RNA viruses as major contributors to Antarctic virioplankton

Abstract

SummaryEarly work on marine algal viruses focused exclusively on those having DNA genomes, but recent studies suggest that RNA viruses, especially those with positive-sense, single-stranded RNA (1ssRNA) genomes, are abundant in tropical and temperate coastal seawater. To test whether this was also true of polar waters, we estimated the relative abundances of RNA and DNA viruses using a mass ratio approach and conducted shotgun metagenomics on purified viral samples collected from a coastal site near Palmer Station, Antarctica on six occasions throughout a summer phytoplankton bloom (NovemberMarch). Our data suggest that RNA viruses contributed up to 65% of the total virioplankton (8-65%), and that, as observed previously in warmer waters, the majority of RNA viruses in these Antarctic RNA virus metagenomes had 1ssRNA genomes most closely related to viruses in the order Picornavirales. Assembly of the metagenomic reads resulted in five novel, nearly complete genomes, three of which had features similar to diatom-infecting viruses. Our data are consistent with the hypothesis that RNA viruses influence diatom bloom dynamics in Antarctic waters.

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics

“…Taken together, the apparent dynamics and abundance of this unclassified Picornavirales suggest this group is a major component of the marine virioplankton, and strengthens previous observations that the Picornavirales phylogenetically distinct from the established families can be dominant members in different marine environments1230. Owing to their small size, detection and quantification of RNA viruses and ssDNA viruses pose significant technical challenges30. Our results, however, clearly point to the power of screening metatranscriptomes for the simultaneous analysis of the dynamics of a large cross-section DNA and RNA viruses.…”

“…These observations suggest a broad ecological role for viral infection during phytoplankton bloom decline, which would not have been resolved with targeted studies of AaV or metagenomic approaches. Taken together, the apparent dynamics and abundance of this unclassified Picornavirales suggest this group is a major component of the marine virioplankton, and strengthens previous observations that the Picornavirales phylogenetically distinct from the established families can be dominant members in different marine environments1230. Owing to their small size, detection and quantification of RNA viruses and ssDNA viruses pose significant technical challenges30.…”

Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing

“…HTS has been used to a large extent in Antarctic environmental virology to study soil (Adriaenssens et al, 2017;Zablocki et al, 2014), lake (Aguirre de Cárcer et al, 2016;Lopez-Bueno et al, 2015, 2009Yau et al, 2011) and marine (Brum et al, 2017;Miranda et al, 2016) viral ecology. Novel viral genomes from various soils and lake samples (Dziewit and Radlinska, 2016;Kerepesi and Grolmusz, 2017;Meiring et al, 2012;Swanson et al, 2012;Zawar-Reza et al, 2014) have been determined using HTS approaches.…”

Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus

“…Until recently, discovery of new RNA viruses proceeded slowly in a mostly hypothesis-driven manner while searching for an agent of a disease, and using antibody cross-reactivity or enough conserved motifs for successful amplification by reverse transcriptase polymerase chain reaction. With improvements in RNA transcriptome sequencing and homology-based search methods, it is now possible to capture the complete infecting RNA virome of an organism by deep-sequencing total intracellular RNA pools (Miranda et al, 2016;Shi et al, 2018Shi et al, , 2016.…”