Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
Identifieur interne : 002147 ( Main/Curation ); précédent : 002146; suivant : 002148Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
Auteurs : Bonnie L. Hurwitz [États-Unis] ; Li Deng [États-Unis] ; Bonnie T. Poulos [États-Unis] ; Matthew B. Sullivan [États-Unis]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2013-05.
Descripteurs français
- KwdFr :
- MESH :
- analyse : Protéines virales.
- génétique : Protéines virales, Virus.
- isolement et purification : Virus.
- virologie : Eau de mer.
- Pascal (Inist)
- MESH :
- Wicri :
- topic : Océan.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Viral Proteins.
- chemical , genetics : Viral Proteins.
- genetics : Viruses.
- isolation & purification : Viruses.
- methods : Virology.
- virology : Seawater.
- Teeft :
- Appl environ microbiol, Biodiversity, Biol, Blackwell publishing, Breitbart, Cscl, Cscl dnase, Database, Deng, Dnase, Dnase cscl, Dnase sucrose, Ecology, Edta, Environ, Environ microbiol, Environmental microbiology, Experimental procedures, Fecl3, Fecl3 dnase, Fecl3 dnase cscl, Fecl3 dnase sucrose, Fecl3 precipitation, Genome, Genus levels, Hurwitz, Linker, Lter, Ltered, Marine viruses, Metagenome, Metagenomes, Metagenomic, Metagenomics, Microbial, Microbial genomes, Microbial metagenome, Microbiol, Microbiology, More variability, Nucleic, Nucleic acid, Other samples, Pfuturbo, Phage, Plo, Plos biol, Poulos, Precipitation, Proc natl acad, Prophage, Prophage regions, Protein clusters, Protein diversity, Qiagen sciences, Rare sequences, Rarefaction, Rarefaction analysis, Rarefaction curves, Replicates, Reproducibility of Results, Rohwer, Scripps pier, Seawater, Sequencing, Simap, Sucrose, Superkingdom, Takara, Taxon, Taxonomic, Total sequences, Triplicate, Triplicate metagenomes, Viral, Viral community, Viral community concentration, Viral concentration, Viral metagenomes, Water Microbiology, Williamson, Wommack.
Abstract
Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF‐concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3‐precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k‐mers (100% of reads) showed 50–53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF‐concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k‐mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture‐independent viral ecology studies.
Url:
- https://api.istex.fr/ark:/67375/WNG-4FWSN1P2-8/fulltext.pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655615
DOI: 10.1111/j.1462-2920.2012.02836.x
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<term>Metagenome</term>
<term>Metagenomics</term>
<term>Method</term>
<term>Ocean</term>
<term>Reproducibility of Results</term>
<term>Seawater (virology)</term>
<term>Viral Proteins (analysis)</term>
<term>Viral Proteins (genetics)</term>
<term>Virology (methods)</term>
<term>Virus</term>
<term>Viruses (genetics)</term>
<term>Viruses (isolation & purification)</term>
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<term>Microbiologie de l'eau</term>
<term>Métagénomique</term>
<term>Protéines virales (analyse)</term>
<term>Protéines virales (génétique)</term>
<term>Reproductibilité des résultats</term>
<term>Virologie ()</term>
<term>Virus (génétique)</term>
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<term>Microbiology</term>
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<front><div type="abstract" xml:lang="en">Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF‐concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3‐precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k‐mers (100% of reads) showed 50–53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF‐concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k‐mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture‐independent viral ecology studies.</div>
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<front><div type="abstract" xml:lang="en">Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl<sub>3</sub>
precipitation and DNase, (iii) FeCl<sub>3</sub>
precipitation and DNase + CsCl and (iv) FeCl<sub>3</sub>
precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycod-naviridae) and more variability among Myoviridae than FeCl<sub>3</sub>
-precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50-53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl<sub>3</sub>
and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for 'rare' reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.</div>
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<front><div type="abstract" xml:lang="en">Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF‐concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3‐precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k‐mers (100% of reads) showed 50–53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF‐concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k‐mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture‐independent viral ecology studies.</div>
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