A remarkably diverse and well-organized virus community in a filter-feeding oyster

• DOI: 10.1186/s40168-022-01431-8
• Publication Date: 2023-01-07T10:05:53Z
• Authors: Jing-Zhe Jiang; Yi-Fei Fang; Hong-Ying Wei; Peng Zhu; Min Liu; Wen-Guang Yuan; Li-Ling Yang; Ying-Xiang Guo; Tao Jin; Mang Shi; Tuo Yao; Jie Lu; Ling-Tong Ye; Shao-Kun Shi; Meng Wang; Ming Duan; Dian-Chang Zhang
• Keywords: Circovirus; 0301 basic medicine; Mollusk; Evolutionary biology; Plant Science; Gene; Microbial ecology; Agricultural and Biological Sciences; 03 medical and health sciences; Viral-like particle enrichment; Crassostrea hongkongensis; Genetics; Animals; Seawater; 14. Life underwater; Crassostrea; Viral Diseases in Livestock and Poultry; Virus-Host Interactions; Biology; Shellfish; Virus classification; Genome; Ecology; Bacteria; Oyster; Research; Microbiota; Bivalve; QR100-130; Human virome; Life Sciences; DNA; Ecology and Evolution of Viruses in Ecosystems; Ostreidae; 3. Good health; Fish; Marine bacteriophage; Fishery; FOS: Biological sciences; Viruses; Environmental Science; Physical Sciences; Viral RNA Silencing and Plant Immunity; Metagenome; Animal Science and Zoology; Aquatic animal; Metagenomics; Zoology

AbstractBackgroundViruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation.ResultsHere, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oysterCrassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels.ConclusionsIn this study, we generated a first “knowledge landscape” of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems.