Metagenomic Characterization of Microbial Communities in Groundwater Associated with Contaminated Land

Bacteriacan be instrumental during the <i>in-situ</i>remediation 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 (<i>e.g.</i><i>Thermoanaerobacteriaceae</i> and<i>Thermoanaerobacterium</i> phage THSA-485A).The hostpopulations identified included several classes of bacteria (<i>e.g.</i> 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 <i>Pseudomonas,Polycyclovorans, Methylocaldum</i> and <i>CandidatusMagnetobacterium</i> species. Gene orthologs for enzymes of the lower hydrocarbon-degradingpathways were amongst the most represented at the site (<i>e.g. pcaC</i> and <i>praC</i>), and thegenomes of various degrader populations were successfully assembled (<i>e.g. Oxalobacteraceae</i> and <i>Rhodocyclaceae</i>). 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 (<i>e.g. adhC</i> and <i>galB</i>). 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.

Name dc:type.qualificationname

Doctor of Philosophy

Level dc:type.qualificationlevel

Doctoral Thesis

Grantor dc:publisher.institution

Queen's University Belfast

Year dc:date.issued

2019

Author dc:creator

• Costeira, Ricardo

Advisors dc:contributor.advisor

• Larkin, Michael
• Allen, Christopher

Language dc:language

eng

Identifier URI

https://pure.qub.ac.uk/files/174377622/SuplementaryFile_SF6.1.xlsx

Identifier

oai:pure.qub.ac.uk/portal:studenttheses/74e888e0-63ff-4b02-afbd-3f3fe5b4f443
https://pure.qub.ac.uk/en/studentTheses/74e888e0-63ff-4b02-afbd-3f3fe5b4f443

OAI identifier oai:identifier

oai:pure.qub.ac.uk/portal:studenttheses/74e888e0-63ff-4b02-afbd-3f3fe5b4f443