Integrated Field Research Challenge Site Research Articles

Stress-related ecophysiology of members of the genus Rhodanobacter isolated from a mixed waste contaminated subsurface

This work examines the physiologic basis of stress tolerance in bacterial strains of the genus Rhodanobacter that dominate in the acidic and highly metal contaminated near-source subsurface zone of the Oak Ridge Integrated Field Research Challenge (ORIFRC) site. Tolerance of R. denitrificans to levels of different stresses were studied in synthetic groundwater medium and R2A broth. Two strains of R. denitrificans, strains 2APBS1T and 116–2, tolerate low to circumneutral pH (4-8), high Uranium (1 mmol/L), elevated levels of nitrate (400 mmol/L) and high NaCl (2.5%). A combination of physiologic traits, such as growth at low pH, increased growth in the presence of high organics concentration, and tolerance of high concentrations of nitrate, NaCl and heavy metals is likely responsible for dominance of Rhodanobacter at the ORIFRC site. Furthermore, extended incubation times and use of low carbon media, better approximating site groundwater conditions, are critical for accurate determination of stress responses. This study expands knowledge of the ecophysiology of bacteria from the genus Rhodanobacter and identifies methodological approaches necessary for acquiring accurate tolerance data.

Efficacy of acetate-amended biostimulation for uranium sequestration: Combined analysis of sediment/groundwater geochemistry and bacterial community structure

Systematic flow-through column experiments were conducted using sediments and ground water collected from different subsurface localities at the U.S. Department of Energy's Integrated Field Research Challenge site in Rifle, Colorado. The principal purpose of this study is to gain a better understanding of the interactive effects of groundwater geochemistry, sediment mineralogy, and indigenous bacterial community structures on the efficacy of uranium removal from the groundwater with/without acetate amendment. Overall, we find that the subtle variations in the sediments' mineralogy, redox conditions, as well as contents of metal(loid) co-contaminants showed a pronounced effect on the associated bacterial population and composition, which mainly determines the system's performance with respect to uranium removal. Positive relationship was identified between the abundance of dissimilatory sulfate-reduction genes (i.e., drsA), markers of sulfate-reducing bacteria, and the sediments' propensity to sequester aqueous uranium. In contrast, no obvious connections were observed between the abundance of common iron-reducing bacteria, e.g., Geobacter spp., and the sediments' ability to sequester uranium. In the sediments with low bacterial biomass and the absence of sulfate-reducing conditions, abiotic adsorption onto mineral surfaces such as phyllosilicates likely played a relatively major role in the attenuation of aqueous uranium; however, in these scenarios, acetate amendment induced detectable rebounds in the effluent uranium concentrations. The results of this study suggest that immobilization of uranium can be achieved under predominantly sulfate-reducing conditions, and provide insight into the integrated roles of various biogeochemical components in long-term uranium sequestration.

Speciation and reactivity of uranium products formed during in situ bioremediation in a shallow alluvial aquifer.

In this study, we report the results of in situ U(VI) bioreduction experiments at the Integrated Field Research Challenge site in Rifle, Colorado, USA. Columns filled with sediments were deployed into a groundwater well at the site and, after a period of conditioning with groundwater, were amended with a mixture of groundwater, soluble U(VI), and acetate to stimulate the growth of indigenous microorganisms. Individual reactors were collected as various redox regimes in the column sediments were achieved: (i) during iron reduction, (ii) just after the onset of sulfate reduction, and (iii) later into sulfate reduction. The speciation of U retained in the sediments was studied using X-ray absorption spectroscopy, electron microscopy, and chemical extractions. Circa 90% of the total uranium was reduced to U(IV) in each reactor. Noncrystalline U(IV) comprised about two-thirds of the U(IV) pool, across large changes in microbial community structure, redox regime, total uranium accumulation, and reaction time. A significant body of recent research has demonstrated that noncrystalline U(IV) species are more suceptible to remobilization and reoxidation than crystalline U(IV) phases such as uraninite. Our results highlight the importance of considering noncrystalline U(IV) formation across a wide range of aquifer parameters when designing in situ remediation plans.

Long-term kinetics of uranyl desorption from sediments under advective conditions

Long-term (>4 months) column experiments were performed to investigate the kinetics of uranyl (U(VI)) desorption in sediments collected from the Integrated Field Research Challenge site at the U.S. Department of Energy Hanford 300 Area. The experimental results were used to evaluate alternative multirate surface complexation reaction (MRSCR) approaches to describe the short and long-term kinetics of U(VI) desorption under flow conditions. The surface complexation reaction (SCR) stoichiometry and equilibrium constants and multirate parameters in the MRSCR models were independently characterized in batch and stirred flow-cell reactors. MRSCR models that were either additively constructed using the MRSCRs for individual size fractions, or composite in nature, could effectively describe short-term U(VI) desorption under flow conditions. The long-term desorption results, however, revealed that using the labile U concentration measured by carbonate extraction underestimated desorbable U(VI) and the long-term rate of U(VI) desorption. This study also found that the gravel size fraction (2–8 mm), which is typically treated as nonreactive in modeling U(VI) reactive transport because of low external surface area, can have an important effect on the U(VI) desorption in the sediment. This study demonstrates an approach to effectively extrapolate U(VI) desorption kinetics for field-scale application and identifies important parameters and uncertainties affecting model predictions.

Geochemical and mineralogical investigation of uranium in multi-element contaminated, organic-rich subsurface sediment

Subsurface regions of alluvial sediments characterized by an abundance of refractory or lignitic organic carbon compounds and reduced Fe and S bearing minerals, which are referred to as naturally reduced zones (NRZ), are present at the Integrated Field Research Challenge site in Rifle, CO (a former U mill site), and other contaminated subsurface sites. A study was conducted to demonstrate that the NRZ contains a variety of contaminants and unique minerals and potential contaminant hosts, investigate micron-scale spatial association of U with other co-contaminants, and determine solid phase-bounded U valence state and phase identity. The NRZ sediment had significant solid phase concentrations of U and other co-contaminants suggesting competing sorption reactions and complex temporal variations in dissolved contaminant concentrations in response to transient redox conditions, compared to single contaminant systems. The NRZ sediment had a remarkable assortment of potential contaminant hosts, such as Fe oxides, siderite, Fe(II) bearing clays, rare solids such as ZnS framboids and CuSe, and, potentially, chemically complex sulfides. Micron-scale inspections of the solid phase showed that U was spatially associated with other co-contaminants. High concentration, multi-contaminant, micron size (ca. 5–30μm) areas of mainly U(IV) (53–100%) which occurred as biogenic UO2 (82%), or biomass – bound monomeric U(IV) (18%), were discovered within the sediment matrix confirming that biotically induced reduction and subsequent sequestration of contaminant U(VI) via natural attenuation occurred in this NRZ. A combination of assorted solid phase species and an abundance of redox-sensitive constituents may slow U(IV) oxidation rates, effectively enhancing the stability of U(IV) sequestered via natural attenuation, impeding rapid U flushing, and turning NRZs into sinks and long-term, slow-release sources of U contamination to groundwater.

Effects of dissimilatory sulfate reduction on FeIII (hydr)oxide reduction and microbial community development

Although dissimilatory iron and sulfate reduction (DIR and DSR) profoundly affect the biogeochemical cycling of C, Fe, and S in subsurface systems, the dynamics of DIR and DSR in the presence of both FeIII (hydr)oxides and sulfate have not been well-studied with mixed microbial populations. This study examined the response of native microbial communities in subsurface sediment from the U.S. Department of Energy’s Integrated Field Research Challenge site in Rifle, CO to the availability of sulfate and specific FeIII (hydr)oxide minerals in experimental systems containing lactate as the electron donor, with ferrihydrite, goethite, or lepidocrocite and high (10.2mM) or low (0.2mM) sulfate as electron acceptors. We observed rapid fermentation of lactate to acetate and propionate. FeIII reduction was slow and limited in the presence of low-sulfate, but the extent of FeIII reduction increased more than 10 times with high-sulfate amendments. Furthermore, the extent of FeIII reduction was higher in ferrihydrite or lepidocrocite incubations than in goethite incubations. Propionate produced during fermentation of lactate was used as the electron donor for DSR. The concurrence of sulfate reduction and FeII production suggests that FeII production was driven primarily by reduction of FeIII by biogenic sulfide. X-ray absorption fine-structure analysis confirmed the formation of ferrous sulfide and the presence of O-coordinated ferrous species. 16S rRNA-based microbial community analysis revealed the development of distinct communities with different FeIII (hydr)oxides. These results highlight the highly coupled nature of C, Fe, and S biogeochemical cycles during DIR and DSR and provide new insight into the effects of electron donor utilization, sulfate concentration, and the presence of specific FeIII (hydr)oxide phases on microbial community development.

Geochemical and geophysical responses during the infiltration of fresh water into the contaminated saprolite of the Oak Ridge Integrated Field Research Challenge site, Tennessee

At the Oak Ridge Integrated Field Research Challenge (IFRC) site, Tennessee, the saprolitic aquifer was contaminated by leaks from the former S‐3 disposal ponds between 1951 and 1983. The chemistry of the contaminant plume is also episodically impacted by fresh meteoritic water infiltrating vertically from a shallow variably saturated perched zone and the ditch surrounding the former S‐3 ponds. We performed a column experiment using saprolite from the contaminated aquifer to understand the geochemical and complex electrical conductivity signatures associated with such events. The changes in the pH and pore water ionic strength are responsible for measurable changes in both the in‐phase and quadrature conductivities. The pore water conductivity can be related to the nitrate concentration (the main ionic species in the plume) while the release of uranium is controlled by the pH. We developed a simple model to determine the pore water conductivity and pH from the recorded complex conductivity. This model is applied to time‐lapse resistivity data at the IFRC site. Time‐lapse inversion of resistivity data, performed with an active time constrain approach, shows the occurrence of an infiltration event during the winter of 2008–2009 with a dilution of the pore water chemistry and an increase of the pH. A simple numerical simulation of the infiltration of fresh water into the unconfined contaminated aquifer is consistent with this scenario.

Genome Sequences for Three Denitrifying Bacterial Strains Isolated from a Uranium- and Nitrate-Contaminated Subsurface Environment

Genome sequences for three strains of denitrifying bacteria (Alphaproteobacteria—Afipia sp. strain 1NLS2 and Hyphomicrobium denitrificans strain 1NES1; Firmicutes—Bacillus sp. strain 1NLA3E) isolated from the nitrate- and uranium-contaminated subsurface of the Oak Ridge Integrated Field Research Challenge (ORIFRC) site, Oak Ridge Reservation, TN, are reported.

Hydrogeophysical investigations of the former S-3 ponds contaminant plumes, Oak Ridge Integrated Field Research Challenge site, Tennessee

At the Oak Ridge Integrated Field Research Challenge site, near Oak Ridge, Tennessee, contaminants from the former S-3 ponds have infiltrated the shallow saprolite for over 60 years. Two- and three-dimensional DC-resistivity tomography is used to characterize the number and location of the main contaminant plumes, which include high concentration of nitrate. These contaminant plumes have typically an electrical resistivity in the range 2–20 ohm-m while the background saprolite resistivity is in the range 60–120 ohm-m, so the difference of resistivity can be easily mapped using DC-resistivity tomography to locate the contaminant pathways. We develop a relationship to derive the in situ nitrate concentrations from the 3D resistivity tomograms accounting for the effect of surface conductivity. The footprint of the contamination upon the resistivity is found to be much stronger than the local variations associated with changes in the porosity and the clay content. With this method, we identified a total of five main plumes (termed CP1 to CP5). Plume CP2 corresponds to the main plume in terms of nitrate concentration (∼50,000 [Formula: see text]). We also used an active time constrained approach to perform time-lapse resistivity tomography over a section crossing the plumes CP1 and CP2. The sequence of tomograms is used to determine the changes in the nitrate concentrations associated with infiltration of fresh (meteoritic) water from a perched aquifer. This study highlights the importance of accounting for surface conductivity when characterizing plume distributions in clay-rich subsurface systems.

Time‐lapse spectral induced polarization imaging of stimulated uranium bioremediation

ABSTRACTTomographic measurements of the spectral induced polarization (SIP) response of aquifer sediments were conducted at the U.S. Department of Energy’s (DOE) Integrated Field Research Challenge site (IFRC) in Rifle, Colorado (USA), where biostimulation research is ongoing with the purpose to immobilize uranium in tailings‐contaminated groundwater. The aims of the SIP surveys were to (a) collect data over a sufficiently broad bandwidth so as to determine the characteristic frequency of the spectral response (at which the strongest polarization response takes places), (b) investigate the distribution of spectral parameters (e.g., characteristic time constant) in an imaging framework and (c) evaluate the potential of these images to delineate changes in the hydraulic properties of the aquifer. Careful field procedures provided high‐quality SIP data from 0.060–256 Hz for three different periods during the remediation experiment. Data quality was evaluated by means of analysis of the discrepancy between normal and reciprocal measurements. A Cole‐Cole model was fitted to pixel values extracted from the inverted images in order to assess changes in the SIP response – particularly in time constant () and chargeability (m) – due to processes accompanying the stimulation of subsurface microbial activity. A significant increase in both and m was observed after halting acetate injection, consistent with the accumulation of semi‐conductive minerals (e.g., FeS) during biostimulation and the post‐injection rebound in aqueous Fe(II). The reliability of the imaged spectral parameters was assessed by means of a numerical study.

Spatial Distribution of Geobacteraceae and Sulfate‐Reducing Bacteria During In Situ Bioremediation of Uranium‐Contaminated Groundwater

AbstractAnalysis of the physiological status of subsurface microbial communities generally relies on the study of unattached microorganisms in the groundwater. These approaches have been employed in studies on bioremediation of uranium‐contaminated groundwater at a study site in Rifle, Colorado, in which Geobacter species typically account for over 90 percent of the microbial community in the groundwater during active uranium reduction. However, to develop efficient in situ bioremediation strategies it is necessary to know the status of sediment‐associated microorganisms as well. In order to evaluate the distribution of the natural community of Geobacter during bioremediation of uranium, subsurface sediments were packed into either passive flux meters (PFMs) or sediment columns deployed in groundwater monitoring wells prior to acetate injection during in situ biostimulation field trials. The trials were performed at the Department of Energy's (DOE's) Rifle Integrated Field Research Challenge site. Sediment samples were removed either during the peak of Fe(III) reduction or the peak of sulfate reduction over the course of two separate field experiments and preserved for microscopy. Direct cell counts using fluorescence in situ hybridization (FISH) probes targeting Geobacter species indicated that the majority of Geobacter cells were unattached during Fe(III) reduction, which typically tracks with elevated rates of uranium reduction. Similar measurements conducted during the sulfate‐reducing phase revealed the majority of Geobacter to be attached following exhaustion of more readily bioavailable forms of iron minerals. Laboratory sediment column studies confirmed observations made with sediment samples collected during field trials and indicated that during Fe(III) reduction, Geobacter species are primarily unattached (90 percent), whereas the majority of sulfate‐reducing bacteria and Geobacter species are attached to sediment surfaces when sulfate reduction is the predominant form of metabolism (75 percent and 77 percent, respectively). In addition, artificial sediment experiments showed that pure cultures of Geobacter uraniireducens, isolated from the Rifle site, were primarily unattached once Fe(III) became scarce. These results demonstrate that, although Geobacter species must directly contact Fe(III) oxides in order to reduce them, cells do not firmly attach to the sediments, which is likely an adaptive response to sparsely and heterogeneously dispersed Fe(III) minerals in the subsurface. © 2013 Wiley Periodicals, Inc.

No Measurable Changes in 238U/235U due to Desorption–Adsorption of U(VI) from Groundwater at the Rifle, Colorado, Integrated Field Research Challenge Site

Groundwater samples were collected from the Integrated Field Research Challenge field site in Rifle, Colorado, over the course of a bicarbonate-induced U desorption-adsorption experiment. Uranium concentrations and high precision U isotopic compositions ((238)U/(235)U) of these groundwater samples were determined and used to assess the impact of bicarbonate-induced U(VI) desorption from contaminated sediments on the (238)U/(235)U of groundwater. The (238)U/(235)U of groundwater was not significantly impacted by bicarbonate-induced desorption of U(VI) from mineral surfaces or by adsorption of advecting U(VI) from upgradient locations onto those surfaces after the treatment. Assuming this absence of a significant shift in U isotopic composition associated with desorption-adsorption applies to other systems, reduction of U(VI) to U(IV) is expected to be the dominant source of U isotopic fractionation associated with removal of U(VI) from pore water as a result of natural and stimulated reductive pathways. Thus, changes in the (238)U/(235)U composition of uranium-bearing fluids should be useful in quantifying the extent of reduction.

Petrophysical properties of saprolites from the Oak Ridge Integrated Field Research Challenge site, Tennessee

At the Oak Ridge Integrated Field Research Challenge site, near Oak Ridge, Tennessee, the shallow saprolitic aquifer is contaminated by nitric acid, uranium, and metals originating from the former S3 settling ponds. To interpret low-frequency geophysical methods used to image contaminant plumes, we have characterized the petrophysical properties of three representative saprolite core samples. Their hydraulic conductivity ranges from [Formula: see text] to [Formula: see text] in agreement with field data. Complex conductivity measurements, in the frequency range of 1 mHz to 45 kHz, were performed with NaCl solutions with electrical conductivities in the range [Formula: see text] to [Formula: see text], a range representative of field conditions. The electrical conductivity data were well reproduced with a simple linear conductivity model between the saprolite conductivity and the pore water conductivity. The conductivity plots were used to estimate the formation factor (the cementation exponent was about [Formula: see text]) and the surface conductivity ([Formula: see text]). The magnitude of the surface conductivity depended on the degree of weathering and therefore on the amount of smectite and mixed layer (illite-smectite) clays present in the saprolite. The chargeability of the core samples was in the range of [Formula: see text] and is strongly dependent on the salinity. We also performed streaming potential measurements with the same pore fluid composition as that used for the complex conductivity measurements. We found an excess of movable electrical charges on the order of 100 to [Formula: see text] in agreement with previous investigations connecting the movable excess charge density to permeability. The zeta potential was in the range of [Formula: see text] to [Formula: see text] independent on the salinity. The electrical measurements were consistent with an average cation exchange capacity in the range of 1.4 to [Formula: see text] and a specific surface area on the order of 4000 to about 30,000 [Formula: see text].

Long-term electrical resistivity monitoring of recharge-induced contaminant plume behavior

Geophysical measurements, and electrical resistivity tomography (ERT) data in particular, are sensitive to properties that are related (directly or indirectly) to hydrological processes. The challenge is in extracting information from geophysical data at a relevant scale that can be used to gain insight about subsurface behavior and to parameterize or validate flow and transport models. Here, we consider the use of ERT data for examining the impact of recharge on subsurface contamination at the S-3 ponds of the Oak Ridge Integrated Field Research Challenge (IFRC) site in Tennessee. A large dataset of time-lapse cross-well and surface ERT data, collected at the site over a period of 12months, is used to study time variations in resistivity due to changes in total dissolved solids (primarily nitrate). The electrical resistivity distributions recovered from cross-well and surface ERT data agrees well, and both of these datasets can be used to interpret spatiotemporal variations in subsurface nitrate concentrations due to rainfall, although the sensitivity of the electrical resistivity response to dilution varies with nitrate concentration. Using the time-lapse surface ERT data interpreted in terms of nitrate concentrations, we find that the subsurface nitrate concentration at this site varies as a function of spatial position, episodic heavy rainstorms (versus seasonal and annual fluctuations), and antecedent rainfall history. These results suggest that the surface ERT monitoring approach is potentially useful for examining subsurface plume responses to recharge over field-relevant scales.

Utility of bromide and heat tracers for aquifer characterization affected by highly transient flow conditions

A tracer test using both bromide and heat tracers conducted at the Integrated Field Research Challenge site in Hanford 300 Area (300A), Washington, provided an instrument for evaluating the utility of bromide and heat tracers for aquifer characterization. The bromide tracer data were critical to improving the calibration of the flow model complicated by the highly dynamic nature of the flow field. However, most bromide concentrations were obtained from fully screened observation wells, lacking depth‐specific resolution for vertical characterization. On the other hand, depth‐specific temperature data were relatively simple and inexpensive to acquire. However, temperature‐driven fluid density effects influenced heat plume movement. Moreover, the temperature data contained “noise” caused by heating during fluid injection and sampling events. Using the hydraulic conductivity distribution obtained from the calibration of the bromide transport model, the temperature depth profiles and arrival times of temperature peaks simulated by the heat transport model were in reasonable agreement with observations. This suggested that heat can be used as a cost‐effective proxy for solute tracers for calibration of the hydraulic conductivity distribution, especially in the vertical direction. However, a heat tracer test must be carefully designed and executed to minimize fluid density effects and sources of noise in temperature data. A sensitivity analysis also revealed that heat transport was most sensitive to hydraulic conductivity and porosity, less sensitive to thermal distribution factor, and least sensitive to thermal dispersion and heat conduction. This indicated that the hydraulic conductivity remains the primary calibration parameter for heat transport.

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.

Rate‐limited U(VI) desorption during a small‐scale tracer test in a heterogeneous uranium‐contaminated aquifer

A tracer test was performed at the Rifle Integrated Field Research Challenge site to assess the effect of addition of bicarbonate on U(VI) desorption from contaminated sediments in the aquifer and to compare equilibrium and rate‐limited reactive transport model descriptions of mass transfer limitations on desorption. The tracer test consisted of injection of a 37 mM NaHCO3solution containing conservative tracers followed by down‐gradient sampling of groundwater at various elevations and distances from the point of injection. Breakthrough curves show that dissolved U(VI) concentrations increased 1.2–2.6‐fold above background levels, resulting from increases in bicarbonate alkalinity (from injectate solution) and Ca concentrations (from cation exchange). In general, more U(VI) was mobilized in shallower zones of the aquifer, where finer‐grained sediments and higher solid phase U content were found compared to deeper zones. An equilibrium‐based reactive transport model incorporating a laboratory‐based surface complexation model derived from the same location predicted the general trends in dissolved U(VI) during the tracer test but greatly overpredicted the concentrations of U(VI), indicating that the system was not at equilibrium. Inclusion of a multirate mass transfer model successfully simulated the nonequilibrium desorption behavior of U(VI). Local sediment properties such as sediment texture (weight percent <2 mm), surface area, cation exchange capacity, and adsorbed U(VI) were heterogeneous at the meter scale, and it was important to incorporate these values into model parameters in order to produce accurate simulations.

Cooperation of Three Denitrifying Bacteria in Nitrate Removal of Acidic Nitrate- and Uranium-Contaminated Groundwater

In uranium-contaminated aquifers co-contaminated with nitrate, denitrifiers play a critical role in bioremediation. Six strains of denitrifying bacteria belonging to Rhizobium, Pseudomonas, and Castellaniella were isolated from the Oak Ridge Integrated Field Research Challenge Site (OR-IFRC), where biostimulation of acidic (pH 3.5–6.5), nitrate-contaminated (up to 140 mM) groundwater occurred. Three isolates were characterized in regards to nitrite tolerance, denitrification kinetic parameters, and growth on different denitrification intermediates. Kinetic and growth experiments showed that Pseudomonas str. GN33#1 reduced NO− 3 most rapidly (Vmax = 15.8 μmol e−·min−1·mg protein−1) and had the fastest generation time (gt) on NO− 3 (2.6 h). Castellaniella str. 4.5A2 was the most low pH and NO− 2 tolerant and grew rapidly on NO− 2 (gt = 4.0 h). Rhizobium str. GN32#2 was also tolerant of low pH values and reduced NO− 2 rapidly (Vmax = 10.6 μmol e−·min−1·mg protein−1) but was far less NO− 2 tolerant than Castellaniella str. 4.5A2. Growth of and denitrification by these three strains incubated together and individually were measured in OR-IFRC groundwater at pHs 5 and 7 to determine whether they cooperate or compete during denitrification. Mixed assemblages reduced NO− 3 more rapidly and more completely than any individual isolate over the course of the experiment. The results described in this article demonstrate 1) that this synthetic assemblage comprised of three physiologically distinct denitrifying bacterial isolates cooperate to achieve more complete levels of denitrification and 2) the importance of pH- and nitrite-tolerant bacteria such as Castellaniella str. 4.5A2 in minimizing NO− 2 accumulation in high-NO− 3 groundwater during bioremediation. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files.

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.

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.