Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

Abstract

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.

Human oral viruses are personal, persistent and gender-consistent

“…nih.gov/refseq/; Supplementary Figure 3). Similar to results found for viromes from different environments (Desnues et al, 2008;Minot et al, 2011;Roux et al, 2012;Wommack et al, 2012;Minot et al, 2013;Yoshida et al, 2013), the majority of the contigs had no known viral homologues. Approximately 32.7±5.9% (range from 20.3 to 48.0%) of the virome contigs were homologous to known viruses, depending on the subject and time point analyzed (Supplementary Figure 3).…”

“…Our findings of a large number of viral genotypes that persist over time are contrary to that presented in our prior study (Pride et al, 2012a); however, they highlight several difficulties encountered when examining large and complex metagenome data sets. These difficulties include the following: (1) assembly related overestimation of viral genotypes, as we likely observed in our previous study (Pride et al, 2012a), (2) lack of available homologs to aid in the identification of virome constituents (Desnues et al, 2008;Minot et al, 2011;Roux et al, 2012;Wommack et al, 2012;Minot et al, 2013;Yoshida et al, 2013) and (3) the relative lack of statistical tools to discern differences in virome compositions. We did not perform detailed comparisons of viral genotypes and the bacteria present in each subject because our BLAST-based techniques for characterizing viruses generally are considered insufficient to accurately predict the hosts of each virus.…”

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

“…To get further insight into the diversity and evolution of CHIVs, we have assembled sequence reads from 103 publicly available viromes and searched the resultant contigs for co-occurrence of genes encoding RC-Reps and RNA virus-like CPs (Supplementary Data 1). As a result, nine contigs were assembled from viromes derived from atmospheric 32 and aquatic 26,33,34 samples. As ssDNA viruses are known to integrate into the genomes of their hosts 35,36 , we also searched for the presence of CHIVs in the eukaryotic genome databases.…”

“…Many of these uncultivated viruses are related to members of the bacteriophage family Microviridae 9 , but perhaps even larger number encode RC-Reps displaying phylogenetic affinity to one of three families of eukaryotic ssDNA viruses-Circoviridae, Geminiviridae and Nanoviridae (for example, see refs [24][25][26][27]. Interestingly, instead of encoding genes for corresponding CPs (circo-, gemini-and nano-like), these viruses typically bear open-reading frames that do not share appreciable similarity with sequences in the databases.…”

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…For example, 249 reads were recruited from the Lake Bourget viral metagenomes while only 4 reads from the Lake Pavin viral metagenomes (Roux et al, 2012). Lake Bourget is an oligo-mesotrophic lake dominated by cyanobacteria (Zhong et al, 2013), whereas Lake Pavin is believed to be dominated by picoeukaryotes (Lefèvre et al, 2008).…”