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Assessing the diversity and specificity of two freshwater viral communities through metagenomics.

Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D - PLoS ONE (2012)

Bottom Line: 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.Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.

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.

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Related in: MedlinePlus

Boxplots of the estimation of species and cluster richness for viromes from different origins.Species richness (A) was estimated with PHACCS for virome subsamples (50,000 sequences, 100 bp). Cluster richness (B) was deduced from the number of different clusters formed from 50,000 input sequences of 100 bp. Viromes associated with extreme points are indicated on the plot, as well as the viromes from Lakes Bourget and Pavin.
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pone-0033641-g002: Boxplots of the estimation of species and cluster richness for viromes from different origins.Species richness (A) was estimated with PHACCS for virome subsamples (50,000 sequences, 100 bp). Cluster richness (B) was deduced from the number of different clusters formed from 50,000 input sequences of 100 bp. Viromes associated with extreme points are indicated on the plot, as well as the viromes from Lakes Bourget and Pavin.

Mentions: Species richness (number of different virotypes) and cluster richness estimated from the two viromes were compared to the ones of 29 previously published viromes [9], [11] from seawater, freshwater, hypersaline and from viral communities associated with different eukaryotes (fish, coral and mosquito) (Table S2). Because numbers of reads of these 31 viromes were different, subsamples of 50,000 randomly-chosen 100-bp reads were generated in order to work with cross-comparable results. Number of virotypes was estimated using PHACCS [14], and plotted for each type of environment (Figure 2A). No significant link could be found between sample origin and virome species richness (one-way ANOVA: p-value = 0.542). The cluster richness of each virome, deduced from the read clustering (Figure 2B), was significantly different between the different environments (one-way ANOVA: p-value = 0.035). Genetic diversity of aquatic viromes (whether marine, freshwater, or hypersaline) was higher than that of viromes associated with eukaryotes, the highest diversity being observed in marine environment.


Assessing the diversity and specificity of two freshwater viral communities through metagenomics.

Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D - PLoS ONE (2012)

Boxplots of the estimation of species and cluster richness for viromes from different origins.Species richness (A) was estimated with PHACCS for virome subsamples (50,000 sequences, 100 bp). Cluster richness (B) was deduced from the number of different clusters formed from 50,000 input sequences of 100 bp. Viromes associated with extreme points are indicated on the plot, as well as the viromes from Lakes Bourget and Pavin.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303852&req=5

pone-0033641-g002: Boxplots of the estimation of species and cluster richness for viromes from different origins.Species richness (A) was estimated with PHACCS for virome subsamples (50,000 sequences, 100 bp). Cluster richness (B) was deduced from the number of different clusters formed from 50,000 input sequences of 100 bp. Viromes associated with extreme points are indicated on the plot, as well as the viromes from Lakes Bourget and Pavin.
Mentions: Species richness (number of different virotypes) and cluster richness estimated from the two viromes were compared to the ones of 29 previously published viromes [9], [11] from seawater, freshwater, hypersaline and from viral communities associated with different eukaryotes (fish, coral and mosquito) (Table S2). Because numbers of reads of these 31 viromes were different, subsamples of 50,000 randomly-chosen 100-bp reads were generated in order to work with cross-comparable results. Number of virotypes was estimated using PHACCS [14], and plotted for each type of environment (Figure 2A). No significant link could be found between sample origin and virome species richness (one-way ANOVA: p-value = 0.542). The cluster richness of each virome, deduced from the read clustering (Figure 2B), was significantly different between the different environments (one-way ANOVA: p-value = 0.035). Genetic diversity of aquatic viromes (whether marine, freshwater, or hypersaline) was higher than that of viromes associated with eukaryotes, the highest diversity being observed in marine environment.

Bottom Line: 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.Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.

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.

Show MeSH
Related in: MedlinePlus