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

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

Dehalobium species implicated in 2,3,7,8-tetrachloro-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary

Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They are naturally occurring and by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g-1) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) the most toxic and concerning of the PCDD/F congeners. Comparison of congener profiles at the contamination source with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as a more amenable growth substrate enriched only the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TCDD and octachlorodibenzo-p-dibenzodioxin to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F degradation in a marine environment.

Heterologous expression of active Dehalobacter spp. respiratory reductive dehalogenases in Escherichia coli

Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, potentially because of their cobamide-dependence. There have been a few successful attempts at RDase production in unconventional heterologous hosts, but a robust method has yet to be developed. Here we outline a novel respiratory RDase expression system using Escherichia coli . The overexpression of E. coli ’s cobamide transport system, btu , and anaerobic expression conditions were found to be essential for production of active RDases from Dehalobacter - an obligate organohalide respiring bacterium. The expression system was validated on six enzymes with amino acid sequence identities as low as 28%. Dehalogenation activity was verified for each RDase by assaying cell-free extracts of small-scale expression cultures on various chlorinated substrates including chloroalkanes, chloroethenes, and hexachlorocyclohexanes. Two RDases, TmrA from Dehalobacter sp. UNSWDHB and HchA from Dehalobacter sp. HCH1, were purified by nickel affinity chromatography. Incorporation of the cobamide and iron-sulfur cluster cofactors was verified; though, the precise cobalamin incorporation could not be determined due to variance between methodologies, and the specific activity of TmrA was consistent with that of the native enzyme. The heterologous expression of respiratory RDases, particularly from obligate organohalide respiring bacteria, has been extremely challenging and unreliable. Here we present a relatively straightforward E. coli expression system that has performed well for a variety of Dehalobacter spp. RDases. IMPORTANCE Understanding microbial reductive dehalogenation is important to refine the global halogen cycle and to improve bioremediation of halogenated contaminants; however, studies of the family of enzymes responsible are limited. Characterization of reductive dehalogenase enzymes has largely eluded researchers due to the lack of a reliable and high-yielding production method. We are presenting an approach to express reductive dehalogenase enzymes from Dehalobacter , a key group of organisms used in bioremediation, in E. coli . This expression system will propel the study of reductive dehalogenases by facilitating their production and isolation, allowing researchers to pursue more in-depth questions about the activity and structure of these enzymes. This platform will also provide a starting point to improve the expression of reductive dehalogenases from many other organisms.

Reductive Dehalogenation – Challenges of Perfluorinated Organics

: In this mini-review, the problem of effective elimination of perfluorinated organic micropollutants from aquatic environment has been touched. The extraordinary chemical stability of common perfluorinated organic surfactants results in unsatisfactory efficiency of conventional treatment processes, which opens perspectives for photocatalytic methods - especially for reductive-dehalogenation. To tackle this challenge by photocatalysis one have to be aware of objective, physical limits set by very nature of the reduction process, electronic structure chemical stability, and formulation of the catalyst as well as emission characteristic of the light source. The paper provides some clues for rational design of reductive-dehalogenation oriented photolytic systems, which are derived on the basis of physical principles, and, rather sparse, experimental examples.

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.

The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation

The Chloroflexi superphylum have been investigated primarily from the perspective of reductive dehalogenation of toxic compounds, anaerobic photosynthesis and wastewater treatment, but remain relatively little studied compared to their close relatives within the larger Terrabacteria group, including Cyanobacteria, Actinobacteria, and Firmicutes. Here, we conducted a detailed phylogenetic analysis of the phylum Chloroflexota, the phylogenetically proximal candidate phylum Dormibacteraeota, and a newly defined sibling phylum proposed in the current study, Eulabeiota. These groups routinely root together in phylogenomic analyses, and constitute the Chloroflexi supergroup. Chemoautotrophy is widespread in Chloroflexi. Two Form I Rubisco ancestral subtypes that both lack the small subunit are prevalent in ca. Eulabeiota and Chloroflexota, suggesting that the predominant modern pathway for CO2 fixation evolved in these groups. The single subunit Form I Rubiscos are inferred to have evolved prior to oxygenation of the Earth's atmosphere and now predominantly occur in anaerobes. Prevalent in both Chloroflexota and ca. Eulabeiota are capacities related to aerobic oxidation of gases, especially CO and H2. In fact, aerobic and anaerobic CO dehydrogenases are widespread throughout every class-level lineage, whereas traits such as denitrification and reductive dehalogenation are heterogeneously distributed across the supergroup. Interestingly, some Chloroflexota have a novel clade of group 3 NiFe hydrogenases that is phylogenetically distinct from previously reported groups. Overall, the analyses underline the very high level of metabolic diversity in the Chloroflexi supergroup, suggesting the ancestral metabolic platform for this group enabled highly varied adaptation to ecosystems that appeared in the aerobic world.

Integration of microbial reductive dehalogenation with persulfate activation and oxidation (Bio-RD-PAO) for complete attenuation of organohalides

Due to the toxicity of bioaccumulative organohalides to human beings and ecosystems, a variety of biotic and abiotic remediation methods have been developed to remove organohalides from contaminated environments. Bioremediation employing organohalide-respiring bacteria (OHRB)-mediated microbial reductive dehalogenation (Bio-RD) represents a cost-effective and environmentally friendly approach to attenuate highly-halogenated organohalides, specifically organohalides in soil, sediment and other anoxic environments. Nonetheless, many factors severely restrict the implications of OHRB-based bioremediation, including incomplete dehalogenation, low abundance of OHRB and consequent low dechlorination activity. Recently, the development of in situ chemical oxidation (ISCO) based on sulfate radicals (SO 4 ·− ) via the persulfate activation and oxidation (PAO) process has attracted tremendous research interest for the remediation of lowly-halogenated organohalides due to its following advantages, e.g., complete attenuation, high reactivity and no selectivity to organohalides. Therefore, integration of OHRB-mediated Bio-RD and subsequent PAO (Bio-RD-PAO) may provide a promising solution to the remediation of organohalides. In this review, we first provide an overview of current progress in Bio-RD and PAO and compare their limitations and advantages. We then critically discuss the integration of Bio-RD and PAO (Bio-RD-PAO) for complete attenuation of organohalides and its prospects for future remediation applications. Overall, Bio-RD-PAO opens up opportunities for complete attenuation and consequent effective in situ remediation of persistent organohalide pollution.

Photoredox Catalysis Using Heterogenized Iridium Complexes

Heterogenized photoredox catalysts provide a path to generating chemicals in an environmentally friendly way, with facile reuse of catalysts in batch or continuous processes. In this study, heterogenized iridium complexes as photoredox catalysts were assembled via covalent attachment to three metal oxide surfaces (ITO, ZrO₂, Al₂O₃) either in the form of thin films or nanopowders and tested as photoredox catalysts for reductive dehalogenation of bromoacetophenone to acetophenone. All catalysts produced acetophenone with high conversions and yields. The fastest reactions were complete in fifteen minutes under mild conditions using Al₂O₃ surfaces, which provided the most robust and reusable supports. The catalytic performance was compared on both nanopowder and thin film supports, showing that both constructs could be used for photoredox catalysis. The nanopowder-based catalysts resulted in faster and more efficient catalysis, while the thin film-immobilized catalysts were more robust and easily reused. Importantly, the thin film constructs show promise for future photoelectrochemical and electrochemical photoredox setups. Finally, all catalysts could be reused 2-3 times, performing at least 1000 turnovers with Al₂O₃supports, highlighting that heterogenized catalysts can perform photoredox catalysis in an environmentally friendly fashion. <br>

Photoredox Catalysis Using Heterogenized Iridium Complexes

Heterogenized photoredox catalysts provide a path to generating chemicals in an environmentally friendly way, with facile reuse of catalysts in batch or continuous processes. In this study, heterogenized iridium complexes as photoredox catalysts were assembled via covalent attachment to three metal oxide surfaces (ITO, ZrO₂, Al₂O₃) either in the form of thin films or nanopowders and tested as photoredox catalysts for reductive dehalogenation of bromoacetophenone to acetophenone. All catalysts produced acetophenone with high conversions and yields. The fastest reactions were complete in fifteen minutes under mild conditions using Al₂O₃ surfaces, which provided the most robust and reusable supports. The catalytic performance was compared on both nanopowder and thin film supports, showing that both constructs could be used for photoredox catalysis. The nanopowder-based catalysts resulted in faster and more efficient catalysis, while the thin film-immobilized catalysts were more robust and easily reused. Importantly, the thin film constructs show promise for future photoelectrochemical and electrochemical photoredox setups. Finally, all catalysts could be reused 2-3 times, performing at least 1000 turnovers with Al₂O₃supports, highlighting that heterogenized catalysts can perform photoredox catalysis in an environmentally friendly fashion. <br>