Analysis Of Virome In The Yangtze River And Study On Genetic Diversity

ObjectiveViruses in aquatic ecosystems are characterized by the extraordinary abundance and diversity.Viruses can be regarded as one of the primary causes of morbidity and mortality for aquatic life.And at the same time,aquatic ecological environment may meditate virus intraspecific and interspecific transmission further.Pathogenic viruses in freshwater might be transmitted to human or animals through drinking,swimming,or inhaling aerosol.Besides,viruses in aquatic ecosystems are usually dominated by bacteriophages,which are capable of controlling bacterial communities and regulating biogeochemical cycles.Thus,it is of great necessity to explore the structure of viral communities in aquatic environments so as to ensure sustainable development of water resources.But limited studies have focused on viral communities in river water systems.The Yangtze River,as the third longest river in the world,rises in the Tanggula Mountains and empties into the East China Sea.Thereinto,the Yangtze River Delta region,located in the lower reaches of the Yangtze River,is one of the most densely populated regions on earth and the most economically developed area of China.Here,this study selected the Yangtze River Delta region as the sampling area,and aimed to explore the virome characteristics in the Yangtze River.MethodsTo explore the freshwater virome from the Yangtze River,water samples were collected from each of the six representative river ports: Anqing,Wuhu,Nanjing,Zhenjiang,Changzhou and Nantong.Using viral metagenomic analysis,the virome in the Yangtze River was investigated.The composition of viral communities from different sampling sites was analyzed and compared.Finally,we phylogenetically analyzed the genetic diversity of main virus groups based on virus hallmark genes.Results(1)The composition and differences of viral communitiesAlthough there were some slight differences with the abundance,the compositions are similar on the whole.The viromes in this study were all dominated by the order Caudovirales,and a group of species Freshwater phage uv FW were particularly prevalent among all the samples.The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae.On the family level,this study identified 17 viral families,including nine ds DNA viral families,four ss DNA viral families and four RNA viral families.Most of the viral reads in the six libraries belong to the order Caudovirales,which was largely dominated by Siphoviridae(37.20% ± 4.27%),Podoviridae(12.96% ± 1.19%),Myoviridae(7.21% ± 2.15%).The most predominant viral family of ss DNA viruses is Microviridae family(2.25% ± 1.84%).Except the virome from Nanjing,which contains predominantly family Parvoviridae(11.88%).Other members of ss DNA group were identified to be homologous to CRESS-DNA viruses,which mainly consist of Circoviridae(0.24% ± 0.11%)and Genomoviridae(0.07% ± 0.09%)families.A small proportion of sequences were assigned to Riboviria Realm including Astroviridae(0.07% ± 0.11%),Hepeviridae(0.01% ± 0.02%),Dicistroviridae(0.11%± 0.18%)and Virgaviridae(0.49% ± 0.55%)families.The principal coordinate composition(PCo A)analysis and the UPGMA dendrogram showed a clear separation between Nanjing and the other five sampling sites.But the Friedman test suggested that there was no statistically significant difference among the samples(P > 0.05).On the species level,201 viral species were detected in the six viral communities,among which we identified 37 overlapping species existing in all samples,accounting for 31 to 45 percent of species found in each of the six samples.Virome from Nanjing cotained the highest number of unique species,accounting for 47% of the total.The most abundant viral species were all bacteriophages.A group of species Freshwater phage uv FW was shared among all the six libraries,accounting for 8.93% to 24.63%.The sample from Nanjing had the largest number of distinctive viral species,such as Aeromonas phage 62 Ahyd R11PP and Viltain virus.In addition,the unique species in Wuhu mainly belong to Synechococcus phages.(2)Phylogenetic analysis of virus hallmark genesPhylogenetic analyses showed that the Caudovirales order and CRESS-DNA viruses present high genetic diversity.The phylogenetic tree constructed using protein sequences of Ter L identified in this study indicated that most of the 248 phage sequences were too divergent to be classified into known families within the order Caudovirales and formed several separate clades.Meanwhile,the phylogenetic tree based on 24 replication proteins(Rep)sequences of CRESS-DNA viruses also fell into unclassified CRESS-DNA viruses and six of them were located between known virus groups and formed several potential new unclassified groups.Instead,viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative.Phylogenetic analysis based on 15 RNA dependent RNA polymerase(Rd Rp)protein sequences indicated that three of them were belonging to Virgaviridae family,one sequence was clustered with bastroviruses.In addition,the remaining sequences were grouped together with several known viral species belonging to unclassified Riboviria.Similarly,the tree based on the major capsid protein(MCP)for Microviridae indicated that the 10 sequences were all phylogenetically grouped into the Gokushovirinae lineage.And as presented in the dendrogram over nonstructural protein 1(NS1)for Parvoviridae,the four sequences were all clustered into the clade of genera Ambidensovirus.ConclusionsOur study first investigated the characteristics of viral communities in the Yangtze River.The composition of viral communities in the Yangtze River contained slightly regional variations but was similar on the whole.The virus hallmark genes presented both diverse and conservative characteristics and formed several new phylogenetic clusters.Our study provided the first insight into viral community composition in large river ecosystem,revealing the diversity and stability of river water virome,contributing to the surveillance and control of water-borne viral diseases,facilitating the proper utilization of freshwater resource.