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

Abstract

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.

Metagenomic Analysis Reveals Microbial Interactions at the Biocathode of a Bioelectrochemical System Capable of Simultaneous Trichloroethylene and Cr(VI) Reduction

“… ** Genes found in Dehalococcoides sp. genome where genomic rearrangement occurred during culture ( Yohda et al, 2017 ). *** Gene from D. mccartyi strain 11a5 where a circular extrachromosomal genetic element and a new tetrachloroethene reductive dehalogenase gene were found ( Zhao et al, 2017 ).…”

“… ** Genes found in Dehalococcoides sp. genome where genomic rearrangement occurred during culture ( Yohda et al, 2017 ). …”

“…We also found RdhAses (GenPept: MBF4481741, MBF4481742, MBF4481741, MBF4481742, MBF4482271) similar to those already found in D. mccartyi strains VS , UCH-ATV1 and 11a5 (8658308VS, 658312VS, DEHALATV1_RS06695, DEHALATV1_RS06700, Dm11a5_1352). The rdhA genes of these strains were found embedded in distinct genomic islands with different predicted integration sites (i.e., 8658308VS, 8658312VS; McMurdie et al, 2009 ), or reported in genomes where genomic rearrangement occurred during culturing (i.e., DEHALATV1_RS06695, DEHALATV1_RS06700; Yohda et al, 2017 ) or found in D. mccartyi strain (11a5) with circular extrachromosomal genetic elements allowing gene mobilization/horizontal transfer ( Zhao et al, 2017 ). Overall, in these strains, gene mobilization occurs.…”

Dehalococcoides mccartyi Strain GEO12 Has a Natural Tolerance to Chloroform Inhibition

“…The low number of rdh genes may be indicative of evolutionary history, suggesting excision of inactive rdh genes in order to gain an advantage in growth, as has been reported for other Dehalococcoides genomes. 54,55 Inhibition of Dechlorination in Dehalococcoides by Chloroform. Previous studies have described the inhibition of TCE dechlorination by chloroform in microbial consortia containing Dehalococcoides.…”

Complete Genome Sequence of Petrimonas sp. Strain IBARAKI, Assembled from the Metagenome Data of a Culture Containing Dehalococcoides spp

“…We obtained single colonies after several rounds of shake agar cultures using the medium for Desulfovibrio species. Then, we supplemented the clone in the culture of the isolate D. mccartyi UCH-ATV1 ( 2 ). As expected, the mixed consortium exhibited significantly high dechlorination activity for trichloroethene.…”