Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture

• Published in: Scientific reports 2017-05, Vol.7 (1), p.2230-11, Article 2230
• Main Authors: Yohda, Masafumi, Ikegami, Kentaro, Aita, Yuto, Kitajima, Mizuki, Takechi, Ayane, Iwamoto, Megumi, Fukuda, Tomomi, Tamura, Noriyoshi, Shibasaki, Junji, Koike, Seiji, Komatsu, Daisuke, Miyagi, Sakari, Nishimura, Minoru, Uchino, Yoshihito, Shiroma, Akino, Shimoji, Makiko, Tamotsu, Hinako, Ashimine, Noriko, Shinzato, Misuzu, Ohki, Shun, Nakano, Kazuma, Teruya, Kuniko, Satou, Kazuhito, Hirano, Takashi, Yagi, Osami
• Format: Article
• Language: English
• Subjects: 38/22; 38/23; 45/77; 631/208/726; 631/326/171; 631/326/171/1818; Chlorides; Chloroflexi - classification; Chloroflexi - genetics; Chloroflexi - metabolism; Dehalococcoides; DNA sequencing; Ethene; Ethylene Dichlorides - metabolism; Ethylenes - metabolism; Gene Rearrangement; Genome, Bacterial; Genomes; Genomics - methods; High-Throughput Nucleotide Sequencing; Humanities and Social Sciences; Metagenome; Metagenomics - methods; Microbial Consortia; multidisciplinary; Nucleotide sequence; rRNA 16S; Science; Science (multidisciplinary); Trichloroethene reductive; Vinyl chloride; Vinyl Chloride - metabolism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-02381-0

We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA , and a trichloroethene reductive dehalogenase gene, tceA . The metagenome analysis of the consortium by the next generation sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp. that is highly homologous to D. mccartyi 195 and equipped with vcrA and tceA exists in the consortium. We isolated this Dehalococcoides sp. and designated it as D. mccartyi UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated conditions, we constructed a consortium by mixing D. mccartyi UCH-ATV1 with several other bacteria and performed metagenomic sequencing using the single molecule DNA sequencer PacBio RS II. We successfully determined the complete genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrA and tceA , but lacks bvcA . Comparison with tag sequences of SOLiD 3 Plus from the original consortium shows a few differences between the sequences. This suggests that a genome rearrangement of Dehalococcoides sp. occurred during culture.