Photolyases are light-dependent DNA repair enzymes that reverse UV-induced DNA damage and are typically associated with sunlit surface environments. Despite the absence of sunlight in the deep ocean, few studies have found photolyase genes retained in microbial genomes from bathypelagic waters (below 1000 m). It is not well characterised whether this observation is limited only to certain microbial taxa or a commonly observed pattern throughout the global ocean. Furthermore, whether these genes remain functionally relevant, selectively maintained, or simply persist through vertical transport from surface waters remains poorly understood. Here, we investigated the diversity, distribution, and evolutionary persistence of photolyase genes (Cryptochrome/photolyase family) across the global ocean using 346 publicly available prokaryotic marine metagenomes and 4190 metagenome-assembled genomes (MAGs) from Tara OCEANS and Malaspina expeditions, together with 1350 previously unpublished MAGs from DEPOCA expedition (Microbial Oceanography group, University of Vienna) spanning epipelagic to bathypelagic depths and including particle-associated (PA) and free-living (FL) ecological lifestyles of the microorganisms. 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 evolutionary distinctness between surface and deep-ocean photolyases, including photolyases from bathypelagic free-living prokaryotes and taxa that are expected to have limited 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. These findings challenge the assumption that UV-response genes are restricted to photic environments and highlight the role of dispersal and evolutionary relation, contributing towards shaping the functional potential of deep-ocean microbial communities.

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