Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

Abstract

Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.In the past century, human activities have released large amounts of chlorinated organic compounds into the environment, and these compounds are among the most pervasive groundwater pollutants. Chloroorganics with fewer chlorines can usually be biodegraded by aerobic microorganisms, whereas more highly chlorinated ones can be reductively dechlorinated by organisms using them as electron acceptors for anaerobic respiration. Several microbial groups carry out respiratory reductive dechlorination 1 , but one genus, Dehalococcoides, seems particularly adapted to a unique niche, and the bacteria are only known to use chloroorganics as electron acceptors and hydrogen as an electron donor for growth. Several studies have now shown successful application of Dehalococcoides-containing cultures for in situ remediation of contaminated sites 2,3 . The recently described genome sequence of D. ethenogenes, strain 195 (ref. 4), an organism that reductively dechlorinates the solvents tetrachloroethene and trichloroethene to vinyl chloride and ethene 5 , reflects this specialization: although only 1.47-megabases (Mb) long, the genome possesses 17 rdhAB pairs potentially encoding reductive dehalogenases and genes predicted to encode five different hydrogenase complexes. We describe here the genome sequence of Dehalococcoides sp. strain CBDB1, a bacterium that has in many ways a different dechlorination spectrum from strain 195. For instance, strain CBDB1 (refs. 6,7) dechlorinated 1,2,3-trichlorobenzene, 1,2,4-trichlorobenzene, 2,3-dichloro-p-dibenzodioxin and the 'Seveso dioxin ' 2,3,7,8-tetrachloro-p-dibenzodioxin, but strain 195 (ref. 8) did not. In contrast to strain 195, strain CBDB1 did not dechlorinate tetrachloroethene past dichloroethene 6 . By sequencing a second Dehalococcoides genome, we can now show that strain CBDB1 has an even greater potential as a reductive dechlorinator than strain 195 and, in addition, the comparison of the two genomes with each other provides insights into the evolution of reductive dechlori...

Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species

“…The upstream region of the RDase gene mbrA (dceA6) is a DNA-binding response regulator, whereas the 5 0 region of the dceA7 gene shares high identity with the SAM domain-containing protein as shown in strain 195. The transcription level of the mbrA gene is lower compared with some other known RDase genes such as the tceA gene, which is possibly due to the tight regulation of transcription by the upstream DNA-binding response regulator protein (Wagner et al, 2009;Kube et al, 2005). The upstream regions of the RDase genes have attracted much interest recently with current genome sequencing projects (Kube et al, 2005;Seshadri et al, 2005).…”

Role of “Dehalococcoides” spp. in the Anaerobic Transformation of Hexachlorobenzene in European Rivers

“…Therefore, it can be speculated that at mesophilic temperatures, besides cbrA and cbdbA1624, some other rdh genes contribute significantly to the metabolic activity. Complex transcriptional responses to various chlorinated compounds were previously reported for Dehalococcoides isolates and cocultures (16,44,45) and were predicted to be tightly regulated by two-component and/or MarR-type regulators (29,35). The majority of rdh genes detected with T-RFLP and sequencing analysis were similar to those of strain CBDB1, which are located close to MarR-type regulators.…”

“…These regulators were shown to have "phenolic-sensing capabilities" (47) and to activate or repress gene expression during aromaticcompound degradation (43) in several other bacteria. It has been suggested that the possibly MarR-regulated rdhA genes might play an important role in haloaromatic compound degradation pathways (29). Since these genes could be detected both in situ and in sediment microcosms, it is tempting to speculate that they carry a great potential to be used as biomarkers of anaerobic haloaromatic-compound degradation capacity.…”

“…can only use chlorinated compounds as their electron acceptor. Sequenced Dehalococcoides genomes have shown no strong indication of the presence of genes encoding enzymes involved in the use of any other electron acceptors (29,32,35). However, the sequenced species were enriched and maintained in the laboratory for a long time solely on chlorinated compounds and might have lost their ability to use other compounds.…”

“…Enzymes catalyzing the reductive dechlorination of HCB have not yet been identified. However, genomes of strains CBDB1 and 195 were shown to have multiple copies of putative reductive dehalogenase (rdh) genes that were predicted to code for enzymes mediating reductive dechlorination (29,35). An rdh gene from strain CBDB1, cbrA, was recently characterized as a 1,2,3,4-tetrachlorobenzene (TeCB) and 1,2,3-TCB reductive dehalogenase gene (2).…”