Metagenomic Characterization of Microbial Communities in Groundwater Associated with Contaminated Land

Abstract

Bacteriacan be instrumental during the in-situremediation of contaminating hydrocarbons. At the same time, bacteriophagepredation may influence the genetic diversity and production of bacterial degraders.This work aimed to characterize the total microbial communities surrounding ahydrocarbon plume. To achieve this, a joint metagenomic study of the virusesand bacteria populating an old gasworks site was carried for one year. Theviral, bacterial and functional gene diversities found were influenced by thepH of the groundwater. Both potential hydrocarbon degraders and theirbacteriophages were dominant at the site (e.g.Thermoanaerobacteriaceae andThermoanaerobacterium phage THSA-485A).The hostpopulations identified included several classes of bacteria (e.g. Clostridia and Proteobacteria), andniche-specific phage-host associations were revealed. These occurred at theedge of the site and at the core of the plume, where pH was the highest (9.52).Thirty-six viral generalists were discovered, with ‘BGW-G9’ having the broadesthost range across 23 taxa, including Pseudomonas,Polycyclovorans, Methylocaldum and CandidatusMagnetobacterium species. Gene orthologs for enzymes of the lower hydrocarbon-degradingpathways were amongst the most represented at the site (e.g. pcaC and praC), and thegenomes of various degrader populations were successfully assembled (e.g. Oxalobacteraceae and Rhodocyclaceae). Biodegradation genes wereleast abundant at the core of the plume. Auxiliary metabolic genes (AMGs) that couldcontribute to the degradation of hydrocarbons were identified in the viromes (e.g. adhC and galB). Altogether, the broad host ranges and AMGs identified arepresumed to affect the biodegradation processes conducted by various bacteriaof the environment studied. This thesis for the first time characterized thephages, their hosts and AMGs associated with a contaminant plume.

Date of Award	Dec 2019
Original language	English
Awarding Institution	Queen's University Belfast
Supervisor	Leonid Kulakov (Supervisor), Mike Larkin (Supervisor) & Christopher C R Allen (Supervisor)