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Title: Metagenomic characterization of microbial communities in groundwater associated with contaminated land
Author: Costeira, Ricardo
ISNI:       0000 0004 8508 1507
Awarding Body: Queen's University Belfast
Current Institution: Queen's University Belfast
Date of Award: 2019
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Bacteria can be instrumental during the in-situ remediation of contaminating hydrocarbons. At the same time, bacteriophage predation may influence the genetic diversity and production of bacterial degraders. This work aimed to characterize the total microbial communities surrounding a hydrocarbon plume. To achieve this, a joint metagenomic study of the viruses and bacteria populating an old gasworks site was carried for one year. The viral, bacterial and functional gene diversities found were influenced by the pH of the groundwater. Both potential hydrocarbon degraders and their bacteriophages were dominant at the site (e.g. Thermoanaerobacteriaceae and Thermoanaerobacterium phage THSA-485A). The host populations identified included several classes of bacteria (e.g. Clostridia and Proteobacteria), and niche-specific phage-host associations were revealed. These occurred at the edge 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 broadest host range across 23 taxa, including Pseudomonas, Polycyclovorans, Methylocaldum and Candidatus Magnetobacterium species. Gene orthologs for enzymes of the lower hydrocarbon-degrading pathways were amongst the most represented at the site (e.g. pcaC and praC), and the genomes 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 could contribute to the degradation of hydrocarbons were identified in the viromes (e.g. adhC and galB). Altogether, the broad host ranges and AMGs identified are presumed to affect the biodegradation processes conducted by various bacteria of the environment studied. This thesis for the first time characterized the phages, their hosts and AMGs associated with a contaminant plume.
Supervisor: Larkin, Michael ; Allen, Christopher Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available