Strain GJ10 Research Articles

Aerobic Dechlorination of Dichloromethane Using Biostimulation Agent BD-C in Continuous and Batch Cultures of Xanthobacter autotrophicus GJ10.

It is important to construct microbiological treatment systems for organic solvent-contaminated water. We developed a continuous culture supplemented with a biostimulation agent named BD-C, which is formulated from canola oil, and Xanthobacter autotrophicus strain GJ10 for an aerobic dichloromethane (DCM)-dechlorinating microorganism. The continuous culture was a chemostat constructed using a 1 L screw-capped bottle containing artificial wastewater medium with 2.0 mM DCM and 1.0% (v/v) BD-C. The expression of genes for DCM metabolism in the dechlorinating aerobe was monitored and analyzed by reverse transcription-quantitative PCR. Strain GJ10 was able to dechlorinate approximately 74% of the DCM in medium supplemented with BD-C during 12 days of incubation. The DCM dechlorination rate was calculated to be 0.11 mM/day. The ΔΔCT method showed that expression of haloalkane dehalogenase increased 5.4 times in the presence of BD-C. Based on batch culture growth tests conducted with mineral salt medium containing three DCM concentrations (0.07, 0.20, 0.43 and 0.65 mM) with BD-C, the apparent maximum specific consumption rate (νmax) and the saturation constant (Ks) determined for DCM degradation in this test were 19.0 nmol/h/CFU and 0.44 mM, respectively. In conclusion, BD-C enhanced the aerobic degradation of DCM by strain GJ10.

A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site.

1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.

Complete detoxification of tris(2-chloroethyl) phosphate by two bacterial strains: Sphingobium sp. strain TCM1 and Xanthobacter autotrophicus strain GJ10

Tris(2-chloroethyl) phosphate (TCEP), a flame retardant, is recently regarded as a potentially toxic and persistent environmental contaminant. We previously isolated TCEP-degrading bacterium, Sphingobium sp. strain TCM1, which, however, produced a toxic metabolite: 2-chloroethanol (2-CE). This study was undertaken to develop a detoxification technique of TCEP using strain TCM1 with a 2-CE-degrading bacterium: Xanthobacter autotrophicus strain GJ10. TCEP degradation by strain TCM1-resting cells was thermally stable for 30 min at 30 °C. It was optimal at 30 °C and at pH 8.5. In the optimum condition, TCM1 cells up to a final cell density of 0.8 at OD(660) in the reaction mixture were unable to hydrolyze the phosphotriester bonds of 10 μM TCEP completely. The addition of 50 μM Co(2+) to reaction mixture enhanced the hydrolysis and caused the complete hydrolysis at the cell density of 0.8. Strain GJ10 resting cells degraded 2-CE only slightly, which might be attributable to lack of coenzyme regeneration of enzymes involved in the degradation. In contrast, the growing cells degraded approximately 180 μM of 2-CE within 24 h. Based on these results, we designed a two-step TCEP detoxification reaction consisting of TCEP hydrolysis to 2-CE by strain TCM1-resting cells and the following degradation of the resulting 2-CE by strain GJ10-growing cells. The combined reaction completely detoxified 10 μM TCEP, and thus opens a way to microbial detoxification of the potential toxic, persistent organophosphorus compound.

Novel method for immobilization of enzymes to magnetic nanoparticles

The value of coupling biological molecules such as enzymes to solid materials has long been recognized. To date, protein immobilization onto such surfaces often involves covalent coupling, encapsulation, or non-specific adsorption techniques. Here we demonstrate the feasibility of specifically attaching a haloalkane dehalogenase enzyme to silica-coated or uncoated iron oxide superparamagnetic nanoparticles using affinity peptides. The enzyme was cloned from Xanthobacter autotrophicus strain GJ10 into Escherichia coli to produce fusion proteins containing dehalogenase sequences with C-terminal polypeptide repeats that have specific affinity for either silica or iron oxide. The fusion proteins serve dual functions, allowing for specific inorganic surface binding and for enzymatic activity. The degree of fusion protein adsorption to nanoparticle surfaces was found to exceed that of enzymes that had not been activated with affinity sequences, particularly for iron-oxide nanoparticles. The ability to specifically adsorb cloned affinity-tagged dehalogenase was further demonstrated by selectively adsorbing dehalogenase fusion proteins containing an iron-oxide affinity tripeptide directly from cell lysate. The retention of enzymatic activity was found to be dependent upon the surface chemistry of the nanoparticles. An increase in activity was observed after adsorption of fusion proteins onto the surface of nanoparticles modified by treatment with hydrophilic polyethylene glycol or 3-glycidoxypropyltrimethoxysilane molecules. As a result of this work, it is possible to tag an active enzyme with specific peptides that bind to inorganic nanoparticle surfaces. Because the conjugates self assemble, the novel surface-specific conjugate formation procedure is highly efficient and easily scalable for use in large-scale applications.

The use of an oil–absorber–bioscrubber system during biodegradation of sequentially alternating loadings of 1,2-dichloroethane and fluorobenzene in a waste gas

This work seeks to improve the robustness of vapour phase bioscrubbing by applying an absorber prior to a bioscrubber during the dynamic treatment of sequentially alternating loads of inhibitory pollutants. Rhizobiales sp. strain F11 and Xanthobacter autotrophicus sp. GJ10, exhibiting specific degradation capabilities for fluorobenzene (FB) and 1,2-dichloroethane (DCE), respectively, were used as a compound-strain model system. The stability of a combined oil–absorber–bioscrubber (OAB) was compared to the stability of a bioscrubber only (BO) system, during sequentially alternating periods (duration 3–6 d) of FB and DCE in the gas feed. The OAB achieved > 66 % degradation of FB, while in the BO system the FB removal efficiency dropped to 0% upon restoring FB feed after a 3 d FB starvation period. Following 6 d of FB starvation the BO failed to recover within 10 d, while the OAB required only 2 d to recover. In contrast, during the DCE treatment periods the OAB system did not show any advantage over the BO system. Further investigation showed that the F - (a main metabolic product from FB degradation) has a strong inhibitory effect on strain GJ10 even at concentrations below 50 mg L - 1 . In the OAB system the inhibitory effect persisted for longer periods due to the absorber, which continued to supply FB to the system, and caused deterioration in the DCE removal efficiency. The inhibition of the microbial culture was confirmed by fluorescence in situ hybridisation (FISH), which showed that the activity of cells was reduced when only FB was fed. The results of this study have shown that in the presence of an inhibitory metabolic product the OAB system may not effectively improve the biological treatment of waste gas during sequential alternations in the feed of inhibitory pollutants.

Metabolism of mono- and dihalogenated C1 and C2 compounds by Xanthobacter autotrophicus growing on 1,2-dichloroethane

The conversion of and toxic effects exerted by several mono- and dihalogenated C1 and C2 compounds on cultures of Xanthobacter autotrophicus GJ10 growing on 1,2-dichloroethane were investigated. Bromochloromethane, dibromomethane and 1-bromo-2-chloroethane were utilized by strain GJ10 in batch culture as a cosubstrate and sole carbon source. The rate of degradation of dihalomethanes by whole cells was lower than that of 1,2-dichloroethane, but a significant increase of the rate of dihalomethane biodegradation was observed when methanol or ethanol were added as a cosubstrate. Products of the degradation of several tested compounds by haloalkane dehalogenase were analyzed and a new metabolic pathway based on hydrolytic conversion to formaldehyde was proposed for the dihalomethanes. Strain GJ10 growing on 1,2-dichloroethane converted 2-fluoroethanol and 1-chloro-2-fluoroethane to 2-fluoroacetate, which was tolerated up to a concentration of 2.5 mM. On the basis of the results from batch cultures an inert (dichloromethane), a growth-supporting (dibromomethane) and a toxic (1,2-dibromoethane) compound were selected for testing their effects on a continuous culture of strain GJ10 growing on 1,2-dichloroethane. The compounds were added as pulses to a steady-state chemostat and the response of the culture was followed. The effects varied from a temporary decrease in cell density for dibromomethane to severe toxicity and culture washout with 1,2-dibromoethane. Our results extend the spectrum of halogenated C1 and C2 compounds that are known to be degraded by strain GJ10 and provide information on toxic effects and transformation of compounds not serving as a carbon source for this bacterium.

Stability and Performance of Xanthobacter autotrophicus GJ10 during 1,2-Dichloroethane Biodegradation

A nucleic acid-based approach was used to investigate the dynamics of a microbial community dominated by Xanthobacter autotrophicus GJ10 in the degradation of synthetic wastewater containing 1,2-dichloroethane (DCE). This study was performed over a 140-day period in a nonsterile continuous stirred-tank bioreactor (CSTB) subjected to different operational regimens: nutrient-limiting conditions, baseline operation, and the introduction of glucose as a cosubstrate. The microbial community was analyzed by a combination of fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Under nutrient-limiting conditions, DCE degradation was restricted, but this did not affect the dominance of strain GJ10, determined by FISH to comprise 85% of the active population. During baseline operation, DCE degradation improved significantly to over 99.5% and then remained constant throughout the subsequent experimental period. DGGE profiles revealed a stable, complex community, while FISH indicated that strain GJ10 remained the dominant species. During the addition of glucose as a cosubstrate, DGGE profiles showed a proliferation of other species in the CSTB. The percentage of strain GJ10 dropped to 8% of the active population in just 5 days, although this did not affect the DCE biodegradation performance. The return to baseline conditions was accompanied by the reestablishment of strain GJ10 as the dominant species, suggesting that this system responds robustly to external perturbations, both at the functional biodegradation level and at the individual strain level.

An Oil-Absorber−Bioscrubber System To Stabilize Biotreatment of Pollutants Present in Waste Gas. Fluctuating Loads of 1,2-Dichloroethane

Biotreatment technologies offer a cost-effective and efficient method for dealing with point-source releases of solvents. However, a major problem hampering these technologies is the fluctuating pollutant loads, which is especially critical for inhibitory pollutants. Provision of biotreatment systems able to cope with this problem is a significant technological and environmental challenge. This study investigates the potential for an absorber to act as buffer for shock loadings of inhibitory pollutants in waste-gas streams undergoing biological treatment. 1,2-Dichloroethane (DCE) was used as an example of a toxic and inhibitory organic pollutant. The stability of a combined oil-absorber-bioscrubber (OAB) system was compared to that of a bioscrubber only (BO) system when each was subjected to shock loads of DCE. The BO system was inoculated with Xanthobacter autotrophicus strain GJ10 and was submitted to sharp, sequential pulses in DCE inlet load, which caused system instability. Complete inhibition of the BO process occurred for a 3 h DCE pulse, leading to 9125 g of DCE m(-3)bioscrubber total organic discharged (TODDCE). Following the pulse, fluorescence in situ hybridization (FISH) showed that the active strain GJ10 was effectively washed-out. In contrast, the performance of the OAB system was stable during DCE shock loads. The carbon dioxide production remained stable, and low levels of effluent DCE and total organic carbon concentrations were found. For the 3 h pulse TODDCE was only 173 g of DCE m(-3)bioscrubber, and FISH indicated that the GJ10 strain remained active. We conclude that the OAB system offers an effective solution to the biological treatment of waste-gas containing fluctuating pollutant concentrations.

Microbial dynamics in an extractive membrane bioreactor exposed to an alternating sequence of organic compounds.

Wastewaters containing organic compounds have been treated using extractive membrane bioreactors (EMBs). During treatment, a biofilm normally develops on the surface of the membrane, on the biological side. This study investigates the dynamics of biofilm growth in an EMB exposed to an alternating sequence of organic compounds. Microbial dynamics of both suspended and attached cultures were investigated experimentally in a single-tube extractive membrane bioreactor (STEMB), which comprised a continuous stirred-tank bioreactor (CSTB) coupled to eight single-tube extractive membrane modules (STEMMs) via a recirculating biomedium. A model microbial culture consisting of a Burkholderia sp. strain JS150 (ATCC No. 51283), able to degrade monochlorobenzene, and a Xanthobacter autotrophicus sp. strain GJ10 (ATCC No. 43050), able to degrade 1, 2-dichloroethane, was used. Both microbial strains exhibited exclusive degradative capabilities. The CSTB was monitored by quantification of individual strains and by product and organic compound evolution. To investigate the biofilm growth dynamics, eight STEMMs were run in parallel with the same operating conditions. Every week, STEMMs were stopped for biofilm analysis and the organic compound in the wastewater was changed. Biofilm growth was investigated by quantification of individual strains, by evaluation of the overall biofilm growth, and by microscopic analysis. A biofilm composed of both strains was developed and maintained during the whole experiment in the STEMMs. The biofilm that developed on the membrane improved the response of the system to changes in the wastewater.

A novel method for characterisation of microbial growth kinetics on volatile organic compounds

A novel method for the determination of microbial growth kinetics on hydrophobic volatile organic compounds (VOC) has been developed. A stirred tank reactor was operated as a fed-batch system to which the VOC was continuously fed via the gas phase, assuring a constant VOC concentration in the mineral medium. A flow of air was saturated with the VOC, and then mixed with a further flow of air, to obtain a predetermined VOC concentration. Thus, different VOC concentrations in the mineral medium could be obtained by altering the VOC concentration in the feed gas. The growth kinetics of Xanthobacter autotrophicus GJ10 on 1,2-dichloroethane (DCE) and of Pseudomonas sp. strain JS150 on MonoChloroBenzene (MCB) were assessed using this method. The growth of strain JS150 was strongly inhibited at MCB concentrations higher than 160 mg l−1, and the results were fitted using a piecewise function. The growth kinetics of strain GJ10 were described by the Luong model where maximum growth rate μmax = 0.12 h−1, substrate saturation constant K S = 7.8 mg l−1, and maximum substrate concentration S m (above which growth is completely inhibited) = 1080 mg l−1. Varying nitrogen and oxygen flows enabled the effect of oxygen concentration on the growth kinetics of Pseudomonas JS150 to be determined.

Heterologous expression in Escherichia coli of soluble active-site random mutants of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 by coexpression of molecular chaperonins GroEL/ES.

A system for heterologous expression in Escherichia coli of dehaloalkane dehalogenase Dh1A from Xanthobacter autotrophicus strain GJ10 is presented. The strategy involved overexpression of E. coli chaperonins GroEL/ES which facilitated the production of soluble Dh1A. When active-site mutant forms were constructed they could not to any detectable degree be expressed in a soluble state in the absence of overproduced GroEL/ES. However, with the described expression system, wild-type Dh1A as well as variant forms randomly mutated in the active-site residues Phe172 and Trp175 were reliably produced. An introduced C-terminal (His)5-tag provided an immunological handle as well as a site for metal ion coordination utilized in affinity chromatography for the purification of recombinant Dh1A. The purified His-tagged enzyme, Dh1A-5His, was confirmed to be catalytically fully active when measuring the dehalogenase activity with dichloroethane as substrate.

Identification of Functional Residues in a 2-Hydroxymuconic Semialdehyde Hydrolase: A NEW MEMBER OF THE α/β HYDROLASE-FOLD FAMILY OF ENZYMES WHICH CLEAVES CARBON-CARBON BONDS

The 2-hydroxymuconic semialdehyde hydrolase, XylF, of the Pseudomonas putida TOL plasmid-encoded pathway for the catabolism of toluene and xylenes, catalyzes one of the rarest types of enzyme reaction (EC 3.7.1.9), the hydrolysis of a carbon-carbon bond in its substrate, the ring-fission product of 3-alkyl-substituted catechols. In this study, amino acid sequence comparisons between XylF and other hydrolases, and analysis of the similarity between the predicted secondary structure of XylF and the known secondary structure of the haloalkane dehalogenase from Xanthobacter autotrophicus strain GJ10, led us to identify several conserved residues likely to have a functional role in the catalytic center of XylF. Three amino acids, Ser107, Asp228, and His256, were found to be arranged in a sequential order similar to that in alpha/beta hydrolase-fold enzymes. Investigations of the potential functional role of these and other residues through amino acid modification and in vitro site-directed mutagenesis experiments provided evidence in support of the hypothesis that XylF is a serine hydrolase of the alpha/beta hydrolase-fold family of enzymes, and pointed to the residues identified above as the catalytic triad of XylF. These studies also provided information on other conserved residues in XylF-related enzymes. Interestingly, the substitution of Phe by Met in position 108 of XylF created an enzyme with increased thermostability and altered substrate specificity.

Identification of Chloroacetaldehyde Dehydrogenase Involved in 1,2-Dichloroethane Degradation

The degradation of 1,2-dichloroethane and 2-chloroethanol by Xanthobacter autotrophicus GJ10 proceeds via chloroacetaldehyde, a reactive and potentially toxic intermediate. The organism produced at least three different aldehyde dehydrogenases, of which one is plasmid encoded. Two mutants of strain GJ10, designated GJ10M30 and GJ10M41, could no longer grow on 2-chloroethanol and were found to lack the NAD-dependent aldehyde dehydrogenase that is the predominant protein in wild-type cells growing on 2-chloroethanol. Mutant GJ10M30, selected on the basis of its resistance to 1,2-dibromoethane, also had lost haloalkane dehalogenase activity and Hg resistance, indicating plasmid loss. From a gene bank of strain GJ10, different clones that complemented one of these mutants were isolated. In both transconjugants, the aldehyde dehydrogenase that was absent in the mutants was overexpressed. The enzyme was purified and was a tetrameric protein of 55-kDa subunits. The substrate range was rather broad, with the highest activity measured for acetaldehyde. The K(m) value for chloroacetaldehyde was 160 muM, higher than those for other aldehydes tested. It is concluded that the ability of GJ10 to grow with 2-chloroethanol is due to the high expression level of an aldehyde dehydrogenase with a rather low activity for chloroacetaldehyde.

Influence of organic nutrients and cocultures on the competitive behavior of 1,2-dichloroethane-degrading bacteria.

The effects of organic nutrients and cocultures on substrate removal by and competitive behavior of 1,2-dichloroethane-degrading bacteria were investigated. Xanthobacter autotrophicus GJ10 needed biotin for optimal growth on 1,2-dichloroethane. In continuous culture, dilution of biotin to a concentration below 0.2 nM resulted in washout. Growth could be restored by inoculation with the 2-chloroethanol utilizer Pseudomonas sp. strain GJ1, leading to a new steady state in which about 1% of the mixed culture consisted of cells of strain GJ1. This indicates that strain GJ1 excreted biotin or a precursor for its synthesis. Inoculation of the mixed culture with Ancylobacter aquaticus AD25 did not result in washout of strain GJ10, although strain AD25 has a 10-fold-lower Ks for growth on 1,2-dichloroethane. Strain AD25 did not become dominant because of the lack of vitamins, which are necessary for its optimal growth. The results indicate that medium composition and the presence of other species strongly influence the effect of substrate limitation on the composition of a bacterial population that degrades a xenobiotic compound in a continuous culture.

Involvement of a Quinoprotein Alcohol Dehydrogenase and an NAD-dependent Aldehyde Dehydrogenase in 2-Chloroethanol Metabolism in Xanthobacter autotrophicus GJ10

An inducible methanol dehydrogenase showing high activity with 2-chloroethanol was purified from 2-chloroethanol-grown cells of the 1, 2-dichloroethane utilizing bacterium Xanthobacter autotrophicus GJ10. The enzyme consisted of a 60 kDa polypeptide that was associated with a 10 kDa polypeptide and contained pyrrolo-quinoline quinone (PQQ) as a prosthetic group. Chloroethanol-grown cells of strain GJ10 also contained an inducible NAD-dependent chloroacetaldehyde dehydrogenase. Its involvement in the metabolism of 2-chloroethanol was inferred from its absence in a 2-chloroethanol non-utilizing mutant. Three different isolates of X. autotrophicus that do not utilize 2-chloroethanol for growth produced chloroethanol dehydrogenase and chloroacetaldehyde dehydrogenase activities at similar levels as strain GJ10. It is concluded that both dehydrogenases are involved in the metabolism of natural compounds and due to their broad substrate specificity fortuitously also play a role in the metabolism of the xenobiotic compounds 1,2-dichloroethane and 2-chloroethanol.