PhD Exit Seminar for Nadia Morson (Edwards Lab)

Phage-mediated mobile genetic elements identified in Dehalococcoidia, Chloroflexi bacteria used for bioremediation

Abstract

Chlorinated compounds, such as vinyl chloride (VC), are persistent, carcinogenic soil and groundwater contaminants. Organohalide-Respiring Bacteria (OHRB) are used for their ability to reductively dechlorinate these chlorinated compounds to decontaminate soil and groundwater in a process called bioremediation. Dehalococcoidia, including Dehalococcoides and Dehalogenimonas, are deep-branching bacteria from the Chloroflexi phylum. Dehalococcoidia are obligate OHRB that use reductive dehalogenase enzymes, RdhA, for organohalide respiration which are encoded by reductive dehalogenase homologous genes, rdhA. There is substantive evidence that rdhA were acquired by horizontal gene transfer and are found on Genomic Islands (GIs), Integrative and Mobilizable Elements (IMEs), transposable elements, and bacteriophages (phages). However, there has been no proven mechanism of horizontal gene transfer to date. The VC reductase-encoded genomic islands, vcrA-GI and bvcA-GI, were the focus of this work. Experiments were designed to selectively induce the vcrA-GI to characterize the mechanism of horizontal gene transfer. While there was evidence for replication and circularization of the vcrA-GI, there was no evidence to support the selective induction of the vcrA-GI nor gene transfer for over 4 years of study. On the other hand, the bvcA-GI was predicted to be incorporated in a phage genome in Dehalococcoides, prompting the isolation and sequencing of phage fractions of Dehalococcoides-containing cultures. A hybrid metagenome sequencing approach was used because it combines short- and long-read technologies for a cost-effective, high-quality assembly. The bvcA-GI was not found in a phage genome but a sub-group of IMEs, called IME1s, were found in extremely high abundance in the metavirome. Upon bioinformatic inspection, IME1s shared a conserved structural organization and met the criteria of Phage-Inducible Chromosomal Islands (PICIs). PICIs are a well-studied class of genetic elements which manipulate the phage lifecycle for their benefit and package into phage particles. Six new IME1s were identified in Dehalococcoides and Dehalogenimonas and were re-categorized as PICIs, revealing the first horizontal gene transfer mechanism in Dehalococcoidia. This work advances our understanding of horizontal gene transfer in OHRB which are difficult to study using classical approaches. An improved understanding of their lifecycle will enhance the efficiency of bioremediation of contaminated sites globally.

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Join Zoom Meeting

Wednesday, December 8th, 2021 at 9:30 am

https://utoronto.zoom.us/j/86259087344

Meeting ID: 862 5908 7344

Host: Elizabeth Edwards (elizabeth.edwards@utoronto.ca)

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