Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

Wetland technology for the treatment of HCH-contaminated water - Case study at Hajek site

Hexachlorocyclohexanes (HCH) isomers and their transformation products, such as chlorobenzenes (ClB), generate severe and persistent environmental problems at many sites worldwide. The Wetland technology employing oxidation-reduction, biosorption, biodegradation and phytoremediation methods can sufficiently treat HCH-contaminated water. The treatment process is inherently natural and requires no supplementary chemicals or energy. The prototype with a capacity of 3 L/s was installed at Hajek quarry spoil heap (CZ), to optimize the technology on a full scale. The system is fed by drainage water with an average concentration of HCH 129 μg/L, ClB 640 μg/L and chlorophenols (ClPh) of 16 μg/L. The system was tested in two years of operation, regularly monitored for HCH, ClB and ClPh, and maintained to improve its efficiency. The assessment was not only for environmental effects but also for socio and economic indicators. During the operation, the removal efficiency of HCH ranged from 53.5 % to 96.9 % (83.9 % on average) depending on the flow rate. Removal efficiency was not uniform for individual HCH isomers but exhibited the trend: α = γ = δ > β = ε. The improved water quality was reflected in a biodiversity increase expressed by a number of phytobenthos (diatoms) species, a common biomarker of aquatic environment quality. The Wetland outranked the conventional WWTP in 10 out of the 15 general categories, and it is the most relevant scenario from the socio, environmental, and economic aspects.

Anaerobic biotransformation of hexachlorocyclohexane isomers in aqueous condition: Dual CCl isotope fractionation and impact on microbial community compositions

Hexachlorocyclohexane (HCH) isomers are persistent organic pollutants (POPs) with high toxicity, lipid solubility, chemical stability. Despite the current ban on usage of Lindane, residual contamination cannot be ignored, and HCH are frequently detected in groundwater and threaten human health. Cultures capable of degrading α-HCH, β-HCH, γ-HCH, and δ-HCH individually have been enriched in anoxic aqueous conditions. Compound-Specific Isotope Analysis (CSIA) was applied to examine the transformation mechanisms of different HCH isomers by the four enrichment cultures. 16S rRNA sequencing techniques were employed to examine the community composition of the enrichment cultures and detect changes in these communities resulting from adding individual HCH isomers. The results indicated that the ability of the enrichment cultures for dichloroelimination of HCH isomers was inconsistent. During dichloroelimination, different bond cleavage mode of β- and δ-HCH led to distinct isotopic effects. HCH isomers had significant impact on the microbial community, while different microbial communities showed comparable isotopic effects during the transformation of a specific HCH isomer. In addition, bacteria in the phyla Proteobacteria and Firmicutes were proposed as the dominant dechlorinators. This study provides a novel perspective on the mode of bond cleavage during HCH dichloroelimination and the effect of HCH on microbial communities, which could potentially support the evaluation of HCH transformation by CSIA and their effects on the microecosystems of groundwater.

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.

Simultaneous regulation of biocathodic γ-HCH dechlorination and CH4 production by tailoring the structure and function of biofilms based on quorum sensing

Dechlorination of chlorinated organic pollutants and methanogenesis are attractive biocathode reductions in microbial electrolysis cells (MECs). Quorum sensing (QS) is applied to regulate microbial communications. However, how acyl-homoserine lactones (AHLs)-dependent QS organize the assembly of the biocathode microbial community, and then regulate multiple biocathode reductions remains unclear. By applying N-butanoyl homoserine lactone (C4-HSL), N-hexanoyl homoserine lactone (C6-HSL) and 3-oxo-hexanoyl homoserine lactone (3OC6-HSL) in γ-hexachlorocyclohexane (γ-HCH) contaminated MECs, this study investigated the changes of biofilm microbial structure and function and the mechanisms of AHLs-QS on γ-HCH dechlorination and CH4 production. Exogenous C4-HSL and 3OC6-HSL increased cytochrome c production and enriched dechlorinators, electroactive bacteria but not methanogens to accelerate γ-HCH dechlorination and inhibit CH4 production. C6-HSL facilitated dechlorination and CH4 production by enhancing biofilm electroactivity and increasing membrane transportation. Besides, exogenous C6-HSL restored the electron transfer capacity that was damaged by the concurrent addition of acylase, an endogenous AHL quencher. From the perspective of microbial assembly, this study sheds insights into and provides an efficient strategy to selectively accelerate dechlorination and CH4 production by harnessing microbial structure based on QS systems to meet various environmental demands.

Impact of clomazone on bacterial communities in two soils

Introduction

Bacterial communities are important for soil functions, but the effect of clomazone on network complexity, composition, and stability is not well studied.

Method

In this study, two agricultural soils were used to test the impact of clomazone on bacterial communities, and the two soils were treated with three concentrations of clomazone (0, 0.8, 8, and 80 mg kg1) in an incubator.

Results and discussion

Bacterial network nodes, links, and average degrees were all decreased by 9-384, 648-829, and 0.703-2.429, respectively. Based on keystone nodes, the topological roles of the nodes were also influenced by clomazone. Bacterial network composition was also impacted based on the analysis of similarity (ANOSIM) and network dissimilarity. Compared with control and clomazone treatments in both soils, the ANOSIM between control and all clomazone treatments was higher than 0.6, network dissimilarities were 0.97-0.98, shared nodes were 131-260, and shared links were 12-100. The bacterial network stability was decreased by clomazone, with decreased robustness by 0.01-0.016 and increased vulnerability by 0.00023-0.00147 in both soils. There were fewer bacterial network modules preserved after clomazone treatment, and the bacterial network community functions were also impacted in both soils. Based on these results, soil bacterial species connections, modularization, and network stability were significantly impacted by clomazone.

Combination of slurry-bioreactors and actinobacteria consortia as strategy to bioremediate chlordane-contaminated soils

Soil contamination caused by pesticides poses a significant environmental challenge, and addressing it requires effective solutions. Bioremediation, combining the utilization of slurry-bioreactors and microbial consortia, emerges as an appropiated strategy to tackle this issue. Therefore, this research evaluated the chlordane (CLD) removal efficiency by a Streptomyces consortium through bioaugmentation of polluted soils, and slurry-bioreactors. For that, a Streptomyces defined consortium with CLD removal abilities was inoculated in soil microcosms and soil-slurry bioreactors (SB), with (SB-TSB) and without stimulation (SB-water). In soil, CLD presence has no negative effect on consortium growth. This was supported by comparing its duplication time (7.48 ± 0.14 h) with the obtained in the biotic control (7.45 ± 0.04 h). Furthermore, 17% of pesticide removal by microbial action was detected in the treated microcosms. In SB, the microbial development was not affected by the pesticide presence. In SB-TSB, the microbial growth was higher than in SB-water. This was supported by its lesser duplication time (7.27 ± 0.17 h) with respect to the non-stimulated systems (10.88 ± 0.29 h). However, SB-water showed the highest CLD removal ability (34.8%), with a concomitant increase in the chloride ion release. In the phytotoxicity test, the vigor index showed that the bioremediation in SB-water did not exert adverse effects greater than those generated by the CLD. Indeed, the root length increased after the treatment. These findings demonstrate the versatility of the Streptomyces consortium to remediate solid and semi-solid matrices impacted with pesticides, and the advantage of using bioaugmented SB to enhance the pollutants removal and accelerating the clean-up time required.

Chlorinated organic pollutants in global flooded soil and sediments: Pollution status and potential risk

Chlorinated organic pollutants (COPs) were widely detected in anaerobic environments while there is limited understanding of their pollution status and potential environmental risks. Here, we applied meta-analysis to identify the occurrence status, pollution sources, and environmental risk of COPs from 246 peer-published literature, including 25 kinds of COPs from 977 sites. The results showed that the median concentrations of COPs were at the ng g^-1 level. By the combination of principal component analysis (PCA) and positive matrix factorization (PMF), we established 7 pollution sources for COPs. Environmental risk assessment found 73.3% of selected sites were at a security level but the rest were not, especially for the wetlands. The environmental risk of COPs was usually underestimated by the existing evaluation methods, such as without the consideration of the non-extractable residues (NER) and the multi-process coupling effect. Especially, the synergetic coupling associations between dechlorination and methanogenesis might increase the risk of methane emission that has barely been previously considered in previous risk assessment approaches. Our results expanded the knowledge for the pollution control and remediation of COPs in anaerobic environments.

Conductive Materials on Biocathodes Altered the Electron-Transfer Paths and Modulated γ-HCH Dechlorination and CH4 Production in Microbial Electrochemical Systems

Adding conductive materials to the cathode of a microbial electrochemical system (MES) can alter the route of interspecies electron transfer and the kinetics of reduction reactions. We tested reductive dechlorination of γ-hexachlorocyclohexane (γ-HCH), along with CH₄ production, in MES systems whose cathodes were coated with conductive magnetite nanoparticles (NaFe), biochar (BC), magnetic biochar (FeBC), or anti-conductive silica biochar (SiBC). Coating with NaFe enriched electroactive microorganisms, boosted electro-bioreduction, and accelerated γ-HCH dechlorination and CH₄ production. In contrast, BC only accelerated dechlorination, while FeBC only accelerated methanogenesis, because of their assemblies of functional taxa that selectively transferred electrons to those electron sinks. SiBC, which decreased electro-bioreduction, yielded the highest CH₄ production and increased methanogens and the mcrA gene. This study provides a strategy to selectively control the distribution of electrons between reductive dechlorination and methanogenesis by adding conductive or anti-conductive materials to the MES's cathode. If the goal is to maximize dechlorination and minimize methane generation, then BC is the optimal conductive material. If the goal is to accelerate electro-bioreduction, then the best addition is NaFe. If the goal is to increase the rate of methanogenesis, adding anti-conductive SiBC is the best.

Remedial trial of sequential anoxic/oxic chemico-biological treatment for decontamination of extreme hexachlorocyclohexane concentrations in polluted soil

During production of γ-hexachlorocyclohexane (γ-HCH), thousands of tons of other isomers were synthesized as byproducts, and after dumping represent sources of contamination for the environment. Several microbes have the potential for aerobic and anaerobic degradation of HCHs, and zero-valent iron is an effective remediation agent for abiotic dechlorination of HCHs, whereas the combination of the processes has not yet been explored. In this study, a sequence of anoxic/oxic chemico-biological treatments for the degradation of HCHs in a real extremely contaminated soil (10-30 g/kg) was applied. Approximately 1500 kg of the soil was employed, and various combinations of reducing and oxygen-releasing chemicals were used for setting up the aerobic and anaerobic phases. The best results were obtained with mZVI/nZVI, grass cuttings, and oxygen-releasing compounds. In this case, 80 % removal of HCHs was achieved in 129 days, and 98 % degradation was achieved after 1106 days. The analysis of HCHs and their transformation products proved active degradation when slight accumulation of the transformation product during the anaerobic phase was followed by aerobic degradation. The results document that switching between aerobic and anaerobic phases, together with the addition of grass, also created suitable conditions for the biodegradation of HCHs and monochlorobenzene/benzene by microbes.

Clomazone impact on fungal network complexity and stability

Introduction

Soil fungal network composition and stability are important for soil functions, but there is less understanding of the impact of clomazone on network complexity and stability.

Methods

In this work, two agricultural soils were used to investigate the impact of clomazone on fungal network complexity, composition, and stability. The two soils were treated with clomazone solution (0, 0.8, 8, and 80  mg kg^-1) and kept in an incubator.

Results and Discussion

Under the influence of clomazone, the fungal network nodes were decreased by 12-42; however, the average degree was increased by 0.169-1.468 and fungal network density was increased by 0.003-0.054. The keystone nodes were significantly changed after clomazone treatment. Network composition was also impacted. Specifically, compared with control and clomazone treatments in both soils, the shared edges were fewer than 54 in all comparisons, and network dissimilarity was 0.97-0.98. These results suggested that fungal network composition was significantly impacted. The network robustness was increased by 0.0018-0.0209, and vulnerability was decreased by 0.00018-0.00059 in both soils, which indicated that fungal network stability was increased by clomazone. In addition, the functions of network communities were also changed in both soils. These results indicated that clomazone could significantly impact soil fungal networks.

Improved understanding on biochar effect in electron supplied anaerobic soil as evidenced by dechlorination and methanogenesis processes

Research interest in biochar as an environmental remediation material has rapidly increased over the past few years. However, the effect of biochar on typical environmental processes in anaerobic soil environment has been insufficiently discussed. By regulating the electron donors with sodium acetate or pyruvate, the effects and underpinning chemical-microbiological coupling mechanisms of biochar under anaerobic conditions were disclosed. Unlike the electron limited condition, the addition of electron donors alleviated the competition for electrons among various reduction processes in the soil. The effect of biochar in regulating the electron transfer processes was lessened. But more than doubled methane emissions were resulted by the exogenous substances, especially with the synergic effect of biochar. Biochar addition increased soil environmental heterogeneity. It might indirectly affect the reductive transformation of γ-HCH via increasing the bioavailability of pollutants through adsorption and promoting the metabolism of some rare microorganisms. Anaerolineaceae, Peptococcaceae and Methanosarcina had coherent phylogenetic patterns and were likely to be the enablers for the reductive dechlorination process in flooded soil. ENVIRONMENTAL IMPLICATION: Previous studies have widely reported the performance characteristics of biochar, but its effects under anaerobic environments are not systematically understood. By regulating the electron donors, the competition for electrons among various reduction processes in the soil might be alleviated, resulting in a lessened effect of biochar in regulating the electron transfer processes. The findings presented in this study highlight the role of biochar to the dynamic changes of reduction processes under anaerobic environments. The relevant soil conditions such as the electron donors and the functional microbial groups should be adequately considered for maximizing the all-around beneficial efficiency of biochar amendments.

Ecological risk assessment of organochlorine pesticide mixture in South China Sea and East China Sea under the effects of seasonal changes and phase-partitioning

Organochlorine pesticides (OCPs), chlorinated hydrocarbon derivatives extensively used in agriculture and chemical industry, have been banned for several decades in most developed countries. However, OCPs act as persistent organic pollutants due to their semi-volatility nature, high ability for wide range transportation and faster bioaccumulation, and thus it has remained as a topical global concern. This study focuses on OCP distributions, sources and associated ecological risks in the globally important OCP source-sink regions of South China Sea (SCS) and East China Sea (ECS). Given the co-exposure of multiple OCPs that undermine the classical risk assessment of single OCP species, a two-tier mixture risk assessment approach has been employed with explicit consideration of seasonal changes and phase-partitioning effects. The results indicate existence of multiple sources varied across the seasons and between the dissolved and particulate phases. Potential sources include the current-use of lindane or historical use of technical HCH, input of technical DDTs, long-range atmospheric transport, and deposition of HCB from land surfaces. There are no wide high-risk zones. Dissolved HCB and DDTs have posed low-to-medium levels of risks broadly distributed across the seasons. Relatively greater risks are observed in summer in the both dissolved and particulate phases. The study has shown the importance of considering mixture risk assessments with the effects of phase-partitioning and seasonal changes for efficient oceanic risk management.

Complete Reductive Dechlorination of 4-Hydroxy-chlorothalonil by Dehalogenimonas Populations

Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile, TePN) is one of the most widely used fungicides all over the world. Its major environmental transformation product 4-hydroxy-chlorothalonil (4-hydroxy-2,5,6-trichloroisophthalonitrile, 4-OH-TPN) is more persistent, mobile, and toxic and is frequently detected at a higher concentration in various habitats compared to its parent compound TePN. Further microbial transformation of 4-OH-TPN has never been reported. In this study, we demonstrated that 4-OH-TPN underwent complete microbial reductive dehalogenation to 4-hydroxy-isophthalonitrile via 4-hydroxy-dichloroisophthalonitrile and 4-hydroxy-monochloroisophthalonitrile. 16S rRNA gene amplicon sequencing demonstrated that Dehalogenimonas species was enriched from 6% to 17-22% after reductive dechlorination of 77.24 μmol of 4-OH-TPN. Meanwhile, Dehalogenimonas copies increased by one order of magnitude and obtained a yield of 1.78 ± 1.47 × 10⁸ cells per μmol Cl^- released (N = 6), indicating that 4-OH-TPN served as the terminal electron acceptor for organohalide respiration of Dehalogenimonas species. A draft genome of Dehalogenimonas species was assembled through metagenomic sequencing, which harbors 30 putative reductive dehalogenase genes. Syntrophobacter, Acetobacterium, and Methanosarcina spp. were found to be the major non-dechlorinating populations in the microbial community, who might play important roles in the reductive dechlorination of 4-OH-TPN by the Dehalogenimonas species. This study first reports that Dehalogenimonas sp. can also respire on the seemingly dead-end product of TePN, paving the way to complete biotransformation of the widely present TePN and broadening the substrate spectrum of Dehalogenimonas sp. to polychlorinated hydroxy-benzonitrile.

Impact of hexachlorocyclohexane addition on the composition and potential functions of the bacterial community in red and purple paddy soil

Soil studies have reported the effect of Hexachlorocyclohexane (HCH) on soil microbial communities. However, how soil microbial communities and function shift after HCH addition into the red and purple soil remains unclear. Here, we analyzed the HCH residue fate, and the functional composition and structure of microbial communities to HCH in the two soils. Under the 100 g/ha and 1000 g/ha treatment, the dissipation rate of HCH was 0.0386 and 0.0273 in the purple soil, 0.0145 and 0.0195 in the red soil. The enrichment of HCH degrading genes leads to a higher HCH dissipation rate in the purple soil. PCoA results demonstrated that HCH addition has a different effect on the community diversity in the two soils, and Proteobacteria and Acidobacteria were the major phyla in the two soils. The soil microbiome average variation degree values of red soil were higher than purple soil, which indicated that the soil microbiome in the purple soil was more stable than in the red soil under HCH addition. PICRUSt2 results indicated that functional genes involved in the carbon, nitrogen biogeochemical cycles and HCH degradation were more tolerant to HCH addition in the purple soil. This study provides new insights into understanding of the effect of HCH addition on soil microbial communities and function in the red and purple paddy soil.

Heterologous expression of active Dehalobacter spp. respiratory reductive dehalogenases in Escherichia coli

Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, potentially because of their cobamide-dependence. There have been a few successful attempts at RDase production in unconventional heterologous hosts, but a robust method has yet to be developed. Here we outline a novel respiratory RDase expression system using Escherichia coli. The overexpression of E. coli's cobamide transport system, btu, and anaerobic expression conditions were found to be essential for production of active RDases from Dehalobacter - an obligate organohalide respiring bacterium. The expression system was validated on six enzymes with amino acid sequence identities as low as 28%. Dehalogenation activity was verified for each RDase by assaying cell-free extracts of small-scale expression cultures on various chlorinated substrates including chloroalkanes, chloroethenes, and hexachlorocyclohexanes. Two RDases, TmrA from Dehalobacter sp. UNSWDHB and HchA from Dehalobacter sp. HCH1, were purified by nickel affinity chromatography. Incorporation of the cobamide and iron-sulfur cluster cofactors was verified; though, the precise cobalamin incorporation could not be determined due to variance between methodologies, and the specific activity of TmrA was consistent with that of the native enzyme. The heterologous expression of respiratory RDases, particularly from obligate organohalide respiring bacteria, has been extremely challenging and unreliable. Here we present a relatively straightforward E. coli expression system that has performed well for a variety of Dehalobacter spp. RDases. IMPORTANCE Understanding microbial reductive dehalogenation is important to refine the global halogen cycle and to improve bioremediation of halogenated contaminants; however, studies of the family of enzymes responsible are limited. Characterization of reductive dehalogenase enzymes has largely eluded researchers due to the lack of a reliable and high-yielding production method. We are presenting an approach to express reductive dehalogenase enzymes from Dehalobacter, a key group of organisms used in bioremediation, in E. coli. This expression system will propel the study of reductive dehalogenases by facilitating their production and isolation, allowing researchers to pursue more in-depth questions about the activity and structure of these enzymes. This platform will also provide a starting point to improve the expression of reductive dehalogenases from many other organisms.

Microbial and abiotic factors of flooded soil that affect redox biodegradation of lindane

Pollution induces pressure to soil microorganism; and conversely, the degradation of pollutants is reported largely regulated by the soil microbiome assembly in situ. However, the specific-dependent core taxa of degraders were barely confirmed, which is not conducive to improving the soil remediation strategy. Taking pollution of a typical organochlorine pesticide (OCP), lindane, as an example, we explored the microbial community assembly in flooded soils and simultaneously quantified the corresponding dynamics of typical soil redox processes. Contrasting initial status of microbial diversity was set up by gamma irradiation or not, with additives (acetate, NaNO_3, acetate + NaNO₃) capable of modifying microbial growth employed simultaneously. Microorganism under lindane stress was reflected by microbial adaptability within complex co-occurrence networks, wherein some environment-dependent core taxa (e.g., Clostridia, Bacteroidia, Bacilli) were highly resilient to pollution and sterilization disturbances. Lindane had higher degradation rate in irradiated soil (0.96 mg kg^-1 d^-1) than non-irradiated soil (0.83 mg kg^-1 d^-1). In non-irradiated soil, addition of acetate promoted lindane degradation and methanogenesis, whereas nitrate inhibited lindane degradation but promoted denitrification. No significant differences in lindane degradation were observed in irradiated soils, which exhibited low-diversity microbiomes in parallel to stronger Fe reduction and methanogenesis. The varied corresponding trigger effects on soil redox processes are likely due to differences of soil microbiome, specifically, deterministic or stochastic assembly, in response to pollution stress under high or low initial microbial diversity conditions. Our results improve the knowledge of the adaptability of disturbed microbiomes and their feedback on microbial functional development in OCP-polluted soils, achieving for a more reliable understanding with respect to the ecological risk of soils resided with OCPs under the fact of global microbial diversity loss.

Potential Role of Methanogens in Microbial Reductive Dechlorination of Organic Chlorinated Pollutants In Situ

Previous studies often attribute microbial reductive dechlorination to organohalide-respiring bacteria (OHRB) or cometabolic dechlorination bacteria (CORB). Even though methanogenesis frequently occurs during dechlorination of organic chlorinated pollutants (OCPs) in situ, the underestimated effect of methanogens and their interactions with dechlorinators remains unknown. We investigated the association between dechlorination and methanogenesis, as well as the performance of methanogens involved in reductive dechlorination, through the use of meta-analysis, incubation experiment, untargeted metabolomic analysis, and thermodynamic modeling approaches. The meta-analysis indicated that methanogenesis is largely synchronously associated with OCP dechlorination, that OHRB are not the sole degradation engineers that maintain OCP bioremediation, and that methanogens are fundamentally needed to sustain microenvironment functional balance. Laboratory results further confirmed that Methanosarcina barkeri (M. barkeri) promotes the dechlorination of γ-hexachlorocyclohexane (γ-HCH). Untargeted metabolomic analysis revealed that the application of γ-HCH upregulated the metabolic functioning of chlorocyclohexane and chlorobenzene degradation in M. barkeri, further confirming that M. barkeri potentially possesses an auxiliary dechlorination function. Finally, quantum analysis based on density functional theory (DFT) indicated that the methanogenic coenzyme F430 significantly reduces the activation barrier to dechlorination. Collectively, this work suggests that methanogens are highly involved in microbial reductive dechlorination at OCP-contaminated sites and may even directly favor OCP degradation.

Biodegradation of Lindane (γ-Hexachlorocyclohexane) To Nontoxic End Products by Sequential Treatment with Three Mixed Anaerobic Microbial Cultures

The γ isomer of hexachlorocyclohexane (HCH), also known as lindane, is a carcinogenic persistent organic pollutant. Lindane was used worldwide as an agricultural insecticide. Legacy soil and groundwater contamination with lindane and other HCH isomers is still a big concern. The biotic reductive dechlorination of HCH to nondesirable and toxic lower chlorinated compounds such as monochlorobenzene (MCB) and benzene, among others, has been broadly documented. Here, we demonstrate that complete biodegradation of lindane to nontoxic end products is attainable using a sequential treatment approach with three mixed anaerobic microbial cultures referred to as culture I, II, and III. Biaugmentation with culture I achieved dechlorination of lindane to MCB and benzene. Culture II was able to dechlorinate MCB to benzene, and finally, culture III carried out methanogenic benzene degradation. Distinct Dehalobacter populations, corresponding to different 16S rRNA amplicon sequence variants in culture I and culture II, were responsible for lindane and MCB dechlorination, respectively. This study continues to highlight key roles of Dehalobacter as chlorobenzene- and HCH -respiring bacteria and demonstrates that sequential treatment with specialized anaerobic cultures may be explored at field sites in order to address legacy soil and groundwater contamination with HCH.

Chloramphenicol biodegradation by enriched bacterial consortia and isolated strain Sphingomonas sp. CL5.1: The reconstruction of a novel biodegradation pathway

Figuring out the comprehensive metabolic mechanism of chloramphenicol (CAP) is critical to improving CAP removal in the bioremediation process. In this study, CAP biodegradation by six consortia and isolated Sphingomonas sp. CL5.1 were systematically investigated using the combination of high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry, second-generation, and third-generation sequencing technologies. The CAP-degrading capability of six consortia was enhanced while CAP mineralization rate declined after long-term enrichment. The microbial community structures of six consortia were all simplified with 69%-82% decline in species richness after continuous passages for one year. The core genera of consortia CL and CH included Sphingomonas, Cupriavidus, Burkholderia, Chryseobacterium, and Pigmentiphaga, which accounted for over 98% of the total population. Sphingomonas was discovered as a new CAP degrader that could subsist on CAP as the sole carbon, nitrogen, and energy sources. Sphingomonas sp. CL5.1 was able to completely remove 120 mg/L CAP within 48 hours with a mineralization rate of 50.4%. The presence of acetate or nitrite could inhibit CAP metabolization by strain CL5.1. Four CAP metabolic pathways were constructed, including modification of the C₃ hydroxyl group of CAP via acetylation, oxidization, dehydration and the bond cleavage between C₁ and C₂. C₃ hydroxyl group dehydration and C₁-C₂ bond-cleavage were first reported regarding to CAP biotransformation. Strain CL5.1 played a core role in the consortia and was responsible for C3 hydroxyl oxidation, C3 dehydration, and C1-C2 bond cleavage. Genomic information of strain CL5.1 revealed the further mineralization pathways of downstream product p-nitrobenzoic acid via ortho- and meta-cleavage.

Genetic Analysis of Citrobacter sp.86 Reveals Involvement of Corrinoids in Chlordecone and Lindane Biotransformations

Chlordecone (Kepone®) and γ-hexachlorocyclohexane (γ-HCH or lindane) have been used for decades in the French West Indies (FWI) resulting in long-term soil and water pollution. In a previous work, we have identified a new Citrobacter species (sp.86) that is able to transform chlordecone into numerous products under anaerobic conditions. No homologs to known reductive dehalogenases or other candidate genes were found in the genome sequence of Citrobacter sp.86. However, a complete anaerobic pathway for cobalamin biosynthesis was identified. In this study, we investigated whether cobalamin or intermediates of cobalamin biosynthesis was required for chlordecone microbiological transformation. For this purpose, we constructed a set of four Citrobacter sp.86 mutant strains defective in several genes belonging to the anaerobic cobalamin biosynthesis pathway. We monitored chlordecone and its transformation products (TPs) during long-term incubation in liquid cultures under anaerobic conditions. Chlordecone TPs were detected in the case of cobalamin-producing Citrobacter sp.86 wild-type strain but also in the case of mutants able to produce corrinoids devoid of lower ligand. In contrast, mutants unable to insert the cobalt atom in precorrin-2 did not induce any transformation of chlordecone. In addition, it was found that lindane, previously shown to be anaerobically transformed by Citrobacter freundii without evidence of a mechanism, was also degraded in the presence of the wild-type strain of Citrobacter sp.86. The lindane degradation abilities of the various Citrobacter sp.86 mutant strains paralleled chlordecone transformation. The present study shows the involvement of cobalt-containing corrinoids in the microbial degradation of chlorinated compounds with different chemical structures. Their increased production in contaminated environments could accelerate the decontamination processes.

Two distinct Dehalobacter strains sequentially dechlorinate 1,1,1-trichloroethane and 1,1-dichloroethane at a field site treated with granular zero valent iron and guar gum

Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic vs. biotic mechanisms as both processes share common transformation products. In this study, we evaluated using the Dhb 16S rRNA gene and specific reductive dehalogenase genes as biomarkers for 1,1,1-TCA and 1,1-dichloroethane (1,1-DCA) dechlorination. We analyzed samples from laboratory groundwater microcosms and from an industrial site where a mixture of granular zero valent iron (ZVI) and guar gum was injected for 1,1,1-TCA remediation. Abiotic and biotic transformation products were monitored and the changes in dechlorinating organisms were tracked using quantitative PCR (qPCR) with primers targeting the Dhb 16S rRNA gene and two functional genes cfrA and dcrA encoding enzymes that dechlorinate 1,1,1-TCA to 1,1-DCA and 1,1-DCA to chloroethane (CA), respectively. The abundance of the cfrA- and dcrA-like genes confirmed that the two dechlorination steps were carried out by two distinct Dhb populations at the site. The biomarkers used in this study proved useful for monitoring different Dhb populations responsible for step-wise dechlorination and tracking biodegradation of 1,1,1-TCA and 1,1-DCA where both abiotic (e.g., with ZVI) and biotic processes co-occur.

Dual C-Cl isotope analysis for characterizing the anaerobic transformation of α, β, γ, and δ-hexachlorocyclohexane in contaminated aquifers

Hexachlorocyclohexanes (HCHs) are widespread and persistent environmental pollutants, which cause heavy contamination in soil, sediment and groundwater. An anaerobic consortium, which was enriched on β-HCH using a soil sample from a contaminated area of a former pesticide factory, was capable to transform α, β, γ, and δ-HCH via tetrachlorocyclohexene isomers stoichiometrically to benzene and chlorobenzene. The carbon and chlorine isotope enrichment factors (ε_C and ε_Cl) of the dehalogenation of the four isomers ranged from -1.9 ± 0.3 to -6.4 ± 0.7‰ and from -1.6 ± 0.2 to -3.2 ± 0.6‰, respectively, and the correlation of δ³⁷Cl and δ¹³C (Λ values) of the four isomers ranged from 1.1 ± 0.1 to 2.4 ± 0.2. The evaluation of Λ and the apparent kinetic isotope effects (AKIE) for carbon and chlorine may lead to the hypothesis that the two eliminated chlorine atoms of α- and γ-HCH were in axial positions, the same as for the β-HCH conformer which has six chlorine atoms in axial positions after ring flip. The dichloroelimination of δ-HCH resulted in distinct AKIE and Λ values as one chlorine atom is in axial whereas the other chlorine atoms are in the equatorial positions. Significant chlorine and carbon isotope fractionations of HCH isomers were observed in the samples from a contaminated aquifer (Bitterfeld, Germany). The ³⁷Cl/³⁵Cl and ¹³C/¹²C isotope fractionation patterns of HCH isomers from laboratory experiments were used diagnostically in a model to characterize microbial dichloroelimination in the field study. The comparison of isotope fractionation patterns indicates that the transformation of HCH isomers at the field was mainly governed by microbial dichloroelimination transformation.