Dataset of Oyster Virome and the Remarkable Virus Diversity in Filter-Feeding Oysters

Background:Viruses are the most abundant biological entities, and they play critical roles in entire ecosystems. Nevertheless, current knowledge about them is no more than 1% of the estimated diversity of the Earth’s virosphere. Oysters are filter-feeding molluscan bivalves and are ideal sentinels for marine virus exploration and viral ecology studies. Results: Here we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit (vOTU) contigs and 3,473 high-quality viral genomes, enabling the first comprehensive overview of viral communities in oysters. As in other marine viromes, families Siphoviridae, Podoviridae, and Myoviridae are dominant in the DOV. However, Circoviridae is the most abundant family among the high-quality genomes, indicating that oysters may be their potential hotspots. Despite performing target amplification for RNA genomes, the diversity of RNA viruses was much lower than the diversity of DNA viruses. Notably, most of the vOTUs in the DOV were previously undescribed viruses and could not be clustered with any sequences in three reference datasets. Three approaches (based on references, vOTUs, and auxiliary metabolic genes) consistently showed that host health status, location, and sampling date had potential impacts on virome structures. Conclusions: This study highlights the practicality of oysters for marine virus exploration and provides a new direction to understand the relationship between marine bivalves and the environment.

RNA Viruses in Aquatic Unicellular Eukaryotes

Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.

Marine Virus Survey Reveals Biodiversity Hot Spots

Ocean samples collected from around the world produced a twelvefold increase in the number of marine viruses known. A portion of the Arctic Ocean has “surprisingly high diversity.”

Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host–Viral Relationships in an Arctic Marine Ecosystem

The Arctic marine environment experiences dramatic seasonal changes in light and nutrient availability. To investigate the influence of seasonality on Arctic marine virus communities, five research cruises to the west and north of Svalbard were conducted across one calendar year, collecting water from the surface to 1000 m in depth. We employed metabarcoding analysis of major capsid protein g23 and mcp genes in order to investigate T4-like myoviruses and large dsDNA viruses infecting prokaryotic and eukaryotic picophytoplankton, respectively. Microbial abundances were assessed using flow cytometry. Metabarcoding results demonstrated that seasonality was the key mediator shaping virus communities, whereas depth exerted a diversifying effect within seasonal virus assemblages. Viral diversity and virus-to-prokaryote ratios (VPRs) dropped sharply at the commencement of the spring bloom but increased across the season, ultimately achieving the highest levels during the winter season. These findings suggest that viral lysis may be an important process during the polar winter, when productivity is low. Furthermore, winter viral communities consisted of Operational Taxonomic Units (OTUs) distinct from those present during the spring-summer season. Our data provided a first insight into the diversity of viruses in a hitherto undescribed marine habitat characterized by extremes in light and productivity.