The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260

Efficient biostimulation of microbial dechlorination of polychlorinated biphenyls by acetate and lactate under nitrate reducing conditions: Insights into dechlorination pathways and functional genes

Microbial-catalyzed reductive dechlorination of polychlorinated biphenyls (PCBs) is largely affected by the indigenous sediment geochemical properties. In this study, the effects of nitrate on PCB dechlorination and microbial community structures were first investigated in Taihu Lake sediment microcosms. And biostimulation study was attempted supplementing acetate/lactate. PCB dechlorination was apparently inhibited under nitrate-reducing conditions. Lower PCB dechlorination rate and less PCB dechlorination extent were observed in nitrate amended sediment microcosms (T-N) than those in non-nitrate amended microcosms (T-1) during 66 weeks of incubation. The total PCB mass reduction in T-N was 17.6% lower than that in T-1. The flanked-para dechlorination was completely inhibited, while the ortho-flanked meta dechlorination was only partially inhibited in T-N. The 7.5 mM of acetate/lactate supplementation recovered PCB dechlorination by resuming ortho-flanked meta dechlorination. Repeated additions of lactate showed more effective biostimulation than acetate. Phylum Chloroflexi, containing most known PCB dechlorinators, was found to play a vital role on stability of the network structures. In T-N, putative dechlorinating Chloroflexi, Dehalococcoides and RDase genes rdh12, pcbA4, pcbA5 all declined. With acetate/lactate supplementation, Dehalococcoides grew by 1-2 orders of magnitude and rdh12, pcbA4, pcbA5 increased by 1-3 orders of magnitude. At Week 66, parent PCBs declined by 86.4% and 80.9% respectively in T-N-LA and T-N-AC compared to 69.9% in T-N. These findings provide insights into acetate/lactate biostimulation as a cost-effective approach for treating PCB contaminated sediments undergoing nitrate inhibition.

Characterizing the bacterial communities associated with Mediterranean sponges: a metataxonomic analysis

The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla (Myxilla) rosacea and Clathria (Clathria) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M. (Myxilla) rosacea, which was mainly associated with soil and plants and involved in biological nitrogen fixation.

Short-chain fatty acids facilitated long-term dechlorination of PCBs in Taihu Lake sediment microcosms: Evidence from PCB congener and microbial community analyses

Microbial reductive dechlorination hosts great promise as an in situ bioremediation strategy for polychlorinated biphenyls (PCBs) contamination. However, the slow dechlorination in sediments limits natural attenuation. Short-chain fatty acids, as preferred carbon sources and electron donors for dechlorinating microorganisms, might stimulate PCB dechlorination. Herein, two sets of short-chain fatty acids, sole acetate and a fatty acid mixture (acetate, propionate, and butyrate), were amended periodically into Taihu Lake (China) sediment microcosms containing nine PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170) after 24 weeks of incubation. Short-chain fatty acids facilitated the long-term PCB dechlorination and the promoting effect of the fatty acid mixture compared favorably with that of sole acetate. By the end of 108 weeks, the total PCB mass concentrations in acetate amended and fatty acid mixture amended microcosms significantly declined by 7.6% and 10.3% compared with non-amended microcosms (P < 0.05), respectively. Short-chain fatty acids selectively favored the removal of flanked meta and single-flanked para chlorines. Notably, a rare ortho dechlorination pathway, PCB25 (24-3-CB) to PCB13 (3-4-CB), was enhanced. Supplementary fatty acids significantly increased reductive dehalogenases (RDase) gene pcbA5 instead of improving the growth of Dehalococcoides. These findings highlight the merits of low cost short-chain fatty acids on in situ biostimulation in treating PCBs contamination.

Exploring the role of microbes for the management of persistent organic pollutants

Persistent organic pollutants (POPs) are chemicals which have been persisting in the environment for many years due to their longer half-lives. POPs have gained attention over the last few decades due to the unsustainable management of chemicals which led to their widespread and massive contamination of biota from different strata and environments. Due to the widespread distribution, bio-accumulation and toxic behavior, POPs have become a risk for organisms and environment. Therefore, a focus is required to eliminate these chemicals from the environment or transform into non-toxic forms. Among the available techniques for the removal of POPs, most of them are inefficient or incur high operational costs. As an alternative to this, microbial bioremediation of POPs such as pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pharmaceuticals and personal care products is much more efficient and cost-effective. Additionally, bacteria play a vital role in the biotransformation and solubilization of POPs, which reduces their toxicity. This review specifies the Stockholm Convention that evaluates the risk profile for the management of existing as well as emerging POPs. The sources, types and persistence of POPs along with the comparison of conventional elimination and bioremediation methods of POPs are discussed comprehensively. This study demonstrates the existing bioremediation techniques of POPs and summaries the potential of microbes which serve as enhanced, cost-effective, and eco-friendly approach for POPs elimination.

Influence of microplastics on microbial anaerobic detoxification of chlorophenols

Microplastics (MPs) can absorb halogenated organic compounds and transport them into marine anaerobic zones. Microbial reductive dehalogenation is a major process that naturally attenuates organohalide pollutants in anaerobic environments. Here, we aimed to determine the mechanisms through which MPs affect the microbe-mediated marine halogen cycle by incubating 2,4,6-trichlorophenol (TCP) dechlorinating cultures with various types of MPs. We found that TCP was dechlorinated to 4-chlorophenol in biotic control and polypropylene (PP) cultures, but essentially terminated at 2,4-dichlorophenol in polyethylene (PE) and polyethylene terephthalate (PET) cultures after incubation for 20 days. Oxygen-containing functional groups such as peroxide and aldehyde were enriched on PE and PET after incubation and corresponded to elevated levels of intracellular reactive oxygen species (ROS) in the microorganisms. Adding PE or PET to the cultures exerted limited effects on hydrogenase and ATPase activities, but delayed the expression of the gene encoding reductive dehalogenase (RDase). Considering the limited changes in the microbial composition of the enriched cultures, these findings suggested that microbial dechlorination is probably affected by MPs through the ROS-induced inhibition of RDase synthesis and/or activity. Overall, our findings showed that extensive MP pollution is unfavorable to environmental xenobiotic detoxification.

Quantitative and Qualitative Changes in the Genetic Diversity of Bacterial Communities in Anaerobic Bioreactors with the Diatomaceous Earth/Peat Cell Carrier

This paper analyses the impact of the diatomaceous earth/peat (DEP; 3:1) microbial carrier on changes in the bacterial microbiome and the development of biofilm in the anaerobic digestion (AD) of confectionery waste, combined with digested sewage sludge as inoculum. The physicochemical properties of the carrier material are presented, with particular focus on its morphological and dispersion characteristics, as well as adsorption and thermal properties. In this respect, the DEP system was found to be a suitable carrier for both mesophilic and thermophilic AD. The evaluation of quantitative and qualitative changes in the genetic diversity of bacterial communities, carried out using next-generation sequencing (NGS), showed that the material has a modifying effect on the bacterial microbiome. While Actinobacteria was the most abundant cluster in the WF-control sample (WF—waste wafers), Firmicutes was the dominant cluster in the digested samples without the carrier (WF-dig.; dig.—digested) and with the carrier (WF + DEP). The same was true for the count of Proteobacteria, which decreased twofold during biodegradation in favor of Synergistetes. The Syntrophomonas cluster was identified as the most abundant genus in the two samples, particularly in WF + DEP. This information was supplemented by observations of morphological features of microorganisms carried out using fluorescence microscopy. The biodegradation process itself had a significant impact on changes in the microbiome of samples taken from anaerobic bioreactors, reducing its biodiversity. As demonstrated by the results of this innovative method, namely the BioFlux microfluidic flow system, the decrease in the number of taxa in the digested samples and the addition of DEP contributed to the microbial adhesion in the microfluidic system and the formation of a stable biofilm.

The amendment of Organic matters enhances the anaerobic dechlorination of Polychlorinated Biphenyls in Paddy Soil

The toxicity of high-chlorinated polychlorinated biphenyls (PCBs) can be efficiently reduced through anaerobic dechlorination. However, this approach suffers a lot in face of in situ microbial remediations, like a shortage of biomass. In this study, we showed that the amendment of organic matters could help microbiota in paddy soil with anaerobic dechlorination and greatly shortened the lag period. The presence of organic matters offered a better environment for dechlorinating bacteria. They provided not only a more strictly anaerobic milieu but also copious carbon sources. By using high-throughput 16S rRNA gene sequencing, genera Dehalobacter, Dehalobacterium, and Desulfitobacterium capable of dechlorination were identified in enriched cultures. Taken together, this study proved that extra organic matters can promote anaerobic dechlorination in paddy soil slurry microcosm systems, which provides new insights into the bioremediation of PCB-contaminated soils.

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.

Presence of bacteria capable of PCB biotransformation in stormwater bioretention cells

Core samples from bioretention cell media as well as surface stormwater sediment samples from seven urban areas were collected to assess the potential for biotransformation activity of polychlorinated biphenyls (PCBs). The presence of putative organohalide-respiring bacteria in these samples was studied. Based on extracted DNA, Dehalobacter, Dehalogenimonas and Dehalococcoides were detected. Other organohalide-respiring bacteria like Desulfitobacterium and Sulfurospirillum were not studied. Bacteria containing the genes encoding for biphenyl 2,3-dioxygenase (bphA) or 2,3-dihydroxybiphenyl 1,2-dioxygenase (bphC) were detected in 29 of the 32 samples. These genes are key factors in PCB aerobic degradation. Transcribed bacterial genes from putative organohalide-respiring bacteria as well as genes encoding for bphA and bphC were obtained from the microbial community, thus showing the potential of organohalide respiration of PCBs and aerobic PCB degradation under both aerobic and anaerobic conditions in the surface samples collected at the bioretention site. Presence and concentrations of 209 PCB congeners in the bioretention media were also assessed. The total PCB concentration ranged from 38.4 ± 2.3 ng/g at the top layer of the inlet to 11.6 ± 1.2 ng/g at 20-30 cm at 3 m from the inlet. These results provide documentation that bacteria capable of PCB transformation, including both anaerobic dechlorination and aerobic degradation, were present and active in the bioretention.

Bioremediation of river sediment polluted with polychlorinated biphenyls: A laboratory study

Persistent organic pollutants (POPs) are lipophilic, constant and bioaccumulative toxic compounds. In general, they are considered resistant to biological, photolytic, and chemical degradation with polychlorinated biphenyls (PCBs) belonging to these chemicals. PCBs were never produced in Serbia, but they were imported and mainly used in electrical equipment, transformers, and capacitors. Our study aimed to analyse sequential multi-stage aerobic/anaerobic microbial biodegradation of PCBs present in the river sediment from the area known for long-term pollution with these chemicals. The study with an autochthonous natural microbial community (NMC model system) and NMC augmented with allochthonous hydrocarbon-degrading (AHD) microorganisms (isolated from location contaminated with petroleum products) (NMC-AHD model system) was performed in order to estimate the potential of these microorganisms for possible use in future bioremediation treatment of these sites. The laboratory biodegradation study lasted 70 days, after which an overall >33 % reduction in the concentration of total PCBs was observed. This study confirmed the strong potential of the NMC for the reduction of the level of PCBs in the river sediment under alternating multi-stage aerobic/anaerobic conditions.

Electrostimulated bio-dechlorination of a PCB mixture (Aroclor 1260) in a marine-originated dechlorinating culture

Aroclor 1260, a commercial polychlorinated biphenyl (PCB) mixture, is highly recalcitrant to biotransformation. A negatively polarized cathode (-0.35 V vs. standard hydrogen electrode) was applied for the first time to a marine-origin PCB dechlorinating culture that substantially increased the microbial dechlorination rate of Aroclor 1260 (from 8.6 to 11.6 μM Cl^- d^-1); meta-chlorine removal was stimulated and higher proportions of tetra-CBs (43.2-46.6%), the predominant dechlorination products, were observed compared to the open circuit conditions (23.7-25.1%). The dechlorination rate was further enhanced (14.1 μM Cl^- d^-1) by amendment with humin as a solid-phase redox mediator. After the suspension culture was renewed using an anaerobic medium, dechlorination activity was effectively maintained solely by cathodic biofilms, where cyclic voltammetry results indicated their redox activity. Electric potential had a significant effect on microbial community structure in the cathodic biofilm, where a greater abundance of Dehalococcoides (2.59-3.02%), as potential dechlorinators, was observed compared to that in the suspension culture (0.41-0.55%). Moreover, Dehalococcoides adhering to the cathode showed a higher chlorine removal rate than in the suspension culture. These findings provide insights into the dechlorination mechanism of cathodic biofilms involving Dehalococcoides for PCB mixtures and extend the application prospects of bioremediation to PCB contamination in the natural environment.

Ultrastructure of organohalide-respiring Dehalococcoidia revealed by cryo-electron tomography

Dehalococcoides mccartyi (Dhc) and Dehalogenimonas spp. (Dhgm) are members of the class Dehalococcoidia, phylum Chloroflexi, characterized by streamlined genomes and a strict requirement for organohalogens as electron acceptors. Here, we used cryo-electron tomography to reveal morphological and ultrastructural features of Dhc strain BAV1 and 'Candidatus Dehalogenimonas etheniformans' strain GP cells at unprecedented resolution. Dhc cells were irregularly shaped discs (890 ± 110 nm long, 630 ± 110 nm wide and 130 ± 15 nm thick) with curved and straight sides that intersected at acute angles, whereas Dhgm cells appeared as slightly flattened cocci (760 ± 85 nm). The cell envelopes were composed of a cytoplasmic membrane (CM), a paracrystalline surface layer (S-layer) with hexagonal symmetry and ∼22 nm spacing between repeating units, and a layer of unknown composition separating the CM and the S-layer. Cell surface appendages were only detected in Dhc cells, whereas both cell types had bundled cytoskeletal filaments. Repetitive globular structures, ∼5 nm in diameter and ∼9 nm apart, were observed associated with the outer leaflet of the CM. We hypothesized that those represent organohalide respiration (OHR) complexes and estimated ∼30,000 copies per cell. In Dhgm cultures, extracellular lipid vesicles (20 - 110 nm in diameter) decorated with putative OHR complexes but lacking an S-layer were observed. The new findings expand our understanding of the unique cellular ultrastructure and biology of organohalide-respiring Dehalococcoidia. Importance: Dehalococcoidia respire organohalogen compounds and play relevant roles in bioremediation of groundwater, sediments and soils impacted with toxic chlorinated pollutants. Using advanced imaging tools, we have obtained 3-dimensional images at macromolecular resolution of whole Dehalococcoidia cells revealing their unique structural components. Our data detail the overall cellular shape, cell envelope architecture, cytoskeletal filaments, the likely localization of enzymatic complexes involved in reductive dehalogenation, and the structure of extracellular vesicles. The new findings expand our understanding of the cell structure-function relationship in Dehalococcoidia with implications for Dehalococcoidia biology and bioremediation.

Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis

Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.

Silica/Lignin Carrier as a Factor Increasing the Process Performance and Genetic Diversity of Microbial Communities in Laboratory-Scale Anaerobic Digesters

The article aims to present results of research on anaerobic digestion (AD) of waste wafers (WF-control) and co-substrate system–waste wafers and cheese (WFC-control), combined with digested sewage sludge, as inoculum. The purpose of this paper is to confirm the outcome of adding silica/lignin (S/L; 4:1) material, as a microbial carrier, on the process performance and genetic diversity of microbial communities. The experiment was conducted in a laboratory under mesophilic conditions, in a periodical operation mode of bioreactors. Selected physicochemical parameters of the tested carrier, along with the microstructure and thermal stability, were determined. Substrates, batches and fermenting slurries were subjected to standard parameter analysis. As part of the conducted analysis, samples of fermented food were also tested for total bacterial count, dehydrogenase activity. Additionally, DNA extraction and next-generation sequencing (NGS) were carried out. As a result of the conducted study, an increase in the volume of produced biogas was recorded for samples fermented with S/L carrier: in the case of WF + S/L by 18.18% to a cumulative biogas yield of 833.35 m3 Mg−1 VS, and in the case of WFC + S/L by 17.49% to a yield of 950.64 m3 Mg−1 VS. The largest total bacterial count, during the process of dehydrogenase activity, was maintained in the WFC + S/L system. The largest bacterial biodiversity was recorded in samples fermented with the addition of cheese, both in the case of the control variant and in the variant when the carrier was used. In contrast, three phyla of bacteria Firmicutes, Proteobacteria and Actinobacteria predominated in all experimental facilities.

Indigenous microbial communities in Albertan sediments are capable of anaerobic benzene biodegradation under methanogenic, sulfate-reducing, nitrate-reducing, and iron-reducing redox conditions

Alberta is a major center for oil and gas production, and correspondingly harbors hundreds of unresolved contamination sites by environmental hazards such as benzene (C₆ H₆ ). Due to its cost-effectiveness, bioremediation has become a promising strategy for C₆ H₆ removal. Contamination sites typically take on an anaerobic context, which complicates the energetics of contamination sites and is a subject that is scarcely broached in studies of Albertan sediments. This study examines the innate potential for indigenous microbial communities in Albertan sediments to remove C₆ H₆ in a multitude of reduced conditions. Community profiles of these sediments were analyzed by 16S rRNA gene amplicon sequencing, and removal rates and reaction stoichiometries were observed by gas chromatography and ion chromatography. Organisms belonging to known primary degrader taxa were identified, including Geobacter (iron-reducing), and Peptococcaceae (nitrate-reducing). Furthermore, benzene removal patterns of the cultures were similar to those observed in previously reported microcosms, with lag times between 70 and 168 days and removal rates between 3.27 and 12.70 µM/day. Such information could support a more comprehensive survey of Albertan sediment consortia, which may eventually be utilized in informing future remediation efforts in the province. PRACTITIONER POINTS: ●Clay and sand sediments originating from Northern Alberta could remove benzene under methanogenic, sulfate-reducing, iron-reducing, and nitrate-reducing conditions. ●Degradation profiles were broadly comparable to those of reported cultures from other geographical locales. ●Key degrader taxa observed included Geobacter (Fe³⁺ -reducing) and Peptococcaceae ( NO 3 - -reducing). ●Knowledge gained can be the start of a more extensive survey of Albertan sediments. Eventually, this collection of information can be used to generate robust C₆ H₆ -degrading cultures that can be implemented for bioaugmentation and be implemented in informing remediation strategies in soil and water matrices for priority contamination cases such as leaking underground storage tanks and orphan wells.

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.

Proteomic insight on the polychlorinated biphenyl degrading mechanism of Pleurotus pulmonarius LBM 105

White-rot fungi are well known bioremediation agents capable of removing recalcitrant xenobiotics. However, the molecular mechanism involved in this process is not well understood. The aim of the present study was to compare the proteomic profiles of Pleurotus pulmonarius LBM 105 in presence and absence of a mixture of polychlorinated biphenyls. Cultures of the fungus were spiked with a mixture of Aroclors and cultivated for 28 days. This strain achieved a peak of PCBs-removal of 65.50 ± 8.09% after 21 days. The ecotoxicological assays showed a toxicity reduction of 46.47%. Based on these findings, a proteomic study was carried out and it was proven that the oxidative metabolism was highly affected. Two proteins that have a function at the transcriptional level and related to the oxidative metabolism, the glyceraldehyde-3-phosphate dehydrogenase and the basal transcription factor 3, presented an increase in their quantity in PCBs presence. Several oxidases and reductases were highly induced, presenting the short chain reductases, aldo/keto reductases, laccases and versatile peroxidases as the enzymes with the most notorious changes. These results indicate a complex response of the fungal metabolism towards these pollutants, which includes a transcriptional response to the oxidative stress and a modification of the intra- and extra-cellular enzymatic profile.

Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review

Chlorinated hydrocarbon contamination in soils and groundwater has a severe negative impact on the human health. Microbial reductive dechlorination is a major degradation pathway of chlorinated hydrocarbon in anaerobic subsurface environments, has been extensively studied. Recent progress on the diversity of the reductive dechlorinators and the key enzymes of chlororespiration has been well reviewed. Here, we present a thorough overview of the studies related to bioremediation of chloroethenes and polychlorinated biphenyls based on enhanced in situ reductive dechlorination. The major part of this review is to provide an up-to-date summary of functional microorganisms which are either detected during in situ biostimulation or applied in bioaugmentation strategies. The applied biostimulants and corresponding reductive dechlorination products are also summarized and the future research needs are finally discussed.

Recent advances in the biodegradation of polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) are typical lasting organic pollutants. Persistence and recalcitrance to biodegradation of PCBs have hampered the transformation of PCB congeners from the environment. Biological transformation of polychlorinated biphenyls could take place through anaerobic dechlorination, aerobic microbial degradation, and a combination of transformation of anaerobic dechlorination and aerobic degradation. Under anaerobic conditions, microbial dechlorination is an important degradation mode for PCBs, especially high-chlorinated congeners. The low-chlorinated compounds formed after reductive dechlorination could be further aerobically degraded and completely mineralized. This paper reviews the recent advances in biological degradation of PCBs, introduces the functional bacteria and enzymes involved in the anaerobic and aerobic degradation of PCBs, and discusses the synergistic action of anaerobic reduction and aerobic degradation. In addition, the different ways to the microbial remediation of PCBs-contaminated environments are discussed. This review provides a theoretical foundation and practical basis to use PCBs-degrading microorganisms for bioremediation.

Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs)

Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.

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.

Diverse dechlorinators and dechlorination genes enriched through amendment of chlorinated natural organic matter fractions

In uncontaminated environments, chlorinated natural organic matter (Cl-NOM) can act as an electron acceptor for organohalide-respiring bacteria. It is unknown, however, whether different types of Cl-NOM are preferentially dechlorinated or whether enrichment with Cl-NOM affects the ability of bacteria to dechlorinate contaminants. In this research NOM was extracted from sediment, fractionated based on hydrophobicity, and either amended to polychlorinated biphenyl-contaminated soil directly or chlorinated and then amended to soil. Amendments of the least hydrophobic Cl-NOM fraction were dechlorinated most rapidly, followed by the moderately hydrophobic Cl-NOM fraction. Soil that had been enriched on the moderately hydrophobic fraction of Cl-NOM was also capable of faster dechlorination of the contaminants trichloroethene and tetrachlorobenzene. Community analysis of the soil during enrichment showed that some known organohalide-respiring bacteria were present and may have played a role in dechlorination; nevertheless, many bacteria appeared to be enriched during both Cl-NOM and contaminant dechlorination. In addition, the quantities of two haloalkane dehalogenase genes increased during enrichment on Cl-NOM. These results show for the first time that Cl-NOM can prime contaminant dechlorination and also suggest that hydrolytic dechlorination processes were involved in both Cl-NOM and contaminant dechlorination.

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.

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.

Distribution of polychlorinated biphenyls in effluent from a large municipal wastewater treatment plant: Potential for bioremediation?

This study involved an evaluation of the potential for bioremediation of polychlorinated biphenyls (PCBs) in the effluent from a large municipal wastewater treatment plant. It was focused on the presence of PCBs in two types of effluents: the continuous effluent present during dry weather conditions and the intermittently present effluent that was present during wet weather due to incoming stormwater. The annual discharge of PCBs for both types of effluent was calculated based on a five-year dataset (2011-2015). In addition, the toxicity and bioremediation potential of the PCBs in the effluent were also assessed. It was found that the continuous effluent was responsible for the majority of the discharged PCB into the receiving river (1821 g for five years), while the intermittent effluent contributed 260 g over the five years. The average number of chlorine per biphenyl for the detected PCB congeners showed a 19% difference between the two types of effluent, which indicated a potential for organohalide respiration of PCBs during the continuous treatment. This was further supported by a high level of tri-, tetra- and penta-chlorinated congeners accounting for 75% of the anaerobically respired PCBs. Potential for aerobic degradation and thus biomineralization of PCBs was identified for both effluents. Furthermore, toxicity of 12 dioxin-like PCBs showed that normal operation of the wastewater reduced the toxicity throughout the wastewater treatment plant.

Solubilization and degradation of polychlorinated biphenyls (PCBs) by naturally occurring facultative anaerobic bacteria

A combination of solubilization and degradation is essential for the bioremediation of environments contaminated with complex polychlorinated biphenyls (PCB) mixtures. However, the application of facultative anaerobic microorganisms that can both solubilize and breakdown hydrophobic PCBs in aqueous media under both anaerobic and aerobic conditions, has not been reported widely. In this comprehensive study, four bacteria discovered from soil and sediments and identified as Achromobacter sp. NP03, Ochrobactrum sp. NP04, Lysinibacillus sp. NP05 and Pseudomonas sp. NP06, were investigated for their PCB degradation efficiencies. Aroclor 1260 (50 mg/L), a commercial and highly chlorinated PCB mixture was exposed to the different bacterial strains under aerobic, anaerobic and two stage anaerobic-aerobic conditions. The results confirmed that all four facultative anaerobic microorganisms were capable of degrading PCBs under both anaerobic and aerobic conditions. The highest chlorine removal (9.16 ± 0.8 mg/L), PCB solubility (14.7 ± 0.93 mg/L) and growth rates as OD₆₀₀ (2.63 ± 0.22) were obtained for Lysinibacillus sp. NP05 under two stage anaerobic-aerobic conditions. The presence of biosurfactants in the culture medium suggested their role in solubility of PCBs. Overall, the positive results obtained suggest that high PCB hydrolysis can be achieved using suitable facultative anaerobic microorganisms under two stage anaerobic-aerobic conditions. Such facultative microbial strains capable of solubilization as well as degradation of PCBs under both anaerobic and aerobic conditions provide an efficient and effective alternative to commonly used bioaugmentation methods utilizing specific obligate aerobic and anaerobic microorganisms, separately.

Strategy for the Rapid Dechlorination of Polychlorinated Biphenyls (PCBs) by Dehalococcoides mccartyi Strains

Anaerobic bacteria play critical roles in the environmental bioremediation of polychlorinated biphenyls (PCBs). However, in situ applications of PCB dechlorinating anaerobes have been largely impeded by difficulties in growing PCB dechlorinators to a high cell abundance in short time periods. Here, we report the accelerated onset of PCB dechlorination by pre-cultivating Dehalococcoides mccartyi strains on chloroethenes as alternative electron acceptors. The extensive dechlorination of Aroclor 1260 was achieved within 1 week by D. mccartyi CG4 pregrown on trichloroethene (TCE) or tetrachloroethene (PCE). Compared to control cultures fed solely with Aroclor 1260, the PCB dechlorination rate was up to 30 times greater in cultures pre-cultivated with chloroethenes. However, when CG4 was simultaneously exposed to multiple potential substrates (PCE, TCE, and PCBs), PCB dechlorination was not observed until PCE was completely depleted. The expression of the bifunctional PCE and PCBs reductive dehalogenase (RDase) gene pcbA4 was inhibited by the presence of both substrates. Furthermore, in the presence of >0.3 mM TCE (produced as an intermediate from PCE dechlorination), the PCB dechlorination rate was an order of magnitude lower than in cultures amended with Aroclor 1260 after the complete depletion of TCE. This reduced PCB dechlorination rate corresponded with a sharp decrease in pcbA4 transcripts in the presence of both TCE and PCBs. The utilization of chloroethenes and PCBs as substrates by CG4 was found to be largely sequential rather than concurrent, suggesting that PCE and TCE are preferred substrates for the RDase responsible for PCE, TCE, and PCB dechlorination.

PCB dechlorination hotspots and reductive dehalogenase genes in sediments from a contaminated wastewater lagoon

Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants that are distributed worldwide. Although industrial PCB production has stopped, legacy contamination can be traced to several different commercial mixtures (e.g., Aroclors in the USA). Despite their persistence, PCBs are subject to naturally occurring biodegradation processes, although the microbes and enzymes involved are poorly understood. The biodegradation potential of PCB-contaminated sediments in a wastewater lagoon located in Virginia (USA) was studied. Total PCB concentrations in sediments ranged from 6.34 to 12,700 mg/kg. PCB congener profiles in sediment sample were similar to Aroclor 1248; however, PCB congener profiles at several locations showed evidence of dechlorination. The sediment microbial community structure varied among samples but was dominated by Proteobacteria and Firmicutes. The relative abundance of putative dechlorinating Chloroflexi (including Dehalococcoides sp.) was 0.01-0.19% among the sediment samples, with Dehalococcoides sp. representing 0.6-14.8% of this group. Other possible PCB dechlorinators present included the Clostridia and the Geobacteraceae. A PCR survey for potential PCB reductive dehalogenase genes (RDases) yielded 11 sequences related to RDase genes in PCB-respiring Dehalococcoides mccartyi strain CG5 and PCB-dechlorinating D. mccartyi strain CBDB1. This is the first study to retrieve potential PCB RDase genes from unenriched PCB-contaminated sediments.

In situ electrochemical manipulation of oxidation-reduction potential in saturated subsurface matrices

Application of a low-intensity electric field is known to influence oxidation-reduction (redox) potential in a saturated matrix. In this study, such redox manipulation was attempted in at a site with contaminated aquifer. At the experiment field site, electrodes connected to a direct current (DC) source provided an electric field with an intensity of 1.82 V m^-1. Redox potentials at locations 3.0 m and 7.9 m from the cathode decreased by 111 mV and 33 mV within a few hours, respectively, indicating that reducing conditions in the aquifer may be established within the electric field. Overall, it is possible to manipulate in situ redox potential in saturated subsurface matrices by applying low-intensity electric fields.

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB-contaminated marine sediments

In this study, six PCE-to-ethene dechlorinating cultures, fed with a fermentable substrate (lactate) or hydrogen as electron donor, were obtained from PCB and PCE dechlorinating microcosms constructed with PCB-contaminated marine sediments. A novel Chloroflexi member (OTU-DIS1) affiliated to Dehalococcoidales Incertae Sedis, only distantly related to known dechlorinating bacteria, dominated the enrichment cultures (up to 86% of total OTUs). Sulfate-, thiosulfate- and sulfur-reducing bacteria affiliated to genera Desulfobacter, Dethiosulfatibacter and Desulfuromusa were also found to lesser extent. Remarkably, tceA, vcrA and the bifunctional PCE/PCB dehalogenase genes pcbA1, pcbA4 and pcbA5 were found in all dechlorinating microbial enrichments indicating the coexistence of different Dehalococcoides mccartyi strains. The reductive dechlorination rate in each culture remained unvaried over long-term operation (≈ 30 months) and ranged between 0.85 and 0.97 mmol Cl-1 released L-1 d-1 in the lactate-fed microbial enrichments and between 0.66 and 0.85 mmol Cl-1 released L-1 d-1 in the H2-fed microbial enrichments. Overall, this study highlights the presence of yet unexplored biodiversity in PCBs contaminated marine sediments and indicates these environments as promising sources of novel organohalide-respiring bacteria.

Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples

The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation). Despite having a detection limit less than the threshold recommended for effective remediation, the application of the assay was limited because of the semi-quantitative nature of the data. Moreover, the assay was prone to false positives due to the aerosolization of amplicons. In this study, deoxyuridine triphosphate (dUTP) and uracil DNA glycosylase (UNG) were incorporated into the assay to reduce the probability of false positives. Optimization experiments revealed a UNG concentration of 0.2units per reaction was adequate for degrading trace levels of AUGC based contamination (~1.4×10⁴ gene copies/reaction) without significant changes to the detection limit (~100 gene copies/reaction). Additionally, the optimized assay was used with the most probable number (MPN) method to quantify RDase genes (vcrA and tceA) in multiple groundwater samples from a chlorinated solvent contaminated site. Using this approach, gene concentrations were significantly correlated to concentrations obtained using traditional methods (qPCR and DNA templates). Although the assay underestimated RDase genes concentrations, a strong correlation (R²=0.78 and 0.94) was observed between the two data sets. The regression equations obtained will be valuable to determine gene copies in groundwater using the newly developed, low cost and time saving method.

Dehalococcoides as a Potential Biomarker Evidence for Uncharacterized Organohalides in Environmental Samples

The massive production and improper disposal of organohalides resulted in worldwide contamination in soil and water. However, their environmental survey based on chromatographic methods was hindered by challenges in testing the extremely wide variety of organohalides. Dehalococcoides as obligate organohalide-respiring bacteria exclusively use organohalides as electron acceptors to support their growth, of which the presence could be coupled with organohalides and, therefore, could be employed as a biomarker of the organohalide pollution. In this study, Dehalococcoides was screened in various samples of bioreactors and subsurface environments, showing the wide distribution of Dehalococcoides in sludge and sediment. Further laboratory cultivation confirmed the dechlorination activities of those Dehalococcoides. Among those samples, Dehalococcoides accounting for 1.8% of the total microbial community was found in an anaerobic granular sludge sample collected from a full-scale bioreactor treating petroleum wastewater. Experimental evidence suggested that the influent wastewater in the bioreactor contained bromomethane which support the growth of Dehalococcoides. This study demonstrated that Dehalococcoides could be employed as a promising biomarker to test the present of organohalides in wastestreams or other environmental samples.

Identification of two organohalide-respiring Dehalococcoidia associated to different dechlorination activities in PCB-impacted marine sediments

Background

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry.

Results

High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 μmol of chlorine removed kg⁻¹ week⁻¹) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 10⁹ 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination.

Conclusions

These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0743-4) contains supplementary material, which is available to authorized users.

Addition of iron oxides in sediments enhances 2,3,4,5-tetrachlorobiphenyl (PCB 61) dechlorination by low-voltage electric fields

The presence of iron oxides in sediments significantly improves anaerobic dechlorination of PCB (i.e., PCB 61) in bioelectrochemical reactors.

Widespread Distribution of Dehalococcoides mccartyi in the Houston Ship Channel and Galveston Bay, Texas, Sediments and the Potential for Reductive Dechlorination of PCDD/F in an Estuarine Environment

Sediments in the Houston Ship Channel and upper Galveston Bay, Texas, USA, are polluted with polychlorinated dibenzo-p-dioxins/furans (PCDD/F; ≤46,000 ng/kg dry weight (wt.)) with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the most toxic congener, contributing >50 % of the total toxic equivalents (TEQ) at most locations. We measured PCDD/F concentrations in sediments and evaluated the potential for enhanced in situ biodegradation by surveying for Dehalococcoides mccartyi, an obligate organohalide respiring bacterium. Dehalococcoides spp. (98 % similar to D. mccartyi) and 22 other members of the class Dehalococcoidia were predominant 16S ribosomal RNA (rRNA) phylotypes. Dehalococcoides spp. were also present in the active fraction of the bacterial community. Presence/absence PCR screening detected D. mccartyi in sediment cores and sediment grab samples having at least 1 ng/kg dry wt. TEQ at salinities ranging from 0.6 to 19.5 PSU, indicating that they are widespread in the estuarine environment. Organic carbon-only and organic carbon + sulfate-amended sediment microcosm experiments resulted in ∼60 % reduction of ambient 2,3,7,8-TCDD in just 24 months leading to reductions in total TEQs by 38.4 and 45.0 %, respectively, indicating that 2,3,7,8-TCDD degradation is occurring at appreciable rates.

First evidence on the occurrence and dynamics of Dehalococcoides mccartyi PCB-dechlorinase genes in marine sediment during Aroclor1254 reductive dechlorination

The present study evaluates the PCB-dehalorespiring capabilities and dynamics of indigenous Dehalococcoides mccartyi population in a PCB contaminated marine sediment. Specialized PCB-dechlorinase genes pcbA1, pcbA4 and pcbA5 previously characterized in pure cultures of D. mccartyi, were here found for the first time in environmental samples. Reductive dechlorination was stimulated by spiking Aroclor1254 to the sediment and by imposing strictly anaerobic conditions both with and without bioaugmentation with a Dehalococcoides mccartyi enrichment culture. In line with the contaminant dechlorination kinetics, Dehalococcoides population increased during the entire incubation period showing growth yields of 4.94E+07 Dehalococcoides per μmolCl^-1 and 7.30E+05 Dehalococcoides per μmolCl^-1 in the marine sediment with and without bioaugmentation respectively. The pcbA4 and pcbA5 dechlorinase genes, and to a lesser extent pcbA1 gene, were enriched during the anaerobic incubation suggesting their role in Aroclor1254 dechlorination under salinity conditions.

Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities

Polychlorobiphenyl (PCB) biodegradation was followed for 1 year in microcosms containing marine sediments collected from Mar Piccolo (Taranto, Italy) chronically contaminated by this class of hazardous compounds. The microcosms were performed under strictly anaerobic conditions with or without the addition of Dehalococcoides mccartyi, the main microorganism known to degrade PCBs through the anaerobic reductive dechlorination process. Thirty PCB congeners were monitored during the experiments revealing that the biodegradation occurred in all microcosms with a decrease in hepta-, hexa-, and penta-chlorobiphenyls (CBs) and a parallel increase in low chlorinated PCBs (tri-CBs and tetra-CBs). The concentrations of the most representative congeners detected in the original sediment, such as 245-245-CB and 2345-245-CB, and of the mixture 2356-34-CB+234-245-CB, decreased by 32.5, 23.8, and 46.7 %, respectively, after only 70 days of anaerobic incubation without any bioaugmentation treatment. Additionally, the structure and population dynamics of the microbial key players involved in the biodegradative process and of the entire mixed microbial community were accurately defined by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in both the original sediment and during the operation of the microcosm. The reductive dehalogenase genes of D. mccartyi, specifically involved in PCB dechlorination, were also quantified using real-time PCR (qPCR). Our results demonstrated that the autochthonous microbial community living in the marine sediment, including D. mccartyi (6.32E+06 16S rRNA gene copy numbers g(-1) sediment), was able to efficiently sustain the biodegradation of PCBs when controlled anaerobic conditions were imposed.

Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

Although polychlorinated biphenyls (PCBs) production was brought to a halt 30 years ago, recalcitrance to degradation makes them a major environmental pollutant at a global scale. Previous studies confirmed that organohalide-respiring bacteria (OHRB) were capable of utilizing chlorinated congeners as electron acceptor. OHRB belonging to the Phyla Chloroflexi and Firmicutes are nowadays considered as the main PCB-dechlorinating organisms. In this study, we aimed at exploring the involvement of other taxa in PCB dechlorination using sediment-free microcosms (SFMs) and the Delor PCB mixture. High rates of congener dehalogenation (up to 96%) were attained in long-term incubations of up to 692 days. Bacterial communities were dominated by Chloroflexi, Proteobacteria, and Firmicutes, among strictly simplified community structures composed of 12 major phyla only. In a first batch of SFMs, Dehalococcoides mccartyi closely affiliated with strains CG4 and CBDB1 was considered as the main actor associated with congener dehalogenation. Addition of 2-bromoethanesulfonate (BES), a known inhibitor of methanogenic activity in a second batch of SFMs had an adverse effect on the abundance of Dehalococcoides sp. Only two sequences affiliated to this Genus could be detected in two (out of six) BES-treated SFMs, contributing to a mere 0.04% of the communities. BES-treated SFMs showed very different community structures, especially in the contributions of organisms involved in fermentation and syntrophic activities. Indirect evidence provided by both statistical and phylogenetic analysis validated the implication of a new cluster of actors, distantly affiliated with the Family Geobacteraceae (Phylum δ-Proteobacteria), in the dehalogenation of low chlorinated PCB congeners. Members of this Family are known already for their dehalogenation capacity of chlorinated solvents. As a result, the present study widens the knowledge for the phylogenetic reservoir of indigenous PCB dechlorinating taxa.

Xanthones of Lichen Source: A 2016 Update

An update of xanthones encountered in lichens is proposed as more than 20 new xanthones have been described since the publication of the compendium of lichen metabolites by Huneck and Yoshimura in 1996. The last decades witnessed major advances regarding the elucidation of biosynthetic schemes leading to these fascinating compounds, accounting for the unique substitution patterns of a very vast majority of lichen xanthones. Besides a comprehensive analysis of the structures of xanthones described in lichens, their bioactivities and the emerging analytical strategies used to pinpoint them within lichens are presented here together with physico-chemical properties (including NMR data) as reported since 1996.

The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis

The compositions of bacterial community in one site contaminated with PCE/TCE after the slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, and surfactants) addition were analyzed. Results show that SPRS caused a rapid enhancement of reductive dechlorination of TCE. The transformation of PCE/TCE into ethene was observed after 20 days of operation. To compare the change of bacterial communities before and after SPRS addition, 16S rRNA amplicon sequencing using the metagenome analysis was performed. Results demonstrated the detection of the increased amounts of Dehalogenimonas by 2.2-fold, Pseudomonas by 3.4-fold and Sulfuricurvum by 4-fold with the analysis of the ribosomal database project (RDP). Metagenomic DNA was extracted from PCE/TCE-contaminated groundwater after SPRS addition, and subjected to sequencing. Results obtained from metagenomic sequencing indicate that genes from Dehalococcoides mccartyi was ranked as the second abundant bacteria among all of the detected bacteria via the analysis of the lowest common ancestor (LCA). Abundance of these bacterial groups, as shown above suggests their role in TCE biodegradation. Functional analysis of the metagenome, with the specific reference to chloroalkane and chloroalkene degradation, revealed the presence of some genes responsible for TCE biodegradation. Overall, results of this study provided new insights for a better understanding of the potential of biostimulation on TCE-contaminated sites.

Ex-Situ Remediation Technologies for Environmental Pollutants: A Critical Perspective

Pollution and the global health impacts from toxic environmental pollutants are presently of great concern. At present, more than 100 million people are at risk from exposure to a plethora of toxic organic and inorganic pollutants. This review is an exploration of the ex-situ technologies for cleaning-up the contaminated soil, groundwater and air emissions, highlighting their principles, advantages, deficiencies and the knowledge gaps. Challenges and strategies for removing different types of contaminants, mainly heavy metals and priority organic pollutants, are also described.

Genomic Characterization of Dehalococcoides mccartyi Strain JNA That Reductively Dechlorinates Tetrachloroethene and Polychlorinated Biphenyls

Dehalococcoides mccartyi strain JNA detoxifies highly chlorinated polychlorinated biphenyl (PCB) mixtures via 85 distinct dechlorination reactions, suggesting that it has great potential for PCB bioremediation. However, its genomic and functional gene information remain unknown due to extremely slow growth of strain JNA with PCBs. In this study, we used tetracholorethene (PCE) as an alternative electron acceptor to grow sufficient biomass of strain JNA for subsequent genome sequencing and functional gene identification. Analysis of the assembled draft genome (1 462 509 bp) revealed the presence of 29 putative reductive dehalogenase (RDase) genes. Among them, JNA_RD8 and JNA_RD11 genes were highly transcribed in both PCE- and PCB-fed cultures. Furthermore, in vitro assays with crude cell lysate from PCE grown cells revealed dechlorination activity against both PCE and 2,2',3,4,4',5,5'-heptachlorobiphenyl. These data suggest that both JNA_RD8 and JNA_RD11 may be bifunctional PCE/PCB RDases. This study deepens the knowledge of organohalide respiration of PCBs and facilitates in situ PCB-bioremediation with strain JNA.

Divergent PCB organohalide-respiring consortia enriched from the efflux channel of a former Delor manufacturer in Eastern Europe

Polychlorinated biphenyl (PCB) organohalide-respiring communities from the efflux channel of a former Delor manufacturer in Eastern Slovakia were assessed using metagenomic, statistical and cultivation-adapted approaches. Multivariate analysis of environmental factors together with terminal restriction fragment length polymorphisms of the bacterial communities in the primary sediments revealed both temporal and spatial heterogeneity in the distribution of microbial populations, which reflects the dynamic pattern of contamination and altered conditions for biodegradation activity along the channel. Anaerobic microcosms were developed from eight sediments sampled along the channel, where high concentrations of PCBs - from 6.6 to 136mg/kg dry weight, were measured. PCB dehalorespiring activity, congruent with changes in the microbial composition in all microcosms, was detected. After 10 months of cultivation, the divergently evolved consortia achieved up to 35.9 percent reduction of the total PCB concentration. Phylogenetic-analysis of the active Chloroflexi-related organohalide-respiring bacteria by partial sequencing of 16S rRNA genes in cDNA from microcosms with the highest PCB dechlorination activity revealed diverse and unique complexity of the populations. The predominant organohalide respirers were either affiliated with Dehalococcoides sp. and Dehalococcoides-like group (DLG) organisms or were composed of currently unknown distant clades of DLG bacteria. The present study should encourage researchers to explore the full potential of the indigenous PCB dechlorinating populations to develop effective bioremediation approaches that can perform the complete mineralization of PCBs in polluted environments.

Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination

Polychlorinated biphenyls (PCBs) pose potential risks to human and environmental health because they are carcinogenic, persistent, and bioaccumulative. In this study, we investigated bacterial communities in soil microcosms spiked with PCB 52, 77, and 153. Switchgrass (Panicum virgatum) was employed to improve overall PCB removal, and redox cycling (i.e., sequential periods of flooding followed by periods of no flooding) was performed in an effort to promote PCB dechlorination. Lesser chlorinated PCB transformation products were detected in all microcosms, indicating the occurrence of PCB dechlorination. Terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis showed that PCB spiking, switchgrass planting, and redox cycling affected the microbial community structure. Putative organohalide-respiring Chloroflexi populations, which were not found in unflooded microcosms, were enriched after 2 weeks of flooding in the redox-cycled microcosms. Sequences classified as Geobacter sp. were detected in all microcosms and were most abundant in the switchgrass-planted microcosm spiked with PCB congeners. The presence of possible organohalide-respiring bacteria in these soil microcosms suggests that they play a role in PCB dechlorination therein.

Dehalococcoides mccartyi strain JNA dechlorinates multiple chlorinated phenols including pentachlorophenol and harbors at least 19 reductive dehalogenase homologous genes

Pentachlorophenol and other chlorinated phenols are highly toxic ubiquitous environmental pollutants. Using gas chromatographic analysis we determined that Dehalococcoides mccartyi strain JNA in pure culture dechlorinated pentachlorophenol to 3,5-dichlorophenol (DCP) via removal of the ortho and para chlorines in all of the three possible pathways. In addition, JNA dechlorinated 2,3,4,6-tetrachlorophenol via 2,4,6-trichlorophenol (TCP) and 2,4,5-TCP to 2,4-DCP and 3,4-DCP, respectively, and dechlorinated 2,3,6-TCP to 3-chlorophenol (CP) via 2,5-DCP. JNA converted 2,3,4-TCP to 3,4-DCP and 2,4-DCP by ortho and meta dechlorination, respectively. 2,3-DCP was dechlorinated to 3-CP, and, because cultures using it could be transferred with a low inoculum (0.5 to 1.5% vol/vol), it may act as an electron acceptor to support growth. Using PCR amplification with targeted and degenerate primers followed by cloning and sequencing, we determined that JNA harbors at least 19 reductive dehalogenase homologous (rdh) genes including orthologs of pcbA4 and pcbA5, pceA, and mbrA, but not tceA or vcrA. Many of these genes are shared with D. mccartyi strains CBDB1, DCMB5, GT, and CG5. Strain JNA has previously been shown to extensively dechlorinate the commercial polychlorinated biphenyl (PCB) mixture Aroclor 1260. Collectively the data suggest that strain JNA may be well adapted to survive in sites contaminated with chlorinated aromatics and may be useful for in situ bioremediation.

Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides mccartyi Strain SG1, Which Carries a Circular Putative Plasmid

Dehalococcoides mccartyi strain SG1, isolated from digester sludge, dechlorinates polychlorinated biphenyls (PCBs) to lower congeners. Here we report the draft genome sequence of SG1, which carries a 22.65 kbp circular putative plasmid.

Bio-beads with immobilized anaerobic bacteria, zero-valent iron, and active carbon for the removal of trichloroethane from groundwater

Chlorinated hydrocarbons are the most common organic pollutants in groundwater systems worldwide. In this study, we developed bio-beads with immobilized anaerobic bacteria, zero-valent iron (ZVI), and activated carbon (AC) powder and evaluated their efficacy in removing 1,1,1-trichloroethane (TCA) from groundwater. Bio-beads were produced by polyvinyl alcohol, alginate, and AC powder. We found that the concentration of AC powder used significantly affected the mechanical properties of immobilized bio-beads and that 1.0 % (w/v) was the optimal concentration. The bio-beads effectively degraded TCA (160 mg L(-1)) in the anaerobic medium and could be reused up to six times. The TCA degradation rate of bio-beads was 1.5 and 2.3 times greater, respectively, than ZVI + AC treatment or microbes + AC treatment. Measuring FeS produced by microbial reactions indicated that TCA removal occurred via FeS-catalyzed dechlorination. Analysis of clonal libraries derived from bio-beads demonstrated that the dominant species in the community were Betaproteobacteria and Gammaproteobacteria, which may contribute to the long-term stability of ZVI reactivity during TCA dechlorination. This study shows that the combined use of immobilized anaerobic bacteria, ZVI, and AC in bio-beads is effective and practical for TCA dechlorination and suggests they may be applicable towards developing a groundwater treatment system for the removal of TCA.

Identifying the Correct Biotransformation Model from Polychlorinated Biphenyl and Dioxin Dechlorination Batch Studies

We performed Monte Carlo simulations of batch transformations of hydrophobic compounds using typical numbers of data points, extent of reaction, and measurement error, to identify the most appropriate biotransformation model to describe such data under different conditions. Highly hydrophobic compounds such as polychlorinated biphenyls (PCBs) and dioxins present special challenges for parameterization due to low environmental concentrations and slow biotransformation rates, which result in high sample variability, few samples, and limited substrate concentration range. Four models of varying complexity (zero-order, first-order, Monod, and Best) were fit to simulated data. Various combinations of initial concentration (S0), half saturation concentration (KS), maximum substrate utilization rate (qmax), measurement error, number of data points per batch run, and extent of biotransformation were simulated. One thousand Monte-Carlo runs were performed for each parameter combination, and AICc (Akaike's information criterion corrected for small numbers of data points) was used to determine the most appropriate model. Neither the Best model nor the zero-order model ever produced the lowest AICc for a majority of simulations under any combination of test conditions. With 10% measurement error, the first-order model always outperformed the others. In the case of 1% measurement error with 10 evenly-spaced data points, the Monod model was the better choice when S0>KS and the system was not mass transfer limited [Formula: see text] otherwise, the first-order model was indicated. S0 is constrained by the compound's aqueous solubility; therefore, for highly hydrophobic compounds such as PCBs or polychlorinated dibenzo-p-dioxins and dibenzofurans, a first-order model is likely to fit batch biotransformation data as well or better than a more complicated model.