Long-Read Metagenomics Reveals Temporal DNA Virome Dynamics and Recovers Sequences of a Major Viral Pathogen at a Sea-Cage Fish Farm

Coastal sea-cage aquaculture environments support dynamic microbial communities, yet their viral components remain poorly characterized. This study profiled DNA viral-like reads recovered from total metagenomes of iron-flocculated seawater concentrates (operationally termed DNA virome) at a rock bream (Oplegnathus fasciatus) sea-cage farm off Geoje Island, Korea, at five time points between July 2024 and May 2025 using long-read Nanopore metagenomics. Multivariate analyses of DNA virome composition indicated temporal patterning in virome composition; samples collected within the cages tended to group together. The DNA virome was dominated overall by bacteriophages of abundant marine bacteria and by viruses infecting picoeukaryotic phytoplankton, and it showed marked temporal turnover during the investigated year: Micromonas-associated viruses became prominent in December, whereas Ostreococcus- and Bathycoccus-associated viruses increased during seasonal rewarming in May, suggesting that environmentally driven changes in microbial host communities may contribute to temporal virome turnover. Pelagibacter phage abundance was positively correlated with that of its potential host Pelagibacter ubique, and both Synechococcus T7-like virus and Synechococcus virus were positively correlated with Parasynechococcus marenigrum, associations that are consistent with, but do not demonstrate, taxon-specific virus–host relationships. Nanopore reads assigned to infectious spleen and kidney necrosis virus, now classified within the species Megalocytivirus pagrus 1, were recovered from samples collected in September 2024 (12,960 bp) and May 2025 (340 bp). Average nucleotide identity analysis indicated that the seawater-derived sequence was most closely related to red seabream iridovirus subtype II, the subtype predominant in Korean cultured marine fish. The seawater virome results and the bioinformatic pipelines developed in this study together may provide a non-invasive approach for tracking temporal virome dynamics and for environmental screening of viral pathogen DNA in sea-cage aquaculture.