Relationships between the Abundance and Expression of Functional Genes from Vinyl Chloride (VC)-Degrading Bacteria and Geochemical Parameters at VC-Contaminated Sites

Reductive dechlorination of 1,1,2-trichloroethane in groundwater by zero valent iron coupled with biostimulation under sulfate stress: Differences and potential mechanisms

Zero-valent iron (ZVI) coupled with biostimulation is recognized as one of the most promising and effective dechlorination methods for chlorinated hydrocarbons in groundwater. However, the heterogeneity of the aquifer environment may affect the dechlorination efficiency of the coupled systems, and the underlying mechanisms remain unclear. In this study, we systematically explored the effect and potential mechanism of sulfate (SO42-) on the removal of 1,1,2-trichloroethane (1,1,2-TCA) by the coupled ZVI and biostimulation. Results revealed that the coupled systems enhanced the degradation rate of 1,1,2-TCA by an order of magnitude compared with that of each individual treatment under SO42- stress. However, the complete dechlorination of the main product, vinyl chloride (VC), remains challenging in the absence of obligate organohalide respiration bacteria (OHRB). SO42- dynamically altered the sulfidation degree of ZVI and microbial interactions, leading to the disappearance of non-chlorinated products in the micron ZVI (mZVI) coupled system and decreased dechlorination efficiency with increasing SO42- concentration. In the nano ZVI (nZVI) coupled system, suitable SO42- concentrations promoted continuous VC degradation, likely due to the inherent high reactivity of the nanometer-size effect. Nevertheless, excessive SO42- reduced ZVI sulfidation, causing differences in dechlorination efficiency and extent trends between mZVI and nZVI coupled systems. These findings will provide scientific support for the optimal application scenarios and limitations of the coupled strategies, thereby facilitating the regulation of technology application according to actual aquifer environmental parameters to achieve low-cost environmental safety control.

Integrating Enzyme-Based Kinetics in Reactive Transport Models to Simulate Spatiotemporal Dynamics of Biomarkers during Chlorinated Ethene Degradation

Biomarkers such as functional gene mRNA (transcripts) and proteins (enzymes) provide direct proof of metabolic regulation during the reductive dechlorination (RD) of chlorinated ethenes (CEs). Yet, current models to simulate their spatiotemporal variability are not flexible enough to mimic the homologous behavior of RDase functional genes. To this end, we developed new enzyme-based kinetics to model the concentrations of CEs together with the transcript and enzyme levels during RD. First, the model was calibrated to existing microcosm data on RD of cis-DCE. The model mirrored the tceA and vcrA gene expression and the production of their enzymes in Dehalococcoides spp. Considering tceA and vcrA as homologous instead of nonhomologous improved fitting of the mRNA time series. Second, CEs and biomarker patterns were explored as a proof of concept under groundwater flow conditions, considering degraders occurring in immobile and mobile states. Under both microcosm and flow conditions, biomarker-rate relationships were nonlinear hysteretic because tceA and vcrA acted as homologous genes. The mobile biomarkers additionally undergo advective-dispersive transport, which increases the nonlinearity and makes the observed patterns even more challenging to interpret. The model offers a thorough mechanistic description of RD while also allowing simulation of spatiotemporal dynamic patterns of various key biomarkers in aquifers.

Natural Attenuation Potential of Vinyl Chloride and Butyl Acrylate Released in the East Palestine, Ohio Train Derailment Accident

The East Palestine, Ohio train derailment released toxic vinyl chloride (VC) and butyl acrylate (BA), which entered the watershed. Streambed sediment, surface water, and private well water samples were collected 128 and 276 days postaccident to assess the natural attenuation potential of VC and BA by quantifying biodegradation biomarker genes and conducting microcosm treatability studies. qPCR detected the aerobic VC degradation biomarkers etnC in ∼40% and etnE in ∼27% of sediments collected in both sampling campaigns in abundances reaching 105 gene copies g-1. The 16S rRNA genes of organohalide-respiring Dehalococcoides and Dehalogenimonas were, respectively, detected in 50 and 64% of sediment samples collected 128 days postaccident and in 63 and 88% of sediment samples collected 276 days postaccident, in abundances reaching 107 cells g-1. Elevated detection frequencies of VC degradation biomarker genes were measured immediately downstream of the accident site (i.e., Sulphur Run). Aerobic VC degradation occurred in all sediment microcosms and coincided with increases of etnC/etnE genes and Mycobacterium, a genus comprising aerobic VC degraders. The conversion of VC to ethene and an increased abundance of VC reductive dechlorination biomarker genes were observed in microcosms established with sediments collected from Sulphur Run. All anoxic microcosms rapidly degraded BA to innocuous products with intermediate formation of n-butanol and acrylate. The results indicate that microbiomes in the East Palestine watershed have natural attenuation capacity for VC and BA. Recommendations are made to improve first-response actions in future contaminant release accidents of this magnitude.

Black Carbon Impacts on Paraburkholderia xenovorans Strain LB400 Cell Enrichment and Activity: Implications toward Lower-Chlorinated Polychlorinated Biphenyls Biodegradation Potential

Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging bioaugmentation approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize the cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. Biphenyl dioxygenase gene (bphA) abundance on four BC types demonstrated corn kernel biochar hosted at least 4 orders of magnitude more attached cells per gram than other feedstocks, and microscopic imaging revealed the attached live cell fraction was >1.5× more on corn kernel biochar than GAC. BC characteristics (i.e., sorption potential, pore size, pH) appear to contribute to cell attachment differences. Reverse transcription qPCR indicated that BC feedstocks significantly influenced bphA expression in attached cells. The bphA transcript-per-gene ratio of attached cells was >10-fold more than suspended cells, confirmed by transcriptomics. RNA-seq also demonstrated significant upregulation of biphenyl and benzoate degradation pathways on attached cells, as well as revealing biofilm formation potential/cell-cell communication pathways. These novel findings demonstrate aerobic PCB-degrading cell abundance and activity could be tuned by adjusting BC feedstocks/attributes to improve LC-PCBs biodegradation potential.

Use of qPCR to monitor 2,4-dinitroanisole degrading bacteria in water and soil slurry cultures

Prediction and process monitoring during natural attenuation, bioremediation, and biotreatment require effective strategies for detection and enumeration of the responsible bacteria. The use of 2,4-dinitroanisole (DNAN) as a component of insensitive munitions leads to environmental contamination of firing ranges and manufacturing waste streams. Nocardioides sp. strain JS1661 degrades DNAN under aerobic conditions via a pathway involving an unusual DNAN demethylase. We used the deeply branched sequences of DNAN degradation functional genes as a target for development of a molecular method for detection of the bacteria. A qPCR assay was designed for the junction between dnhA and dnhB, the adjacent genes encoding DNAN demethylase. The assay allowed reproducible enumeration of JS1661 during growth in liquid media and soil slurries. Results were consistent with biodegradation of DNAN, accumulation of products, and classical biomass estimates, including most probable number and OD600. The results provide a sensitive and specific molecular method for prediction of degradation potential and process evaluation during degradation of DNAN.

ONE-SENTENCE SUMMARY

A unique target sequence in functional genes enables the design of a simple and specific qPCR assay for enumeration of aerobic 2,4-dinitroanisole-degrading bacteria in soil and water.

Biodiversity in wetland+ system: a passive solution for HCH dump effluents

The hexachlorocyclohexane isomers (HCH) are long-banned pesticides. Even though their use has been prohibited for decades, their presence in the environment is still reported worldwide. Wetland + is a registered trademark of the remedial treatment technology consisting of an aerobic sedimentary tank, a permeable reactive barrier, a biosorption system, and an aerobic wetland. This proven method combines a reductive treatment known from PRBs with the natural wetland self-cleaning processes. The average efficiency of the system is 96.8% for chlorobenzenes (ClB) and 81.7% for HCH, during the first 12 months of the system operation. The presence of the genes encoding enzymes involved in the degradation of the HCH compounds indicates that the removal of HCH and ClB occurs not only by chemical removal but also through aerobic and anaerobic combining biodegradation. Changes in abundance and the composition of the diatom community were found to be suitable indicators of the water quality and of the impact of the Wetland + operation on the water ecosystem. The system's annual operation exhibited a markedly higher number of diatom species in the closing profiles of the Ostrovský Creek, the Wetland + effluent recipient.

Reciprocal Interactions of Abiotic and Biotic Dechlorination of Chloroethenes in Soil

Chloroethenes (CEs) as common organic pollutants in soil could be attenuated via abiotic and biotic dechlorination. Nonetheless, information on the key catalyzing matter and their reciprocal interactions remains scarce. In this study, FeS was identified as a major catalyzing matter in soil for the abiotic dechlorination of CEs, and acetylene could be employed as an indicator of the FeS-mediated abiotic CE-dechlorination. Organohalide-respiring bacteria (OHRB)-mediated dechlorination enhanced abiotic CEs-to-acetylene potential by providing dichloroethenes (DCEs) and trichloroethene (TCE) since chlorination extent determined CEs-to-acetylene potential with an order of trans-DCE > cis-DCE > TCE > tetrachloroethene/PCE. In contrast, FeS was shown to inhibit OHRB-mediated dechlorination, inhibition of which could be alleviated by the addition of soil humic substances. Moreover, sulfate-reducing bacteria and fermenting microorganisms affected FeS-mediated abiotic dechlorination by re-generation of FeS and providing short chain fatty acids, respectively. A new scenario was proposed to elucidate major abiotic and biotic processes and their reciprocal interactions in determining the fate of CEs in soil. Our results may guide the sustainable management of CE-contaminated sites by providing insights into interactions of the abiotic and biotic dechlorination in soil.

Meta-omics elucidates key degraders in a bacterial tris(2-butoxyethyl) phosphate (TBOEP)-degrading enrichment culture

Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation of OPEs. In this study, we investigated the biotransformation of tris(2-butoxyethyl) phosphate (TBOEP), a frequently detected alkyl-OPE by a bacterial enrichment culture under aerobic conditions. The enrichment culture degraded 5 mg/L TBOEP following the first-order kinetics with a reaction rate constant of 0.314 h^-1. TBOEP was mainly degraded via ether bond cleavage, evidenced by the production of bis(2-butoxyethyl) hydroxyethyl phosphate, 2-butoxyethyl bis(2-hydroxyethyl) phosphate, and 2-butoxyethyl (2-hydroxyethyl) hydrogen phosphate. Other transformation pathways include terminal oxidation of the butoxyethyl group and phosphoester bond hydrolysis. Metagenomic sequencing generated 14 metagenome-assembled genomes (MAGs), showing that the enrichment culture primarily consisted of Gammaproteobacteria, Bacteroidota, Myxococcota, and Actinobacteriota. One MAG assigned to Rhodocuccus ruber strain C1 was the most active in the community, showing upregulation of various monooxygenase, dehydrogenase, and phosphoesterase genes throughout the degradation process, and thus was identified as the key degrader of TBOEP and the metabolites. Another MAG affiliated with Ottowia mainly contributed to TBOEP hydroxylation. Our results provided a comprehensive understanding of the bacterial TBOEP degradation at community level.

Contrasting regulatory effects of organic acids on aerobic vinyl chloride biodegradation in etheneotrophs

Vinyl chloride (VC) is a common groundwater pollutant generated during anaerobic biodegradation of chlorinated solvents (e.g., trichloroethene (TCE) or tetrachloroethene (PCE)). Aerobic VC biodegradation by etheneotrophs can support anaerobic PCE and TCE bioremediation to achieve complete removal in situ. However, anaerobic bioremediation strategies necessitate biostimulation with electron donors that are fermented in situ, generating organic acids that could influence aerobic VC biodegradation processes. We examined the effect of organic acids (lactate, acetate, propionate, and butyrate) on aerobic VC biodegradation by VC-assimilating etheneotrophs Mycobacterium strain JS60 and Nocardioides strain JS614. Strain JS60 grew on all organic acids tested, while strain JS614 did not respond to lactate. VC-grown strain JS60 fed VC and one or more organic acids showed carbon catabolite repression (CCR) behavior where VC biodegradation occurred only after organic acids were depleted. In contrast, CCR was not evident in VC-grown strain JS614, which degraded VC and organic acids simultaneously. Acetate-grown JS60 showed similar CCR behavior when fed VC and a single organic acid, except that extended lag periods (5-12 days) occurred before VC oxidation ensued. Acetate-grown JS614 fed VC and either acetate or butyrate displayed 5-8 day lag periods before simultaneous VC and organic acid biodegradation. In contrast, acetate-grown JS614 degraded VC and propionate without a significant lag, suggesting a regulatory link between propionate and VC oxidation in JS614. Different global regulatory mechanisms controlling VC biodegradation in the presence of organic acids in etheneotrophs have implications for developing combined anaerobic-aerobic bioremediation strategies at chlorinated ethene-contaminated sites. KEY POINTS: • With organic acids present, VC utilization was repressed in JS60, but not in JS614 • Strain JS60 grew readily on lactate, while strain JS614 did not • Propionate alleviated lag periods for VC utilization in acetate-grown JS614.

Microbiome Composition and Dynamics of a Reductive/Oxidative Bioelectrochemical System for Perchloroethylene Removal: Effect of the Feeding Composition

Chlorinated solvents still represent an environmental concern that requires sustainable and innovative bioremediation strategies. This study describes the microbiome composition of a novel bioelectrochemical system (BES) based on sequential reductive/oxidative dechlorination for complete perchloroethylene (PCE) removal occurring in two separate but sequential chambers. The BES has been tested under various feeding compositions [i.e., anaerobic mineral medium (MM), synthetic groundwater (SG), and real groundwater (RG)] differing in presence of sulfate, nitrate, and iron (III). In addition, the main biomarkers of the dechlorination process have been monitored in the system under various conditions. Among them, Dehalococcoides mccartyi 16S rRNA and reductive dehalogenase genes (tceA, bvcA, and vcrA) involved in anaerobic dechlorination have been quantified. The etnE and etnC genes involved in aerobic dechlorination have also been quantified. The feeding composition affected the microbiome, in particular when the BES was fed with RG. Sulfuricurvum, enriched in the reductive compartment, operated with MM and SG, suggesting complex interactions in the sulfur cycle mostly including sulfur oxidation occurring at the anodic counter electrode (MM) or coupled to nitrate reduction (SG). Moreover, the known Mycobacterium responsible for natural attenuation of VC by aerobic degradation was found abundant in the oxidative compartment fed with RG, which was in line with the high VC removal observed (92 ± 2%). D. mccartyi was observed in all the tested conditions ranging from 8.78E + 06 (with RG) to 2.35E + 07 (with MM) 16S rRNA gene copies/L. tceA was found as the most abundant reductive dehalogenase gene in all the conditions explored (up to 2.46 E + 07 gene copies/L in MM). The microbiome dynamics and the occurrence of biomarkers of dechlorination, along with the kinetic performance of the system under various feeding conditions, suggested promising implications for the scale-up of the BES, which couples reductive with oxidative dechlorination to ensure the complete removal of highly chlorinated ethylene and mobile low-chlorinated by-products.

Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants

Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.

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.

Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning

Microbial respiration is critical for soil carbon balance and ecosystem functioning. Previous studies suggest that plant diversity influences soil microbial communities and their respiration. Yet, the linkages between tree diversity, microbial biomass, microbial diversity, and microbial functioning have rarely been explored. In this study, we measured two microbial functions (microbial physiological potential, and microbial respiration), together with microbial biomass, microbial taxonomic and functional profiles, and soil chemical properties in a tree diversity experiment in South China, to disentangle how tree diversity affects microbial respiration through the modifications of the microbial community. Our analyses show a significant positive effect of tree diversity on microbial biomass (+25% from monocultures to 24-species plots), bacterial diversity (+12%), and physiological potential (+12%). In addition, microbial biomass and physiological potential, but not microbial diversity, were identified as the key drivers of microbial respiration. Although soil chemical properties strongly modulated soil microbial community, tree diversity increased soil microbial respiration by increasing microbial biomass rather than changing microbial taxonomic or functional diversity. Overall, our findings suggest a prevalence of microbial biomass over diversity in controlling soil carbon dynamics.

Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis

Chlorinated ethenes (CEs) are most problematic pollutants in groundwater. Dehalogenating bacteria, and in particular organohalide-respiring bacteria (OHRB), can transform PCE to ethene under anaerobic conditions, and thus contribute to bioremediation of contaminated sites. Current approaches to characterize in situ biodegradation of CEs include hydrochemical analyses, quantification of the abundance of key species (e.g. Dehalococcoides mccartyi) and dehalogenase genes (pceA, vcrA, bvcA and tceA) involved in different steps of organohalide respiration (OHR) by qPCR, and compound-specific isotope analysis (CSIA) of CEs. Here we combined these approaches with sequencing of 16S rRNA gene amplicons to consider both OHRB and bacterial taxa involved in CE transformation at a multi-contaminated site. Integrated analysis of hydrogeochemical characteristics, gene abundances and bacterial diversity shows that bacterial diversity and OHRB mainly correlated with hydrogeochemical conditions, suggesting that pollutant exposure acts as a central driver of bacterial diversity. CSIA, abundances of four reductive dehalogenase encoding genes and the prevalence of Dehalococcoides highlighted sustained PCE, DCE and VC degradation in several wells of the polluted plume. These results suggest that bacterial taxa associated with OHR play an essential role in natural attenuation of CEs, and that representatives of taxa including Dehalobacterium and Desulfosporosinus co-occur with Dehalococcoides. Overall, our study emphasizes the benefits of combining several approaches to evaluate the interplay between the dynamics of bacterial diversity in CE-polluted plumes and in situ degradation of CEs, and to contribute to a more robust assessment of natural attenuation at multi-polluted sites.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Vapor Intrusion Investigations and Decision-Making: A Critical Review

At sites impacted by volatile organic compounds (VOCs), vapor intrusion (VI) is the pathway with the greatest potential to result in actual human exposure. Since sites with VI were first widely publicized in late 1990s, the scientific understanding of VI has evolved considerably. The VI conceptual model has been extended beyond relatively simple scenarios to include nuances, such as biological and hydrogeological factors that may limit the potential for VI and alternative pathways, such as preferential pathways and direct building contact/infiltration that may enhance VI in some cases. Regulatory guidance documents typically recommend initial concentration- or distance-based screening to evaluate whether VI may be a concern, followed by a multiple-lines-of-evidence (MLE) investigation approach for sites that do not screen out. These recommendations for detailed evaluation of VI currently focus on monitoring of VOC concentrations in groundwater, soil gas, and indoor air and can be supplemented by other lines of evidence. In this Critical Review, we summarize key elements important to VI site characterization, provide the status and current understanding, and highlight data interpretation challenges, as well as innovative tools developed to help overcome the challenges. Although there have been significant advances in the understanding of VI in the past 20 years, limitations and knowledge gaps in screening, investigation methods, and modeling approaches still exist. Potential areas for further research include improved initial screening methods that account for the site-specific role of barriers, improved understanding of preferential pathways, and systematic study of buildings and infrastructure other than single-family residences.

Combining nanoscale zero-valent iron with electrokinetic treatment for remediation of chlorinated ethenes and promoting biodegradation: A long-term field study

Nanoscale zero-valent iron (nZVI) is recognized as a powerful tool for the remediation of groundwater contaminated by chlorinated ethenes (CEs). This long-term field study explored nZVI-driven degradation of CEs supported by electrokinetic (EK) treatment, which positively affects nZVI longevity and migration, and its impact on indigenous bacteria. In particular, the impact of combined nZVI-EK treatment on organohalide-respiring bacteria, ethenotrophs and methanotrophs (all capable of CE degradation) was assessed using molecular genetic markers detecting Dehalococcoides spp., Desulfitobacterium spp., the reductive dehalogenase genes vcrA and bvcA and ethenotroph and methanotroph functional genes. The remediation treatment resulted in a rapid decrease of the major pollutant cis-1,2-dichloroethene (cDCE) by 75% in the affected area, followed by an increase in CE degradation products methane, ethane and ethene. The newly established geochemical conditions in the treated aquifer not only promoted growth of organohalide-respiring bacteria but also allowed for the concurrent presence of vinyl chloride- and cDCE-oxidizing methanotrophs and (especially) ethenotrophs, which proliferated preferentially in the vicinity of an anode where low levels of oxygen were produced. The nZVI treatment resulted in a temporary negative impact on indigenous bacteria in the application well close to the cathode; but even there, the microbiome was restored within 15 days. The nZVI-EK treatment proved highly effective in reducing CE contamination and creating a suitable environment for subsequent biodegradation by changing groundwater conditions, promoting transport of nutrients and improving CE availability to soil and groundwater bacteria.

Potential for co-metabolic oxidation of TCE and evidence for its occurrence in a large-scale aquifer survey

Trichloroethylene (TCE) is a groundwater pollutant that is prevalent worldwide. In contaminated groundwater, TCE can be biodegraded following either reductive dechlorination or aerobic co-metabolic oxidation. However, since the co-metabolic process is not accompanied by indicative and easily detectable transformation products, little is known about its prominence in the environment. To estimate the environmental importance of the oxidative process, a regional groundwater survey was conducted. In this survey, polluted water from 100 wells along the Israeli Coastal Aquifer was sampled. Geochemical data indicated oxic conditions prevailing in most sites. The sampled groundwater was used for microcosm experiments, functional gene analysis, and TCE compound-specific isotope analysis (δ¹³C and δ³⁷Cl). Enrichments of methane and toluene oxidizers in microcosms indicated the high potential of the indigenous microbial community to co-metabolically oxidize TCE. This was further reinforced by the high abundance of mmoX and PHE functional genes quantified in some of the sites (yet lower abundance of TOD functional gene was found). Finally, compound-specific isotope analysis was used to assess the magnitude of TCE oxidation in practice. Applying the isotopic tool for scattered points on a regional scale demanded the consideration of a wide δ¹³C range of source TCE, hampering the ability to detect small shifts of a single permil. Thus, despite the high potential for the oxidation process, no evidence was attained for the natural occurrence of the process, and significant isotopic shifts were restricted to actively treated sites only. This limitation should be considered in future regional scale studies, in which no single source is defined.

Variable carbon and chlorine isotope fractionation in TCE co-metabolic oxidation

Identifying co-metabolic TCE oxidation in polluted groundwater is challenging due to lack of indicative by-products. This challenge may theoretically be resolved if the oxidation process can be characterized by a distinct dual isotope enrichment. In this work, we aimed to explore the carbon and chlorine isotope effects associated with TCE oxidation by a variety of oxygenases. These included pure strains and enrichment cultures of methane, toluene and ammonia oxidizers, as well as experiments with crude extracts. Isotope effects determined for TCE oxidation by toluene and ammonia oxidizers were mostly in line with expected values for epoxidation mechanism (ϵ¹³C -11.0 ± 0.7 to -24.8 ± 0.2‰ and ϵ³⁷Cl +0.9 ± 0.5 to +1.0 ± 0.4‰), whereas, the methanotrophs resulted in distinctively different isotope effects (ϵ¹³C -2.4 ± 0.4 to -3.4 ± 0.8‰ and ϵ³⁷Cl -1.8 ± 0.2 to -2.9 ± 0.9‰). It is suggested that in TCE oxidation by methanotrophs, substrate binding rather than bond cleavage is rate limiting, leading to this unexpected isotope effect. On the environmental level, our results imply that the oxidative process can be differentiated if catalyzed by toluene and ammonia oxidizers or by methanotrophs. Additionally, the oxidative process can be distinguished from the reductive one. However, using dual isotope analysis in the field may result in an under-estimation of the overall co-metabolic process if methanotrophs are to be excluded due to low isotope effects.

Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment

A stall of cis-1,2-DCE and vinyl chloride (VC) is frequently observed during bioremediation of groundwater chloroethenes via reductive dechlorination. These chloroethenes may be oxidised by aerobic methanotrophs or ethenotrophs co-metabolically and/or metabolically. We assessed the potential for such oxidation at 12 sites (49 groundwater samples) using hydrochemical and molecular biological tools. Both ethenotroph (etnC and etnE) and methanotroph (mmoX and pmoA) functional genes were identified in 90% of samples, while reductive dehalogenase functional genes (vcrA and bvcA) were identified in 82%. All functional genes were simultaneously detected in 78% of samples, in actively biostimulated sites in 88% of samples. Correlation analysis revealed that cis-1,2-DCE concentration was positively correlated with vcrA, etnC and etnE, while VC concentration was correlated with etnC, etnE, vcrA and bvcA. However, feature selection based on random forest classification indicated a significant relationship for the vcrA in relation to cis-1,2-DCE, and vcrA, bvcA and etnE for VC and no prove of relationship between cis-1,2-DCE or VC and the methanotroph functional genes. Analysis of hydrochemical parameters indicated that aerobic oxidation of chloroethenes by ethenotrophs may take place under a range of redox conditions of aquifers and coincide with high ethene and VC concentrations.

Chlorinated ethene plume evolution after source thermal remediation: Determination of degradation rates and mechanisms

The extent, mechanism(s), and rate of chlorinated ethene degradation in a large tetrachloroethene (PCE) plume were investigated in an extensive sampling campaign. Multiple lines of evidence for this degradation were explored, including compound-specific isotope analysis (CSIA), dual C-Cl isotope analysis, and quantitative real-time polymerase chain reaction (qPCR) analysis targeting the genera Dehalococcoides and Dehalogenimonas and the genes vcrA, bvcA, and cerA. A decade prior to this sampling campaign, the plume source was thermally remediated by steam injection. This released dissolved organic carbon (DOC) that stimulated microbial activity and created reduced conditions within the plume. Based on an inclusive analysis of minor and major sampling campaigns since the initial site characterization, it was estimated that reduced conditions peaked 4 years after the remediation event. At the time of this study, 11 years after the remediation event, the redox conditions in the aquifer are returning to their original state. However, the DOC released from the remediated source zone matches levels measured 3 years prior and plume conditions are still suitable for biotic reductive dechlorination. Dehalococcoides spp., Dehalogenimonas spp., and vcrA, bvcA, and cerA reductive dehalogenase genes were detected close to the source, and suggest that complete, biotic PCE degradation occurs here. Further downgradient, qPCR analysis and enriched δ¹³C values for cis-dichloroethene (cDCE) suggest that cDCE is biodegraded in a sulfate-reducing zone in the plume. In the most downgradient portion of the plume, lower levels of specific degraders supported by dual C-Cl analysis indicate that the biodegradation occurs in combination with abiotic degradation. Additionally, 16S rRNA gene amplicon sequencing shows that organizational taxonomic units known to contain organohalide-respiring bacteria are relatively abundant throughout the plume. Hydraulic conductivity testing was also conducted, and local degradation rates for PCE and cDCE were determined at various locations throughout the plume. PCE degradation rates from sampling campaigns after the thermal remediation event range from 0.11 to 0.35 yr^-1. PCE and cDCE degradation rates from the second to the third sampling campaigns ranged from 0.08 to 0.10 yr^-1 and 0.01 to 0.07 yr^-1, respectively. This is consistent with cDCE as the dominant daughter product in the majority of the plume and cDCE degradation as the time-limiting step. The extensive temporal and spatial analysis allowed for tracking the evolution of the plume and the lasting impact of the source remediation and illustrates that the multiple lines of evidence approach is essential to elucidate the primary degradation mechanisms in a plume of such size and complexity.

Cryogenic soil coring reveals coexistence of aerobic and anaerobic vinyl chloride degrading bacteria in a chlorinated ethene contaminated aquifer

Vinyl chloride (VC) is a common groundwater contaminant and known human carcinogen. Three major bacterial guilds are known to participate in VC biodegradation: aerobic etheneotrophs and methanotrophs, and anaerobic organohalide-respiring VC-dechlorinators. We investigated the spatial relationships between functional genes representing these three groups of bacteria (as determined by qPCR) with chlorinated ethene concentrations in a surficial aquifer at a contaminated site. We used cryogenic soil coring to collect high-resolution aquifer sediment samples and to preserve sample geochemistry and nucleic acids under field conditions. All samples appeared to be anaerobic (i.e., contained little to no dissolved oxygen). VC biodegradation associated functional genes from etheneotrophs (etnC and/or etnE), methanotrophs (mmoX and/or pmoA), and anaerobic VC-dechlorinators (bvcA and/or vcrA) coexisted in 48% of the samples. Transcripts of etnC/etnE and bvcA/vcrA were quantified in contemporaneous groundwater samples, indicating co-located gene expression. Functional genes from etheneotrophs and anaerobic VC-dechlorinators were correlated to VC concentrations in the lower surficial aquifer (p < 0.05). Methanotroph functional genes were not correlated to VC concentrations. Cryogenic soil coring proved to be a powerful tool for capturing high-spatial resolution trends in geochemical and nucleic acid data in aquifer sediments. We conclude that both aerobic etheneotrophs and anaerobic VC-dechlorinators may play a significant role in VC biodegradation in aquifers that have little dissolved oxygen.

Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing

Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.