Isolation of two newDehalococcoides mccartyistrains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis

CO-driven electron and carbon flux fuels synergistic microbial reductive dechlorination

BACKGROUND

Carbon monoxide (CO), hypothetically linked to prebiotic biosynthesis and possibly the origin of the life, emerges as a substantive growth substrate for numerous microorganisms. In anoxic environments, the coupling of CO oxidation with hydrogen (H2) production is an essential source of electrons, which can subsequently be utilized by hydrogenotrophic bacteria (e.g., organohalide-respring bacteria). While Dehalococcoides strains assume pivotal roles in the natural turnover of halogenated organics and the bioremediation of chlorinated ethenes, relying on external H2 as their electron donor and acetate as their carbon source, the synergistic dynamics within the anaerobic microbiome have received comparatively less scrutiny. This study delves into the intriguing prospect of CO serving as both the exclusive carbon source and electron donor, thereby supporting the reductive dechlorination of trichloroethene (TCE).

RESULTS

The metabolic pathway involved anaerobic CO oxidation, specifically the Wood-Ljungdahl pathway, which produced H2 and acetate as primary metabolic products. In an intricate microbial interplay, these H2 and acetate were subsequently utilized by Dehalococcoides, facilitating the dechlorination of TCE. Notably, Acetobacterium emerged as one of the pivotal collaborators for Dehalococcoides, furnishing not only a crucial carbon source essential for its growth and proliferation but also providing a defense against CO inhibition.

CONCLUSIONS

This research expands our understanding of CO's versatility as a microbial energy and carbon source and unveils the intricate syntrophic dynamics underlying reductive dechlorination.

Underexplored Organohalide-Respiring Bacteria in Sewage Sludge Debrominating Polybrominated Diphenyl Ethers

Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants prevalent in the environment. Organohalide-respiring bacteria (OHRB) can attenuate PBDEs via reductive debromination, but often producing toxic end-products. Debromination of PBDEs to diphenyl ether remains a rare phenomenon and is so far specifically associated with Dehalococcoides isolated from e-waste polluted sites. The occurrence of PBDE debromination in other ecosystems and underpinning OHRB are underexplored. Here we found that debromination of PBDEs is a common trait of sewage sludge microbiota, and diphenyl ether was produced as the end-product at varying quantities (0.6-52.9% mol of the parent PBDEs) in 76 of 84 cultures established with bioreactor sludge. Diverse debromination pathways converting PBDEs to diphenyl ether, including several new routes, were identified. Although Dehalococcoides contributed to PBDE debromination, Dehalogenimonas, Dehalobacter, and uncultivated Dehalococcoidia likely played more important roles than previously recognized. Multiple reductive dehalogenase genes (including bdeA, pcbA4, pteA, and tceA) were also prevalent and coexisted in bioreactor sludge. Collectively, these findings contribute to enhancing our comprehension of the environmental fate of PBDEs, expanding the diversity of microorganisms catalyzing PBDE debromination, and developing consortia for bioremediation application.

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.

Alleviating Chlorinated Alkane Inhibition on Dehalococcoides to Achieve Detoxification of Chlorinated Aliphatic Cocontaminants

Cocontamination by multiple chlorinated solvents is a prevalent issue in groundwater, presenting a formidable challenge for effective remediation. Despite the recognition of this issue, a comprehensive assessment of microbial detoxification processes involving chloroethenes and associated cocontaminants, along with the underpinning microbiome, remains absent. Moreover, strategies to mitigate the inhibitory effects of cocontaminants have not been reported. Here, we revealed that chloroform exhibited the most potent inhibitory effects, followed by 1,1,1-trichloroethane and 1,1,2-trichloroethane, on dechlorination of dichloroethenes (DCEs) in Dehalococcoides-containing consortia. The observed inhibition could be attributed to suppression of biosynthesis and enzymatic activity of reductive dehalogenases and growth of Dehalococcoides. Notably, cocontaminants more profoundly inhibited Dehalococcoides populations harboring the vcrA gene than those possessing the tceA gene, thereby explaining the accumulation of vinyl chloride under cocontaminant stress. Nonetheless, we successfully ameliorated cocontaminant inhibition by augmentation with Desulfitobacterium sp. strain PR owing to its ability to attenuate cocontaminants, resulting in concurrent detoxification of DCEs, trichloroethanes, and chloroform. Microbial community analyses demonstrated obvious alterations in taxonomic composition, structure, and assembly of the dechlorinating microbiome in the presence of cocontaminants, and introduction of strain PR reshaped the dechlorinating microbiome to be similar to its original state in the absence of cocontaminants. Altogether, these findings contribute to developing bioremediation technologies to clean up challenging sites polluted with multiple chlorinated solvents.

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.

Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge

Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.

Diversity of organohalide respiring bacteria and reductive dehalogenases that detoxify polybrominated diphenyl ethers in E-waste recycling sites

Widespread polybrominated diphenyl ethers (PBDEs) contamination poses risks to human health and ecosystems. Bioremediation is widely considered to be a less ecologically disruptive strategy for remediation of organohalide contamination, but bioremediation of PBDE-contaminated sites is limited by a lack of knowledge about PBDE-dehalogenating microbial populations. Here we report anaerobic PBDE debromination in microcosms established from geographically distinct e-waste recycling sites. Complete debromination of a penta-BDE mixture to diphenyl ether was detected in 16 of 24 investigated microcosms; further enrichment of these 16 microcosms implicated microbial populations belonging to the bacterial genera Dehalococcoides, Dehalogenimonas, and Dehalobacter in PBDE debromination. Debrominating microcosms tended to contain either both Dehalogenimonas and Dehalobacter or Dehalococcoides alone. Separately, complete debromination of a penta-BDE mixture was also observed by axenic cultures of Dehalococcoides mccartyi strains CG1, CG4, and 11a5, suggesting that this phenotype may be fairly common amongst Dehalococcoides. PBDE debromination in these isolates was mediated by four reductive dehalogenases not previously known to debrominate PBDEs. Debromination of an octa-BDE mixture was less prevalent and less complete in microcosms. The PBDE reductive dehalogenase homologous genes in Dehalococcoides genomes represent plausible molecular markers to predict PBDE debromination in microbial communities via their prevalence and transcriptions analysis.

Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review

Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.

Efficient and Complete Detoxification of Polybrominated Diphenyl Ethers in Sediments Achieved by Bioaugmentation with Dehalococcoides and Microbial Ecological Insights

Polybrominated diphenyl ethers (PBDEs) are prevalent environmental pollutants, but bioremediation of PBDEs remains to be reported. Here we report accelerated remediation of a penta-BDE mixture in sediments by bioaugmentation with Dehalococcoides mccartyi strains CG1 and TZ50. Bioaugmentation with different amounts of each Dehalococcoides strain enhanced debromination of penta-BDEs compared with the controls. The sediment microcosm spiked with 6.8 × 10⁶ cells/mL strain CG1 showed the highest penta-BDEs removal (89.9 ± 7.3%) to diphenyl ether within 60 days. Interestingly, co-contaminant tetrachloroethene (PCE) improved bioaugmentation performance, resulting in faster and more extensive penta-BDEs debromination using less bioinoculants, which was also completely dechlorinated to ethene by introducing D. mccartyi strain 11a. The better bioaugmentation performance in sediments with PCE could be attributed to the boosted growth of the augmented Dehalococcoides and capability of the PCE-induced reductive dehalogenases to debrominate penta-BDEs. Finally, ecological analyses showed that bioaugmentation resulted in more deterministic microbial communities, where the augmented Dehalococcoides established linkages with indigenous microorganisms but without causing obvious alterations of the overall community diversity and structure. Collectively, this study demonstrates that bioaugmentation with Dehalococcoides is a feasible strategy to completely remove PBDEs in sediments.

Long-term dechlorination of cis-DCE to ethene with co-immobilized Dehalococcoides mccartyi BAV1 and Clostridium butyricum in silica gel system

Chloroethenes are common groundwater pollutants, and have been classified as toxic and carcinogenic to humans. The metabolites of chloroethenes, cis-dichloroethene (cis-DCE) and vinyl chloride (VC) commonly accumulate in groundwater due to their recalcitrant reductive dechlorination under anaerobic conditions. Dehalococcoides mccartyi (Dhc) is the key anaerobic bacteria for complete dechlorination of chloroethene, and Clostridium butyricum (C. butyricum) can provide hydrogen for supporting the growth of Dhc. In this study, we co-immobilized Dhc strain BAV1 and C. butyricum in a silica gel to determine the ability of the complete dechlorination of cis-DCE. Our results showed that our immobilized system could protect BAV1 from a high concentration (8 mM) of cis-DCE to carry out complete dechlorination. After the long-term use of our immobilized system, the activity of complete dechlorination was maintained for more than 180 consecutive days. Furthermore, we applied the immobilized system to remediate contaminated groundwater and uncovered the complete dechlorination of cis-DCE into ethene, a non-toxic product, within 28 days. Therefore, this novel co-immobilized system could serve a solution for bioremediation at chloroethene-contaminated sites.

Influence of nitrate concentration on trichloroethylene reductive dechlorination in weak electric stimulation system

The co-existence of volatile chlorinated hydrocarbons (VCHs) and nitrate pollution in groundwater is prominent, but how nitrate exposure affects weak-electrical stimulated bio-dechlorination activity of VCH is largely unknown. Here, by establishing weak-electrical stimulated trichloroethylene (TCE) dechlorination systems, the influence on TCE dechlorination by exposure to the different concentrations (25-100 mg L^-1) of nitrate was investigated. The existence of nitrate in general decreased TCE dechlorination efficiency to varying degrees, and the higher nitrate concentration, the stronger the inhibitory effects, verified by the gradually decreased transcription levels of tceA. Although the TCE dechlorination kinetic rate constant decreased by 36% the most, under all nitrate concentration ranges, TCE could be completely removed within 32 h and no difference in generated metabolites was found, revealing the well-maintained dechlorination activity. This was due to the quickly enriched bio-denitrification activity, which removed nitrate completely within 9 h, and thus relieved the inhibition on TCE dechlorination. The obvious bacterial community structure succession was also observed, from dominating with dechlorination genera (e.g., Acetobacterium, Eubacterium) to dominating with both dechlorination and denitrification genera (e.g., Acidovorax and Brachymonas). The study proposed the great potential for the in situ simultaneous denitrification and dehalogenation in groundwater contaminated with both nitrate and VCHs.

Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis

As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.

Debromination of TetraBromoBisphenol-A (TBBPA) depicting the metabolic versatility of Dehalococcoides

TetraBromoBisphenol-A (TBBPA) is a widely used brominated flame retardant and an emerging contaminant that has amassed significant environmental impacts. Though there are a few studies that report the bioremediation of TBBPA, there is no direct evidence to suggest a metabolic use of TBBPA as the sole electron acceptor, which offers an advantage in the complete and energy-efficient process of debromination under anaerobic conditions. In this study, Dehalococcoides mccartyi strain CG1 was identified to be capable of utilizing TBBPA as the sole electron acceptor at its maximum soluble concentrations (7.3 μM) coupled with cell growth. A previously characterized reductive dehalogenase (RDase), PcbA1, and six other RDases of strain CG1 were detected during TBBPA debromination via transcriptional and proteomic analyses. Furthermore, as a commonly co-contaminated brominated flame retardant of TBBPA, penta-BDEs were debrominated synchronously with TBBPA by strain CG1. This study provides deeper insights into the versatile dehalogenation capabilities of D. mccartyi strain CG1 and its role in in situ remediations of persistent organic pollutants in the environment.

Remediation of soil contaminated with organic compounds by nanoscale zero-valent iron: A review

In recent years, nanoscale zero-valent iron (nZVI) has been gradually applied in soil remediation due to its strong reducing ability and large specific surface area. Compared to conventional remediation solutions, in situ remediation using nZVI offers some unique advantages. In this review, respective merits and demerits of each approach to nZVI synthesis are summarized in detail, particularly the most commonly used aqueous-phase reduction method featuring surface modification. In order to overcome undesired oxidation and agglomeration of fresh nZVI due to its high reactivity, modifications of nZVI have been developed such as doping with transition metals, stabilization using macromolecules or surfactants, and sulfidation. Mechanisms underlying efficient removal of organic pollutants enabled by the modified nZVI lie in alleviative oxidation and agglomeration of nZVI and enhanced electron utilization efficiency. In addition to chemical modification, other assisting methods for further improving nZVI mobility and reactivity, such as electrokinetics and microbial technologies, are evaluated. The effects of different remediation technologies and soil physicochemical properties on remediation performance of nZVI are also summarized. Overall, this review offers an up-to-date comprehensive understanding of nZVI-driven soil remediation from scientific and practical perspectives.

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.

Abundance of organohalide respiring bacteria and their role in dehalogenating antimicrobials in wastewater treatment plants

Anthropogenic organohalide contaminants present in wastewater treatment plants (WWTPs) often remain untreated and can be discharged into the environment. Although organohalide respiring bacteria (OHRB) contribute to the elimination of anthropogenic organohalides in natural anaerobic environments, reductive dehalogenation by OHRB in mainstream WWTPs remains poorly understood. In this study, we quantified OHRB during a long-term operation of a municipal WWTP with short hydraulic and sludge retention times (3 h and 1.5-5 days, respectively). The obligate OHRB were detected at high levels (averaging 2.56 ± 1.73 × 10⁷ and 3.11 ± 1.16 × 10⁷ 16S rRNA gene copies/ml MLSS sludge in anoxic and aerobic zones, respectively) over the entire sampling period and throughout the wastewater treatment train. Microcosms derived from mainstream activated sludge contained an unidentified member of the Dehalococcoides genus that metabolically dechlorinated triclosan, used as a representative emerging organohalide antimicrobial, to diclosan, suggesting the potential of anaerobic degradation of emerging contaminants in WWTPs. To further understand the mechanisms for such antimicrobials' removal, an investigation of dechlorination of triclosan by Dehalococcoides strains was conducted. Dechlorination of environmentally relevant concentrations of triclosan to diclosan was observed in Dehalococcoides mccartyi strain CG1, yielding 4.59 ± 0.34 × 10⁸ cells/μmole Cl^- removed at a rate of 0.062 μM/day and a minimal inhibitory concentration of 0.5 mg/L. Notably, both the tolerance of strain CG1 to triclosan and the rate of triclosan dechlorination increased when CG1 was cultured in the presence of both triclosan and tetrachloroethene. Taken together, our results suggest that anaerobic degradation of organohalide antimicrobials might be more prevalent in mainstream WWTPs than previously speculated, though the low growth yields that are supported by triclosan dechlorination seem to indicate that other organohalide substrates could be necessary to sustain OHRB populations in these systems.

Dehalococcoides mccartyi Strain GEO12 Has a Natural Tolerance to Chloroform Inhibition

Cocontamination by chloroform and chloroethenes often confounds bioremediation efforts. Here, we describe Dehalococcoides mccartyi strain GEO12 that dechlorinates trichloroethene to ethene in 14 μM (1.6 mg·L^-1) chloroform. The same chloroform concentration effectively inhibited dechlorination in Dehalococcoides strains ANAS2, 11a, and BAV1. Successive transfers of strain GEO12 in increasing concentrations of chloroform led to culture GEO12CF that tolerated 83 μM (10 mg·L^-1) chloroform. The genome of strain GEO12 revealed seven reductive dehalogenase homologous (rdh) genes, including tceA and vcrA. Transcriptional analyses showed that chloroform (45 μM; 5.3 mg·L^-1) in culture GEO12CF enhanced the transcription of tceA to a statistically significant degree (the median increase was 55.4 transcripts per 10⁴ 16S rRNA, CI_95% = [12.9, 125]). The increase of vcrA transcripts in the presence of chloroform (45 μM; 5.3 mg·L^-1) in culture GEO12CF was not statistically significant because the CI_95% range spanned 0 (the median increase was 109 transcripts per 10⁴ 16S rRNA, CI_95% = [-13.6, 246]). Inhibition of dehalogenation by chloroform is often seen in Dehalococcoides, but the mechanism remains unknown. Our results suggest that culture GEO12CF may overcome chloroform inhibition by rdh upregulation. The chloroform-adapted culture GEO12CF provides insights into the metabolic flexibility of Dehalococcoides and could be used to fight chloroethene contamination where chloroform is a cocontaminant.

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.

Electrokinetics applied in remediation of subsurface soil contaminated with chlorinated ethenes - A review

Electrokinetics is being applied in combination with common insituremediation technologies, e.g. permeable reactive barriers, bioremediation and in-situ chemical oxidation, to overcome experienced limitations in remediation of chlorinated ethenes in low-permeable subsurface soils. The purpose of this review is to evaluate state-of-theart for identification of major knowledge gaps to obtain robust and successful field-implementations. Some of the major knowledge gaps include the behavior and influence of induced transient changes in soil systems, transport velocities of chlorinated ethenes, and significance of site-specific parameters on transport velocities, e.g. heterogeneous soils and hydrogeochemistry. Furthermore, the various ways of reporting voltage distribution and transport rates complicate the comparison of transport velocities across studies. It was found, that for the combined EK-techniques, it is important to control the pH and redox changes caused by electrolysis for steady transport, uniform distribution of the electric field etc. Specifically for electrokinetically enhanced bioremediation, delivery of lactate and biodegrading bacteria is of the same order of magnitude. This review shows that enhancement of remediation technologies can be achieved by electrokinetics, but major knowledge gaps must be examined to mature EK as robust methods for successful remediation of chlorinated ethene contaminated sites.

Electron Fluxes in Biocathode Bioelectrochemical Systems Performing Dechlorination of Chlorinated Aliphatic Hydrocarbons

Bioelectrochemical systems (BESs) are regarded as a promising approach for the enhanced dechlorination of chlorinated aliphatic hydrocarbons (CAHs). However, the electron distribution and transfer considering dechlorination, methanogenesis, and other bioprocesses in these systems are little understood. This study investigated the electron fluxes in biocathode BES performing dechlorination of three typical CAHs, 1,1,2,2-tetrachloroethene (PCE), 1,1,2-trichloroethene (TCE) and 1,2-dichloroethane (1,2-DCA). Anaerobic sludge was inoculated to cathode and biocathode was acclimated by the direct acclimation and selection. The constructed biocathode at −0.26 V had significantly higher dechlorination efficiency (E_24h > 99.0%) than the opened circuit (E_24h of 17.2–27.5%) and abiotic cathode (E_24h of 5.5–10.8%), respectively. Cyclic voltammetry analysis demonstrated the enhanced cathodic current and the positive shift of onset potential in the cathodic biofilm. Under autotrophic conditions with electrons from the cathode as sole energy source (columbic efficiencies of 80.4–90.0%) and bicarbonate as sole carbon source, CAHs dechlorination efficiencies were still maintained at 85.0 ± 2.0%, 91.4 ± 1.8%, and 84.9 ± 3.1% for PCE, TCE, and 1,2-DCA, respectively. Cis-1,2-dichloroethene was the final product for PCE and TCE, while 1,2-DCA went through a different dechlorination pathway with the non-toxic ethene as the final metabolite. Methane was the main by-product of the heterotrophic biocathode, and methane production could be enhanced to some extent by electrochemical stimulation. The various electron fluxes originating from the cathode and oxidation of organic substrates might be responsible for the enhanced CAHs dechlorination, while methane generation and bacterial growth would probably reduce the fraction of electrons provided for CAH dechlorination. The study deals with the dechlorination and competitive bioprocesses in CAH-dechlorinating biocathodes with a focus on electron fluxes.

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.

Effects of 1,1,1-Trichloroethane and Triclocarban on Reductive Dechlorination of Trichloroethene in a TCE-Reducing Culture

Chlorinated compounds were generally present in the environment due to widespread use in the industry. A short-term study was performed to evaluate the effects of 1,1,1- trichloroethane (TCA) and triclocarban (TCC) on trichloroethene (TCE) removal in a reactor fed with lactate as the sole electron donor. Both TCA and TCC inhibited TCE reduction, but the TCC had a more pronounced effect compared to TCA. The TCE-reducing culture, which had never been exposed to TCA before, reductively dechlorinated TCA to 1,1-dichloroethane (DCA). Below 15 μM, TCA had little effect on the transformation of TCE to cis-dichloroethene (DCE); however, the reduction of cis-DCE and vinyl chloride (VC) were more sensitive to TCA, and ethene production was completely inhibited when the concentration of TCA was above 15 μM. In cultures amended with TCC, the reduction of TCE was severely affected, even at concentrations as low as 0.3 μM; all the cultures stalled at VC, and no ethene was detected. The cultures that fully transformed TCE to ethene contained 5.2–8.1% Dehalococcoides. Geobacter and Desulfovibrio, the bacteria capable of partially reducing TCE to DCE, were detected in all cultures, but both represented a larger proportion of the community in TCC-amended cultures. All cultures were dominated by Clostridium_sensu_stricto_7, a genus that belongs to Firmicutes with proportions ranging from 40.9% (in a high TCC (15 μM) culture) to 88.2%. Methanobacteria was detected at levels of 1.1–12.7%, except in cultures added with 15 and 30 μM TCA, in which they only accounted for ∼0.4%. This study implies further environmental factors needed to be considered in the successful bioremediation of TCE in contaminated sites.

Microbial degradation of chloroethenes: a review

Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.

Interaction of perchlorate and trichloroethene bioreductions in mixed anaerobic culture

This work evaluated the interaction of perchlorate and trichloroethene (TCE), two common co-contaminants in groundwater, during bioreduction in serum bottles containing synthetic mineral salts media and microbial consortia. TCE at concentrations up to 0.3mM did not significantly affect perchlorate reduction; however, perchlorate concentrations higher than 0.1mM made the reduction of TCE significantly slower. Perchlorate primarily inhibited the reduction of vinyl chloride (VC, a daughter product of TCE) to ethene. Mechanistic analysis showed that the inhibition was mainly because perchlorate reduction is thermodynamically more favorable than reduction of TCE and its daughter products and not because of toxicity due to accumulation of dissolved oxygen produced during perchlorate reduction. As the initial perchlorate concentration increased from 0 to 600mg/L in a set of serum bottles, the relative abundance of Rhodocyclaceae (a putatively perchlorate-reducing genus) increased from 6.3 to 80.6%, while the relative abundance of Dehalococcoides, the only known genus that is able to reduce TCE all the way to ethene, significantly decreased. Similarly, the relative abundance of Proteobacteria (a phylum to which most known perchlorate-reducing bacteria belong) increased from 22% to almost 80%.

Rising Strengths Hong Kong SAR in Bioinformatics

Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

Reductive dechlorination of tetrachloroethene in marine sediments: Biodiversity and dehalorespiring capabilities of the indigenous microbes

Chlorinated compounds pose environmental concerns due to their toxicity and wide distribution in several matrices. Microorganisms specialized in leading anaerobic reductive dechlorination (RD) processes, including Dehalococcoides mccartyi (Dhc), are able to reduce chlorinated compounds to harmless products or to less toxic forms. Here we report the first detailed study dealing with the RD potential of heavy polluted marine sediment by evaluating the biodegradation kinetics together with the composition, dynamics and activity of indigenous microbial population. A microcosm study was conducted under strictly anaerobic conditions on marine sediment collected near the marine coast of Sarno river mouth, one of the most polluted river in Europe. Tetrachloroethene (PCE), used as model pollutant, was completely converted to ethene within 150 days at reductive dechlorination rate equal to 0.016 meq L(-1) d(-1). Consecutive spikes of PCE allowed increasing the degradation kinetics up to 0.1 meq L(-1)d(-1) within 20 days. Strictly anaerobiosis and repeated spikes of PCE stimulated the growth of indigenous Dhc cells (growth yield of ~7.0 E + 07 Dhc cells per μM Cl(-1) released). Dhc strains carrying the reductive dehalogenase genes tceA and vcrA were detected in the original marine sediment and their number increased during the treatment as demonstrated by the high level of tceA expression at the end of the microcosm study (2.41 E + 05 tceA gene transcripts g(-1)). Notably, the structure of the microbial communities was fully described by Catalysed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) as wells as the dynamics of the dechlorinating bacteria during the microcosms operation. Interestingly, a direct role of Dhc cells was ascertained suggesting the existence of strains adapted at salinity conditions. Additionally, non-Dhc Chloroflexi were retrieved in the original sediment and were kept stable over time suggesting their likely flanking role of the RD process.

A comparative genomics and reductive dehalogenase gene transcription study of two chloroethene-respiring bacteria, Dehalococcoides mccartyi strains MB and 11a

Genomes of two trichloroethene (TCE)-respiring Dehalococcoides (Dhc) mccartyi, strains MB and 11a, were sequenced to identify reductive dehalogenases (RDase) responsible for oraganohalide respiration. Transcription analyses were conducted to verify the roles of RDase subunit A genes (rdhA) in chloroethene respiration. Some interesting features of the strain MB draft genome include a large genome size, two CRISPR-cas type I systems, and 38 rdhA genes. Strain 11a has a stream-lined genome with 11 rdhA genes, of which nine are distinct. Quantitative real-time PCR transcription analysis of RDase gene transcripts showed that a single RDase gene, designated mbrA, was up-regulated upon exposure to TCE and no other RDase genes were considerably expressed in strain MB. A single RDase gene, designated vcrA, was up-regulated upon exposure to TCE and expressed at a steady level until all chloroethenes were completely dechlorinated to ethene at 147 h in strain 11a. Overall, this study reports the genomes of two distinct Dhc strains; both contain numerous uncharacterized RDase genes, but in each strain only one such gene was expressed highly during organohalide respiration.

Detoxification of 1,1,2-trichloroethane to ethene by desulfitobacterium and identification of its functional reductase gene

1,1,2-trichloroethane (1,1,2-TCA) has become a common groundwater pollutant due to historically extensive utilization, improper disposal, as well as from incomplete dechlorination of 1,1,2,2-tetrachloroethane. Currently, limited information is available on microbial detoxification of 1,1,2-TCA. Desulfitobacterium sp. strain PR, which was isolated from an anaerobic bioreactor maintained to dechlorinate chloroethenes/ethanes, exhibited the capacity to dechlorinate 1,1,1-trichloroethane and chloroform. In this study, the dechlorinating ability of strain PR was further explored. Strain PR showed the capability to dechlorinate 1,1,2-TCA (~1.12 mM) predominantly to 1,2-dichloroethane (1,2-DCA) and chloroethane, and to trace amounts of vinyl chloride and ethene within 20 days. Strain PR coupled growth with dechlorination of 1,1,2-TCA to 1,2-DCA, while no cell growth was observed with dechlorination of 1,2-DCA to chloroethane. Later, through transcriptomic and enzymatic analysis, the reductive dehalogenase CtrA, which was previously reported to be responsible for 1,1,1-trichloroethane and chloroform dechlorination, was identified as the 1,1,2-TCA reductive dehalogenase. Since trichloroethene (TCE) is usually co-contaminated with 1,1,2-TCA, a co-culture containing Dehalococcoides mccartyi strain 11a capable of detoxifying TCE and 1,2-DCA and strain PR was established. Interestingly, this co-culture dechlorinated 1,1,2-TCA and TCE to the non-toxic end-product ethene within 48 days without chloroethane production. This novel pathway avoids production of the carcinogenic intermediate dechlorination product vinyl chloride, providing a more environmentally friendly strategy to treat 1,1,2-TCA.

Chloroethene degradation and expression of Dehalococcoides dehalogenase genes in cultures originating from Yangtze sediments

The anaerobic Dehalococcoides spp. is the only microorganism known to completely dechlorinate the hazardous compounds tetrachloroethene (PCE) or trichloroethene (TCE) via dichloroethene (DCE) and vinyl chloride (VC) to the terminal product, ethene. In this study, growth of Dehalococcoides spp. (DHC) and the expression of DHC dehalogenase genes were demonstrated for Yangtze enrichment cultures. Reductive dechlorination of chloroethenes occurred in Yangtze sediment without the addition of any external auxiliary substrates. All Yangtze enrichment cultures completely dechlorinated PCE and cis-DCE to ethene. To investigate expression of the dehalogenase genes pceA, tceA, vcrA, and bvcA, a protocol for messenger RNA (mRNA) extraction followed by reverse transcription and quantitative PCR analysis was established. During dechlorination, an increase in gene copy numbers of pceA, tceA, and vcrA was observed. However, temporary formation of mRNA was only measured in the case of the dehalogenase genes tceA and vcrA. Comparison of DHC dehalogenase patterns indicated that the Yangtze DHC community does not match any of the previously published enrichment cultures that were obtained from contaminated areas in the USA or Europe.

A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1-trichloroethane and chloroform

1,1,1-Trichloroethane (TCA) and chloroform are two notorious groundwater pollutants. Here we report the isolation and characterization of Desulfitobacterium sp. strain PR that rapidly dechlorinates both compounds. In pyruvate-amended medium, strain PR reductively dechlorinates ∼ 1.0 mM TCA completely to monochloroethane within 15 days. Under the same conditions, strain PR dechlorinates ∼ 1.2 mM chloroform to predominantly dichloromethane (∼ 1.14 mM) and trace amount of monochloromethane (∼ 0.06 mM) within 10 days. Strain PR shares 96.7% 16S rRNA gene sequence similarity with its closest relative - Desulfitobacterium metallireducens strain 853-15; however, it distinguishes itself from known Desulfitobacterium strains by its inability of utilizing several of their commonly shared substrates such as lactate, thiosulfate and sulfite. A reductive dehalogenase gene (ctrA) in strain PR was identified to be responsible for dechlorination of both TCA and chloroform, showing a maximum expression level of 5.95 ∼ 6.25 copies of transcripts cell(-1) . CtrA shares 94% amino acid sequence identity with CfrA in Dehalobacter sp. strain CF50 and DcrA in Dehalobacter sp. strain DCA. Interestingly, strain PR could tolerate high aqueous concentrations (up to 0.45 mM) of trichloroethene, another groundwater pollutant that often coexists with TCA/chloroform. As the first chloroform-respiring and the second TCA-respiring isolate that has been identified, Desulfitobacterium sp. strain PR may prove useful in remediation of halogenated alkanes with trihalomethyl (-CX₃) groups.