Virome Diversity in Three Bat Species in Different Environments in Southern Spain

Viruses represent a major component of global biodiversity and are integral to ecological and evolutionary processes shaping host populations and communities. Bats, with high species richness and ecological diversity, provide a system to examine how host traits and environmental context structure viral communities. Here, we characterize viral diversity from three bat species (Pipistrellus kuhlii, Cnephaeus isabellinus, and Nyctalus lasiopterus) using samples across two environments in southern Spain: a well-preserved Mediterranean forest (Sierras de Cazorla, Segura, and Las Villas Natural Park, CSVNP) and a human-modified wetland-agrosystem mosaic (Doñana National Park, DNP). Metagenomics detected 72 eukaryotic virus species, including viruses reported in mammals, insects, arachnids, and plants. Viral richness and composition varied among samples, bat species, and environments. Samples of P. kuhlii exhibited the highest richness, driven by insect-associated viruses. C. isabellinus showed a higher contribution of vertebrate-related viruses, whereas N. lasiopterus exhibited the lowest richness. CSVNP samples showed higher viral richness and more exclusive taxa, whereas DNP samples exhibited lower richness, with a greater contribution of arthropod-associated viruses, potentially reflecting prey communities. Despite this, diversity metrics were similar between environments, indicating structurally comparable communities composed of distinct taxa. Bat viromes appear to be associated with host ecology, trophic behavior, and environmental context.