BACTERIA-PHAGE ANTAGONISTIC COEVOLUTION

Prokaryotes are faced with a constant threat of predation, and have developed a broad range of antiviral defense mechanisms that act at every stage of the phage life cycle. While previous studies of bacterial defense systems were focused on the mechanistic basis for their activity, little is known about what determines the choice of anti-phage strategies at the population level. Using bacteria-phage co-evolution approach one can not only study known defense strategies, but also detect novel ones, as the memory of host-predator interactions could be recorded in the genomes of bacteria as rearrangements at specific loci, and could be monitored during real-time evolutionary experiments.

In this work we performed over 70 separate coevolution experiments with dozens of strains of Bacillus and Thermus and their phages. Each bacterial strain was infected with one of its phages in 500 μl of liquid media, allowing coevolution for seven days with serial daily transfers. Whole genome sequencing of bacterial and phage genomes was performed, followed by analysis of genome changes suspected as responsible for phage and bacterial survival during the multiple coevolution passages.

Different bacteria-phage growths dynamics were observed during co-incubation, indicating different defense strategies of bacteria. Mutations in phage receptors, diversification of cell wall receptors, lysogenisation, and rearrangements in CRISPR arrays were among most common defense strategies of bacteria. In addition, multiple short fragment inversions were detected in the genome of Thermus strains after phage infection; further experiments are required to discover the mechanisms of these rearrangements.