Analysis Of Diversity Of RNA Viruses From Deep-sea Sediments

Virus is one of the most abundant biological entities in the marine environment,can infect all of the marine organisms.After a virus infect its host,the virus can influence the host's life activities and metabolic processes to directly affect the biochemical cycles of marine environment.At present,the researches of marine viruses mainly focus on the DNA viruses of shallow oceans.However,the investigation on deep-sea viruses,especially on deep-sea RNA viruses,is very limited.in this study,therefore,the RNA viruses from deep-sea sediments were characterized at a large scale,which will be helpful to comprehensively understand the deep-sea RNA viruses.To explore the diversity of RNA viruses in deep-sea environment,79 deep-sea sediment samples from five deep-sea habitats(hydrothermal vent,cold seep,seamount,ocean basin and mid-ocean ridge)of the Pacific Ocean,Atlantic Ocean and Indian Ocean were used.Based on virus isolation,nucleic acid extraction,amplification and metagenome sequencing,the deep-sea RNA viruses were characterized.The results showed that there were 384902 RNA viruses in deep sea,of which only 7.27% viruses were homologous with the known viruses and 92.73% viruses were unknown,indicating that there existed a large number of unknown RNA viruses in deep sea.Among the known RNA viruses,69.23%viruses belonged to the viruses of prokaryotes,while 26.26% viruses were eukaryotes' viruses.The known RNA viruses in deep sea belonged to 22 viral families,of which the relative abundance of 8 viral families were more than 1%.They were Microviridae,Poxviridae,Herelleviridae,Rudiviridae,Genomoviridae,Myoviridae,Inoviridae and Geminiviridae.In addition,the relative abundance of 14 viral families were less than 1%,including Picornaviridae,Siphoviridae,Podoviridae,Nimaviridae,Phycodnaviridae,Circoviridae,Retroviridae,Coronaviridae,Betaflexiviridae,Caliciviridae,Closteroviridae,Iridoviridae,Paramyxoviridae and Baculoviridae.The results indicated that among the 22 viral families,12 viral families(Microviridae,Poxviridae,Podoviridae,Rudiviridae,Genomoviridae,Herelleviridae,Picornaviridae,Retroviridae,Iridoviridae,Myoviridae,Siphoviridae and Nimaviridae)were distributed in hydrothermal vents,cold seeps,seamounts,ocean basins and mid-ocean ridges.Geminiviridae appeared in four deep-sea habitats except for cold seep.Paramyxoviridae only appeared in mid-ocean ridge,while Iridoviridae appeared in cold seep at a low abundance.The results of viral diversity analysis showed that the diversity of RNA viruses in mid-ocean ridge was the highest.These results indicated that the diversity of viruses in deep-sea sediment samples was high and the distribution of viruses was related to the deep-sea environment.Our findings were helpful to understand the diversity of RNA viruses in deep sea,and enrich our knownledge about marine viruses.Based on the analysis of circular genomes,925 deep-sea RNAs with complete genomes(circular genomes)were obtained.Among them,the largest circular viral genome was 22612 bp,while the shortest genome was 1381 bp.The results showed that only 16 circular genomes shared homology with the known viruses.The hosts of these 16 RNA viruses were eukaryotes,of which 68.75% hosts were vertebrates and 18.75% hosts were invertebrates.These known RNA viruses with circular genomes belonged to 6 viral families,including Picornaviridae,Retroviridae,Coronaviridae,Betaflexiviridae,Caliciviridae and Closteroviridae.The results revealed that there was a high diversity of viruses in deep sea,and the distribution of viruses was associated to the deep-sea environment.Our findings on the RNA viruses with circular genomes in deep sea would be helpful for us to enrich the knowledgement about the diversity of deep-sea RNA viruses.The analysis of functional genes revealed that the genes encoded by deep-sea RNA viruses were involved in the host metabolisms,such as carbohydrate transport and metabolism,lipid transport and metabolism,biosynthesis and decomposition of secondary metabolites,indicating that the deep-sea RNA viruses had a pool of functional genes.In this study,it was found that 5418 genes of RNA viruses were related to the replication of genome and the expression of genes.Among them,5007 genes encoded RNA dependent RNA polymerase and 411 genes encodes reverse transcriptase,which were the marker genes of RNA viruses.The results showed that the genes related to methane metabolism were mainly distributed in cold seeps,hydrothermal vents and ocean basins.The genes related to sulfur metabolism mainly appeared in hydrothermal vents,cold seeps,mid-ocean ridges and seamounts.The RNA viruses in deep sea encoded a large number of genes related to sulfur metabolism and methane metabolism,the distribution of these genes was closely related to different deep-sea environments.These results was helpful to understand the important roles of viruses in deep sea and the interactions between viruses and hosts.Among the 22 known viral families revealed in this study,some viruses of Poxviridae,Retroviridae and Paramyxoviridae had potential pathogenicity to humans.Among them,the abundance of Poxviridae was the highest,which was widely distributed in 79 deep-sea sediment samples.The abundance of Retroviridae was slightly low,which mainly appeared in DP210,DP209,DP214,DP218,DP192,DP220,DP188 and DP095 samples.Paramyxoviridae had a low abundance,which was only distributed in DP091.Therefore,there were the deep-sea RNA viruses that had a potential threat to human health.The results of this study on the pathogenic RNA viruses in deep sea could provide a biosecurity support for the exploration and utilization of deep-sea resources.