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

Enhanced resilience to oxygen exposure and toxicity of chlorinated solvents in immobilized Dehalococcoides mccartyi

Members of Dehalococcoides mccartyi (Dhc) are strictly anaerobic and play crucial roles in the restoration of many industrial sites impacted by chlorinated solvents, such as tetrachloroethene (PCE) and trichloroethene (TCE). In situ bioremediation with Dhc involves intricate procedures intended to minimize oxygen intrusion, and achieving optimal dechlorination performance in aquifers near the dense non-aqueous phase liquids source zone is challenging. Here, we respectively embedded Dhc strain 195 and the biomass of a Dhc-containing, PCE-dechlorinating consortium in poly(vinyl alcohol)-alginate hydrogel beads. The ethene-forming potential was well-retained in immobilized Dhc following a prolonged oxygen exposure spanning from 12 hours to 7 days, with dechlorination rates ranging from 54.6 ± 4.2-101.9 ± 13.5 µM Cl- released day-1. In contrast, suspended strain 195 and the Dhc-containing biomass exposed to oxygen for a shorter duration were completely deactivated, or suffered a substantial reduction in dechlorination potential. Cell immobilization also significantly improved the ability of Dhc to tolerate the toxic effects of chlorinated solvents. When exposed to 300 mg L-1 TCE or free-phase PCE, an immobilized Dhc inoculum enabled more rapid recovery of dechlorination activity with shorter lag phases and up to 2.1-fold higher dechlorination rate compared to the use of their suspended counterparts. Our results demonstrate the effectiveness of cell immobilization for shielding Dhc from various environmental stresses (e.g., oxygen exposure).

Mechanistic insights into chloroethene dechlorination by Dehalococcoides mccartyi strain CWV2: A multi-omics perspective

This study provides an in-depth investigation of the novel Dehalococcoides mccartyi (Dhc) strain CWV2, isolated from Taiwan, for its effectiveness in dechlorinating various chloroethenes, including PCE, TCE, DCEs, and VC, to ethene. Through multi-omics analyses, including genomic, transcriptomic, translatomic and proteomic profiling, we uncovered the mechanisms behind TCE dechlorination by strain CWV2. The genomic analysis identified key reductive dehalogenase (RDase) genes, pceA and vcrA, which enhance our understanding of the versatile dechlorination pathways in Dhc. Ribosome profiling provided detailed insights into the translational regulation of vcrA, revealing sophisticated genetic control over protein synthesis. Complementary BN-PAGE and proteomic analyses identified key RDase VcrA, offering further insights into the activity of the organohalide respiration (OHR) complex within CWV2 and its metabolic pathways. Multi-omics analyses provide a comprehensive understanding of the mechanisms behind TCE dechlorination and organohalide respiration, offering valuable insights to advance bioremediation strategies for chloroethene-contaminated environments.

Iron-reduction driven extracellular electron transfer widely promotes microbial reductive dechlorination metabolism

Biological iron reduction and reductive dehalogenation occur in similar ecological environments, however, how Fe(III)/Fe(II) redox cycles impact the microbial dehalogenation processes remains controversial. In this study, the favorable microbial reductive dechlorination activity has been widely observed in iron-rich river sediments by national sampling, with the dechlorination efficiency showing a positive correlation with the concentration of Fe(III). Microcosm experiments demonstrated that the addition of nano-hematite resulted in a maximum increase of 2.16 times in the dechlorination rate constant (k) for 2,4,6-trichlorophenol, achieved via synergistic interactions with Fe(III) reduction. Multi-tools, including transcriptomic analyses, revealed that the addition of nano-hematite enhanced the process of Fe(III) reduction by upregulating genes associated with extracellular electron transfer (e.g., CYC, pliM) and conductive biofilm formation (e.g., livH, secY, wza). This synergistic Fe(III) reduction further facilitated intracellular carbon metabolism, energy production, and reductive dechlorination, as confirmed by the upregulated functional genes identified through transcriptomics and RT-qPCR. The discovery of the novel phenomenon involving synergistic Fe(III) reduction and dehalogenation broadens our understanding of the biochemical cycling of organohalides (e.g., chlorinated phenols) in iron-rich environment, and provides a feasible strategy for improving biodehalogenation through the regulation of carbon and electron flow at sites contaminated with organohalides.

Reductive dechlorination of trichloroethene at concentrations approaching saturation by a Desulfitobacterium-containing community

In dense nonaqueous phase liquid (DNAPL) contaminant source zones, aqueous concentrations of trichloroethene (TCE) in groundwater may approach saturation levels (8.4 mM). It is generally believed that such saturation concentrations are toxic to organohalide-respiring bacteria (OHRB), thus limiting the effectiveness of bioremediation. Here, we describe a Desulfitobacterium-containing culture capable of dechlorinating TCE to cis-dichloroethene (cis-DCE) at aqueous concentrations as high as 8.0 mM. A novel Desulfitobacterium population, designated as strain THU1, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Illumina MiSeq sequencing. Microbial community analysis revealed that TCE concentrations above 4.6 mM significantly affected the composition of the microbial community but had little effect on the Shannon index. The genome of strain THU1 revealed two reductive dehalogenases (RdhA), and the RdhA2 is a putative pceA. Additionally, its genome encodes proteins involved in stress response and regulatory pathways, enabling tolerance to near-saturation TCE concentrations. Our findings provide insights into the metabolic flexibility of Desulfitobacterium, suggesting its potential use as a candidate for source zone bioremediation to enhance the dissolution of TCE DNAPL by increasing the concentration gradient at the DNAPL-water interface.

Analyzing Dehalochip: A functional DNA microarray for reductive dichlorination in chloroethene-contaminated sites

Interpreting high-throughput transcriptomic and metagenomic data from non-model microorganisms presents a challenge due to the significant number of genes with unknown functions and sequences. In this study, we applied an innovative microarray, Dehalochip, for detecting the expression of genes in various microorganisms, particularly focusing on genes involved in chloroethene degradation. Our results demonstrated that this approach can effectively identify dechlorination genes, such as 16S rRNA, tceA, bvcA, and vcrA, in Dehalococcoides mccartyi from samples of groundwater contaminated with chloroethene. Noticeably, the sensitivity and specificity of our Dehalochip are comparable to that of quantitative PCR. However, it stands out as a more viable option for in-situ applications due to its greater capacity to infer potential dechlorination genes. Consequently, we believe our dechlorination microarray offers valuable insights into the role of known microorganisms and their associated functional genes in chloroethene-contaminated environments. This contributes to a deeper understanding of the in-situ reductive dechlorination process.

Construction of a synthetic anaerobic dechlorination microbiome to degrade chlorinated ethenes by application of metabolic interactions principle

Bioaugmentation is a bioremediation approach to treat groundwater contaminated with chlorinated ethenes, but currently it faces challenges such as poor microbiome stability and effectiveness, due to blind species integration and metabolic inhibition. The objective of this study was to create a controllable and functionally stable microbial community for dichlorination application. For this, we utilized targeted screening to identify dechlorinating bacteria from contaminated groundwater, that in combination would form an anaerobic dechlorination microbial community with stabilizing metabolic interactions between the constituents. The results showed that two organohalide-respiring bacterial (OHRB) species were isolated, and these were identified as Enterobacter bugandensis X4 and Enterobacter sichuanensis C4. Upon co-cultivation with lactic acid as the carbon source, the strains demonstrated metabolic interactions and synergistic dehalogenation ability towards trichloroethene (TCE). It was further demonstrated that the functional microbiome constructed with the strains was stable over time and exhibited a robust TCE degradation rate of 80.85% at 13.13 mg/L TCE within 10 days. Additionally, the complete conversion of TCE was achieved through microbiome bioaugmentation, this augmented microbiome increased the degradation rate towards 52.55 mg/L TCE by approximately 30% within 6 days. Additionally, bioaugmentation stimulated the growth of indigenous OHRB, such as Dehalobacter and Desulfovibrio. It also promoted a positive succession of the microbial community. These findings offer valuable insights into the microbial remediation of chlorinated ethenes-contaminated groundwater and offers novel ideas for the construction of an artificial functional microbiome.

Bioremediation of trichloroethylene-contaminated groundwater using green carbon-releasing substrate with pH control capability

In this research, a sustainable substrate, termed green and long-lasting substrate (GLS), featuring a blend of emulsified substrate (ES) and modified rice husk ash (m-RHA) was devised. The primary objective was to facilitate the bioremediation of groundwater contaminated with trichloroethylene (TCE) using innovative GLS for slow carbon release and pH control. The GLS was concocted by homogenizing a mixture of soybean oil, surfactants (Simple Green™ and soya lecithin), and m-RHA, ensuring a gradual release of carbon sources. The hydrothermal synthesis was applied for the production of m-RHA production. The analyses demonstrate that m-RHA were uniform sphere-shape granules with diameters in micro-scale ranges. Results from the microcosm study show that approximately 83% of TCE could be removed (initial TCE concentration = 7.6 mg/L) with GLS supplement after 60 days of operation. Compared to other substrates without RHA addition, higher TCE removal efficiency was obtained, and higher Dehalococcoides sp. (DHC) population and hydA gene (hydrogen-producing gene) copy number were also detected in microcosms with GLS addition. Higher hydrogen concentrations enhanced the DHC growth, which corresponded to the increased DHC populations. The addition of the GLS could provide alkalinity at the initial stage to neutralize the acidified groundwater caused by the produced organic acids after substrate biodegradation, which was advantageous to DHC growth and TCE dechlorination. The addition of m-RHA reached an increased TCE removal efficiency, which was due to the fact that the m-RHA had the zeolite-like structure with a higher surface area and lower granular diameter, and thus, it resulted in a more effective initial adsorption effect. Therefore, a significant amount of TCE could be adsorbed onto the surface of m-RHA, which caused a rapid TCE removal through adsorption. The carbon substrates released from m-RHA could then enhance the subsequent dechlorination. The developed GLS is an environmentally-friendly and green substrate.

An innovative permeable reactive bio-barrier to remediate trichloroethene-contaminated groundwater: A field study

Permeable reactive bio-barrier (PRBB), an innovative technology, could treat many contaminants via the natural gradient flow of groundwater based on immobilization or transformation of pollutants into less toxic and harmful forms. In this field study, we developed an innovative PRBB system comprising immobilized Dehalococcoides mccartyi (Dhc) and Clostridium butyricum embedded into the silica gel for long-term treatment of trichloroethene (TCE) polluted groundwater. Four injection wells and two monitoring wells were installed at the downstream of the TCE plume. Without PRBB, results showed that the TCE (6.23 ± 0.43 μmole/L) was converted to cis-dichloroethene (0.52 ± 0.63 μmole/L), and ethene was not detected, whereas TCE was completely converted to ethene (3.31 μmole/L) with PRBB treatment, indicating that PRBB could promote complete dechlorination of TCE. Noticeably, PRBB showed the long-term capability to maintain a high dechlorinating efficiency for TCE removal during the 300-day operational period. Furthermore, with qPCR analysis, the PRBB application could stably maintain the populations of Dhc and functional genes (bvcA, tceA, and vcrA) at >108 copies/L within the remediation course and change the bacterial communities in the contaminated groundwater. We concluded that our PRBB was first set up for cleaning up TCE-contaminated groundwater in a field trial.

Application of dissimilatory iron-reducing bacteria for the remediation of soil and water polluted with chlorinated organic compounds: Progress, mechanisms, and directions

Chlorinated organic compounds are widely used as solvents, but they are pollutants that can have adverse effects on the environment and human health. Dissimilatory iron-reducing bacteria (DIRB) such as Shewanella and Geobacter have been applied to treat a wide range of halogenated organic compounds due to their specific biological properties. Until now, there has been no systematic review on the mechanisms of direct or indirect degradation of halogenated organic compounds by DIRB. This work summarizes the discussion of DIRB's ability to enhance the dechlorination of reaction systems through different pathways, both biological and biochemical. For biological dechlorination, some DIRB have self-dechlorination capabilities that directly dechlorinate by hydrolysis. Adjustment of dechlorination genes through genetic engineering can improve the dechlorination capabilities of DIRB. DIRB can also adjust the capacity for the microbial community to dechlorinate and provide nutrients to enhance the expression of dechlorination genes in other bacteria. In biochemical dechlorination, DIRB bioconverts Fe(III) to Fe(II), which is capable of dichlorination. On this basis, the DIRB-driven Fenton reaction can efficiently degrade chlorinated organics by continuously maintaining anoxic conditions to generate Fe(II) and oxic conditions to generate H2O2. DIRB can drive microbial fuel cells due to their electroactivity and have a good dechlorination capacity at low levels of energy consumption. The contribution of DIRB to the removal of pesticides, antibiotics and POPs is summarized. Then the DIRB electron transfer mechanism is discussed, which is core to their ability to dechlorinate. Finally, the prospect of future work on the removal of chlorine-containing organic pollutants by DIRB is presented, and the main challenges and further research directions are suggested.

New dechlorination products and mechanisms of tris(2-chloroethyl) phosphate by an anaerobic enrichment culture from a vehicle dismantling site

End-of-life vehicles (ELVs) dismantling sites are the notorious hotspots of chlorinated organophosphate esters (Cl-OPEs). However, the microbial-mediated dechlorination of Cl-OPEs at such sites has not yet been explored. Herein, the dechlorination products, pathways and mechanisms of tris(2-chloroethyl) phosphate (TCEP, a representative Cl-OPE) by an anaerobic enrichment culture (ZNE) from an ELVs dismantling plant were investigated. Our results showed that dechlorination of TCEP can be triggered by reductive transformation to form bis(2-chloroethyl) phosphate (BCEP), mono-chloroethyl phosphate (MCEP) and by hydrolytic dechlorination to form bis(2-chloroethyl) 2-hydroxyethyl phosphate (TCEP-OH), 2-chloroethyl bis(2-hydroxyethyl) phosphate (TCEP-2OH), 2-chloroethyl (2-hydroxyethyl) hydrogen phosphate (BCEP-OH). The combination of 16S rRNA gene amplicon sequencing, quantitative real-time PCR (qPCR) and metagenomics revealed that the Dehalococcoides played an important role in the reductive transformation of TCEP to BCEP and MCEP. A high-quality metagenome-assembled genome (completeness >99% and contamination <1%) of Dehalococcoides was obtained. The sulfate-reducing bacteria harboring haloacid dehalogenase genes (had) may be responsible for the hydrolytic dechlorination of TCEP. These findings provide insights into microbial-mediated anaerobic transformation products and mechanisms of TCEP at ELVs dismantling sites, having implications for the environmental fate and risk assessment of Cl-OPEs at those sites.

Reutilization of scrap tyre for the enhanced removal of phthalate esters from water: immobilization performance, interaction mechanisms, and application

Waste scrap tyre as microbial immobilization matrix enhanced degradation of phthalate esters (PAEs), di (2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), and diethyl phthalate (DEP). The hybrid (physical adsorption and microbial immobilization) degradation process performance of scrap tyres was examined for the PAEs degradation. The scrap tyre was shown with competitive adsorption capacity toward PAEs, influenced by pH, temperature, dosage of adsorbent (scrap tyre), and concentration of PAE. The primary adsorption mechanism for tyres toward PAEs was considered hydrophobic. The immobilization of previously isolated Bacillus sp. MY156 on tyre surface significantly enhanced PAEs degradation as well as bacterial growth. The enzymatic activity results implied immobilization promoted dehydrogenase activity and decreased esterase activity. The cell surface response during PAEs degradation, in terms of morphological observation, FTIR and XRD analyses, and extracellular polymeric substance (EPS) release, was further assessed to better understand the interactions between microorganisms and tyre surface. Waste scrap tyres could be a promising potential candidate to be reused for sustainable environmental management, including contaminants removal.