Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium.

The chloroform-respiring bacterium Dehalobacter UNSWDHB was isolated from subsurface soil contaminated with a mixture of organohalides, including chloroform. Here, we present its 3.2-Mb genome.

GENOME ANNOUNCEMENT

Trichloromethane, commonly known as chloroform (CF), is a toxic and recalcitrant organohalide with an aqueous half-life of 3,100 years (1), and it is currently ranked 11th on the U.S. Environmental Protection Agency (EPA) priority list of hazardous substances (see http://www.atsdr.cdc.gov/substances/toxsubstance.asp?toxid=16). CF was formerly used as an anesthetic and a precursor chemical in the manufacture of chlorofluorocarbons used as refrigerant gases. For these reasons, CF has been manufactured in vast quantities; for example, from 1983 to 1993, the production of CF averaged 203 million kg per annum in the United States alone (http://www.atsdr.cdc.gov/substances/toxsubstance.asp?toxid=16). Large-scale production and use of CF have led to large-scale pollution due to poor handling and storage practices. Currently, CF exists in 474 of the 1,287 priority polluted sites in the United States (http://toxmap.nlm.nih.gov/). Additionally, CF is a strong inhibitor of microbial metabolic processes, including organohalide respiration (2, 3). This property of CF means that microbial remediation of organohalide-polluted sites is problematic where CF is part of the organohalide mixture.

In recent years, there have been two reports of microbial populations that are capable of using CF as a terminal electron acceptor. The first, in 2010, showed the transformation of CF to dichloromethane (DCM) by a mixed Dehalobacter population (4), and the second (from our laboratory) showed CF respiration to DCM; DCM was then transformed to acetate and hydrogen also by a mixed community containing Dehalobacter (5). Here, we report the genome sequence of the CF-respiring Dehalobacter sp. strain UNSWDHB, isolated from the mixed community completely degrading CF (5).

The UNSWDHB strain was sequenced using an Illumina MiSeq sequencer. A total of 3,787,713 paired-end reads were generated with a read length of 251 bases. This represents the equivalent of 230× coverage. Low-quality bases were trimmed from sequence reads before assembly using the SolexaQA software package (6). De novo assembly of the reads was carried out using Velvet 1.2.06 (7) and ABySS 1.3.4 (8) and was tested over a range of k-mers, from 51 to 99 bases. The draft assembly generated using ABySS with a k-mer value of 63 was found to be optimal when evaluated with parameters, such as cohesiveness (number of contigs, 220), N50 (38,707 bp), and the genome size (3,209,125 bp). The draft genome sequence of UNSWDHB has a G+C content of 44.9%.

Initially, the genome of UNSWDHB was compared with that of Dehalobacter sp. CF (9), the only other known CF-respiring bacteria. The comparison showed that 246 genes are specific to the UNSWDHB strain, whereas 226 genes are present in the Dehalobacter sp. CF strain but absent in UNSWDHB. In a more comprehensive analysis, UNSWDHB was compared with all sequenced Dehalobacter strains (9–11). This comparison identified 2,243 core genes common to all sequenced Dehalobacter strains. Of five genes specific to the UNSWDHB strain, three genes showed phage-related functional annotations. Also identified in the UNSWDHB genome were genes encoding 17 reductive dehalogenases, 14 of which were shared with Dehalobacter sp. CF and three that appeared to be unique to UNSWDHB.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AUUR00000000. The version described in this paper is version AUUR01000000. The NCBI locus ID for this submission is UNSWDHB.