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

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.

Biomolecular insights into the inhibition of heavy metals on reductive dechlorination of 2,4,6-trichlorophenol in Pseudomonas sp. CP-1

Influences of heavy metal exposure to the organohalide respiration process and the related molecular mechanism remain poorly understood. In this study, a non-obligate organohalide respiring bacterium, Pseudomonas sp. strain CP-1, was isolated and its molecular response to the five types of commonly existed heavy metal ions were thoroughly investigated. All types of heavy metal ions posed inhibitory effects on 2,4,6-trichlorophenol dechlorination activity and cell growth with the varied degree. Exposure to Cu (II) showed the most serious inhibitive effects on dechlorination even at the lowest concentration of 0.05 mg/L, while the inhibition by As (V) was the least with the removal kinetic constant k decreased to 0.05 under 50 mg/L. Further, multi-omics analysis found compared with Cu (II), As (V) exposure led to the insignificant downregulation of a variety of biosynthesis processes, which would be one possible account for the less inhibited activity. More importantly, the inhibited mechanisms on the organohalide respiration catabolism of strain CP-1 were firstly revealed. Cu (II) stress severely downregulated NADH generation during TCA cycle and electron donation of organohalide respiration process, which might decrease the reducing power required for organohalide respiration. While both Cu (II) and As (Ⅴ) inhibited substrate level phosphorylation during TCA cycle, as well as electron transfer and ATP generation during organohalide respiration. Meanwhile, CprA-2 was confirmed as the responsible reductive dehalogenase in charge of 2,4,6-TCP dechlorination, and transcriptional and proteomic studies confirmed the directly inhibited gene transcription and expression of CprA-2. The in-depth reveal of inhibitory effects and mechanism gave theoretical supports for alleviating heavy metal inhibition on organohalide respiration activity in groundwater co-contaminated with organohalides and heavy metals.

Impact of different zero valent iron-based particles on anaerobic microbial dechlorination of 2,4-dichlorophenol: Comparison of dechlorination performance and the underlying mechanism

The integration of iron-based materials and anaerobic microbial consortia has been extensively studied owing to its potential to enhance pollutant degradation. However, few studies have compared how different iron materials enhance the dechlorination of chlorophenols in coupled microbial systems. This study systematically compared the combined performances of microbial community (MC) and iron materials (Fe0/FeS2 +MC, S-nZVI+MC, n-ZVI+MC, and nFe/Ni+MC) for the dechlorination of 2,4-dichlorophenol (DCP) as one representative of chlorophenols. DCP dechlorination rate was significantly higher in Fe0/FeS2 +MC and S-nZVI+MC (1.92 and 1.67 times, with no significant difference between two groups) than in nZVI+MC and nFe/Ni+MC (1.29 and 1.25 times, with no significant difference between two groups). Fe0/FeS2 had better performance for the reductive dechlorination process as compared with other three iron-based materials via the consumption of any trace amount of oxygen in anoxic condition and accelerated electron transfer. On the other hand, nFe/Ni could induce different dechlorinating bacteria as compared to other iron materials. The enhanced microbial dechlorination was mainly due to some putative dechlorinating bacteria (Pseudomonas, Azotobacter, Propionibacterium), and due to improved electron transfer of sulfidated iron particles. Therefore, Fe0/FeS2 as a biocompatible as well as low-cost sulfidated material can be a good alternative for possible engineering applications in groundwater remediation.

Development and microbial characterization of Bio-RD-PAOP for effective remediation of polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) as typical halogenated persistent organic pollutants are widely distributed in natural environments, and can be enriched and magnified in organisms via food webs. It is consequently urgent and necessary to develop techniques to completely remove these persistent organohalides. In this study, we developed a process (Bio-RD-PAOP) by integrating microbial reductive dechlorination (Bio-RD) with subsequent persulfate activation and oxidation process (PAOP) for effective remediation of PCBs. Results showed the synergistic combination of advantages of Bio-RD and PAOP in dechlorination of higher-chlorinated PCBs and of PAOP in degradation/mineralization of lower-chlorinated PCBs, respectively. For the PAOP, both experimental evidences and theoretical calculations suggested that degradation rate and efficiency decreased with the increased PCB chlorine numbers. Relative to the Bio-RD and PAOP, Bio-RD-PAOP had significantly higher PCB removal efficiencies, of which values were PCB congener-specific. For example, removal efficiency of Bio-RD-PAOP in removing PCB88 is 2.50 and 1.86 times of that of Bio-RD and PAOP, respectively. In contrast, the efficiency is 1.66 and 3.35 times of Bio-RD and PAOP, respectively, for PCB180 removal. The PAOP-derived oxidizing species (mainly sulfate free radical) significantly decreased microbial abundance, particularly of the organohalide-respiring Dehalococcoides. Notably, co-existence of other microorganisms alleviated the inhibitive effect of oxidizing species on the Dehalococcoides, possibly due to formation of microbial flocs or biofilm. This study provided a promising strategy for extensive remediation of organohalide-contaminated sites, as well as new insight into impact of PAOP-derived oxidizing species on the organohalide-respiring community.

The multi-process reaction model and underlying mechanisms of 2,4,6-trichlorophenol removal in lab-scale biochar-microorganism augmented ZVI PRBs and field-scale PRBs performance

This work developed calcium alginate (CA) embedded zero-valent iron (ZVI@CA) and CA embedded biochar (BC) immobilized microorganism (BC&Cell@CA) gel beads as alternative to conventional Fe⁰ permeable reactive barriers for treating groundwater contaminated with 2,4,6-trichlorophenol (2,4,6-TCP). Lab-scale and field-scale biochar-microorganism augmented PRBs (Bio-PRBs) were constructed and tested. The underlying mechanisms were revealed by a multi-source data calibrated multi-process reaction model, X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and high-throughput sequencing. Moreover, calibrated advection-dispersion (a) coupled with the two-site sorption (K_d) and chemical-biological multi-process reaction (λ) model were used for revealing 2,4,6-TCP transport behavior and optimizing Bio-PRBs. Compared to that in the ZVI@CA (0.004 h^-1) system, the reaction rate (0.011 h^-1) of 2,4,6-TCP increased by 175% in the combined chemical-biological batch system. Moreover, chemical-biological augmentation significantly improved the retardation effect of Bio-PRBs for 2,4,6-TCP. It came from that chemical-biological augmentation significantly decreased the dispersivity a (0.53 to 0.20 cm), and increased the distribution coefficient K_d (2.20 to 19.00 cm³ mg^-1), the reaction rate λ (2.40 to 3.60 day^-1), and the fraction (30% to 80%) of first-order kinetic sorption of 2,4,6-TCP in the lab-scale one-dimensional Bio-PRBs. Moreover, versatile functional bacteria Desulfitobacterium was crucial in the transformation of Fe (III) iron oxides. The diversity and richness of archaea in the reaction solution were improved by ZVI@CA gel beads addition. Furthermore, the field-scale reaction system was designed to remediate the chlorinated organic compounds and Benzene Toluene Ethylbenzene & Xylene contaminated groundwater in a pesticide factory site. The field test results demonstrated it is a promising technology to construct vertical reaction columns or horizontal Bio-PRBs for the efficient remediation of actually contaminated groundwater.

Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants

Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.

Concurrent anaerobic chromate bio-reduction and pentachlorophenol bio-degradation in a synthetic aquifer

Chromate [Cr(VI)] and pentachlorophenol (PCP) coexist widely in the environment and are highly toxic to public health. However, whether Cr(VI) bio-reduction is accompanied by PCP bio-degradation and how microbial communities can keep long-term stability to mediate these bioprocesses in aquifer remain elusive. Herein, we conducted a 365-day continuous column experiment, during which the concurrent removals of Cr(VI) and PCP were realized under anaerobic condition. This process allowed for complete Cr(VI) bio-reduction and PCP bio-degradation at an efficiency of 92.8 ± 4.2% using ethanol as a co-metabolic substrate. More specifically, Cr(VI) was reduced to insoluble chromium (III) and PCP was efficiently dechlorinated with chloride ion release. Collectively, Acinetobacter and Spirochaeta regulated Cr(VI) bio-reduction heterotrophically, while Pseudomonas mediated not only Cr(VI) bio-reduction but also PCP bio-dechlorination. The bio-dechlorinated products were further mineralized by Azospira and Longilinea. Genes encoding proteins for Cr(VI) bio-reduction (chrA and yieF) and PCP bio-degradation (pceA) were upregulated. Cytochrome c and intracellular nicotinamide adenine dinucleotide were involved in Cr(VI) and PCP detoxification by promoting electron transfer. Taken together, our findings provide a promising bioremediation strategy for concurrent removal of Cr(VI) and PCP in aquifers through bio-stimulation with supplementation of appropriate substrates.

Efficient biodegradation of tetrabromobisphenol A by the novel strain Enterobacter sp. T2 with good environmental adaptation: Kinetics, pathways and genomic characteristics

T2, a gram-positive bacterium capable of rapidly degrading tetrabromobisphenol A (TBBPA), and affiliated with the genus Enterobacter, was isolated for the first time from sludge that had been contaminated for several years. The TBBPA degradation data fitted the first-order model well. Under optimal conditions (pH of 7, temperature of 31 °C, TBBPA concentration of 5 mg L^-1, and inoculum size of 5%), 99.4% of the initially added TBBPA was degraded after 48 h. TBBPA degradation fitted the first-order model with the half-life of 3.3 h. These results illustrated that the TBBPA degradation capability of strain T2 was significantly better than that of previously reported bacteria. A total of 17 intermediates were detected, among which five were reported for the first time. Whole-genome sequencing revealed that strain T2 had a chromosome with the total length of 4 854 376 bp and a plasmid with the total length of 21 444 bp. It harbored essential genes responsible for debromination, such as cyp450, gstB, gstA, and HADH, and genes responsible for subsequent complete mineralization, such as bioC, yrrM, Tam, and Ubil. A key protein of haloacid dehalogenases responsible for the biodegradation of TBBPA may also be involved in the regulation of TBBPA degradation in natural environment. In soil bioremediation experiments, strain T2 showed excellent environmental adaptation. It was able to biodegrade TBBPA and its typical intermediate bisphenol A efficiently. Therefore, it could potentially be applied to treat TBBPA-contaminated sites.

Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis

As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.

DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X12Y12 (X = Al, B, and Y = N, P)

Adsorption of 2,4,6-tribromoaniline (BA), 2,4,6-trifluoroaniline (FA) and 2,4,6-trichloroaniline (CA) onto the surface of coronene/fullerene/fullerene-like nanocages was investigated by theoretical calculations. Due to the adsorption of BA/FA/CA, there are significant changes in chemical descriptors and nonlinear optical properties. Energy gap values of all nanoclusters are lowered, giving an increase in conductivity of complexes except for fullerene. All complex's ultraviolet visible wavenumber is blue-shifted and especially for fullerene complex, the values are very high. The enhancement of Raman intensities shows that it is possible to design a nanocage sensor for detecting these compounds by surface-enhanced Raman scattering (SERS).Communicated by Ramaswamy H. Sarma.

Microbial Enzymes Used in Bioremediation

Emerging pollutants in nature are linked to various acute and chronic detriments in biotic components and subsequently deteriorate the ecosystem with serious hazards. Conventional methods for removing pollutants are not efficient; instead, they end up with the formation of secondary pollutants. Significant destructive impacts of pollutants are perinatal disorders, mortality, respiratory disorders, allergy, cancer, cardiovascular and mental disorders, and other harmful effects. The pollutant substrate can recognize different microbial enzymes at optimum conditions (temperature/pH/contact time/concentration) to efficiently transform them into other rather unharmful products. The most representative enzymes involved in bioremediation include cytochrome P450s, laccases, hydrolases, dehalogenases, dehydrogenases, proteases, and lipases, which have shown promising potential degradation of polymers, aromatic hydrocarbons, halogenated compounds, dyes, detergents, agrochemical compounds, etc. Such bioremediation is favored by various mechanisms such as oxidation, reduction, elimination, and ring-opening. The significant degradation of pollutants can be upgraded utilizing genetically engineered microorganisms that produce many recombinant enzymes through eco-friendly new technology. So far, few microbial enzymes have been exploited, and vast microbial diversity is still unexplored. This review would also be useful for further research to enhance the efficiency of degradation of xenobiotic pollutants, including agrochemical, microplastic, polyhalogenated compounds, and other hydrocarbons.

Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with ¹³C-/¹⁵N-labeled peptides determined 1.8 × 10³ TceA and 1.2 × 10² VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.

Maize straw biochar addition inhibited pentachlorophenol dechlorination by strengthening the predominant soil reduction processes in flooded soil

Biochar has received increasing attention for its multifunctional applications as a soil amendment. The dual effect of biochar on reductive organic pollutants and soil biogeochemical processes under anaerobic environments in parallel has yet to be fully explored. In this study, anaerobic batch experiments were conducted to examine the effect of biochar on both reductive transformation of pentachlorophenol (PCP) and soil redox processes in flooded soil. Compared to biochar-free controls, the reductive dechlorination of PCP was significantly inhibited following biochar addition, with the inhibition degree increased with increasing amount of biochar. Dissimilatory iron and sulfate reduction, as well as the production of methane, were significantly enhanced following biochar addition. The bacterial and archaeal communities showed a functional selection responded to the addition of biochar and PCP, with the core functional groups at the genus level including Dethiobacter, Clostridium, Geosporobacter, Desulfuromonas, Desulfatitalea, and Methanosarcina. These findings indicated that biochar could affect soil microbial redox processes and may act as an electron mediator altering electron distribution from PCP dechlorination to the predominant soil reduction processes, and increase understanding regarding biochar's comprehensive effects on the remediation of natural flooded soil polluted by chlorinated organic pollutants that can be degraded reductively.

Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions

Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.

Purification, molecular characterization and metabolic mechanism of an aerobic tetrabromobisphenol A dehalogenase, a key enzyme of halorespiration in Ochrobactrum sp. T

Due to the detoxification of tetrabromobisphenol A (TBBPA) varies from different bacterial strains and depends on their specific enzymatic machinery, it is necessary to understand them for potential in situ bioremediation application. The special ability of our previously isolated Ochrobactrum sp. T to simultaneously debrominate and aerobic mineralize TBBPA urgent us to continuously study its degradation molecular mechanism. Herein, the purification and characterization of the dehalogenase which can debrominate TBBPA was investigated based on its corresponding encoding gene tbbpaA. Results showed that an enzyme with molecular mass of 117 kDa, K_m of 26.6 μM and V_max of 0.133 μM min^-1 mg^-1 was purified and designated as bromophenol dehalogenase. It was the only detected dehalogenase which exhibited TBBPA degradation ability (78%). Moreover, its activity was significantly enhanced by adding NADPH or methyl viologen to the reaction solution. The high similarity of substrate spectrum between the dehalogenase from the recombinant strain and the wild strain further indicated that it was the main dehalogenase responsible for the debromination in wild strain. Based on three identified metabolites, a metabolic pathway of TBBPA by purified enzyme under oxic condition was proposed. This study provides an excellent dehalogenase candidate for mechanistic study of aerobic dehalogenation of brominated aromatic compound.

Reduction in sulfate inhibition of microbial dechlorination of polychlorinated biphenyls in Hudson and Grasse River sediments through fatty acid supplementation

Microbial dechlorination of polychlorinated biphenyls (PCBs) in aquatic sediments may reduce the need for dredging for remediation. To better understand this biotransformation route under different geochemical conditions, the influence of sulfate on dechlorination in sediments from the Hudson River and the Grasse River spiked with two PCB mixtures (PCB 5/12, 64/71, 105/114 and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, 144/170 in Mixture 2) was investigated. The results showed that PCB dechlorination was partially inhibited in the sulfate-amended sediment microcosms. The rate, extent and preference of dechlorination were mainly controlled by the indigenous differences (sulfate, carbon content etc.) in sediment, but also affected by the PCB mixture composition. An increase of Dehalococcoides 16S rRNA genes coincided with the resumption of dechlorination. Dechlorination preferences were identified using a modified dechlorination pathway analysis approach. The low carbon content and high background sulfate Hudson sediment exhibited more para dechlorination targeting flanked para chlorines. The high carbon content and low background sulfate Grasse sediment preferentially removed more para-flanked meta chlorines than flanked para chlorines. The supplementation of fatty acids (acetate or a mixture of acetate, propionate and butyrate) dramatically increased PCB dechlorination in the Grasse sediment by resuming ortho-flanked meta dechlorination. Rare ortho removals were found in the Grasse sediment after adding fatty acids. This study suggests that supplementary fatty acids might be used to stimulate PCB dechlorination under sulfate reducing conditions, but the effectiveness largely depends on sediment geochemistry.

Acclimation of 2-chlorophenol-biodegrading activated sludge and microbial community analysis

Using glucose as cosubstrate, activated sludge that could effectively biodegrade 40 mg/L 2-chlorophenol was successfully domesticated in sequencing batch reactors. To acclimate the sludge, 2-chlorophenol was increased stepwise from 0 to 40 mg/L. High-throughput sequencing revealed that the microbial community richness increased during the first 5 days of acclimation to 5 mg/L 2-chlorophenol and then decreased after another 20 days as 2-chlorophenol was increased. The original sludge obtained from a water resource recovery facility had the highest microbial diversity. As the acclimation continued further, community richness and diversity both increased, but they decreased again, significantly, when 2-chlorophenol reached 40 mg/L. Saccharibacteria_norank, Bacillus, Saprospiraceae_uncultured, and Lactococcus were the dominant bacteria. Bacillus and Pseudomonas were the main known chlorophenol-degrading bacteria. WCHB1-60_norank, Tetrasphaera, Comamonadaceae_unclassified, and Haliangium showed poor tolerance to 2-chlorophenol. Higher bacterial tolerance to chlorophenols does not mean higher degrading capability. The degradation of chlorophenols was not positively correlated with the detected abundance of known 2-chlorophenol-degrading bacteria. PRACTITIONER POINTS: Activated sludge that could effectively biodegrade 40 mg/L 2-chlorophenol was successfully domesticated using glucose as cosubstrate in sequencing batch reactors. Saccharibacteria_norank, Bacillus, Saprospiraceae_uncultured, and Lactococcus were the dominant bacteria. Bacillus and Pseudomonas were the main known chlorophenol-degrading bacteria detected in this study. The degrading capability and tolerance of bacteria to chlorophenols were relatively independent and the degradation of chlorophenols may be the synergistic effect of various bacteria.

The microbial community responsible for dechlorination and benzene ring opening during anaerobic degradation of 2,4,6‑trichlorophenol

This study describes the dechlorination ability of acclimated biomass, the high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene of such microorganisms, and the analysis of their community structure in relation to special functions. Two types of acclimated biomass (AB-1 and AB-2) were obtained via different acclimated treatment processes and were used to degrade 2,4,6‑trichlorophenol. The degradation pathway and characteristics of trichlorophenol degradation were different between the two groups. AB-1 degraded trichlorophenol only to 4-chlorophenol. AB-2 completely dechlorinated trichlorophenol and opened the benzene ring. The 16S rRNA high-throughput sequencing method was employed to examine the microbial diversity. It was found that the microbial richness and diversity of AB-1 were higher than those of AB-2. Firmicutes and Bacteroidetes were 2.7-fold and 4.3-fold more abundant, respectively, in AB-1 than in AB-2. Dechlorination bacteria in AB-1 mainly included Desulfobulbus, Desulfovibrio, Dechloromonas, and Geobacter. The above-mentioned bacteria were less abundant in AB-2, but the abundance of Desulfomicrobium was twofold higher in AB-2 than in AB-1. The two types of acclimated biomass contained different hydrogen (H₂)-producing bacteria. AB-2 showed higher abundance and diversity of hydrogen-producing bacteria. There was no Ignavibacteriae in AB-1, whereas its abundance in AB-2 was 8.4%. In this biomass, Ignavibacteriae was responsible for opening of the benzene ring. This study indicates that the abundance and diversity of microorganisms are not necessarily beneficial to the formation of a functional dechlorinating community. The H₂-producing bacteria (which showed greater abundance and diversity) and Ignavibacterium were assumed to be core functional populations that gave AB-2 stronger dechlorination and phenol-degradation abilities. Control of lower oxidation reduction potential (E_h) and higher temperatures by means of fresh aerobic activated sludge as the starting microbial group, caused rapid complete dechlorination of 2,4,6‑trichlorophenol and benzene ring opening.

Application of a novel gene encoding bromophenol dehalogenase from Ochrobactrum sp. T in TBBPA degradation

Tetrabromobisphenol-A (TBBPA), a typical brominated flame retardant, leaked from commercial products into the environments has attracted people's attention around the world. Ochrobactrum sp. T capable of degradation and mineralization of TBBPA was isolated in our early work. In this study, the identification of TBBPA-degrading gene from the strain was further carried out by combining whole-genome sequencing with gene cloning and expression procedures. In total, 3877 open reading frames were found within 3.9 Mb genome and seven of them were identified as dehalogenating-relating genes. One gene with a significant ability to degrade TBBPA was designated as tbbpaA. Sequence alignments analysis showed that it shared 100% identity with haloacid dehalogenases. Furthermore, tbbpaA gene was cloned and expressed into E. coli to achieve a constructed strain. Like the original strain, the constructed strain could degrade TBBPA (6 mg L^-1) with 78% of debromination efficiency and 37.8% mineralization efficiency within 96 h. Gene expression study revealed that tbbpaA was up-regulated in the presence of TBBPA. Overall, we report the identification of a functional TBBPA-degrading gene in an aerobe, which can deepen the knowledge of enhancing TBBPA removal by Strain T at the genetic level and facilitate in situ TBBPA bioremediation.

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.

Reconstruction of microbial community structures as evidences for soil redox coupled reductive dechlorination of PCP in a mangrove soil

The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics. The phylum Bacteroidetes predominated during the earlier PCP dechlorination period and then was progressively replaced by Proteobacteria and Firmicutes groups when PCP was mostly transformed into 2,3,4,5-TeCP and 3,4,5-TCP. Heatmap and hierarchical cluster analysis revealed the Clostridium-like, Geobacter-like and Dehalococcoides-like organisms enriched concurrently during PCP reductive dechlorination processes. The relative abundance changes of the redox-active microorganisms, together with their relevance to the corresponding biogeochemical redox processes, showed that PCP dechlorination, Fe(III) and SO₄^2- reduction, as well as methanogenesis were coupled terminal electron accepting processes. The combined analysis of the microbial function, the affinity for substrates (H₂ and acetate) and the sensitivity for PCP toxicity by microorganisms might explain why electron transport chain has changed in soil biogeochemical redox process. Our study offers a comprehensive description of the impact of PCP on the soil microbial community structures, which could be very useful for understanding the regulation of soil nutrient and energy transfer during biogeochemical cycling processes in soils with significant inputs of exogenous pollutants.

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.

Acclimation of 2-chlorophenol Biodegrading Activated Sludge and Microbial Community Analysis

Taking glucose as co-substrate, the activated sludge which could effectively biodegrade 2-chlorophenol (2-CP) of 40 mg/L　was successfully domesticated after acclimation for 49 days in sequencing batch reactors. High-throughput sequencing (HTS) analysis revealed that the community richness initially increased for 5 days and then decreased after another 20 days with the increase of 2-CP. The original sludge obtained from water resource recovery facility had the highest diversity. At the beginning of acclimation, the community diversity decreased. With the acclimation going on, both richness and diversity of community increased, but decreased significantly when the concentration of 2-CP was increased to 40 mg/L. Saccharibacteria_norank, Bacillus, Saprospiraceae_uncultured and Lactococcus were the dominant bacteria detected in this study. Bacillus and Pseudomonas were the main chlorophenol-degrading bacteria. WCHB1-60_norank, Tetrasphaera, Comamonadaceae_unclassified and Haliangium had lower tolerance to 2-CP. Higher bacterial tolerance to CPs does not mean higher degrading capability. The degradation of CPs was not positively correlated with the abundance of known 2-CP degrading bacteria detected in this study.

Electrocatalytic dechlorination of 2,3,5-trichlorophenol on palladium/carbon nanotubes-nafion film/titanium mesh electrode

Palladium/carbon nanotubes-nafion film-modified titanium mesh electrode (Pd/CNTs-nafion film/Ti electrode) was prepared and used for catalytic dechlorination of 2,3,5-trichlorophenol (2,3,5-TCP). The influences of factors, such as Pd²⁺ concentration, plating solution pH, and electrodeposition time and current, on the preparation of the electrode were studied by cyclic voltammetry (CV) to establish the optimal electrode preparation conditions. Additionally, the CV results highlighted that the addition of the CNTs-nafion film could enhance the electrochemical performance of the electrode. The Pd/CNTs-nafion film/Ti electrode was characterized by field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), and inductively coupled plasma-atomic emission spectrometry (ICP-AES). The electrode exhibited good stability and high catalytic dechlorination capacity on 2,3,5-TCP-100 mg L^-1 2,3,5-TCP was completely dechlorinated within 100 min at a dechlorination current of 5 mA and an initial solution pH of 2.3. High-performance liquid chromatography (HPLC) was used to detect the chlorinated phenolic intermediates, and the results revealed that the final products were mainly phenol. The kinetics studies revealed that the dechlorination of 2,3,5-TCP followed two-stage mixed order kinetics, and a possible degradation pathway for 2,3,5-TCP was proposed.

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.

Spatial Abundance and Distribution of Potential Microbes and Functional Genes Associated with Anaerobic Mineralization of Pentachlorophenol in a Cylindrical Reactor

Functional interplays of microbial activity, genetic diversity and contaminant transformation are poorly understood in reactors for mineralizing halogenated aromatics anaerobically. Here, we investigated abundance and distribution of potential microbes and functional genes associated with pentachlorophenol (PCP) anaerobic mineralization in a continuous-flow cylindrical reactor (15 cm in length). PCP dechlorination and the metabolite (phenol) were observed at segments 0–8 cm from inlet, where key microbes, including potential reductive dechlorinators (Dehalobacter, Sulfurospirillum, Desulfitobacterium and Desulfovibrio spp.) and phenol degraders (Cryptanaerobacter and Syntrophus spp.), as well as putative functional genes, including putative chlorophenol reductive dehalogenase (cprA) and benzoyl-CoA reductase (bamB), were highly enriched simultaneously. Five types of putative cprAs, three types of putative bamBs and seven types of putative nitrogenase reductase (nifHs) were determined, with their copy numbers decreased gradually from inlet to outlet. Distribution of chemicals, bacteria and putative genes confirmed PCP dechlorination and phenol degradation accomplished in segments 0–5 cm and 0–8 cm, respectively, contributing to a high PCP mineralization rate of 3.86 μM d⁻¹. Through long-term incubation, dechlorination, phenol degradation and nitrogen fixation bacteria coexisted and functioned simultaneously near inlet (0–8 cm), verified the feasibility of anaerobic mineralization of halogenated aromatics in the compact reactor containing multiple functional microbes.

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.

Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans-Dichloroethene Reductive Dehalogenase, TdrA

The Dehalogenimonas population in a dechlorinating enrichment culture referred to as WBC-2 was previously shown to be responsible for trans-dichloroethene (tDCE) hydrogenolysis to vinyl chloride (VC). In this study, blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzymatic assays and protein identification using liquid chromatography coupled with mass spectrometry (LC-MS/MS) led to the functional characterization of a novel dehalogenase, TdrA. This new reductive dehalogenase (RDase) catalyzes the dechlorination of tDCE to VC. A metagenome of the WBC-2 culture was sequenced, and a complete Dehalogenimonas genome, only the second Dehalogenimonas genome to become publicly available, was closed. The tdrA dehalogenase found within the Dehalogenimonas genome appears to be on a genomic island similar to genomic islands found in Dehalococcoides. TdrA itself is most similar to TceA from Dehalococcoides sp. strain FL2 with 76.4% amino acid pairwise identity. It is likely that the horizontal transfer of rdhA genes is not only a feature of Dehalococcoides but also a feature of other Dehalococcoidia, including Dehalogenimonas. A set of primers was developed to track tdrA in WBC-2 subcultures maintained on different electron acceptors. This newest dehalogenase is an addition to the short list of functionally defined RDases sharing the usual characteristic motifs (including an AB operon, a TAT export sequence, two iron-sulfur clusters, and a corrinoid binding domain), substrate flexibility, and evidence for horizontal gene transfer within the Dehalococcoidia.