. This contrasts with typical, empirical microbial models that assume fixed growth yields and the possibility for complete metabolism of the substrates. The coupled genome-scale and reactive transport model predicted acetate concentrations and U(VI) reduction rates in a field trial of in situ uranium bioremediation that were comparable to the predictions of a calibrated conventional model, but without the need for empirical calibration, other than specifying the initial biomass of Geobacter. These results suggest that coupling genome-scale metabolic models with reactive transport models may be a good approach to developing models that can be truly predictive, without empirical calibration, for evaluating the probable response of subsurface microorganisms to possible bioremediation approaches prior to implementation.