AbstractEnvironmental DNA analysis using metagenomics can provide an insight into the taxonomy and functional potential of microbial communities ex situ, without the need for culturing or DNA amplification. However, metagenomics has had limited application to environmental microbial ecology, in particular, to microbial communities in proglacial regions. This thesis aims to contribute to the body of literature on environmental metagenomics through evaluating assemblers for soil microbial ecologists, and subsequently applying metagenomics to investigate microbial communities in proglacial environments.
Assembly of metagenome sequencing reads can improve sequence alignment to taxonomic and functional databases, thereby improving ecological conclusions. However, limited guidance is available for assembler choice by microbial ecologists. The first study in this thesis compares assemblers for soil metagenome data, demonstrating the importance of assembler evaluation and parameterization. The guidance produced was applied to investigate microbial communities in proglacial regions, including fjords and forefields. Proglacial forefields present a unique opportunity to understand microbial colonization in land exposed by glacier retreat. Here, metagenomics was used to investigate microbial diversity and functional potential during forefield succession, alongside comparing the diversity of nitrogen-fixing bacteria between Arctic forefields. This work contributes to our understanding of Arctic microbial ecology, which has significance given the continued exposure of forefield soils during global warming. In addition, metagenomics was used to investigate microbial communities in oligotrophic, dark, saline fjord waters, fed by glacial meltwater. This work highlights the potential of metagenomics to understand uncultured microbial samples and demonstrate areas for further analysis, such as targeting novel genomes.
This thesis has contributed to the literature on metagenomics by providing methodological guidance for microbial ecologists, alongside enhancing understanding of microbial diversity in proglacial regions. It is hoped that this work will inspire others to use metagenomics to explore uncultured microbial samples and to target further analysis or exploration for unique genomes.
|Date of Award
|1 Oct 2019
|Patricia Sanchez-Baracaldo (Supervisor), Alexandre M B Anesio (Supervisor) & Gary L A Barker (Supervisor)