Genome-resolved biogeography reveals multidimensional structuring of freshwater giant viruses across global deep lakes

Giant viruses (GV) are increasingly recognized as important ecosystem regulators, yet their global biogeography remains poorly understood. In this preprint, researchers reconstructed GV metagenome-assembled genomes (MAGs) from 35 globally distributed deep freshwater lakes across five continents, yielding 1,663 non-redundant MAGs and expanding known freshwater GV diversity by an estimated 84% novel species. The MAGs grouped into cosmopolitan and geographically restricted lineages, with 27 cosmopolitan GV species spanning viral lineages including Imitervirales, Pimascovirales, and mirusviruses order Styxvirales. Cosmopolitan species tended to have larger genomes and expanded gene repertoires for host-interaction functions, potentially enabling interactions with diverse hosts. The authors observed stronger distance-decay in community similarity in freshwater than marine ecosystems, indicating that physical connectivity limits GV dispersal. Additionally, 312 and 177 MAGs were almost exclusively associated with the epilimnion and hypolimnion, respectively, with consistent vertical partitioning across lakes, likely tied to thermal stratification. These findings show that GV biogeography in deep lakes is structured by horizontal dispersal limitation, vertical partitioning, and lineage-specific evolutionary histories, providing new insight into how these viruses distribute across global freshwater systems.