Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
Identifieur interne : 000983 ( Ncbi/Curation ); précédent : 000982; suivant : 000984Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
Auteurs : Bonnie L. Hurwitz ; Li Deng ; Bonnie T. Poulos ; Matthew B. SullivanSource :
- Environmental Microbiology [ 1462-2912 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
- analyse : Protéines virales.
- génétique : Protéines virales, Virus.
- isolement et purification : Virus.
- virologie : Eau de mer.
- Biodiversité, Microbiologie de l'eau, Métagénomique, Reproductibilité des résultats, Virologie.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Viral Proteins.
- chemical , genetics : Viral Proteins.
- genetics : Viruses.
- isolation & purification : Viruses.
- methods : Virology.
- virology : Seawater.
- Biodiversity, Metagenomics, Reproducibility of Results, Water Microbiology.
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 (
Url:
DOI: 10.1111/j.1462-2920.2012.02836.x
PubMed: 22845467
PubMed Central: 3655615
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PMC:3655615Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics</title><author><name sortKey="Hurwitz, Bonnie L" sort="Hurwitz, Bonnie L" uniqKey="Hurwitz B" first="Bonnie L" last="Hurwitz">Bonnie L. Hurwitz</name></author><author><name sortKey="Deng, Li" sort="Deng, Li" uniqKey="Deng L" first="Li" last="Deng">Li Deng</name></author><author><name sortKey="Poulos, Bonnie T" sort="Poulos, Bonnie T" uniqKey="Poulos B" first="Bonnie T" last="Poulos">Bonnie T. Poulos</name></author><author><name sortKey="Sullivan, Matthew B" sort="Sullivan, Matthew B" uniqKey="Sullivan M" first="Matthew B" last="Sullivan">Matthew B. Sullivan</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22845467</idno><idno type="pmc">3655615</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655615</idno><idno type="RBID">PMC:3655615</idno><idno type="doi">10.1111/j.1462-2920.2012.02836.x</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000C38</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000C38</idno><idno type="wicri:Area/Pmc/Curation">000C38</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000C38</idno><idno type="wicri:Area/Pmc/Checkpoint">001227</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001227</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:22845467</idno><idno type="wicri:Area/PubMed/Corpus">001D60</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001D60</idno><idno type="wicri:Area/PubMed/Curation">001D60</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001D60</idno><idno type="wicri:Area/PubMed/Checkpoint">001B49</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001B49</idno><idno type="wicri:Area/Ncbi/Merge">000983</idno><idno type="wicri:Area/Ncbi/Curation">000983</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics</title><author><name sortKey="Hurwitz, Bonnie L" sort="Hurwitz, Bonnie L" uniqKey="Hurwitz B" first="Bonnie L" last="Hurwitz">Bonnie L. Hurwitz</name></author><author><name sortKey="Deng, Li" sort="Deng, Li" uniqKey="Deng L" first="Li" last="Deng">Li Deng</name></author><author><name sortKey="Poulos, Bonnie T" sort="Poulos, Bonnie T" uniqKey="Poulos B" first="Bonnie T" last="Poulos">Bonnie T. Poulos</name></author><author><name sortKey="Sullivan, Matthew B" sort="Sullivan, Matthew B" uniqKey="Sullivan M" first="Matthew B" last="Sullivan">Matthew B. Sullivan</name></author></analytic><series><title level="j">Environmental Microbiology</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biodiversity</term><term>Metagenomics</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>Viruses (genetics)</term><term>Viruses (isolation & purification)</term><term>Water Microbiology</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biodiversité</term><term>Eau de mer (virologie)</term><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><term>Virus (isolement et purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines virales</term><term>Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Virology</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Eau de mer</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Seawater</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>Metagenomics</term><term>Reproducibility of Results</term><term>Water Microbiology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biodiversité</term><term>Microbiologie de l'eau</term><term>Métagénomique</term><term>Reproductibilité des résultats</term><term>Virologie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 (<italic>Podoviridae</italic> and <italic>Phycodnaviridae</italic>) and more variability among <italic>Myoviridae</italic> 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Allen, Lz" uniqKey="Allen L">LZ Allen</name></author><author><name sortKey="Ishoey, T" uniqKey="Ishoey T">T Ishoey</name></author><author><name sortKey="Novotny, Ma" uniqKey="Novotny M">MA Novotny</name></author><author><name sortKey="Mclean, Js" uniqKey="Mclean J">JS McLean</name></author><author><name sortKey="Lasken, Rs" uniqKey="Lasken R">RS Lasken</name></author><author><name sortKey="Williamson, Sj" uniqKey="Williamson S">SJ Williamson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name></author><author><name sortKey="Schaffer, Aa" uniqKey="Schaffer A">AA 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sortKey="Crielaard, Jw" uniqKey="Crielaard J">JW Crielaard</name></author><author><name sortKey="Claas, Ec" uniqKey="Claas E">EC Claas</name></author><author><name sortKey="Templeton, Ke" uniqKey="Templeton K">KE Templeton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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