Plants host a vast array of microorganisms, crucial for their productivity. With the Food and Agriculture Organization (FAO) highlighting the need to boost global food production by 70% by 2050 to feed the increasing population, scientists are now focusing on plant microbes to enhance yields. As bacteriophages significantly shape host microbiomes, understanding the complex plant virome is vital for developing effective microbiome-assisted agricultural strategies.

Therefore, this project explores bacteriophage diversity in the wheat phyllosphere and its associated drivers. This project was divided into three stages. Stage I included sampling, viral purification, and whole genome shotgun (WGS) sequencing. Stage II involved the construction of a genome catalog encompassing the diversity of bacteriophages on the wheat phyllosphere. Finally, Stage III incorporated further bioinformatics analyses to study specific aspects of the diversity and ecology of phyllosphere phages.

Computational tools reflect a broader shift in phage research, where understanding the genetic and functional diversity of phages has implications for ecology, microbiology, and potential applications in medicine and biotechnology. Therefore, this project focused on bioinformatics tools to address these stages. The introduction of this thesis presents the field of viral metagenomics and the phyllosphere microbiome. Additionally, the discussion outlines the different steps of viral bioinformatic analysis and discusses important factors to consider.

Outcomes from this project were disseminated in peer-reviewed open-access journals and relevant conferences. Also, the two bioinformatics workflows designed for this project are public on GitHub repositories. Overall, five manuscripts were produced. The articles are divided into two main areas of research 1) Case studies on Viral bioinformatics and 2) Reviews on Viral Bioinformatics.

Manuscript I describes the first sequenced bacteriophage population of a phyllosphere environment. Manuscript II focuses on understanding the diversity of Pseudomonas phages in organic waste, and how this diversity changes when cultured with the plant pathogen Pseudomonas syringae DC3000. Finally, Manuscript III characterizes the activity of spontaneously induced prophages of Erwinia and Pseudomonas strains isolated from the wheat phyllosphere.

The second area of research is composed of two manuscripts.
Manuscript IV includes a comprehensive description of computational
tools for the analysis of uncultivated phage genomes. Finally,
Manuscript V is an opinion paper on the different DNA modifications
present in bacteriophages and bacteria. It focuses on state-of-the-art
bioinformatics tools and their implementations for modification
detection using long-read sequencing.