Bioaugmentation for chlorinated ethene detoxification: Bioaugmentation and molecular diagnostics in the bioremediation of chlorinated ethene-contaminated sites

An innovative permeable reactive bio-barrier to remediate trichloroethene-contaminated groundwater: A field study

Permeable reactive bio-barrier (PRBB), an innovative technology, could treat many contaminants via the natural gradient flow of groundwater based on immobilization or transformation of pollutants into less toxic and harmful forms. In this field study, we developed an innovative PRBB system comprising immobilized Dehalococcoides mccartyi (Dhc) and Clostridium butyricum embedded into the silica gel for long-term treatment of trichloroethene (TCE) polluted groundwater. Four injection wells and two monitoring wells were installed at the downstream of the TCE plume. Without PRBB, results showed that the TCE (6.23 ± 0.43 μmole/L) was converted to cis-dichloroethene (0.52 ± 0.63 μmole/L), and ethene was not detected, whereas TCE was completely converted to ethene (3.31 μmole/L) with PRBB treatment, indicating that PRBB could promote complete dechlorination of TCE. Noticeably, PRBB showed the long-term capability to maintain a high dechlorinating efficiency for TCE removal during the 300-day operational period. Furthermore, with qPCR analysis, the PRBB application could stably maintain the populations of Dhc and functional genes (bvcA, tceA, and vcrA) at >108 copies/L within the remediation course and change the bacterial communities in the contaminated groundwater. We concluded that our PRBB was first set up for cleaning up TCE-contaminated groundwater in a field trial.

Decoupling Fe0 Application and Bioaugmentation in Space and Time Enables Microbial Reductive Dechlorination of Trichloroethene to Ethene: Evidence from Soil Columns

Fe⁰ is a powerful chemical reductant with applications for remediation of chlorinated solvents, including tetrachloroethene and trichloroethene. Its utilization efficiency at contaminated sites is limited because most of the electrons from Fe⁰ are channeled to the reduction of water to H₂ rather than to the reduction of the contaminants. Coupling Fe⁰ with H₂-utilizing organohalide-respiring bacteria (i.e., Dehalococcoides mccartyi) could enhance trichloroethene conversion to ethene while maximizing Fe⁰ utilization efficiency. Columns packed with aquifer materials have been used to assess the efficacy of a treatment combining in space and time Fe⁰ and aD. mccartyi-containing culture (bioaugmentation). To date, most column studies documented only partial conversion of the solvents to chlorinated byproducts, calling into question the feasibility of Fe⁰ to promote complete microbial reductive dechlorination. In this study, we decoupled the application of Fe⁰ in space and time from the addition of organic substrates andD. mccartyi-containing cultures. We used a column containing soil and Fe⁰ (at 15 g L^-1 in porewater) and fed it with groundwater as a proxy for an upstream Fe⁰ injection zone dominated by abiotic reactions and biostimulated/bioaugmented soil columns (Bio-columns) as proxies for downstream microbiological zones. Results showed that Bio-columns receiving reduced groundwater from the Fe⁰-column supported microbial reductive dechlorination, yielding up to 98% trichloroethene conversion to ethene. The microbial community in the Bio-columns established with Fe⁰-reduced groundwater also sustained trichloroethene reduction to ethene (up to 100%) when challenged with aerobic groundwater. This study supports a conceptual model where decoupling the application of Fe⁰ and biostimulation/bioaugmentation in space and/or time could augment microbial trichloroethene reductive dechlorination, particularly under oxic conditions.

Biotrickling Filtration for the Reduction of N2O Emitted during Wastewater Treatment: Results from a Long-Term In Situ Pilot-Scale Testing

Wastewater treatment plants (WWTPs) are a major source of N₂O, a potent greenhouse gas with 300 times higher global warming potential than CO₂. Several approaches have been proposed for mitigation of N₂O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining biotrickling filtration, an end-of-the-pipe treatment technology, was tested in situ at a full-scale WWTP under realistic operational conditions. Temporally varying untreated wastewater was used as trickling medium, and no temperature control was applied. The off-gas from the covered WWTP aerated section was conveyed through the pilot-scale reactor, and an average removal efficiency of 57.9 ± 29.1% was achieved during 165 days of operation despite the generally low and largely fluctuating influent N₂O concentrations (ranging between 4.8 and 96.4 ppmv). For the following 60-day period, the continuously operated reactor system removed 43.0 ± 21.2% of the periodically augmented N₂O, exhibiting elimination capacities as high as 5.25 g N₂O m^-3·h^-1. Additionally, the bench-scale experiments performed abreast corroborated the resilience of the system to short-term N₂O starvations. Our results corroborate the feasibility of biotrickling filtration for mitigating N₂O emitted from WWTPs and demonstrate its robustness toward suboptimal field operating conditions and N₂O starvation, as also supported by analyses of the microbial compositions and nosZ gene profiles.

Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing

Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.

Anaerobic microbial dehalogenation and its key players in the contaminated Bitterfeld-Wolfen megasite

The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins. Various methods and concepts were applied including ex situ cultivation and isolation, and in situ analysis of hydrochemical parameters, compound-specific stable isotope analysis of contaminants, 13C-tracer studies and molecular markers. Overall, biotransformation of organohalides is ongoing at the field site and Dehalococcoides mccartyi species play an important role in the detoxification process in the Bitterfeld-Wolfen region.

Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns

The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems. Bioaugmentation of one column of each treatment with Bachman Road enrichment culture did not change Dhc populations nor the eventual degree of TCE dehalogenation. Pyrosequencing revealed high diversity among Dhc strains. There were 13 OTUs that were represented by more than 1000 sequences each. Cornell group-related populations dominated in complete TCE dehalogenating columns, while Pinellas group related Dhc dominated in all other treatments. General microbial communities varied with biostimulation, and three distinct microbial communities were established: one each for whey, oils, and control treatments. Bacterial genera, including Dehalobacter, Desulfitobacterium, Sulfurospirillum, Desulfuromonas, and Geobacter, all capable of partial TCE dehalogenation, were abundant in the limited and partial TCE dehalogenating systems. Dhc strain diversity was wider than previously reported and their composition within the community varied significantly depending on the nature of the carbon source applied and/or changes in the Dhc associated partners that fostered different biogeochemical conditions across the columns.

Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.

Dehalococcoides abundance and alternate electron acceptor effects on large, flow-through trichloroethene dechlorinating columns

Trichloroethene (TCE) in groundwater is a major health concern and biostimulation/bioaugmentation-based strategies have been evaluated to achieve complete reductive dechlorination with varying success. Different carbon sources were hypothesized to stimulate different extents of TCE reductive dechlorination. Ecological conditions that developed different dechlorination stages were investigated by quantitating Dehalococcoides 16S rRNA (Dhc) and reductive dehalogenase gene abundance, and by describing biogeochemical properties of laboratory columns in response to this biostimulation. Eight large columns (183 cm × 15.2 cm), packed with aquifer material from Hill AFB, Utah, that were continuously fed TCE for 7.5 years. Duplicate columns were biostimulated with whey or one of two different Newman Zone® emulsified oil formulations containing either nonionic surfactant (EOLN) or standard surfactant (EOL). Two columns were non-stimulated controls. Complete (whey amended), partial (EOLN amended), limited (EOL), and non-TCE dehalogenating systems (controls) developed over the course of the study. Bioaugmentation of half of the columns with Bachman Road culture 3 years prior to dismantling did not influence the extent of TCE dehalogenation. Multivariate analysis clustered samples by biostimulation treatments and extent of TCE dehalogenation. Dhc, tceA, and bvcA gene concentrations did not show a consistent relationship with TCE dehalogenation but the vcrA gene was more abundant in completely dehalogenating, whey-treated columns. The whey columns developed strongly reducing conditions producing Fe(II), sulfide, and methane. Biostimulation with different carbon and energy sources can support high concentrations of diverse Dhc, but carbon addition has a major influence on biogeochemical processes effecting the extent of TCE dehalogenation.

Distribution of organohalide-respiring bacteria between solid and aqueous phases

Contemporary microbial monitoring of aquifers relies on groundwater samples to enumerate nonattached cells of interest. One-dimensional column studies quantified the distribution of bacterial cells in solid and the aqueous phases as a function of microbial species, growth substrate availability and porous medium (i.e., Appling soil versus Federal Fine Ottawa sand with 0.75% and 0.01% [w/w] organic carbon, respectively). Without supplied growth substrates, effluent from columns inoculated with the tetrachloroethene- (PCE-) to-ethene-dechlorinating bacterial consortium BDI-SZ containing Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ), or inoculated with Anaeromyxobacter dehalogenans strain W (AdehalW), captured 94-96, 81-99, and 73-84% of the Dhc, GeoSZ, and AdehalW cells, respectively. Cell retention was organism-specific and increased in the order Dhc < GeoSZ < AdehalW. When amended with 10 mM lactate and 0.11 mM PCE, aqueous samples accounted for 1.3-27 and 0.02-22% of the total Dhc and GeoSZ biomass, respectively. In Appling soil, up to three orders-of-magnitude more cells were associated with the solid phase, and attachment rate coefficients (katt) were consistently greater compared to Federal Fine sand. Cell-solid interaction energies ranged from -2.5 to 787 kT and were consistent with organism-specific deposition behavior, where GeoSZ and AdehalW exhibited greater attachment than Dhc cells. The observed disparities in microbial cell distributions between the aqueous and solid phases imply that groundwater analysis can underestimate the total cell abundance in the aquifer by orders-of-magnitude under conditions of growth and in porous media with elevated organic carbon content. The implications of these findings for monitoring chlorinated solvent sites are discussed.

Bioaugmentation with distinct Dehalobacter strains achieves chloroform detoxification in microcosms

Chloroform (CF) is a widespread groundwater contaminant not susceptible to aerobic degradation. Under anoxic conditions, CF can undergo abiotic and cometabolic transformation but detoxification is generally not achieved. The recent discovery of distinct Dehalobacter strains that respire CF to dichloromethane (DCM) and ferment DCM to nonchlorinated products promises that bioremediation of CF plumes is feasible. To track both strains, 16S rRNA gene-based qPCR assays specific for either Dehalobacter strain were designed and validated. A laboratory treatability study explored the value of bioaugmentation and biostimulation to achieve CF detoxification using anoxic microcosms established with aquifer material from a CF-contaminated site. Microcosms that received 6% (v/v) of the CF-to-DCM-dechlorinating culture Dhb-CF to achieve an initial Dehalobacter cell titer of 1.6 ± 0.9 × 10(4) mL(-1) dechlorinated CF to stoichiometric amounts of DCM. Subsequent augmentation with 3% (v/v) of the DCM-degrading consortium RM to an initial Dehalobacter cell abundance of 1.2 ± 0.2 × 10(2) mL(-1) achieved complete DCM degradation in microcosms amended with 10 mM bicarbonate. Growth of the CF-respiring and the DCM-degrading Dehalobacter populations and detoxification were also observed in microcosms that received both inocula simultaneously. These findings suggest that anaerobic bioremediation (e.g., bioaugmentation) is a possible remedy at CF- and DCM-contaminated sites without CT, which strongly inhibited CF organohalide respiration and DCM organohalide fermentation.

Dechlorination and organohalide-respiring bacteria dynamics in sediment samples of the Yangtze Three Gorges Reservoir

Several groups of bacteria such as Dehalococcoides spp., Dehalobacter spp., Desulfomonile spp., Desulfuromonas spp., or Desulfitobacterium spp. are able to dehalogenate chlorinated pollutants such as chloroethenes, chlorobenzenes, or polychlorinated biphenyls under anaerobic conditions. In order to assess the dechlorination potential in Yangtze sediment samples, the presence and activity of the reductively dechlorinating bacteria were studied in anaerobic batch tests. Eighteen sediment samples were taken in the Three Gorges Reservoir catchment area of the Yangtze River, including the tributaries Jialing River, Daning River, and Xiangxi River. Polymerase chain reaction analysis indicated the presence of dechlorinating bacteria in most samples, with varying dechlorinating microbial community compositions at different sampling locations. Subsequently, anaerobic reductive dechlorination of tetrachloroethene (PCE) was tested after the addition of electron donors. Most cultures dechlorinated PCE completely to ethene via cis-dichloroethene (cis-DCE) or trans-dichloroethene. Dehalogenating activity corresponded to increasing numbers of Dehalobacter spp., Desulfomonile spp., Desulfitobacterium spp., or Dehalococcoides spp. If no bacteria of the genus Dehalococcoides spp. were present in the sediment, reductive dechlorination stopped at cis-DCE. Our results demonstrate the presence of viable dechlorinating bacteria in Yangtze samples, indicating their relevance for pollutant turnover.

Quantifying the effects of 1,1,1-trichloroethane and 1,1-dichloroethane on chlorinated ethene reductive dehalogenases

Mixtures of chlorinated ethenes and ethanes are often found at contaminated sites. In this study, we undertook a systematic investigation of the inhibitory effects of 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA) on chlorinated ethene dechlorination in three distinct Dehalococcoides-containing consortia. To focus on inhibition acting directly on the reductive dehalogenases, dechlorination assays used cell-free extracts prepared from cultures actively dechlorinating trichloroethene (TCE) to ethene. The dechlorination assays were initiated with TCE, cis-1,2-dichloroethene (cDCE), or vinyl chloride (VC) as substrates and either 1,1,1-TCA or 1,1-DCA as potential inhibitors. 1,1,1-TCA inhibited VC dechlorination similarly in cell suspension and cell-free extract assays, implicating an effect on the VC reductases associated with the dechlorination of VC to nontoxic ethene. Concentrations of 1,1,1-TCA in the range of 30-270 μg/L reduced VC dechlorination rates by approximately 50% relative to conditions without 1,1,1-TCA. 1,1,1-TCA also inhibited reductive dehalogenases involved in TCE and cDCE dechlorination. In contrast, 1,1-DCA had no pronounced inhibitory effects on chlorinated ethene reductive dehalogenases, indicating that removal of 1,1,1-TCA via reductive dechlorination to 1,1-DCA is a viable strategy to relieve inhibition.

Stable carbon isotope enrichment factors for cis-1,2-dichloroethene and vinyl chloride reductive dechlorination by Dehalococcoides

Compound-specific stable isotope analysis (CSIA) is a promising tool for monitoring in situ microbial activity, and enrichment factors (ε values) determined using CSIA can be employed to estimate compound transformation. Although ε values for some dechlorination reactions catalyzed by Dehalococcoides (Dhc) have been reported, reproducibility between independent experiments, variability between different Dhc strains, and congruency between pure and mixed cultures are unknown. In experiments conducted with pure cultures of Dhc sp. strain BAV1, ε values for 1,1-DCE, cis-DCE, trans-DCE, and VC were -5.1, -14.9, -20.8, and -23.2‰, respectively. The ε value for 1,1-DCE dechlorination was 48.9% higher than the value reported in a previous study, but ε values for other chlorinated ethenes were equal between independent experiments. For the dechlorination of cis-DCE and VC by Dhc strains BAV1, FL2, GT, and VS, average ε values were -18.4 and -23.2‰, respectively. cis-DCE and VC ε values determined in pure Dhc cultures with different reductive dehalogenase genes (e.g., vcrA vs bvcA) varied by less than 36.8 and 8.3%, respectively. In the BDI consortium, ε values for cis-DCE and VC dechlorination were -25.3‰ and -19.9‰, 31.6% higher and 15.3% lower, respectively, compared to the average ε value for Dhc pure cultures. As cis-DCE and VC ε values are all within the same order-of-magnitude and fractionation is always measured during Dhc dechlorination, CSIA may be a valuable approach for monitoring in situ cis-DCE and VC reductive dechlorination.

Effects of elevated temperature on Dehalococcoides dechlorination performance and DNA and RNA biomarker abundance

Coupling thermal treatment with microbial reductive dechlorination is a promising remedy for tetrachloroethene (PCE) and trichloroethene (TCE) contaminated source zones. Laboratory experiments evaluated Dehalococcoides (Dhc) dechlorination performance, viability, and biomarker gene (DNA) and transcript (mRNA) abundances during exposure to elevated temperatures. The PCE-dechlorinating consortia BDI and OW produced ethene when incubated at temperatures of 30 °C, but vinyl chloride (VC) accumulated when cultures were incubated at 35 or 40 °C. Cultures incubated at 40 °C for less than 49 days resumed VC dechlorination following cooling; however, incubation at 45 °C resulted in complete loss of dechlorination activity. Dhc 16S rRNA, bvcA, and vcrA gene abundances in cultures showing complete dechlorination to ethene at 30 °C exceeded those measured in cultures incubated at higher temperatures, consistent with observed dechlorination activities. Conversely, biomarker gene transcript abundances per cell in cultures incubated at 35 and 40 °C were generally at least one order-of-magnitude greater than those measured in ethene-producing cultures incubated at 30 °C. Even in cultures accumulating VC, transcription of the vcrA gene, which is implicated in VC-to-ethene dechlorination, was up-regulated. Temperature stress caused the up-regulation of Dhc reductive dehalogenase gene expression indicating that Dhc gene expression measurements should be interpreted cautiously as Dhc biomarker gene transcript abundances may not correlate with dechlorination activity.

Tetrachloroethene conversion to ethene by a Dehalococcoides-containing enrichment culture from Bitterfeld

A Dehalococcoides-dominated culture coupling reductive dechlorination of tetrachloroethene (PCE) to ethene to growth was enriched from a European field site for the first time. Microcosms were set up using groundwater from a chlorinated ethene-contaminated anaerobic aquifer in Bitterfeld (Germany). Active, lactate-amended microcosms capable of PCE dechlorination to ethene without the accumulation of intermediates were used for further enrichment. After three transfers on lactate as an electron donor and PCE as an electron acceptor, the enrichment was transferred to parallel cultures with one of the chlorinated ethenes as an electron acceptor and acetate and hydrogen as the carbon and energy source, respectively. After three more transfers, a highly purified culture was derived that was capable of dechlorinating PCE with hydrogen and acetate as the electron donor and carbon source, respectively. PCR, followed by denaturing gradient gel electrophoresis, cloning and sequencing revealed that this culture was dominated by a Dehalococcoides sp. belonging to the Pinellas group. Investigation of substrate specificity in the parallel cultures suggested the presence of a novel Dehalococcoides that can couple all dechlorination steps, from PCE to ethene, to energy conservation. Quantitative real-time PCR confirmed growth with PCE, cis-dichloroethene, 1,1-dichloroethene or vinyl chloride as electron acceptors. The culture was designated BTF08 due to its origin in Bitterfeld.

Comparing on-site to off-site biomass collection for Dehalococcoides biomarker gene quantification to predict in situ chlorinated ethene detoxification potential

Biostimulation and bioaugmentation have emerged as constructive remedies for chlorinated ethene-contaminated aquifers, and a link between Dehalococcoides (Dhc) bacteria and chlorinated ethene detoxification has been established. To quantify Dhc biomarker genes, groundwater samples are shipped to analytical laboratories where biomass is collected on membrane filters by vacuum filtration for DNA extraction and quantitative real-time PCR analysis. This common practice was compared with a straightforward, on-site filtration approach to Sterivex cartridges. In initial laboratory studies with groundwater amended with known amounts of Dhc target cells, Sterivex cartridges yielded one-third of the total DNA and 9-18% of the Dhc biomarker gene copies compared with vacuum filtration. Upon optimization, DNA yields increased to 94 +/- 38% (+/-SD, n = 10), and quantification of Dhc biomarker genes exceeded the values obtained with the vacuum filtration procedure up to 5-fold. Both methods generated reproducible results when volumes containing >10(4) total Dhc target gene copies were collected. Analysis of on-site and off-site biomass collection procedures corroborated the applicability of the Sterivex cartridge for Dhc biomarker quantification in groundwater. Ethene formation coincided with Dhc cell titers of >2 x 10(6) L(-1) and high (i.e., >10(5)) abundance of the vinyl chloride reductive dehalogenase genes vcrA and/or bvcA; however, high Dhc cell titers alone were insufficient to predict ethene formation. Further, ethene formation occurred at sites with high Dhc cell titers but low or no detectable vcrA or bvcA genes, suggesting that other, not yet identified vinyl chloride reductive dehalogenases contribute to ethene formation. On-site biomass collection with Sterivex cartridges avoids problems associated with shipping groundwater and has broad applicability for biomarker monitoring in aqueous samples.

Bioaugmentation for chlorinated ethenes using Dehalococcoides sp.: comparison between batch and column experiments

Batch and column experiments were performed to evaluate the transport, growth and dechlorination activity of Dehalococcoides sp. (DHC) during bioaugmentation for chlorinated ethenes. Batch experiments showed that the reductive dechlorination of trichloroethene (TCE), cis-1,2-dichloroethene (DCE), and vinyl chloride (VC), as well as growth of the DHC, were well described by the Monod kinetic model. The measured maximum utilization rate coefficients for TCE, DCE, and VC were 1.3x10(-12), 5.2x10(-13), and 1.4x10(-12)mmol Cl(-) (cellh)(-1), respectively. Results of the column experiments showed that dechlorination occurred throughout the length of the column, and that extractable DHC concentrations associated with the soil phase throughout the column were negligible relative to the aqueous phase concentrations. Dechlorination rates relative to aqueous DHC concentrations in the column were approximately 200-times greater than in the batch experiments. Additional batch experiments performed using column effluent water confirmed this result. Incorporation of these enhanced dechlorination kinetics in the transport model provided a reasonable prediction of the column data. Overall results of this study suggest that aqueous phase (as opposed to soil phase) DHC concentrations can be used to estimate dechlorination activity in saturated soils, and DHC dechlorination activity in porous media may be substantially greater than DHC dechlorination activity measured in batch experiments.

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.

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.

Distinguishing abiotic and biotic transformation of tetrachloroethylene and trichloroethylene by stable carbon isotope fractionation

Significant carbon isotope fractionation was observed during FeS-mediated reductive dechlorination of tetrachloroethylene (PCE) and trichloroethylene (TCE). Bulk enrichment factors (E(bulk)) for PCE were -30.2 +/- 4.3 per thousand (pH 7), -29.54 +/- 0.83 per thousand (pH 8), and -24.6 +/- 1.1 per thousand (pH 9). For TCE, E(bulk) values were -33.4 +/- 1.5 per thousand (pH 8) and -27.9 +/- 1.3 per thousand (pH 9). A smaller magnitude of carbon isotope fractionation resulted from microbial reductive dechlorination by two isolated pure cultures (Desulfuromonas michiganensis strain BB1 (BB1) and Sulfurospirillum multivorans (Sm)) and a bacterial consortium (BioDechlor INOCULUM (BDI)). The E(bulk) values for biological PCE microbial dechlorination were -1.39 +/- 0.21 per thousand (BB1), -1.33 +/- 0.13 per thousand (Sm), and -7.12 +/- 0.72 per thousand (BDI), while those for TCE were -4.07 +/- 0.48 per thousand (BB1), -12.8 +/- 1.6 per thousand (Sm), and -15.27 +/- 0.79 per thousand (BDI). Reactions were investigated by calculation of the apparent kinetic isotope effect for carbon (AKIEc), and the results suggest that differences in isotope fractionation for abiotic and microbial dechlorination resulted from the differences in rate-limiting steps during the dechlorination reaction. Measurement of more negative E(bulk) values at sites contaminated with PCE and TCE may suggest the occurrence of abiotic reductive dechlorination by FeS.

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.

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.

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.

Harnessing microbial activities for environmental cleanup

Human activities have released large amounts of toxic organic and inorganic chemicals into the environment. Toxic waste streams threaten dwindling drinking water supplies and impact terrestrial, estuarine and marine ecosystems. Cleanup is technically challenging and the costs based on traditional technologies are exceeding the economic capabilities of even the richest countries. Recent advances in our understanding of the microbiology contributing to contaminant transformation and detoxification has led to successful field demonstrations. Hence, harnessing the activity of naturally occurring bacteria, particularly the power of anaerobic reductive processes, is a promising approach to restore contaminated subsurface environments, protect drinking water reservoirs and to safeguard ecosystem health.

Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate

A novel Dehalococcoides isolate capable of metabolic trichloroethene (TCE)-to-ethene reductive dechlorination was obtained from contaminated aquifer material. Growth studies and 16S rRNA gene-targeted analyses suggested culture purity; however, the careful quantitative analysis of Dehalococcoides 16S rRNA gene and chloroethene reductive dehalogenase gene (i.e., vcrA, tceA, and bvcA) copy numbers revealed that the culture consisted of multiple, distinct Dehalococcoides organisms. Subsequent transfers, along with quantitative PCR monitoring, yielded isolate GT, possessing only vcrA. These findings suggest that commonly used qualitative 16S rRNA gene-based procedures are insufficient to verify purity of Dehalococcoides cultures. Phylogenetic analysis revealed that strain GT is affiliated with the Pinellas group of the Dehalococcoides cluster and shares 100% 16S rRNA gene sequence identity with two other Dehalococcoides isolates, strain FL2 and strain CBDB1. The new isolate is distinct, as it respires the priority pollutants TCE, cis-1,2-dichloroethene (cis-DCE), 1,1-dichloroethene (1,1-DCE), and vinyl chloride (VC), thereby producing innocuous ethene and inorganic chloride. Strain GT dechlorinated TCE, cis-DCE, 1,1-DCE, and VC to ethene at rates up to 40, 41, 62, and 127 micromol liter-1 day-1, respectively, but failed to dechlorinate PCE. Hydrogen was the required electron donor, which was depleted to a consumption threshold concentration of 0.76+/-0.13 nM with VC as the electron acceptor. In contrast to the known TCE dechlorinating isolates, strain GT dechlorinated TCE to ethene with very little formation of chlorinated intermediates, suggesting that this type of organism avoids the commonly observed accumulation of cis-DCE and VC during TCE-to-ethene dechlorination.