Enzymes involved in the biodegradation of hexachlorocyclohexane: a mini review

Integrated landfarming strategy for remediation of HCH-contaminated soil: Synergistic effects of bioaugmentation, organic amendments, and nanoscale zero-valent iron

Hexachlorocyclohexane (HCH) isomers are toxic and persistent pollutants that pose serious risks to the environment and human health. Here we tested the capacity of various nature-based solutions to degrade HCH in contaminated soils of O Porriño area (Galicia, Spain). To this end, eight microcosms were established using combinations of tailor-made biostabilized organic amendments, nanoscale zero-valent iron (nZVI), and an autochthonous microbial inoculum. Throughout a 60-day experiment, we conducted HCH quantification, leachability tests, bacterial community analysis, and soil health assessment. Our results showed that landfarming alone achieved a reduction of up to 83 % in ∑HCH concentrations, demonstrating its cost-effectiveness, facilitated by the physical disruption of HCH aggregates and the presence of HCH-degrading bacteria as Sphingobium, Mesorhizobium and Cupriavidus. Organic amendments did not improve the HCH degradation rate of landfarming, but, notably, reduced HCH leachability and improved soil properties; the combination of the inoculum with the organic amendments revealed the same positive effects but a higher HCH depletion similar to that of landfarming. Thus, the synergistic effects of organic amending and inoculum in an integrated landfarming allows a reduction of the environmental risk and a potential long-term soil restoration, while a landfarming without amendments appear as a cost-effective option but only to reduce HCH contents. These findings aim to provide valuable insights into integrated approach for HCH large-scale landfarming remediation.

XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes

Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141 200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38 000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.

Physical-chemical transformations for the remediation and valorization of hexachlorocyclohexanes (HCHs) including lindane: A review

The production of the former insecticide lindane (γ-HCH) resulted in the generation of vast quantities of hexachlorocyclohexanes (HCH) residues, creating one of the most significant environmental challenges related to persistent organic pollutants in the world. This contamination is present today in different scenarios, including stockpiles and highly concentrated mixed waste, contaminated surface soils, subsoil, and waters. In particular, Dense Non-Aqueous Phase Liquids (DNAPLs) represent challenging subsurface and groundwater contamination. This review provides a comprehensive and critical overview of the physical-chemical methodologies and remediation projects reported in the literature for addressing lindane contamination through separation, transformation, disposal, and valorization approaches. The available physicochemical techniques include dehydrochlorination, oxidation, reduction, substitution, isomerization, as well as electrochemical, photochemical, sonochemical, plasma, and other high energy treatments. Key aspects, such as advantages and limitations, remediation effectiveness, technological maturity, scalability, estimated costs, and applicability to different contamination scenarios are thoroughly analyzed for each method. The review culminates in a detailed comparison of these methodologies for various contamination contexts, providing valuable insights for the identification of optimal solutions to this global environmental challenge. In addition, the review assesses, for the first time, the potential for valorization of the products formed during HCH treatment or remediation. This aspect highlights the opportunity to transform HCH residues into higher value-added chemicals, thereby enhancing the circular economy of the remediation process. Finally, the integration of physicochemical methods with separation and biological tools offers a holistic perspective that underscores the importance of comprehensive strategies for addressing HCH contamination effectively and sustainably.

Biodegradation of DDT using multi-species mixtures: From genome-mining prediction to practical assessment

DDT (dichlorodiphenyltrichloroethane) is a commonly used insecticide that is recalcitrant and highly stable in the environment. Currently, DDT residue contamination, especially in agricultural soil, is still a concern in many countries, threatening human health and the environment. Among the approaches to resolve such an issue, novel biodegradation-based methods are now preferred to physicochemical methods, due to the sustainability and the effectiveness of the former. In this study, we explored the possibility of building mixed microbial cultures that can offer improved DDT-degrading efficiencies and be more environmentally transilient, based on genome annotation using the KEGG database and prediction of interactions between single strains using the obtained metabolic maps. We then proposed 10 potential DDT-degrading mixed cultures of different strain combinations and evaluated their DDT degradation performances in liquid, semi-solid and solid media. The results demonstrated the superiority of the mixtures over the single strains in terms of degrading DDT, particularly in a semi-solid medium, with up to 40-50% more efficiency. Not only did the mixed cultures degrade DDT more efficiently, but they also adapted to broader spectra of environmental conditions. The three best DDT-degrading and transilient mixtures were selected, and it turned out that their component strains seemed to have more metabolic interactions than those in the other mixtures. Thus, our study demonstrates the effectiveness of exploiting genome-mining techniques and the use of constructed mixed cultures in improving biodegradation.

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.

Bioaugmentation treatment of polycyclic aromatic hydrocarbon-polluted soil in a slurry bioreactor with a bacterial consortium and hydroxypropyl-β-cyclodextrin

The aim of the study was to verify the effect of bioaugmentation by the bacterial consortium YS with hydroxypropyl-β-cyclodextrin (HPCD) in a soil slurry. The bacterial consortium YS was enriched from a petroleum-polluted soil using pyrene as sole carbon resource. After 3 weeks, the degradation rate of phenanthrene in CK increased from 22.58% to 55.23 and 78.21% in bioaugmentation (B) and HPCD + bioaugmentation (MB) respectively. The degradation rate of pyrene in CK increased from 17.33% to 51.10% and 60.32% in B and MB respectively in the slurry. The augmented YS persisted in the slurry as monitored by 16S rRNA gene high-throughput sequencing and outcompeted some indigenous bacteria. Enhanced polycyclic aromatic hydrocarbon (PAH) degradation was observed in the addition of HPCD due to the enhanced bioavailability of phenanthrene and pyrene. Additionally, the amount of PAH-degrading bacteria and enzymatic activity in bioaugmentation with HPCD were higher than that in the CK group. The results indicated that bioaugmentation with a bacterial consortium and HPCD is an environmentally friendly method for the bioremediation of PAH-polluted soil.

Microbial debromination of hexabromocyclododecanes

Hexabromocyclododecanes (HBCDs), a new sort of brominated flame retardants (BFRs), are globally prevalent and recalcitrant toxic environmental pollutants. HBCDs have been found in many environmental media and even in the human body, leading to serious health concerns. HBCDs are biodegradable in the environment. By now, dozens of bacteria have been discovered with the ability to transform HBCDs. Microbial debromination of HBCDs is via HBr-elimination, HBr-dihaloelimination, and hydrolytic debromination. Biotic transformation of HBCDs yields many hydroxylated and lower brominated compounds which lack assessment of ecological toxicity. Bioremediation of HBCD pollution has only been applied in the laboratory. Here, we review the current knowledge about microbial debromination of HBCDs, aiming to promote the bioremediation applied in HBCD contaminated sites. KEY POINTS: • Microbial debromination of HBCDs is via hydrolytic debromination, HBr-elimination, and HBr-dihaloelimination. • Newly occurred halogenated contaminants such as HBCDs hitch the degradation pathway tamed by previously discharged anthropogenic organohalides. • Strategy that combines bioaugmentation with phytoremediation for bioremediation of HBCD pollution is promising.

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.

Complete dechlorination of lindane over N-doped porous carbon supported Pd catalyst at room temperature and atmospheric pressure

Transfer hydrogenation is highly effective for dechlorinating priority organic pollutants in wastewater. Lindane could be completely dechlorinated at room temperature and atmospheric pressure via transfer hydrogenation, in which Pd (3.1 wt%) supported on chitosan-derived porous carbon (3.1Pd@A600) and formic acid (FA) were used as catalyst and hydrogen source, respectively. Favorable catalytic activity of 3.1Pd@A600 is attributed to pyridinic N of the support that allowed Pd nanoparticles to be well-dispersed in the solid and to pyridinic N-Pd interactions that enhanced FA decomposition over that observed for commercial carbon supported Pd catalyst (5Pd@AC). In the reaction system containing 3.1Pd@A600 and FA, 99.7% lindane conversion and 100% dechlorination efficiency could be achieved at 25 °C and atmospheric pressure within 60 min. Benzene and cyclohexane were identified as end-products of lindane dechlorination. The transfer hydrogenation strategy developed in this study has wide application to chlorinated organic pollutants contained in actual waste streams.

Insights Into the Biodegradation of Lindane (γ-Hexachlorocyclohexane) Using a Microbial System

Lindane (γ-hexachlorocyclohexane) is an organochlorine pesticide that has been widely used in agriculture over the last seven decades. The increasing residues of lindane in soil and water environments are toxic to humans and other organisms. Large-scale applications and residual toxicity in the environment require urgent lindane removal. Microbes, particularly Gram-negative bacteria, can transform lindane into non-toxic and environmentally safe metabolites. Aerobic and anaerobic microorganisms follow different metabolic pathways to degrade lindane. A variety of enzymes participate in lindane degradation pathways, including dehydrochlorinase (LinA), dehalogenase (LinB), dehydrogenase (LinC), and reductive dechlorinase (LinD). However, a limited number of reviews have been published regarding the biodegradation and bioremediation of lindane. This review summarizes the current knowledge regarding lindane-degrading microbes along with biodegradation mechanisms, metabolic pathways, and the microbial remediation of lindane-contaminated environments. The prospects of novel bioremediation technologies to provide insight between laboratory cultures and large-scale applications are also discussed. This review provides a theoretical foundation and practical basis to use lindane-degrading microorganisms for bioremediation.

Biotransformation of hexachlorocyclohexanes contaminated biomass for energetic utilization demonstrated in continuous anaerobic digestion system

Lindane, the γ-hexachlorocyclohexane (HCH) isomer, was among the most used pesticides worldwide. Although it was banned in 2009, residues of Lindane and other HCH-isomers are still found with high concentrations in contaminated fields. For clean-up, phytoremediation combined with anaerobic digestion (AD) of contaminated biomass to produce biogas and fertilizer could be a promising strategy and was tested in two 15 L laboratory-scale continuous stirred tank reactors. During operation over one year by adding HCH isomers (γ, α and β) consecutively, no negative influence on conventional reactor parameters was observed. The γ- and α-HCH isomers were transformed to chlorobenzene and benzene, and transformation became faster along with time, while β-HCH was not removed. Genus Methanosaeta and order Clostridiales, showing significant enhancement on abundance with HCH addition, may be used as bioindicators for HCH dehalogenation in AD process. The potential for HCH degradation in AD system was restricted to axial Cl atoms of HCH and it showed slight enantioselective preference towards transformation of (+) α-HCH. Moreover, metabolite benzene was mineralized to CO₂ and methane, deducing from tracer experiments with benzene-¹³C₆. Overall, AD appears to be a feasible option for treatment of γ and α-HCHs contaminated biomass.

Understanding fungal potential in the mitigation of contaminated areas in the Czech Republic: tolerance, biotransformation of hexachlorocyclohexane (HCH) and oxidative stress analysis

The study of the soil microbial community represents an important step in better understanding the environmental context. Therefore, biological characterisation and physicochemical integration are keys when defining contaminated sites. Fungi play a fundamental role in the soil, by providing and supporting ecological services for ecosystems and human wellbeing. In this research, 52 soil fungal taxa were isolated from in situ pilot reactors installed to a contaminated site in Czech Republic with a high concentration of hexachlorocyclohexane (HCH). Among the identified isolates, 12 strains were selected to evaluate their tolerance to different isomers of HCH by using specific indices (Rt:Rc; T.I.) and to test their potential in xenobiotic biotransformation. Most of the selected taxa was not significantly affected by exposure to HCH, underlining the elevated tolerance of all the tested fungal taxa, and different metabolic intermediates of HCH dechlorination were observed. The oxidative stress responses to HCH for two selected species, Penicillium simplicissimum and Trichoderma harzianum, were investigated in order to explore their toxic responses and to evaluate their potential functioning in bioremediation of contaminated environments. This research suggests that the isolated fungal species may provide opportunities for new eco-friendly, integrated and cost-effective solutions for environmental management and remediation, considering their efficient adaptation to stressful conditions.

Rhizospheric Microbacterium sp. P27 Showing Potential of Lindane Degradation and Plant Growth Promoting Traits

Lindane is an organochlorine pesticide that is highly persistent in the environment. The amassing of lindane has been identified worldwide and has been found to be very toxic to the environment, human, and animal health. Therefore, urgent consideration and management of the problem is necessary. The current study intends to isolate and identify lindane degrading rhizospheric bacteria from Phragmites karka and to study its degradation kinetics. Also, plant growth promoting potential of the bacterium was evaluated in the presence and absence of studied pesticide. Rhizospheric bacteria were isolated by standard enrichment technique in Mineral Salt Medium. Microbacterium sp. P27 showed the highest degradation percentage, 82.7 ± 1.79% for 50 mg l^-1 lindane, after 15 days. Degradation was also studied at different concentrations of lindane. Maximum degradation was achieved at 10 mg l^-1 followed by 50 mg l^-1 and 100 mg l^-1 lindane. Microbacterium sp. P27 showed positive result for Indole-3-acetic acid production, ammonia production, and 1-aminocyclopropane-1-carboxylate deaminase activity. Presence of lindane revealed a concentration-dependent decrease in plant growth promoting activity. Since the isolated bacterial strain possesses lindane degrading capacity and also other characters that help in plant growth promotion, the isolate can be an important candidate for the progress of bioremediation strategy.

Lindane degradation by root epiphytic bacterium Achromobacter sp. strain A3 from Acorus calamus and characterization of associated proteins

Lindane degrading root epiphytic bacteria were isolated from wetland plant Acorus calamus. Bacterial strain A3 identified as Achromobacter sp. A3, showed maximum degradation potential of 88.7 ± 1.24% for 50 mg l^-1 lindane. Lindane biodegradation was followed by decrease in pH as well as increase in concentration of chloride ions in the culture medium. Lindane degradation potential of Achromobacter sp. A3 was also studied at different concentrations of lindane. Maximum degradation was at 10 mg l^-1 followed by 50 mg l^-1 and 100 mg l^-1 lindane. Also, lindane induced proteins were studied using SDS-PAGE. The induced proteins were identified as alpha/beta hydrolase fold-3 domain-containing protein, involved in lindane hydrolysis and extracellular solute-binding family protein having role in transmembrane transport of lindane for utilization of lindane by bacteria. The appearance of unique polypeptides in lane corresponding to media supplemented with lindane showed that the exposure of bacterial cells to lindane has resulted in regulative expression of certain proteins. So far as known, this is the first report to isolate and study lindane degrading root epiphytic bacteria from A. calamus.

An effective immobilized haloalkane dehalogenase DhaA from Rhodococcus rhodochrous by adsorption, crosslink and PEGylation on meso-cellular foam

Haloalkane dehalogenase DhaA catalyzes the hydrolysis of halogenated compounds by cleavage of the carbon-halogen bond. However, DhaA suffers from poor environmental stability and difficult recovery, which significantly increase the cost of DhaA. Here, an effective enzyme immobilization strategy was developed to overcome the disadvantages of DhaA. DhaA was physically absorbed with amine-functionalized meso-cellular foam (MCF). The MCF-absorbed DhaA (MD) was intermolecularly crosslinked with 8-arm PEG N‑hydroxysuccinimide ester and then PEGylated by maleimide-thiol chemistry. DhaA from Rhodococcus rhodochrous was absorbed at a loading capacity of 100 mg/g in MD. The bulk crystallinity and morphology of MCF were largely maintained. The immobilized DhaA (MD-P1-P2) showed a lower Michaelis constant (K_m, 0.588 mM) than DhaA (0.905 mM), along with an extremely low leaching ratio of DhaA (1.1%) from MCF. MD-P1-P2 exhibited a high stability in the extreme environmental conditions, as reflected by the remaining activity of 99.8% in 40% (v/v) DMSO for 5 h, 87.3% in 3 M urea solution for 1 h, 25.9% at pH 3.0, and 51.8% at room temperature for 30 days. Thus, our study was expected to develop an effective immobilized DhaA for practical application.

Strengthening calcium alginate microspheres using polysulfone and its performance evaluation: Preparation, characterization and application for enhanced biodegradation of chlorpyrifos

Bacterial cell immobilization offer considerable advantages over traditional biotreatment systems using free cells. Calcium alginate matrix usually used for bacterial immobilization is susceptible to biodegradation in harsh environment. Current study aimed to produce and characterize stable macrocapsules (MCs) of Chlorpyrifos (CP) degrading bacterial consortium using biocompatible calcium alginate matrix coupled with environmentally stable polysulfone. In current study bacterial consortium capable of CP biodegradation was immobilized using calcium alginate in a form of microcapsule (MC) reinforced by being coated with a synthetic polymer polysulfone (PSf) through phase inversion. Consortium comprised of five bacterial strains was immobilized using optimized concentration of sodium alginate (2.5gL^-1), calcium chloride (6gL^-1), biomass (600mgL^-1) and polysulfone (10gL^-1). It has been observed that MCs have high thermal, pH and chemical stability than CAMs. In synthetic media complete biodegradation of CP (100-600mgL^-1) was achieved using macrocapsules (MCs) within 18h. CAMs could be reused effectively only upto 5cycles, contrary to this MCs could be used 13 times to achieve more than >96% CP degradation. Shelf life and reusability studies conducted for MCs indicated unaltered biomass retention and CP biodegradation activity (95%) over 16weeks of storage. MCs achieved complete biodegradation of CP (536mgL^-1) in real industrial wastewater and reused several times effectively. Metabolites (3,5,6-trichloro-2-pyridinol (TCP), 3,5,6-trichloro-2-methoxypyridine (TMP) and diethyl-thiophosphate (DETP) were traced using GC-MS and possible metabolic pathway was constructed. Study indicated MCs could be used for cleanup of CP contaminated wastewater repeatedly, safely, efficiently for a longer period of time.

Biotransformation and inhibition effects of hexachlorocyclohexanes during biogas production from contaminated biomass characterized by isotope fractionation concepts

Hexachlorocyclohexane (HCH) production for pesticides was banned by Stockholm Convention (2009) due to its harmful and adverse effects on the environment. Despite this measure, many areas contaminated with former HCH production-waste products still require management. As a potential solution contributing to clean-up of these sites, anaerobic digestion (AD) of pesticide-contaminated biomass to produce biogas is a promising strategy. High pesticide concentrations, however, may inhibit biogas production. Therefore, laboratory-scale batch reactors were set up to investigate biogas reactor performance in presence of HCH. Inhibitory effects on biogas yield was observed with concentrations of HCH ≥ 150 mg/L. Carbon isotope composition of methane (δ¹³C_CH4) showed significant fluctuation after an inhibition phase, indicating that HCH toxicity can affect the activity of acetoclastic methanogens. Furthermore, combined results of metabolites and carbon isotope fractionation factors (ε_c) demonstrated that α- and γ-HCH can be degraded to chlorobenzene and benzene via anaerobic reductive dechlorination.

Streptomyces sp. is a powerful biotechnological tool for the biodegradation of HCH isomers: biochemical and molecular basis

Actinobacteria are well-known degraders of toxic materials that have the ability to tolerate and remove organochloride pesticides; thus, they are used for bioremediation. The biodegradation of organochlorines by actinobacteria has been demonstrated in pure and mixed cultures with the concomitant production of metabolic intermediates including γ-pentachlorocyclohexene (γ-PCCH); 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN); 1,2-dichlorobenzene (1,2-DCB), 1,3-dichlorobenzene (1,3-DCB), or 1,4-dichlorobenzene (1,4-DCB); 1,2,3-trichlorobenzene (1,2,3-TCB), 1,2,4-trichlorobenzene (1,2,4-TCB), or 1,3,5-trichlorobenzene (1,3,5-TCB); 1,3-DCB; and 1,2-DCB. Chromatography coupled to mass spectrometric detection, especially GC-MS, is typically used to determine HCH-isomer metabolites. The important enzymes involved in HCH isomer degradation metabolic pathways include hexachlorocyclohexane dehydrochlorinase (LinA), haloalkane dehalogenase (LinB), and alcohol dehydrogenase (LinC). The metabolic versatility of these enzymes is known. Advances have been made in the identification of actinobacterial haloalkane dehydrogenase, which is encoded by linB. This knowledge will permit future improvements in biodegradation processes using Actinobacteria. The enzymatic and genetic characterizations of the molecular mechanisms involved in these processes have not been fully elucidated, necessitating further studies. New advances in this area suggest promising results. The scope of this paper encompasses the following: (i) the aerobic degradation pathways of hexachlorocyclohexane (HCH) isomers; (ii) the important genes and enzymes involved in the metabolic pathways of HCH isomer degradation; and (iii) the identification and quantification of intermediate metabolites through gas chromatography coupled to mass spectrometry (GC-MS).

Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon perlevis

Lindane is an organochlorine pesticide belonging to persistent organic pollutants (POPs) that has been widely used to treat agricultural pests. It is of particular concern because of its toxicity, persistence and tendency to bioaccumulate in terrestrial and aquatic ecosystems. In this context, we assessed the role of bacteria associated with the sponge Hymeniacidon perlevis in lindane degradation. Seven bacteria isolates were characterized and identified. These isolates showed a remarkable capacity to utilize lindane as a sole carbon source leading to a percentage of residual lindane ranging from 3% to 13% after 12 days of incubation with the pesticide. The lindane metabolite, 1,3–6-pentachloro-cyclohexene, was identified as result of lindane degradation and determined by gas chromatography–mass spectrometry (GC–MS). The bacteria capable of lindane degradation were identified on the basis of the phenotypic characterization by morphological, biochemical and cultural tests, completed with 16S rDNA sequence analysis, and assigned to Mameliella phaeodactyli, Pseudovibrioascidiaceicola, Oceanicaulis stylophorae, Ruegeria atlantica and to three new uncharacterized species. The results obtained are a prelude to the development of future strategies for the in situ bioremediation of lindane.

Compound-Specific Stable Isotope Analysis: Implications in Hexachlorocyclohexane in-vitro and Field Assessment

Assessment of biotic and abiotic degradation reactions by studying the variation in stable isotopic compositions of organic contaminants in contaminated soil and aquifers is being increasingly considered during the last two decades with development of Compound specific stable isotope analysis (CSIA) technique. CSIA has been recognized as a potential tool for evaluating both qualitative and quantitative degradation with measurement of shifts in isotope ratios of contaminants and their degradation products as its basis. Amongst a wide variety of environmental pollutants including monoaromatics, chlorinated ethenes and benzenes etc., it is only recently that its efficacy is being tested for assessing biodegradation of a noxious pollutant namely hexachlorocyclohexane (HCH), by pure microbial cultures as well as directly at the field site. Anticipating the increase in demand of this technique for monitoring the microbial degradation along with natural attenuation, this review highlights the basic problems associated with HCH contamination emphasizing the applicability of emerging CSIA technique to absolve the major bottlenecks in assessment of HCH. To this end, the review also provides a brief overview of this technique with summarizing the recent revelations put forward by both in vitro and in situ studies by CSIA in monitoring HCH biodegradation.

Effect of coating on the environmental applications of zero valent iron nanoparticles: the lindane case

Commercial stabilized slurry of zero-valent iron nanoparticles (nZVI) as well as laboratory-synthesized polymer-stabilized NZVI nanoparticles were used for lindane (γ-hexachlorocyclohexane) degradation studies in aqueous solution. In the present study, polymer-stabilized iron nanoparticles were stabilized using polyethylene glycol (PEG, Mn ~400 and ~950-1050) and polytetrahydrofuran (PTHF, Mn ~650). To study the effectiveness of the different nanoparticles, a quantitative monitorization of lindane degradation by using solid-phase extraction (SPE) and a qualitative measurement of generated volatile by-products by headspace-solid phase microextraction (HS-SPME) followed by GC/MS were carried out. The obtained data were compared and contrasted with the results obtained in previous work. Results showed that the nanoparticles studied in this work possess superior dechlorination performance compared with previous observations. The freshly prepared Fe(0)-PEG400, Fe(0)-PEG1050 and Fe(0)-PTHF exhibited high reactivity during the dechlorination process of lindane in a very short time. The results obtained with the synthesized nanoparticles were similar to those obtained with commercial nanoparticles. However, in all cases reactivity decreased at reaction's late stage. Degradation of lindane by the studied nanoparticles removed 99.9% of the lindane initial concentration after 72h, except for Fe(0)-PTHF nanoparticles, for which the reaction stopped after 5min. In all cases, the reaction followed a second order kinetics. Finally, comparing the results from this study with our previous work, where different nature polymers were considered (Fe(0)-CMC, Fe(0)-PAA and Fe(0)-PAP), more gradual degradation profile of lindane was observed for Fe(0)-PAA and Fe(0)-CMC. It should be noted that in the present case, the reaction of lindane was speeded up with commercial and Fe(0)-PEG nanoparticles. Nevertheless, in the later case, the composition of by-products was affected by the presence of partially degraded intermediates. Taking into account the current technologies, the high removal rates obtained and the acceptable degradation times required, the proposed technology is suitable for its aimed purpose.

Genome Sequence of Pseudomonas sp. HUK17, Isolated from Hexachlorocyclohexane-Contaminated Soil

Pseudomonas sp. HUK17 has been isolated from hexachlorocyclohexane (HCH) long-term contaminated soil. The genome of strain HUK17 was sequenced to elucidate its adaptation toward HCH and to evaluate the presence of pesticide degradation pathways. Here, we report the annotated draft genome sequence (~2.6 Mbp) of this strain.

Evidence of α-, β- and γ-HCH mixture aerobic degradation by the native actinobacteria Streptomyces sp. M7

The organochlorine insecticide γ-hexachlorocyclohexane (γ-HCH, lindane) and its non-insecticidal α- and β-isomers continue to pose serious environmental and health concerns, although their use has been restricted or completely banned for decades. In this study we report the first evidence of the growth ability of a Streptomyces strain in a mineral salt medium containing high doses of α- and β-HCH (16.6 mg l(-1)) as a carbon source. Degradation of HCH isomers by Streptomyces sp. M7 was investigated after 1, 4, and 7 days of incubation, determining chloride ion release, and residues in the supernatants by GC with µECD detection. The results show that both the α- and β-HCH isomers were effectively metabolized by Streptomyces sp. M7, with 80 and 78 % degradation respectively, after 7 days of incubation. Moreover, pentachlorocyclohexenes and tetrachlorocyclohexenes were detected as metabolites. In addition, the formation of possible persistent compounds such as chlorobenzenes and chlorophenols were studied by GC-MS, while no phenolic compounds were detected. In conclusion, we have demonstrated for the first time that Streptomyces sp. M7 can degrade α- and β-isomers individually or combined with γ-HCH and could be considered as a potential agent for bioremediation of environments contaminated by organochlorine isomers.

Biodegradability of HCH in agricultural soils from Guadeloupe (French West Indies): identification of the lin genes involved in the HCH degradation pathway

Banana has been a main agricultural product in the French West Indies (Guadeloupe and Martinique) since the 1960s. This crop requires the intensive use of pesticides to prevent attacks by insect pests. Chlorinated pesticides, such as hexachlorocyclohexane (HCH), chlordecone and dieldrin, were used until the beginning of the 1990s, resulting in a generalized diffuse contamination of the soil and water in the areas of banana production, hence the need to develop solutions for cleanup of the polluted sites. The aims of this work were (i) to assess lindane degradation in soil slurry microcosms treated with lindane at 10 mg/L and (ii) to detect the catabolic genes involved in the HCH degradation pathway. The soil slurry microcosm system showed a 40% lindane degradation efficiency at the end of a 30-day experiment. Lower lindane removal was also detected in the abiotic controls, probably caused by pesticide adsorption to soil particles. Indeed, the lindane concentration decreased from 6000 to 1330 ng/mL and from 800 to 340 ng/mL for the biotic and abiotic soils, respectively. Nevertheless, some of the genes involved in the HCH degradation pathway were amplified by polymerase chain reaction (PCR) from crude deoxyribonucleic acid (DNA) extracted from the Guadeloupe agricultural soil, suggesting that HCH degradation is probably mediated by bacteria closely related to the family Sphingomonadaceae.

Analytical investigations on the lindane bioremediation capability of the demosponge Hymeniacidon perlevis

Lindane is an organochlorine pesticide that has been widely used to treat agricultural pests. It is of particular concern because of its toxicity, persistence and tendency to bioaccumulate in terrestrial and aquatic ecosystems. In this context, we investigated the ability of the demosponge Hymeniacidon perlevis to bioremediate lindane polluted seawater during in vitro experimentation. Lindane was extracted by solid-phase micro-extraction (SPME) and determined by gas chromatography-mass spectrometry (GC-MS). Furthermore, we assessed the role exerted in lindane degradation by bacteria isolated from the sponge. Sponges showed low mortality in experimental conditions (lindane concentration 1 μg/L) and were able to remove about 50% of the lindane content from seawater in 48 h. Bacteria isolated from sponges showed a remarkable remediating capacity (up to 97% of lindane removed after 8-days). A lindane metabolite was identified, 1,3,4,5,6-pentachloro-cyclohexene. The results obtained are a prelude to the development of future strategies for the in situ bioremediation of this pollutant.

Ti/ZnO–MxOy composites (M = Al, Cr, Fe, Ce): synthesis, characterization and application as highly efficient photocatalysts for hexachlorobenzene degradation

A series of novel organic–inorganic nanoscale layered materials were synthesized by intercalating the Ti-containing Schiff base complex into the interlayer of the ZnM layered double hydroxides (LDHs, M = Al, Cr, Fe, Ce).

Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126

We present a novel fragment-based approach that tackles some of the challenges for chemical biology of predicting protein function. The general approach, which we have termed biofragments, comprises two key stages. First, a biologically relevant fragment library (biofragment library) can be designed and constructed from known sets of substrate-like ligands for a protein class of interest. Second, the library can be screened for binding to a novel putative ligand-binding protein from the same or similar class, and the characterization of hits provides insight into the basis of ligand recognition, selectivity, and function at the substrate level. As a proof-of-concept, we applied the biofragments approach to the functionally uncharacterized Mycobacterium tuberculosis (Mtb) cytochrome P450 isoform, CYP126. This led to the development of a tailored CYP biofragment library with notable 3D characteristics and a significantly higher screening hit rate (14%) than standard drug-like fragment libraries screened previously against Mtb CYP121 and 125 (4% and 1%, respectively). Biofragment hits were identified that make both substrate-like type-I and inhibitor-like type-II interactions with CYP126. A chemical-fingerprint-based substrate model was built from the hits and used to search a virtual TB metabolome, which led to the discovery that CYP126 has a strong preference for the recognition of aromatics and substrate-like type-I binding of chlorophenol moieties within the active site near the heme. Future catalytic analyses will be focused on assessing CYP126 for potential substrate oxidative dehalogenation.

Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments

The abundance and diversity of biodegradation genes (BDGs) and potential degradation pathways of dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexane (HCH), and atrazine (ATZ) in freshwater and marine sediments were investigated by metagenomic analysis using 6 datasets (16Gb in total). The datasets were derived using Illumina high-throughput sequencing and were based on BLAST against self-established databases of BDGs, DDT degradation genes (DDGs), HCH degradation genes (HDGs), and ATZ degradation genes (ADGs). The results showed that the abundance and diversity of BDGs, DDGs, HDGs, and ADGs varied with sample source and locations. The lip and mnp genes, which encode for peroxidase, and the carA gene, which encodes for laccase, were detected as the dominant genes for degradation of organic pollutants. The hdt, hdg, and atzB genes, which encode for hydratase, dehalogenase, and ethylaminohydrolase, were found to be the most abundant genes involved in DDT, HCH, and ATZ degradation, respectively. The identified 69 genera capable of degrading organic pollutants were mostly affiliated with Proteobacteria (49.3%) and Actinobacteria (21.7%). Four genera, including Plesiocystis, Anaerolinea, Jannaschia, and Mycobacterium, were the major biodegradation populations in all sediments. In this study, the nearly complete biodegradation pathways of DDT and ATZ were found, and the partial degradation pathway of HCH was detected in all sediments.

Biodegradation of α-, β-, and γ-hexachlorocyclohexane by Arthrobacter fluorescens and Arthrobacter giacomelloi

The organochlorine pesticide γ-hexachlorocyclohexane (γ-HCH, lindane) and its non-insecticidal isomers α-, β-, and δ- continue to pose serious environmental and health concerns, although their use has been restricted or completely banned for decades. The present study reports the first results on the ability of two Arthrobacter strains, not directly isolated from a HCH-polluted site, to grow in a mineral salt medium containing α-, β-, or γ-HCH (100 mgl(-1)) as sole source of carbon. Growth of cultures and HCHs degradation by Arthrobacter fluorescens and Arthrobacter giacomelloi were investigated after 1, 2, 3, 4, and 7 days of incubation by enumerating colony forming units and GC with ECD detection, respectively. Both bacteria are able to metabolize the HCHs: A. giacomelloi is the most effective one, as after 72 h of incubation it produces 88 % degradation of α-, 60 % of β-, and 56 % of γ-HCH. The formation of possible persistent compounds was studied by GC/MS and by HPLC analysis. Pentachlorocyclohexenes and tetrachlorocyclohexenes have been detected as metabolites, which are almost completely eliminated after 72 h of incubation, while no phenolic compounds were found.

Bacterial bio-resources for remediation of hexachlorocyclohexane

In the last few decades, highly toxic organic compounds like the organochlorine pesticide (OP) hexachlorocyclohexane (HCH) have been released into the environment. All HCH isomers are acutely toxic to mammals. Although nowadays its use is restricted or completely banned in most countries, it continues posing serious environmental and health concerns. Since HCH toxicity is well known, it is imperative to develop methods to remove it from the environment. Bioremediation technologies, which use microorganisms and/or plants to degrade toxic contaminants, have become the focus of interest. Microorganisms play a significant role in the transformation and degradation of xenobiotic compounds. Many Gram-negative bacteria have been reported to have metabolic abilities to attack HCH. For instance, several Sphingomonas strains have been reported to degrade the pesticide. On the other hand, among Gram-positive microorganisms, actinobacteria have a great potential for biodegradation of organic and inorganic toxic compounds. This review compiles and updates the information available on bacterial removal of HCH, particularly by Streptomyces strains, a prolific genus of actinobacteria. A brief account on the persistence and deleterious effects of these pollutant chemical is also given.