Phycodnavirus diversification and biogeographic dynamics across Cascadian lakes

Background/Question/Methods

Phycodnaviruses are a clade of extraordinarily diverse viruses with exceptionally large genomes. These viruses are best studied as algal pathogens and show patterns of epidemiological variation throughout the year linked to the abundance of host species. Phycodnaviruses have the potential to affect aquatic environments through influencing bloom termination, nutrient cycling, and community composition. Studies of viral isolates using quantitative PCR indicate that phycodnaviruses can be readily detected in marine and freshwater environments around the globe. The aim of our research is to study the phylogenetic relationships, patterns of diversification, and spatial-temporal dynamics of phycodnaviruses.

We hypothesized that our metagenomic and PCR-based approaches would characterize novel virus lineages in the Cascadian ecoregion, and phycodnavirus phylogenetic patterns would reflect environmental influence on diversification either within a virus lineage or across multiple lineages.

We collected samples from lakes across the ecoregion, which enabled comparisons based on variation in environmental conditions, phytoplankton community structure, and biogeographic proximity. We isolated phycodnavirus DNA from aquatic samples by collecting water and filtering it through a Whatman #1 filter, spin in an ultracentrifuge, and the pellet virus is subjected to freeze-thaw cycles. The DNA polymerase B (polB) gene is the most widely available sequence in public databases and is the focal locus for our study.

Results/Conclusions

Our work using conserved primers has successfully amplified a 550bp fragment of the phycodnavirus pol sequence from our Cascadian lakes and has identified new clades of phycodnaviruses. We have also generated draft phycodnavirus genome scaffolds from a 300pe Illumina MiSeq run using environmental DNA isolated from one of our focal lakes. While our viral genomes share sequence similarity with conserved core genes from reference phycodnavirus genomes, they show substantial differences in gene content and genome organization.

Using primers specific to two of our newly identified virus lineages, we have performed PCR analysis of all lake samples, spanning 3 years. Our results indicate that one lineage was only present in two lake samples from 2014, whereas other lineages were present across multiple years and multiple lakes. We can detect new phycodnaviral lineages and track the evolution of these specific lineages across seasons and geography. Our phylogenetic analyses and comparisons of DNA sequence variation from our pol data indicate that phycodnaviruses within our sampled lakes are diverse, showing silent and coding polymorphisms. Collectively, our research describes unique phycodnavirus lineages, genome architectures, and lineage-specific seasonal and spatial variation.