Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

Abstract

Freshwater microeukaryotes contribute to aquatic productivity, yet the RNA viruses associated with these communities remain incompletely characterized compared with their marine counterparts. Here, we used metatranscriptomics to profile viral diversity across five Finnish freshwater sites (one river and four lakes) and one coastal marine sample from Hiroshima Bay in the Seto Inland Sea, Japan. We recovered 399 viral operational taxonomic units (vOTUs), of which 285 (71.4%) represented RNA viruses distributed across five viral phyla and putatively associated with fungal, plant or algal, metazoan and bacterial hosts. DNA viruses formed a smaller component of the dataset, including bacteriophage-like vOTUs with transcripts encoding replication, structural, packaging, and lysis proteins. Two vOTUs, which were detected in the Vantaanjoki river sample, were putatively classified within the family Marnaviridae, which comprises RNA viruses that infect protists in marine and freshwater environments. Both vOTUs encoded conserved replication and picornavirus-like capsid domains, and one represented a near-complete dicistronic genome. RNA-dependent RNA polymerase (RdRp) -based phylogeny placed these vOTUs in a strongly supported lineage outside the currently recognized genera within the family Marnaviridae, supporting their provisional assignment to the candidate genus Vandarnavirus proposed here within Marnaviridae. Whole-genome comparisons using the IMG/VR v4 database revealed genetic similarities between the vOTUs representing the candidate Vandarnavirus genus and picorna-like virus sequences from freshwater, wetland, saltmarsh, and estuarine metatranscriptomes. These findings expand the known ecological range of marnavirus-like RNA viruses and identify freshwater habitats as under-sampled reservoirs of microalgae-associated viral sequences.