Arctic microbial exploration: a bioinformatics approach

Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)

Abstract

The Arctic environment is a microbe-driven biome where microorganisms actively shape the environment and mediate biogeochemical cycles. Due to the life-challenging conditions that this environment poses (e.g. subzero temperatures, water and nutrient depletion), microorganisms have developed coping metabolic pathways and enzyme adaptations, constituting a reservoir for the bioprospecting of new molecules and cold-adapted enzymes. The advent of cheap and diffused sequencing technologies has boosted the study of environmental biodiversity and genome reconstruction. In this thesis I use different sequencing technologies (i.e. Illumina and Nanopore), bioinformatics approaches (i.e. amplicon and whole shotgun metagenomics, and metatranscriptomics) and pipelines for the characterization of Arctic microorganisms. In particular, this thesis presents i) PhyloPrimer, a new online user-friendly software for the semi-automated design of taxon-specific primers to perform taxonomic and functional driven studies, ii) the characterization of microbial community distribution in unexplored englacial channels using the universal 16S ribosomal RNA gene. I then present iii) the LongMeta pipeline used to screen whole shotgun metagenomic sequencing data and used to explore microbial communities and their role in rock weathering and nitrogen fixation processes in proglacial systems. Finally, iv) I explore cold-adapted microbial communities in the active layer of proglacial permafrost to create the cold-adapted predicted protein (CAPP) database to provide sequence data to cold-adapted protein bioengineering studies. Overall, this thesis presents the application and development of several sequencing technologies and computational pipelines available for microbial characterization and bioprospecting, exploring the microbial communities of rapidly changing environments in the Arctic: the glacier, its proglacial system and soil permafrost.
Date of Award21 Jan 2021
Original languageEnglish
Awarding Institution
  • The University of Bristol
SupervisorGary L A Barker (Supervisor) & Marian L Yallop (Supervisor)

Keywords

  • bioinformatics
  • microbial diversity
  • Arctic
  • metagenomics
  • metatranscriptomics

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