Field evidence for co-metabolism of trichloroethene stimulated by addition of electron donor to groundwater

External carbon source as a viable tool for controlling antibiotics and antibiotic resistance genes (ARGs) in effluent: Influence on antibiotic removal and ARGs dissemination

Fluoroquinolone antibiotics and antibiotic resistance genes (ARGs) regarded as emerging contaminants were poorly removed in conventional wastewater treatment plants (WWTPs). Nitrogen-containing heterocyclic organics were found to be biodegraded through denitrification co-metabolism. The feasibility to enhance antibiotics removal efficiency in WWTPs through denitrification co-metabolism needs to be further verified. Meanwhile, due to significant correlation between ARGs profiles and nitrogen removal that was previously observed, the dissemination of ARGs during denitrification was worthy of in-depth understanding. Herein, the antibiotic removal and ARGs dissemination in denitrification co-metabolism condition were investigated with different denitrifying consortiums that acclimated under different conditions in terms of carbon source and the exposure of Ofloxacin (OFL). The results suggest that the removal of OFL can be enhanced by the denitrification co-metabolism. The tolerance to OFL is different among various denitrifying communities. For the denitrifying consortiums acclimated with methanol, long-term exposure to trace OFL (1 μg/L) could reduce the capabilities of removal and tolerance to OFL. On the contrary, those acclimated with sodium acetate (NaAc), the capabilities of removal and tolerance to OFL, were enhanced by long-term exposure to trace OFL. According to the quantitative determination to 384 target genes with high-throughput quantitative PCR, the abundance of ARGs in consortiums greatly increased when exposed to OFL at the concentration of comparable to sewage, which was also much larger than that acclimated with methanol. It can be confirmed and supported by DNA sequencing results that the antibiotic removal and the dissemination of ARGs were determined by microbial community that could be shaped with carbon source. These conclusions suggest that selecting the right external carbon source can be a useful strategy for WWTPs to control antibiotics and ARGs in the effluent. From a new perspective on mitigating ARGs dissemination, NaAc was not an appropriate carbon source.

Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation

Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.

Biodegradation of chloroethene compounds under microoxic conditions

The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic conditions are unknown. Here, we report the biostimulated (BIOST: addition of lactate) and natural attenuated (NAT) degradation of chloroethene compounds under microoxic conditions by bacterial communities from chloroethene compounds-contaminated groundwater. The degradation of tetrachloroethene was significantly higher in NAT (15.14% on average) than in BIOST (10.13% on average) conditions at the end of the experiment (90 days). Sporomusa, Paracoccus, Sedimentibacter, Pseudomonas, and Desulfosporosinus were overrepresented in NAT and BIOST compared to the source groundwater. The NAT metagenome contains phenol hydrolase P1 oxygenase (dmpL), catechol-1,2-dioxygenase (catA), catechol-2,3-dioxygenases (dmpB, todE, and xylE) genes, which could be involved in the cometabolic degradation of chloroethene compounds; and chlorate reductase (clrA), that could be associated with partial reductive dechlorination of chloroethene compounds. Our data provide a better understanding of the bacterial communities, genes, and pathways potentially implicated in the reductive and cometabolic degradation of chloroethene compounds under microoxic conditions.

Bioremediation of contaminated soil and groundwater by in situ biostimulation

Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.

Electrochemical biostimulation of aerobic metabolic TCE degradation in a bioaugmentation approach

Chloroethenes are globally prevalent groundwater contaminants. Since 2014, TCE has been shown to be degradable in an aerobic metabolic process where it is used as sole energy source and growth substrate by a mixed bacteria culture (SF culture). In 2019, the SF culture was shown to be successfully used in bioaugmentation approaches under field-relevant conditions. In this study, a combined bio-/electro-approach to stimulate the TCE degradation by the SF culture was investigated in laboratory experiments. Column experiments were set up to compare a bioaugmentation approach with an electrochemical biostimulated bioaugmentation approach. Low strength direct current increased the amount of degraded TCE to about 150 % of the control. Through lowering the inflow concentration of oxygen, the effect of the electro-biostimulation in a low oxygen setting confirmed the potential of the bio-electro process for treatment of oxygen-deprived, TCE-contaminated sites.

Identifying and Understanding Microbial Methanogenesis in CO2 Storage

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO₂ can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO₂, yet there has been little consideration of the subsurface microbial impact on CO₂ storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO₂ that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO₂ storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H₂ generation. We expect that the bioavailability of H₂ (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO₂ storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO₂ storage sites and its potential impact.

Coupled microscale zero valent iron-autotrophic hydrogen bacteria dechlorination system is not always superior to its standalone counterparts: A sustainable remediation perspective

The coupling of microscale zero-valent iron with autotrophic hydrogen bacteria (mZVI-AHB) are often believed to show greater potential than the single abiotic or biotic systems in remediating chlorinated aliphatic hydrocarbon-contaminated groundwater. However, our understanding of the remediation performance of this system under real field conditions, especially by incorporating the concept of sustainable remediation, remains limited. In this study, the performances of the mZVI, H₂-AHB, and mZVI-AHB systems in dechlorinating groundwater containing complex electron acceptors were compared by evaluating their removal efficiency (RE), reaction products, and electron efficiency (EE), using trichloroethylene (TCE) as the target contaminant and NO₃^- and SO₄^2- as the coexisting natural electron acceptors. Ultimately, which of these systems had TCE removal superiority was dependent on the coexisting electron acceptor. mZVI-AHB and mZVI resulted in more complete dechlorination, whereas H₂-AHB exhibited higher N₂ selectivity in reducing NO₃^-. Regardless of the coexisting electron acceptor, the mZVI-alone system showed the highest EE. Finally, the sustainability concerns and applicability of the three systems were evaluated on the basis of their TCE RE, complete dechlorination ratio, N₂ selectivity, EE, and cost, which were integrated into a comparison of overall benefits. Our findings provide comprehensive and insightful information on the factors that determine remediation scheme selection in real practice.

Recent advances and trends of trichloroethylene biodegradation: A critical review

Trichloroethylene (TCE) is a ubiquitous chlorinated aliphatic hydrocarbon (CAH) in the environment, which is a Group 1 carcinogen with negative impacts on human health and ecosystems. Based on a series of recent advances, the environmental behavior and biodegradation process on TCE biodegradation need to be reviewed systematically. Four main biodegradation processes leading to TCE biodegradation by isolated bacteria and mixed cultures are anaerobic reductive dechlorination, anaerobic cometabolic reductive dichlorination, aerobic co-metabolism, and aerobic direct oxidation. More attention has been paid to the aerobic co-metabolism of TCE. Laboratory and field studies have demonstrated that bacterial isolates or mixed cultures containing Dehalococcoides or Dehalogenimonas can catalyze reductive dechlorination of TCE to ethene. The mechanisms, pathways, and enzymes of TCE biodegradation were reviewed, and the factors affecting the biodegradation process were discussed. Besides, the research progress on material-mediated enhanced biodegradation technologies of TCE through the combination of zero-valent iron (ZVI) or biochar with microorganisms was introduced. Furthermore, we reviewed the current research on TCE biodegradation in field applications, and finally provided the development prospects of TCE biodegradation based on the existing challenges. We hope that this review will provide guidance and specific recommendations for future studies on CAHs biodegradation in laboratory and field applications.

Direct aerobic oxidation (DAO) of chlorinated aliphatic hydrocarbons: A review of key DAO bacteria, biometabolic pathways and in-situ bioremediation potential

Contamination of aquifers and vadose zones with chlorinated aliphatic hydrocarbons (CAH) is a world-wide issue. Unlike other reactions, direct aerobic oxidation (DAO) of CAHs does not require growth substrates and avoids the generation of toxic by-products. Here, we critically review the current understanding of chlorinated aliphatic hydrocarbons-DAO and its application in bioreactors and at the field scale. According to reports on chlorinated aliphatic hydrocarbons-DAO bacteria, isolates mainly consisted of Methylobacterium and Proteobacterium. Chlorinated aliphatic hydrocarbons-DAO bacteria are characterized by tolerance to a high concentration of CAHs and highly efficient removal of CAHs. Trans-1,2-dichloroethylene (t-DCE) is easily transformed biomass for bacteria, followed by 1,2-dichloroethane (1,2-DCA), dichloromethane (DCM), vinyl chloride (VC) and cis-1,2-dichloroethylene (c-DCE). Significant differences in the maximum specific growth rates were observed with different CAHs and biometabolic pathways for DCM, 1,2-DCA, VC and c-DCE degradation have been successfully parsed. Detection of the functional genes etnC and etnE is useful for the determination of active VC DAO bacteria. Additionally, DAO bacteria have been successfully applied to CAHs in new types of bioreactors with satisfactory results. To the best of the authors' knowledge, only one study on DAO-CAHs was conducted in-situ and resulted in 99% CAH removal. Lastly, we put forward future development prospect of chlorinated aliphatic hydrocarbons-DAO.

Insights into carbon isotope fractionation on trichloroethene degradation in base activated persulfate process: The role of multiple reactive oxygen species

Understanding the role of reactive oxygen species (ROS) is essential to elucidate the mechanism of contaminants degradation in in-situ chemical oxidation (ISCO). In this study, compound specific isotope analysis (CSIA) and radicals quenching methods were integrated to investigate the roles of hydroxyl radical (HO), sulfate radical (SO₄^-), and superoxide radical (O₂^-) on trichloroethene (TCE) degradation during persulfate (PS) activated with base. The carbon isotope fractionation of TCE was found to be dependent of the base:PS ratios, yielding carbon enrichment factors (ε values) from -9.8 ± 0.5‰ to -16.7 ± 1.0‰ at base:PS molar ratios between 0.5:1 and 10:1, which was attributed to multi-pathways degradation of TCE by multiple ROS. The expected ε value (-31.6 ± 1.6‰) for TCE degradation via O₂^- attacking pathway, was more negative than those values via SO₄^- or HO pathways. The relative contributions of HO, SO₄^- and O₂^- for TCE degradation during base activated PS were estimated with observed ε values. HO and O₂^- were the predominant ROS for TCE degradation (with the relative contribution of 55-69% and 22-45%, respectively) in base activated PS. This work highlights the prospect of CSIA application for identifying degradation pathways of contaminants with ROS in environment.

Sequential anaerobic and aerobic bioaugmentation for commingled groundwater contamination of trichloroethene and 1,4-dioxane

Chlorinated solvents, notably trichloroethene (TCE), and the cyclic ether stabilizer, 1,4-dioxane (dioxane), have been frequently detected commingling in contaminated aquifers. Here we developed a sequential anaerobic and aerobic treatment strategy effective to mitigate the co-contamination of TCE and dioxane, particularly when dioxane is present at ppb levels relevant to many impacted sites. After the primary anaerobic treatment by a halorespiring consortium SDC-9, TCE was effectively removed, though lingering less-chlorinated metabolites, vinyl chloride (VC) and cis-dichloroethene (cDCE). Subsequent aerobic bioaugmentation with Azoarcus sp. DD4, a cometabolic dioxane degrader, demonstrated the ability of DD4 to degrade dioxane at an initial concentration of 20 μg/L to below 0.4 μg/L and its dominance (~7%) in microcosms fed with propane. Even better, DD4 can also transform VC and cDCE in tandem, though cDCE and VC at relatively high concentrations (e.g., 1 mg/L) posed inhibition to propane assimilation and cell growth of DD4. Mutagenesis of DD4 revealed group-2 toluene monooxygenase and group-5 propane monooxygenase are responsible for cDCE and VC co-oxidation, respectively. Overall, we demonstrated the feasibility of a treatment train combining reductive dehalogenation and aerobic co-oxidation processes in tandem to not only effectively clean up prevalent co-contamination of TCE and dioxane at trace levels but also mitigate persistent products (e.g., cDCE and VC) when complete reductive dehalogenation of less-chlorinated ethenes occurs slowly in the field.

Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review

Chlorinated hydrocarbon contamination in soils and groundwater has a severe negative impact on the human health. Microbial reductive dechlorination is a major degradation pathway of chlorinated hydrocarbon in anaerobic subsurface environments, has been extensively studied. Recent progress on the diversity of the reductive dechlorinators and the key enzymes of chlororespiration has been well reviewed. Here, we present a thorough overview of the studies related to bioremediation of chloroethenes and polychlorinated biphenyls based on enhanced in situ reductive dechlorination. The major part of this review is to provide an up-to-date summary of functional microorganisms which are either detected during in situ biostimulation or applied in bioaugmentation strategies. The applied biostimulants and corresponding reductive dechlorination products are also summarized and the future research needs are finally discussed.

Microbial and Geochemical Dynamics of an Aquifer Stimulated for Microbial Induced Calcite Precipitation (MICP)

Microbially induced calcite precipitation (MICP) is an alternative to existing soil stabilization techniques for construction and erosion. As with any biologically induced process in soils or aquifers, it is important to track changes in the microbial communities that occur as a result of the treatment. Our research assessed how native microbial communities developed in response to injections of reactants (dilute molasses as a carbon source; urea as a source of nitrogen and alkalinity) that promoted MICP in a shallow aquifer. Microbial community composition (16S rRNA gene) and ureolytic potential (ureC gene copy numbers) were also measured in groundwater and artificial sediment. Aquifer geochemistry showed evidence of sulfate reduction, nitrification, denitrification, ureolysis, and iron reduction during the treatment. The observed changes in geochemistry corresponded to microbial community succession in the groundwater and this matched parallel geophysical and mineralogical evidence of calcite precipitation in the aquifer. We detected an increase in the number of ureC genes in the microbial communities at the end of the injection period, suggesting an increase in the abundance of microbes possessing this gene as needed to hydrolyze urea and stimulate MICP. We identify geochemical and biological markers that highlight the microbial community response that can be used along with geophysical and geotechnical evidence to assess progress of MICP.

Aerobic metabolic trichloroethene biodegradation under field-relevant conditions

Chloroethenes belong to the most widely distributed groundwater contaminants. Since 2014, it has been known that trichloroethene (TCE) can be degraded aerobically and metabolically as growth substrate by a mixed bacterial enrichment culture (named SF culture). In this study, the degradation capabilities under a range of field-relevant conditions were investigated in fixed-bed reactors as well as in batch experiments. Aerobic metabolic TCE degradation was stable over the long term, with degradation optima at 22 °C and pH 7. Degradation of up to 400 μM TCE was observed. The longest starvation period after which degradation of TCE was regained was 112 days. The possible co-contaminants perchloroethene, trans-1,2-dichloroethene, and cis-1,2-dichloroethene did not inhibit TCE degradation, even though they were not degraded themselves. The presence of equimolar amounts of 1,1-dichloroethene and vinyl chloride inhibited TCE degradation. Experiments with groundwater from different chloroethene-contaminated field sites proved the potential of the SF culture for bioaugmentation. Thus, aerobic metabolic TCE degradation should be considered as a promising method for the bioremediation of field sites with TCE as the main contaminant.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential

Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.

Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana

Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.

Simultaneous biodegradation of carbon tetrachloride and trichloroethylene in a coupled anaerobic/aerobic biobarrier

Simultaneous biodegradation of carbon tetrachloride (CT) and trichloroethylene (TCE) in a biobarrier with polyethylene glycol (PEG) carriers was studied. Toluene/methanol and hydrogen peroxide (H2O2) were used as electron donors and an electron acceptor source, respectively, in order to develop a biologically active zone. The average removal efficiencies for TCE and toluene were over 99.3%, leaving the respective residual concentrations of ∼12 and ∼57μg/L, which are below or close to the groundwater quality standards. The removal efficiency for CT was ∼98.1%, with its residual concentration (65.8μg/L) slightly over the standards. TCE was aerobically cometabolized with toluene as substrate while CT was anaerobically dechlorinated in the presence of electron donors, with the respective stoichiometric amount of chloride released. The oxygen supply at equivalent to 50% chemical oxygen demand of the injected electron donors supported successful toluene oxidation and also allowed local anaerobic environments for CT reduction. The originally augmented (immobilized in PEG carriers) aerobic microbes were gradually outcompeted in obtaining substrate and oxygen. Instead, newly developed biofilms originated from indigenous microbes in soil adapted to the coupled anaerobic/aerobic environment in the carrier for the simultaneous and almost complete removal of CT, TCE, and toluene. The declined removal rates when temperature fell from 28 to 18°C were recovered by doubling the retention time (7.2 days).

Dynamics of organohalide-respiring bacteria and their genes following in-situ chemical oxidation of chlorinated ethenes and biostimulation

Application of Fenton's reagent and enhanced reductive dechlorination are currently the most common remediation strategies resulting in removal of chlorinated ethenes. In this study, the influence of such techniques on organohalide-respiring bacteria was assessed at a site contaminated by chlorinated ethenes using a wide spectrum of molecular genetic markers, including 16S rRNA gene of the organohalide-respiring bacteria Dehaloccocoides spp., Desulfitobacterium and Dehalobacter; reductive dehalogenase genes (vcrA, bvcA) responsible for dechlorination of vinyl chloride and sulphate-reducing and denitrifying bacteria. In-situ application of hydrogen peroxide to induce a Fenton-like reaction caused an instantaneous decline in all markers below detection limit. Two weeks after application, the bvcA gene and Desulfitobacterium relative abundance increased to levels significantly higher than those prior to application. No significant decrease in the concentration of a range of chlorinated ethenes was observed due to the low hydrogen peroxide dose used. A clear increase in marker levels was also observed following in-situ application of sodium lactate, which resulted in a seven-fold increase in Desulfitobacterium and a three-fold increase in Dehaloccocoides spp. after 70 days. An increase in the vcrA gene corresponded with increase in Dehaloccocoides spp. Analysis of selected markers clearly revealed a positive response of organohalide-respiring bacteria to biostimulation and unexpectedly fast recovery after the Fenton-like reaction.

The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis

The compositions of bacterial community in one site contaminated with PCE/TCE after the slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, and surfactants) addition were analyzed. Results show that SPRS caused a rapid enhancement of reductive dechlorination of TCE. The transformation of PCE/TCE into ethene was observed after 20 days of operation. To compare the change of bacterial communities before and after SPRS addition, 16S rRNA amplicon sequencing using the metagenome analysis was performed. Results demonstrated the detection of the increased amounts of Dehalogenimonas by 2.2-fold, Pseudomonas by 3.4-fold and Sulfuricurvum by 4-fold with the analysis of the ribosomal database project (RDP). Metagenomic DNA was extracted from PCE/TCE-contaminated groundwater after SPRS addition, and subjected to sequencing. Results obtained from metagenomic sequencing indicate that genes from Dehalococcoides mccartyi was ranked as the second abundant bacteria among all of the detected bacteria via the analysis of the lowest common ancestor (LCA). Abundance of these bacterial groups, as shown above suggests their role in TCE biodegradation. Functional analysis of the metagenome, with the specific reference to chloroalkane and chloroalkene degradation, revealed the presence of some genes responsible for TCE biodegradation. Overall, results of this study provided new insights for a better understanding of the potential of biostimulation on TCE-contaminated sites.

Evaluation of the fate and transport of chlorinated ethenes in a complex groundwater system discharging to a stream in Wonju, Korea

Chlorinated ethenes such as trichloroethylene (TCE) are common and persistent groundwater contaminants. If contaminated groundwater discharges to a stream, then stream water pollution near the contamination site also becomes a problem. In this respect, the fate and transport of chlorinated ethenes around a stream in an industrial complex were evaluated using the concentration of each component, and hydrogeochemical, microbial, and compound-specific carbon isotope data. Temporal and spatial monitoring reveal that a TCE plume originating from main and local source zones continues to be discharged to a stream. Groundwater geochemical data indicate that aerobic conditions prevail in the upgradient area of the studied aquifer, whereas conditions become anaerobic in the downgradient. The TCE molar fraction is high at the main and local source zones, ranging from 87.4 to 99.2% of the total volatile organic compounds (VOCs). An increasing trend in the molar fraction of cis-1, 2-Dichloroethene (cis-DCE) and vinyl chloride (VC) was observed in the downgradient zone of the study area. The enriched δ(13)C values of TCE and depleted values of cis-DCE in the stream zone, compared to those of the source zone, also suggest biodegradation of VOCs. Microbial community structures in monitoring wells adjacent to the stream zone in the downgradient area were analyzed using 16S rRNA gene-based pyrosequencing to identify the microorganisms responsible for biodegradation. This was attributed to the high relative abundance of dechlorinating bacteria in monitoring wells under anaerobic conditions farthest from the stream in the downgradient area. The multilateral approaches adopted in this study, combining hydrogeochemical and biomolecular methods with compound-specific analyses, indicate that contaminants around the stream were naturally attenuated by active anaerobic biotransformation processes.

In situ aerobic cometabolism of chlorinated solvents: a review

The possible approaches for in situ aerobic cometabolism of aquifers and vadose zones contaminated by chlorinated solvents are critically evaluated. Bioaugmentation of resting-cells previously grown in a fermenter and in-well addition of oxygen and growth substrate appear to be the most promising approaches for aquifer bioremediation. Other solutions involving the sparging of air lead to satisfactory pollutant removals, but must be integrated by the extraction and subsequent treatment of vapors to avoid the dispersion of volatile chlorinated solvents in the atmosphere. Cometabolic bioventing is the only possible approach for the aerobic cometabolic bioremediation of the vadose zone. The examined studies indicate that in situ aerobic cometabolism leads to the biodegradation of a wide range of chlorinated solvents within remediation times that vary between 1 and 17 months. Numerous studies include a simulation of the experimental field data. The modeling of the process attained a high reliability, and represents a crucial tool for the elaboration of field data obtained in pilot tests and for the design of the full-scale systems. Further research is needed to attain higher concentrations of chlorinated solvent degrading microbes and more reliable cost estimates. Lastly, a procedure for the design of full-scale in situ aerobic cometabolic bioremediation processes is proposed.

Aerobic biodegradation of trichloroethene without auxiliary substrates

Trichloroethene (TCE) represents a priority pollutant and is among the most frequently detected contaminants in groundwater. The current bioremediation measures have certain drawbacks like e.g. the need for auxiliary substrates. Here, the aerobic biodegradation of TCE as the sole growth substrate is demonstrated. This new process of metabolic TCE degradation was first detected in groundwater samples. TCE degradation was stable in an enriched mixed bacterial culture in mineral salts medium for over five years and repeated transfers of the culture resulting in a 10(10) times dilution of the original groundwater. Aerobic TCE degradation resulted in stoichiometric chloride formation. Stable carbon isotope fractionation was observed providing a reliable analytical tool to assess this new biodegradation process at field sites. The results suggest that aerobic biodegradation of TCE without auxiliary substrate could be considered as an option for natural attenuation or engineered bioremediation of contaminated sites.

Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals

In this review, the strategies being employed to exploit the inherent durability of biofilms and the diverse nutrient cycling of the microbiome for bioremediation are explored. Focus will be given to halogenated compounds, hydrocarbons, pharmaceuticals, and personal care products as well as some heavy metals and toxic minerals, as these groups represent the majority of priority pollutants. For decades, industrial processes have been creating waste all around the world, resulting in contaminated sediments and subsequent, far-reaching dispersal into aquatic environments. As persistent pollutants have accumulated and are still being created and disposed, the incentive to find suitable and more efficient solutions to effectively detoxify the environment is even greater. Indigenous bacterial communities are capable of metabolizing persistent organic pollutants and oxidizing heavy metal contaminants. However, their low abundance and activity in the environment, difficulties accessing the contaminant or nutrient limitations in the environment all prevent the processes from occurring as quickly as desired and thus reaching the proposed clean-up goals. Biofilm communities provide among other things a beneficial structure, possibility for nutrient, and genetic exchange to participating microorganisms as well as protection from the surrounding environment concerning for instance predation and chemical and shear stresses. Biofilms can also be utilized in other ways as biomarkers for monitoring of stream water quality from for instance mine drainage. The durability and structure of biofilms together with the diverse array of structural and metabolic characteristics make these communities attractive actors in biofilm-mediated remediation solutions and ecosystem monitoring.

Bacterial communities in tetrachloroethene-polluted groundwaters: a case study

The compositions of bacterial groundwater communities of three sites contaminated with chlorinated ethenes were analyzed by pyrosequencing their 16S rRNA genes. For each location, the entire and the active bacterial populations were characterized by independent molecular analysis of the community DNA and RNA. The sites were selected to cover a broad range of different environmental conditions and contamination levels, with tetrachloroethene (PCE) and trichloroethene (TCE) being the primary contaminants. Before sampling the biomass, a long-term monitoring of the polluted locations revealed high concentrations of cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC), which are toxic by-products of the incomplete bacterial degradation of PCE and TCE. The applied pyrosequencing technique enabled known dechlorinators to be identified at a very low detection level (<0.25%) without compromising the detailed analysis of the entire bacterial community of these sites. The study revealed that only a few species dominated the bacterial communities, with Albidiferax ferrireducens being the only highly prominent member found at all three sites. Only a limited number of OTUs with abundances of up to 1% and high sequence identities to known dechlorinating microorganisms were retrieved from the RNA pools of the two highly contaminated sites. The dechlorinating consortium was likely to be comprised of cDCE-assimilating bacteria (Polaromonas spp.), anaerobic organohalide respirers (mainly Geobacter spp.), and Burkholderia spp. involved in cometabolic dechlorination processes, together with methylotrophs (Methylobacter spp.). The deep sequencing results suggest that the indigenous dechlorinating consortia present at the investigated sites can be used as a starting point for future bioremediation activities by stimulating their anaerobic and aerobic chloroethene degradation capacities (i.e. reductive dechlorination, and metabolic and cometabolic oxidation).

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants.

Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.