Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China

Abstract

Viruses are the most abundant biological entities in the oceans, and encompass a significant reservoir of genetic diversity. However, little is known about their biodiversity in estuary environments, which represent a highly dynamic and potentially more diverse habitat. Here, we report a metagenomic analysis of the dsDNA viral community from the Jiulong River Estuary (JRE), China, and provide a comparative analysis with other closely related environments. The results showed that the majority of JRE virome did not show any significant similarity to the database. For the major viral group (Caudovirales) detected in the sample, Podoviridae (44.88%) were the most abundant family, followed by Siphoviridae (32.98%) and Myoviridae (17.32%). The two most abundant viruses identified in the virome were phages HTVC010P and HMO-2011, which infect bacteria belonging to marine SAR11 and SAR116 clades, respectively. Two contigs larger than 20 kb, which show similar overall genome architectures to Celeribacter phage P12053L and Thalosomonas phage BA3, respectively, were generated during assembly. Comparative analysis showed that the JRE virome was more similar to marine viromes than to freshwater viromes, and shared a relative coarse-grain genetic overlap (averaging 14.14% ± 1.68%) with other coastal viromes. Our study indicated that the diversity and community structure of the virioplankton found in JRE were mainly affected by marine waters, with less influence from freshwater discharge.

Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

“…Previous reports on aquatic viromes suggested high prevalence of Caudovirales in the marine environments of Sargasso Sea 33 , and Iquique- Chile 34 . Recent reports from other aquatic environments also suggest a high dominance of Myoviridae , such as from Goseong Bay (South Sea, Korea) 41 , and some freshwater lakes 42 , 43 . Similar dominance of bacteriophages making up most of the viral fraction has been reported previously 11 , 34 , 35 , 44 – 46 .…”

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

“…The prevalence of Microviridae as the dominant taxon was observed in freshwater viromes of Lake Limnopolar, Antarctica33 and Lake Bourget in France424344, sediment viromes in Izu-Ogasaware Trench and Shimokita Peninsula26 and partial soil samples in Scotland28. The higher presence of ssDNA viruses might have been caused by the use of phi29 applied during metagenomic DNA preparation, which have been reproted to result in biased amplification of ssDNA viruses30.…”

Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon

“…As the cosmopolitan viral families in the Amazon infect bacteria or archaea and as two of them are members of Caudovirales ( Myoviridae and Podoviridae ) ( 51 ), it is plausible that these tailed viruses can move between river and plume. Recent viral metagenomic studies of a rural river in Australia ( 52 ) and of the estuary of the Jiulong River in China ( 53 ) indicate that Caudovirales (e.g., Myoviridae , Siphoviridae , and Podoviridae ) were the most abundant viruses. In the Amazon River, members of Caudovirales were also abundant, but the higher abundance of Microviridae , and also of Circoviridae , suggests that the ssDNA families, which are significant pathogens of the phytoplankton and microzooplankton in marine food webs ( 54 ), are also very important along the continuum.…”