Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis

Abstract

Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom-designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase-encoding genes.

A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1‐trichloroethane and chloroform

“…While strain PR exhibits higher chloroform and TCA dechlorination rates than most of the Dehalococcoides strains (He et al, 2003;Lee et al, 2013), the growth yields of strain PR from dehalorespiration are comparable with those of Dehalococcoides [1.73 (TCA) and 0.67 (chloroform) by strain PR versus 0.31 to 2.20 (chloroethenes) by Dehalococcoides, unit: gram cell dry weight per mole chlorine removed] (Supporting Information Table S2). This is also consistent with the similar Gibbs free energy changes [ΔG 0′ (pH 7, 25°C)] between reductive dechlorination of chlorinated ethanes/methanes [134.9 kJ/reaction for TCA (Dolfing, 2000) and 170 kJ/ reaction for chloroform (Olivas et al, 2002)] and chlorinated ethenes [166.1 kJ/reaction for TCE (Dolfing, 2000)].…”

Rising Strengths Hong Kong SAR in Bioinformatics

“…Another study aimed to understand the dissimilarity of two new Dehalococcoides mccartyi strains through collaboration between US and Hong Kong scientists. In this study, Lee et al [38] performed a comparative genomics analysis via a microarray and concluded that the observed functional incongruence between the activity and core genome phylogenies of D. mccartyi strains is probably caused by a horizontal shift in significant reductive dehalogenase- [39,40]. The authors of this paper are themselves performing collaborative research.…”

Effects of 1,1,1-Trichloroethane and Triclocarban on Reductive Dechlorination of Trichloroethene in a TCE-Reducing Culture

“…Microbially mediated anaerobic reductive dechlorination is a good strategy for the remediation of chlorinated compounds. For example, TCE can be converted to dichloroethene (DCE), vinyl chloride (VC), and finally non-toxic ethene in a stepwise manner ( Lee et al, 2013 ; Wen et al, 2017 ) by various microorganisms. Dehalococcoides (which belong to Chloroflexi) are the only known bacteria that completely transform TCE all way down to ethene, although many other microorganisms have been found to partially reduce TCE to DCE or VC, including Geobacter, Desulfovibrio, Desulfuromonas (which belong to Proteobacteria), Dehalobacter and Desulfitobacterium (which belong to Firmicutes), and Dehalobium , and Dehalogenimonas (which belong to Chloroflexi) ( Duhamel and Edwards, 2006 ; Maphosa et al, 2010 ).…”