A substantial proportion of CRISPR spacers, up to three times higher than self-targeting spacers, are acquired from DNA of other prokaryotes in subsurface environments.
CRISPR systems in (MAGs) from two subsurface environments were analyzed using over 1 Tb of sequencing data.
The acquisition of foreign DNA spacers is partly influenced by the abundance of the MAG containing the protospacer and the total number of CRISPR arrays it has.
Almost all types of exhibit spacer acquisition from foreign prokaryotic DNA, with varying preferences for subtypes depending on the ecosystem.
These findings provide insights into the diversity of CRISPR spacers in natural microbial communities and clarify the origins of unmatched spacers in public databases.
Simplified
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer analyses revealed a very specific acquisition of CRISPR spacers derived from genomes of related species or from closely interacting episymbiont genomes as recently shown for subsurface archaea. However, the origin of most of the spacers that can be found in from natural environments has not been deciphered. Here, by analyzing CRISPR-Cas systems of (MAGs) from two subsurface environments spanning more than 1 Tb of sequencing data, we show that a substantial proportion of CRISPR spacers are acquired from DNA of other prokaryotes inhabiting the same environment. As such, we found that the number of respective spacers can be up to three times higher than the number of self-targeting spacers. Statistical analyses demonstrated that the acquisition of CRISPR spacers from other prokaryotic genomes is partly explained by the relative abundance of the MAG containing the protospacer, as well as by other factors, such as the total number of CRISPR arrays present in a MAG with the respective spacers. Further, we found that spacer acquisition from foreign prokaryotic DNA occurs in almost all types of CRISPR-Cas systems, but shows preferences for subtypes of CRISPR-Cas systems that differ across the investigated ecosystems. Taken together, our results shed new light on the diversity of CRISPR spacers in natural microbial communities and provide an explanation for some of the many unmatched spacers in public databases.
Key numbers
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Proportion of with Foreign Matches
Percentage of clusters in Guaymas Basin with .
3×
Prokaryote-targeting Clusters vs. Self-targeting
Number of prokaryote-targeting clusters compared to self-targeting clusters.
141,557
Total Clusters Detected
Total number of clusters extracted from metagenomic reads.
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