Enantioselective Dechlorination of Polychlorinated Biphenyls in Dehalococcoides mccartyi CG1

Field test of a bioaugmentation agent for the bioremediation of chlorinated ethene contaminated sites

Chlorinated ethenes are toxic compounds that were widely used in the past, and their improper handling and storage caused notable pollutions worldwide. In situ bioremediation by reductive dechlorination of bacteria is a cost-effective and ecologically friendly way to eliminate these pollutions. During the present study, the efficiency of a previously developed bioaugmentation agent combined with biostimulation was tested under field conditions in contaminated soil. Furthermore, the preservation of dechlorinating ability was also investigated in a long-term experiment. Initially, aerobic conditions were present in the groundwater with possible presence of anaerobic micro-niches providing habitat for Brocadia related anammox bacteria. "Candidatus Omnitrophus" was also identified as a dominant member of community then. Significant changes were detected after the biostimulation, anaerobic conditions established and most of the dominant OTUs were related to fermentative taxa (e.g. Clostridium, Trichococcus and Macillibacteroides). Dominant presence of vinyl-chloride coupled with the lack of vinyl-chloride reductase gene was observed. The most notable change after the bioaugmentation was the significant decrease in the pollutant quantities and the parallel increase in the vcrA gene copy numbers. Similar to post-biostimulation state, fermentative bacteria dominated the community. Bacterial community composition transformed considerably with time after the treatment, dominance of fermentative-mainly Firmicutes related-taxa decreased and chemolithotrophic bacteria became abundant, but the dechlorinating potential of the community remained and could be induced by the reappearance of the pollutants even after 4 years.

Comprehensive exploration of the anaerobic biotransformation of polychlorinated biphenyls in Dehalococcoides mccartyi CG1: Kinetics, enantioselectivity, and isotope fractionation

Anaerobic microbial transformation is a key pathway in the natural attenuation of polychlorinated biphenyls (PCBs). Much less is known about the transformation behaviors induced by pure organohalide-respiring bacteria, especially kinetic isotope effects. Therefore, the kinetics, pathways, enantioselectivity, and carbon and chlorine isotope fractionation of PCBs transformation by Dehalococcoides mccartyi CG1 were comprehensively explored. The results indicated that the PCBs were mainly dechlorinated via removing their double-flanked meta-chlorine, with their first-order kinetic constants following the order of PCB132 > PCB174 > PCB85 > PCB183 > PCB138. However, PCBs occurred great loss of stoichiometric mass balance during microbial transformation, suggesting the generation of other non-dehalogenation products and/or stable intermediates. The preferential transformation of (-)-atropisomers and generation of (+)-atropisomers were observed during PCB132 and PCB174 biotransformation with the enantiomeric enrichment factors of -0.8609 ± 0.1077 and -0.4503 ± 0.1334 (first half incubation times)/-0.1888 ± 0.1354 (second half incubation times), respectively, whereas no enantioselectivity occurred during PCB183 biotransformation. More importantly, although there was no carbon and chlorine isotope fractionation occurring for studied substrates, the δ13C values of dechlorination products, including PCB47 (-28.15 ± 0.35‰ ∼ -27.77 ± 0.20‰), PCB91 (-36.36 ± 0.09‰ ∼ -34.71 ± 0.49‰), and PCB149 (-28.08 ± 0.26‰ ∼ -26.83 ± 0.10‰), were all significantly different from those of their corresponding substrates (PCB85: -30.81 ± 0.02‰ ∼ -30.22 ± 0.21‰, PCB132: -33.57 ± 0.15‰ ∼ -33.13 ± 0.14‰, and PCB174: -26.30 ± 0.09‰ ∼ -26.01 ± 0.07‰), which further supported the generation of other non-dehalogenation products and/or stable intermediates with enrichment or depletion of 13C. These findings provide deeper insights into the anaerobic microbial transformation behaviors of PCBs.

Enantioselectivity in ecotoxicity of pharmaceuticals, illicit drugs, and industrial persistent pollutants in aquatic and terrestrial environments: A review

At present, there is a serious concern about the alarming number of recalcitrant contaminants that can negatively affect biodiversity threatening the ecological status of marine, estuarine, freshwater, and terrestrial ecosystems (e.g., agricultural soils and forests). Contaminants of emerging concern (CEC) such as pharmaceuticals (PHAR), illicit drugs (ID), industrial persistent pollutants, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) and chiral ionic solvents are globally spread and potentially toxic to non-target organisms. More than half of these contaminants are chiral and have been measured at different enantiomeric proportions in diverse ecosystems. Enantiomers can exhibit different toxicodynamics and toxicokinetics, and thus, can cause different toxic effects. Therefore, the enantiomeric distribution in occurrence cannot be neglected as the toxicity and other adverse biological effects are expected to be enantioselective. Hence, this review aims to reinforce the recognition of the stereochemistry in environmental risk assessment (ERA) of chiral CEC and gather up-to-date information about the current knowledge regarding the enantioselectivity in ecotoxicity of PHAR, ID, persistent pollutants (PCBs and PBDEs) and chiral ionic solvents present in freshwater and agricultural soil ecosystems. We performed an online literature search to obtain state-of-the-art research about enantioselective studies available for assessing the impact of these classes of CEC. Ecotoxicity assays have been carried out using organisms belonging to different trophic levels such as microorganisms, plants, invertebrates, and vertebrates, and considering ecologically relevant aquatic and terrestrial species or models organisms recommended by regulatory entities. A battery of ecotoxicity assays was also reported encompassing standard acute toxicity to sub-chronic and chronic assays and different endpoints as biomarkers of toxicity (e.g., biochemical, morphological alterations, reproduction, behavior, etc.). Nevertheless, we call attention to the lack of knowledge about the potential enantioselective toxicity of many PHAR, ID, and several classes of industrial compounds. Additionally, several questions regarding key species, selection of most appropriate toxicological assays and ERA of chiral CEC are addressed and critically discussed.

Effect of fertilization on the degradation and enantioselectivity of fipronil in soil

BACKGROUND

Fertilizers and pesticides are commonly used simultaneously in agriculture. However, the effects of common fertilizers on the dissipation, enantioselectivity, and metabolites of the chiral insecticide fipronil in soil are yet to be reported.

RESULT

An enantioselective method for detecting fipronil enantiomers and their metabolites in different soil matrices was developed using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The results showed that organic and compound fertilizers significantly decreased the degradation of S- and R-fipronil, whereas phosphate and microbial fertilizers slightly reduced fipronil dissipation. The half-life values for S- and R-fipronil were 43.3 and 28.9 days, 99.0 and 63.0 days, 69.3 and 43.3 days, 46.2 and 30.1 days, and 43.3 and 31.5 days, respectively, in the control and the four fertilizer treatments, respectively. The enantioselectivity of fipronil enantiomers occurred and R-fipronil exhibited preferential degradation with an enantiomeric fraction (EF) of 0.4900-0.6238 in all treatments; but the four tested fertilizers decreased enantioselectivity with EF values changed from 0.4970 to 0.6238 in the control to 0.4900-0.6171 in fertilizer treatments. Two metabolites, fipronil sulfone and sulfide, were produced, and their amounts increased with culture time in all treatments. Fertilization reduced the content of fipronil sulfide and sulfone but hardly reduced the total amount of fipronil and its metabolites.

CONCLUSION

Fertilizers affect the environmental behavior of fipronil in the soil. Fertilization alters the soil bacterial community, which may be an important factor. This influence is relatively complicated and should be comprehensively considered in the environmental risk assessment of pesticides. © 2023 Society of Chemical Industry.

Improve Niche Colonization and Microbial Interactions for Organohalide-Respiring-Bacteria-Mediated Remediation of Chloroethene-Contaminated Sites

Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation is promising in in situ bioremediation of chloroethene-contaminated sites. The bioremediation efficiency of this approach is largely determined by the successful colonization of fastidious OHRB, which is highly dependent on the presence of proper growth niches and microbial interactions. In this study, based on two ecological principles (i.e., Priority Effects and Coexistence Theory), three strategies were developed to enhance niche colonization of OHRB, which were tested both in laboratory experiments and field applications: (i) preinoculation of a niche-preparing culture (NPC, being mainly constituted of fermenting bacteria and methanogens); (ii) staggered fermentation; and (iii) increased inoculation of CE40 (a Dehalococcoides-containing tetrachloroethene-to-ethene dechlorinating enrichment culture). Batch experimental results show significantly higher dechlorination efficiencies, as well as lower concentrations of volatile fatty acids (VFAs) and methane, in experimental sets with staggered fermentation and niche-preconditioning with NPC for 4 days (CE40_NPC-4) relative to control sets. Accordingly, a comparatively higher abundance of Dehalococcoides as major OHRB, together with a lower abundance of fermenting bacteria and methanogens, was observed in CE40_NPC-4 with staggered fermentation, which indicated the balanced syntrophic and competitive interactions between OHRB and other populations for the efficient dechlorination. Further experiments with microbial source tracking analyses suggested enhanced colonization of OHRB by increasing the inoculation ratio of CE40. The optimized conditions for enhanced colonization of OHRB were successfully employed for field bioremediation of trichloroethene (TCE, 0.3-1.4 mM)- and vinyl chloride (VC, ∼0.04 mM)-contaminated sites, resulting in 96.6% TCE and 99.7% VC dechlorination to ethene within 5 and 3 months, respectively. This study provides ecological principles-guided strategies for efficient bioremediation of chloroethene-contaminated sites, which may be also employed for removal of other emerging organohalide pollutants.

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

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

Mechanistic insight into co-metabolic dechlorination of hexachloro-1,3-butadiene in Dehalococcoides

Hexachloro-1,3-butadiene (HCBD) as one of emerging persistent organic pollutants (POPs) poses potential risk to human health and ecosystems. Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation represents a promising strategy to remediate HCBD-contaminated sites. Nonetheless, information on the HCBD-dechlorinating OHRB and their dechlorination pathways remain unknown. In this study, both in vivo and in vitro experiments, as well as quantum chemical calculation, were employed to successfully identify and characterize the reductive dechlorination of HCBD by Dehalococcoides. Results showed that some Dehalococcoides extensively dechlorinated HCBD to (E)-1,2,3-tri-CBD via (E)-1,1,2,3,4-penta-CBD and (Z,E)-1,2,3,4-tetra-CBD in a co-metabolic way. Both qPCR and 16S rRNA gene amplicon sequencing analyses suggested that the HCBD-dechlorinating Dehalococcoides coupled their cell growth with dechlorination of perchloroethene (PCE), rather than HCBD. The in vivo and in vitro ATPase assays indicated ≥78.89% decrease in ATPase activity upon HCBD addition, which suggested HCBD inhibition on ATPase-mediated energy harvest and provided rationality on the Dehalococcoides-mediated co-metabolic dechlorination of HCBD. Interestingly, dehalogenation screening of organohalides with the HCBD-dechlorinating enrichment cultures showed that debromination of bromodichloromethane (BDCM) was active in the in vitro RDase assays but non-active in the in vivo experiments. Further in vitro assays of hydrogenase activity suggested that significant inhibition of BDCM on the hydrogenase activity could block electron derivation from H₂ for consequent reduction of organohalides in the in vivo experiments. Therefore, our results provided unprecedented insight into metabolic, co-metabolic and RDase-active-only dehalogenation of varied organohalides by specific OHRB, which could guide future screening of OHRB for remediation of sites contaminated by HCBD and other POPs.

Dehalogenation of Polybrominated Diphenyl Ethers and Polychlorinated Biphenyls Catalyzed by a Reductive Dehalogenase in Dehalococcoides mccartyi Strain MB

Polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) are notorious persistent organic pollutants. However, few organohalide-respiring bacteria that harbor reductive dehalogenases (RDases) capable of dehalogenating these pollutants have been identified. Here, we report reductive dehalogenation of penta-BDEs and PCBs byDehalococcoides mccartyi strain MB. The PCE-pregrown cultures of strain MB debrominated 86.6 ± 7.4% penta-BDEs to di- to tetra-BDEs within 5 days. Similarly, extensive dechlorination of Aroclor1260 and Aroclor1254 was observed in the PCE-pregrown cultures of strain MB, with the average chlorine per PCB decreasing from 6.40 ± 0.02 and 5.40 ± 0.03 to 5.98 ± 0.11 and 5.19 ± 0.07 within 14 days, respectively; para-substituents were preferentially dechlorinated from PCBs. Moreover, strain MB showed distinct enantioselective dechlorination of different chiral PCB congeners. Dehalogenation activity and cell growth were maintained during the successive transfer of cultures when amended with penta-BDEs as the sole electron acceptors but not when amended with only PCBs, suggesting metabolic and co-metabolic dehalogenation of these compounds, respectively. Transcriptional analysis, proteomic profiling, and in vitro activity assays indicated that MbrA was involved in dehalogenating PCE, PCBs, and PBDEs. Interestingly, resequencing of mbrA in strain MB identified three nonsynonymous mutations within the nucleotide sequence, although the consequences of which remain unknown. The substrate versatility of MbrA enabled strain MB to dechlorinate PCBs in the presence of either penta-BDEs or PCE, suggesting that co-metabolic dehalogenation initiated by multifunctional RDases may contribute to PCB attenuation at sites contaminated with multiple organohalide pollutants.

Offshore Marine Sediment Microbiota Respire Structurally Distinct Organohalide Pollutants

Marine sediments are a major sink of organohalide pollutants, but the potential for offshore marine microbiota to transform these pollutants remains underexplored. Here, we report dehalogenation of diverse organohalide pollutants by offshore marine microbiota. Dechlorination of polychlorinated biphenyls (PCBs) was observed in four marine sediment microcosms, which was positively correlated with in situ PCB contamination. Three distinct enrichment cultures were enriched from these PCB-dechlorinating microcosms using tetrachloroethene (PCE) as the sole organohalide. All enrichment cultures also dehalogenated polybrominated diphenyl ethers (PBDEs), tetrabromobisphenol A (TBBPA), and 2,4,6-trichlorophenol (2,4,6-TCP). Particularly, two enrichments completely debrominated penta-BDEs, the first observation of complete debromination of penta-BDEs in marine cultures. Multiple Dehalococcoides and uncultivated Dehalococcoidia were identified in the initial sediment microcosms, but only Dehalococcoides was dominant in all enrichments. Transcription of a gene encoding a PcbA5-like reductive dehalogenase (RDase) was observed during dehalogenation of different organohalides in each enrichment culture. When induced by a single organohalide substrate, the PcbA5-like RDase dehalogenated all tested organohalides (PCE, PCBs, PBDEs, TBBPA, and 2,4,6-TCP) in in vitro tests, suggesting its involvement in dehalogenation of structurally distinct organohalides. Our results demonstrate the versatile dehalogenation capacity of marine Dehalococcoidia and contribute to a better understanding of the fate of these pollutants in marine systems.

Indigenous functional microbial communities for the preferential degradation of chloroacetamide herbicide S-enantiomers in soil

This study investigated indigenous functional microbial communities associated with the degradation of chloroacetamide herbicides acetochlor (ACE), S-metolachlor (S-MET) and their enantiomers in repeatedly treated soils. The results showed that biodegradation was the main process for the degradation of ACE, S-MET and their enantiomers. Eight dominant bacterial genera associated with the degradation were found: Amycolatopsis, Saccharomonospora, Mycoplasma, Myroides, Mycobacterium, Burkholderia, Afipia, and Kribbella. The S-enantiomers of ACE and S-MET were preferentially degraded, which mainly relied on Amycolatopsis, Saccharomonospora and Kribbella for the ACE S-enantiomer and Amycolatopsis and Saccharomonospora for the S-MET S-enantiomer. Importantly, the relative abundances of Amycolatopsis and Saccharomonospora increased by 146.3%-4467.2% in the S-enantiomer treatments of ACE and S-MET compared with the control, which were significantly higher than that in the corresponding R-enantiomer treatments (25.3%-4168.2%). Both metagenomic and qPCR analyses demonstrated that four genes, ppah, alkb, benA, and p450, were the dominant biodegradation genes (BDGs) potentially involved in the preferential degradation of the S-enantiomers of ACE and S-MET. Furthermore, network analysis suggested that Amycolatopsis, Saccharomonospora, Mycoplasma, Myroides, and Mycobacterium were the potential hosts of these four BDGs. Our findings indicated that Amycolatopsis and Saccharomonospora might play pivotal roles in the preferential degradation of the S-enantiomers of ACE and S-MET.

Long-Term Dechlorination of Polychlorinated Biphenyls (PCBs) in Taihu Lake Sediment Microcosms: Identification of New Pathways, PCB-Driven Shifts of Microbial Communities, and Insights into Dechlorination Potential

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) is regarded as an alternative approach for in situ remediation and detoxification in the environment. To better understand the process of PCB dechlorination in freshwater lake sediment, a long-term (108 weeks) dechlorination study was performed in Taihu Lake sediment microcosms with nine parent PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170). Within 108 weeks, the total PCBs declined by 32.8%, while parent PCBs declined by 84.8%. PCB dechlorinators preferred to attack meta- and para-chlorines, principally para-flanked meta and single-flanked para chlorines. A total of 58 dechlorination pathways were observed, and 20 of them were not in 8 processes, suggesting the broad spectrum of PCB dechlorination in the environment. Rare ortho dechlorination was confirmed to target the unflanked ortho chlorine, indicating a potential for complete dechlorination. PCBs drove the shifts of the microbial community structures, and putative dechlorinating bacteria were growth-linked to PCB dechlorination. The distinct jump of RDase genes ardA, rdh12, pcbA4, and pcbA5 was found to be consistent with the commencement of dechlorination. The maintained high level of putative dechlorinating phylum Chloroflexi (including Dehalococcoides and o-17/DF-1), genus Dehalococcoides, and four RDase genes at the end of incubation revealed the long-term dechlorination potential. This work provided insights into dechlorination potential for long-term remediation strategies at PCB-contaminated sites.

Acceleration of polychlorinated biphenyls remediation in soil via sewage sludge amendment

Bioremediation of polychlorinated biphenyls (PCBs) is impeded by difficulties in massively cultivating bioinoculant. Meanwhile, sewage sludge is rich in pollutant-degrading microorganisms and nutrients, drawing our attention to investigate their potential to be used as a supplement for bioremediation of PCBs. Here we reported extensive microbial reductive dechlorination of PCBs by waste activated sludge (WAS) and digestion sludge (DS), which were identified to harbor multiple putative organohalide-respiring bacteria (i.e., Dehalococcoides, Dehalogenimonas, Dehalobacter, and uncultivated Dehalococcoidia) and PCB reductive dehalogenase genes (i.e., pcbA4 and pcbA5). Consequently, amendment of 1-20% (w/w) fresh WAS/DS enhanced the attenuation of PCBs by 126-544% in a soil microcosm compared with the control soil, with the fastest dechlorination of PCBs being achieved when spiked with 20% fresh WAS. Notably, dechlorination pathways of PCBs were also changed by sludge amendment. Microbial and physicochemical analyses revealed that the enhanced dechlorination of PCBs by sludge amendment was largely attributed to the synergistic effects of sludge-derived nutrients, PCB-dechlorinating bacteria, and stimulated growth of beneficial microorganisms (e.g., fermenters). Finally, risk assessment of heavy metals suggests low potential ecological risks of sludge amendment in soil. Collectively, our study demonstrates that sewage sludge amendment could be an efficient, cost-effective and environment-friendly approach for in situ bioremediation of PCBs.

Spatial Distribution, Bioconversion and Ecological Risk of PCBs and PBDEs in the Surface Sediment of Contaminated Urban Rivers: A Nationwide Study in China

Surface sediments of polluted urban rivers can be a reservoir of hydrophobic persistent organic pollutants (POPs). In this study, we comprehensively assessed the contamination of two groups of POPs, that is, polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), in 173 black-odorous urban rivers in China. Spatial distribution of PCBs and PBDEs showed similar patterns but very different contamination levels in surface sediments, that is, average concentrations of 10.73 and 401.16 ng/g dw for the ∑PCBs and ∑PBDEs, respectively. Tetra-/di-CBs and deca-BDE are major PCBs and PBDEs and accounted for 59.11 and 95.11 wt % of the ∑PCBs and ∑PBDEs, respectively. Compared with the persistence of PBDEs, the EF changes of chiral PCBs together with previous cultivation evidence indicated indigenous bioconversion of PCBs in black-odorous urban rivers, particularly the involvement of uncharacterized Dehalococcoidia in PCB dechlorination. Major PCB sources (and their relative contributions) included pigment/painting (25.36%), e-waste (22.92%), metallurgical industry (13.25%), and e-waste/biological degradation process (10.95%). A risk assessment indicated that exposure of resident organisms in urban river sediments to deca-/penta-BDEs could pose a high ecological risk. This study provides the first insight into the contamination, conversion and ecological risk of PCBs and PBDEs in nationwide polluted urban rivers in China.

Waste activated sludge stimulates in situ microbial reductive dehalogenation of organohalide-contaminated soil

Due to its enriched organic matter, nutrients and growth cofactors, as well as a diverse range of microorganisms, waste activated sludge (WAS) might be an ideal additive to stimulate organohalide respiration for in situ bioremediation of organohalide-contaminated sites. In this study, we investigated the biostimulation and bioaugmentation impacts of WAS-amendment on the performance and microbiome in tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) dechlorinating microcosms. Results demonstrated that WAS-amendment increased PCE- and PCBs-dechlorination rate as much as 6.06 and 10.67 folds, respectively. The presence of WAS provided a favorable growth niche for organohalide-respiring bacteria (OHRB), including redox mediation and generation of electron donors and carbon sources. Particularly for the PCE dechlorination, indigenous Geobacter and WAS-derived Dehalococcoides were identified to play key roles in PCE-to-dichloroethene (DCE) and DCE-to-ethene dechlorination, respectively. Similar biostimulation and bioaugmentation effects of WAS-amendment were observed on both PCE- and PCBs-dechlorination in three different soils, i.e., laterite, brown loam and paddy soil. Risk assessment suggested low potential ecological risk of WAS amendment in remediation of organohalide-contaminated soil. Overall, this study provided an economic and efficient strategy to stimulate the organohalide respiration-based bioremediation in field applications.

Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: a review

Electronic waste is termed as e-waste and on recycling it produces environmental pollution. Among these e-waste pollutants, polychlorinated biphenyls (PCBs) are significantly important due to ubiquitous, organic in nature and serious health and environmental hazards. PCBs are used in different electrical equipment such as in transformers and capacitors for the purposes of exchange of heat and hydraulic fluids. Bioremediation is a reassuring technology for the elimination of the PCBs from the environment. In spite of their chemical stability, there are several microbes which can bio-transform or mineralize the PCBs aerobically or anaerobically. In this review paper, our objective was to summarize the information regarding PCB-degrading enzymes and microbes. The review suggested that the most proficient PCB degraders during anaerobic condition are Dehalobacter, Dehalococcoides, and Desulfitobacterium and in aerobic condition are Burkholderia, Achromobacter, Comamonas, Ralstonia, Pseudomonas, Bacillus, and Alcaligenes etc., showing the broadest substrate among bacterial strains. Enzymes found in soil such as dehydrogenases and fluorescein diacetate (FDA) esterases have the capability to breakdown PCBs. Biphenyl upper pathway involves four enzymes: dehydrogenase (bphB), multicomponent dioxygenase (bphA, E, F, and G), second dioxygenase (bphC), hydrolase, and (bphD). Biphenyl dioxygenase is considered as the foremost enzyme used for aerobic degradation of PCBs in metabolic pathway. It has been proved that several micro-organisms are responsible for the PCB metabolization. The review provides novel strategies for e-waste-contaminated soil management.

Water content as a primary parameter determines microbial reductive dechlorination activities in soil

Organohalide-respiring bacteria (OHRB) remove halogens from a variety of organohalides, which have been utilized for in situ remediation of different contaminated sites, e.g., groundwater, sediment and soil. Nonetheless, dehalogenation activities of OHRB and consequent remediation efficiencies can be synergistically affected by water content, soil type and inoculated/indigenous OHRB, which need to be disentangled to identify the key driving parameter and to elucidate the underlying mechanism. In this study, we investigated the impacts of water content (0-100%), soil type (laterite, brown soil and black soil) and inoculated OHRB (Dehalococcoides mccartyi CG1 and a river sediment culture) on reductive dechlorination of perchloroethene (PCE) and polychlorinated biphenyls (PCBs), as well as on associated microbial communities. Results suggested that the water content as a primary rate-limiting parameter governed dechlorination activities in environmental matrices, particularly in the soil, possibly through mediation of cell-to-organohalide mobility of OHRB. By contrast, interestingly, organohalide-dechlorinating microbial communities were predominantly clustered based on soil types, rather than water contents or inoculated OHRB. This study provided knowledge on the impacts of major parameters on OHRB-mediated reductive dechlorination in groundwater, sediment and soil for future optimization of in situ bioremediation of organohalides.

Effects of antibiotic norfloxacin on the degradation and enantioselectivity of the herbicides in aquatic environment

Antibiotics are currently extensively used in human medicine, animal farming, agriculture and aquaculture, and their residue has become a global environmental problem. However, the effects of antibiotic on other pollutants in aquatic environment are still poorly understood. In this study, the influences of norfloxacin on the residue, degradation and distribution of the herbicides (simazine, atrazine, terbuthylazine, acetochlor and metolachlor) and the enantioselectivity of acetochlor in sediment and water-sediment microcosm system were investigated. Sediment was spiked with norfloxacin and water was contaminated by herbicides to simulate environmental pollution. The amounts of herbicides in water and sediment samples were analyzed within 30 days of cultivation. The results showed that norfloxacin could significantly inhibit the dissipation, lengthen the half-lives and enhance the residues of herbicides in sediment. Take simazine as an example, its half-life significantly increased from 16.1 days to 19.3 days and its residual percentage grew from 24.2% to 30.4% when sediment was contaminated with 5 mg·kg^-1 norfloxacin. However, only acetochlor degradation was significantly inhibited by norfloxacin in water-sediment microcosm and the distribution of the herbicides were not affected. Enantioselective degradation of acetochlor was observed both in control and norfloxacin-treated water-sediment system, with R-acetochlor preferential elimination, suggesting the co-existence of norfloxacin had very limited influence on the enantioselectivity. The findings indicated that co-contamination with norfloxacin could increase the persistence of herbicides in aquatic environment, thus increasing the environmental risks to aquatic organisms.

Tracing the sources and microbial degradation of PCBs in field sediments by a multiple-line-of-evidence approach including compound-specific stable isotope analysis

Comprehensive monitoring is crucial for tracing micropollutants in the natural environment. To better evaluate the sources and natural attenuation of polychlorinated biphenyls (PCBs), three composite sediment cores were sampled from a closed pond near e-waste recycling plants, and a multiple-line-of-evidence approach (MLEA) including quantification, enantiomer analysis, microbial community profiling, and compound-specific isotope analysis (CSIA) was used to investigate the fate of PCBs in sediment cores. The difference in the maximum PCB concentrations and associated depths between sites 1/2 and 3 and the corresponding significant (p < 0.01) difference in δ¹³C values strongly indicated two different PCB inputs at sites 1/2 and 3. A significant (p < 0.01) negative correlation between the variation in chlorine per biphenyl (CPB) and Log the abundance of Dehalococcoides/total molar concentration of PCBs (Log Dhc/TPCB) along the cores suggested that different degrees of PCB degradation occurred and that Dehalococcoides likely participated in PCB degradation in these sediments. Nonracemic compositions and pronounced stable carbon isotope fractionation (Δδ¹³C > 1‰) of PCB congeners were observed, confirming that in situ degradation occurred in the sediment cores. The progressive enrichment in ¹³C with increasing core depth suggested strengthened microbial degradation of the residual congener pools. The results of this study suggested that MLEA analysis of PCBs can provide reliable information to better monitor the sources and fate of these compounds in the environment.

Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds

Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and tonB2 (SLG_34540), one of the six tonB comprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds.

Organohalide-Respiring Bacteria in Polluted Urban Rivers Employ Novel Bifunctional Reductive Dehalogenases to Dechlorinate Polychlorinated Biphenyls and Tetrachloroethene

Polluted urban river sediments could be a sink of persistent and toxic polychlorinated biphenyls (PCBs) in urban areas and provide desired growth niches for organohalide-respiring bacteria (OHRB). In this study, microcosms were set up with surface sediments of nationwide polluted urban rivers in China, of which 164 cultures could dechlorinate tetrachloroethene (PCE) to dichloroethenes (DCEs) and to vinyl chloride and/or ethene. Further in vivo tests showed extensive PCB dechlorination with different pathways in 135 PCE pregrown cultures. Taking reductive dechlorination of PCB180 (2345-245-CB) as an example, 121 and 14 cultures preferentially removed flanked para- and meta-chlorines, respectively. Strikingly, all in vitro assays with the 135 PCE pregrown cultures showed identical PCB dechlorination pathways with their living cultures, implying the involvement of bifunctional reductive dehalogenases (RDases) to dechlorinate both PCBs and PCE. Further 16S rRNA and RDase gene-based analyses, together with enantioselective dechlorination of chiral PCBs, suggested that Dehalococcoides and Dehalogenimonas in the 135 cultures largely employed distinctively different novel bifunctional RDases to catalyze PCB/PCE dechlorination. Quantitative assessment of the community assembly process with the modified stochasticity ratio (MST) indicated three different stages in enrichment of OHRB. The second stage, as the only one controlled by stochastic processes (MST > 0.5), required extra attention in monitoring community successional patterns to minimize stochastic variance for enriching the PCB/PCE-dechlorinating OHRB.

Generation of zero valent sulfur from dissimilatory sulfate reduction under methanogenic conditions

Dissimilatory sulfate reduction mediated by sulfate-reducing microorganisms (SRMs) has a pivotal role in the sulfur cycle, from which the generation of zero valent sulfur (ZVS) represents a novel pathway. Nonetheless, information on ZVS production from the dissimilatory sulfate reduction remains scarce. This study successfully showed the ZVS production from the dissimilatory sulfate reduction both in a bioreactor and batch experiments under the methanogenic condition. The ZVS was produced in the form of polysulfide and largely located at extracellular sites. In the bioreactor, interestingly, ZVS could be generated first from partial sulfide oxidation mediated by sulfide-oxidizing bacteria (e.g., Thiobacillus) and later from the dissimilatory sulfate reduction in SRMs when changing the reactor operation from anoxic to obligate anaerobic and black condition. In batch experiments, increasing sulfate concentration was shown to enhance ZVS production. Based on these results, together with thermodynamic calculations, a scenario was proposed for the ZVS production from dissimilatory sulfate reduction, in which SRMs might utilize sulfate-to-ZVS as an alternative pathway to sulfate-to-sulfide to increase the thermodynamic favorability and alleviate the inhibitive effects of sulfide. This study expands our understanding of the SRMs-mediated dissimilatory sulfate reduction and may have important implications in environmental bioremediation.

Inhibitory effects of metal ions on reductive dechlorination of polychlorinated biphenyls and perchloroethene in distinct organohalide-respiring bacteria

Bioremediation of sites co-contaminated with organohalides and metal pollutants may have unsatisfactory performance, since metal ions can potentially inhibit organohalide respiration. To understand the detailed impact of metals on organohalide respiration, we tested the effects of four metal ions (i.e., Cu²⁺, Cd²⁺, Cr³⁺ and Pb²⁺), as well as their mixtures, on reductive dechlorination of perchloroethene (PCE) and polychlorinated biphenyls (PCBs) in three different cultures, including a pure culture of Dehalococcoides mccartyi CG1, a Dehalococcoides-containing microcosm and a Dehalococcoides-Geobacter coculture. Results showed that the inhibitive impact on organohalide respiration depended on both the type and concentration of metal ions. Interestingly, the metal ions might indirectly inhibit organohalide respiration through affecting non-dechlorinating populations in the Dehalococcoides-containing microcosm. Nonetheless, compared to the CG1 pure culture, the Dehalococcoides-containing microcosm had higher tolerance to the individual metal ions. In addition, no synergistic inhibition was observed for reductive dechlorination of PCE and PCBs in cultures amended with metal ion mixtures. These results provide insights into the impact of metal ions on organohalide respiration, which may be helpful for future in situ bioremediation of organohalide-metal co-contaminated sites.

Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities

Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.

Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls

Dehalococcoides usually work closely with other beneficial microorganisms for removal of halogenated organic compounds at contaminated sites. Traditional microbial cultivation is necessary but not enough to gain insights into key microbial populations and their interactions in complex communities. In this study, we cultivated and characterized two D. mccartyi strains (CG3 and SG1), and further revealed interspecies synergistic interactions in PCB-dechlorinating microbial communities via metagenomic analysis. Strain CG3 and SG1 originated from distinct geographic sites employ reductive dehalogenase CG3-RD11 (PcbA1-like) and SG1-RD28 (PcbA4/5-like), respectively, to catalyze chlorine-removal from PCBs. In their parent mixed cultures CG-3 and SG-1, as well as in previously enriched PCB-dechlorinating cultures CG-1, CG-4 and CG-5, Methanosarcina and Desulfovibrio were found as major non-dechlorinating populations which may play roles in mediating acetate- and H₂-sources for D. mccartyi. They together form a stable microbial community for interspecies carbon- and electron-transfers to facilitate organohalide respiration of D. mccartyi, being confirmed in a synthetic microbial community consisting of the Dehalococcoides, Methanosarcina and Desulfovibrio. The results provide insights into which and how other microorganisms support D. mccartyi to dechlorinate PCBs, and suggest that Methanosarcina may play a larger role in PCB-dechlorinating communities than currently appreciated.

Microbial transformation of chiral organohalides: Distribution, microorganisms and mechanisms

Chiral organohalides including dichlorodiphenyltrichloroethane (DDT), Hexabromocyclododecane (HBCD) and polychlorinated biphenyls (PCBs) raise a significant concern in the environmental occurrence, fate and ecotoxicology due to their enantioselective biological effects. This review provides a state-of-the-art overview on enantioselective microbial transformation of the chiral organohalides. We firstly summarized worldwide field assessments of chiral organohalides in a variety of environmental matrices, which suggested the pivotal role of microorganisms in enantioselective transformation of chiral organohalides. Then, laboratory studies provided experimental evidences to further link enantioselective attenuation of chiral organohalides to specific functional microorganisms and enzymes, revealing mechanistic insights into the enantioselective microbial transformation processes. Particularly, a few amino acid residues in the functional enzymes could play a key role in mediating the enantioselectivity at the molecular level. Finally, major challenges and further developments toward an in-depth understanding of the enantioselective microbial transformation of chiral organohalides are identified and discussed.

Tetrachloroethene primes reductive dechlorination of polychlorinated biphenyls in a river sediment microcosm

Halo-priming is an effective approach to initiate microbial reductive dechlorination of polychlorinated biphenyls (PCBs) at contaminated sites, of which the application has been restricted by introducing extra pollutants generated from priming organohalides. In this study, tetrachloroethene (PCE) was demonstrated to be an effective priming compound to enhance PCB dechlorination both in a PCB-dechlorinating pure culture and a river sediment microcosm. In the isolated PCB-dechlorinating Dehalococcoides mccartyi CG1, PCB dechlorination activities were stimulated by adding 0.05-0.2 mM PCE, and were inhibited when further increasing PCE concentrations. Both in vivo and in vitro experiments showed that PCBs and PCE were synchronously dechlorinated in D. mccartyi CG1. In a river sediment microcosm, which was established to mimic in situ biostimulation of PCB dechlorination, 0.2 mM PCE could significantly improve para-chlorine removal from both PCB180 (2345-245-CB) and Aroclor 1260, and increase the relative abundance of indigenous dechlorinating Dehalococcoides for more than 20 times (from <0.1% to 2.3-5.0%). At the same time, PCE as a priming compound was completely dechlorinated to non-toxic ethene. Overall, this study provided an efficient strategy to stimulate in situ bioremediation of PCBs.