Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M

Functional analysis of microorganisms and metabolites in the cecum of different sheep populations and their effects on production traits

The purpose of this study was to investigate the effects of intestinal microbiota on the growth and production performance of different groups of sheep, focusing on the role of cecal microbiota in regulating intestinal function, enhancing digestion and absorption, and improving feed utilization. The production performance of MG × STH (Mongolia × Small Tailed Han) F1 hybrids and purebred STH (Small Tailed Han) sheep by measuring various factors, including enzyme activities and VFAs (volatile fatty acids), to analyze changes in cecal fermentation parameters across different sheep groups. Metagenomic and metabolomic sequencing combined with bioinformatics to analyze the cecal contents of the two sheep populations. The study findings indicated that the MG × STH F1 hybrids outperformed the purebred STH in terms of body weight, height, oblique body length, and VFAs (p < 0.05). Additionally, the MG × STH F1 higher levels of protease and cellulase in the cecum compared to the purebred sheep (p < 0.05). Metagenomic analysis identified 4,034 different microorganisms at the species level. Five differential organisms (Akkermansiaceae bacterium, Escherichia coli, unclassified p Firmicutes, Streptococcus equinus, Methanobrevibacter millerae) positively regulated sheep performance. Metabolomics identified 822 differential metabolites indoleacetaldehyde, 2-aminobenzoic acid, phenyl-Alanine, enol-phenylpyruvate and n-acetylserotonin were associated with improved performance of sheep. The combined results from the metagenomic and metabolomic studies suggest a positive correlation between specific microbes and metabolites and the performance of the sheep. In conclusion, the MG × STH F1 hybrids demonstrated superior growth performance compared to the purebred STH sheep. The identified microorganisms and metabolites have promising roles in positively regulating sheep growth and can be considered key targets for enhancing sheep performance.

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.

Enhanced thyroxine removal from micro-polluted drinking water resources in a bio-electrochemical reactor amended with TiO2@GAC particles: Efficiency, mechanism and energy consumption

A three-dimensional bioelectrochemical system (3D-BES) with both electrocatalytic and biodegradation functions was designed and developed to enhance iodine-containing hormone removal from micro-polluted oligotrophic drinking water sources and to reduce energy consumption. Thyroxine (T4) removal efficiency was 99.0% in the 3D-BES amendment with TiO2@GAC as the particle electrodes, which was 20.5% higher than the total efficiency of single biodegradation (28.7%) plus electrochemical decomposition (49.8%). The high T4 removal efficiency was a result of biochemical synergistic degradation, enhancement of electron transfer and utilization, enrichment of functional microorganisms, and the expression of dehalogenation functional genes. The electron transfer was increased by 1.63 times in 3D-BES compared to the 2D-BES, which contributed to: (i) ∼17.8% enhancement of dehalogenation, (ii) 2.35 times enhancement of the attenuation rate, and (iii) 60% reduction in energy consumption. Moreover, the aggregation of microorganisms and the hydrophobic T4 onto TiO2@GAC shortened the transfer distance of matter and energy, which induced the degradation steps to be shortened and the toxic decay to be accelerated from T4 and its metabolites. These comprehensive functions also enhanced the 31.8% ATPase activity, 7.3% abundance of the functional reductive dehalogenation genera, and 52.3% dehalogenation genes expression for Pseudomonas, Ancylobacter, and Dehalogenimonas, which contributed to an increase in T4 removal. This work provides an environmental-friendly biochemical synergistic method for the detoxification of T4 polluted water.

Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses

Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.

Dehalogenimonas etheniformans sp. nov., a formate-oxidizing, organohalide-respiring bacterium isolated from grape pomace

A strictly anaerobic, organohalide-respiring bacterium, designated strain GP^T, was characterized using a polyphasic approach. GP^T is Gram-stain-negative, non-spore-forming and non-motile. Cells are irregular cocci ranging between 0.6 and 0.9 µm in diameter. GP^T couples growth with the reductive dechlorination of 1,2-dichloroethane, vinyl chloride and all polychlorinated ethenes, except tetrachloroethene, yielding ethene and inorganic chloride as dechlorination end products. H₂ and formate serve as electron donors for organohalide respiration in the presence of acetate as carbon source. Major cellular fatty acids include C_16 : 0, C_18 : 1ω9c, C_16 : 1, C_14 : 0 and C_18 : 0. On the basis of 16S rRNA gene phylogeny, GP^T is most closely related to Dehalogenimonas formicexedens NSZ-14^T and Dehalogenimonas alkenigignens IP3-3^T with 99.8 and 97.4 % sequence identities, respectively. Genome-wide pairwise comparisons based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization do not support the inclusion of GP^T in previously described species of the genus Dehalogenimonas with validly published names. On the basis of phylogenetic, physiological and phenotypic traits, GP^T represents a novel species within the genus Dehalogenimonas, for which the name Dehalogenimonas etheniformans sp. nov. is proposed. The type strain is GP^T (= JCM 39172^T = CGMCC 1.17861^T).

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.

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.

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.

Dehalococcoides mccartyi NIT01, a novel isolate, dechlorinates high concentrations of chloroethenes by expressing at least six different reductive dehalogenases

This study presents the isolation of a novel strain of Dehalococcoides mccartyi, NIT01, which can completely dechlorinate up to 4.0 mM of trichloroethene to ethene via 1,2-cis-dichroroethene and vinyl chloride within 25 days. Strain NIT01 dechlorinated chloroethenes (CEs) at a temperature range of 25-32 °C and pH range of 6.5-7.8. The activity of the strain was inhibited by salt at more than 1.3% and inactivated by 1 h exposure to 2.0% air or 0.5 ppm hypochlorous acid. The genome of NIT01 was highly similar to that of the Dehalococcoides strains DCMB5, GT, 11a5, CBDB1, and CG5, and all included identical 16S rRNA genes. Moreover, NIT01 had 19 rdhA genes including NIT01-rdhA7 and rdhA13, which are almost identical to vcrA and pceA that encode known dehalogenases for tetrachloroethene and vinyl chloride, respectively. We also extracted RdhAs from the membrane fraction of NIT01 using 0.5% n-dodecyl-β-d-maltoside and separated them by anion exchange chromatography to identify those involved in CE dechlorination. LC/MS identification of the LDS-PAGE bands and RdhA activities in the fractions indicated cellular expression of six RdhAs. NIT01-RdhA7 (VcrA) and NIT01-RdhA15 were highly detected and NIT01-RdhA6 was the third-most detected. Among these three RdhAs, NIT01-RdhA15 and NIT01-RdhA6 had no biochemically identified relatives and were suggested to be novel functional dehalogenases for CEs. The expression of multiple dehalogenases may support bacterial tolerance to high concentrations of CEs.

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.