From CRISPR-Cas to Argonautes: Defense systems of bacteria and archaea in the hydrothermal deep subsurface

Microbial defense systems are central to virus-host interactions and thus to microbial survival but remain poorly studied in microbial communities of extreme environments. Here we examine the repertoire and distribution of microbial defense genes in hydrothermally influenced deep subsurface sediments and rocks of the Guaymas Basin (Gulf of California). Restriction-modification and abortive infection systems were broadly distributed across the examined sediment depths, and clustered, regularly interspaced short palindromic repeats-Cas systems were primarily detected within temperate surficial sediments. Prokaryotic Argonaute genes were found mostly in archaeal MAGs at elevated temperatures up to 81.8°C. Overall defense gene repertoire declines downcore, as temperature increases and phylogenetic host range narrows, with phylogeny as the decisive control factor. We suggest that these defense systems, together with DNA repair mechanisms, protein maintenance activities, and RNA modification pathways, constitute a survival toolkit for the hydrothermally influenced subsurface, where energy limitation and temperature extremes select for resilient microbial communities.