Persistence of photolyase genes in the deep ocean

Despite the absence of sunlight in the deep ocean, microbial genomes from bathypelagic waters (below 1000 m) may retain genes associated with ultraviolet (UV) stress responses. Whether these genes remain functionally relevant, selectively maintained, or simply persist through vertical transport from surface waters remains poorly understood. Photolyases are light-dependent DNA repair enzymes that reverse UV-induced DNA damage and are typically associated with sunlit surface environments. Here, we investigated the diversity, distribution, and evolutionary persistence of photolyase genes (Cryptochrome/photolyase family) across the global ocean using 346 publicly available marine metagenomes and 4190 metagenome-assembled genomes (MAGs) from Tara OCEANS and Malaspina expeditions, together with 1350 previously unpublished MAGs spanning epipelagic to bathypelagic depth from multiple marine expeditions. We identified 37,947 photolyase genes across diverse bacterial and archaeal lineages, including a substantial proportion recovered from bathypelagic depths, although their relative abundance declined with depth. Phylogenetic analyses revealed no clear separation between surface and deep ocean photolyases, including taxa with limited expected connectivity to surface waters. These results suggest that the persistence of photolyases in the deep ocean is shaped not only by the vertical transport of particle-associated microorganisms from surface waters, but also by long-term evolutionary conservation of retained DNA repair capabilities.