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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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Composition and taxonomic affiliations of Lake Bourget and Lake Pavin virome reads as determined by similarity to known sequences.(A) The percent of “known” virome sequences when compared to the NR protein database. A read was considered “known” if it had a significant similarity in NR (BLASTx using thresholds of 10−3 on e-value and 50 on bit score). (B) Breakdown of the “known” sequences into Viruses, Bacteria, Archaea, or Eukarya using similarity results against NR. Hatched parts were reads having a best BLAST hit against a non-viral sequence, but still presenting significant similarity against a complete virus genome sequence of the RefseqVirus database (tBLASTx using thresholds of 10−3 on e-value and 50 on bit score) and thus designated as reads “similar to at least one viral sequence”. (C) Taxonomic composition at the viral family level of these reads “similar to at least one viral sequence” computed using the GAAS pipeline. The “Other” category pools families which represented less than 1% of the full virome sequences. The number of sequences represented in each chart are as follow : 593,084 ; 156 772 ; 95,905 for charts A, B and C of Lake Bourget virome, and 649,290 ; 92,834 ; 47,345 for the Lake Pavin virome.
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pone-0033641-g001: Composition and taxonomic affiliations of Lake Bourget and Lake Pavin virome reads as determined by similarity to known sequences.(A) The percent of “known” virome sequences when compared to the NR protein database. A read was considered “known” if it had a significant similarity in NR (BLASTx using thresholds of 10−3 on e-value and 50 on bit score). (B) Breakdown of the “known” sequences into Viruses, Bacteria, Archaea, or Eukarya using similarity results against NR. Hatched parts were reads having a best BLAST hit against a non-viral sequence, but still presenting significant similarity against a complete virus genome sequence of the RefseqVirus database (tBLASTx using thresholds of 10−3 on e-value and 50 on bit score) and thus designated as reads “similar to at least one viral sequence”. (C) Taxonomic composition at the viral family level of these reads “similar to at least one viral sequence” computed using the GAAS pipeline. The “Other” category pools families which represented less than 1% of the full virome sequences. The number of sequences represented in each chart are as follow : 593,084 ; 156 772 ; 95,905 for charts A, B and C of Lake Bourget virome, and 649,290 ; 92,834 ; 47,345 for the Lake Pavin virome.

Mentions: After 454 pyrosequencing and data filtering, viromes of 593,084 and 649,290 reads with an average length of 420 bp were available for Lake Bourget and Lake Pavin, respectively. The proportion of reads similar to protein sequences of the non-redundant NCBI database (NR) were 26.4% and 14.3% for Lakes Bourget and Pavin, respectively (Figure 1A). These proportions of “known” reads (reads with a BLAST hit against NR) are among the highest compared to published viromes (range 1%–28% with an average of 6,3% for aquatic environments [9], [11]). Yet, as read length influences these proportions of “known” reads [12] and as our reads are 400 bp versus 100 to 250 bp in previous studies, a direct comparison of BLAST hit ratios is questionable, so the “known” fractions were also determined using reads randomly reduced to 100 bp. Using shorter reads, the “known” fractions dropped to 2.2% in Lake Bourget and to 0.7% in Lake Pavin, the one of the Lake Pavin being the lowest among aquatic viromes (Table S2).


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)

Composition and taxonomic affiliations of Lake Bourget and Lake Pavin virome reads as determined by similarity to known sequences.(A) The percent of “known” virome sequences when compared to the NR protein database. A read was considered “known” if it had a significant similarity in NR (BLASTx using thresholds of 10−3 on e-value and 50 on bit score). (B) Breakdown of the “known” sequences into Viruses, Bacteria, Archaea, or Eukarya using similarity results against NR. Hatched parts were reads having a best BLAST hit against a non-viral sequence, but still presenting significant similarity against a complete virus genome sequence of the RefseqVirus database (tBLASTx using thresholds of 10−3 on e-value and 50 on bit score) and thus designated as reads “similar to at least one viral sequence”. (C) Taxonomic composition at the viral family level of these reads “similar to at least one viral sequence” computed using the GAAS pipeline. The “Other” category pools families which represented less than 1% of the full virome sequences. The number of sequences represented in each chart are as follow : 593,084 ; 156 772 ; 95,905 for charts A, B and C of Lake Bourget virome, and 649,290 ; 92,834 ; 47,345 for the Lake Pavin virome.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3303852&req=5

pone-0033641-g001: Composition and taxonomic affiliations of Lake Bourget and Lake Pavin virome reads as determined by similarity to known sequences.(A) The percent of “known” virome sequences when compared to the NR protein database. A read was considered “known” if it had a significant similarity in NR (BLASTx using thresholds of 10−3 on e-value and 50 on bit score). (B) Breakdown of the “known” sequences into Viruses, Bacteria, Archaea, or Eukarya using similarity results against NR. Hatched parts were reads having a best BLAST hit against a non-viral sequence, but still presenting significant similarity against a complete virus genome sequence of the RefseqVirus database (tBLASTx using thresholds of 10−3 on e-value and 50 on bit score) and thus designated as reads “similar to at least one viral sequence”. (C) Taxonomic composition at the viral family level of these reads “similar to at least one viral sequence” computed using the GAAS pipeline. The “Other” category pools families which represented less than 1% of the full virome sequences. The number of sequences represented in each chart are as follow : 593,084 ; 156 772 ; 95,905 for charts A, B and C of Lake Bourget virome, and 649,290 ; 92,834 ; 47,345 for the Lake Pavin virome.
Mentions: After 454 pyrosequencing and data filtering, viromes of 593,084 and 649,290 reads with an average length of 420 bp were available for Lake Bourget and Lake Pavin, respectively. The proportion of reads similar to protein sequences of the non-redundant NCBI database (NR) were 26.4% and 14.3% for Lakes Bourget and Pavin, respectively (Figure 1A). These proportions of “known” reads (reads with a BLAST hit against NR) are among the highest compared to published viromes (range 1%–28% with an average of 6,3% for aquatic environments [9], [11]). Yet, as read length influences these proportions of “known” reads [12] and as our reads are 400 bp versus 100 to 250 bp in previous studies, a direct comparison of BLAST hit ratios is questionable, so the “known” fractions were also determined using reads randomly reduced to 100 bp. Using shorter reads, the “known” fractions dropped to 2.2% in Lake Bourget and to 0.7% in Lake Pavin, the one of the Lake Pavin being the lowest among aquatic viromes (Table S2).

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