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Open AccessArticle

Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour

1
Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
2
Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Scarborough, ON M1C 1A4, Canada
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(9), 792; https://doi.org/10.3390/v11090792
Received: 9 July 2019 / Revised: 13 August 2019 / Accepted: 25 August 2019 / Published: 28 August 2019
(This article belongs to the Special Issue Viromics: Approaches, Advances, and Applications)
Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize virus communities captured in the >0.22 µm size-fraction seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus groups (i.e., order or family) Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Diverse Mimiviridae contigs were detected in the samples and the two sites contained distinct Mimiviridae communities, suggesting that Mimiviridae are important algal viruses in this system. Caudovirales and Phycodnaviridae were present at low abundances in most samples. Of the 18 environmental parameters tested, only chlorophyll a explained the variation in the data at the order or family level of classification. Overall, our findings provide insight into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales. View Full-Text
Keywords: viral ecology; freshwater environments; microbial communities; mimiviruses; virophages viral ecology; freshwater environments; microbial communities; mimiviruses; virophages
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Palermo, C.N.; Fulthorpe, R.R.; Saati, R.; Short, S.M. Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour. Viruses 2019, 11, 792.

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