Comparing the diversity and relative abundance of free and particle-associated aquatic viruses

Metagenomics has enabled rapid increases in virus discovery, in turn permitting revisions of viral taxonomy and our understanding of the ecology of viruses and their hosts. Inspired by recent discoveries of large viruses prevalent in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before sequencing. We studied assembled contigs derived from 0.45 {micro}m size fractions that were annotated as viral to determine the diversity and relative abundances of virus groups from each fraction. Virus communities were vastly different when comparing the size fractions, indicating that analysis of either fraction alone would provide only a partial perspective of environmental viruses. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 {micro}m size fractions, whereas the 0.45 {micro}m size fractions potentially indicating replication within cells during ongoing infections. Many of the Mimiviridae and Phycodnaviridae, and all Iridoviridae and Poxviridae were detected exclusively in the often disregarded > 0.45 {micro}m size fractions. In addition to observing unique virus communities associated with each size fraction, we detected viruses common to both fractions and argue that these are candidates for further exploration because they may be the product of ongoing or recent lytic events.