Perchlorate and chlorate degradation by two organisms isolated from wastewater: Microbial identification and kinetics Prata, F. P., Costa C., Reis M. A. M., Lemos, P. C. The biological removal of perchlorate (ClO4-) and chlorate (ClO3-) can be viewed as a very promising water treatment technology. The process is based on the ability of specific bacteria to use (per)chlorate as an electron acceptor in the absence of oxygen. The present research work was focused on the isolation and kinetic characterization of perchlorate reducing bacteria. The enrichment process started with a sludge sample taken from an anaerobic digester of a domestic wastewater treatment plant (Beirolas, Portugal). Two perchlorate-reducing bacteria (per1) and (per2) were isolated using different selection methods, platting and liquid transfer respectively. The purity of the isolates was confirmed by genetic characterization of 16S rDNA. The BLAST search showed that the microorganims shared a 99% sequence similarities to the 16S rDNA of Dechlorospirillum sp. DB (per1) and Dechlorosoma sp. PCC (per2). Batch tests were performed under anaerobic conditions with acetate as the electron donor and perchlorate and/or chlorate as electron acceptor. During perchlorate reduction by Dechlorospirillum sp. DB it was observed transient accumulation of chlorate. The isolates showed different behaviour concerning perchlorate and chlorate reduction. Chlorate was preferentially reduced when both electron acceptors were present, being perchlorate reduced after completely depletion of chlorate. The former performance was observed in both bacteria. Keywords: Bioremediation, perchlorate/chlorate reduction, competitive inhibition, Dechlorospirillum sp. DB, Dechloromona sp. PCC. 1 INTRODUCTION Perchlorate (ClO4-) and chlorate (ClO3-) have been produced on a large scale by the chemical industry for use in a wide range of applications. The improper storage and/or disposal of these oxyanions have led to harmful concentrations in surface and groundwater, as they are extremely soluble and not significantly broken down in the environment. These characteristics make them persistent and problematic environmental pollutants of drinking waters. The biological removal of theses anions can be viewed as a very promising water treatment technology. ClO4- is a strong oxidizing agent, mostly used as ammonium perchlorate (NH4ClO4) in the manufacturing of solid rocket fuel, missiles and explosives for various military munitions and also in industrial products (e.g., fireworks, air bag inflators and paint). The presence of perchlorate in water supplies and soils is also linked to the earlier use of Chilean nitrate as fertilizer (Urbansky et al., 2001), and recently its natural formation was reported (Dasgupta et al. 2005). Perchlorate competitively blocks thyroid iodine uptake and inhibit normal thyroid hormone production, which may lead to metabolic problems in adults and anomalous development in children (Greer et al., 2002). ClO3- is also a potential chlorine oxyanion pollutant, which has been used as an herbicide in agriculture, and it is used for the on-site generation of the bleaching agent chlorine dioxide (ClO2) in the paper and pulp industry (Rosemarin et al., 1990). It can also be formed through the ozonation of drinking waters treated with chlorine (Siddiqui, 1996). ClO3- and also chlorite (ClO2-) added to drinking water can cause haemolytic anaemia in rats (Condie, 1986), due to oxidative damage of red blood cells. Perchlorate is on drinking water contaminant candidate list, but in the meantime the US Environmental Protection Agency (EPA) has established an official reference dose (RfD) corresponding to a drinking water level of 24.5 ppb od ClO4-. Chlorate has no legislation yet. The high oxidation state of (per)chlorate makes them ideal electron acceptors for microbial metabolism, and the microbial reduction of these compounds is energetically favourable. Many perchlorate-reducing bacteria (PRB) have now been isolate. Perchlorate-reducing strains reported in the literature include: Vibrio dechloraticans Cuznesove B-1168 (Korenkov et al., 1976), Wolinella succinogenes HAP-1 (Wallace et al., 1996), Dechlorosoma suillum (Chaudhuri et al., 2002) and isolates GR-1 (Rikken et al., 1996), perclace (Herman et al., 1998), and CKB (Bruce et al., 1999). These PRB are mainly Gram-negative, nonfermentative facultative anaerobes. Analysis of the 16S rDNA demonstrated that these organisms are phylogenetically diverse with members in the α-, β-, γ-, and ε-subclasses of the Proteobacteria (Coates et al., 1999; Wallace et al., 1996). However, the majority resides in the β-subclass of the Proteobacteria, being members of the genus Dechloromonas or Dechlorosoma (Coates et al., 1999). In 1996, Rikken and his colleagues proposed a three-step mechanism of perchlorate reduction (Equation 1): ClO4- ClO3- ClO2- O2 + Cl- (1) The perchlorate reduction pathway consist in three steps, the first two steps via two electrons transfers by (per)chlorate reductase, which sequentially reduces perchlorate to chlorate, then chlorate to chlorite (Kengen et al., 1999; Bender et al., 2005). The third step with chlorite dismutase, which transforms chlorite into 2 chloride and oxygen by disproportionation, does not consume electrons and therefore does not directly produce energy for the cells (van Ginkel et al., 1996; Bender et al., 2002). Chlorate accumulation has only been reported for a mixed culture growing on nitrate and perchlorate (Nerenberg et al., 2002) and for a pure culture growing on perchlorate (Nerenberg et al., 2006). Chlorite dismutase and (per)chlorate reductase are the only enzymes in the perchlorate reduction pathway that have been isolated and characterized (Coates et al., 1999; Kengen et al., 1999;). However, it is still not clear if only a single enzyme is used by PRB for perchlorate and chlorate reduction, or if there are separate enzymes used for perchlorate and chlorate reduction. Evidence for different enzymes was provided indirectly by the fact that not all chlorate-reducing bacteria (CRB) were capable of respiring perchlorate, although this question will require further research in order to be solved. Up to now, at least three enzymes that can reduce chlorate have been purified and characterized. A chlorate reductase C was purified from the denitrifying strain Proteus mirabilis (Oltmann et al., 1976), as well as from Pseudomonas chloritidismutans (Wolterink et al., 2003) and Pseudomonas sp. PDA (Steinberg et al., 2005). Improved understanding of the biological perchlorate reduction kinetics and its biochemical mechanisms will lead to better biological remediation processes. Since there are hardly any perchlorate degradation kinetic data available, the present work was focused on isolation of possible new perchlorate reducing bacteria as well as its kinetic characterization. MATERIALS AND METHODS Media. For the enrichment process it was used Basal medium amended with 1 mL/L of mineral solution SL10. For growth kinetics of Dechlorospirillum sp. DB, to the Basal medium was added 1 mL/L of Medium KL and for growth kinetics of Dechlorosoma sp. PCC, the Basal medium was amended with 1 mL/L of Medium SLA (Table 1, page 4). All media were prepared using ultrapure water (Milli Q system) and research grade chemicals in the amounts indicated (per liter). Sodium acetate was used in 1:2 molar ratio to sodium perchlorate and/or sodium chlorate. Solid agar plates were prepared by adding 15 g/L agar on the media previous described. Bacterial isolation procedures. A sludge sample was collected at the anaerobic digester of a wastewater treatment plant (Beirolas, Portugal). To start the enrichment a primary inoculum was obtained by dilution of the sludge sample. The medium used for the enrichment process was Basal medium + SL-10. The culture became turbid in 7 to 14 days and continuous transfers (10% by volume) were made during a period of two months. The enrichment process was performed in 50 mL glass flasks under anaerobic conditions. For further enrichment, ClO4- concentration was increased from 5 to 10 mM. Subsequently, two different selection methods were applied to reach pure cultures. In the first one, a sample of the enriched culture was serially diluted to 10-3 and spread onto agar plates. Select colonies were picked and then re-grown in fresh medium. The second method applied consisted in the continuous transfers (10% by volume) of the enriched 3 liquid culture at exponential phase to fresh medium during a period of 20 days. The enrichments were followed by microscopic examination and the purity of the isolates obtained was further confirmed by molecular methods. Table 1 – Media and reagents used for enrichment and isolation. Reagent Basal Medium K2HPO4 1.55 NaH2PO4.H2O 0.85 NH4Cl 0.25 MgSO4.7H2O 0.1 SL-10 HCl (37%) 10 ml Na2SeO3 0.0017 Na2SeO3.5H2O FeCl2.4H2O Medium KL Medium SLA 0.15 0.1 1.5 FeSO4.7H2O 18 4 Na2MoO4.2H2O 0.036 0.4 0.3 NiCl2.6H2O 0.024 0.1 0.1 EDTA 3 H3BO3 ZnCl2 0.6 0.07 5 1 MnCl2.4H2O 0.1 0.7 CoCl2.6H2O 0.19 2.5 CuCl2.2H2O 0.002 0.1 16S ribosomal DNA extraction and sequencing. DNA extraction of the isolates was performed using FastDNA® SPIN Kit (for soil). Some changes were performed in order to adjust the kit to our sample. The extraction was confirmed by gel electrophoresis. The 16S ribosomal DNAs were amplified by conventional PCR. The amplification program included initial denaturation at 94oC for 5 minutes followed by three steps repeated 30 times. Step 1: 94oC for 30 seconds; step 2: 48oC for 30 seconds; and step 3: 72oC for 2 minutes. The final elongation was at 72oC for 5 minutes. The primers 27f and 1492r, and Taq polymerase (Invritogen) were used in this amplification. The PCR products were purified and sequenced by BaseClear, DNA sequencing services, The Netherlands. Phylogenetic analysis. For establishing the identity of the isolates by 16S rDNA nucleotide-nucleotide sequence homology, the BLAST (Basic Local Alignment Search Tool) network service at the National Center for Biotechnological Information (NCBI) was used. (http://www.ncbi.nih.gov, 2007). 4 Batch growth kinetics. Isolate (per1) was grown on basal medium + medium KL and (per2) was grown on basal medium + medium SLA. The batch tests were performed in a reactor filled with 0.5 L of the appropriate medium with electron acceptor and donor under anaerobic conditions. The growth kinetics was conduct at controlled temperature (37oC) and the redox potential was measured with a redox electrode insitu. The pH measurements were made ex-situ and samples were taken (5 mL) in sterilized conditions, at regular time intervals for further analysis. Analytical techniques. Culture growth was monitored by optical density at 600nm (OD600nm) with a spectrophotometer and converted to dry weight (DW) using a calibration curve. The DW determination was made using the method described elsewhere (Olsson and Nielsen, 1997). The anions concentration was analyzed by HPLC. The concentration of perchlorate was determined by ion chromatography equipped with a Ion Pac AS16 column and a AG16 guard column (4mm, Dionex), a selfregenerating suppressor (SRS Ultra II), and an autosampler. The samples were analyzed with a 50mM NaOH mobile phase at a flow rate of 1 ml min-1. The injection loop volume was 30µl. The chlorate, chlorite, chloride and acetate were determined with the same ion chromatography system described before while an Ion Pac AS9 column and a AG9 guard column was used this time. The eluent used was 9 mM Na2CO3 at a flow rate of 1ml min-1. The injection loop volume was 30µl and the suppressor controller was set at 50 mA for all the analysis. RESULTS AND DISCUSSION Microbiologic characterization of the isolates. With the first selection method (platting) it was obtained a spirillum-shaped enriched culture (per1). The individual cells were highly motile and occasionally growing as clusters. The purity was confirmed by genetic characterization of 16S rDNA. The BLAST search showed that the first isolate (per1) shared a 99% sequence similarities to the 16S rDNA of Dechlorospirillum sp. DB. Dechlorospirillum sp. DB has its complete sequence of 16S rDNA with the accession number AY530551 (Bender et al., 2004). Phylogenetically belongs to the α-subclasse of Proteobacteria and was first isolated during a cld (chlorite dismutase) primer development (J. Coates, unpublished data). The chlorite dismutase gene was also sequenced (Bender et al., 2004), but no kinetic parameters were determined so far. Through the second isolation method (liquid) it was achieved a rod-shaped enriched culture (per2). The cells were in its majority non-motile and clusters were not observed. Concerning the genetic characterization by 16S rDNA of the second isolate (per2), the sequencing showed that the microorganim shared a 99% sequence similarities to the 16S rDNA of Dechlorosoma sp. PCC. This bacteria have the 16S rDNA partially sequenced with the accession number AY126453 (Nerenberg et al., 2002), but no other publication related with this bacteria is available at the moment. Phylogenetically belongs to the β-subclasse of Proteobacteria. 5 Growth and kinetic parameters. The growth kinetic of Dechlorospirillum sp. DB and Dechlorosoma sp. PCC were performed in batch tests under anaerobic conditions with acetate as the electron donor and perchlorate and/or chlorate as electron acceptor. Both bacteria were grown in medium amended with 20mM of CH3COO- as electron donor and 10 mM of ClO4- as final electron acceptor (Figure 1). Dechlorospirillum sp. DB 25 Dechlorosoma sp. PCC 25 -ClO4 0.4 -CH3COO 0.35 ClO4 -ClO3 20 CH3COO 20 0.2 10 0.15 Acet, ClO4- (mM) 0.25 15 ClO3- (mM) Acet, ClO4- (mM) 0.3 15 10 0.1 5 5 0.05 0 0 0 0 1 2 3 4 5 6 7 8 9 10 11 0 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Time (h) Tim e (h) Figure 1 – Perchlorate reduction by Dechlorospirillum sp. DB and Dechlorosoma sp. PCC. Chlorate formation and subsequent degradation was observed during the reduction of 10mM of ClO4- by Dechlorospirillum sp. DB. Note the different concentration scale for ClO3-. It was observed with Dechlorospirillum sp. DB accumulation and subsequent degradation of the intermediate chlorate. Around 3.4% on a molar basis of perchlorate concentration was accumulated by Dechlorospirillum sp. DB. The same was not observed with Dechlorosoma sp. PCC. Chlorate accumulation by Dechlorospirillum sp. DB indicates that perchlorate reduction have different systems within perchlorate reducing bacteria. In order to study the growth kinetic with chlorate as the final electron acceptor, it was performed a kinetic study with 10mM ClO3-. Again CH3COO- was used as electron donor in a concentration of 20mM (Figure 2). Dechlorosoma sp. PCC 25 25 0.8 ClO3CH3COOClDW (g/l) 20 0.6 0.4 10 0.6 15 mM mM 15 DW (g/l) 20 0.8 ClO3CH3COOClDW (g/l) 0.4 10 0.2 5 DW (g/l) Dechlorospirillum sp. DB 0.2 5 0 0 0 1 2 3 4 5 Time (h) 6 7 8 9 10 0 0.0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Time (h) Figure 2 – Chlorate reduction by Dechlorospirillum sp. DB and Dechlorosoma sp. PCC. 6 Concerning chlorate as the sole final electron acceptor, different behaviours were also observed in both bacteria. This fact emphasizes once more the presence of different (per)chlorate reduction system within perchlorate reducing bacteria. Dechlorospirillum sp. DB showed specific growth rate as well as acetate and chlorate uptake rates higher than Dechlorosoma sp. PCC (Table 2). Comparing each one individually with the former test with perchlorate, Dechlorospirillum sp. DB showed higher specific growth rate during chlorate reduction. In this way, it should not be expected chlorate accumulation by Dechlorospirillum sp. DB in the former test. Chlorate was completely reduced to chloride in both bacteria, which proves the conversion of chlorate into chloride. It was also performed a kinetic study with 5mM ClO4- and 5mM ClO3- simultaneously in the media in order to study the growth kinetic of Dechlorospirillum sp. DB and Dechlorosoma sp. PCC (Figure 3). Dechlorospirillum sp. DB Dechlorosoma sp. PCC 20 1.2 ClO4CH3COOClO3DW (g/l) 25 1.0 20 15 mM DW (g/L) mM 0.6 10 0.6 10 0.4 0.4 5 0.2 0 0.0 0 1 2 3 4 5 Time (h) 6 7 8 9 10 1.0 0.8 0.8 15 1.2 DW (g/l) -ClO3 -CH3COO -Cl -ClO4 DW 25 5 0.2 0 0.0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Time (h) Figure 3 – Acetate and chlorate uptake as function of time during the reduction of 5mM of ClO4- and 5mM of ClO3- simultaneously, by Dechlorospirillum sp. DB and Dechlorosoma sp. PCC. In this kinetics it should be stressed the preference for chlorate when both were present in the media. Perchlorate was not reduced unless chlorate was almost totally reduced. This observation indicates that chlorate could inhibit perchlorate reduction when both were present in the same concentration of 5mM. Concerning acetate, it can be observed in each kinetic study two different uptake rates, clearly related with chlorate and perchlorate reduction respectively (Table 2). The chloride produced was identical to the sum of perchlorate and chlorate amounts, showing once more a completely conversion of both electron donors into chloride. Batch tests with Dechlorospirillum sp. DB and Dechlorosoma sp. PCC were performed in order to determine kinetic parameters such as specific growth rate (µmax), specific acetate uptake rates (qCH3COO-), specific perchlorate reduction rates (qClO4-), specific chlorate reduction rates (qClO3-) and biomass yield (g [DW] / gCH3COO-). They were grown on acetate as the electron donor and perchlorate and/or chlorate as the electron acceptor. 7 Table 2 – Resume of all kinetic parameters (n, number of data points considered for parameter calculations Isolate electron acceptor ClO4- ClO3DB ClO4+ ClO3- ClO4ClO3PCC µmax (h-1) -qCH3COO-1 (mmol h g-1 DW) -qe- Y Y Y Y (mmol h g-1 DW) e- acceptor /CH3COO e-acceptor / Cl g[DW] / g acet g[DW] / g e- acceptor acceptor -1 0.166 ± 0.004 5.3 ± 0.2 2.9 ± 0.1 0.578 ± 0.008 0.85 ± 0.04 1.04 ± 0.04 1.41 ± 0.04 (n = 9) (n = 5) (n = 5) (n = 9) (n = 7) (n = 5) (n= 5) 0.192 ± 0.007 20.5 ± 1.8 11.5 ± 0.9 0.69 ± 0.04 0.84 ± 0.03 0.51 ± 0.07 0.42 ± 0.08 (n = 4) (n = 4) (n = 3) (n = 5) (n= 5) (n= 8) (n= 5) 5.6 ± 0.4 2.5 ± 0.2 0.472 ± 0.004 0.247 ± 0.01 (n = 4) (n = 4) (n=4) 0.81 ± 0.04 1.14 ± 0.03 (n= 3) (n = 5) 17.7 ± 1.8 5.2 ± 0.4 0.43 ± 0.1 (n= 5) (n= 7) 2.44± 0.01 (n= 3) (n=3) (n= 5) 10.9 ± 0.5 7.3 ± 0.4 0.72 ± 0.03 0.167 ± 0.004 0.93 ± 0.05 (n= 7) 0.93 ± 0.04 0.70 ± 0.02 0.56 ± 0.06 (n = 11) (n= 4) (n= 4) (n = 7) (n= 7) (n=16) (n= 11) 0.132 ± 0.005 4.14± 0.07 2.4 ± 0.1 0.64 ± 0.03 0.86 ± 0.03 0.83 ± 0.03 0.72 ± 0.02 (n = 6) (n= 5) (n= 5) (n= 3) (n= 11) (n=16) (n= 16) 3.1± 0.1 1.8 ± 0.1 0.64 ± 0.02 ClO4- 0.149 ± 0.004 (n= 6) (n= 5) (n= 6) 0.95 ± 0.02 + (n = 9) 14.1 ± 0.6 4.8 ± 0.2 0.924 ± 0.03 (n= 15) (n= 4) (n= 5) (n= 3) ClO3- 0.80 ± 0.04 1.18 ± 0.02 (n= 11) (n= 5) 0.88 ± 0.03 (n=7) The specific growth rates determined in this study were within the values found in the literature, ranging from 0.07 to 0.26 h-1 (Figure 4). Figure 4 – Specific growth rate determined for both bacteria, Dechlorospirillum sp. DB and Dechlorosoma sp. PCC with perchlorate and chlorate and values found in the literature: KJ (Logan et al., 2001); GR1 (Rikken et al.,1996); PDX (Logan et al., 2001) and perclace (Herman and Frankenberger, 1998) Among the cell yield found in the literature it was observed that Dechlorospirillum sp. DB showed higher values for perchlorate reduction and that Dechlorosoma sp. PCC showed the highest values for chlorate reduction compared with the other isolates. In this study, an interesting observation was that for chlorate reduction the values of the specific growth rate vary indirectly to the cell yield (Figure 5). 8 Figure 5 – Cell yield determined for both bacteria, Dechlorospirillum sp. DB and Dechlorosoma sp. PCC with perchlorate and chlorate and values found in the literature: KJ (Logan et al., 2001); GR1 (Rikken et al.,1996) and AB1 (Olsen et al., 1997). CONCLUSIONS AND FURTHER RESEARCH Each one of the bacteria isolated in this research work had different perchlorate reduction system. The main evidence was the transient accumulation of chlorate by Dechlorospirillum sp. DB during perchlorate reduction, which was not observed in Dechlorosoma sp. PCC. Chlorate accumulation can be explained based on the existence of two enzymes responsible for the conversion of perchlorate into chlorite, in which the conversion of chlorate into chlorite was the rate-limiting step. If a unique enzyme was present, then chlorate accumulation could be explained based on the idea that chlorate reduction decreased when perchlorate is present at 10mM. However, the results found were not sufficient to predict if one enzyme was responsible for both reduction (perchlorate and chlorate) or if different enzymes were present. Chlorate accumulation during perchlorate reduction was hardly studied and for further investigation, the enzymes involved in the perchlorate reduction pathway of these two bacteria, should be purified and studied concerning its biochemical characterization. Also kinetic test starting with different perchlorate and chlorate concentration should be done to observe the effect of the initial concentration over the reduction of each electron acceptor. Regarding the batch test done with chlorate and perchlorate present in the same medium, it was observed the preference for chlorate over perchlorate in both bacteria. This observation could also indicate that chlorate inhibit perchlorate reduction, although this finding was not in agreement with chlorate accumulation observed during perchlorate reduction in the first test. For further elucidation, the effect of chlorate during perchlorate reduction should be studied. In order to do so a test in which a chlorate spike is added during perchlorate reduction should be performed. The genetic characterization of 16S rDNA showed that both isolates have already its sequence deposited, but no other description was made. For further research concerning characterization it should be done the construction of the phylogenetic tree. Concerning description of the bacteria it should be done the G + C content, microbial size and all the tests in order to clarify their characteristics. 9 BIBLIOGRAPHY Bender, K. S., C. Shang, R. Chakraborty, S. M. Belchik, J. D. Coates, and L. A. Achenbach. 2005. Identification, characterization, and classification of genes encoding perchlorate reductase. J. Bacteriol., 187:5090-5096. Bender, K. S., S. M. O’Connor, R. Chakraborty, J. D. Coates, and L. A. Achenbach. 2002. Sequencing and transcriptional analysis of the chlorite dismutase gene of Dechloromonas agitata and its use as a metabolic probe. Appl. Environ. 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