Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses

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Abstract

Author links open overlay panelXinyi Zhang a, Haitao Wan a, Min Jin b, Liquan Huang a, Xiaobo Zhang aShow morehttps://doi.org/10.1016/j.jare.2023.04.003Get rights and contentHighlights•Global deep-sea sediment RNA viromes reveal 85,059 viral operational taxonomic units (vOTUs), the largest number of RNA viruses known so far.•Most vOTUs (98.28%) are unclassified, indicating a vast reservoir of novel RNA viruses in the deep sea.•A total of 1,463 complete RNA viral genomes are found, expanding our understanding of the RNA viruses in the deep-sea ecosystems.•Ecosystems rather than geographical locations drive the differentiation of deep-sea RNA viral communities.•Viral metabolic genes participate in the ecosystem-driven viral community differentiation via mediating the energy metabolism.AbstractIntroductionViruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles.ObjectivesHowever, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses.MethodsThe viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses.ResultsIn this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems.ConclusionsTherefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.KeywordsDeep-sea sedimentvirome of RNA virusesviral communityvirus-encoded geneRecommended articles© 2023 The Authors. Published by Elsevier B.V. on behalf of Cairo University.



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