Diversity of algal viruses in various North American freshwater environments

Abstract

To examine algal virus (Phycodnaviridae) genetic diversity in freshwater environments, gene fragments were cloned and sequenced from a river and a reservoir in Colorado, USA, and 2 different lakes in Ontario, Canada using PCR methods that target a diverse subset of known Phycodnaviridae DNA polymerase genes. Numerous phycodnavirus gene sequences were obtained from every sample, and rarefaction analysis of the sequence libraries demonstrated that virus richness was variable among different sample locations, and among samples collected from the same location at different times. Phylogenetic analysis of the unique sequences from each sample indicated that most sequences from the same geographic region (i.e. Colorado or Ontario) clustered together, but several exceptions were also observed. Phylogenetic analysis also demonstrated that the sequences obtained were more closely related to sequences from cultivated marine phycodnaviruses belonging to the genus Prasinovirus than to those from cultivated freshwater phycodnaviruses from the genus Chlorovirus. Overall, phycodnavirus sequences originating from cultivated marine viruses and marine clone libraries were not genetically distinct from the freshwater phycodnavirus sequences reported in this study.

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

“…Clades and sequences followed by a green circle are from phycodnavirus isolates with classifications recognized by the International Committee on Taxonomy of Viruses (ICTV). All others shown are environmental sequences from previously published investigations of seawater (black type; Chen et al, 1996;Suttle, 2002, 2003) or freshwater (blue type; Short and Short, 2008). The number of sequences that comprise each clade is in parentheses adjacent to the clade.…”

“…Sequences sharing p97% identity on the nucleotide level (Short and Short, 2008) were considered to be different phylotypes. Sequences were labeled with a code indicating the location from which they were derived (KB for Kāne'ohe Bay) and the nature of the sequence (vp for viral polymerase; vi for viral intein).…”

“…Most culture-independent surveys of phycodnavirus populations have involved PCR amplification and sequence analysis of a fragment of the DNA polymerase gene (DNA pol) using degenerate primers (Chen et al, 1996;Suttle, 2002, 2003;Short and Short, 2008), although one recent study has evaluated the utility of using the major capsid protein . The diverse sequences detected by these PCR assays in various marine and freshwater environments suggest that a wide range of protists is prone to infection by members of the family Phycodnaviridae and that much of the diversity remains undescribed.…”

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

“…The earliest effort to characterize phycodnavirus communities while circumventing difficulties associated with virus cultivation involved designing algal-virus specific (AVS) PCR primers that targeted DNA polymerase (polB) genes . Clone libraries of polB amplicons, and more recently amplicons of a gene encoding the major capsid protein (Larsen et al, 2008), demonstrated that phycodnavirus communities are diverse, environmental sequences are distinct from cultivated phycodnavirus genes, and closely related sequences can be found in geographically distant locations (Short and Suttle, 2002;Larsen et al, 2008;Short and Short, 2008;Clasen and Suttle, 2009). Although studies of phycodnavirus diversity have provided many insights into their ecology, they do not yield quantitative information to infer their influence on phytoplankton mortality and succession, or the flow of energy and material in aquatic systems.…”

“…Initially, Lake Ontario algal virus community richness was examined by sequencing clone libraries of polB gene fragments (Short and Short, 2008). Using sequences from autumn clone libraries, qPCR was used to monitor the abundances of three operational taxonomic units (OTUs) for an entire year demonstrating that they achieved maximum abundances in the autumn months of 2007 and 2008, and two were persistent throughout the year while the other was ephemeral (Short and Short, 2009).…”