Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls

Abstract

Fastidious anaerobic bacteria play critical roles in environmental bioremediation of halogenated compounds. However, their characterization and application have been largely impeded by difficulties in growing them in pure culture. Thus far, no pure culture has been reported to respire on the notorious polychlorinated biphenyls (PCBs), and functional genes responsible for PCB detoxification remain unknown due to the extremely slow growth of PCB-respiring bacteria. Here we report the successful isolation and characterization of three Dehalococcoides mccartyi strains that respire on commercial PCBs. Using high-throughput metagenomic analysis, combined with traditional culture techniques, tetrachloroethene (PCE) was identified as a feasible alternative to PCBs to isolate PCB-respiring Dehalococcoides from PCB-enriched cultures. With PCE as an alternative electron acceptor, the PCBrespiring Dehalococcoides were boosted to a higher cell density (1.2 × 10 8 to 1.3 × 10 8 cells per mL on PCE vs. 5.9 × 10 6 to 10.4 × 10 6 cells per mL on PCBs) with a shorter culturing time (30 d on PCE vs. 150 d on PCBs). The transcriptomic profiles illustrated that the distinct PCB dechlorination profile of each strain was predominantly mediated by a single, novel reductive dehalogenase (RDase) catalyzing chlorine removal from both PCBs and PCE. The transcription levels of PCB-RDase genes are 5-60 times higher than the genome-wide average. The cultivation of PCB-respiring Dehalococcoides in pure culture and the identification of PCB-RDase genes deepen our understanding of organohalide respiration of PCBs and shed light on in situ PCB bioremediation.P olychlorinated biphenyls (PCBs) as priority persistent organic pollutants (1) are ranked fifth on the US Environmental Protection Agency Superfund Priority List of Hazardous Compounds (2). PCBs were massively produced and sold as complex mixtures (e.g., Aroclor 1260) for industrial uses, resulting in their widespread distribution in sediments of lakes, rivers, and harbors (2). Although the production of PCBs was banned in most countries by the late 1970s, their persistence in nature and bioaccumulation in food chains continue to pose a significant health risk for humans (3). The pitfalls of the most commonly used chemical methods for PCB remediation via dredging include risk of leaking contaminants, identifying suitable disposal methods for large quantities of contaminated soil, and the invasive and disruptive impact on the surrounding ecosystem (4).In as early as 1987, detoxification of PCBs through reductive dechlorination by indigenous anaerobic bacteria was reported at contaminated sites (5) and confirmed in laboratory studies (6), opening up the possibility of an environmentally attractive in situ microbial detoxification strategy. However, progress in this direction has been slow due to the challenges involved in cultivation of PCB-respiring bacteria. Correspondingly, to date, only three bacterial strains showed PCB dechlorination activity, Dehalobium chlorocoercia DF-1 (7), Dehalococ...

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

“…(Bedard, 2008), Bacterium o-17 (Cutter et al, 1998) and Dehalobium chlorocoercia DF-1 (Wu et al, 2002) were shown to be involved in the reductive dechlorination of PCB congeners. The difficulty in cultivating PCB dechlorinators in pure culture impedes further characterization, optimization, and application in in-situ bioremediation (Wang et al, 2014). Recently, Wang et al used traditional culture techniques with tetrachloroethene as an alternative electron acceptor and successfully isolated and characterized three PCB-respiring Dehalococcoides mccartyi strains.…”

The MarR-Type Regulator Rdh2R Regulates rdh Gene Transcription in Dehalococcoides mccartyi Strain CBDB1

“…This gene cluster is conserved in sequence (Ն98% identity) and synteny in three other D. mccartyi strains, DCMB5, GT, and CG5 (7,23,24). Transcription of the rdhA gene (cbdbA1453) was shown previously to be upregulated in the presence of 1,2,3-trichlorobenzene (TCB) (25).…”

“…The genomes of D. mccartyi strains contain between 11 and 36 nonidentical rdhAB genes encoding the catalytic subunit A and the putative membrane anchor B of reductive dehalogenase homologous (Rdh) proteins, respectively, (3)(4)(5)(6)(7). This high number probably reflects the diversity of organohalogen compounds, which can be reductively dehalogenated by Dehalococcoides strains.…”

Ecophysiology and environmental distribution of organohalide-respiring bacteria

“…Recently, more strains from this species were isolated including strain JNA [85,86], CG1 [87,88], CG4 [87,88], CG5 [87,88], SG1 [87,88], AD14-1 [89] and AD14-2 [89].…”

“…Sand and silt near Liangjiang River 2014 [87,88] Dehalococcoides mccartyi CG4 Sand and silt of ditch sediment near electronic waste dump site 2014 [87,88] Dehalococcoides mccartyi CG5 Sand and silt of ditch sediment near electronic waste dump site 2014 [87,88] Dehalococcoides mccartyi SG1 Digester sludge of an industrial wastewater treatment plant 2014 [87,88] Dehalococcoides mccartyi AD14-1 An anaerobic digester in a wastewater treatment plant 2013 [89] Dehalococcoides mccartyi AD14-2 An anaerobic digester in a wastewater treatment plant 2013 [89] Dehalococcoides mccartyi MB [48,50,178,179] from pristine environments where naturally-occurring organohalides are believed to feed OHRB.…”