Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms-race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies.
Phage-host relationships have been studied intensively since the early days of molecular biology. In the late 1970s, while viruses were found to be ubiquitous, it was assumed that they were present in relatively low numbers and that their effect on microbial communities was low. With the increasing availability of new molecular techniques that allow studies of microbial communities without the need to culture them, it is now realized that viruses greatly outnumber bacteria in the ocean and other environments, with viral numbers (~10E7–10E8 ml−1) often tenfold larger than bacterial cell counts (~10E6ml−1). Thus, bacteria are confronted with a constant threat of phage predation.
The Red Queen hypothesis posits that competitive environmental interactions, such as those displayed by hosts and parasites, will lead to continuous variation and selection towards adaptation of the host, and counter-adaptations on the side of the parasite. Arguably, nowhere is this evolutionary trend so pronounced as in phage-microbe interactions. This is due to the extremely rapid evolution and turnover of phage particles, causing acute pressure on microbial communities to evade infection and killing by phages. In fact, the arms-race between phage and bacteria is predicted to have had an impact on global nutrient cycling, on global climate, on the evolution of the biosphere, and also on the evolution of virulence in human pathogens.
A recent study focuses on the evolution of three of the most well studied microbial defense mechanisms against phage: the restriction-modification system, the recently discovered CRISPR (clustered regularly interspersed palindromic repeats) loci together with their associated cas genes, and the abortive infection system (summarized in Table 1). This research first describes these defense systems, as well as the counter-adaptations that evolved in the phage to allow escape from bacterial defense. It also discusses features that are common to many microbial defense systems, such as rapid evolution, tendency for lateral gene transfer (LGT), and the selfish nature of these systems.