Isolation of novel bacteria within theChloroflexicapable of reductive dechlorination of 1,2,3-trichloropropane

Sequential Reductive Dechlorination of Triclosan by Sediment Microbiota Harboring Organohalide-Respiring Dehalococcoidia

Aquatic ecosystems represent a prominent reservoir of xenobiotic compounds, including triclosan (TCS), a broad-spectrum biocide extensively used in pharmaceuticals and personal care products. As a biogeochemical hotspot, the potential of aquatic sediments for the degradation of TCS remains largely unexplored. Here, we demonstrated anaerobic biotransformation of TCS in a batch microcosm established with freshwater sediment. The initial 43.4 ± 2.2 μM TCS was completely dechlorinated to diclosan, followed by subsequent conversion to 5-chloro-2-phenoxyphenol, a monochlorinated TCS (MCS) congener. Analyses of community profile and population dynamics revealed substrate-specific, temporal-growth of Dehalococcoides and Dehalogenimonas, which are organohalide-respiring bacteria (OHRB) affiliated with class Dehalococcoidia. Dehalococcoides growth was linked to the formation of diclosan but not MCS, yielding 3.6 ± 0.4 × 107 cells per μmol chloride released. A significant increase in Dehalogenimonas cells, from 1.5 ± 0.4 × 104 to 1.5 ± 0.3 × 106 mL-1, only occurred during the reductive dechlorination of diclosan to MCS. Dehalococcoidia OHRB gradually disappeared following consecutive transfers, likely due to the removal of sediment materials with strong adsorption capacity that could alleviate TCS's antimicrobial toxicity. Consequently, a solid-free, functionally stable TCS-dechlorinating consortium was not obtained. Our results provide insights into the microbial determinants controlling the environmental fate of TCS.

Developing a microbial community structure index (MCSI) as an approach to evaluate and optimize bioremediation performance

Much attention is placed on organohalide-respiring bacteria (OHRB), such as Dehalococcoides, during the design and performance monitoring of chlorinated solvent bioremediation systems. However, many OHRB cannot function effectively without the support of a diverse group of other microbial community members (MCMs), who play key roles fermenting organic matter into more readily useable electron donors, producing corrinoids such as vitamin B12, or facilitating other important metabolic processes or biochemical reactions. While it is known that certain MCMs support dechlorination, a metric considering their contribution to bioremediation performance has yet to be proposed. Advances in molecular biology tools offer an opportunity to better understand the presence and activity of specific microbes, and their relation to bioremediation performance. In this paper, we test the hypothesis that a specific microbial consortium identified within 16S ribosomal ribonucleic acid (rRNA) gene next generation sequencing (NGS) data can be predictive of contaminant degradation rates. Field-based data from multiple contaminated sites indicate that increasing relative abundance of specific MCMs correlates with increasing first-order degradation rates. Based on these results, we present a framework for computing a simplified metric using NGS data, the Microbial Community Structure Index, to evaluate the adequacy of the microbial ecosystem during assessment of bioremediation performance.

Role of Nitrogenous Functional Group Identity in Accelerating 1,2,3-Trichloropropane Degradation by Pyrogenic Carbonaceous Matter (PCM) and Sulfide Using PCM-like Polymers

Groundwater contamination by 1,2,3-trichloropropane (TCP) poses a unique challenge due to its human toxicity and recalcitrance to degradation. Previous work suggests that nitrogenous functional groups of pyrogenic carbonaceous matter (PCM), such as biochar, are important in accelerating contaminant dechlorination by sulfide. However, the reaction mechanism is unclear due, in part, to PCM's structural complexity. Herein, PCM-like polymers (PLPs) with controlled placement of nitrogenous functional groups [i.e., quaternary ammonium (QA), pyridine, and pyridinium cations (py+)] were employed as model systems to investigate PCM-enhanced TCP degradation by sulfide. Our results suggest that both PLP-QA and PLP-py+ were highly effective in facilitating TCP dechlorination by sulfide with half-lives of 16.91 ± 1.17 and 0.98 ± 0.15 days, respectively, and the reactivity increased with surface nitrogenous group density. A two-step process was proposed for TCP dechlorination, which is initiated by reductive ß-elimination, followed by nucleophilic substitution by surface-bound sulfur nucleophiles. The TCP degradation kinetics were not significantly affected by cocontaminants (i.e., 1,1,1-trichloroethane or trichloroethylene), but were slowed by natural organic matter. Our results show that PLPs containing certain nitrogen functional groups can facilitate the rapid and complete degradation of TCP by sulfide, suggesting that similarly functionalized PCM might form the basis for a novel process for the remediation of TCP-contaminated groundwater.

Dual C-Cl isotope fractionation offers potential to assess biodegradation of 1,2-dichloropropane and 1,2,3-trichloropropane by Dehalogenimonas cultures

1,2-dichloropropane (1,2-DCP) and 1,2,3-trichloropropane (1,2,3-TCP) are hazardous chemicals frequently detected in groundwater near agricultural zones due to their historical use in chlorinated fumigant formulations. In this study, we show that the organohalide-respiring bacterium Dehalogenimonas alkenigignens strain BRE15 M can grow during the dihaloelimination of 1,2-DCP and 1,2,3-TCP to propene and allyl chloride, respectively. Our work also provides the first application of dual isotope approach to investigate the anaerobic reductive dechlorination of 1,2-DCP and 1,2,3-TCP. Stable carbon and chlorine isotope fractionation values for 1,2-DCP (ƐC = -13.6 ± 1.4 ‰ and ƐCl = -27.4 ± 5.2 ‰) and 1,2,3-TCP (ƐC = -3.8 ± 0.6 ‰ and ƐCl = -0.8 ± 0.5 ‰) were obtained resulting in distinct dual isotope slopes (Λ12DCP = 0.5 ± 0.1, Λ123TCP = 4 ± 2). However direct comparison of ΛC-Cl among different substrates is not possible and investigation of the C and Cl apparent kinetic isotope effects lead to the hypothesis that concerted dichloroelimination mechanism is more likely for both compounds. In fact, whole cell activity assays using cells suspensions of the Dehalogenimonas-containing culture grown with 1,2-DCP and methyl viologen as electron donor suggest that the same set of reductive dehalogenases was involved in the transformation of 1,2-DCP and 1,2,3-TCP. This study opens the door to the application of isotope techniques for evaluating biodegradation of 1,2-DCP and 1,2,3-TCP, which often co-occur in groundwaters near agricultural fields.

Abiotic natural attenuation of 1,2,3-trichloropropane by natural magnetite under O2 perturbation

1,2,3-Trichloropropane (TCP) is an emerging groundwater pollutant, but there is a lack of reported studies on the abiotic natural attenuation of TCP by iron minerals. Furthermore, perturbation by O2 is common in the shallow subsurface by both natural and artificial processes. In this study, natural magnetite was selected as the reactive iron mineral to investigate its role in the degradation of TCP under O2 perturbation. The results indicated that the mineral structural Fe(II) on magnetite reacted with dissolved oxygen to generate O2-· and HO·. Both O2-· and HO· contributed to TCP degradation, with O2-· playing a more important role. After 56 days of reaction, 66.7% of TCP was completely dechlorinated. This study revealed that higher magnetite concentrations, smaller magnetite particle sizes, and lower initial TCP concentrations favored TCP degradation. The presence of <10 mg/L natural organic matter (NOM) did not affect TCP degradation. These findings significantly advance our understanding of the abiotic natural attenuation mechanisms facilitated by iron minerals under O2 perturbation, providing crucial insights for the study of natural attenuation.

Degradation of Atrazine by an Anaerobic Microbial Consortium Enriched from Soil of an Herbicide-Manufacturing Plant

Atrazine is an important herbicide that has been widely used for weed control in recent decades. However, with the extensive use of atrazine, its residue seriously pollutes the environment. Therefore, the microbial degradation and detoxification of atrazine have received extensive attention. To date, the aerobic degradation pathway of atrazine has been well studied; however, little is known about its anaerobic degradation in the environment. In this study, an anaerobic microbial consortium capable of efficiently degrading atrazine was enriched from soil collected from an herbicide-manufacturing plant. Six metabolites including hydroxyatrazine, deethylatrazine, N-isopropylammelide, deisopropylatrazine, cyanuric acid, and the novel metabolite 4-ethylamino-6-isopropylamino-1,3,5-triazine (EIPAT) were identified, and two putative anaerobic degradation pathways of atrazine were proposed: a hydrolytic dechlorination pathway is similar to that seen in aerobic degradation, and a novel pathway initiated by reductive dechlorination. During enrichment, Denitratisoma, Thiobacillus, Rhodocyclaceae_unclassified, Azospirillum, and Anaerolinea abundances significantly increased, dominating the enriched consortium, indicating that they may be involved in atrazine degradation. These findings provide valuable evidence for elucidating the anaerobic catabolism of atrazine and facilitating anaerobic remediation of residual atrazine pollution.

A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide

IMPORTANCE

Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.

Effect of weak electrical stimulation on m-dichlorobenzene biodegradation in biotrickling filters: Insights from performance and microbial community analysis

The microbial electrolysis cell coupled with the biotrickling filters (MEC-BTF) was developed for enhancing the biodegradation of gaseous m-dichlorobenzene (m-DCB) through weak electrical stimulation. The maximum removal efficiency and elimination capacity in MEC-BTF were 1.48 and 1.65 times higher than those in open-circuit BTF (OC-BTF), respectively. Weak electrical stimulation had a positive impact on the characteristics of the biofilm. Additionally, microbial community analysis revealed that weak electrical stimulation increased the abundance of key functional genera (e.g., Rhodanobacter and Bacillus) and genes (e.g., catA/E and E1.3.1.32), thereby accelerating reductive dechlorination and ring-opening of m-DCB. Macrogenomic sequencing further revealed that electron transfer pathway in MEC-BTF might be mediated through extracellular electroactive mediators and cytochromes.

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Intermittent Oxygen Supply Facilitates Codegradation of Trichloroethene and Toluene by Anaerobic Consortia

Biodegradation is commonly employed for remediating trichloroethene- or toluene-contaminated sites. However, remediation methods using either anaerobic or aerobic degradation are inefficient for dual pollutants. We developed an anaerobic sequencing batch reactor system with intermittent oxygen supply for the codegradation of trichloroethylene and toluene. Our results showed that oxygen inhibited anaerobic dechlorination of trichloroethene, but dechlorination rates remained comparable to that at dissolved oxygen levels of 0.2 mg/L. Intermittent oxygenation engendered reactor redox fluctuations (-146 to -475 mV) and facilitated rapid codegradation of targeting dual pollutants, with trichloroethene degradation constituting only 27.5% of the noninhibited dechlorination. Amplicon sequencing analysis revealed the predominance of Dehalogenimonas (16.0% ± 3.5%) over Dehalococcoides (0.3% ± 0.2%), with ten times higher transcriptomic activity in Dehalogenimonas. Shotgun metagenomics revealed numerous genes related to reductive dehalogenases and oxidative stress resistance in Dehalogenimonas and Dehalococcoides, as well as the enrichment of diversified facultative populations with functional genes related to trichloroethylene cometabolism and aerobic and anaerobic toluene degradation. These findings suggested that the codegradation of trichloroethylene and toluene may involve multiple biodegradation mechanisms. Overall results of this study demonstrate the effectiveness of intermittent micro-oxygenation in aiding trichloroethene-toluene degradation, suggesting the potential for the bioremediation of sites with similar organic pollutants.

Dual C-Br Isotope Fractionation Indicates Distinct Reductive Dehalogenation Mechanisms of 1,2-Dibromoethane in Dehalococcoides- and Dehalogenimonas-Containing Cultures

Brominated organic compounds such as 1,2-dibromoethane (1,2-DBA) are highly toxic groundwater contaminants. Multi-element compound-specific isotope analysis bears the potential to elucidate the biodegradation pathways of 1,2-DBA in the environment, which is crucial information to assess its fate in contaminated sites. This study investigates for the first time dual C-Br isotope fractionation during in vivo biodegradation of 1,2-DBA by two anaerobic enrichment cultures containing organohalide-respiring bacteria (i.e., either Dehalococcoides or Dehalogenimonas). Different ε_bulk^C values (-1.8 ± 0.2 and -19.2 ± 3.5‰, respectively) were obtained, whereas their respective ε_bulk^Br values were lower and similar to each other (-1.22 ± 0.08 and -1.2 ± 0.5‰), leading to distinctly different trends (Λ_C-Br = Δδ¹³C/Δδ⁸¹Br ≈ ε_bulk^C/ε_bulk^Br) in a dual C-Br isotope plot (1.4 ± 0.2 and 12 ± 4, respectively). These results suggest the occurrence of different underlying reaction mechanisms during enzymatic 1,2-DBA transformation, that is, concerted dihaloelimination and nucleophilic substitution (S_N2-reaction). The strongly pathway-dependent Λ_C-Br values illustrate the potential of this approach to elucidate the reaction mechanism of 1,2-DBA in the field and to select appropriate ε_bulk^C values for quantification of biodegradation. The results of this study provide valuable information for future biodegradation studies of 1,2-DBA in contaminated sites.

Using Compound Specific Isotope Analysis to decipher the 1,2,3-trichloropropane-to-Allyl chloride transformation by groundwater microbial communities

1,2,3-trichloropropane (TCP), a refractory contaminant, can be reductive dehalogenated to allyl chloride (AC) by microorganisms, which has been shown a potential in situ bioremediation (ISB) strategy for TCP remediation in groundwater. In practice, however, it is hard to monitor the bioreduction extent because the TCP concentrations may also be decreased by non-biodegradation processes. Compound specific isotope analysis (CSIA) can be promising in determining the extent of degradation by quantifying the isotope enrichment factors (ε) of relevant degradation mechanisms. To date, no CSIA study has been reported on TCP degradation. In this study, a novel TCP-to-AC transformation enrichment culture (dominated by Azotobacter, Parabacteroides, Fusibacter, Hydrogenophaga, Trichococcus Desulfovibrio, etc) in the absence of the already identified TCP anaerobic reductive dechlorinating microorganisms (e.g., Dehalogenimonas) was derived from a chlorinated hydrocarbon-contaminated aquifer. A TCP degradation experiment was carried out by adding yeast extract to produce hydrogen as an electron donor. The TCP-to-AC transformation was found to conform to zero-order conversion kinetics with the rate constant 11 ± 0.34 μmol L^-1 d^-1 during the main biodegradation stage. The bulk carbon isotope enrichment factor (ε_bulk) of the TCP-to-AC transformation was firstly evaluated as -5.2 ± 0.1‰. This study for the first time characterized the carbon isotope fractionations during TCP biodegradation using a novel enrichment culture, which would provide a promising tool for the incorporation of ISB for TCP removal in the future.

Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil

Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.

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

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

Complete Reductive Dechlorination of 4-Hydroxy-chlorothalonil by Dehalogenimonas Populations

Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile, TePN) is one of the most widely used fungicides all over the world. Its major environmental transformation product 4-hydroxy-chlorothalonil (4-hydroxy-2,5,6-trichloroisophthalonitrile, 4-OH-TPN) is more persistent, mobile, and toxic and is frequently detected at a higher concentration in various habitats compared to its parent compound TePN. Further microbial transformation of 4-OH-TPN has never been reported. In this study, we demonstrated that 4-OH-TPN underwent complete microbial reductive dehalogenation to 4-hydroxy-isophthalonitrile via 4-hydroxy-dichloroisophthalonitrile and 4-hydroxy-monochloroisophthalonitrile. 16S rRNA gene amplicon sequencing demonstrated that Dehalogenimonas species was enriched from 6% to 17-22% after reductive dechlorination of 77.24 μmol of 4-OH-TPN. Meanwhile, Dehalogenimonas copies increased by one order of magnitude and obtained a yield of 1.78 ± 1.47 × 10⁸ cells per μmol Cl^- released (N = 6), indicating that 4-OH-TPN served as the terminal electron acceptor for organohalide respiration of Dehalogenimonas species. A draft genome of Dehalogenimonas species was assembled through metagenomic sequencing, which harbors 30 putative reductive dehalogenase genes. Syntrophobacter, Acetobacterium, and Methanosarcina spp. were found to be the major non-dechlorinating populations in the microbial community, who might play important roles in the reductive dechlorination of 4-OH-TPN by the Dehalogenimonas species. This study first reports that Dehalogenimonas sp. can also respire on the seemingly dead-end product of TePN, paving the way to complete biotransformation of the widely present TePN and broadening the substrate spectrum of Dehalogenimonas sp. to polychlorinated hydroxy-benzonitrile.

Organohalide Respiration with Diclofenac by Dehalogenimonas

Diclofenac (DCF) is a pharmaceutically active contaminant frequently found in aquatic ecosystems. The transformation pathways and microbiology involved in the biodegradation of DCF, particularly under anoxic conditions, remain poorly understood. Here, we demonstrated microbially mediated reductive dechlorination of DCF in anaerobic enrichment culture derived from contaminated river sediment. Over 90% of the initial 76.7 ± 3.6 μM DCF was dechlorinated at a maximum rate of 1.8 ± 0.3 μM day^-1 during a 160 days' incubation. Mass spectrometric analysis confirmed that 2-(2-((2-chlorophenyl)amino)phenyl)acetic acid (2-CPA) and 2-anilinophenylacetic acid (2-APA) were formed as the monochlorinated and nonchlorinated DCF transformation products, respectively. A survey of microbial composition and Sanger sequencing revealed the enrichment and dominance of a new Dehalogenimonas population, designated as Dehalogenimonas sp. strain DCF, in the DCF-dechlorinating community. Following the stoichiometric conversion of DCF to 2-CPA (76.0 ± 2.1 μM) and 2-APA (3.7 ± 0.8 μM), strain DCF cell densities increased by 24.4 ± 4.4-fold with a growth yield of 9.0 ± 0.1 × 10⁸ cells per μmol chloride released. Our findings expand the metabolic capability in the genus Dehalogenimonas and highlight the relevant roles of organohalide-respiring bacteria for the natural attenuation of halogenated contaminants of emerging concerns (e.g., DCF).

Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review

Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.

Dehalogenation of Chlorinated Ethenes to Ethene by a Novel Isolate, "Candidatus Dehalogenimonas etheniformans"

Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, "Candidatus Dehalogenimonas etheniformans" strain GP, capable of respiratory dechlorination of VC to ethene. This bacterium couples formate and hydrogen (H₂) oxidation to the reduction of trichloro-ethene (TCE), all dichloroethene (DCE) isomers, and VC with acetate as the carbon source. Cultures that received formate and H₂ consumed the two electron donors concomitantly at similar rates. A 16S rRNA gene-targeted quantitative PCR (qPCR) assay measured growth yields of (1.2 ± 0.2) × 10⁸ and (1.9 ± 0.2) × 10⁸ cells per μmol of VC dechlorinated in cultures with H₂ or formate as electron donor, respectively. About 1.5-fold higher cell numbers were measured with qPCR targeting cerA, a single-copy gene encoding a putative VC RDase. A VC dechlorination rate of 215 ± 40 μmol L^-1 day^-1 was measured at 30°C, with about 25% of this activity occurring at 15°C. Increasing NaCl concentrations progressively impacted VC dechlorination rates, and dechlorination ceased at 15 g NaCl L^-1. During growth with TCE, all DCE isomers were intermediates. Tetrachloroethene was not dechlorinated and inhibited dechlorination of other chlorinated ethenes. Carbon monoxide formed and accumulated as a metabolic by-product in dechlorinating cultures and impacted reductive dechlorination activity. The isolation of a new Dehalogenimonas species able to effectively dechlorinate toxic chlorinated ethenes to benign ethene expands our understanding of the reductive dechlorination process, with implications for bioremediation and environmental monitoring. IMPORTANCE Chlorinated ethenes are risk drivers at many contaminated sites, and current bioremediation efforts focus on organohalide-respiring Dehalococcoides mccartyi strains to achieve detoxification. We isolated and characterized the first non-Dehalococcoides bacterium, "Candidatus Dehalogenimonas etheniformans" strain GP, capable of metabolic reductive dechlorination of TCE, all DCE isomers, and VC to environmentally benign ethene. In addition to hydrogen, the new isolate utilizes formate as electron donor for reductive dechlorination, providing opportunities for more effective electron donor delivery to the contaminated subsurface. The discovery that a broader microbial diversity can achieve detoxification of toxic chlorinated ethenes in anoxic aquifers illustrates the potential of naturally occurring microbes for biotechnological applications.

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 XR_DCA and XR_TCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XR_TCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XR_DCA and XR_TCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XR_TCA 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.

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

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

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.

Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi

Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B₁₂ (B₁₂) is provided. Strain FL2 cultures that received 50 μg L^-1 B₁₂ completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day^-1 and attained 1.64 ± 0.11 × 10⁸ cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 10⁸ cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.

Genome Sequence of "Candidatus Dehalogenimonas etheniformans" Strain GP, a Vinyl Chloride-Respiring Anaerobe

“Candidatus Dehalogenimonas etheniformans” strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.

“Candidatus Dehalogenimonas etheniformans” strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase genes.

Isolation, characterization and bioaugmentation of an acidotolerant 1,2-dichloroethane respiring Desulfitobacterium species from a low pH aquifer

A Desulfitobacterium sp. strain AusDCA of the Peptococcaceae family capable of respiring 1,2-dichloroethane (1,2-DCA) to ethene anaerobically with ethanol or hydrogen as electron donor at pH 5.0 with optimal range between pH 6.5-7.5 was isolated from an acidic aquifer near Sydney, Australia. Strain AusDCA is distant (94% nucleotide identity) from its nearest phylogenetic neighbor, D. metallireducens, and could represent a new species. Reference gene-based quantification of growth indicated a doubling time of 2 days in cultures buffered at pH 7.2, and a yield of 7.66 (± 4.0) × 106 cells µmol-1 of 1,2-DCA. A putative 1,2-DCA reductive dehalogenase was translated from a dcaAB locus and had high amino acid identity (97.3% for DcaA and 100% for DcaB) to RdhA1B1 of the 1,2-DCA respiring Dehalobacter strain WL. Proteomic analysis confirmed DcaA expression in the pure culture. Dehalogenation of 1,2-DCA (1.6 mM) was observed in batch cultures established from groundwater at pH 5.5 collected 38 days after in situ bioaugmentation but not in cultures established with groundwater collected at the same time from wells not receiving bioaugmentation. Overall, strain AusDCA can tolerate lower pH than previously characterized organohalide respiring bacteria and remained viable in groundwater at pH 5.5.

Perspectives of genetically engineered microbes for groundwater bioremediation

Biodegradation is the main process for the removal of organic compounds from the environment, but proceeds slowly for many synthetic chemicals of environmental concern. Research on microbial biodegradation pathways revealed that recalcitrance is - among other factors - caused by biochemical blockages resulting in dysfunctional catabolic routes. This has raised interest in the possibility to construct microorganisms with improved catabolic activities by genetic engineering. Although this goal has been pursued for decades, no full-scale applications have emerged. This perspective explores the lagging implementation of genetically engineered microorganisms in practical bioremediation. The major technical and scientific issues are illustrated by comparing two examples, that of 1,2-dichloroethane where successful full-scale application of pump-and-treat biotreatment processes has been achieved, and 1,2,3-trichloropropane, for which protein and genetic engineering yielded effective bacterial cultures that still await application.

Reduction of 1,2,3-trichloropropane (TCP): pathways and mechanisms from computational chemistry calculations

The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dihalocarbons, reductive dechlorination can include hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various structural and energetic factors. To better understand how these factors influence the degradation rates and products of the lesser halogenated hydrocarbons (in contrast to the widely studied per-halogenated hydrocarbons, like trichloroethylene and carbon tetrachloride), density functional theory calculations were performed to compare all of the possible pathways for reduction and elimination of 1,2,3-trichloropropane (TCP). The results showed that free energies of each species and reaction step are similar for all levels of theory, although B3LYP differed from the others. In all cases, the reaction coordinate diagrams suggest that β-elimination of TCP to allyl chloride followed by hydrogenolysis to propene is the thermodynamically favored pathway. This result is consistent with experimental results obtained using TCP, 1,2-dichloropropane, and 1,3-dichloropropane in batch experiments with zerovalent zinc (Zn⁰, ZVI) as a reductant.

Phytoplankton and Bacterial Community Structure in Two Chinese Lakes of Different Trophic Status

Phytoplankton are the primary producers at the basis of aquatic food webs, and bacteria play an important role in energy flow and biochemical cycling in aquatic ecosystems. In this study, both the bacterial and phytoplankton communities were examined in the oligotrophic Lake Basomtso and the eutrophic Lake South (China). The results of this study showed that the phytoplankton density and diversity in the eutrophic lake were higher than those in the oligotrophic lake. Furthermore, Chlorophyta (68%) and Cryptophyta (24%) were the dominant groups in the eutrophic lake, while Bacillariophyta (95%) dominated in the oligotrophic lake. The bacterial communities in the waters and sediments of the two lakes were mainly composed of Proteobacteria (mean of 32%), Actinobacteria (mean of 25%), Bacteroidetes (mean of 12%), and Chloroflexi (mean of 6%). Comparative analysis showed that the abundance of bacteria in the eutrophic lake was higher than that in the oligotrophic lake (p < 0.05), but the bacterial diversity in the oligotrophic lake was higher than that in the eutrophic lake (p < 0.05). Finally, the bacterial abundance and diversity in the sediments of the two lakes were higher than those in the water samples (p < 0.05), and the Latescibacteria and Nitrospinae groups were identified only in the sediments. These results suggest that both the phytoplankton and bacterial communities differed considerably between the oligotrophic lake and the eutrophic lake.

Assessment of PCB contamination, the potential for in situ microbial dechlorination and natural attenuation in an urban watershed at the East Coast of the United States

Sediment contamination is a major environmental issue in many urban watersheds and coastal areas due to the potential toxic effects of contaminants on biota and human health. Characterizing and delineating areas of sediment contamination and toxicity are important goals of coastal resource management in terms of ecological and economical perspectives. Core and surficial sediment samples were collected from an industrialized urban watershed at the East Coast of the United Stated and analyzed to evaluate the PCB contamination profile and toxicity resulting from dioxin-like PCBs as well as reductive dechlorination potential of indigenous PCB halorespiring bacteria through dechlorination activity assays. To support the experimental results an anaerobic dechlorination model was applied to identify microbial dechlorination pathways. The total PCB concentration in core samples ranged from 3.9 to 225.6 ng/g·dry weight (dw) decreasing with depth compared to 353.2 to 1213.7 ng/g·dw in surficial samples. The results of this study indicated an increase in PCB contamination over the last century as the industrial activity intensified. The toxicity resulting from dioxin-like PCBs was reduced up to 94% in core samples via 21 pathways resulting from the dechlorination model. Dechlorination rates in surficial sediment were between 1.8 and 13.2 · 10^-3 mol% PCB116/day, while lower rates occurred in the core sediment samples. Dechlorination was achieved mainly through meta followed by para dechlorination. However, the rarer ortho dechlorination was also observed. Detection of indigenous PCB dechlorinating bacteria in the sediments and reduction of toxicity indicated potential for natural attenuation when point and nonpoint source PCBs in the urban watershed are controlled and PCB loading reduced.

Dual carbon - chlorine isotope fractionation during dichloroelimination of 1,1,2-trichloroethane by an enrichment culture containing Dehalogenimonas sp

Chlorinated ethanes are frequent groundwater contaminants but compound specific isotope analysis (CSIA) has been scarcely applied to investigate their degradation pathways. In this study, dual carbon and chlorine isotope fractionation was used to investigate for the first time the anoxic biodegradation of 1,1,2-trichloroethane (1,1,2-TCA) using a Dehalogenimonas-containing culture. The isotopic fractionation values obtained for the biodegradation of 1,1,2-TCA were ɛ_C = -6.9 ± 0.4‰ and ɛ_Cl = -2.7 ± 0.3‰. The detection of vinyl chloride (VC) as unique byproduct and a closed carbon isotopic mass balance corroborated that dichloroelimination was the degradation pathway used by this strain. Combining the values of δ¹³C and δ³⁷Cl resulted in a dual element C-Cl isotope slope of Λ = 2.5 ± 0.2‰. Investigation of the apparent kinetic isotope effects (AKIEs) expected for cleavage of a CCl bond showed an important masking of the intrinsic isotope fractionation. Theoretical calculation of Λ suggested that dichloroelimination of 1,1,2-TCA was taking place via simultaneous cleavage of two CCl bonds (concerted reaction mechanism). The isotope data obtained in this study can be useful to monitor natural attenuation of 1,1,2-TCA via dichloroelimination and provide insights into the source and fate of VC in contaminated groundwaters.

Preliminary analysis of Chloroflexi populations in full-scale UASB methanogenic reactors

AIMS

The phylum Chloroflexi is frequently found in high abundance in methanogenic reactors, but their role is still unclear as most of them remain uncultured and understudied. Hence, a detailed analysis was performed in samples from five up-flow anaerobic sludge blanket (UASB) full-scale reactors fed different industrial wastewaters.

METHODS AND RESULTS

Quantitative PCR show that the phylum Chloroflexi was abundant in all UASB methanogenic reactors, with higher abundance in the reactors operated for a long period of time, which presented granular biomass. Both terminal restriction fragment length polymorphism and 16S rRNA gene amplicon sequencing revealed diverse Chloroflexi populations apparently determined by the different inocula. According to the phylogenetic analysis, the sequences from the dominant Chloroflexi were positioned in branches where no sequences of the cultured representative strains were placed. Fluorescent in situ hybridization analysis performed in two of the reactors showed filamentous morphology of the hybridizing cells.

CONCLUSIONS

While members of the Anaerolineae class within phylum Chloroflexi were predominant, their diversity is still poorly described in anaerobic reactors. Due to their filamentous morphology, Chloroflexi may have a key role in the granulation in methanogenic UASB reactors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results bring new insights about the diversity, stability, dynamics and abundance of this phylum in full-scale UASB reactors which aid in understanding their function within the reactor biomass. However, new methodological approaches and analysis of bulking biomass are needed to completely unravel their role in these reactors. Combining all this knowledge with reactor operational parameters will allow to understand their participation in granulation and bulking episodes and design strategies to prevent Chloroflexi overgrowth.

A Dehalogenimonas Population Respires 1,2,4-Trichlorobenzene and Dichlorobenzenes

Chlorobenzenes are ubiquitous contaminants in groundwater and soil at many industrial sites. Previously, we demonstrated the natural attenuation of chlorobenzenes and benzene at a contaminated site inferred from a 5 year site investigation and parallel laboratory microcosm studies. To identify the microbes responsible for the observed dechlorination of chlorobenzenes, the microbial community was surveyed using 16S rRNA gene amplicon sequencing. Members of the Dehalobacter and Dehalococcoides are reported to respire chlorobenzenes; however, neither were abundant in our sediment microcosms. Instead, we observed a significant increase in the relative abundance of Dehalogenimonas from <1% to 16-30% during dechlorination of 1,2,4-trichlorobenzene (TCB), 1,2-dichlorobenzene (DCB), and 1,3-DCB over 19 months. Quantitative PCR (qPCR) confirmed that Dehalogenimonas gene copies increased by 2 orders of magnitude with an average yield of 3.6 ± 2.3 g cells per mol Cl^- released ( N = 12). In transfer cultures derived from sediment microcosms, dechlorination of 1,4-DCB and monochlorobenzene (MCB) was carried out by Dehalobacter spp. with a growth yield of 3.0 ± 2.1 g cells per mol Cl^- released ( N = 5). Here we show that a Dehalogenimonas population respire 1,2,4-TCB and 1,2-/1,3-DCB isomers. This finding emphasizes the need to monitor a broader spectrum of organohalide-respiring bacteria, including Dehalogenimonas, at sites contaminated with halogenated organic compounds.

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.

Detoxification of 1,1,2-trichloroethane to ethene in a bioreactor co-culture of Dehalogenimonas and Dehalococcoides mccartyi strains

1,1,2-Trichloroethane (1,1,2-TCA) is a non-flammable organic solvent and common environmental contaminant in groundwater. Organohalide-respiring bacteria are key microorganisms to remediate 1,1,2-TCA because they can gain metabolic energy during its dechlorination under anaerobic conditions. However, all current isolates produce hazardous end products such as vinyl chloride, monochloroethane or 1,2-dichloroethane that accumulate in the medium. Here, we constructed a syntrophic co-culture of Dehalogenimonas and Dehalococcoides mccartyi strains to achieve complete detoxification of 1,1,2-TCA to ethene. In this co-culture, Dehalogenimonas transformed 1,1,2-TCA via dihaloelimination to vinyl chloride, whereas Dehalococcoides reduced vinyl chloride via hydrogenolysis to ethene. Molasses, pyruvate, and lactate supported full dechlorination of 1,1,2-TCA in serum bottle co-cultures. Scale up of the cultivation to a 5-L bioreactor operating for 76d in fed-batch mode was successful with pyruvate as substrate. This synthetic combination of bacteria with known complementary metabolic capabilities demonstrates the potential environmental relevance of microbial cooperation to detoxify 1,1,2-TCA.

Dehalogenimonas formicexedens sp. nov., a chlorinated alkane-respiring bacterium isolated from contaminated groundwater

A strictly anaerobic, Gram-stain-negative, non-spore-forming bacterium designated NSZ-14T, isolated from contaminated groundwater in Louisiana (USA), was characterized using a polyphasic approach. Strain NSZ-14T reductively dehalogenated a variety of polychlorinated aliphatic alkanes, producing ethene from 1,2-dichloroethane, propene from 1,2-dichloropropane, a mixture of cis- and trans-1,2-dichloroethene from 1,1,2,2-tetrachloroethane, vinyl chloride from 1,1,2-trichloroethane and allyl chloride (3-chloro-1-propene) from 1,2,3-trichloropropane. Formate or hydrogen could both serve as electron donors. Dechlorination occurred between pH 5.5 and 7.5 and over a temperature range of 20-37 °C. Major cellular fatty acids included C18 : 1ω9c, C14 : 0 and C16 : 0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the strain clusters within the class Dehalococcoidia of the phylum Chloroflexi, most closely related to but distinct from type strains of the species Dehalogenimonas alkenigignens (97.63 % similarity) and Dehalogenimonas lykanthroporepellens (95.05 %). A complete genome sequence determined for strain NSZ-14T revealed a DNA G+C content of 53.96 mol%, which was corroborated by HPLC (54.1±0.2 mol% G+C). Genome-wide comparisons based on average nucleotide identity by orthology and estimated DNA-DNA hybridization values combined with phenotypic and chemotaxonomic traits and phylogenetic analysis indicate that strain NSZ-14T represents a novel species within the genus Dehalogenimonas, for which the name Dehalogenimonas formicexedens sp. nov. is proposed. The type strain is NSZ-14T (=HAMBI 3672T=JCM 19277T=VKM B-3058T). An emended description of Dehalogenimonas alkenigignens is also provided.

Cometabolic biodegradation of 1,2,3-trichloropropane by propane-oxidizing bacteria

1,2,3-Trichloropropane (TCP) is an emerging groundwater pollutant and suspected human carcinogen. TCP, a recalcitrant contaminant, has been detected in the subsurface near TCP manufacture facilities and many superfund sites. Considering the toxicity and the occurence of TCP, there is a need to seek for cost-effective treatment technologies for TCP-contaminated sites. This paper investigated TCP biodegradation by propane-oxidizing bacteria (PrOB) which are known to express propane monooxygenase (PrMO). PrMO can cometabolically degrade many different contaminants. Four PrOB, Rhodococus jostii RHA1, Mycobacterium vaccae JOB5, Rhodococcus rubber ENV425 and one isolate Sphingopyxis sp. AX-A were examined for their ability to degrade TCP. All the four PrOB resting cells were able to degrade TCP. Strain JOB5 exhibited the best TCP degradation ability (v_initial = 9.7 ± 0.7 μg TCP (mg protein)^-1h^-1). No TCP was degraded in the presence of acetylene (an inhibitor for PrMO), suggesting that PrMO might be responsible for TCP degradation. Furthermore, competitive inhibition was observed between propane and TCP, and between trichloroethylene (TCE) and TCP.

Bacterial community compositions of propylene oxide saponification wastewater treatment plants

In this study, the bacterial community structures of propylene oxide saponification wastewater treatment plants were explored for the first time.

Distribution of bacterial communities across plateau freshwater lake and upslope soils

Microorganisms are involved in a variety of biogeochemical processes in natural environments. The differences between bacterial communities in freshwaters and upslope soils remain unclear. The present study investigated the bacterial distribution in a plateau freshwater lake, Erhai Lake (southwestern China), and its upslope soils. Illumina MiSeq sequencing illustrated high bacterial diversity in lake sediments and soils. Sediment and soil bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Planctomycetes. However, a distinctive difference in bacterial community structure was found between soil and sediment ecosystems. Water content, nitrogen and pH affected the distribution of the bacterial community across Erhai Lake and its upslope soils. Moreover, the soil bacterial community might also be shaped by plant types. This work could provide some new insights into plateau aquatic and terrestrial microbial ecology.

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

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

Stable Carbon Isotope Fractionation During 1,2-Dichloropropane-to-Propene Transformation by an Enrichment Culture Containing Dehalogenimonas Strains and a dcpA Gene

A stable enrichment culture derived from Besòs river estuary sediments stoichiometrically dechlorinated 1,2-dichloropropane (1,2-DCP) to propene. Sequential transfers in defined anaerobic medium with the inhibitor bromoethanesulfonate produced a sediment-free culture dechlorinating 1,2-DCP in the absence of methanogenesis. Application of previously published genus-specific primers targeting 16S rRNA gene sequences revealed the presence of a Dehalogenimonas strain, and no amplification was obtained with Dehalococcoides-specific primers. The partial sequence of the 16S rRNA amplicon was 100% identical with Dehalogenimonas alkenigignens strain IP3-3. Also, dcpA, a gene described to encode a corrinoid-containing 1,2-DCP reductive dehalogenase was detected. Resistance of the dehalogenating activity to vancomycin, exclusive conversion of vicinally chlorinated alkanes, and tolerance to short-term oxygen exposure is consistent with the hypothesis that a Dehalogenimonas strain is responsible for 1,2-DCP conversion in the culture. Quantitative PCR showed a positive correlation between the number of Dehalogenimonas 16S rRNA genes copies in the culture and consumption of 1,2-DCP. Compound specific isotope analysis revealed that the Dehalogenimonas-catalyzed carbon isotopic fractionation (εC(bulk)) of the 1,2-DCP-to-propene reaction was -15.0 ± 0.7‰ under both methanogenic and nonmethanogenic conditions. This study demonstrates that carbon isotope fractionation is a valuable approach for monitoring in situ 1,2-DCP reductive dechlorination by Dehalogenimonas strains.

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.

A Pseudomonas putida strain genetically engineered for 1,2,3-trichloropropane bioremediation

1,2,3-Trichloropropane (TCP) is a toxic compound that is recalcitrant to biodegradation in the environment. Attempts to isolate TCP-degrading organisms using enrichment cultivation have failed. A potential biodegradation pathway starts with hydrolytic dehalogenation to 2,3-dichloro-1-propanol (DCP), followed by oxidative metabolism. To obtain a practically applicable TCP-degrading organism, we introduced an engineered haloalkane dehalogenase with improved TCP degradation activity into the DCP-degrading bacterium Pseudomonas putida MC4. For this purpose, the dehalogenase gene (dhaA31) was cloned behind the constitutive dhlA promoter and was introduced into the genome of strain MC4 using a transposon delivery system. The transposon-located antibiotic resistance marker was subsequently removed using a resolvase step. Growth of the resulting engineered bacterium, P. putida MC4-5222, on TCP was indeed observed, and all organic chlorine was released as chloride. A packed-bed reactor with immobilized cells of strain MC4-5222 degraded >95% of influent TCP (0.33 mM) under continuous-flow conditions, with stoichiometric release of inorganic chloride. The results demonstrate the successful use of a laboratory-evolved dehalogenase and genetic engineering to produce an effective, plasmid-free, and stable whole-cell biocatalyst for the aerobic bioremediation of a recalcitrant chlorinated hydrocarbon.

Reassessment of PCR primers targeting 16S rRNA genes of the organohalide-respiring genus Dehalogenimonas

Representatives from the genus Dehalogenimonas have the metabolic capacity to anaerobically transform a variety of environmentally important polychlorinated aliphatic compounds. In light of the recent isolation of additional strains, description of a new species, and an expanded number of uncultured DNA sequences, PCR primers and protocols intended to uniquely target members of this organohalide-respiring genus were reevaluated. Nine of fourteen primer combinations reported previously as genus-specific failed to amplify 16S rRNA genes of recently isolated Dehalogenimonas strains. Use of alternative combinations or modified genus-specific primers, however, allowed detection of all presently known Dehalogenimonas strains. Use of a modified primer set in qPCR revealed an approximately two-order of magnitude increase in concentration of Dehalogenimonas 16S rRNA gene copies following subsurface injection of electron donors at a Louisiana Superfund site, demonstrating the utility of the newly developed protocol and suggesting that the genus Dehalogenimonas can respond to biostimulation remediation strategies in a manner similar to that previously reported for other dechlorinating genera such as Dehalococcoides.

Immobilized synthetic pathway for biodegradation of toxic recalcitrant pollutant 1,2,3-trichloropropane

The anthropogenic compound 1,2,3-trichloropropane (TCP) has recently drawn attention as an emerging groundwater contaminant. No living organism, natural or engineered, is capable of the efficient aerobic utilization of this toxic industrial waste product. We describe a novel biotechnology for transforming TCP based on an immobilized synthetic pathway. The pathway is composed of three enzymes from two different microorganisms: engineered haloalkane dehalogenase from Rhodococcus rhodochrous NCIMB 13064, and haloalcohol dehalogenase and epoxide hydrolase from Agrobacterium radiobacter AD1. Together, they catalyze consecutive reactions converting toxic TCP to harmless glycerol. The pathway was immobilized in the form of purified enzymes or cell-free extracts, and its performance was tested in batch and continuous systems. Using a packed bed reactor filled with the immobilized biocatalysts, 52.6 mmol of TCP was continuously converted into glycerol within 2.5 months of operation. The efficiency of the TCP conversion to the intermediates was 97%, and the efficiency of conversion to the final product glycerol was 78% during the operational period. Immobilized biocatalysts are suitable for removing TCP from contaminated water up to a 10 mM solubility limit, which is an order of magnitude higher than the concentration tolerated by living microorganisms.

Potential for Polychlorinated Biphenyl Biodegradation in Sediments from Indiana Harbor and Ship Canal

Polychlorinated biphenyls (PCBs) are carcinogenic, persistent, and bioaccumulative contaminants that pose risks to human and environmental health. In this study, we evaluated the PCB biodegradation of sediments from Indiana Harbor and Ship Canal (IHSC), a PCB-contaminated site (average PCB concentration = 12,570 ng/g d.w.). PCB congener profiles and bacterial community structure in a core sediment sample (4.57 m long) were characterized. Analysis of vertical PCB congener profile patterns in sediment and pore water strongly suggest that in situ dechlorination occurred in sediments. However, 16S rRNA genes from putative PCB-dechlorinating Chloroflexi were relatively more abundant in upper 2 m sediments, as were genes indicative of aerobic biodegradation potential (i.e. biphenyl dioxygenase (bphA)). Characterization of the bacterial community by terminal restriction fragment length polymorphism and comparison of these with sediment and pore water PCB congener profiles with the Mantel test revealed a statistical correlation (p<0.001). Sequences classified as Acinetobacter and Acidovorax were highly abundant in deep sediments. Overall, our results suggest that PCB dechlorination has already occurred, and that IHSC sediments have the potential for further aerobic and anaerobic PCB biodegradation.

Novel Firmicutes group implicated in the dechlorination of two chlorinated xanthones, analogues of natural organochlorines

Although the abundance and diversity of natural organochlorines are well established, much is still unknown about the degradation of these compounds. Triplicate microcosms were used to determine whether, and which, bacterial communities could dechlorinate two chlorinated xanthones (2,7-dichloroxanthone and 5,7-dichloro-1,3-dihydroxylxanthone), analogues of a diverse class of natural organochlorines. According to quantitative-PCR (qPCR) results, several known dechlorinating genera were either not present or not enriched during dechlorination of the xanthones. Denaturing gradient gel electrophoresis, however, indicated that several Firmicutes were enriched in the dechlorinating cultures compared to triplicate controls amended with nonchlorinated xanthones. One such group, herein referred to as the Gopher group, was further studied with a novel qPCR method that confirmed enrichment of Gopher group 16S rRNA genes in the dechlorinating cultures. The enrichment of the Gopher group was again tested with two new sets of triplicate microcosms. Enrichment was observed during chlorinated xanthone dechlorination in one set of these triplicate microcosms. In the other set, two microcosms showed clear enrichment while a third did not. The Gopher group is a previously unidentified group of Firmicutes, distinct from but related to the Dehalobacter and Desulfitobacterium genera; this group also contains clones from at least four unique cultures capable of dechlorinating anthropogenic organochlorines that have been previously described in the literature. This study suggests that natural chlorinated xanthones may be effective biostimulants to enhance the remediation of pollutants and highlights the idea that novel genera of dechlorinators likely exist and may be active in bioremediation and the natural cycling of chlorine.

Identification and environmental distribution of dcpA, which encodes the reductive dehalogenase catalyzing the dichloroelimination of 1,2-dichloropropane to propene in organohalide-respiring chloroflexi

Dehalococcoides mccartyi strains KS and RC grow with 1,2-dichloropropane (1,2-D) as an electron acceptor in enrichment cultures derived from hydrocarbon-contaminated and pristine river sediments, respectively. Transcription, expression, enzymatic, and PCR analyses implicated the reductive dehalogenase gene dcpA in 1,2-D dichloroelimination to propene and inorganic chloride. Quantitative real-time PCR (qPCR) analyses demonstrated a D. mccartyi cell increase during growth with 1,2-D and suggested that both D. mccartyi strains carried a single dcpA gene copy per genome. D. mccartyi strain RC and strain KS produced 1.8 × 10(7) ± 0.1 × 10(7) and 1.4 × 10(7) ± 0.5 × 10(7) cells per μmol of propene formed, respectively. The dcpA gene was identified in 1,2-D-to-propene-dechlorinating microcosms established with sediment samples collected from different geographical locations in Europe and North and South America. Clone library analysis revealed two distinct dcpA phylogenetic clusters, both of which were captured by the dcpA gene-targeted qPCR assay, suggesting that the qPCR assay is useful for site assessment and bioremediation monitoring at 1,2-D-contaminated sites.

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.