Oxidation of the cyclic ethers 1,4-dioxane and tetrahydrofuran by a monooxygenase in two Pseudonocardia species.

The bacterium Pseudonocardia dioxanivorans CB1190 grows on the cyclic ethers 1,4-dioxane (dioxane) and tetrahydrofuran (THF) as sole carbon and energy sources. Prior transcriptional studies indicated that an annotated THF monooxygenase (THF MO) gene cluster, thmADBC, located on a plasmid in CB1190 is upregulated during growth on dioxane. In this work, transcriptional analysis demonstrates that upregulation of thmADBC occurs during growth on the dioxane metabolite ß-hydroxyethoxyacetic acid (HEAA) and on THF. Comparison of the transcriptomes of CB1190 grown on THF and succinate (an intermediate of THF degradation) permitted the identification of other genes involved in THF metabolism. Dioxane and THF oxidation activity of the THF MO was verified in Rhodococcus jostii RHA1 cells heterologously expressing the CB1190 thmADBC gene cluster. Interestingly, these thmADBC expression clones accumulated HEAA as a dead-end product of dioxane transformation, indicating that despite its genes being transcriptionally upregulated during growth on HEAA, the THF MO enzyme is not responsible for degradation of HEAA in CB1190. Similar activities were also observed in RHA1 cells heterologously expressing the thmADBC gene cluster from Pseudonocardia tetrahydrofuranoxydans K1.

RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans†CB1190.

Pseudonocardia is an actinobacterial genus of interest due to its potential biotechnological, medical and environmental remediation applications, as well as for the ecologically relevant symbiotic relationships it forms with attine ants. Some Pseudonocardia spp. can grow autotrophically, but the genetic basis of this capability has not previously been reported. In this study, we examined autotrophy in Pseudonocardia dioxanivorans CB1190, which can grow using H2 and CO2, as well as heterotrophically. Genomic and transcriptomic analysis of CB1190 cells grown with H2/bicarbonate implicated the Calvin-Benson-Bassham (CBB) cycle in growth-supporting CO2 fixation, as well as a [NiFe] hydrogenase-encoding gene cluster in H2 oxidation. The CBB cycle genes are evolutionarily most related to actinobacterial homologues, although synteny has not been maintained. Ribulose-1,5-bisphosphate carboxylase activity was confirmed in H2/bicarbonate-grown CB1190 cells and was detected in cells grown with the C1 compounds formate, methanol and carbon monoxide. We also demonstrated the upregulation of CBB cycle genes upon exposure of CB1190 to these C1 substrates, and identified genes putatively involved in generating CO2 from the C1 substrates by using RT-qPCR. Finally, the potential for autotrophic growth of other Pseudonocardia spp. was explored, and the ecological implications of autotrophy in attine ant- and plant root-associated Pseudonocardia discussed.

The impact of chlorinated solvent co-contaminants on the biodegradation kinetics of 1,4-dioxane.

1,4-Dioxane (dioxane), a probable human carcinogen, is used as a solvent stabilizer for 1,1,1-trichloroethane (TCA) and other chlorinated solvents. Consequently, TCA and its abiotic breakdown product 1,1-dichloroethene (DCE) are common co-contaminants of dioxane in groundwater. The aerobic degradation of dioxane by microorganisms has been demonstrated in laboratory studies, but the potential effects of environmentally relevant chlorinated solvent co-contaminants on dioxane biodegradation have not yet been investigated. This work evaluated the effects of TCA and DCE on the transformation of dioxane by dioxane-metabolizing strain Pseudonocardia dioxanivorans CB1190, dioxane co-metabolizing strain Pseudonomas mendocina KR1, as well as Escherichia coli expressing the toluene monooxygenase of strain KR1. In all experiments, both TCA and DCE inhibited the degradation of dioxane at the tested concentrations. The inhibition was not competitive and was reversible for strain CB1190, which did not transform the chlorinated solvents. For both strain KR1 and toluene monooxygenase-expressing E. coli, inhibition of dioxane degradation by chlorinated solvents was competitive and irreversible, and the chlorinated solvents were degraded concurrently with dioxane. These data suggest that the strategies for biostimulation or bioaugmentation of dioxane will need to consider the presence of chlorinated solvents during site remediation.

Glyoxylate metabolism is a key feature of the metabolic degradation of 1,4-dioxane by Pseudonocardia dioxanivorans strain CB1190.

The groundwater contaminant 1,4-dioxane (dioxane) is transformed by several monooxygenase-expressing microorganisms, but only a few of these, including Pseudonocardia dioxanivorans strain CB1190, can metabolize the compound as a sole carbon and energy source. However, nothing is yet known about the genetic basis of dioxane metabolism. In this study, we used a microarray to study differential expression of genes in strain CB1190 grown on dioxane, glycolate (a previously identified intermediate of dioxane degradation), or pyruvate. Of eight multicomponent monooxygenase gene clusters carried by the strain CB1190 genome, only the monooxygenase gene cluster located on plasmid pPSED02 was upregulated with dioxane relative to pyruvate. Plasmid-borne genes for putative aldehyde dehydrogenases, an aldehyde reductase, and an alcohol oxidoreductase were also induced during growth with dioxane. With both dioxane and glycolate, a chromosomal gene cluster encoding a putative glycolate oxidase was upregulated, as were chromosomal genes related to glyoxylate metabolism through the glyoxylate carboligase pathway. Glyoxylate carboligase activity in cell extracts from cells pregrown with dioxane and in Rhodococcus jostii strain RHA1 cells expressing the putative strain CB1190 glyoxylate carboligase gene further demonstrated the role of glyoxylate metabolism in the degradation of dioxane. Finally, we used (13)C-labeled dioxane amino acid isotopomer analysis to provide additional evidence that metabolites of dioxane enter central metabolism as three-carbon compounds, likely as phosphoglycerate. The routing of dioxane metabolites via the glyoxylate carboligase pathway helps to explain how dioxane is metabolized as a sole carbon and energy source for strain CB1190.

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

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

Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190.

Pseudonocardia dioxanivorans CB1190 is the first bacterium reported to be capable of growth on the environmental contaminant 1,4-dioxane and the first member of the genus Pseudonocardia for which there is an annotated genome sequence. Preliminary analysis of the genome (chromosome and three plasmids) indicates that strain CB1190 possesses several multicomponent monooxygenases that could be involved in the aerobic degradation of 1,4-dioxane and other environmental contaminants.

Insights into enzyme kinetics of chloroethane biodegradation using compound specific stable isotopes.

While compound specific isotope analysis (CSIA) has been used extensively to investigate remediation of chlorinated ethenes, to date considerably less information is available on its applicability to chlorinated ethanes. In this study, biodegradation of 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA) was carried out by a Dehalobacter-containing mixed culture. Carbon isotope fractionation factors (ε) measured during whole cell degradation demonstrated that values for 1,1,1-TCA and 1,1-DCA (-1.8‰ and -10.5‰, respectively) were significantly smaller than values reported for abiotic reductive dechlorination of these same compounds. Similar results were found in experiments degrading these two priority pollutants by cell free extracts (CFE) where values of -0.8‰ and -7.9‰, respectively, were observed. For 1,1,1-TCA in particular, the large kinetic isotope effect expected for cleavage of a C-Cl bond was almost completely masked during biodegradation by both whole cells and CFE. Comparison to previous studies demonstrates that these patterns of isotopic fractionation are not attributable to transport effects across the cell membrane, as had been seen for other compounds such as PCE. In contrast these results reflect significant differences in the kinetics of the enzymes catalyzing chlorinated ethane degradation.

Chloroform respiration to dichloromethane by a Dehalobacter population.

Chloroform (CF), or trichloromethane, is an ubiquitous environmental pollutant because of its widespread industrial use, historically poor disposal and recalcitrance to biodegradation. Chloroform is a potent inhibitor of metabolism and no known organism uses it as a growth substrate. We discovered that CF was rapidly and sustainably dechlorinated in the course of investigating anaerobic reductive dechlorination of 1,1,1-trichloroethane in a Dehalobacter-containing culture. Like 1,1,1-trichloroethane dechlorination in this culture, CF dechlorination was a growth-linked respiratory process, requiring H(2) as an electron donor and CF as an electron acceptor. Moreover, the same specific reductive dehalogenase likely catalyzed both reactions. This Dehalobacter population appears specialized for substrates with three halogen substituents on the same carbon atom, with widespread implications for bioremediation.

1,1,1-trichloroethane and 1,1-dichloroethane reductive dechlorination kinetics and co-contaminant effects in a Dehalobacter-containing mixed culture.

1,1,1-Trichloroethane (1,1,1-TCA) is a common groundwater contaminant that can be reductively dechlorinated to 1,1-dichloroethane (1,1-DCA) and monochloroethane, and can support the growth of certain dehalorespiring strains of Dehalobacter We used reductive dehalogenase cell-free extract assays (with reduced methyl viologen) and whole cell suspension dechlorination assays (with hydrogen) and a Dehalobacter-containing enrichment culture to explore the kinetics of l,1,1-TCA and 1,1-DCA reductive dechlorination in the presence of the common co-contaminants trichloroethene (TCE), cis-dichloroethene (cDCE), and vinyl chloride (VC). These chlorinated ethenes were most significant inhibitors of 1,1,1-TCA dechlorination in cell-free extracts, indicating direct effects on the reductive dehalogenase enzyme(s). The inhibition was present but less pronounced in whole cell suspension assays. None of the chlorinated ethenes inhibited 1,1-DCA dechlorination in cell-free extract assays, yet cDCE and particularly VC were inhibitors in whole cell assays, indicating an effect on Dehalobacter, but not on the dehalogenase enzyme(s). Marked differences in kinetic parameters for 1,1,1-TCA and 1,1-DCA, and an uncoupling of these two activities in cultures grown on 1,1-DCA compared to those grown on 1,1,1-TCA was strong evidence for the existence of distinct 1,1,1-TCA and 1,1-DCA reductive dehalogenase enzymes.

Characterization of a Dehalobacter coculture that dechlorinates 1,2-dichloroethane to ethene and identification of the putative reductive dehalogenase gene.

Dehalobacter and "Dehalococcoides" spp. were previously shown to be involved in the biotransformation of 1,1,2-trichloroethane (1,1,2-TCA) and 1,2-dichloroethane (1,2-DCA) to ethene in a mixed anaerobic enrichment culture. Here we report the further enrichment and characterization of a Dehalobacter sp. from this mixed culture in coculture with an Acetobacterium sp. Through a series of serial transfers and dilutions with acetate, H(2), and 1,2-DCA, a stable coculture of Acetobacterium and Dehalobacter spp. was obtained, where Dehalobacter grew during dechlorination. The isolated Acetobacterium strain did not dechlorinate 1,2-DCA. Quantitative PCR with specific primers showed that Dehalobacter cells did not grow in the absence of a chlorinated electron acceptor and that the growth yield with 1,2-DCA was 6.9 (+/-0.7) x 10(7) 16S rRNA gene copies/mumol 1,2-DCA degraded. PCR with degenerate primers targeting reductive dehalogenase genes detected three distinct Dehalobacter/Desulfitobacterium-type sequences in the mixed-parent culture, but only one of these was present in the 1,2-DCA-H(2) coculture. Reverse transcriptase PCR revealed the transcription of this dehalogenase gene specifically during the dechlorination of 1,2-DCA. The 1,2-DCA-H(2) coculture could dechlorinate 1,2-DCA but not 1,1,2-TCA, nor could it dechlorinate chlorinated ethenes. As a collective, the genus Dehalobacter has been show to dechlorinate many diverse compounds, but individual species seem to each have a narrow substrate range.

Quantification of biotransformation of chlorinated hydrocarbons in a biostimulation study: added value via stable carbon isotope analysis.

Stable carbon isotope analysis of chlorinated aliphatic compounds was performed at an in situ biostimulation pilot test area (PTA) at a site where 1,2-dichloroethane (1,2-DCA) and trichloroethene (TCE) were present in groundwater. Chlorinated products of TCE reductive dechlorination (cis-dichloroethene (cDCE) and vinyl chloride (VC)) were present at concentrations of 17.5 to 126.4 micromol/L. Ethene, a potential degradation product of both 1,2-DCA dihaloelimination and TCE reductive dechlorination was also present in the PTA. Emulsified soybean oil and lactate were added as electron donors to stimulate anaerobic dechlorination in the PTA. Stable carbon isotope analysis provided evidence that dechlorination was occurring in the PTA during biostimulation, and a means of monitoring changes in dechlorination efficiency over the 183 day monitoring period. Stable carbon isotope analysis was also used to determine if ethene production in the PTA was due to dechlorination of TCE, 1,2-DCA, or both. Fractionation factors (alpha) were determined in the laboratory during anaerobic biotransformation of 1,2-DCA via a dihaloelimination reaction in four separate enrichment cultures. These alpha values (as well as the previously published ranges of alpha for the dechlorination of TCE, cDCE and 1,2-DCA) were used, along with isotopic values measured during the pilot test, to derive quantitative estimates of biotransformation during the pilot test. Dechlorination was found to account for 10.7 to 35.9%, 21.9 to 74.9%, and 54.4 to 67.8% of 1,2-DCA, TCE and cDCE concentration loss respectively in the PTA. Stable carbon isotope analysis indicates that dechlorination of 1,2-DCA, TCE and cDCE were all significant processes during the pilot test, while ethene production during the pilot test was dominated by 1,2-DCA dihaloelimination. This study demonstrates how stable carbon isotope analysis can provide more conservative estimates of the extent of biotransformation than do conventional protocols. In addition, in a complex mixed plume such as this, compound specific isotope analysis is shown to be one of the few methods available for clarifying dominant biotransformation pathways where breakdown products are non-exclusive (i.e. ethene).

A 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes.

1,1,1-trichloroethane (1,1,1-TCA) is a common groundwater pollutant as a result of improper disposal and accidental spills. It is often found as a cocontaminant with trichloroethene (TCE) and inhibits some TCE-degrading microorganisms. 1,1,1-TCA removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. This study characterized MS, a 1,1,1-TCA-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-TCA-contaminated site in the northeastern United States. MS reductively dechlorinated 1,1,1-TCA to 1,1-dichloroethane (1,1-DCA) and then to monochloroethane (CA) but not further. Cloning of bacterial 16S rRNA genes revealed among other organisms the presence of a Dehalobacter sp. and a Desulfovibrio sp., which are both phylogenetically related to known dehalorespiring strains. Monitoring of these populations with species-specific quantitative PCR during degradation of 1,1,1-TCA and 1,1-DCA showed that Dehalobacter proliferated during dechlorination. Dehalobacter growth was dechlorination dependent, whereas Desulfovibrio growth was dechlorination independent. Experiments were also performed to test whether MS could enhance TCE degradation in the presence of inhibiting levels of 1,1,1-TCA. Dechlorination of cis-dichloroethene (cDCE) and vinyl chloride (VC) in KB-1, a chloroethene-degrading culture used for bioaugmentation, was inhibited with 1,1,1-TCA present. When KB-1 and MS were coinoculated, degradation of cDCE and VC to ethene proceeded as soon as the 1,1,1-TCA was dechlorinated to 1,1-DCA by MS. This demonstrated the potential application of the MS and KB-1 cultures for cobioaugmentation of sites cocontaminated with 1,1,1-TCA and TCE.

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.