Periodic Reporting for period 2 - PredProkDef (Predicting of Prokaryotic Defence Distributions)
Okres sprawozdawczy: 2022-02-01 do 2023-01-31
Bacteria are one of the most highly abundant organisms on earth, and are crucial for global geochemical cycling. Phages are estimated to outnumber bacteria by 10-100 : 1, depending on the environment. Therefore the scale alone of these interactions warrants the need for a deep understanding of their evolution and ecology. Moreover, phage biology has a long history of contributing to biotechnology advances, and in recent years the study of bacterial immune systems has continued this trend. For example, the discovery and use of CRISPR has led to advances in genome editing, gene-drives and diagnostic technologies. Newly discovered phage immune defence systems may provide similar advances. Overall, a better understanding of the role of ecology in shaping these systems may provide unique insights.
There are 3 major objectives of this action, with the steps involved divided into work packages (WP). Objective I aims to study the impact of spatial structure on bacterial defence in a model system. This system is the environmental bacterium Serratia sp. ATCC39006 and will contrast the abortive infection system, toxIN, and a selfish immune system, CRISPR, by manipulating spatial structure and quantifying the relative benefits to each system during phage infections Objective II uses metagenomic data and newly developed models to identify these forms of immune system in natural environments. Objective III uses the insights gathered from objectives I and II to classify a newly discovered immune system as other selfish or altruistic, and characterise the mechanism of this system experimentally.
In addition to research results, the action has achieved the auxiliary objectives of developing technical skills and independence via training and conference attendance. I presented the paper mentioned above at CRISPR 2021, Paris and FAOBMB, Christchurch, and delivered a research seminar to my host institution (Dept. of Microbiology and Immunology, University of Otago). I also attended training for computational biology at the Research Bazaar events at the University of Otago. Lastly, an outreach workshop was held at the end of the fellowship using nanopore sequencing to profile microbial communities in a popular UK botanical garden (The Eden Project).