Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution

Quantifying genes and transcripts to assess the in situ physiology of "Dehalococcoides" spp. in a trichloroethene-contaminated groundwater site

Quantitative PCR (qPCR) was coupled with reverse transcription (RT) to analyze both gene copy numbers and transcripts of the 16S rRNA gene and three reductive dehalogenase (RDase) genes (tceA, vcrA, and bvcA) as biomarkers of "Dehalococcoides" spp. in the groundwater of a trichloroethene-dense nonaqueous-phase liquid site at Fort Lewis, WA, that was sequentially subjected to biostimulation and bioaugmentation. Dehalococcoides cells carrying the tceA, vcrA, and bvcA genes were indigenous to the site. The sum of the three identified RDase gene copy numbers closely correlated to 16S rRNA gene copy numbers throughout the biostimulation and bioaugmentation activity, suggesting that these RDase genes represented the major Dehalococcoides metabolic functions at this site. Biomarker quantification revealed an overall increase of more than 3 orders of magnitude in the total Dehalococcoides population through the 1-year monitoring period (spanning biostimulation and bioaugmentation), and measurement of the respective RDase gene concentrations indicated different growth dynamics among Dehalococcoides cells. The Dehalococcoides cells containing the tceA gene consistently lagged behind other Dehalococcoides cells in population numbers and made up less than 5% of the total Dehalococcoides population, whereas the vcrA- and bvcA-containing cells represented the dominant fractions. Quantification of transcripts in groundwater samples verified that the 16S rRNA gene and the bvcA and vcrA genes were consistently highly expressed in all samples examined, while the tceA transcripts were detected inconsistently, suggesting a less active physiological state of the cells with this gene. The production of vinyl chloride and ethene toward the end of treatment supported the physiological activity of the bvcA- and vcrA-carrying cells. A clone library of the expressed RDase genes in field samples produced with degenerate primers revealed the expression of two putative RDase genes that were not previously monitored with RT-qPCR. The level of abundance of one of the putative RDase genes (FtL-RDase-1638) identified in the cDNA clone library tracked closely in field samples with abundance of the bvcA gene, suggesting that the FtL-RDase-1638 gene was likely colocated in genomes containing the bvcA gene. Overall, results from this study demonstrate that quantification of biomarker dynamics at field sites can provide useful information about the in situ physiology of Dehalococcoides strains and their associated activity.

Positive impact of microorganisms on the performance of laboratory-scale permeable reactive iron barriers

Degradation efficiencies of zerovalent iron (Fe0) containing different bacterial inocula, i.e., an iron(III)-reducing Geobacter sulfurreducens strain and/or a bacterial consortium, were compared to degradation efficiencies of noninoculated Fe0 in a laboratory-scale column experiment. Contaminant removal efficiencies and hydrogen production rates indicated an increasing reactivity in time for all inoculated iron columns, while reactivity of the noninoculated columns remained the same. The main mineral precipitates, including carbonate green rust, ferrous hydroxy carbonate, aragonite, and to a lesser extent goethite, were observed under all imposed conditions. The higher reactivity of the inoculated column material is explicable by the reduction of ferric iron species by iron(III)-reducing bacteria, resulting in the observed higher amounts of highly reactive carbonate green rust. However, contributions of other bacteria could not be excluded. Although different groups of hydrogen-consuming bacteria were detected in the columns, no indication was found that hydrogen consumption was sufficiently high to affect reactivity or permeability of the iron matrix, as the abiotic generation of H2 was substantially exceeding its potential consumption.

Bioreduction of trichloroethene using a hydrogen-based membrane biofilm reactor

A H2-based, denitrifying membrane-biofilm reactor (MBfR) was effective for removing trichloroethene (TCE) by reductive dechlorination. When TCE was first added to the MBfR, reductive dechlorination took place immediately and then increased over 18 weeks, and TCE was completely dechlorinated to ethene by about 120 days. These results indicate that TCE-dechlorinating bacteria were present naturally in the H2-based biofilm, and that enrichment for TCE-dechlorinating bacteria occurred. Dehalococcoides were documented in the MBfR biofilm before and after TCE feeding. Their proportion, quantified using the 16S rRNA gene, increased from 2.9 to 12% after TCE addition. This is the first report in which Dehalococcoides are proven to be present as part of an autotrophic biofilm community active in reductive dechlorination of TCE to ethene in a laboratory controlled experiment. Based on the complete reduction of TCE to ethene, the 16S rRNA clone libraries results, and the amount of tceA and bvcA, it appears that at least two Dehalococcoides strains were present in the enriched biofilm. One of them seems to be a new strain that is unique for having tceA and bvcA reductive dehalogenases.

Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes

DNA and RNA transcripts, particularly of genes of functional importance in the reductively dechlorinating microbe Dehalococcoides, are increasingly being studied as potential molecular bioindicators of reductive dechlorination. Ideally, mRNA bioindicators would be informative both qualitatively (with respect to dechlorination end point and substrate range) and quantitatively (with respectto activity rates). Here, we examined pseudo-steady-state mRNA levels in Dehalococcoides-containing microcosms continuously fed PCE at various loading rates. We characterized gene transcript abundance of potential Dehalococcoides bioindicators of reductive dechlorination, including 16S rRNA, and genes encoding an annotated formate dehydrogenase (Fdh), the hydrogenase (H2ase) Hup, and the reductive dehalogenases (RDases) TceA, DET1559, PceA, and DET1545. Increases in steady PCE loading rate led to corresponding increases in PCE respiration rate (1.5 +/- 0.1, 2.5 +/- 0.3, 4.8 +/- 0.1, and 9.2 +/- 0.5 micromol/L/hr). We also observed that pseudo-steady-state expression levels of most functional targets increase linearly over PCE respiration rates of 1.5-4.8 micromol/L/hr, with Fdh, Hup, and TceA transcripts increasing by approximately 2 x 10(10) copies per mL of culture for every micromol/L/hr increase in chloroethene respiration rate, and DET1559 and PceAtranscripts increasing by approximately9 x 10(9) copies per mL of culture, butthat increased respiration rates of 9.2 micromol/L/hr did not necessarily lead to corresponding increases in transcript levels.

Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1

A chlorobenzene reductive dehalogenase of the anaerobic dehalorespiring bacterium Dehalococcoides sp. strain CBDB1 was identified. Due to poor biomass yields, standard protein isolation procedures were not applicable. Therefore, cell extracts from cultures grown on trichlorobenzenes were separated by native polyacrylamide gel electrophoresis and analyzed directly for chlorobenzene reductive dehalogenase activity within gel fragments. Activity was found in a single band, even though electrophoretic separation was performed under aerobic conditions. Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and nano-liquid chromatography-MALDI MS analysis of silver-stained replicas of the active band on native polyacrylamide gels identified a protein product of the cbdbA84 gene, now called cbrA. The cbdbA84 gene is one of 32 reductive dehalogenase homologous genes present in the genome of strain CBDB1. The chlorobenzene reductive dehalogenase identified in our study represents a member of the family of corrinoid/iron-sulfur cluster-containing reductive dehalogenases. No orthologs of cbdbA84 were found in the completely sequenced genomes of Dehalococcoides sp. strains 195 and BAV1 nor among the genes amplified from Dehalococcoides sp. strain FL2 or mixed cultures containing Dehalococcoides. Another dehalogenase homologue (cbdbA80) was expressed in cultures that contained 1,2,4-trichlorobenzene, but its role is unclear. Other highly expressed proteins identified with our approach included the major subunit of a protein annotated as formate dehydrogenase, transporter subunits, and a putative S-layer protein.

Reductive dechlorination of chloroethenes by Dehalococcoides-containing cultures enriched from a polychlorinated-dioxin-contaminated microcosm

The reductive dechlorinating abilities for chloroethenes of seven enrichment cultures from polychlorinated-dioxin-dechlorinating microcosm were investigated using culture-independent and -dependent methods. These cultures were constructed and maintained with 1,2,3-trichlorobenzene (1,2,3-TCB) or fthalide as an electron acceptor and hydrogen as an electron donor. Denaturing gradient gel electrophoresis (DGGE) analysis of the amplified fragments targeting the 16S rRNA gene showed one or two major bands, whose nucleotide sequences were then analyzed and were found to suggest that Dehalococcoides was one of the dominant bacteria in all enrichment cultures. The nucleotide sequence data revealed that the identity of the major band was 100% identical to the 16S rRNA gene sequence of the Pinellas subgroup of the Dehalococcoides clusters, that is, strains CBDB1 and FL2. Genetic diagnosis targeting the pceA, tceA, bvcA, vcrA and reductive dehalogenase homologous (rdh) gene was performed to investigate the potential for reductive chloroethene dechlorination of cultures. The required length of PCR-amplified fragments was not observed, suggesting that these cultures are not capable of reductively dechlorinating chloroethenes. However, a culture-dependent test indicated that two cultures, TUT1903 and TUT1952, reductively dechlorinated tetrachloroethene (PCE) to trichloroethene (TCE), although not completely. While, TUT2260 and TUT2264 completely converted PCE to TCE and dichloroethenes, but not further. These results suggest that these TUT cultures might include a novel type of bacteria belonging to the Dehalococcoides group and that currently available information on both the 16S rRNA gene and rdh gene sequences is insufficient to definitively evaluate the potential abilities for reductive dechlorination.

Natural attenuation processes during in situ capping

Chlorinated solvents are common groundwater contaminants that threaten surface water quality and benthic health when present in groundwater seeps. Aquatic sediments can act as natural biobarriers to detoxify chlorinated solvent plumes via reductive dechlorination. In situ sediment capping, a remedial technique in which clean material is placed at the sediment-water interface, may alter sedimentary natural attenuation processes. This research explores the potential of Anacostia River sediment to naturally attenuate chlorinated solvents under simulated capping conditions. Results of microcosm studies demonstrated that intrinsic dechlorination of dissolved-phase PCE to ethene was possible, with electron donor availability controlling microbial activity. A diverse microbial community was present in the sediment, including multiple Dehalococcoides strains indicated by the amplification of the reductive dehalogenases tceA, vcrA, and bvcA. An upflow column simulating a capped sediment bed subject to PCE-contaminated groundwater seepage lost dechlorination activity with time and only achieved complete dechlorination when microorganisms present in the sediment were provided electron donor. Increases in effluent chloroethene concentrations during the period of biostimulation were attributed to biologically enhanced desorption and the formation of less sorptive dechlorination products. These findings suggest that in situ caps should be designed to account for reductions in natural biobarrier reactivity and for the potential breakthrough of groundwater contaminants.

Isolation and quantitative detection of tetrachloroethene (PCE)-dechlorinating bacteria in unsaturated subsurface soils contaminated with chloroethenes

The estimation of tetrachloethene (PCE) dechlorinating-activity and identification of PCE-dechlorinating bacteria were performed in 65 unsaturated subsurface soils (at a depth 30-60 cm) that were collected from 21 noncontaminated soils and 44 chloroethene-contaminated soils including four soils that dechlorinated PCE to 1,2-cis-dichloroethene (cisDCE) in situ. Sixteen out of the 44 PCE-contaminated soils and three out of the 21 noncontaminated soils dechlorinated PCE to trichloroethene and cisDCE but not vinyl chloride or ethene after a month of incubation with 0.1% yeast extract at 30 degrees C. Desulfitobacterium sp. strain B31e3 that can dechlorinate PCE to cisDCE was isolated from a soil that dechlorinated PCE to cisDCE in situ. 16S rRNA gene of this strain showed the closest similarity of 99.1% with that of Desulfitobacterium hafniense (formally frappieri) strain DP7. Real-time PCR using specific primer sets targeted to the 16S rRNA genes of the representative PCE-dechlorinating bacteria, Dehalococcoides spp., Desulfitobacterium spp., and Dehalobacter spp. were performed using five unsaturated subsurface soils that dechlorinated PCE and three that did not dechlorinate PCE. In two out of the five soils that dechlorinated PCE, Desulfitobacterium spp. (0.12, 0.38% of total bacteria) and Dehalobacter spp. (0.0045, 0.0061% of total bacteria) were detected, and in one of the five soils, only Desulfitobacterium spp. (0.042% of total bacteria) was detected. None of these representative PCE-dechlorinating bacteria were detected in two out of the five soils that dechlorinated PCE and in all of the three soils that did not dechlorinate PCE. Dehalococcoides spp. were not detected in any unsaturated subsurface soils used in this study. These results suggested the involvement of Desulfitobacterium spp. and probably Dehalobacter spp. rather than Dehalococcoides spp. in the dechlorination of PCE to cisDCE in unsaturated subsurface soils.

Cellular therapy using microglial cells

Recent insights into the function and dysfunction of microglia may inform future therapies to combat neurodegeneration. We hypothesise how different aspects of microglial activity including migration, activation, oxidative response, phagocytosis, proteolysis, and replenishment could be targeted by novel therapeutic approaches. A combined approach is suggested, encompassing opsonization and anti-inflammatory strategies in conjunction with an engineering of microglial precursors. Xenoproteases for bioremediation could be used to enhance intracellular and extracellular proteolytic capacity. The capacity of microglial precursors to cross the blood-brain barrier and to home in on sites of neural damage and inflammation might prove to be particularly useful for future therapeutic strategies.

Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol

Reductive dehalogenase (RD) gene transcript levels in Dehalococcoides ethenogenes strain 195 were investigated using reverse transcriptase quantitative PCR during growth and reductive dechlorination of tetrachloroethene (PCE), trichloroethene (TCE), or 2,3-dichlorophenol (2,3-DCP). Cells grown with PCE or TCE had high transcript levels (greater than that for rpoB) for tceA, which encodes the TCE RD, pceA, which encodes the PCE RD, and DET0162, which contains a predicted stop codon and is considered nonfunctional. In cells grown with 2,3-DCP, tceA mRNA was less than 1% of that for rpoB, indicating that its transcription was regulated. pceA and DET0162 were the only RD genes with high transcript levels in cells grown with 2,3-DCP. Proteomic analysis of PCE-grown cells detected both PceA and TceA with high peptide coverage but not DET0162, and analysis of 2,3-DCP-grown cells detected PceA with high coverage but not TceA, DET0162, or any other potential RD. Cells grown with PCE or 2,3-DCP were tested for the ability to dechlorinate PCE, TCE, or 2,3-DCP with H2 as the electron donor. 2,3-DCP-grown cells were unable to dechlorinate TCE but dechlorinated PCE to TCE without a lag, and PCE-grown cells dechlorinated 2,3-DCP without a lag. These results show that 2,3-DCP-grown cells do not produce TceA and that DET0162 is transcribed but its translation product is not detectable in cells and are consistent with PceA's being bifunctional, also serving as the 2,3-DCP RD. Chlorophenols naturally occur in soils and are good candidates for the original substrates for PceA.

Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species

Vinyl chloride reductases (VC-RDase) are the key enzymes for complete microbial reductive dehalogenation of chloroethenes, including the groundwater pollutants tetrachloroethene and trichloroethene. Analysis of the codon usage of the VC-RDase genes vcrA and bvcA showed that these genes are highly unusual and are characterized by a low G+C fraction at the third position. The third position of codons in VC-RDase genes is biased toward the nucleotide T, even though available Dehalococcoides genome sequences indicate the absence of any tRNAs matching codons that end in T. The comparatively high level of abnormality in the codon usage of VC-RDase genes suggests an evolutionary history that is different from that of most other Dehalococcoides genes.

The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260

Microbial reductive dechlorination of commercial polychlorinated biphenyl (PCB) mixtures (e.g., Aroclors) in aquatic sediments is crucial to achieve detoxification. Despite extensive efforts over nearly two decades, the microorganisms responsible for Aroclor dechlorination remained elusive. Here we demonstrate that anaerobic bacteria of the Dehalococcoides group derived from sediment of the Housatonic River (Lenox, MA) simultaneously dechlorinate 64 PCB congeners carrying four to nine chlorines in Aroclor 1260 in the sediment-free JN cultures. Quantitative real-time PCR showed that the Dehalococcoides cell titer in JN cultures amended with acetate and hydrogen increased from 7.07 x 10(6) +/- 0.42 x 10(6) to 1.67 x 10(8) +/- 0.04 x 10(8) cells/ml, concomitant with a 64.2% decrease of the PCBs with six or more chlorines in Aroclor 1260. No Dehalococcoides growth occurred in parallel cultures without PCBs. Aroclor 1260 dechlorination supported the growth of 9.25 x 10(8) +/- 0.04 x 10(8) Dehalococcoides cells per mumol of chlorine removed. 16S rRNA gene-targeted PCR analysis of known dechlorinators (i.e., Desulfitobacterium, Dehalobacter, Desulfuromonas, Sulfurospirillum, Anaeromyxobacter, Geobacter, and o-17/DF-1-type Chloroflexi organisms) ruled out any involvement of these bacterial groups in the dechlorination. Our results suggest that the Dehalococcoides population present in the JN cultures also catalyzes in situ dechlorination of Aroclor 1260 in the Housatonic River. The identification of Dehalococcoides organisms as catalysts of extensive Aroclor 1260 dechlorination and our ability to propagate the JN cultures under defined conditions offer opportunities to study the organisms' ecophysiology, elucidate nutritional requirements, identify reductive dehalogenase genes involved in PCB dechlorination, and design molecular tools required for bioremediation applications.

Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes

Besides 19 potential reductive dehalogenase genes, the genome of Dehalococcoides ethenogenes strain 195 contains over 60 genes annotated as encoding oxidoreductases, including five hydrogenase complexes and a formate dehydrogenase (Fdh). Using quantitative reverse transcriptase polymerase chain reaction, we found that genes encoding a periplasmic Hup hydrogenase and the Fdh were the most highly expressed in batch-grown pure cultures, in which the H2 partial pressure was >0.1 atm, and in butyrate/tetrachloroethene-mixed cultures, in which H2 partial pressures were 10(-4)-10(-5) atm. Shotgun electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry were used to identify multiple peptides in pure culture membrane-enriched fractions matching several highly expressed respiratory enzymes, including three hydrogenases, two reductive dehalogenases, Fdh and DET1407, a 105.5-kDa protein we propose to be part of an S-layer cell wall. Both transcript and mass spectrometric approaches indicated that the putative Fdh was an important oxidoreductase in these cells; nevertheless, D. ethenogenes cultures could not use formate as an electron donor for reductive dechlorination. Analysis of the gene encoding the large subunit of Fdh indicated that while it was related to other Fdh proteins, its sequence encodes serine rather than cysteine or selenocysteine at a critical position, casting doubt on its function. Overall, genomic and proteomic approaches have provided novel insights into the metabolism of this difficult to culture organism.

Hydrogen metabolism in Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a facultative sediment microorganism which uses diverse compounds, such as oxygen and fumarate, as well as insoluble Fe(III) and Mn(IV) as electron acceptors. The electron donor spectrum is more limited and includes metabolic end products of primary fermenting bacteria, such as lactate, formate, and hydrogen. While the utilization of hydrogen as an electron donor has been described previously, we report here the formation of hydrogen from pyruvate under anaerobic, stationary-phase conditions in the absence of an external electron acceptor. Genes for the two S. oneidensis MR-1 hydrogenases, hydA, encoding a periplasmic [Fe-Fe] hydrogenase, and hyaB, encoding a periplasmic [Ni-Fe] hydrogenase, were found to be expressed only under anaerobic conditions during early exponential growth and into stationary-phase growth. Analyses of DeltahydA, DeltahyaB, and DeltahydA DeltahyaB in-frame-deletion mutants indicated that HydA functions primarily as a hydrogen-forming hydrogenase while HyaB has a bifunctional role and represents the dominant hydrogenase activity under the experimental conditions tested. Based on results from physiological and genetic experiments, we propose that hydrogen is formed from pyruvate by multiple parallel pathways, one pathway involving formate as an intermediate, pyruvate-formate lyase, and formate-hydrogen lyase, comprised of HydA hydrogenase and formate dehydrogenase, and a formate-independent pathway involving pyruvate dehydrogenase. A reverse electron transport chain is potentially involved in a formate-hydrogen lyase-independent pathway. While pyruvate does not support a fermentative mode of growth in this microorganism, pyruvate, in the absence of an electron acceptor, increased cell viability in anaerobic, stationary-phase cultures, suggesting a role in the survival of S. oneidensis MR-1 under stationary-phase conditions.

Comparison of bioaugmentation and biostimulation for the enhancement of dense nonaqueous phase liquid source zone bioremediation

Two 11.7-m(3) experimental controlled release systems (ECRS), packed with sandy model aquifer material and amended with tetrachloroethene (PCE) dense nonaqueous phase liquid (DNAPL) source zone, were operated in parallel with identical flow regimes and electron donor amendments. Hydrogen Releasing Compound (Regenesis Bioremediation Products, Inc., San Clemente, California), and later dissolved lactate, served as electron donors to promote dechlorination. One ECRS was bioaugmented with an anaerobic dechlorinating consortium directly into the source zone, and the other served as a control (biostimulated only) to determine the benefits of bioaugmentation. The presence of halorespiring bacteria in the aquifer matrix before bioaugmentation, shown by nested polymerase chain reaction with phylogenetic primers, suggests that dechlorinating catabolic potential may be somewhat widespread. Results obtained corroborate that source zone reductive dechlorination of PCE is possible at near field scale and that a system bioaugmented with a competent halorespiring consortium can enhance DNAPL dissolution and dechlorination processes at significantly greater rates than in a system that is biostimulated only.

Comparative proteomics of Dehalococcoides spp. reveals strain-specific peptides associated with activity

Anaerobic reductive dehalogenation by Dehalococcoides spp. is an ideal system for studying functional diversity of closely related strains of bacteria. In Dehalococcoides spp., reductive dehalogenases (RDases) are key respiratory enzymes involved in the anaerobic detoxification of halogenated compounds at contaminated sites globally. Although housekeeping genes sequenced from Dehalococcoides spp. are >85% identical at the amino acid level, different strains are capable of dehalogenating diverse ranges of compounds, depending largely on the suite of RDase genes that each strain harbors and expresses. We identified RDase proteins that corresponded to known functions in four characterized cultures and predicted functions in an uncharacterized Dehalococcoides-containing mixed culture. Homologues within RDase subclusters containing PceA, TceA, and VcrA were among the most frequently identified proteins. Several additional proteins, including a formate dehydrogenase-like protein (Fdh), had high coverage in all strains and under all growth conditions.

Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp

This study characterizes the transcriptional expression of the reductive dehalogenase (RDase)-encoding tceA and vcrA genes and evaluates their applicability as potential biological markers of Dehalococcoides activity. When Dehalococcoides ethenogenes 195 was provided with trichloroethene (TCE) as the electron acceptor, the expression of the tceA gene increased by 90-fold relative to that in cells starved of chlorinated ethenes, demonstrating that tceA gene expression is indicative of the active physiological state of this strain. In a Dehalococcoides-containing enrichment culture that contains both the tceA and vcrA genes, the tceA gene was up-regulated in response to TCE and cis-1,2-dichloroethene (cDCE) exposure, while the vcrA gene was up-regulated in response to TCE, cDCE, and vinyl chloride (VC). When chlorinated ethenes were depleted, the RDase-encoding gene transcripts decayed exponentially, with a half-life between 4.8 and 6.1 h, until they reached a stable background level after 2 days. We found that while gene expression correlated generally to the presence of chlorinated ethenes, there was no apparent direct relationship between RDase-encoding transcript numbers and respective rates of TCE, cDCE, and VC dechlorination activities. However, elevated tceA and vcrA expression did correlate with chlorinated-ethene reduction beyond cDCE, suggesting that elevated RDase-encoding transcript numbers could serve as a biomarker for the physiological ability of Dehalococcoides spp. to dechlorinate beyond cDCE.

Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes

While many anaerobic microbial communities are capable of reductively dechlorinating tetrachloroethene (PCE) and trichloroethene (TCE) to dichloroethene (DCE), vinyl chloride (VC), and finally ethene, the accumulation of the highly toxic intermediates, cis-DCE (cDCE) and VC, presents a challenge for bioremediation processes. Members of the genus Dehalococcoides are apparently solely responsible for dechlorination beyond DCE, but isolates of Dehalococcoides each metabolize only a subset of PCE dechlorination intermediates and the interactions among distinct Dehalococcoides strains that result in complete dechlorination are not well understood. Here we apply quantitative PCR to 16S rRNA and reductase gene sequences to discriminate and track Dehalococcoides strains in a TCE enrichment derived from soil taken from the Alameda Naval Air Station (ANAS) using a four-gene plasmid standard. This standard increased experimental accuracy such that 16S rRNA and summed reductase gene copy numbers matched to within 10%. The ANAS culture was found to contain only a single Dehalococcoides 16S rRNA gene sequence, matching that of D. ethenogenes 195, but both the vcrA and tceA reductive dehalogenase genes. Quantities of these two genes in the enrichment summed to the quantity of the Dehalococcoides 16S rRNA gene. Further, between ANAS subcultures enriched on TCE, cDCE, or VC, the relative copy number of the two dehalogenases shifted 14-fold, indicating that the genes are present in two different Dehalococcoides strains. Comparison of cell yields in VC-, cDCE-, and TCE-enriched subcultures suggests that the tceA-containing strain is responsible for nearly all of the TCE and cDCE metabolism in ANAS, whereas the vcrA-containing strain is responsible for all of the VC metabolism.

The Desulfitobacterium genus

Desulfitobacterium spp. are strictly anaerobic bacteria that were first isolated from environments contaminated by halogenated organic compounds. They are very versatile microorganisms that can use a wide variety of electron acceptors, such as nitrate, sulfite, metals, humic acids, and man-made or naturally occurring halogenated organic compounds. Most of the Desulfitobacterium strains can dehalogenate halogenated organic compounds by mechanisms of reductive dehalogenation, although the substrate spectrum of halogenated organic compounds varies substantially from one strain to another, even with strains belonging to the same species. A number of reductive dehalogenases and their corresponding gene loci have been isolated from these strains. Some of these loci are flanked by transposition sequences, suggesting that they can be transmitted by horizontal transfer via a catabolic transposon. Desulfitobacterium spp. can use H2 as electron donor below the threshold concentration that would allow sulfate reduction and methanogenesis. Furthermore, there is some evidence that syntrophic relationships occur between Desulfitobacterium spp. and sulfate-reducing bacteria, from which the Desulfitobacterium cells acquire their electrons by interspecies hydrogen transfer, and it is believed that this relationship also occurs in a methanogenic consortium. Because of their versatility, desulfitobacteria can be excellent candidates for the development of anaerobic bioremediation processes. The release of the complete genome of Desulfitobacterium hafniense strain Y51 and information from the partial genome sequence of D. hafniense strain DCB-2 will certainly help in predicting how desulfitobacteria interact with their environments and other microorganisms, and the mechanisms of actions related to reductive dehalogenation.

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.

Growth of Dehalobacter and Dehalococcoides spp. during degradation of chlorinated ethanes

Mixed anaerobic microbial subcultures enriched from a multilayered aquifer at a former chlorinated solvent disposal facility in West Louisiana were examined to determine the organism(s) involved in the dechlorination of the toxic compounds 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA) to ethene. Sequences phylogenetically related to Dehalobacter and Dehalococcoides, two genera of anaerobic bacteria that are known to respire with chlorinated ethenes, were detected through cloning of bacterial 16S rRNA genes. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments after starvation and subsequent reamendment of culture with 1,2-DCA showed that the Dehalobacter sp. grew during the dichloroelimination of 1,2-DCA to ethene, implicating this organism in degradation of 1,2-DCA in these cultures. Species-specific real-time quantitative PCR was further used to monitor proliferation of Dehalobacter and Dehalococcoides during the degradation of chlorinated ethanes and showed that in fact both microorganisms grew simultaneously during the degradation of 1,2-DCA. Conversely, Dehalobacter grew during the dichloroelimination of 1,1,2-TCA to vinyl chloride (VC) but not during the subsequent reductive dechlorination of VC to ethene, whereas Dehalococcoides grew only during the reductive dechlorination of VC but not during the dichloroelimination of 1,1,2-TCA. This demonstrated that in mixed cultures containing multiple dechlorinating microorganisms, these organisms can have either competitive or complementary dechlorination activities, depending on the chloro-organic substrate.

Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures

Degenerate primers were used to amplify 14 distinct reductive-dehalogenase-homologous (RDH) genes from the Dehalococcoides-containing mixed culture KB1. Most of the corresponding predicted proteins were highly similar (97 to >99% amino acid identity) to previously reported Dehalococcoides reductive dehalogenases. To examine the differential transcription of these RDH genes, KB1 was split into five subcultures amended with either trichloroethene, cis-1,2-dichloroethene, vinyl chloride, 1,2-dichlorethane, or no chlorinated electron acceptor. Total RNA was extracted following the onset of reductive dechlorination, and RDH transcripts were reverse transcribed and amplified using degenerate primers. The results indicate that the transcription of RDH genes requires the presence of a chlorinated electron acceptor, and for all treatments, multiple RDH genes were simultaneously transcribed, with transcripts of two of the genes being present under all four electron-accepting conditions. Two of the transcribed sequences were highly similar to reported vinyl chloride reductase genes, namely, vcrA from Dehalococcoides sp. strain VS and bvcA from Dehalococcoides sp. strain BAV1. These findings suggest that multiple RDH genes are induced by a single chlorinated substrate and that multiple reductive dehalogenases contribute to chloroethene degradation in KB1.

Enzyme Electrochemistry — Biocatalysis on an Electrode

Oxidoreductase enzymes catalyze single- or multi-electron reduction/oxidation reactions of small molecule inorganic or organic substrates, and they are integral to a wide variety of biological processes including respiration, energy production, biosynthesis, metabolism, and detoxification. All redox enzymes require a natural redox partner such as an electron-transfer protein (e.g. cytochrome, ferredoxin, flavoprotein) or a small molecule cosubstrate (e.g. NAD(P)H, dioxygen) to sustain catalysis, in effect to balance the substrate/product redox half-reaction. In principle, the natural electron-transfer partner may be replaced by an electrochemical working electrode. One of the great strengths of this approach is that the rate of catalysis (equivalent to the observed electrochemical current) may be probed as a function of applied potential through linear sweep and cyclic voltammetry, and insight to the overall catalytic mechanism may be gained by a systematic electrochemical study coupled with theoretical analysis. In this review, the various approaches to enzyme electrochemistry will be discussed, including direct and indirect (mediated) experiments, and a brief coverage of the theory relevant to these techniques will be presented. The importance of immobilizing enzymes on the electrode surface will be presented and the variety of ways that this may be done will be reviewed. The importance of chemical modification of the electrode surface in ensuring an environment conducive to a stable and active enzyme capable of functioning natively will be illustrated. Fundamental research into electrochemically driven enzyme catalysis has led to some remarkable practical applications. The glucose oxidase enzyme electrode is a spectacularly successful application of enzyme electrochemistry. Biosensors based on this technology are used worldwide by sufferers of diabetes to provide rapid and accurate analysis of blood glucose concentrations. Other applications of enzyme electrochemistry are in the sensing of macromolecular complexation events such as antigen–antibody binding and DNA hybridization. The review will include a selection of enzymes that have been successfully investigated by electrochemistry and, where appropriate, discuss their development towards practical biotechnological applications.

Transcriptional expression of the tceA gene in a Dehalococcoides-containing microbial enrichment

Dynamic changes in the transcriptional expression of the tceA gene, which encodes a trichloroethene reductive dehalogenase, were characterized in a Dehalococcoides-containing microbial enrichment culture. Expression was quantified by real-time PCR as the number of tceA transcripts per tceA gene. Expression of tceA increased 40-fold after chlorinated ethene-starved cells were exposed to trichloroethene (TCE), cis-dichloroethene (DCE), or 1,1-DCE but did not increase after exposure to tetrachloroethene or vinyl chloride. Surprisingly, tceA expression also increased 30-fold after cellular exposure to the nonmetabolic substrate trans-DCE, indicating that expression of tceA is induced by both growth-supporting and non-growth-supporting chlorinated ethenes. Additional experiments revealed that the level of tceA expression was independent of the concentration of chlorinated ethenes (sum concentrations of TCE and DCEs of 2.2 to 333 microM), the concentration of the electron donor hydrogen (concentrations of 12 nM to 17 microM), and the presence of alternate bacterial electron acceptors (5 mM concentrations of fumarate, sulfate, sulfite, thiosulfate, nitrate, or nitrite) but was highly dependent on incubation temperature.

Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe

A strictly anaerobic bacterium was isolated from tetrachloroethene (PCE)-to-ethene dechlorinating microcosms established with river sediment without prior exposure to chlorinated solvents. The isolation procedure included the addition of 2-bromoethanesulfonate to select against methanogenic archaea, >50 consecutive 1-2% (v/v) transfers to reduced mineral salts medium amended with trichloroethene (TCE), acetate, and hydrogen, the addition of ampicillin, and the dilution-to-extinction principle. Culture-dependent and 16S rRNA gene-targeted approaches suggested culture purity. Microscopic examination revealed a homogeneous culture of an organism with a distinct, disc-shaped morphology. The isolate shared >99% 16S rRNA gene sequence similarity with members of the Pinellas group of the Dehalococcoides cluster, and was designated Dehalococcoides sp. strain FL2. Strain FL2 could be propagated with TCE, cis-1,2-dichloroethene (cis-DCE), or trans-DCE as the electron acceptors, acetate as the carbon source, and hydrogen as the electron donor in defined, completely synthetic medium. No other growth-supporting redox couples were identified. Trichloroethene, cis-DCE and trans-DCE were dechlorinated at rates of 27.5, 30.4 and 18.8 micromol l-1 day-1 respectively. Quantitative real-time polymerase chain reaction (PCR) with a fluorescently labelled linear hybridization probe confirmed growth with these electron acceptors, and suggested that strain FL2 captures energy from both the TCE-to-cis-DCE and 1,2-DCE-to-VC dechlorination steps. Tetrachloroethene and vinyl chloride (VC) were slowly and cometabolically dechlorinated in the presence of a growth-supporting chloroethene, but ethene formation was incomplete, even after prolonged incubation. At room temperature, strain FL2 grew with a doubling time of 2.4 days, and yielded 166.1+/-10.2 mg of protein per mole of chloride released. In the presence of excess electron acceptor, strain FL2 consumed hydrogen to a concentration of 0.061+/-0.016 nM. Dechlorination ceased following the addition of 0.5 mM sulfite, whereas sulfate (10 mM) and nitrate (5 mM) had no inhibitory effects.

Isolation and transcriptional analysis of novel tetrachloroethene reductive dehalogenase gene from Desulfitobacterium sp. strain KBC1

Strain KBC1, an anaerobic bacterium, that dechlorinates tetrachloroethene (PCE) to trichloroethene was isolated. This strain also dechlorinated high concentrations of PCE at a temperature range of 10 to 40 degrees C and showed high oxygen tolerance. Based on the 16S rRNA gene sequence analysis, this microorganism was identified as a species of the genus Desulfitobacterium. Several species of this genus have been reported to be potent ortho-chlorophenol and PCE dechlorinators; however, the gene coding PCE-specific dehalogenase had not been cloned thus far. In this report, we identified a novel PCE reductive dehalogenase (PrdA) gene from the Desulfitobacterium sp. strain KBC1. These prd genes, including putative membrane anchor protein, were classified as novel type of PCE reductive dehalogenase (approximately 40% homology with the general PCE dehalogenase). It was revealed that the two open reading frames had been transcribed as identical mRNA and were induced strictly in the presence of PCE. This transcriptional regulation appeared to be controlled by the transcriptional activator located downstream of prdAB operon. According to the substrate utility of the strain KBC1 and phylogenetic analysis of PrdA, this microorganism may be expected to play the role of a primary dechlorinator of PCE in the environment.

Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1

Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.

Natural attenuation and enhanced bioremediation of organic contaminants in groundwater

An area of intense scientific and practical interest is the biogeochemical and microbial processes determining the success of natural attenuation, biostimulation and/or bioaugmentation treatments for organic contaminants in groundwater. Recent studies in this area have focused on the reductive dechlorination of chlorinated solvents, the degradation of the fuel additive methyl tert-butyl ether, and the removal of long-term hydrocarbon contamination. These studies have been facilitated by the use of stable isotope analysis to demonstrate in situ bioremediation and push-pull tests, in which isotopes are injected into aquifers and then quickly retrieved and analyzed, to measure in situ activity. Molecular tools such as quantitative PCR, the detection of mRNA expression, and numerous DNA fingerprinting methods have also proved valuable, being employed to identify and sometimes quantify environmentally important organisms or changes in communities. Methods to track bacteria and tools to characterize bacterial attachment properties have also offered insight into bacterial transport in situ.

Enrichment, cultivation, and detection of reductively dechlorinating bacteria

Strategies and procedures for enriching, isolating, and cultivating reductively dechlorinating bacteria that use chloroorganic compounds as metabolic electron acceptors from environmental samples are described. Further, nucleic acid-based approaches used to detect and quantify dechlorinator (i.e., Dehalococcoides)-specific genes are presented.

Anaerobic microbial dehalogenation

The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating--or completely mineralizing--halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.

Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1

Dehalococcoides sp. strain BAV1 couples growth with the reductive dechlorination of vinyl chloride (VC) to ethene. Degenerate primers targeting conserved regions in reductive dehalogenase (RDase) genes were designed and used to PCR amplify putative RDase genes from strain BAV1. Seven unique RDase gene fragments were identified. Transcription analysis of VC-grown BAV1 cultures suggested that bvcA was involved in VC reductive dechlorination, and the complete sequence of bvcA was obtained. bvcA was absent in Dehalococcoides isolates that failed to respire VC, yet was detected in four of eight VC-respiring mixed cultures.