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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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Maximum-likelihood tree for T4-like phage (GP23).The two main reference groups are indicated (near-T4 in red and T4-like cyanophages in blue). The Far-T4 group is highlighted in yellow. Leaves corresponding to virome sequences are colored (red for Lake Pavin and blue for Lake Bourget). Far-T4 sequences described by Comeau et al. are highlighted in green. Nodes with at least 80% bootstrap support are flagged with black circles. The sample origin of PCR-obtained sequences is designated on the leaf label (seaw stands for seawater, flood for floodwater, and fresh for freshwater). Rhodothermus RM378, the only cultured representative within the Far-T4 clade, is marked with a black dot.
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pone-0033641-g007: Maximum-likelihood tree for T4-like phage (GP23).The two main reference groups are indicated (near-T4 in red and T4-like cyanophages in blue). The Far-T4 group is highlighted in yellow. Leaves corresponding to virome sequences are colored (red for Lake Pavin and blue for Lake Bourget). Far-T4 sequences described by Comeau et al. are highlighted in green. Nodes with at least 80% bootstrap support are flagged with black circles. The sample origin of PCR-obtained sequences is designated on the leaf label (seaw stands for seawater, flood for floodwater, and fresh for freshwater). Rhodothermus RM378, the only cultured representative within the Far-T4 clade, is marked with a black dot.

Mentions: A significant number of these sequences (20%) were related to T4-like phages (Figure 6) within the Myoviridae family. The diversity of this group has been previously explored using GP23 and G20 markers [19], [20] leading to the identification of different sub-groups: “Near-T4”, “T4-like cyanophages” and “Far-T4”, a group composed of only one sequenced genome (Rhodothermus phage RM378) and identified in marine waters by PCR approach on the GP23 gene [20]. According to G20-based phylogenetic analyses (Figure S2 and Figure S3), 11% of the 190 virome reads from Bourget and Pavin were affiliated to “T4-Like cyanophages” and 89% of these reads formed a new group including Rhodothermus phage RM378. Similar proportions were obtained with the GP23 marker, with 16% of the 251 reads affiliated to “T4-Like Cyanophage” and 84% forming a group containing the “Far-T4” group identified by Comeau et al. [20] (Figure S4 and Figure 7). Thus, freshwater virome sequences greatly expand the diversity of the previously identified Far-T4 group.


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)

Maximum-likelihood tree for T4-like phage (GP23).The two main reference groups are indicated (near-T4 in red and T4-like cyanophages in blue). The Far-T4 group is highlighted in yellow. Leaves corresponding to virome sequences are colored (red for Lake Pavin and blue for Lake Bourget). Far-T4 sequences described by Comeau et al. are highlighted in green. Nodes with at least 80% bootstrap support are flagged with black circles. The sample origin of PCR-obtained sequences is designated on the leaf label (seaw stands for seawater, flood for floodwater, and fresh for freshwater). Rhodothermus RM378, the only cultured representative within the Far-T4 clade, is marked with a black dot.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0033641-g007: Maximum-likelihood tree for T4-like phage (GP23).The two main reference groups are indicated (near-T4 in red and T4-like cyanophages in blue). The Far-T4 group is highlighted in yellow. Leaves corresponding to virome sequences are colored (red for Lake Pavin and blue for Lake Bourget). Far-T4 sequences described by Comeau et al. are highlighted in green. Nodes with at least 80% bootstrap support are flagged with black circles. The sample origin of PCR-obtained sequences is designated on the leaf label (seaw stands for seawater, flood for floodwater, and fresh for freshwater). Rhodothermus RM378, the only cultured representative within the Far-T4 clade, is marked with a black dot.
Mentions: A significant number of these sequences (20%) were related to T4-like phages (Figure 6) within the Myoviridae family. The diversity of this group has been previously explored using GP23 and G20 markers [19], [20] leading to the identification of different sub-groups: “Near-T4”, “T4-like cyanophages” and “Far-T4”, a group composed of only one sequenced genome (Rhodothermus phage RM378) and identified in marine waters by PCR approach on the GP23 gene [20]. According to G20-based phylogenetic analyses (Figure S2 and Figure S3), 11% of the 190 virome reads from Bourget and Pavin were affiliated to “T4-Like cyanophages” and 89% of these reads formed a new group including Rhodothermus phage RM378. Similar proportions were obtained with the GP23 marker, with 16% of the 251 reads affiliated to “T4-Like Cyanophage” and 84% forming a group containing the “Far-T4” group identified by Comeau et al. [20] (Figure S4 and Figure 7). Thus, freshwater virome sequences greatly expand the diversity of the previously identified Far-T4 group.

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