Organohalide-respiring Bacteria Research Articles

Biocathode regulates enrofloxacin degradation by coupling with different co-metabolism conditions

In this study, biocathode system coupled with different co-metabolism conditions (NaAc, glucose and NaHCO3) were developed to degrade quinolones enrofloxacin (ENR) due to its poorly metabolization, easily accumulation and potential toxicity. Simultaneously, ENR reduction kinetic rate constant in NaAc-fed, glucose-fed and NaHCO3-fed biocathodes, and sole biocathode were increased by 343.62%, 320.46%, 189.19% and 130.88% when compared with that of abiotic cathode when the operational time and ENR concentration were set to 48 h and 25 mg/L. In addition, transformation pathways of ENR revealed pathway II were dominantly occurred in NaAc- and glucose-fed biocathode while pathway IV acting as key metabolic process were shown in NaHCO3-fed biocathode. Moreover, 16S rRNA high-throughput sequencing analysis indicated that biocathodic communities were sensitive to switch-over of carbon source, namely Delftia and Bosea as organohalide-respiring bacteria (OHRB) were abundant in NaAc- and glucose-fed biocathodes while Mesotoga and Syntrophorhabdus that responsible for benzoyl-CoA metabolic process were enriched in NaHCO3-fed biocathode. Overall, this study could unravel the underlying relationship between biocathode degradation pattern of ENR and different co-metabolism conditions, and further offer valuable scientific information on treating refractory quinolones antibiotics via green bioelectrochemical method.

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

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

Insight into microbial degradation of hexabromocyclododecane (HBCD) in lake sediments under different hydrodynamic conditions

Hexabromocyclododecane (HBCD), an emerging persistent organic pollutant, has been widely detected in aquatic ecosystems with various hydrodynamic conditions, however, the effects of hydrodynamic changes on microbial degradation of HBCD in aquatic sediment remains unclear. Here, we conducted an annular flume experiment to characterize variation in HBCD removal from contaminated sediment under three hydrodynamic conditions with different flow velocities, as well as clarify the underlying microbial mechanisms. We detected significant HBCD removal and bromine ion generation in all contaminated sediments, and microbial reduction debromination was an important process for HBCD removal. At the end of the 49-day experiment, both HBCD removal percentage and the bromine ion concentration were significantly lower under dynamic water condition with higher sediment redox potential, compared with static water conditions. The dynamic water conditions resulted a relatively high sediment redox potential and decreased the iron reduction rate and the abundance of organohalide-respiring bacteria (OHRB) in the genera Geobatcer, Dehalogenimonas, Dehalobacter, and Dehalococcoide, which reduced the microbial degradation of HBCD in contaminated sediments. The community composition of both total bacteria and OHRB also differed significantly among hydrodynamic conditions. Some bacterial groups with HBCD degradation abilities such as Pseudomonas and Sulfuricurvum were less abundant under dynamic water conditions, and the HBCD degradation efficiencies were lower. These findings enhance our understanding of the bioremediation potential of HBCD-contaminated sediments in different hydrodynamic areas.

Geobacter sp. Strain IAE Dihaloeliminates 1,1,2-Trichloroethane and 1,2-Dichloroethane.

Chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XRDCA and XRTCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XRTCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XRDCA and XRTCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XRTCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 × 107 and 1.18 ± 0.14 × 107 cells per μmol Cl- released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.

Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains.

ABSTRACTSulfurospirillum species strains are frequently detected in various pristine and contaminated environments and participate in carbon, sulfur, nitrogen, and halogen elements cycling. Recently we obtained the complete genome sequences of two newly isolated Sulfurospirillum strains, ACSDCE and ACSTCE, capable of dechlorinating tetrachloroethene to cis-1,2-dichloroethene and trichloroethene under low-pH conditions, but a detailed analysis of these two genomes in reference to other Sulfurospirillum genomes for an improved understanding of Sulfurospirillum evolution and ecophysiology has not been accomplished. Here, we performed phylogenetic and pangenome analyses with 12 completed Sulfurospirillum genomes, including those of strain ACSTCE and strain ACSDCE, to unravel the evolutionary and metabolic potentials in the genus Sulfurospirillum. Based on 16S rRNA gene and whole-genome phylogenies, strains ACSTCE, ACSDCE, and JPD-1 could be clustered into a single species, proposed as “Candidatus Sulfurospirillum acididehalogenans.” TimeTree analysis suggested that the organohalide-respiring (OHR) Sulfurospirillum might acquire the ability to use chlorinated electron acceptors later than other energy conservation processes. Nevertheless, the ambiguity of the phylogenetic relations among Sulfurospirillum strains complicated the interpretation of acquisition and loss of metabolic traits. Interestingly, all OHR Sulfurospirillum genomes except the ones of Sulfurospirillum multivorans strains harbor a well-aligned and conserved region comprising the genetic components required for the organohalide respiration chain. Pangenome results further revealed that a total of 34,620 gene products, annotated from the 12 Sulfurospirillum genomes, can be classified into 4,118 homolog families and 2,075 singleton families. Various Sulfurospirillum species strains have conserved metabolisms as well as individual enzymes and biosynthesis capabilities. For instance, only the OHR Sulfurospirillum species strains possess the quinone-dependent pyruvate dehydrogenase (PoxB) gene, and only “Ca. Sulfurospirillum acididehalogenans” strains harbor urea transporter and urease genes. The plasmids found in strain ACSTCE and strain ACSDCE feature genes coding for type II toxin-antitoxin systems and transposases and are promising tools for the development of robust gene editing tools for Sulfurospirillum.IMPORTANCE Organohalide-respiring bacteria (OHRB) play critical roles in the detoxification of chlorinated pollutants and bioremediation of subsurface environments (e.g., groundwater and sediment) impacted by anthropogenic chlorinated solvents. The majority of known OHRB cannot perform reductive dechlorination below neutral pH, hampering the applications of OHRB for remediating acidified groundwater due to fermentation and reductive dechlorination. Previously we isolated two Sulfurospirillum strains, ACSTCE and ACSDCE, capable of dechlorinating tetrachloroethene under acidic conditions (e.g., pH 5.5), and obtained the complete genomes of both strains. Notably, two plasmid sequences were identified in the genomes of strain ACSTCE and strain ACSDCE that may be conducive to unraveling the genetic modification mechanisms in the genus Sulfurospirillum. Our findings improve the current understanding of Sulfurospirillum species strains regarding their biogeographic evolution, genome dynamics, and functional diversity. This study has applied values for the bioremediation of toxic and persistent organohalide pollutants in low-pH environments.

Soil microorganisms facilitated the electrode-driven trichloroethene dechlorination to ethene by Dehalococcoides species in a bioelectrochemical system

Bioelectrochemical dechlorination using organohalide-respiring bacteria (ORBs) is a promising technique for remediating contaminated groundwater. Generally, a longer enrichment period is required for selecting the ORB consortia to achieve bioelectrochemical dechlorination. However, the full dechloriantion is difficult to be achieved due to the absence of functional species (e.g. Dehalococcoides) in previously used enrich cultures. To overcome these challenges, bioelectrochemical dechlorination using a culture enriched with the pre-augmented Dehalococcoides was performed for the first time in this study. A two-chamber bioelectrochemical system (BES) inoculated with a pure Dehalococcoides culture and paddy soil with an applied voltage of −0.3 V (versus a standard hydrogen electrode) as the sole electron donor was used to achieve dechlorination. The ethene formation rate was 10–100 times higher than that in previous studies, indicating that inoculating the system with a pure Dehalococcoides culture and soil microorganisms gave effective full dechlorination performance. Microbial community analysis and bioelectrochemical analysis indicated that Desulfosporosinus species may have facilitated dechlorination through syntrophic interactions with Dehalococcoides. The results indicated that adding Dehalococcoides cells before operating a bioelectrochemical system is an effective way of achieving full dechlorination.

Anaerobic Microbial Dechlorination of 6:2 Chlorinated Polyfluorooctane Ether Sulfonate and the Underlying Mechanisms.

The microbial transformation potential of 6:2 chlorinated polyfluorooctane ether sulfonate (6:2 Cl-PFESA) was explored in anaerobic microbial systems. Microbial communities from anaerobic wastewater sludge, an anaerobic digester, and anaerobic dechlorinating cultures enriched from aquifer materials reductively dechlorinated 6:2 Cl-PFESA to 6:2 hydrogen-substituted polyfluorooctane ether sulfonate (6:2 H-PFESA), which was identified as the sole metabolite by non-target analysis. Rapid and complete reductive dechlorination of 6:2 Cl-PFESA was achieved by the anaerobic dechlorinating cultures. The microbial community of the anaerobic dechlorinating cultures was impacted by 6:2 Cl-PFESA exposure. Organohalide-respiring bacteria originally present in the anaerobic dechlorinating cultures, including Geobacter, Dehalobacter, and Dehalococcoides, decreased in relative abundance over time. As the relative abundance of organohalide-respiring bacteria decreased, the rates of 6:2 Cl-PFESA dechlorination decreased, suggesting that the most likely mechanism for reductive dechlorination of 6:2 Cl-PFESA was co-metabolism rather than organohalide respiration. Reductive defluorination of 6:2 Cl-PFESA was not observed. Furthermore, 6:2 H-PFESA exhibited 5.5 times lower sorption affinity to the suspended biosolids than 6:2 Cl-PFESA, with the prospect of increased mobility in the environment. These results show the susceptibility of 6:2 Cl-PFESA to microbially mediated reductive dechlorination and the likely persistence of the product, 6:2 H-PFESA, in anaerobic environments.

Presence of bacteria capable of PCB biotransformation in stormwater bioretention cells.

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

Microbiome composition resulting from different substrates influences trichloroethene dechlorination performance

Hydrogen-releasing substrates can stimulate the reductive dechlorination of trichloroethene (TCE) mediated by organohalide-respiring bacteria (OHRB) at contaminated sites. However, how the substrate affects microbiome assembly and the accompanying influences on the growth of OHRB and reductive TCE dechlorination remains unclear. We evaluated the effects of microbial community structures and potential functions on the reductive dechlorination of TCE in three anaerobic reactors with acetate, soybean oil, or molasses as the substrate and no cobalamin or amino acid supplementation. The molasses-fed reactor exhibited superior performance and dechlorination of TCE loadings to ethene, and the oil-fed reactor exhibited a high growth rate of the key OHRB, Dehalococcoides. This finding suggests an effect of the substrate on reductive dechlorination and the growth of Dehalococcoides. The three reactors developed distinct microbial community structures and the predicted metagenomes were distinguished on the basis of vitamin and amino acid metabolisms as well as fermentation pathways. In addition to the diversified hydrogen-producing pathways, the molasses-induced microbiome exhibited high potential to synthesize the cobalamin, which may account for its high Dehalococcoides activity and thus effective dechlorination performance. The substrate dependence of microbiomes may provide insight into strategies of exogenous amino acid supplementation to benefit Dehalococcoides growth. This study adds novel insight into the interplay of hydrogen-releasing substrates and OHRB. The results may contribute to the development of tailored and cost-effective management for the reductive dechlorination of chlorinated solvents in bioremediation.

Advances of using Dehalogenimonas in anaerobic degradation of chlorinated compounds and bioremediation of contaminated sites

The genus Dehalogenimonas (Dhgm) is a recently discovered taxonomic group within the class Dehalococcoidia of the phylum Chloroflexi. To date, Dhgm consists of three formally described species including Dehalogenimonas lykanthroporepellens, Dehalogenimonas alkenigignens and Dehalogenimonas formicexedens. All isolates of these three Dhgm species are obligate organohalide-respiring bacteria. They use hydrogen and formate as electron donors and chlorinated ethanes (e.g., 1,2,3-trichloropropane, 1,2-dichloropropane, 1,2-dichloroethane) as electron acceptors in energy-conserving reductive dechlorination reaction. Chlorinated ethanes are common groundwater contaminants in China. The unique metabolic capacities of Dhgm strains implicate it may play important roles in site remediation. The recently reported Dhgm sp. strain WBC-2 and 'Candidatus Dehalogenimonas etheniformans' strain GP are capable of dechlorinating certain chlorinated ethenes. More importantly, strain GP can completely detoxify the carcinogenic vinyl chloride (VC) to ethene. These findings expand the diversity of microorganisms involved in the respiratory VC reductive dechlorination and improve the understanding of Dhgm's ecological functions. Here, we summarize the advances in physiological and biochemical characteristics, ecological functions and genomic features of Dhgm, with the aim to develop effective and sustainable strategies to facilitate the bioremediation of chlorinated compounds contaminated sites.

Effectiveness of Permeable Reactive Bio-Barriers for Bioremediation of an Organohalide-Polluted Aquifer by Natural-Occurring Microbial Community

In this study, a bioremediation approach was evaluated for the decontamination of an aquifer affected by the release of organohalides by an industrial landfill. After preliminary physicochemical and microbiological characterization of the landfill groundwater, the stimulation of natural organohalide respiration by the addition of a reducing substrate (i.e., molasse) was tested both at microcosm and at field scales, by the placement of an anaerobic permeable reactive bio-barrier. Illumina sequencing of cDNA 16S rRNA gene revealed that organohalide-respiring bacteria of genera Geobacter, Sulfurospirillum, Dehalococcoides, Clostridium and Shewanella were present within the aquifer microbial community, along with fermentative Firmicutes and Parvarchaeota. Microcosm experiments confirmed the presence of an active natural attenuation, which was boosted by the addition of the reducing substrate. Field tests showed that the bio-barrier decreased the concentration of chloroethenes at a rate of 23.74 kg d−1. Monitoring of organohalide respiration biomarkers by qPCR and Illumina sequencing revealed that native microbial populations were involved in the dechlorination process, although their specific role still needs to be clarified. The accumulation of lower-chloroethenes suggested the need of future improvement of the present approach by supporting bacterial vinyl-chloride oxidation, to achieve a complete degradation of chloroethenes.

Acceleration of polychlorinated biphenyls remediation in soil via sewage sludge amendment

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

Effects of iron-carbon materials on microbial-catalyzed reductive dechlorination of polychlorinated biphenyls in Taihu Lake sediment microcosms: Enhanced chlorine removal, detoxification and shifts of microbial community

Nano zero-valent iron particles (nZVI, 0.09 wt%), micro zero-valent iron particles (mZVI, 0.09 wt%), granular activated carbon (GAC, 3.03 wt%), GAC supported nZVI (nZVI/GAC, 3.12 wt%) and nZVI&GAC (nZVI 0.09 wt%, GAC 3.03 wt%) were evaluated for their effects on polychlorinated biphenyls (PCBs) anaerobic reductive dechlorination, detoxification, as well as microbial community structure in Taihu Lake (China) sediment microcosms. The results showed that all of these five materials could stimulate PCBs reductive dechlorination, especially for dioxin-like PCB congeners, and nZVI&GAC had the best removal effect on PCBs. The reduction of total PCBs increased from 13.5% to 33.2%. H2 generated by zero-valent iron corrosion was utilized by organohalide-respiring bacteria (OHRB) to enhance the dechlorination of PCBs predominantly via meta chlorine removal in the short term. The addition of ZVI had little impact on the total bacterial abundance and the microbial community structure. The adsorption of GAC and potential bioremediation properties of attached biofilm could promote the long-term removal of PCBs. GAC, nZVI/GAC, nZVI&GAC had different influences on the microbial structure. These findings provide insights into the biostimulation technique for in situ remediations of PCBs contaminated sediments.

Substrate-dependent competition and cooperation relationships between Geobacter and Dehalococcoides for their organohalide respiration

Obligate and non-obligate organohalide-respiring bacteria (OHRB) play central roles in the geochemical cycling and environmental bioremediation of organohalides. Their coexistence and interactions may provide functional redundancy and community stability to assure organohalide respiration efficiency but, at the same time, complicate isolation and characterization of specific OHRB. Here, we employed a growth rate/yield tradeoff strategy to enrich and isolate a rare non-obligate tetrachloroethene (PCE)-respiring Geobacter from a Dehalococcoides-predominant microcosm, providing experimental evidence for the rate/yield tradeoff theory in population selection. Surprisingly, further physiological and genomic characterizations, together with co-culture experiments, revealed three unique interactions (i.e., free competition, conditional competition and syntrophic cooperation) between Geobacter and Dehalococcoides for their respiration of PCE and polychlorinated biphenyls (PCBs), depending on both the feeding electron donors (acetate/H2 vs. propionate) and electron acceptors (PCE vs. PCBs). This study provides the first insight into substrate-dependent interactions between obligate and non-obligate OHRB, as well as a new strategy to isolate fastidious microorganisms, for better understanding of the geochemical cycling and bioremediation of organohalides.

Enhanced dechlorination of 1,2-dichloropropane to propene in a bioelectrochemical system mediated by Dehalogenimonas

Bioelectrochemical systems (BES) are promising technologies to enhance the growth of organohalide-respiring bacteria and to treat chlorinated aliphatic hydrocarbons. In this study, two carbon-based cathodic electrode materials, a graphite brush and a carbon cloth, were used as hydrogen suppliers to couple growth of Dehalogenimonas and dechlorination of 1,2-DCP to nontoxic propene in the cathode vessel. The BES with graphite brush electrode consumed ~4000 µM 1,2-DCP during 110 days and exhibited a degradation rate 5.6-fold higher than the maximum value obtained with the carbon cloth electrode, with a cathode potential set at −0.7 V. Quantitative PCR confirmed that Dehalogenimonas gene copies increased by two orders of magnitude in the graphite brush BES, with an average yield of 1.2·108±5·107 cells per µmol of 1,2-DCP degraded. The use of a pulsed voltage operation (cathode potential set at −0.6 V for 16 h and −1.1 V for 8 h) increased the coulombic efficiency and degradation of 1,2-DCP when compared with a continuous voltage operation of −1.1 V. Bacterial cell aggregates were observed in the surface of the graphite brush electrodes by electron scanning microscopy, suggesting biofilm formation. This study expands the range of chlorinated compounds degradable and organohalide-respiring bacteria capable of growing in BES.

2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples

2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D’s high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0—40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.

Potential Role of Methanogens in Microbial Reductive Dechlorination of Organic Chlorinated Pollutants In Situ.

Previous studies often attribute microbial reductive dechlorination to organohalide-respiring bacteria (OHRB) or cometabolic dechlorination bacteria (CORB). Even though methanogenesis frequently occurs during dechlorination of organic chlorinated pollutants (OCPs) in situ, the underestimated effect of methanogens and their interactions with dechlorinators remains unknown. We investigated the association between dechlorination and methanogenesis, as well as the performance of methanogens involved in reductive dechlorination, through the use of meta-analysis, incubation experiment, untargeted metabolomic analysis, and thermodynamic modeling approaches. The meta-analysis indicated that methanogenesis is largely synchronously associated with OCP dechlorination, that OHRB are not the sole degradation engineers that maintain OCP bioremediation, and that methanogens are fundamentally needed to sustain microenvironment functional balance. Laboratory results further confirmed that Methanosarcina barkeri (M. barkeri) promotes the dechlorination of γ-hexachlorocyclohexane (γ-HCH). Untargeted metabolomic analysis revealed that the application of γ-HCH upregulated the metabolic functioning of chlorocyclohexane and chlorobenzene degradation in M. barkeri, further confirming that M. barkeri potentially possesses an auxiliary dechlorination function. Finally, quantum analysis based on density functional theory (DFT) indicated that the methanogenic coenzyme F430 significantly reduces the activation barrier to dechlorination. Collectively, this work suggests that methanogens are highly involved in microbial reductive dechlorination at OCP-contaminated sites and may even directly favor OCP degradation.

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

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

Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils.

Recent work revealed an active biological chlorine cycle in coastal Arctic tundra of northern Alaska. This raised the question of whether chlorine cycling was restricted to coastal areas or if these processes extended to inland tundra. The anaerobic process of organohalide respiration, carried out by specialized bacteria like Dehalococcoides, consumes hydrogen gas and acetate using halogenated organic compounds as terminal electron acceptors, potentially competing with methanogens that produce the greenhouse gas methane. We measured microbial community composition and soil chemistry along an ∼262-km coastal-inland transect to test for the potential of organohalide respiration across the Arctic Coastal Plain and studied the microbial community associated with Dehalococcoides to explore the ecology of this group and its potential to impact C cycling in the Arctic. Concentrations of brominated organic compounds declined sharply with distance from the coast, but the decrease in organic chlorine pools was more subtle. The relative abundances of Dehalococcoides were similar across the transect, except for being lower at the most inland site. Dehalococcoides correlated with other strictly anaerobic genera, plus some facultative ones, that had the genetic potential to provide essential resources (hydrogen, acetate, corrinoids, or organic chlorine). This community included iron reducers, sulfate reducers, syntrophic bacteria, acetogens, and methanogens, some of which might also compete with Dehalococcoides for hydrogen and acetate. Throughout the Arctic Coastal Plain, Dehalococcoides is associated with the dominant anaerobes that control fluxes of hydrogen, acetate, methane, and carbon dioxide. Depending on seasonal electron acceptor availability, organohalide-respiring bacteria could impact carbon cycling in Arctic wet tundra soils.IMPORTANCE Once considered relevant only in contaminated sites, it is now recognized that biological chlorine cycling is widespread in natural environments. However, linkages between chlorine cycling and other ecosystem processes are not well established. Species in the genus Dehalococcoides are highly specialized, using hydrogen, acetate, vitamin B12-like compounds, and organic chlorine produced by the surrounding community. We studied which neighbors might produce these essential resources for Dehalococcoides species. We found that Dehalococcoides species are ubiquitous across the Arctic Coastal Plain and are closely associated with a network of microbes that produce or consume hydrogen or acetate, including the most abundant anaerobic bacteria and methanogenic archaea. We also found organic chlorine and microbes that can produce these compounds throughout the study area. Therefore, Dehalococcoides could control the balance between carbon dioxide and methane (a more potent greenhouse gas) when suitable organic chlorine compounds are available to drive hydrogen and acetate uptake.

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

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