Trichloroethylene biodegradation by a methane-oxidizing bacterium

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH₄ ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH₄ , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH₄ monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

Electrochemical reductive remediation of trichloroethylene contaminated groundwater using biomimetic iron-nitrogen-doped carbon

Electrochemical dechlorination is a prospective strategy to remediate trichloroethylene (TCE)-contaminated groundwater. In this work, iron-nitrogen-doped carbon (FeNC) mimicking microbiological dechlorination coenzymes was developed for TCE removal under environmentally related conditions. The biomimetic FeNC-900, FeNC-1000, and FeNC-1100 materials were synthesized via pyrolysis at different temperatures (900, 1000, and 1100 °C). Due to the synergistic effect of Fe-N₄ active sites and graphitic N sites, FeNC-1000 had the highest electron transfer efficiency and the largest electrochemical active surface area among the as-synthesized FeNC catalysts. The pseudo-first-order rate constants for TCE reduction using FeNC-1000 catalyst are 0.19, 0.28 and 0.36 h^-1 at potentials of -0.8 V, -1.0 V and -1.2 V, respectively. Active hydrogen and direct electrons transfer both contribute to the dechlorination from TCE to C₂H₄ and C₂H₆. FeNC maintain a high reactivity after five reuse cycles. Our study provides a novel approach for the dechlorination of chlorinated organic contaminants in groundwater.

Biotechnology and nanotechnology for remediation of chlorinated volatile organic compounds: current perspectives

Chlorinated volatile organic compounds (CVOCs) are persistent organic pollutants which are harmful to public health and the environment. Many CVOCs occur in substantial quantities in groundwater and soil, even though their use has been more carefully managed and restricted in recent years. This review summarizes recent data on several innovative treatment solutions for CVOC-affected media including bioremediation, phytoremediation, nanoscale zero-valent iron (nZVI)-based reductive dehalogenation, and photooxidation. There is no optimally developed single technology; therefore, the possibility of using combined technologies for CVOC remediation, for example bioremediation integrated with reduction by nZVI, is presented. Some methods are still in the development stage. Advantages and disadvantages of each treatment strategy are provided. It is hoped that this paper can provide a basic framework for selection of successful CVOC remediation strategies.

Degradation of tetra- and trichloroethylene under iron reducing conditions by Acidimicrobiaceae sp. A6

The degradation of trichloroethylene (TCE) and tetrachloroethylene (PCE), in incubations where ammonium was oxidized while iron was being reduced indicates that these compounds can be degraded during the Feammox process by Acidimicrobiaceae sp. A6 (ATCC, PTA-122488). None of these compounds were degraded in incubations to which no ammonium was added, indicating that they were degraded during the oxidation of ammonium. Degradation of TCE and PCE (ranging between 32% and 55%) was observed in incubations with a pure Acidimicrobiaceae sp. A6 culture as well as an Acidimicrobiaceae sp. A6 enrichment culture over a 2-week period. In addition to these batch studies, a column study, with a 5-h hydraulic residence time, was conducted contrasting the degradation of TCE in iron-rich soil columns that were either seeded with a pure or an enrichment culture of Acidimicrobiaceae sp. A6 to achieve ammonium oxidation under iron reduction, and a control column that was initially not seeded and later seeded with Geobacter metallireducens. While there was ∼22% TCE removal in the columns seeded with Acidimicrobiaceae sp. A6, there was no removal in the unseeded column or the column seeded with G. metallireducens which was being operated under iron reducing conditions. Feammox is an anoxic process that requires acidic conditions. Hence, these results indicate that this process might be harnessed where other bioremediation strategies are difficult, since many require neutral or alkaline conditions, and supplying ammonium to an anoxic aquifer is relatively easy, since there are not many processes that will oxidize ammonium in the absence of dissolved oxygen.

Development of a novel chem-bio hybrid process using biochar supported nanoscale iron sulfide composite and Corynebacterium variabile HRJ4 for enhanced trichloroethylene dechlorination

A sequential chem-bio hybrid process was developed using a novel biochar supported carboxymethyl cellulose-stabilized nanoscale iron sulfide (CMC-FeS@biochar) as a chemical remover and Corynebacterium variabile HRJ4 as a biological agent for trichloroethylene (TCE) degradation. Compared with CMC-FeS, FeS@biochar600, bare FeS and biochar600, the CMC-FeS@biochar600 composite displayed better physiochemical properties (smaller hydrodynamic diameter and higher stability) and demonstrated excellent removal capacity for TCE from aqueous phase. A facultative bacterial strain, Corynebacterium variabile HRJ4, growing well in the presence of CMC-FeS@biochar (added up to 0.25 g L^-1), further enhanced TCE removal after chemical treatment. The dechlorination pathway proposed based on the gas chromatography-mass spectrometry (GC-MS) analysis revealed that TCE was dechlorinated to cis-1,2-dichloroethene (cis-DCE) and acetylene via hydrogenolysis and β-elimination, respectively within 12 h by CMC-FeS@biochar. Addition of HRJ4 strain into the reaction system effectively enhanced the degradation of the residual TCE, cis-DCE and acetylene to ethylene. Acetylene was the main product in chemical process, whereas ethylene was the main product in biological process as strain HRJ4 could reduce acetylene to ethylene effectively. The results of this study signify the potential application of CMC-FeS@biochar600/HRJ4 chem-bio hybrid system for complete degradation of TCE in the anaerobic environment.

Composition and emission of VOC from biogas produced by illegally managed waste landfills in Giugliano (Campania, Italy) and potential impact on the local population

The composition in Volatile Organic Compounds (VOC) of the biogas produced by seven landfills of Giugliano (Naples, Campania, Italy) was determined and VOC emission rates assessed to verify if these compounds represent a potential threat to the population living nearby. VOC composition in the biogas could not be predicted, as heterogeneous waste was dumped from the late 1980s to the early 2000s and then underwent biological degradation. No data are available on the amount and composition of VOC in the biogas before the landfills closure as no operational biogas collection system was present. In this study, VOC composition was determined by gas chromatography-mass spectrometry (GC-MS), after collecting samples from collection pipes and from soil fractures in cover soil or capping. Individual VOC were quantified and data compared with those collected at two landfills in Latium, when they were still in operation. Relevant differences were observed, mainly due to waste aging, but no specific VOC revealing toxic waste dumping was found, although the concurrent presence of certain compounds suggested that dumping of industrial wastes might have occurred. The average VOC emission was assessed and a dispersion model was run to find out if the emitted plume could affect the health of population. The results suggested that fugitive emissions did not represent a serious danger, since the concentrations simulated at the neighboring cities were below the threshold limits for acute and chronic diseases. However, VOC plume could cause annoyance at night when the steady state conditions of the atmosphere enhance pollutants accumulation in the lower layers. In addition, some of the emitted VOC, such as alkylbenzenes and monoterpenes, can contribute to tropospheric ozone formation.

Development of a novel methanotrophic process with the helper micro-organism Hyphomicrobium sp. NM3

AIMS

Microbial consortia can be more efficient at biological processes than single isolates. The purposes of this study were to design and evaluate a synthetic microbial consortium containing the methanotroph Methylocystis sp. M6 and the helper Hyphomicrobium sp. NM3, and develop a novel methanotrophic process for this consortium utilizing a dialysis membrane.

METHODS AND RESULTS

Hyphomicrobium increased the methane-oxidation rate (MOR), biomass and stability at a dilution rate of 0·067 day^-1 in fed-batch co-culture. qRT-PCR showed that Methylocystis population increased gradually with time, whereas Hyphomicrobium population remained stable despite cell washing, confirming synergistic population interaction. At 0·1 day^-1 , spiking of Hyphomicrobium effectively increased the methanotrophic activity, after which Hyphomicrobium population decreased with time, indicating that the consortium is optimal at <0·1 day^-1 . When Hyphomicrobium was grown in dialysis membrane within the bioreactor, MOR increased linearly up to 155·1 ± 1·0 mmol l^-1  day^-1 at 0·067, 0·1, 0·2 and 0·4 day^-1 , which is the highest observed value for a methanotrophic reactor.

CONCLUSIONS

Hyphomicrobium sp. NM3 is a promising helper micro-organism for methanotrophs. Hyphomicrobium-methanotroph consortia used concurrently with existing methods can produce an efficient and stable methane oxidation system.

SIGNIFICANCE AND IMPACT OF THE STUDY

This novel methanotrophic process is superior to those previously reported in the literature, and can provide efficient and stable methane oxidation.

Novel approaches and reasons to isolate methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives

The recent drop in the price of natural gas has rekindled the interests in methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse methanotrophs with relatively high growth rates. For long, isolation of methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.

Evaluating alternate biokinetic models for trace pollutant cometabolism

Mathematical models of cometabolic biodegradation kinetics can improve our understanding of the relevant microbial reactions and allow us to design in situ or in-reactor applications of cometabolic bioremediation. A variety of models are available, but their ability to describe experimental data has not been systematically evaluated for a variety of operational/experimental conditions. Here five different models were considered: first-order; Michaelis-Menten; reductant; competition; and combined models. The models were assessed on their ability to fit data from simulated batch experiments covering a realistic range of experimental conditions. The simulated observations were generated by using the most complex model structure and parameters based on the literature, with added experimental error. Three criteria were used to evaluate model fit: ability to fit the simulated experimental data, identifiability of parameters using a colinearity analysis, and suitability of the model size and complexity using the Bayesian and Akaike Information criteria. Results show that no single model fits data well for a range of experimental conditions. The reductant model achieved best results, but required very different parameter sets to simulate each experiment. Parameter nonuniqueness was likely to be due to the parameter correlation. These results suggest that the cometabolic models must be further developed if they are to reliably simulate experimental and operational data.

Degradation kinetics of chlorinated aliphatic hydrocarbons by methane oxidizers naturally-associated with wetland plant roots

Chlorinated aliphatic hydrocarbons (CAHs) are common groundwater contaminants that can be removed from the environment by natural attenuation processes. CAH biodegradation can occur in wetland environments by reductive dechlorination as well as oxidation pathways. In particular, CAH oxidation may occur in vegetated wetlands, by microorganisms that are naturally associated with the roots of wetland plants. The main objective of this study was to evaluate the cometabolic degradation kinetics of the CAHs, cis-1,2-dichloroethene (cisDCE), trichloroethene (TCE), and 1,1,1-trichloroethane (1,1,1TCA), by methane-oxidizing bacteria associated with the roots of a typical wetland plant in soil-free system. Laboratory microcosms with washed live roots investigated aerobic, cometabolic degradation of CAHs by the root-associated methane-oxidizing bacteria at initial aqueous [CH4] ~1.9mgL(-1), and initial aqueous [CAH] ~150μgL(-1); cisDCE and TCE (in the presence of 1,1,1TCA) degraded significantly, with a removal efficiency of approximately 90% and 46%, respectively. 1,1,1TCA degradation was not observed in the presence of active methane oxidizers. The pseudo first-order degradation rate-constants of TCE and cisDCE were 0.12±0.01 and 0.59±0.07d(-1), respectively, which are comparable to published values. However, their biomass-normalized degradation rate constants obtained in this study were significantly smaller than pure-culture studies, yet they were comparable to values reported for biofilm systems. The study suggests that CAH removal in wetland plant roots may be comparable to processes within biofilms. This has led us to speculate that the active biomass may be on the root surface as a biofilm. The cisDCE and TCE mass losses due to methane oxidizers in this study offer insight into the role of shallow, vegetated wetlands as an environmental sink for such xenobiotic compounds.

Density-dependent enhancement of methane oxidation activity and growth of Methylocystis sp. by a non-methanotrophic bacterium Sphingopyxis sp

Methanotrophs are a biological resource as they degrade the greenhouse gas methane and various organic contaminants. Several non-methanotrophic bacteria have shown potential to stimulate growth of methanotrophs when co-cultured, and however, the ecology is largely unknown. Effects of Sphingopyxis sp. NM1 on methanotrophic activity and growth of Methylocystis sp. M6 were investigated in this study. M6 and NM1 were mixed at mixing ratios of 9:1, 1:1, and 1:9 (v/v), using cell suspensions of 7.5 × 10¹¹ cells L^-1. Methane oxidation of M6 was monitored, and M6 population was estimated using fluorescence in situ hybridization (FISH). Real-time PCR was applied to quantify rRNA and expression of transcripts for three enzymes involved in the methane oxidation pathway. NM1 had a positive effect on M6 growth at a 1:9 ratio (p < 0.05), while no significant effects were observed at 9:1 and 1:1 ratios. NM1 enhanced the methane oxidation 1.34-fold at the 1:9 ratio. NM1 increased the population density and relative rRNA level of M6 by 2.4-fold and 5.4-fold at the 1:9 ratio, indicating that NM1 stimulated the population growth of M6. NM1 increased the relative transcriptional expression of all mRNA targets only at the 1:9 ratio. These results demonstrated that NM1 enhanced the methanotrophic activity and growth of M6, which was dependent on the proportion of NM1 present in the culture. This stimulation can be used as management and enhancement strategies for methanotrophic biotechnological processes.

Revisiting methanotrophic communities in sewage treatment plants

The methanotrophic potential in sewage treatment sludge was investigated. We detected a diverse aerobic methanotrophic community that potentially plays a significant role in mitigating methane emission in this environment. The results suggest that community structure was determined by conditions specific to the processes in a sewage treatment plant.

Current trends in trichloroethylene biodegradation: a review

Over the past few years biodegradation of trichloroethylene (TCE) using different microorganisms has been investigated by several researchers. In this review article, an attempt has been made to present a critical summary of the recent results related to two major processes--reductive dechlorination and aerobic co-metabolism used for TCE biodegradation. It has been shown that mainly Clostridium sp. DC-1, KYT-1, Dehalobacter, Dehalococcoides, Desulfuromonas, Desulfitobacterium, Propionibacterium sp. HK-1, and Sulfurospirillum bacterial communities are responsible for the reductive dechlorination of TCE. Efficacy of bacterial communities like Nitrosomonas, Pseudomonas, Rhodococcus, and Xanthobacter sp. etc. for TCE biodegradation under aerobic conditions has also been examined. Mixed cultures of diazotrophs and methanotrophs have been used for TCE degradation in batch and continuous cultures (biofilter) under aerobic conditions. In addition, some fungi (Trametes versicolor, Phanerochaete chrysosporium ME-446) and Actinomycetes have also been used for aerobic biodegradation of TCE. The available information on kinetics of biofiltration of TCE and its degradation end-products such as CO2 are discussed along with the available results on the diversity of bacterial community obtained using molecular biological approaches. It has emerged that there is a need to use metabolic engineering and molecular biological tools more intensively to improve the robustness of TCE degrading microbial species and assess their diversity.

Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation

Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.

Phenylalanine as a hydroxyl radical-specific probe in pyrite slurries

The abundant iron sulfide mineral pyrite has been shown to catalytically produce hydrogen peroxide (H2O2) and hydroxyl radical (.OH) in slurries of oxygenated water. Understanding the formation and fate of these reactive oxygen species is important to biological and ecological systems as exposure can lead to deleterious health effects, but also environmental engineering during the optimization of remediation approaches for possible treatment of contaminated waste streams. This study presents the use of the amino acid phenylalanine (Phe) to monitor the kinetics of pyrite-induced .OH formation through rates of hydroxylation forming three isomers of tyrosine (Tyr) - ortho-, meta-, and para-Tyr. Results indicate that about 50% of the Phe loss results in Tyr formation, and that these products further react with .OH at rates comparable to Phe. The overall loss of Phe appeared to be pseudo first-order in [Phe] as a function of time, but for the first time it is shown that initial rates were much less than first-order as a function of initial substrate concentration, [Phe]o. These results can be rationalized by considering that the effective concentration of .OH in solution is lower at a higher level of reactant and that an increasing fraction of .OH is consumed by Phe-degradation products as a function of time. A simplified first-order model was created to describe Phe loss in pyrite slurries which incorporates the [Phe]o, a first-order dependence on pyrite surface area, the assumption that all Phe degradation products compete equally for the limited supply of highly reactive .OH, and a flux that is related to the release of H2O2 from the pyrite surface (a result of the incomplete reduction of oxygen at the pyrite surface). An empirically derived rate constant, Kpyr, was introduced to describe a variable .OH-reactivity for different batches of pyrite. Both the simplified first-order kinetic model, and a more detailed numerical simulation, yielded results that compare well to the observed kinetic data describing the effects of variations in concentrations of both initial Phe and pyrite. This work supports the use of Phe as a useful probe to assess the formation of .OH in the presence of pyrite, and its possible utility for similar applications with other minerals.

Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils

The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation.

Reductive Dechlorination of Trichloroethylene and Tetrachloroethylene under Aerobic Conditions in a Sediment Column

Biodegradation of trichloroethylene and tetrachloroethylene under aerobic conditions was studied in a sediment column. Cumulative mass balances indicated 87 and 90% removal for trichloroethylene and tetrachloroethylene, respectively. These studies suggest the potential for simultaneous aerobic and anaerobic biotransformation processes under bulk aerobic conditions.

Biodegradation of trichloroethylene in continuous-recycle expanded-bed bioreactors

Experimental bioreactors operated as recirculated closed systems were inoculated with bacterial cultures that utilized methane, propane, and tryptone-yeast extract as aerobic carbon and energy sources and degraded trichloroethylene (TCE). Up to 95% removal of TCE was observed after 5 days of incubation. Uninoculated bioreactors inhibited with 0.5% Formalin and 0.2% sodium azide retained greater than 95% of their TCE after 20 days. Each bioreactor consisted of an expanded-bed column through which the liquid phase was recirculated and a gas recharge column which allowed direct headspace sampling. Pulses of TCE (20 mg/liter) were added to bioreactors, and gas chromatography was used to monitor TCE, propane, methane, and carbon dioxide. Pulsed feeding of methane and propane with air resulted in 1 mol of TCE degraded per 55 mol of substrate utilized. Perturbation studies revealed that pH shifts from 7.2 to 7.5 decreased TCE degradation by 85%. The bioreactors recovered to baseline activities within 1 day after the pH returned to neutrality.

Soluble Methane Monooxygenase Production and Trichloroethylene Degradation by a Type I Methanotroph, Methylomonas methanica 68-1

A methanotroph (strain 68-1), originally isolated from a trichloroethylene (TCE)-contaminated aquifer, was identified as the type I methanotroph Methylomonas methanica on the basis of intracytoplasmic membrane ultrastructure, phospholipid fatty acid profile, and 16S rRNA signature probe hybridization. Strain 68-1 was found to oxidize naphthalene and TCE via a soluble methane monooxygenase (sMMO) and thus becomes the first type I methanotroph known to be able to produce this enzyme. The specific whole-cell sMMO activity of 68-1, as measured by the naphthalene oxidation assay and by TCE biodegradation, was comparatively higher than sMMO activity levels in Methylosinus trichosporium OB3b grown in the same copper-free conditions. The maximal naphthalene oxidation rates of Methylomonas methanica 68-1 and Methylosinus trichosporium OB3b were 551 +/- 27 and 321 +/- 16 nmol h mg of protein , respectively. The maximal TCE degradation rates of Methylomonas methanica 68-1 and Methylosinus trichosporium OB3b were 2,325 +/- 260 and 995 +/- 160 nmol h mg of protein, respectively. The substrate affinity of 68-1 sMMO to naphthalene (K(m), 70 +/- 4 muM) and TCE (K(m), 225 +/- 13 muM), however, was comparatively lower than that of the sMMO of OB3b, which had affinities of 40 +/- 3 and 126 +/- 8 muM, respectively. Genomic DNA slot and Southern blot analyses with an sMMO gene probe from Methylosinus trichosporium OB3b showed that the sMMO genes of 68-1 have little genetic homology to those of OB3b. This result may indicate the evolutionary diversification of the sMMOs.

Cometabolism of chlorinated solvents by nitrifying bacteria: kinetics, substrate interactions, toxicity effects, and bacterial response

Pure cultures of ammonia-oxidizing bacteria, Nitrosomonas europaea, were exposed to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), chloroform (CF), 1,2-dichloroethane (1,2-DCA), or carbon tetrachloride (CT), in the presence of ammonia, in a quasi-steady-state bioreactor. Estimates of enzyme kinetics constants, solvent inactivation constants, and culture recovery constants were obtained by simultaneously fitting three model curves to experimental data using nonlinear optimization techniques and an enzyme kinetics model, referred to as the inhibition, inactivation, and recovery (IIR) model, that accounts for inhibition of ammonia oxidation by the solvent, enzyme inactivation by solvent product toxicity, and respondent synthesis of new enzyme (recovery). Results showed relative enzyme affinities for ammonia monooxygenase (AMO) of 1,1-DCE approximately TCE > CT > NH(3) > CF > 1,2-DCA. Relative maximum specific substrate transformation rates were NH(3) > 1,2-DCA > CF > TCE approximately 1,1-DCE > CT (=0). The TCE, CF, and 1,1-DCE inactivated the cells, with 1,1-DCE being about three times more potent than TCE or CF. Under the conditions of these experiments, inactivating injuries caused by TCE and 1,1-DCE appeared limited primarily to the AMO enzyme, but injuries caused by CF appeared to be more generalized. The CT was not oxidized by N. europaea while 1,2-DCA was oxidized quite readily and showed no inactivation effects. Recovery capabilities were demonstrated with all solvents except CF. A method for estimating protein yield, the relationship between the transformation capacity model and the IIR model, and a condition necessary for sustainable cometabolic treatment of inactivating substrates are presented. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 520-534, 1997.

A review: advances in microbial remediation of trichloroethylene (TCE)

Research works in the recent past have revealed three major biodegradation processes leading to the degradation of trichloroethylene. Reductive dechlorination is an anaerobic process in which chlorinated ethenes are used as electron acceptors. On the other hand, cometabolism requires oxygen for enzymatic degradation of chlorinated ethenes, which however yields no benefit for the bacteria involved. The third process is direct oxidation under aerobic conditions whereby chlorinated ethenes are directly used as electron donors by microorganisms. This review presented the current research trend in understanding biodegradation mechanisms with regard to their field applications. All the techniques used are evaluated, with the focus being on various factors that influence the process and the outcome.

Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods

The occurrence of chlorinated ethene transformation in a streambed was investigated using concentration and carbon isotope data from water samples taken at different locations and depths within a 15 x 25 m study area across which a tetrachloroethene (PCE) plume discharges. Furthermore, it was evaluated how the degree of transformation is related to groundwater discharge rates, redox conditions, solid organic matter content (SOM) and microbial factors. Groundwater discharge rates were quantified based on streambed temperatures, and redox conditions using concentrations of dissolved redox-sensitive species. The degree of chlorinated ethene transformation was highly variable in space from no transformation to transformation beyond ethene. Complete reductive dechlorination to ethane and ethene occurred at locations with at least sulfate-reducing conditions and with a residence time in the samples streambed zone (80 cm depth) of at least 10 days. Among these locations, Dehalococcoides was detected using a PCR method where SOM contents were >2% w/w and where transformation proceeded beyond ethene. However, it was not detected at locations with low SOM, which may cause an insufficient H(2) supply to sustain a detectably dense Dehalococcoides population. Additionally, it is possible that other organisms are responsible for the biodegradation. A microcosm study with streambed sediments demonstrated the potential of VC oxidation throughout the site even at locations without a pre-exposure to VC, consistent with the detection of the epoxyalkane:coenzyme M transferase (EaCoMT) gene involved in the degradation of chlorinated ethenes via epoxidation. In contrast, no aerobic transformation of cDCE in microcosms over a period of 1.5 years was observed. In summary, the study demonstrated that carbon isotope analysis is a sensitive tool to identify the degree of chlorinated ethene transformation even in hydrologically and geochemically complex streambed systems. In addition, it was observed that the degree of transformation is related to redox conditions, which in turn depend on groundwater discharge rates.

Environmentally relevant microorganisms

The development of molecular microbial ecology in the 1990s has allowed scientists to realize that microbial populations in the natural environment are much more diverse than microorganisms so far isolated in the laboratory. This finding has exerted a significant impact on environmental biotechnology, since knowledge in this field has been largely dependent on studies with pollutant-degrading bacteria isolated by conventional culture methods. Researchers have thus started to use molecular ecological methods to analyze microbial populations relevant to pollutant degradation in the environment (called environmentally relevant microorganisms, ERMs), although further effort is needed to gain practical benefits from these studies. This review highlights the utility and limitations of molecular ecological methods for understanding and advancing environmental biotechnology processes. The importance of the combined use of molecular ecological and physiological methods for identifying ERMs is stressed.

Trichloroethylene degradation by Ralstonia sp. KN1-10A constitutively expressing phenol hydroxylase: transformation products, NADH limitation, and product toxicity

Ralstonia sp. KN1-10A, which was constructed by inserting the tac promoter upstream of the phenol hydroxylase (PH) gene in the chromosomal DNA of the wild-type strain, Ralstonia sp. KN1, is a useful recombinant strain for eliminating trichloroethylene (TCE) from contaminated sites because it exhibits constitutive TCE oxidation activity. During TCE degradation by Ralstonia sp. KN1-10A, noxious chlorinated compounds, such as dichloroacetic acid, trichloroacetic acid, 2,2,2-trichloroethanol, and chloral, were not detected, and more than 95% of chlorine in TCE was released as chloride ions. Among the possible TCE transformation products, only carbon monoxide was detected, and its conversion percentage was 7 mol%. The addition of formate, which Ralstonia sp. KN1-10A could use as an exogenous electron donor, did not enhance the TCE degradation performance, suggesting that NADH depletion did not limit the degradation. The phenol degradation activity of Ralstonia sp. KN1-10A that previously degraded TCE was not markedly lower than that of cells not exposed to TCE, suggesting that Ralstonia sp. KN1-10A was not susceptible to product toxicity associated with TCE degradation. Furthermore, to clarify the mechanisms underlying TCE degradation by PH from Ralstonia sp. KN1, this enzyme was compared with another enzyme, a hybrid aromatic ring dioxygenase exhibiting a high TCE degradation activity in Escherichia coli and Pseudomonas sp. The initial TCE degradation rate of Ralstonia sp. KN1 (pKTP100), which produced PH, was 1 50 lower than that of Ralstonia sp. KN1 (pKTF200), which produced the hybrid aromatic ring dioxygenase. However, because of its lower product toxicity, the strain producing PH could degrade 2.3 times more TCE than that generated by the strain producing the hybrid aromatic ring dioxygenase.

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.

Diversity of oxygenase genes from methane- and ammonia-oxidizing bacteria in the Eastern Snake River Plain aquifer

PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus Methylocystis. A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.

The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria

Methane gas is produced from many natural and anthropogenic sources. As such, methane gas plays a significant role in the Earth's climate, being 25 times more effective as a greenhouse gas than carbon dioxide. As with nearly all other naturally produced organic molecules on Earth, there are also micro-organisms capable of using methane as their sole source of carbon and energy. The microbes responsible (methanotrophs) are ubiquitous and, for the most part, aerobic. Although anaerobic methanotrophs are believed to exist, so far, none have been isolated in pure culture. Methanotrophs have been known to exist for over 100 years; however, it is only in the last 30 years that we have begun to understand their physiology and biochemistry. Their unique ability to use methane for growth is attributed to the presence of a multicomponent enzyme system-methane monooxygenase (MMO)-which has two distinct forms: soluble (sMMO) and membrane-associated (pMMO); however, both convert methane into the readily assimilable product, methanol. Our understanding of how bacteria are capable of effecting one of the most difficult reactions in chemistry-namely, the controlled oxidation of methane to methanol-has been made possible by the isolation, in pure form, of the enzyme components.The mechanism by which methane is activated by sMMO involves abstraction of a hydrogen atom from methane by a high-valence iron species (FeIV or possibly FeV) in the hydroxylase component of the MMO complex to form a methyl radical. The radical combines with a captive oxygen atom from dioxygen to form the reaction product, methanol, which is further metabolized by the cell to produce multicarbon intermediates. Regulation of the sMMO system relies on the remarkable properties of an effector protein, protein B. This protein is capable of facilitating component interactions in the presence of substrate, modifying the redox potential of the diiron species at the active site. These interactions permit access of substrates to the hydroxylase, coupling electron transfer by the reductase with substrate oxidation and affecting the rate and regioselectivity of the overall reaction. The membrane-associated form is less well researched than the soluble enzyme, but is known to contain copper at the active site and probably iron. From an applied perspective, methanotrophs have enjoyed variable successes. Whole cells have been used as a source of single-cell protein (SCP) since the 1970s, and although most plants have been mothballed, there is still one currently in production. Our earlier observations that sMMO was capable of inserting an oxygen atom from dioxygen into a wide variety of hydrocarbon (and some non-hydrocarbon) substrates has been exploited to either produce value added products (e.g. epoxypropane from propene), or in the bioremediation of pollutants such as chlorinated hydrocarbons. Because we have shown that it is now possible to drive the reaction using electricity instead of expensive chemicals, there is promise that the system could be exploited as a sensor for any of the substrates of the enzyme.

In situ bioremediation of a cis-dichloroethylene-contaminated aquifer utilizing methane-rich groundwater from an uncontaminated aquifer

At a trichloroethylene (TCE)-contaminated site in Chikura, Chiba, Japan, TCE had spread over to the first and second aquifers over years. After 8 years of pumping and treatment, finally derivative of TCE, cis-dichloroethylene (c-DCE) remained only in the second aquifer. In this study, feasibility of a low cost in situ bioremediation utilizing groundwater of the third aquifer, which contained natural dissolved methane possibly derived from natural gas field nearby, to stimulate methane-oxidizing bacteria was examined. In vitro experiment showed that a mixture of the groundwater from the second and third aquifers stimulated a growth of methane oxidizing bacteria and enhanced c-DCE degradation. The groundwater of the third aquifer was introduced into the second aquifer in situ. The population of methanotrophs with high V(max) and K(m) for methane uptake increased, resulting in successful degradation of c-DCE at a monitoring well 2m downgradient of the injection well.

Microbial community structure and trichloroethylene degradation in groundwater

Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon–Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.Key words: community structure, trichloroethylene, degradation, groundwater.

Chlorinated aliphatic hydrocarbon-induced degradation of trichloroethylene in Wautersia numadzuensis sp. nov

Two strains of trichloroethylene (TCE)-degrading bacteria were isolated from soils at polluted and unpolluted sites. The isolates, strains TE26(T) and K6, showed co-substrate-independent TCE-degrading activity. TCE degradation was accelerated by preincubation with tetrachloroethylene, cis-dichloroethylene (DCE) and 1,1-DCE. TCE-degrading activities of strains TE26(T) and K6 were 0.23, 0.24 micromol min(-1) g(-1) dry cells, respectively. 16S rDNA sequences of strains TE26(T) and K6 were almost identical (99.7% similarity), and most closely related to Ralstonia basilensis (ATCC17697(T)) (98.5% similarity). From the results of DNA-DNA hybridizations, strain TE26(T) was genetically coherent to strain K6 (94 and 88% hybridization), and exhibited lower relatedness to R. basilensis (DSM11853(T)) (44% and 15%). In addition, because of the differences in chemotaxonomic properties, strain TE26(T) and strain K6 appear to be distinct from all established species of the Ralstonia group. Based on these results and the proposal of transferring R. basilensis and related species to Wautersia gen. nov., we propose that these strains should be assigned to the genus Wautersia as Wautersia numadzuensis sp. nov.

Pilot studies for in-situ aerobic cometabolism of trichloroethylene using toluene-vapor as the primary substrate

In-situ pilot studies of aerobic cometabolism were conducted to evaluate the injection of toluene-vapor and air into TCE-contaminated aquifer. Delivery of primary substrate (toluene) in a vapor state with air enhanced the growth of indigenous toluene-utilizing bacteria that would degrade TCE by aerobic cometabolism. Meanwhile, delivering toluene in a vapor state effectively reduced potential clogging near the injection points due to excessive microbial growth, which was observed in the field when the injection of neat toluene was employed. Over 90% removal of TCE was achieved with primary substrate (toluene) degraded to a concentration below 10 microg/L.

Characterization of methanogenic and methanotrophic assemblages in landfill samples

A greater understanding of the tightly linked trophic groups of anaerobic and aerobic bacteria residing in municipal solid waste landfills will increase our ability to control methane emissions and pollutant fate in these environments. To this end, we characterized the composition of methanogenic and methanotrophic bacteria in samples taken from two regions of a municipal solid waste landfill that varied in age. A method combining polymerase chain reaction amplification, restriction fragment length polymorphism analysis and phylogenetic analysis was used for this purpose. 16S rDNA sequence analysis revealed a rich assemblage of methanogens in both samples, including acetoclasts, H2/CO2-users and formate-users in the newer samples and H2/CO2-users and formate-users in the older samples, with closely related genera including Methanoculleus, Methanofollis, Methanosaeta and Methanosarcina. Fewer phylotypes of type 1 methanotrophs were observed relative to type 2 methanotrophs. Most type 1 sequences clustered within a clade related to Methylobacter, whereas type 2 sequences were broadly distributed among clades associated with Methylocystis and Methylosinus species. This genetic characterization tool promises rapid screening of landfill samples for genotypes and, therefore, degradation potentials.

Trichloroethylene degradation in a coupled anaerobic/aerobic reactor oxygenated using hydrogen peroxide

In this work, trichloroethylene (TCE) degradation under combined anaerobic-aerobic conditions was studied in an ethanol-fed biofilm reactor oxygenated using hydrogen peroxide. The reactor was inoculated with a biomass originating from an anaerobic digestor. Granulated peat was added to the reactor as a substratum for biofilm development. Extensive characterization of reactor populations using activity tests and PCR analysis revealed the development of a mutualistic consortium, particularly methanotrophic and methanogenic microorganisms. This consortium was shown to degrade TCE by a combination of reductive and oxidative pathways. A near complete degradation of TCE at a load of 18 mg L(R)(-1) day(-1) was evidenced by a stoichiometric release of inorganic chloride.

Evolution of the soluble diiron monooxygenases

Based on structural, biochemical, and genetic data, the soluble diiron monooxygenases can be divided into four groups: the soluble methane monooxygenases, the Amo alkene monooxygenase of Rhodococcus corallinus B-276, the phenol hydroxylases, and the four-component alkene/aromatic monooxygenases. The limited phylogenetic distribution of these enzymes among bacteria, together with available genetic evidence, indicates that they have been spread largely through horizontal gene transfer. Phylogenetic analyses reveal that the alpha- and beta-oxygenase subunits are paralogous proteins and were derived from an ancient gene duplication of a carboxylate-bridged diiron protein, with subsequent divergence yielding a catalytic alpha-oxygenase subunit and a structural beta-oxygenase subunit. The oxidoreductase and ferredoxin components of these enzymes are likely to have been acquired by horizontal transfer from ancestors common to unrelated diiron and Rieske center oxygenases and other enzymes. The cumulative results of phylogenetic reconstructions suggest that the alkene/aromatic monooxygenases diverged first from the last common ancestor for these enzymes, followed by the phenol hydroxylases, Amo alkene monooxygenase, and methane monooxygenases.