Freshwater community DNA from < 0.45 um and > 0.45 um size fractions

Metagenomic analysis of virus communities has enabled rapid increases in virus discovery and expansion of sequence databases, in turn permitting revisions of viral taxonomy and our understanding of ecological interactions between viruses and hosts. Given the recent discoveries of large viruses that are prevalent in the environment, we aimed to assess the longstanding methodological approach of filtering water through small pore-size filters to separate viruses from cellular communities prior to sequencing. We used shotgun metagenomics to study assembled contigs derived from the < 0.45 um and > 0.45 um size fractions that were annotated as viral, allowing us to determine the diversity and relative abundance of virus groups from each size fraction. At the level of virus order/family we observed highly diverse and different virus communities in the > 0.45 um size fractions, whereas the < 0.45 um size fractions were similar and comprised primarily of Caudovirales. Highly diverse Caudovirales communities were detected in the < 0.45 um size fractions, but the relative abundances of Caudovirales for which hosts could be inferred varied widely between the size fractions. Higher relative abundances of cyanophages were observed in the > 0.45 um size fractions, potentially indicating replication within cells during ongoing infections. Many of the Mimiviridae and Phycodnaviridae, and all Iridoviridae and Poxviridae were detected only in the often disregarded > 0.45 um size fractions. Virus communities were vastly different when comparing the size fractions, indicating that analysis of either size fraction alone will provide only a partial perspective of environmental viruses.