Environ. Sci. Technol. 2008, 42, 5718–5726
Oxygen Effect on Dehalococcoides Viability and Biomarker Quantification BENJAMIN K. AMOS,† KIRSTI M. RITALAHTI,† CLARIBEL CRUZ-GARCIA,† ELIZABETH PADILLA-CRESPO,‡ AND F R A N K E . L Ö F F L E R * ,†,‡ School of Civil and Environmental Engineering and School of Biology, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30332-0512
Received December 22, 2007. Revised manuscript received May 16, 2008. Accepted May 22, 2008.
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 e4 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.
Introduction Chlorinated ethenes are common groundwater pollutants with stringent regulatory standards that mandate corrective * Corresponding author phone: (404) 894-0279; fax: (404) 8948266; e-mail:
[email protected]. † School of Civil and Environmental Engineering. ‡ School of Biology. 5718
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action(s) at many contaminated sites. Traditionally, pumpand-treat systems have been deployed to prevent expansion of contaminant plumes, but this technology is inefficient, has high operating costs, and must be maintained for decades. The need for affordable remedial technologies has driven substantial research investment to identify alternative approaches that yield near- and long-term benefits. Remarkable progress has been made in understanding the microbiology involved in detoxification of chlorinated ethenes (1), and bioremediation has emerged as a viable remedy (2). A milestone for the success of chlorinated ethene bioremediation was the identification of Dehalococcoides organisms as the key catalysts for reductive dechlorination of dichloroethenes (DCEs) and vinyl chloride (VC) to innocuous products (i.e., ethene and inorganic chloride) (3–6). Laboratory and field-scale investigations demonstrated a causeand-effect relationship between the presence of Dehalococcoides spp. and ethene formation (7–10). Hence, assessment of chlorinated ethene-impacted sites where bioremediation is considered a treatment option includes one key objective: determining if Dehalococcoides spp. are present or not. To address this question, Dehalococcoides-specific, PCR-based tools targeting the 16S rRNA gene and reductive dehalogenase (RDase) genes (i.e., tceA, bvcA, and vcrA) implicated in chlorinated ethene reductive dechlorination (11–13) are applied to DNA extracted from site samples (e.g., groundwater). These tools allow for sensitive, specific detection and quantification of Dehalococcoides biomarker genes (7, 8, 14–21) and are offered commercially. Dehalococcoides spp. are native to many contaminated sites but are often heterogeneously distributed throughout the aquifer and/or are present in very low numbers (9, 10). At sites where native Dehalococcoides spp. occur, the lack of substrates and/or suitable redox conditions often limit (i.e., control) reductive dechlorination and detoxification. To overcome the nutritional limitations, biostimulation with organic (e.g., lactate) and inorganic (i.e., N and P) substrates has been successfully implemented at the field scale (9). Although biostimulation has been employed productively at several sites, this approach may be insufficient to sustain desirable dechlorination rates and only works at sites that have native Dehalococcoides spp. capable of efficient ethene formation. As an alternative approach, bioaugmentation with Dehalococcoides-containing consortia has been implemented at numerous sites (9, 10, 22, 23), and bioaugmentation inocula are commercially available. To accompany biostimulation and bioaugmentation field efforts, detailed laboratory studies with Dehalococcoides pure and mixed cultures have been performed to elucidate the organisms’ nutritional requirements. Dehalococcoides spp. are very difficult to grow and maintain in pure culture (3, 5). The reasons for the intricate growth of Dehalococcoides spp. in pure culture are unclear but may be due to unknown nutritional requirements and/or sensitivity to oxygen (3, 5). The effects of oxygen on Dehalococcoides viability have not been thoroughly explored, but several studies reported that brief exposure of Dehalococcoides cultures to air or oxygen completely and irreversibly inhibited dechlorination (8, 24, 25). Commercial vendors of Dehalococcoides-containing bioaugmentation consortia recognize that proper diligence is required to limit oxygen exposure during inoculum transport to the contaminanted site and/or delivery to the subsurface (26). The state-of-the-art practice of bioaugmentation includes techniques (e.g., shipping consortia in sealed and pressurized containers, injecting consortia into the subsurface under pressure with argon or nitrogen) that reduce 10.1021/es703227g CCC: $40.75
2008 American Chemical Society
Published on Web 06/27/2008
exposure of the bioaugmentation culture to air (26). The ability to manage exposure of subsurface Dehalococcoides organisms to oxygen during biostimulation and bioaugmentation field efforts, however, can be challenging due to infiltration of oxygenated surface water (e.g., rain events) or migration of oxygenated groundwater into treatment areas. Such oxygen exposure, if not adequately controlled, may have a profound impact on the success of the biological remedy. Hence, the aim of this study was to explore the effects of oxygen on Dehalococcoides viability and dechlorination performance in more detail, and evaluate if the current PCRbased tools are useful to detect oxygen exposure and distinguish viable, dechlorinating cells from inactive, oxygenexposed cells. To this end, we also explored the use of RNA in addition to DNA biomarkers as useful indicators of oxygen exposure. Information on Dehalococcoides survivability (i.e., resistance and resilience) following oxygen exposure and knowledge of the resolution of the current molecular tools to detect oxygen exposure has practical relevance for bioremediation applications.
Materials and Methods Chemicals. Trichloroethene (TCE; g99.5%) was obtained from Sigma-Aldrich Co. (St. Louis, MO). cis-1,2-Dichloroethene (cis-DCE; 99.9%) and trans-1,2-dichloroethene (transDCE; 99.9%) were purchased from Supelco Co. (Bellefonte, PA). Gaseous VC (g99.5%) was purchased from Fluka Chemical Corp. (Ronkonkoma, NY), and gaseous ethene (99.5%) was obtained from Scott Specialty Gases (Durham, NC). All other chemicals used were reagent grade or better unless otherwise specified. Culture, Medium Preparation, and Growth Conditions. Bio-Dechlor INOCULUM (BDI), a tetrachloroethene- (PCE-) to-ethene dechlorinating consortium has been successfully used in bioaugmentation field applications (22) and contains at least three Dehalococcoides strains: FL2, GT, and BAV1 (15). Strain FL2 metabolically dechlorinates TCE to VC and cometabolically transforms VC to ethene (4). Strain GT metabolically dechlorinates TCE to ethene (6), while strain BAV1 metabolically dechlorinates all DCE isomers and VC to ethene (3). These Dehalococcoides strains can be tracked via quantitative real-time PCR (qPCR; (15)) by targeting specific RDase genes: the TCE-to-VC RDase gene (tceA) of strain FL2 (11), the VC-to-ethene RDase gene (vcrA) of strain GT (6, 13), and the putative VC-to-ethene RDase gene (bvcA) of strain BAV1 (12). Reduced anaerobic mineral salts medium was prepared as described (25), except the concentration of Na2S × 9H2O was 0.1 mM. The medium contained resazurin (1 µM; 0.25 mg/L) as a redox indicator (27–30). Resazurin, which can be oxidized by oxygen (27), is useful as a redox indicator in a narrow range of redox potentials (-51 mV ( 60 mV at pH 7 (29)). Solutions containing resazurin are bright pink at redox potentials above +10 mV, clear at redox potentials below -110 mV, and various intensities of pink at redox potentials between -110 mV and +10 mV. The BDI consortium was grown in 160-mL (nominal volume; Wheaton Co, Millville, NJ) glass serum bottles containing 100 mL ( 1 mL of medium and a N2/CO2 (80%/20% [vol/vol]) headspace. Bottles were sealed with Teflon-lined, gray butylrubber septa (West Pharmaceuticals, Lionville, PA) held in place with aluminum crimp caps (Wheaton). Lactate (5 mM) and hydrogen (10 mL) served as electron donors and were provided in excess (i.e., were not limiting dechlorination activity). Lactate was added by syringe from sterile, anoxic stocks. Acetate, which was produced by lactate fermentation, served as the carbon source for Dehalococcoides organisms in BDI. TCE (4 µL of neat liquid) or VC (3 mL of sterile gas) were provided as electron acceptors. TCE was added with a 5-µL gastight syringe (model 95 with a reproducibility adapter; Hamilton Co., Reno, NV); VC was added via 3-mL disposable
syringe. Triplicate or duplicate cultures were incubated statically, in an upside-down position, at room temperature. Oxygen Exposure. Sterile oxygen gas was amended to triplicate bottles containing autoclaved mineral salts medium via syringe and 30-gauge needle at an initial amount of 10% (vol/vol) of the headspace. Assuming equilibrium partitioning, the initial dissolved oxygen concentration was approximately 4 mg/L (31), which is in the range of dissolved oxygen concentrations when surface water or oxygenated groundwater migrate into biobarriers. Triplicate positive control cultures did not receive oxygen but instead were amended with equal volumes of sterile nitrogen gas. The bottles received TCE or VC and were allowed to equilibrate for 2 days before inoculation with 5% (vol/vol) from a dechlorinating BDI stock culture maintained with TCE as electron acceptor and lactate as electron donor. Before inoculation of individual bottles, two 100-mL aliquots of the BDI stock culture were dispensed into sterile, N2-flushed serum bottles. Filter-sterilized streams of N2/CO2 (80%/20% [vol/vol]) were bubbled through each cell suspension for 15 min to remove residual chlorinated ethenes and ethene. Three 5-mL samples of each cell suspension were collected for qPCR and reverse transcription qPCR (RT-qPCR) analyses before distribution of the inoculum to the VC-fed or TCE-fed bottles. The oxygen exposure experiment was repeated in an independent experiment with duplicate, VC-fed cultures and the following modifications: the inoculum size was increased to 15% (vol/vol) and oxygen was initially provided at 3.5% (vol/vol) of the headspace. The bottles received additional oxygen (12.6 and 2.1 mL) on Days 10 and 12, respectively, of the 21-day incubation. Liquid samples were taken periodically for qPCR and/or RT-qPCR analyses as described below. Oxygen Consumption Experiments. To determine abiotic and/or biotic oxygen consumption, oxygen concentrations were measured in an independent experiment with triplicate cultures not amended with chlorinated ethenes. The bottles were allowed to equilibrate for 2 days after oxygen addition before inoculation (5%, vol/vol) from a dechlorinating BDI stock culture. Triplicate abiotic control cultures received 5% (vol/vol) of sterile medium 2 days after oxygen addition. Headspace samples were taken for oxygen analysis immediately after oxygen addition and periodically thereafter. Reversibility Experiments. Aqueous 1-mL samples from triplicate VC- and TCE-fed, oxygen-amended cultures were transferred on Day 30 of the incubation to triplicate vessels containing reduced, oxygen-free medium equilibrated with VC and TCE, respectively. Aqueous 1-mL samples were also transferred from the triplicate VC- and TCE-fed positive control cultures (i.e., not exposed to oxygen) to triplicate vessels containing reduced, oxygen-free medium. Separate reversibility experiments were conducted with washed cell suspensions as described by Amos et al. (25) to ensure complete removal of oxygen from the transferred culture suspensions. Briefly, biomass was collected by centrifugation (4300g, 30 min) in an anoxic glovebox (Coy Laboratory Products, Ann Arbor, MI) from 5 mL of triplicate VC- or TCEfed, oxygen-amended or positive control cultures on Day 30 of the incubation. The resulting cell pellets were washed once with reduced (i.e., oxygen-free) medium and suspended in 1 mL of reduced medium. The washed cell suspensions served as inocula to triplicate (duplicate for the VC-fed, positive control cultures) vessels containing reduced, oxygen-free medium amended with VC or TCE, respectively. In the independent, repeated oxygen-exposure experiment, reversibility experiments were performed with washed cell suspensions collected from 15 mL of culture on Day 21. DNA and RNA Extraction. Biomass was collected periodically from aqueous samples by centrifugation at 16,000g for 10 min. The supernatant was decanted, and the biomass VOL. 42, NO. 15, 2008 / ENVIRONMENTAL SCIENCE & TECHNOLOGY
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from five 1-mL samples of culture suspension was collected in the same tube. The resulting pellet was suspended in 500 µL of RNAprotect Bacteria Reagent (Qiagen, Valencia, CA) to stabilize and protect RNA inside intact cells. The suspension was homogenized by vortexing, incubated at room temperature for 5 min, and centrifuged at 16,000g for 10 min. Genomic DNA and total RNA were extracted with the AllPrep DNA/RNA Mini Kit (Qiagen) from previously frozen cell pellets. The cell pellets were suspended in 250 µL of TrisEDTA (TE) buffer (RNase-free, pH 8; Ambion, Austin, TX) containing 15 mg/mL lysozyme (Sigma). Each sample received 1 µL of 10% SDS solution (20% RNase-free SDS stock [Ambion] diluted with diethyl pyrocarbonate- [DEPC-] treated water) and 600 µL of RTL lysis buffer (supplied with AllPrep DNA/RNA Mini Kit) containing 0.14 M β-mercaptoethanol (Sigma). All samples were then vortexed for 5 min before following the remainder of the Qiagen protocol. DNA was obtained in a final volume of 100 µL of buffer EB (provided with the AllPrep DNA/RNA Mini Kit) and stored at -20 °C until qPCR analysis. RNA was obtained in a final volume of 100 µL of RNase-free water, amended with 1 µL of RNaseOUT Ribonuclease Inhibitor (Invitrogen, Carlsbad, CA), and stored at -80 °C until further processing. In the independent experiment with VC-fed, oxygenamended cultures, biomass was collected periodically from 10 mL of culture fluid by centrifugation as described (25). The cell pellet was stored at -20 °C until genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) following a modified protocol (15). DNA was obtained in a final volume of 200 µL of buffer AE (provided with the QIAamp DNA Mini Kit) and stored at -20 °C until qPCR analysis. RNA Purification and Reverse Transcription. To remove contaminating DNA, the RNA was DNase treated with the TURBO DNA-free kit (Ambion) according to the manufacturer’s recommendations. After the DNase treatment, RNA was purified by successive phenol, phenol/chloroform/ isoamyl alcohol (25:24:1 vol/vol/vol), and chloroform/isoamyl alcohol (24:1 vol/vol) extractions, and recovered by ethanol precipitation with 0.3 M sodium acetate as described (32). The precipitated RNA was dissolved in 20 µL RNase-free water, amended with 1 µL of RNaseOUT Ribonuclease Inhibitor (Invitrogen), and stored at -80 °C until use. Removal of contaminating DNA was confirmed via PCR with universal bacterial 16S rRNA gene-targeted primers (14). Reverse transcription was performed with the SuperScript First-Strand Synthesis System for RT-PCR (Invitrogen). Before reverse transcription, the volumes of the RNA samples were reduced to
