Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.
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Hurwitz, Bonnie L.
Poulos, Bonnie T.
Sullivan, Matthew B.
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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% .....
Essential Ocean Variables (EOV)Microbe biomass and diversity
Best Practice TypeBest Practice
CitationHurwitz, B. L.,; Deng, L. ; Poulos, B. T. and Sullivan, M. B. (2013) Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environmental Microbiology, 15, pp.1428-1440. DOI:10.1111/j.1462-2920.2012.02836.x
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