Invaders (and evaders) from the deep!

Hyperthermophilic Archaea of the order Thermococcales have served as an important model for understanding CRISPR-Cas immunity. Yet remarkably little is known about the viruses that have driven the evolution of these archaeal immune systems. To address this gap, we sequenced more than 120 newly isolated Thermococcales genomes together with 70 deep-sea vent metagenomes. Comparative genomics identified six CRISPR-Cas subtypes, including twelve examples of the previously uncharacterized type IV-C family. Functional and structural analyses established the first molecular mechanism of type IV-C immunity, revealing a distinct mode of CRISPR-mediated antiviral defense. To identify the mobile genetic elements that have driven the evolution of these immune systems, we combined CRISPR spacers from cultivated Thermococcales isolates with publicly available and newly generated hydrothermal vent metagenomes. This CRISPR-guided approach uncovered >3000 previously unknown viruses and plasmids infecting Thermococcales, dramatically expanding the known archaeal virosphere. These mobile genetic elements also encode a diverse repertoire of anti-CRISPR proteins, including broad-spectrum inhibitors capable of simultaneously disabling multiple CRISPR-Cas subtypes through previously unrecognized mechanisms. Together, these findings reveal an evolutionary arms race still unfolding beneath the seafloor, where archaeal hosts and their viruses continue to shape one another’s evolution in one of Earth’s most extreme environments.