Metagenomic CRISPR reconstruction disentangle bacteria-phage dynamics

Abstract

The high number of bacteriophages in microbial-dominated ecosystems has led to the hypothesis that they are key components that affect the structure and dynamics of microbial populations. However, it remains poorly understood how phages and bacteria manage to coexist, avoiding complete host and virus eradication. This is largely due to the experimental challenge of monitoring the coevolutionary dynamics of phages and their host within complex natural environments. CRISPR sequences provide an unequivocal signal of interaction and the spacers acquisition by the CRISPR-Cas machinery keep an organized record of previous phage infections in the population across time. This concept was validated in a longitudinal metagenomic study of a wastewater treatment plant, which allowed us the reconstruction of different coexisting CRISPR variants in a bacteria of the genus Gordonia and two of their infecting phage genomes. Analysis of CRISPR arrays showed that different Gordonia subpopulations have evolved from an almost clonal population through the acquisition of new spacers against the coexisting phages. Although almost all bacterial cells have one of the CRISPR variants, approximately half of the population has a variant devoid of spacers sequences against the circulating phages. On the other hand, phages have evolved introducing directional changes without preference for CRISPR targeted regions. These observations, contrary to what has been seen under laboratory conditions, which resembles an arm-race dynamics, revealed the complexity of the bacteria-phage dynamics suggesting that the study of communities in natural conditions is crucial to understand such complex interactions.