Abstract

--- - Background The fjords of Chilean Patagonia (similar to 41.5-55.9 degrees S) lie at the forefront of global warming, where rising temperatures threaten to disrupt microbial processes central to ocean productivity and carbon cycling. Despite their ecological relevance, the diversity and environmental drivers of viral communities, both giant viruses and prokaryotic viruses, remain poorly understood in high-latitude fjords. - Results Here, we leveraged metagenomics across a 500 km latitudinal gradient in Chilean Patagonia (4-10 degrees C; salinity 18-33 PSU) to decode the structure and distribution of marine viral communities. We recovered 126 giant viruses (polB sequences dereplicated at 100% average nucleotide identity) and 9213 prokaryotic viruses (viral contigs dereplicated at 95% average nucleotide identity), primarily affiliated with Prasinoviridae (proposed genus g177, order Algavirales) and Caudoviricetes, respectively. Consistent with global-scale studies, temperature emerged as the strongest driver structuring viral communities, outpacing the effects of salinity, depth, dissolved oxygen, chlorophyll-a, and geography. Viral diversity was consistently higher in the northern warmer waters (7.5-10.4 degrees C), while southern colder sites (4.0-7.4 degrees C) harbored less diverse and compositionally distinct communities. Giant viruses shift from Pandoravirales and AG_04 (Algavirales) at lower temperatures to increasing dominance of IM_01 (Imitervirales) and Prasinoviridae (AG_01) in warmer habitats. Prokaryotic virus communities also displayed strong temperature structuring, with additional influence from salinity. - Conclusions Together, our findings underscore the environmental sensitivity of viral communities in subpolar marine systems and highlight their vulnerability to climate-driven changes. Given the critical role of viruses in microbial turnover, nutrient cycling, and ecosystem resilience, shifts in their diversity and structure may have far-reaching consequences for biogeochemical fluxes and food web dynamics in the fjords of Chilean Patagonia.