Trichloroethene and cis-1,2-dichloroethene concentration-dependent toxicity model simulates anaerobic dechlorination at high concentrations. II: continuous flow and attached growth reactors

Exploration of processes governing microbial reductive dechlorination in a heterogeneous aquifer flow cell

Although microbial reductive dechlorination (MRD) has proven to be an effective approach for in situ treatment of chlorinated ethenes, field implementation of this technology is complicated by many factors, including subsurface heterogeneity, electron donor availability, and distribution of microbial populations. This work presents a coupled experimental and mathematical modeling study designed to explore the influence of heterogeneity on MRD and to assess the suitability of microcosm-derived rate parameters for modeling complex heterogeneous systems. A Monod-based model is applied to simulate a bioremediation experiment conducted in a laboratory-scale aquifer cell packed with aquifer material from the Commerce Street Superfund site in Williston, VT. Results reveal that (uncalibrated) model application of microcosm-derived dechlorination and microbial growth rates for transformation of trichloroethene (TCE), cis-1,2-dichloroethene (cis-DCE), and vinyl chloride (VC) reproduced observed aquifer cell concentration levels and trends. Mean relative errors between predicted and measured effluent concentrations were quantified as 6.7%, 27.0%, 41.5%, 32.0% and 21.6% over time for TCE, cis-DCE, VC, ethene and total volatile fatty acids (fermentable electron donor substrate and carbon source), respectively. The time-averaged extent of MRD (i.e., ethene formation) was well-predicted (4% underprediction), with modeled MRD exhibiting increased deviation from measured values under electron donor limiting conditions (maximum discrepancy of 14%). In contrast, simulations employing a homogeneous (uniform flow) domain resulted in underprediction of MRD extent by an average of 13%, with a maximum discrepancy of 45%. Model sensitivity analysis suggested that trace amounts of natural dissolved organic carbon served as an important fermentable substrate, providing up to 69% of the reducing equivalents consumed for MRD under donor-limiting conditions. Aquifer cell port concentration data and model simulations revealed that ethene formation varied spatially within the domain and was associated with regions of longer residence times. These results demonstrate the strong influence of subsurface heterogeneity on the accuracy of MRD predictions, and highlight the importance of subsurface characterization and the incorporation of flow field uncertainty in model applications for successful design and assessment of in situ bioremediation.

Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs)

Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.

Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor

A trichloroethene (TCE)-dechlorinating community (CANAS) maintained in a completely mixed flow reactor was established from a semi-batch enrichment culture (ANAS) and was monitored for 400 days at a low solids retention time (SRT) under electron acceptor limitation. Around 85% of TCE supplied to CANAS (0.13 mmol d^-1) was converted to ethene at a rate of 0.1 mmol d^-1, with detection of low production rates of vinyl chloride (6.8 × 10^-3 mmol d^-1) and cis-dichloroethene (2.3 × 10^-3 mmol d^-1). Two distinct Dehalococcoides mccartyi strains (ANAS1 and ANAS2) were stably maintained at 6.2 ± 2.8 × 10⁸ cells mL^-1 and 5.8 ± 1.2 × 10⁸ cells mL^-1, respectively. Electron balance analysis showed 107% electron recovery, in which 6.1% were involved in dechlorination. 16 S rRNA amplicon sequencing revealed a structural regime shift between ANAS and CANAS while maintaining robust TCE dechlorination due to similar relative abundances of D. mccartyi and functional redundancy among each functional guild supporting D. mccartyi activity. D. mccartyi transcriptomic analysis identified the genes encoding for ribosomal RNA and the reductive dehalogenases tceA and vcrA as the most expressed genes in CANAS, while hup and vhu were the most critical hydrogenases utilized by D. mccartyi in the community.

Interaction of perchlorate and trichloroethene bioreductions in mixed anaerobic culture

This work evaluated the interaction of perchlorate and trichloroethene (TCE), two common co-contaminants in groundwater, during bioreduction in serum bottles containing synthetic mineral salts media and microbial consortia. TCE at concentrations up to 0.3mM did not significantly affect perchlorate reduction; however, perchlorate concentrations higher than 0.1mM made the reduction of TCE significantly slower. Perchlorate primarily inhibited the reduction of vinyl chloride (VC, a daughter product of TCE) to ethene. Mechanistic analysis showed that the inhibition was mainly because perchlorate reduction is thermodynamically more favorable than reduction of TCE and its daughter products and not because of toxicity due to accumulation of dissolved oxygen produced during perchlorate reduction. As the initial perchlorate concentration increased from 0 to 600mg/L in a set of serum bottles, the relative abundance of Rhodocyclaceae (a putatively perchlorate-reducing genus) increased from 6.3 to 80.6%, while the relative abundance of Dehalococcoides, the only known genus that is able to reduce TCE all the way to ethene, significantly decreased. Similarly, the relative abundance of Proteobacteria (a phylum to which most known perchlorate-reducing bacteria belong) increased from 22% to almost 80%.

Motile Geobacter dechlorinators migrate into a model source zone of trichloroethene dense non-aqueous phase liquid: experimental evaluation and modeling

Microbial migration towards a trichloroethene (TCE) dense non-aqueous phase liquid (DNAPL) could facilitate the bioaugmentation of TCE DNAPL source zones. This study characterized the motility of the Geobacter dechlorinators in a TCE to cis-dichloroethene dechlorinating KB-1(™) subculture. No chemotaxis towards or away from TCE was found using an agarose in-plug bridge method. A second experiment placed an inoculated aqueous layer on top of a sterile sand layer and showed that Geobacter migrated several centimeters in the sand layer in just 7days. A random motility coefficient for Geobacter in water of 0.24±0.02cm(2)·day(-1) was fitted. A third experiment used a diffusion-cell setup with a 5.5cm central sand layer separating a DNAPL from an aqueous top layer as a model source zone to examine the effect of random motility on TCE DNAPL dissolution. With top layer inoculation, Geobacter quickly colonized the sand layer, thereby enhancing the initial TCE DNAPL dissolution flux. After 19days, the DNAPL dissolution enhancement was only 24% lower than with an homogenous inoculation of the sand layer. A diffusion-motility model was developed to describe dechlorination and migration in the diffusion-cells. This model suggested that the fast colonization of the sand layer by Geobacter was due to the combination of random motility and growth on TCE.

Enhanced reductive dechlorination of tetrachloroethene dense nonaqueous phase liquid with EVO and Mg(OH)2

In situ treatment of dense nonaqueous phase liquids (DNAPL) by enhanced reductive dechlorination (ERD) can be limited by contaminant toxicity, low pH, and challenges in effectively delivering electron donor. Flushing emulsified vegetable oil (EVO), colloidal Mg(OH)2 buffer, and a bioaugmentation culture (BC) through a zone containing neat tetrachloroethene (PCE) was effective in reducing contaminant toxicity, limiting pH declines, and accelerating bioenhanced dissolution of the DNAPL. In the effluent of porous media columns with little fine material, PCE concentrations reached a maximum of 40-50 times PCE aqueous solubility in water, demonstrating NAPL PCE was distributed throughout the 1.5 m column length. In a column treated with only EVO+BC, reductive dechlorination was limited. However, a single injection of EVO+Mg(OH)2+BC was effective in reducing PCE to below detection for over 400 days with a large increase in Cl(-) and dichloroethene (DCE), accelerating bioenhanced DNAPL dissolution. Dechlorination rates gradually increased over time with the rate of total ethene (TE) release from the Mg(OH)2+EVO+BC column reaching 5-6 times the TE release rate from the EVO+BC column. The accelerated dechlorination was likely due to both Mg(OH)2 addition which limited pH declines from HCl, volatile fatty acids (VFAs), and inorganic carbon (IC) production, and formation of a mixed PCE-vegetable oil NAPL which provided a readily accessible electron donor, resulting in rapid PCE degradation with reduced PCE toxicity.

Successful operation of continuous reactors at short retention times results in high-density, fast-rate Dehalococcoides dechlorinating cultures

The discovery of Dehalococcoides mccartyi reducing perchloroethene and trichloroethene (TCE) to ethene was a key landmark for bioremediation applications at contaminated sites. D. mccartyi-containing cultures are typically grown in batch-fed reactors. On the other hand, continuous cultivation of these microorganisms has been described only at long hydraulic retention times (HRTs). We report the cultivation of a representative D. mccartyi-containing culture in continuous stirred-tank reactors (CSTRs) at a short, 3-d HRT, using TCE as the electron acceptor. We successfully operated 3-d HRT CSTRs for up to 120 days and observed sustained dechlorination of TCE at influent concentrations of 1 and 2 mM TCE to ≥ 97 % ethene, coupled to the production of 10(12) D. mccartyi cells Lculture (-1). These outcomes were possible in part by using a medium with low bicarbonate concentrations (5 mM) to minimize the excessive proliferation of microorganisms that use bicarbonate as an electron acceptor and compete with D. mccartyi for H2. The maximum conversion rates for the CSTR-produced culture were 0.13 ± 0.016, 0.06 ± 0.018, and 0.02 ± 0.007 mmol Cl(-) Lculture (-1) h(-1), respectively, for TCE, cis-dichloroethene, and vinyl chloride. The CSTR operation described here provides the fastest laboratory cultivation rate of high-cell density Dehalococcoides cultures reported in the literature to date. This cultivation method provides a fundamental scientific platform for potential future operations of such a system at larger scales.

Molecular biomarker-based biokinetic modeling of a PCE-dechlorinating and methanogenic mixed culture

Bioremediation of chlorinated ethenes via anaerobic reductive dechlorination relies upon the activity of specific microbial populations--most notably Dehalococcoides (DHC) strains. In the lab and field Dehalococcoides grow most robustly in mixed communities which usually contain both fermenters and methanogens. Recently, researchers have been developing quantitative molecular biomarkers to aid in field site diagnostics and it is hoped that these biomarkers could aid in the modeling of anaerobic reductive dechlorination. A comprehensive biokinetic model of a community containing Dehalococcoides mccartyi (formerly D. ethenogenes) was updated to describe continuously fed reactors with specific biomass levels based on quantitative PCR (qPCR)-based population data (DNA and RNA). The model was calibrated and validated with subsets of chemical and molecular biological data from various continuous feed experiments (n = 24) with different loading rates of the electron acceptor (1.5 to 482 μeeq/L-h), types of electron acceptor (PCE, TCE, cis-DCE) and electron donor to electron acceptor ratios. The resulting model predicted the sum of dechlorination products vinyl chloride (VC) and ethene (ETH) well. However, VC alone was under-predicted and ETH was over predicted. Consequently, competitive inhibition among chlorinated ethenes was examined and then added to the model. Additionally, as 16S rRNA gene copy numbers did not provide accurate model fits in all cases, we examined whether an improved fit could be obtained if mRNA levels for key functional enzymes could be used to infer respiration rates. The resulting empirically derived mRNA "adjustment factors" were added to the model for both DHC and the main methanogen in the culture (a Methanosaeta species) to provide a more nuanced prediction of activity. Results of this study suggest that at higher feeding rates competitive inhibition is important and mRNA provides a more accurate indicator of a population's instantaneous activity than 16S rRNA gene copies alone as biomass estimates.

Kinetics and inhibition of reductive dechlorination of trichloroethene, cis-1,2-dichloroethene and vinyl chloride in a continuously fed anaerobic biofilm reactor

Anaerobic bioreactors containing Dehalococcoides spp. can be effective for the treatment of trichloroethene (TCE) contamination. However, reductive dehalogenation of TCE often results in partial conversion to harmless ethene, and significant production of undesired cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC) is frequently observed. Here, a detailed modeling study was conducted focusing on the determination of biokinetic constants for the dechlorination of TCE and its reductive dechlorination intermediates cis-DCE and VC as well as any biokinetic inhibition that may exist between these compounds. Dechlorination data from an anaerobic biotrickling filter containing Dehalococcoides spp. fed with single compounds (TCE, cis-DCE, or VC) were fitted to the model to determine biokinetic constants. Experiments with multiple compounds were used to determine inhibition between the compounds. It was found that the Michaelis-Menten half-saturation constants for all compounds were higher than for cells grown in suspended cultures, indicating a lower enzyme affinity in biofilm cells. It was also observed that TCE competitively inhibited the dechlorination of cis-DCE and had a mild detrimental effect on the dechlorination of VC. Thus, careful selection of biotreatment conditions, possibly with the help of a model such as the one presented herein, is required to minimize the production of partially dechlorinated intermediates.

Trichloroethene and cis-1,2-dichloroethene concentration-dependent toxicity model simulates anaerobic dechlorination at high concentrations: I. batch-fed reactors

A model was developed to describe toxicity from high concentrations of chlorinated aliphatic hydrocarbons (CAHs) on reductively dechlorinating cultures under batch-growth conditions. A reductively dechlorinating anaerobic Evanite subculture (EV-cDCE) was fed trichloroethene (TCE) and excess electron donor to accumulate cis-1,2-dichloroethene (cDCE) in batch-fed reactors. A second Point Mugu (PM) culture was also studied in the cDCE accumulating batch-fed experiment, as well as in a time- and concentration-dependent cDCE exposure experiment. Both cultures accumulated cDCE to concentrations ranging from 9,000 to 12,000 microM before cDCE production from TCE ceased. Exposure to approximately 3,000 and 6,000 microM cDCE concentrations for 5 days during continuous TCE dechlorination exhibited greater loss in activity proportional to both time and concentration of exposure than simple endogenous decay. Various inhibition models were analyzed for the two cultures, including the previously proposed Haldane inhibition model and a maximum threshold inhibition model, but neither adequately fit all experimental observations. A concentration-dependent toxicity model is proposed, which simulated all the experimental observations well. The toxicity model incorporates CAH toxicity terms that directly increase the cell decay coefficient in proportion with CAH concentrations. We also consider previously proposed models relating toxicity to partitioning in the cell wall (K(M/B)), proportional to octanol-water partitioning (K(OW)) coefficients. A reanalysis of previously reported modeling of batch tests using the Haldane model of Yu and Semprini, could be fit equally well using the toxicity model presented here, combined with toxicity proportioned to cell wall partitioning. A companion paper extends the experimental analysis and our modeling approach to a completely mixed reactor and a fixed film reactor.