PhD defence by Laura Milena Forero-Junco
PhylloVir: Exploring viral populations’ diversity patterns and their associated drivers on the wheat phyllosphere.
With the Food and Agriculture Organization (FAO) emphasizing the need to increase global food production by 70% by 2050 to meet the growing population's demands, scientists are turning their attention to plant microbes as a strategy to improve plant health. Bacteriophages, which significantly influence the composition of microbial communities in plants, are a crucial aspect to consider. Exploring their diversity is essential for developing effective strategies to improve agriculture through microbiomebased approaches. This research project specifically focuses on exploring the diversity of bacteriophages in the phyllosphere of wheat plants and the factors driving this diversity. The project's emphasis is on harnessing computational tools to advance our understanding of phages, reflecting a broader shift in phage research. This understanding spans genetic and functional aspects of phages, with implications not only in ecology and microbiology but also in potential applications in medicine and biotechnology. This thesis takes a deep dive into the field of viral metagenomics and phyllosphere microbiomes. It employs bioinformatics tools to navigate the stages of analysis, addressing key considerations along the way.
The project's outcomes are available in peer-reviewed open-access journals. Additionally, two bioinformatics workflows created for this project are made publicly available on GitHub repositories. In total, the project yields six manuscripts, divided into two primary research areas: the first area presents case studies on viral bioinformatics, including population composition in the wheat phyllosphere, diversity of Pseudomonas phages in organic waste, and the activity of spontaneously induced prophages in Erwinia and Pseudomonas strains from the wheat phyllosphere. The second research area comprises two manuscripts, one providing a comprehensive overview of computational tools for analyzing uncultivated phage genomes and the other discussing DNA modifications in bacteriophages and bacteria, focusing on bioinformatics tools for modification detection using long-read sequencing.
Assessment Committee
Professor Rob Edwards, Flinders University, Australia
Senior lecturer Gemma Atkinson, Lund University, Sweden
Associate Professor Mette H. Nicolaisen (Chairman), PLEN, University of Copenhagen, Denmark
Supervisors
Professor Lars Hestbjerg Hansen, PLEN, University of Copenhagen, Denmark
Assistant Professor Witold Piotr Kot, PLEN, University of Copenhagen, Denmark
The defence is followed by a reception in meeting room B212 on 2nd floor. Everybody is welcome.