Metagenomic identification, seasonal dynamics, and potential transmission mechanisms of a Daphnia‐associated single‐stranded DNA virus in two temperate lakes

Abstract

We used a metagenomic approach to identify viruses that may be involved in the ecology of Daphnia spp. in Oneida and Cayuga lakes (upstate New York). We identified several highly represented, putative eukaryotic, circular, single-stranded deoxyribonucleic acid (DNA) viral genomes. Among these, we discovered a genotype similar in both sequence and genomic architecture to a virus previously reported from a hyperthermal lake that shares characteristics of both single-stranded ribonucleic acid (RNA) and single-stranded DNA viruses. We used quantitative polymerase chain reactions to study the prevalence and viral load of both positive-sense and negative-sense strands of the Daphnia mendotae-associated (Cladocera) hybrid virus (DMClaHV) over a summer season in Oneida and Cayuga lakes. DMClaHV had high prevalence within Daphnia populations, where viral load and the proportion of virus-positive individuals were higher preceding host population decline. DMClaHV viral load was different between two species of Daphnia (D. mendotae and D. retrocurva), and the dynamics between viruses and their hosts varied between the two lakes. We detected DMClaHV in eggs (ephippia) retrieved from Oneida Lake sediments with an estimated age of 30 yr. Using transmission electron microscopy, we observed small (20 nm diameter) virus-like particles in Daphnia that were well away from gut tissues and not associated with intracellular parasites. Because Daphnia plays a critical role in many lake ecosystems, DMClaHV may have important effects on herbivory and thus carbon flow through the lake ecosystem.

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…Note added in proof: Following the revision of this article, Hewson et al have described the identification of a new CHIV genome in samples collected from Oneida and Cayuga lakes (upstate New York, USA) 71 , further expanding our knowledge on the genetic diversity and environmental distribution of this peculiar group of chimeric viruses. Interestingly, the new ssDNA virus appears to be associated with planktonic crustaceans of the genus Daphnia.…”

Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi

“…Specifically, these viruses have been identified in insects [2,5,16,17], copepods [6], mollusks [4] and water fleas [8]. Although recent studies have identified linear ssDNA densoviruses in echinoderms [7,9], AfaCV is the first CRESS-DNA virus identified in echinoderms and provides further support that these viruses may infect a wider host range than previously thought.…”

Densovirus associated with sea-star wasting disease and mass mortality

“…Quantitative PCR (qPCR) was performed following the approach of Hewson et al (17), where template material comprised DNA extracted from small excisions of body wall or tube feet and where SSaDV copy number was divided by weight of tissue extracted.…”