Development and characterization of stable sediment-free anaerobic bacterial enrichment cultures that dechlorinate aroclor 1260

Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights

Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 h. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced beta diversity (community composition) but had only a minor effect on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05 % yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1 % to 32 %). Comparative genomic analysis indicated that Bin3 has undergone specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.

Halogenated organic compounds in mangrove sediments from Bintan Island, Indonesia: Occurrence, profiles, sources, and potential ecological risk

The first comprehensive analysis of halogenated organic compounds (HOCs), including 209 full congeners of polychlorinated biphenyls (PCBs), 26 organochlorinated pesticides (OCPs), 41 polybrominated diphenyl ethers (PBDEs), and four other brominated flame retardants (BFRs), was performed on surface mangrove sediments from Bintan Island, Province of the Riau Archipelago, Indonesia. Among the measured HOC contaminants, the mean concentration of ∑209PCBs (2.3 ± 0.96 ng g-1 dw) was higher than that of p,p'-DDE (1.8 ± 0.70 ng g-1 dw), ∑41PBDEs (1.8 ± 1.1 ng g-1 dw), trans-nonachlor (0.42 ± 0.13 ng g-1 dw), and other BFRs (0.20 ± 0.29 ng g-1 dw), while other OCP related compounds less than 0.2 ng g-1 dw. In addition, concentrations of unintentionally produced PCBs such as PCB-11 and PCB-47/48/75 ranged from 0.57 to 1.5 ng g-1 dw. Variations in HOCs accumulation and profiles among mangrove habitats and species indicate different anthropogenic stressors and species-specific accumulations. The ecological risk estimation from HOCs exposure on dwelling sediment biota in mangrove sediments varied from no risk to potentially causing adverse effects in several locations. Overall, this study provides fundamental information on the function of mangrove ecosystems as an accumulation zone for HOCs in tropical regions.

Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant

Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.

Microbial and chemically induced reductive dechlorination of polychlorinated biphenyls in the environment

Polychlorinated biphenyls (PCBs) are persistent organic pollutants and are emitted during e-waste activities. Once they enter into the environment, PCBs could pose toxic effects to environmental compartments and public health. Reductive dechlorination offers a sustainable solution to manage the PCBs-contaminated environment. Under anaerobic conditions, reductive dechlorination of PCBs occurs, and PCBs congeners serve as potential electron acceptors which stimulate the growth of PCBs-dechlorinating microorganisms. In this review, microbial and chemically induced reductive dechlorination was summarized. During anaerobic conditions, highly chlorinated PCBs undergo reductive dechlorination and are converted into less chlorinated PCBs. The mechanisms involved in reductive dechlorination are mainly attacks on meta and/or para chlorines of PCBs mixtures in a contaminated environment and ortho dechlorination of PCBs. Based on methods, PCBs removal efficiency was as chemical > biological. Activated carbon (90%) showed more treatment efficiency than bacterial (84%). The review suggested that microbial remediation is a slow process; however, efficiency could be enhanced after amendments. Different microorganisms appear to be responsible for different dechlorination activities and the occurrence of various dehalogenation routes. However, PCBs dechlorination rate, extent, and route are influenced by pH, temperature, availability of carbon sources, and the presence or absence of H2 or competing electron acceptors and other electron donors.

Enhanced microbial dechlorination of PCBs by anaerobic digested sludge and enrichment of low-abundance PCB dechlorinators

The slow rate of anaerobic microbial dechlorination in natural environments limits the application of polychlorinated biphenyl (PCB) bioremediation. Anaerobic digested sludge (ADS), abundant in nutrients and microorganisms, could be an effective additive to improve microbial dechlorination. This research investigates the influence of ADS on Aroclor 1260 dechlorination performance, microbial community composition, and the abundance of functional genes. Moreover, further enrichment of organohalide-respiring bacteria (OHRB) was examined using tetrachloroethene (PCE) as the electron acceptor, followed by the serial dilution-to-extinction method in conjunction with resuscitation promoting factor (Rpf) supplementation. The results demonstrated that the addition of 5 g/L ADS achieved more extensive and efficient dechlorination of PCBs. ADS enhanced the removal of meta- and para-chlorine without significantly changing the dechlorination pathways. The abundances of dechlorinators, including Dehalobium and Dehalobacter within the Chloroflexi and Firmicutes phyla, as well as non-dechlorinators from the Desulfobacterota, Euryarchaeota, and Bacteroidetes phyla, were significantly increased with ADS amendment. Similarly, an increased abundance of bacteria, OHRB, reductive dehalogenase (RDase) genes, and archaeal 16S rRNA genes was observed. Additionally, obligate OHRB, such as Dehalobacter and Dehalobium, were further enriched. These findings indicate that ADS effectively enhances microbial reductive dechlorination and highlight the potential for enriching and isolating OHRB with Rpf.

Unlocking the potential of resuscitation-promoting factor for enhancing anaerobic microbial dechlorination of polychlorinated biphenyls

Microbial dechlorination of polychlorinated biphenyls (PCBs) is limited by the slow growth rate and low activity of dechlorinators. Resuscitation promoting factor (Rpf) of Micrococcus luteus, has been demonstrated to accelerate the enrichment of highly active PCB-dechlorinating cultures. However, it remains unclear whether the addition of Rpf can further improve the dechlorination performance of anaerobic dechlorination cultures. In this study, the effect of Rpf on the performance of TG4, an enriched PCB-dechlorinating culture obtained by Rpf amendment, for reductive dechlorination of four typical PCB congeners (PCBs 101, 118, 138, 180) was evaluated. The results indicated that Rpf significantly enhanced the dechlorination of the four PCB congeners, with residual mole percentages of PCBs 101, 118, 138 and 180 in Rpf-amended cultures being 16.2-29.31 %, 13.3-20.1 %, 11.9-14.4 % and 9.4-17.3 % lower than those in the corresponding cultures without Rpf amendment after 18 days of incubation. Different models were identified as appropriate for elucidating the dechlorination kinetics of distinct PCB congeners, and it was observed that the dechlorination rate constant is significantly influenced by the PCB concentration. The supplementing Rpf did not obviously change dechlorination metabolites, and the removal of chlorines occurred mainly at para- and meta- positions. Analysis of microbial community and functional gene abundance suggested that Rpf-amended cultures exhibited a significant enrichment of Dehalococcoides, Dehalogenimonas and Desulfitobacterium, as well as non-dechlorinators belonging to Desulfobacterota and Bacteroidetes. These findings highlight the potential of Rpf as an effective additive for enhancing PCB dechlorination, providing new insights into the survival of functional microorganisms involved in anaerobic reductive dechlorination.

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.

Positive Matrix Factorization analysis shows dechlorination of polychlorinated biphenyls during domestic wastewater collection and treatment

Polychlorinated biphenyls (PCBs) are persistent, toxic and bioaccumulative pollutants. One of the few pathways via which they break down is microbial dechlorination, which has been shown to occur in sewers. Questions remain about where within sewers this process takes place and which conditions encourage dechlorination. These issues were examined using a large data set on PCBs in influent and effluents from a main and bypass outfall from a wastewater treatment facility in the Mid-Atlantic region of the USA. A data set containing 64 chromatographic peaks representing 103 PCB congeners measured in 74 whole water samples was analyzed by Positive Matrix Factorization (PMF). PMF resolved four factors, three of which represented Aroclors 1242, 1254, and 1260. The remaining factor represented an advanced dechlorination regime of PCBs characterized by high proportions of PCBs 4 and 19 and comprised about 35% of the PCBs in the treated effluent, among the highest levels of dechlorination observed in previous studies. Concentrations of dechlorination products were not correlated with total suspended solids, indicating they were mostly dissolved and explaining the poor removal via sedimentation during the treatment process. The factors representing Aroclors were positively correlated with total influent flow, but the dechlorination signal was not, suggesting that the dechlorination signal arises from different locations and/or processes than the Aroclors. Even though treatment and dechlorination reduced the dioxin-like toxicity of the PCB mixture, this effect might be offset by the incomplete removal of dechlorination products.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

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.

An anoxic-aerobic system for simultaneous biodegradation of phenol and ammonia in a sequencing batch reactor

A laboratory-scale sequencing batch reactor (SBR) was investigated to treat artificial pretreated coal gasification wastewater that was mainly contained of ammonia and phenol. The efficiency of SBR fed with increasing phenol concentrations (from 150 to 300 mg l^-1) and the relationship among phenol, nitrogen removal, and the microbial community structure were evaluated. When the phenol feeding concentration was increased to about 300 mg l^-1, the removal efficiency was above 99.0%, demonstrating the robustness of phenol removal capacity. The study showed that most phenol was degraded in anoxic stage. The average removal efficiencies of ammonia and total nitrogen were 98.4 and 81.9%, respectively, with average NH₄⁺-N concentration of 107.5 mg l^-1 and COD/N 7.5. Low temperature caused sludge loss that led to the decreased performance. Increasing the temperature could not recover the performance effectively. The data from bacterial analysis revealed that Delftia, Hydrogenophaga, and unclassified Xanthomonadaceae played a significant role in phenol degradation before the temperature increase, while uncultured Syntrophococcus sp. and unclassified Rhodocyclaceae were responsible for phenol degradation after the temperature increase. These results imply that the SBR holds potential for the simultaneous removal of phenolic compounds and nitrogen through aerobic ammonia oxidation and anoxic denitrification with phenol as the co-organic carbon source.

Potential risk reduction of Aroclor 1254 by microbial dechlorination in anaerobic Grasse River sediment microcosms

Aroclor 1254 was the second most produced commercial PCB mixture and is found in soils, sediments and sewage throughout the globe. This commercial PCB mixture is considered particularly toxic because of the relatively high concentrations of congeners with dioxin-like properties. The potential for risk reduction by microbial reductive dechlorination of Aroclor 1254 (A1254) was investigated in sediment microcosms from Grasse River (GR), Massena, NY. The specificity of A1254 dechlorination was doubly- and singly-flanked chlorines in meta positions and to a less extent doubly-flanked para chlorines of 2345-substituted chlorobiphenyl rings. The average dechlorination rate of A1254 was 0.0153 Cl^-/biphenyl/day, and dechlorination rates of single congeners ranged between 0.001 and 0.0074 Cl^-/biphenyl/day. Potential risk associated with A1254 based on the toxic equivalency factors of the dioxin-like congeners was reduced by 83%. Additional potential risk associated with bioaccumulation in fish was reduced by 35% based on biota-sediment accumulation factor estimates for all detected congeners. Finally, the dechlorination end-products were tri- and tetra-chlorobiphenyls with unflanked chlorines, all of which are susceptible to further degradation by aerobic microorganisms. The combined results indicate that microbial reductive dechlorination has the potential for reducing risk associated with toxicity and bioaccumulation in fish in sites contaminated with A1254.

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.

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.

High levels of dioxin-like PCBs found in organic-farmed eggs caused by coating materials of asbestos-cement fiber plates: A case study

During a regional monitoring project of organic-farmed, free-range and cage-free eggs, high levels of dioxin-like compounds were detected in organic-farmed eggs, using the dioxin responsive chemical-activated luciferase gene expression (DR-CALUX®) bioassay. Further evaluations performed with GC-HRMS (gas chromatography in combination with high resolution mass spectrometry) revealed elevated amounts of non-dioxin-like (non-dl) polychlorinated biphenyls (PCBs) dominated by most lipophilic congeners like PCB 138, 153 and 180 and of dioxin-like (dl) PCBs, with a congener pattern in the descending order of PCB 118, 156, 167, 105, 189, 157, 105, 126 and PCB 77. Contaminations with polychlorinated dibenzo-p-dioxins (PCDDs) appeared of minor priority, with only hepta- and octa-substituted dioxins above their limits of quantification (LOQs). The pattern of polychlorinated dibenzofurans (PCDFs) was dominated by low amounts of tetra- and penta-chlorinated congeners. To identify the source of contamination, several samples of organic-farmed eggs, soil, laying hens, feedstuff, corrugated asbestos-cement cover plates (ACPs), stable dust and debris collected in the gutter of the stable, were analyzed. Comparing PCB congener-pattern of individual samples, the source was traced back to the coating of ACPs, which covered roof and sidewalls of the stable. Because coating materials probably have been used for roofing and cladding in many countries worldwide, there is a high probability that the presented case report is not a local incident but rather describes a new source of PCB contamination, yet widely unknown or underestimated.

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.

Dehalococcoides mccartyi strain JNA in pure culture extensively dechlorinates Aroclor 1260 according to polychlorinated biphenyl (PCB) dechlorination Process N

We isolated Dehalococcoides mccartyi strain JNA from the JN mixed culture which was enriched and maintained using the highly chlorinated commercial PCB mixture Aroclor 1260 for organohalide respiration. For isolation we grew the culture in minimal liquid medium with 2,2',3,3',6,6'-hexachlorobiphenyl (236-236-CB)(20 μM) as respiratory electron acceptor. We repeatedly carried out serial dilutions to extinction and recovered dechlorination activity from transfers of 10(-7) and 10(-8) dilutions. Fluorescence microscopy, DGGE and RFLP analysis of PCR amplified16S rRNA genes, and multilocus sequence typing of three housekeeping genes confirmed culture purity. No growth occurred on complex media. JNA dechlorinated most hexa- and heptachlorobiphenyls in Aroclor 1260 (50 μg/mL) leading to losses of 51% and 20%, respectively. Dechlorination was predominantly from flanked meta positions of 34-, 234-, 235-, 236-, 245-, 2345-, 2346-, and 2356-chlorophenyl rings, as indicated by the underscores. The major products were 24-24-CB, 24-26-CB, 24-25-CB, and 25-26-CB. We identified 85 distinct PCB dechlorination reactions and 56 different PCB dechlorination pathways catalyzed by JNA. Dechlorination pathways were confirmed by mass balance of substrates and products. This dechlorination pattern matches PCB Dechlorination Process N. JNA is the first pure culture demonstrated to carry out this extensive and environmentally relevant PCB dechlorination pattern.

vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense

The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D. hafniense, D. chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D. chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D. hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase.

Reductive dechlorination of 1,2,3,7,8-pentachlorodibenzo-p-dioxin and Aroclor 1260, 1254 and 1242 by a mixed culture containing Dehalococcoides mccartyi strain 195

A mixed culture containing Dehalococcoides mccartyi strain 195 dechlorinated 1,2,3,7,8-pentachlorodibenzo-p-dioxin (1,2,3,7,8-PeCDD) and selected polychlorinated biphenyl (PCB) congeners in Aroclors 1260, 1254 and 1242. 1,2,3,7,8-PeCDD was dechlorinated to 1,3,7-trichlorodibenzo-p-dioxin (1,3,7-TrCDD) and/or 1,3,8-TrCDD via 1,3,7,8-tetrachlorodibenzo-p-dioxin (1,3,7,8-TeCDD), a pathway that excludes the production of the toxic congener 2,3,7,8-TeCDD. Dechlorination rate and extent was greatly enhanced by the addition of 1,2,3,4-tetrachlorobenzene (1,2,3,4-TeCB) as an alternate halogenated substrate and/or incubation temperature increase from 25 °C to 35 °C. The most extensive dechlorination of PCBs occurred for Aroclor 1260 with 13 major congeners making up 44.1 mol% of the original PCBs dechlorinated by 42% over 250 days at 25 °C. When 1,2,3,4-TeCB was amended as co-substrate, the extent of dechlorination increased to 82%, over 250 days. The mixed culture primarily dechlorinated the doubly-flanked chlorines on 2,3,4-, 2,3,4,6-, and 2,3,4,5,6-substituted chlorophenyl rings, whereas it primarily removed the doubly-flanked para chlorine from the 2,3,4,5-substituted chlorophenyl ring. Experiments using a 20% dilution of culture with 31.8 μg/mL 1,2,3,4-TeCDD or 2,3,4,4',5-pentachlorobiphenyl (PCB 114) as sole halogenated substrate exhibited less than 0.1 mol% dechlorination over 120 days. Further, dechlorination of PCBs and PCDDs by the fully grown culture in the absence of 1,2,3,4-TeCB eventually stopped or greatly slowed over the incubation period. Since Dehalococcoides spp. only gain energy for growth from organohalide respiration, absence of reductive dechlorination upon transfer and dilution or cessation of dechlorination after long incubation times suggest that it is unlikely that strain 195 can grow using the PCDDs or PCBs utilized in this study.

Dechlorination of commercial PCBs and other multiple halogenated compounds by a sediment-free culture containing Dehalococcoides and Dehalobacter

At the contaminated sites, polychlorinated biphenyls (PCBs) frequently coexist with other halogenated compounds, such as polybrominated diphenyl ethers (PBDEs), chloroethanes, and chloroethenes. The presence of multiple halogenated compounds usually poses toxicity to dehalogenating microbes, because few cultures are capable of detoxifying a broad spectrum of halogenated compounds. In this study, a sediment-free culture, designed as AD14, is able to sequentially remove halogens from PCBs and other cocontaminants. Culture AD14 dechlorinated the commercial PCB mixture-Aroclor 1260-mainly by removing flanked para- and doubly flanked meta-chlorines. It also dehalogenated octa-brominated diphenyl ether mixture predominantly to tetra-BDEs, 2,4,6-trichlorophenol (2,4,6-TCP) to 4-CP, and tetrachloroethene (PCE)/1,2-dichloroethane (1,2-DCA) completely to ethene. When applied to a mixture of the above-mentioned compounds, culture AD14 stepwise removed halogens from 2,4,6-TCP, 1,2-DCA, PCE, PBDEs, and PCBs. Illumina sequencing analysis of 16S rRNA genes showed that only two known dechlorinating genera, Dehalococcoides and Dehalobacter, were present in culture AD14. Quantitative real-time PCR analysis showed that the 16S rRNA gene copies of Dehalococcoides and Dehalobacter increased from 1.14 × 10(5) to 7.04 × 10(6) copies mL(-1) and from 1.15 × 10(5) to 8.20 × 10(6) copies mL(-1) after removing 41.13 μM of total chlorine from PCBs. The above results suggest that both Dehalobacter and Dehalococcoides could be responsible for PCB dechlorination. Although two Dehalococoides mccartyi strains with identical 16S rRNA genes were isolated from the PCBs-dechlorinating mixed culture using trichloroethene (TCE) and vinyl chloride (VC) as alternatives to PCBs, the two isolates are incapable of dechlorinating PCBs. In all, culture AD14 is promising for bioremediation applications at sites cocontaminated with PCBs and other halogenated compounds.

In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet?

The remediation of polychlorinated biphenyls (PCBs) in soils and sediments remains a particularly difficult problem to solve. The possibility of in situ degradation by microorganisms has been pursued for many years since this approach has the potential to provide a cost-effective and environmentally sustainable alternative to dredging for treatment of PCB impacted sites. Being hydrophobic, PCBs partition into organic material and accumulate in anoxic environments well poised to support anaerobic dechlorination of highly chlorinated congeners; products of which are susceptible to complete aerobic degradation. Laboratory research over the past 25 years is now leading to new microbial technologies that could soon be tested for treatment of PCB impacted sediments in the field.

Phylogenetically distinct bacteria involve extensive dechlorination of aroclor 1260 in sediment-free cultures

Microbial reductive dechlorination of the persistent polychlorinated biphenyls (PCBs) is attracting much attention in cleanup of the contaminated environment. Nevertheless, most PCB dechlorinating cultures require presence of sediment or sediment substitutes to maintain their dechlorination activities which hinders subsequent bacterial enrichment and isolation processes. The information on enriching sediment-free PCB dechlorinating cultures is still limited. In this study, 18 microcosms established with soils and sediments were screened for their dechlorination activities on a PCB mixture – Aroclor 1260. After one year of incubation, 10 out of 18 microcosms showed significant PCB dechlorination with distinct dechlorination patterns (e.g., Process H, N and T classified based on profiles of PCB congeners loss and new congeners formation). Through serial transfers in defined medium, six sediment-free PCB dechlorinating cultures (i.e., CW-4, CG-1, CG-3, CG-4, CG-5 and SG-1) were obtained without amending any sediment or sediment-substitutes. PCB dechlorination Process H was the most frequently observed dechlorination pattern, which was found in four sediment-free cultures (CW-4, CG-3, CG-4 and SG-1). Sediment-free culture CG-5 showed the most extensive PCB dechlorination among the six cultures, which was mediated by Process N, resulting in the accumulation of penta- (e.g., 236-24-CB) and tetra-chlorobiphenyls (tetra-CBs) (e.g., 24-24-CB, 24-25-CB, 24-26-CB and 25-26-CB) via dechlorinating 30.44% hepta-CBs and 59.12% hexa-CBs after three months of incubation. For culture CG-1, dechlorinators mainly attacked double flanked meta-chlorines and partially ortho-chlorines, which might represent a novel dechlorination pattern. Phylogenetic analysis showed distinct affiliation of PCB dechlorinators in the microcosms, including Dehalogenimonas and Dehalococcoides species. This study broadens our knowledge in microbial reductive dechlorination of PCBs, and provides essential information for culturing and stimulating PCB dechlorinators for in situ bioremediation applications.

Microbial communities involved in methane production from hydrocarbons in oil sands tailings

Microbial metabolism of residual hydrocarbons, primarily short-chain n-alkanes and certain monoaromatic hydrocarbons, in oil sands tailings ponds produces large volumes of CH(4) in situ. We characterized the microbial communities involved in methanogenic biodegradation of whole naphtha (a bitumen extraction solvent) and its short-chain n-alkane (C(6)-C(10)) and BTEX (benzene, toluene, ethylbenzene, and xylenes) components using primary enrichment cultures derived from oil sands tailings. Clone libraries of bacterial 16S rRNA genes amplified from these enrichments showed increased proportions of two orders of Bacteria: Clostridiales and Syntrophobacterales, with Desulfotomaculum and Syntrophus/Smithella as the closest named relatives, respectively. In parallel archaeal clone libraries, sequences affiliated with cultivated acetoclastic methanogens (Methanosaetaceae) were enriched in cultures amended with n-alkanes, whereas hydrogenotrophic methanogens (Methanomicrobiales) were enriched with BTEX. Naphtha-amended cultures harbored a blend of these two archaeal communities. The results imply syntrophic oxidation of hydrocarbons in oil sands tailings, with the activities of different carbon flow pathways to CH(4) being influenced by the primary hydrocarbon substrate. These results have implications for predicting greenhouse gas emissions from oil sands tailings repositories.

A Chloroflexi bacterium dechlorinates polychlorinated biphenyls in marine sediments under in situ-like biogeochemical conditions

We investigated the reductive dechlorination of Aroclor 1254 PCBs by a coplanar PCB-dechlorinating microbial community enriched from an actual site contaminated marine sediment of the Venice lagoon in sterile slurry microcosms of the same sediment suspended in its site water, i.e., under biogeochemical conditions that closely mime those occurring in situ. The culture dechlorinated more than 75% of the penta- through hepta-chlorinated biphenyls to tri- and tetra-chlorinated congeners in 30 weeks. The dechlorination rate was reduced by the addition of H(2) and short chain fatty acids, which stimulated sulfate-reduction and methane production, and markedly increased by the presence of vancomycin or ampicillin. DGGE analysis of 16S rRNA genes on PCB-spiked and PCB-free cultures ruled out sulfate-reducing and methanogenic bacteria and revealed the presence of a single Chloroflexi phylotype closely related to the uncultured bacteria m-1 and SF1 associated to PCB dechlorination. These findings suggest that a single dechlorinator is responsible for the observed extensive dechlorination of Aroclor 1254 and that a Chloroflexi species similar to those already detected in freshwater and estuarine contaminated sediments mediates PCB dechlorination in the marine sediment adopted in this study under biogeochemical conditions resembling those occurring in situ in the Brentella Canal of Venice Lagoon.

Isolation and characterization of an environmental cadmium- and tellurite-resistant Pseudomonas strain

A Pseudomonas strain (TeU), resistant to tellurite (TeO(2)(3)(-) and cadmium (Cd(2+)) ions, was isolated from heavy-metal-contaminated sediments by enrichment. Black precipitates, presumably the product of the reduction of tellurite, such as tellurium, occurred in cultures of the isolate after growth in medium containing tellurite. Quantitative determination of the TeO(2)(3)(-) concentration in the liquid culture demonstrated a decreased concentration of tellurite (to less than 100 µM) from initial concentrations of approximately 1,000 µM within 24 h of growth. Strain TeU was resistant to TeO(2)(3)(-) and Cd(2+) concentrations as high as 2,000 µM and 500 µM, respectively. Transposon mutagenesis of strain TeU resulted in mutants exhibiting Cd(2+) sensitivity (Strain BU21) and one with decreased ability to reduce tellurite (strain AU08). Strain BU21 was less tolerant to Cd(2+) (100 µM) compared with the wild-type strain TeU (500 µM) but was still able to reduce tellurite to 80% of that of strain TeU. Although strain AU08 possesses the ability for Cd(2+) resistance, it reduced less than 20% of the initial concentrations of tellurite compared with strain TeU. Genes encoding an HflKC complex and a putative metallopeptidase were associated with the bacterium's capacity for tellurite reduction and Cd resistance, respectively. The ability to reduce tellurite therefore may not be necessary for this bacterium's heavy metal and metalloid tellurite resisting ability.

Potential fossil endoliths in vesicular pillow basalt, Coral Patch Seamount, eastern North Atlantic Ocean

The chilled rinds of pillow basalt from the Ampère-Coral Patch Seamounts in the eastern North Atlantic were studied as a potential habitat of microbial life. A variety of putative biogenic structures, which include filamentous and spherical microfossil-like structures, were detected in K-phillipsite-filled amygdules within the chilled rinds. The filamentous structures (∼2.5 μm in diameter) occur as K-phillipsite tubules surrounded by an Fe-oxyhydroxide (lepidocrocite) rich membranous structure, whereas the spherical structures (from 4 to 2 μm in diameter) are associated with Ti oxide (anatase) and carbonaceous matter. Several lines of evidence indicate that the microfossil-like structures in the pillow basalt are the fossilized remains of microorganisms. Possible biosignatures include the carbonaceous nature of the spherical structures, their size distributions and morphology, the presence and distribution of native fluorescence, mineralogical and chemical composition, and environmental context. When taken together, the suite of possible biosignatures supports the hypothesis that the fossil-like structures are of biological origin. The vesicular microhabitat of the rock matrix is likely to have hosted a cryptoendolithic microbial community. This study documents a variety of evidence for past microbial life in a hitherto poorly investigated and underestimated microenvironment, as represented by the amygdules in the chilled pillow basalt rinds. This kind of endolithic volcanic habitat would have been common on the early rocky planets in our Solar System, such as Earth and Mars. This study provides a framework for evaluating traces of past life in vesicular pillow basalts, regardless of whether they occur on early Earth or Mars.

Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions

The prokaryotic activity, diversity and culturability of diffusion-controlled Aarhus Bay sediments, including the sulphate-methane transition zone (SMTZ), were determined using a combination of geochemical, molecular (16S rRNA and mcrA genes) and cultivation techniques. The SMTZ had elevated sulphate reduction and anaerobic oxidation of methane, and enhanced cell numbers, but no active methanogenesis. The prokaryotic population was similar to that in other SMTZs, with Deltaproteobacteria, Gammaproteobacteria, JS1, Planctomycetes, Chloroflexi, ANME-1, MBG-D and MCG. Many of these groups were maintained in a heterotrophic (10 mM glucose, acetate), sediment slurry with periodic low sulphate and acetate additions (~2 mM). Other prokaryotes were also enriched including methanogens, Firmicutes, Bacteroidetes, Synergistetes and TM6. This slurry was then inoculated into a matrix of substrate and sulphate concentrations for further selective enrichment. The results demonstrated that important SMTZ bacteria can be maintained in a long-term, anaerobic culture under specific conditions. For example, JS1 grew in a mixed culture with acetate or acetate/glucose plus sulphate. Chloroflexi occurred in a mixed culture, including in the presence of acetate, which had previously not been shown to be a Chloroflexi subphylum I substrate, and was more dominant in a medium with seawater salt concentrations. In contrast, archaeal diversity was reduced and limited to the orders Methanosarcinales and Methanomicrobiales. These results provide information about the physiology of a range of SMTZ prokaryotes and shows that many can be maintained and enriched under heterotrophic conditions, including those with few or no cultivated representatives.

Common key acidogen populations in anaerobic reactors treating different wastewaters: molecular identification and quantitative monitoring

Bacterial population dynamics during the start-up of three lab-scale anaerobic reactors treating different wastewaters, i.e., synthetic glucose wastewater, whey permeate, and liquefied sewage sludge, were assessed using a combination of denaturing gradient gel electrophoresis (DGGE) and real-time PCR techniques. The DGGE results showed that bacterial populations related to Aeromonas spp. and Clostridium sticklandii emerged as common and prominent acidogens in all reactors. Two real-time PCR primer/probe sets targeting Aeromonas or C. sticklandii were developed, and successfully applied to quantitatively investigate their dynamics in relation to changes in reactor performance. Quantitative analysis demonstrated that both Aeromonas- and C. sticklandii-related populations were highly abundant for acidogenic period in all reactors. Aeromonas populations accounted for up to 86.6-95.3% of total bacterial 16S rRNA genes during start-up, suggesting that, given its capability of utilizing carbohydrate, Aeromonas is likely the major acidogen group responsible for the rapid initial fermentation of carbohydrate. C. sticklandii, able to utilize specific amino acids only, occupied up to 8.5-55.2% of total bacterial 16S rRNA genes in the reactors tested. Growth of this population is inferred to be supported, at least in part, by non-substrate amino acid sources like cell debris or extracellular excretions, particularly in the reactor fed on synthetic glucose wastewater with no amino acid source. The quantitative dynamics of the two acidogen groups of interest, together with their putative functions, suggest that Aeromonas and C. sticklandii populations were numerically as well as functionally important in all reactors tested, regardless of the differences in substrate composition. Particularly, the members of Aeromonas supposedly play vital roles in anaerobic digesters treating various substrates under acidogenic, fermentative start-up conditions.

Effect of coplanar PCB concentration on dechlorinating microbial communities and dechlorination in estuarine sediments

The effect of concentration of coplanar PCB on the dechlorinating microbial community and dechlorination were investigated in anoxic estuarine sediment collected from Er-Jen River and enriched with 10 and 50 mg L⁻¹ of 3,4,4',5-tetrachlorobiphenyl, 3,3',4,4',5-pentachlorobiphenyl, and 3,3',4,4',5,5'-hexachlorobipheny. Dechlorination rates were similar in the cultures enriched with 10 and 50 mg L⁻¹ of 3,4,4',5-tetrachlorobiphenyl, whereas significantly higher dechlorination rates were observed in cultures enriched with 10 mg L⁻¹ of 3,3',4,4',5-pentachlorobiphenyl. No dechlorination was observed in sediment slurries enriched with 3,3',4,4',5,5'-hexachlorobipheny. Para dechlorination occurred prior to meta dechlorination during reductive dechlorination of 3,4,4',5-tetrachlorobiphenyl and 3,3',4,4',5-pentachlorobiphenyl. GC-MS and denaturing gradient gel electrophoresis (DGGE) were used to detect dechlorination products and dechlorinating microorganisms in the enriched sediment cultures during the process of degradation. Two Chloroflexi phylotypes observed in DGGE were responsible for para and meta dechlorination respectively. Phylotype Cp-1 has 98% similarity to uncultured bacterium N5-12. Phylotype Cm-1 has 99% similarity to uncultured dechlorinating bacterium m1 or SF1 belonging to the ο-17/DF-1 group of PCB-dechlorinating bacteria.

Evidence for widespread dechlorination of polychlorinated biphenyls in groundwater, landfills, and wastewater collection systems

One of the few pathways for environmental transformation of polychlorinated biphenyls (PCBs) is microbial dechlorination under anaerobic conditions, which is reported to occur in contaminated sediments of rivers, lakes and harbors. The goal of this work was to determine whether PCB dechlorination occurs in built waste treatment environments. We analyzed a large database on PCB congener concentrations in effluents and some influents of facilities in the Delaware River Basin. Positive matrix factorization was used to identify the sources of PCBs and to look for evidence of dechlorination. Seven factors were resolved from the data set of 89 congeners in 645 samples. Two of the resolved factors represented dechlorination signals. One of these was dominated by PCBs 4 and 19 and represents an advanced stage of dechlorination of Aroclors to di- and trichlorinated congeners. This dechlorination signal was most prevalent in effluents from sites with contaminated groundwater and from wastewater treatment plants (WWTPs) that serve combined sewers or treat landfill leachate. The other dechlorination signal appeared to represent an intermediate stage of dechlorination, because it was dominated by two coeluting groups of tetrachlorinated congeners: PCBs 44 + 47 + 65 and 45 + 51. This partial dechlorination signal was most prevalent in the 40 WWTPs with separate (sanitary) sewer systems, where it often comprised more than 20% of the PCBs in the effluents. Both dechlorination signals were present in WWTP influents, but were not observed in stormwater runoff, suggesting that dechlorination occurs in sewers. This work represents the first convincing evidence of PCB dechlorination occurring outside of contaminated aquatic sediments or anaerobic digesters. The results suggest that PCBs are dechlorinated by anaerobic bacteria in sewers, landfills, and contaminated groundwater. These two dechlorination signals comprise about 19% of the total loads of PCBs to the Delaware River from the sampled dischargers.

Characterization of the microbial community from the marine sediment of the Venice lagoon capable of reductive dechlorination of coplanar polychlorinated biphenyls (PCBs)

The native microbial community of a contaminated sediment from Brentella Canal (Venice Lagoon, Italy) was enriched in slurry microcosms consisting of sterile sediment suspended in sterile site water in the presence of 3,3',4,4'-tetrachlorobiphenyl, 3,3',4,4',5- and 2,3',4,4',5-pentachlorobiphenyls, 3,3',4,4',5,5'- and 2,3,3',4,4',5-hexachlorobiphenyls. The enrichment cultures were characterized at each subculturing step by 16S rRNA gene Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE) analysis. About 90% of spiked polychlorinated biphenyls (PCBs) were stoichiometrically converted into di- and tri-chlorinated congeners by each enriched culture via dechlorination of flanked para chlorines and ortho-flanked meta chlorines. A 2-fold increase in PCB-dechlorination rate, the disappearance of lag phase, as well as a remarkable increase of sulfate consumption and a decline of methanogenic activity, were observed throughout subculturing. A reduction of complexity of the archaeal community, which was composed by Methanomicrobiales and Methanosarcinales, was also observed as a result of culture enrichment. The bacterial community included members of the Alpha, Gamma, Delta and Epsilon divisions of Proteobacteria, Firmicutes and Chloroflexi. Two sequence phylotypes related to the genus Sulforovum and the species Desulfococcus multivorans and two Chloroflexi enriched throughout subculturing, thus suggesting that these bacteria were involved in PCB dechlorination in the marine sediments of Brentella canal.

Identification of structural properties associated with polychlorinated biphenyl dechlorination processes

Polychlorinated biphenyl molecules can be biologically dechlorinated through sequential losses of a chlorine atom, following 840 pathways from higher chlorinated to lesser-chlorinated congeners and biphenyl. Previously, eight recurring sets of pathways, herein referred to as explicitly reported pathways in dechlorination processes, have been identified through qualitative analysis of shifts in congener masses in field and laboratory studies. Dechlorination process generalizations were qualitatively extrapolated based on limited attributes of the congeners dechlorinated in the explicitly reported pathways. They are valuable because they allow comparisons of dechlorination patterns across laboratory experiments and contaminated sites. However, due to analytical limitations and a paucity of studies, the explicitly reported pathways in dechlorination processes likely do not represent all of the pathways that could occur at contaminated sites. This work presents an alternative, quantitative, and replicable approach to the identification of candidate pathways for inclusion in dechlorination process generalizations through use of classification trees. This method considers 46 structural and property attributes of dechlorination pathways. Trees fit for pathway inclusion in each of the eight dechlorination processes with alternative assumptions are compared in terms of critical congener attributes. The classification trees correctly classify explicitly reported pathways into dechlorination processes at rates of 0.90 to 0.99. While many of the attributes used in the original generalizations were also selected as predictors by the classification trees, the extra attributes allow identification of additional dechlorination pathways that can be considered as candidates for monitoring in future studies.

Phytoremediation of polychlorinated biphenyls: new trends and promises

Transgenic plants and associated bacteria constitute a new generation of genetically modified organisms for efficient and environment-friendly treatment of soil and water contaminated with polychlorinated biphenyls (PCBs). This review focuses on recent advances in phytoremediation for the treatment of PCBs, including the development of transgenic plants and associated bacteria. Phytoremediation, or the use of higher plants for rehabilitation of soil and groundwater, is a promising strategy for cost-effective treatment of sites contaminated by toxic compounds, including PCBs. Plants can help mitigate environmental pollution by PCBs through a range of mechanisms: besides uptake from soil (phytoextraction), plants are capable of enzymatic transformation of PCBs (phytotransformation); by releasing a variety of secondary metabolites, plants also enhance the microbial activity in the root zone, improving biodegradation of PCBs (rhizoremediation). However, because of their hydrophobicity and chemical stability, PCBs are only slowly taken up and degraded by plants and associated bacteria, resulting in incomplete treatment and potential release of toxic metabolites into the environment. Moreover, naturally occurring plant-associated bacteria may not possess the enzymatic machinery necessary for PCB degradation. To overcome these limitations, bacterial genes involved in the metabolism of PCBs, such as biphenyl dioxygenases, have been introduced into higher plants, following a strategy similar to the development of transgenic crops. Similarly, bacteria have been genetically modified that exhibit improved biodegradation capabilities and are able to maintain stable relationships with plants. Transgenic plants and associated bacteria bring hope for a broader and more efficient application of phytoremediation for the treatment of PCBs.

Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer

BACKGROUND

Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water) represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ.

RESULTS

We report the characterization of the response of an enriched bacterial community of a 1,2-dichloroethane (1,2-DCA) contaminated aquifer to the spiking with 5 mM lactate as electron donor in microcosm studies. After 15 days of incubation, the microbial community structure was analyzed. The bacterial 16S rRNA gene clone library showed that the most represented phylogenetic group within the consortium was affiliated with the phylum Firmicutes. Among them, known degraders of chlorinated compounds were identified. A reductive dehalogenase genes clone library showed that the community held four phylogenetically-distinct catalytic enzymes, all conserving signature residues previously shown to be linked to 1,2-DCA dehalogenation.

CONCLUSIONS

The overall data indicate that the enriched bacterial consortium shares the metabolic functionality between different members of the microbial community and is characterized by a high functional redundancy. These are fundamental features for the maintenance of the community's functionality, especially under stress conditions and suggest the feasibility of a bioremediation treatment with a potential prompt dehalogenation and a process stability over time.

"Dehalococcoides" sp. strain CBDB1 extensively dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260

"Dehalococcoides" sp. strain CBDB1 in pure culture dechlorinates a wide range of PCB congeners with three to eight chlorine substituents. Congener-specific high-resolution gas chromatography revealed that CBDB1 extensively dechlorinated both Aroclor 1248 and Aroclor 1260 after four months of incubation. For example, 16 congeners comprising 67.3% of the total PCBs in Aroclor 1260 were decreased by 64%. We confirmed the dechlorination of 43 different PCB congeners. The most prominent dechlorination products were 2,3',5-chlorinated biphenyl (25-3-CB) and 24-3-CB from Aroclor 1248 and 235-25-CB, 25-25-CB, 24-25-CB, and 235-236-CB from Aroclor 1260. Strain CBDB1 removed flanked para chlorines from 3,4-, 2,4,5-, and 3,4,5-chlorophenyl rings, primarily para chlorines from 2,3,4,5-chlorophenyl rings, primarily meta chlorines from 2,3,4- and 2,3,4,6-chlorophenyl rings, and either meta or para chlorines from 2,3,4,5,6-chlorophenyl rings. The site of attack on the 2,3,4-chorophenyl ring was heavily influenced by the chlorine configuration on the opposite ring. This dechlorination pattern matches PCB Process H dechlorination, which was previously observed in situ both in the Acushnet Estuary (New Bedford, MA) and in parts of the Hudson River (New York). Accordingly, we propose that Dehalococcoides bacteria similar to CBDB1 are potential agents of Process H PCB dechlorination in the environment. This is the first time that a complex naturally occurring PCB dechlorination pattern has been reproduced in the laboratory using a single bacterial strain.

A case study for microbial biodegradation: anaerobic bacterial reductive dechlorination of polychlorinated biphenyls-from sediment to defined medium

The history of anaerobic microbial polychlorinated biphenyl (PCB) dechlorination is traced over 20 years using a case study of PCB dechlorination in the Housatonic River (Massachusetts) as an example. The history progresses from the characterization of the PCBs in the sediment, to cultivation in sediment microcosms, to the identification of four distinct types of PCB dechlorination, to a successful field test, to the cultivation in defined medium of the organisms responsible for extensive dechlorination of Aroclor 1260, and finally to the identification of a Dehalococcoides population that links its growth to the dechlorination of Aroclor 1260. Other PCB dechlorinators have also been identified. Two bacterial strains, o-17 and DF-1, that link their growth to the dechlorination of several PCB congeners belong to a novel clade of putative dechlorinating bacteria within the phylum Chloroflexi. Dehalococcoides ethenogenes strain 195 also dechlorinates several PCB congeners when grown on chlorinated ethenes. Evidence is mounting that Dehalococcoides and other dechlorinating Chloroflexi may play a significant role in the dechlorination of commercial PCBs in situ.

Microbial transformation and degradation of polychlorinated biphenyls

This paper reviews the potential of microorganisms to transform polychlorinated biphenyls (PCBs). In anaerobic environments, higher chlorinated biphenyls can undergo reductive dehalogenation. Meta- and para-chlorines in PCB congeners are more susceptible to dechlorination than ortho-chlorines. Anaerobes catalyzing PCB dechlorination have not been isolated in pure culture but there is strong evidence from enrichment cultures that some Dehalococcoides spp. and other microorganisms within the Chloroflexi phylum can grow by linking the oxidation of H(2) to the reductive dechlorination of PCBs. Lower chlorinated biphenyls can be co-metabolized aerobically. Some aerobes can also grow by utilizing PCB congeners containing only one or two chlorines as sole carbon/energy source. An example is the growth of Burkholderia cepacia by transformation of 4-chlorobiphenyl to chlorobenzoates. The latter compounds are susceptible to aerobic mineralization. Higher chlorinated biphenyls therefore are potentially fully biodegradable in a sequence of reductive dechlorination followed by aerobic mineralization of the lower chlorinated products.

Pathways for the anaerobic microbial debromination of polybrominated diphenyl ethers

The debromination pathways of seven polybrominated diphenyl ethers (PBDEs) by three different cultures of anaerobic dehalogenating bacteria were investigated using comprehensive two-dimensional gas chromatography (GC x GC). The congeners analyzed were the five major components of the industrially used octa-BDE mixture (octa-BDEs 196, 203, and 197, hepta-BDE 183, and hexa-BDE 153) as well as the two most commonly detected PBDEs in the environment, penta-BDE 99 and tetra-BDE 47. Among the dehalogenating cultures evaluated in this study were a trichloroethene-enriched consortium containing multiple Dehalococcoides species, and two pure cultures, Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense PCP-1. PBDE samples were analyzed by GC x GC coupled to an electron capture detector to maximize separation and identification of the product congeners. All studied congeners were debrominated to some extent by the three cultures and all exhibited similar debromination pathways with preferential removal of para and meta bromines. Debromination of the highly brominated congeners was extremely slow, with usually less than 10% of nM concentrations of PBDEs transformed after three months. In contrast, debromination of the lesser brominated congeners, such as penta 99 and tetra 47, was faster, with some cultures completely debrominating nM levels of tetra 47 within weeks.