Bioprospecting is the process by which organisms are investigated for natural products (NPs) that can be of societal benefit. The cryosphere is a prime region for bioprospecting because it has extreme environmental conditions that increase the probability of NP novelty, it is underexplored, and it is threatened by global climate change. Initially, 16S rRNA gene amplicon analysis was used to identify environments with high bioprospecting potential in a Svalbard glacier system (Chapter 3). Bacteria showed strong habitat preference, suggesting niche specialisation and subsequent vulnerability to climate change. Phylotypes do not provide functional information about microbes, therefore, shotgun metagenomics was used to understand the high potential environments better. Following the construction and testing of a bioinformatics workflow (Chapter 8), a collection of 74 metagenome assembled genomes (MAGs) from Svalbard cryoconite, soil and seawater (Chapter 4) and 121 MAGs from the Scărișoara Ice Cave (Chapter 7) were constructed. These MAGs were taxonomically classified, revealing several novel species. The spatial distribution of MAGs across several sites, together with identification of genes in major biogeochemical pathways was explored to understand microbe nutrient needs and look for signs of cooperation between co-occurring MAGs. Genome-mining was used to screen the MAGs for potentially useful secondary metabolites (Chapter 5). The MAGs were rich in biosynthetic gene clusters (BGCs) for exopolysaccharides (EPS), carotenoids, and non-ribosomal peptide synthases (NRPS), all of which find utility in the food, cosmetic and pharmaceutical industries. Bioinformatics predictions are limited by information in databases, and functional studies are needed to describe novel functions. Therefore, a functional metagenomic screen was conducted to search for novel coldactive polymerases by cloning soil and cryoconite environmental DNA into cold-sensitive E. coli mutants (Chapter 6). This thesis confirmed enormous diversity and novelty in cryospheric bacteria. Furthermore, adaptations that enable survival in the extreme conditions lend themselves to biotechnological applications.
|Date of Award||2020|
|Supervisor||Arwyn Edwards (Supervisor) & Andy Mitchell (Supervisor)|
Metagenomics to Explore the Biotechnological Potential of Cryospheric Bacteria
Hay, M. C. (Author). 2020
Student thesis: Doctoral Thesis › Doctor of Philosophy