Unique ecophysiology among U(VI)-reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter dehalogenans strain 2CP-C.

Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2x10(7)+/-8.6x10(6) to 1.0x10(8)+/-2.2x10(7) cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3x10(4)+/-1.1x10(4) cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [micro=(-0.09xpO2)+0.051; R2=0.923] was observed between the instantaneous specific growth rate micro and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. dehalogenans from other known U(VI)-reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.

Microbial activity and distribution during enhanced contaminant dissolution from a NAPL source zone.

Laboratory experiments were conducted to assess microbial reductive dechlorination in one-dimensional sand columns containing a 10 cm long source zone of uniformly distributed residual tetrachloroethene (PCE) nonaqueous phase liquid (NAPL), a 10 cm long transition zone directly down-gradient of the source zone containing some nonuniformly distributed NAPL ganglia, and a 40 cm long plume region down-gradient of the transition zone. The activity and distribution of Sulfurospirillum multivorans, a PCE-to-1,2-cis-dichloroethene (cis-DCE) dechlorinating bacterium, was evaluated in columns containing either a mixed-NAPL (0.25 mol/mol PCE in hexadecane) or pure PCE-NAPL. Significant dechlorination of PCE to cis-DCE was observed in the mixed-NAPL column, resulting in 53% PCE-NAPL mass recovery in the effluent with PCE-NAPL dissolution enhanced by up to 13.6-fold (maximum) and 4.6-fold (cumulative) relative to abiotic dissolution. Quantitative real-time PCR targeting pceA, the PCE reductive dehalogenase gene of S. multivorans, revealed that S. multivorans cells were present in the NAPL source zone, and increased in numbers (i.e., grew) throughout the source and transition zones. In contrast, minimal reductive dechlorination and microbial growth were observed in the column containing pure PCE-NAPL, where aqueous-phase PCE concentrations reached saturation. These results demonstrate that microbial growth within NAPL source zones is possible, provided that contaminant concentrations remain below levels toxic to the dechlorinating organisms, and that microbial growth can result in significant bioenhanced NAPL dissolution.

Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: model validation and sensitivity analysis.

Reductive dechlorination catalyzed by organohalide-respiring bacteria is often considered for remediation of non-aqueous phase liquid (NAPL) source zones due to cost savings, ease of implementation, regulatory acceptance, and sustainability. Despite knowledge of the key dechlorinators, an understanding of the processes and factors that control NAPL dissolution rates and detoxification (i.e., ethene formation) is lacking. A recent column study demonstrated a 5-fold cumulative enhancement in tetrachloroethene (PCE) dissolution and ethene formation (Amos et al., 2009). Spatial and temporal monitoring of key geochemical and microbial (i.e., Geobacter lovleyi and Dehalococcoides mccartyi strains) parameters in the column generated a data set used herein as the basis for refinement and testing of a multiphase, compositional transport model. The refined model is capable of simulating the reactive transport of multiple chemical constituents produced and consumed by organohalide-respiring bacteria and accounts for substrate limitations and competitive inhibition. Parameter estimation techniques were used to optimize the values of sensitive microbial kinetic parameters, including maximum utilization rates, biomass yield coefficients, and endogenous decay rates. Comparison and calibration of model simulations with the experimental data demonstrate that the model is able to accurately reproduce measured effluent concentrations, while delineating trends in dechlorinator growth and reductive dechlorination kinetics along the column. Sensitivity analyses performed on the optimized model parameters indicate that the rates of PCE and cis-1,2-dichloroethene (cis-DCE) transformation and Dehalococcoides growth govern bioenhanced dissolution, as long as electron donor (i.e., hydrogen flux) is not limiting. Dissolution enhancements were shown to be independent of cis-DCE accumulation; however, accumulation of cis-DCE, as well as column length and flow rate (i.e., column residence time), strongly influenced the extent of reductive dechlorination. When cis-DCE inhibition was neglected, the model over-predicted ethene production ten-fold, while reductions in residence time (i.e., a two-fold decrease in column length or two-fold increase in flow rate) resulted in a more than 70% decline in ethene production. These results suggest that spatial and temporal variations in microbial community composition and activity must be understood to model, predict, and manage bioenhanced NAPL dissolution.

Spatial and temporal distributions of Geobacter lovleyi and Dehalococcoides spp. during bioenhanced PCE-NAPL dissolution.

The spatial and temporal distributions of multiple reductively dechlorinating bacteria were simultaneously assessed in a one-dimensional sand column containing a tetrachloroethene (PCE) nonaqueous phase liquid (NAPL) source and associated plume zones. The column was uniformly inoculated with a PCE-to-ethene dechlorinating microbial consortium that contained Dehalococcoides spp., Dehalobacter spp., and Geobacter lovleyi strain SZ. Geobacter and Dehalococcoides populations grew and colonized the column material, including the mixed-NAPL (0.25 mol/mol PCE in hexadecane) source zone. In contrast, Dehalobacter cells did not colonize the porous column material, and planktonic Dehalobacter cell titers remained below the detection limit of ca. 2.6 x 10(2) cells/mL throughout the experiment. Significant PCE dechlorination was observed and resulted in bioenhanced NAPL dissolution up to 21-fold (maximum) and 5.2-fold (cumulative) relative to abiotic dissolution. cis-1,2-Dichloroethene (cis-DCE) wasthe primary dechlorination product although vinyl chloride (VC) was also formed throughout the experiment. Ethene production occurred after significant depletion of PCE from the NAPL and when cis-DCE concentrations dropped below 6 microM. Data obtained after increasing the column residence time from 1.1 to 2.8 days and introducing a VC pulse to the column indicated that both the residence time and cis-DCE inhibition limited significant VC and ethene production. Although both Geobacter and Dehalococcoides cells were present and active in the mixed-NAPL source zone and plume region, Geobacter cell numbers were typically more than 1 order of magnitude higher than Dehalococcoides cell numbers, which is consistent with the production of predominantly cis-DCE. Analysis of both liquid- and solid-phase samples indicated that Geobacter cells grew and remained attached to the porous medium within the source zone but were largely planktonic in the plume region. In contrast Dehalococcoides cell were attached throughoutthecolumn,and Dehalococcoides cell titers increased by 1 to 2 orders of magnitude over the length of the column, correlating to increases in VC concentrations. The results from this study highlight that bioenhanced dissolution is governed by a complex interplay between resident dechlorinators, contaminant concentrations, and other aquifer-specific characteristics (e.g., hydrology).

Oxygen effect on Dehalococcoides viability and biomarker quantification.

Oxygen-sensitive Dehalococcoides bacteria play crucial roles in detoxification of chlorinated contaminants (e.g., chlorinated ethenes), and bioremediation monitoring relies on quantification of Dehalococcoides DNA and RNA biomarkers. To explore the effects of oxygen on Dehalococcoides activity, viability, and biomarker quantification, batch experiments with a tetrachloroethene-to-ethene dechlorinating consortium (Bio-Dechlor INOCULUM [BDI]) harboring multiple Dehalococcoides strains were performed to quantify the effects of < or = 4 mg/L dissolved oxygen. Oxygen inhibited reductive dechlorination, and only incomplete dechlorination to vinyl chloride (VC) occurred following oxygen consumption and extended incubation periods (89 days). Following 30 days of oxygen exposure and subsequent oxygen removal (i.e., reversibility experiments), all trichloroethene- (TCE-) fed cultures dechlorinated TCE to VC, but VC dechlorination to ethene occurred in only one out of fourteen replicates. These results suggest that Dehalococcoides strains respond differently to oxygen exposure, and strains catalyzing the VC-to-ethene dechlorination step are more susceptible to oxygen inhibition. Quantitative real-time PCR (qPCR) analysis detected a 1-1.5 order-of-magnitude decrease in the number of Dehalococcoides biomarker genes (i.e., 16S rRNA gene and the reductive dehalogenase [RDase] genes tceA, vcrA, bvcA) in the oxygen-amended cultures, but qPCR analysis failed to distinguish viable, dechlorinating from irreversibly inhibited (nonviable) Dehalococcoides cells. Reverse transcriptase qPCR (RT-qPCR) detected Dehalococcoides gene transcripts in the oxygen-amended, non-dechlorinating cultures, and biomarker transcription did not always correlate with dechlorination (in)activity. Enhanced molecular tools that complement existing protocols and provide quantitative information on the viability and activity of the Dehalococcoides population are desirable.

Experimental evaluation and mathematical modeling of microbially enhanced tetrachloroethene (PCE) dissolution.

Experiments to assess metabolic reductive dechlorination (chlororespiration) at high concentration levels consistent with the presence of free-phase tetrachloroethene (PCE) were performed using three PCE-to-cis-1,2-dichloroethene (cis-DCE) dechlorinating pure cultures (Sulfurospirillum multivorans, Desulfuromonas michiganensis strain BB1, and Geobacter lovleyi strain SZ) and Desulfitobacterium sp. strain Viet1, a PCE-to-trichloroethene (TCE) dechlorinating isolate. Despite recent evidence suggesting bacterial PCE-to-cis-DCE dechlorination occurs at or near PCE saturation (0.9-1.2 mM), all cultures tested ceased dechlorinating at approximately 0.54 mM PCE. In the presence of PCE dense nonaqueous phase liquid (DNAPL), strains BB1 and SZ initially dechlorinated, but TCE and cis-DCE production ceased when aqueous PCE concentrations reached inhibitory levels. For S. multivorans, dechlorination proceeded at a rate sufficient to maintain PCE concentrations below inhibitory levels, resulting in continuous cis-DCE production and complete dissolution of the PCE DNAPL. A novel mathematical model, which accounts for loss of dechlorinating activity at inhibitory PCE concentrations, was developed to simultaneously describe PCE-DNAPL dissolution and reductive dechlorination kinetics. The model predicted that conditions corresponding to a bioavailability number (Bn) less than 1.25 x 10(-2) will lead to dissolution enhancement with the tested cultures, while conditions corresponding to a Bn greater than this threshold value can result in accumulation of PCE to inhibitory dissolved-phase levels, limiting PCE transformation and dissolution enhancement. These results suggest that microorganisms incapable of dechlorinating at high PCE concentrations can enhance the dissolution and transformation of PCE from free-phase DNAPL.

Effects of the nonionic surfactant tween 80 on microbial reductive dechlorination of chlorinated ethenes.

Recent field studies have indicated synergistic effects of coupling microbial reductive dechlorination with physicochemical remediation (e.g., surfactant flushing) of dense nonaqueous phase liquid (DNAPL) source zones. This study explored chlorinated ethene (e.g., tetrachloroethene [PCE]) dechlorination in the presence of 50-5000 mg/L Tween 80, a nonionic surfactant employed in source zone remediation. Tween 80 did not inhibit dechlorination by four pure PCE-to-cis-1,2-dichloroethene (cis-DCE) or PCE-to-trichloroethene (TCE) dechlorinating cultures. In contrast, cis-DCE-dechlorinating Dehalococcoides isolates (strain BAV1 and strain FL2) failed to dechlorinate in the presence of Tween 80. Bio-Dechlor INOCULUM (BDI), a PCE-to-ethene dechlorinating consortium, produced cis-DCE in the presence of Tween 80, further suggesting that Tween 80 inhibits dechlorination by Dehalococcoides organisms. Quantitative real-time PCR analysis applied to BDI revealed that the number of Dehalococcoides cells decayed exponentially (R(2) = 0.85) according to the Chick-Watson disinfection model (pseudo first-order decay rate of 0.13+/-0.02 day(-1)) from an initial value of 6.6 +/-1.5 x 10(8) to 1.3+/-0.8 x 10(5) per mL of culture after 58 days of exposure to 250 mg/L Tween 80. Although Tween 80 exposure prevented ethene formation and reduced Dehalococcoides cell numbers, Dehalococcoides organisms remained viable, and dechlorination activity pist cis-DCE was recovered following the removal of Tween 80. These findings suggest that sequential Tween 80 flushing followed by microbial reductive dechlorination is a promising strategy for remediation of chlorinated ethene-impacted source zones.

Hexavalent uranium supports growth of Anaeromyxobacter dehalogenans and Geobacter spp. with lower than predicted biomass yields.

The stimulation of bacteria capable of reducing soluble U(VI) to sparingly soluble U(IV) is a promising approach for containing U(VI) plumes. Anaeromyxobacter dehalogenans is capable of mediating this activity; however, its ability to couple U(VI) reduction to growth has not been established. Monitoring the increase in 16S rRNA gene copy numbers using quantitative real-time PCR (qPCR) in cultures provided with U(VI) as an electron acceptor demonstrated growth, and 7.7-8.6 x 10(6) cells were produced per mumole of U(VI) reduced. This biomass yield was lower than predicted based on the theoretical free energy changes associated with U(VI)-to-U(IV) reduction. Lower than predicted growth yields with U(VI) as electron acceptor were also determined in cultures of Geobacter lovleyi and Geobacter sulfurreducens suggesting that U(VI) reduction is inefficient or imposes an additional cost to growing cells. These findings have implications for U(VI) bioremediation because Anaeromyxobacter spp. and Geobacter spp. contribute to radionuclide immobilization in contaminated subsurface environments.

Detection and quantification of Geobacter lovleyi strain SZ: implications for bioremediation at tetrachloroethene- and uranium-impacted sites.

Geobacter lovleyi strain SZ reduces hexavalent uranium, U(VI), to U(IV) and is the first member of the metal-reducing Geobacter group capable of using tetrachloroethene (PCE) as a growth-supporting electron acceptor. Direct and nested PCR with specific 16S rRNA gene-targeted primer pairs distinguished strain SZ from other known chlorinated ethene-dechlorinating bacteria and closely related Geobacter isolates, including its closest cultured relative, G. thiogenes. Detection limits for direct and nested PCR were approximately 1 x 10(6) and 1 x 10(4) 16S rRNA gene copies per mul of template DNA, respectively. A quantitative real-time PCR (qPCR) approach increased the sensitivity to as few as 30 16S rRNA gene copies per mul of template DNA but was less specific. Melting curve analysis and comparison of the shapes of amplification plots identified false-positive signals and distinguished strain SZ from G. thiogenes when analyzed separately. These indicators were less reliable when target (strain SZ) DNA and nontarget (G. thiogenes) DNA with high sequence similarity were mixed, indicating that the development of qPCR protocols should not only evaluate specificity but also explore the effects of nontarget DNA on the accuracy of quantification. Application of specific tools detected strain SZ-like amplicons in PCE-dechlorinating consortia, including the bioaugmentation consortium KB-1, and two chlorinated ethene-impacted groundwater samples. Strain SZ-like amplicons were also detected in 13 of 22 groundwater samples following biostimulation at the uranium- and chlorinated solvent-contaminated Integrated Field-Scale Subsurface Research Challenge (IFC) site in Oak Ridge, TN. The numbers of strain SZ-like cells increased from below detection to 2.3 x 10(7) +/- 0.1 x 10(7) per liter groundwater, suggesting that strain SZ-like organisms contribute to contaminant transformation. The G. lovleyi strain SZ-specific tools will be useful for monitoring bioremediation efforts at uranium- and/or chlorinated solvent-impacted sites such as the Oak Ridge IFC site.

Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains.

The 16S rRNA gene provides insufficient information to infer the range of chloroorganic electron acceptors used by different Dehalococcoides organisms. To overcome this limitation and provide enhanced diagnostic tools for growth measurements, site assessment, and bioremediation monitoring, a quantitative real-time PCR (qPCR) approach targeting 16S rRNA genes and three Dehalococcoides reductive dehalogenase (RDase) genes with assigned function (i.e., tceA, bvcA, and vcrA) was designed and evaluated. qPCR standard curves generated for the RDase genes by use of genomic DNA from Dehalococcoides pure cultures correlated with standard curves obtained for both Bacteria- and Dehalococcoides-targeted 16S rRNA genes, suggesting that the RDase genes are useful targets for quantitative assessment of Dehalococcoides organisms. RDase gene probe/primer pairs were specific for the Dehalococcoides strains known to carry the diagnostic RDase gene sequences, and the qPCR method allowed the detection of as few as 1 to 20 and quantification of as few as 50 to 100 tceA, bvcA, or vcrA gene targets per PCR volume. The qPCR approach was applied to dechlorinating enrichment cultures, microcosms, and samples from a contaminated site. In characterized enrichment cultures where known Dehalococcoides strains were enumerated, the sum of the three RDase genes equaled the total Dehalococcoides cell numbers. In site samples and chloroethane-dechlorinating microcosms, the sum of the three RDase genes was much less than that predicted by Dehalococcoides-targeted qPCR, totaling 10 to 30% of the total Dehalococcoides cell numbers. Hence, a large number of Dehalococcoides spp. contain as-yet-unidentified RDase genes, indicating that our current understanding of the dechlorinating Dehalococcoides community is incomplete.

Activity of Desulfitobacterium sp. strain Viet1 demonstrates bioavailability of 2,4-dichlorophenol previously sequestered by the aquatic plant Lemna minor.

Aquatic plants take up and sequester organic contaminants such as chlorophenols through incorporation in cell wall materials and storage in vacuoles. The ultimate fate of plant-sequestered chlorophenols, however, remains unclear. This research investigated 2,4-dichlorophenol (2,4-DCP) sequestration by the aquatic plant Lemna minor and evaluated contaminant release and bioavailability after plant death and cellular disruption. 14C-labeled 2,4-DCP was used to establish that contaminant removed from the aqueous phase was retained internal to L. minor. An assay with Desulfitobacterium sp. strain Viet1 was used to assess the readily bioavailable fraction of plant-sequestered 2,4-DCP and plant metabolites of 2,4-DCP. In plant-free systems, strain Viet1 dechlorinated 2,4-DCP to stoichiometric amounts of 4-chlorophenol (4-CP) as a stable and quantifiable end product. Anaerobic microcosms containing inactivated L. minor, which had accumulated 3.8 micromol of 2,4-DCP equivalents/g of plant material (fresh weight) during a preceding aerobic exposure, were inoculated with strain Viet1. After 118 d of incubation with strain Viet1, 43.5% (+/-1.4%) of the contaminant was recovered as 4-CP, indicating a large portion of plant-sequestered 2,4-DCP was bioavailable for dechlorination by strain Viet1. In contrast, 4-CP formation was not observed in autoclaved microcosms, and only 26.1% (+/-1.0%) of plant-sequestered 2,4-DCP was recovered in the aqueous phase. These findings demonstrate contaminant cycling between plants and microorganisms, and emphasize that understanding the mechanisms and pathways of contaminant sequestration by plants is critical for predicting long-term contaminant fate.

Stimulated microbial reductive dechlorination following surfactant treatment at the Bachman Road site.

A pilot-scale demonstration of surfactant-enhanced aquifer remediation (SEAR) was conducted in July 2000 at the Bachman Road site located in Oscoda, MI. The Bachman aquifer is a shallow, relatively homogeneous, unconfined aquifer formation composed primarily of sandy glacial outwash with relatively low organic carbon content (0.02 wt %). A 6 wt % aqueous solution of Tween 80 (a nonionic, food-grade surfactant) was flushed through a localized dense nonaqueous phase liquid (DNAPL) source zone to recover approximately 19 L of tetrachloroethene (PCE). Post-treatment monitoring revealed PCE concentrations were reduced by up to 2 orders of magnitude within the source zone, and there was no evidence of concentration rebound after more than 450 d. Concentrations of PCE dechlorination products (trichloroethene, cis-1,2-dichloroethene) 450 d after SEAR operations ceased were more than 2 orders of magnitude greater than pretreatment values, suggesting stimulation of native dechlorination activity. Post-treatment monitoring detected increased concentrations of volatile fatty acids generated from the fermentation of residual-level Tween 80 surfactant. These field data suggest that Tween 80 not only induced and maintained anaerobiosis but also provided reducing equivalents to reductively dechlorinating populations present in the oligotrophic Bachman aquifer. Experience from this site supports application of staged treatment strategies that couple SEAR and microbial reductive dechlorination to enhance mass removal and reduce contaminant mass flux emanating from treated source zones.