Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method

Area of Science:

• Environmental microbiology
• Genomics
• Bioremediation

Background:

• Dehalococcoides bacteria are crucial for bioremediation of chlorinated ethenes but are difficult to cultivate.
• Genome sequencing of Dehalococcoides strains presents significant challenges due to their recalcitrant nature.

Observation:

• A novel Dehalococcoides sp. strain, UCH007, was isolated from Japanese groundwater contaminated with chlorinated ethenes.
• Strain UCH007 demonstrated the ability to dechlorinate trichloroethene, cis-1,2-dichloroethene, and vinyl chloride to ethene.
• A differential reads picking method was developed and applied for sequencing mixed genomic DNA from a co-culture of strain UCH007.

Findings:

• The genome of strain UCH007 comprises a 1,473,548-bp chromosome with 1509 coding sequences.
• The genome encodes 29 putative reductive dehalogenase genes, including pceA, tceA, and vcrA.
• Strain UCH007 is the first identified strain in the Victoria subgroup possessing the pceA, tceA, and vcrA genes.

Implications:

• This study provides valuable genomic insights into Dehalococcoides bacteria, aiding in understanding their bioremediation capabilities.
• The novel sequencing method overcomes challenges in culturing these bacteria, enabling further genomic research.
• The identified dehalogenase genes in strain UCH007 offer potential targets for enhancing bioremediation strategies for chlorinated ethene pollution.