Random targeting of prokaryotic genomes by bacterial CRISPR-Cas systems in natural environments

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes provide archaea and bacteria with adaptive immunity to invading mobile genetic elements (MGEs), like viruses. Recently, we showed that CRISPR-Cas systems of uncultivated archaea do not only target MGEs, but also harbour spacers matching protospacers in their episymbiont's genome. However, this alone does not explain the tremendous diversity of spacers that is generally found in CRISPR-Cas systems from natural environments. We therefore tested the hypothesis that bacterial CRISPR spacers match genomic DNA of other prokaryotes inhabiting the same environments. Applying metagenomics, we investigated the CRISPR-Cas systems of metagenome-assembled genomes (MAGs) from (non-)hydrothermal sediments in the Guaymas Basin (Gulf of California, Mexico) and groundwater of the cold-water geyser Wallender Born (Wallenborn, Germany). We found that bacterial CRISPR-Cas systems have acquired spacers matching a large diversity of different prokaryotic genomes in their respective environment. Analyses of bacterial CRISPR-Cas systems did not reveal a subtype associated with increased uptake of spacers from prokaryotic DNA. However, our results indicate that the selectivity of spacer acquisition is influenced by the number of different CRISPR-Cas subtypes found in a genome. Our data show that the respective bacterial genomes encode for proteins potentially involved in the uptake and subsequent degradation of environmental DNA. We consequently posit that DNA uptake for either horizontal gene transfer or as a source of nutrients facilitates the acquisition of spacers from prokaryotic DNA. Our results shed new light on the diversity of spacer populations in natural communities and provide an explanation for some of the many unmatched spacers in public databases.