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Viruses 2017, 9(3), 47; doi:10.3390/v9030047

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater

1
Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
2
Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK
3
University of Exeter Sequencing Service, Biosciences, Stocker Rd., University of Exeter, Exeter EX4 4QD, UK
4
Department of Environmental Affairs, Oceans and Coasts, P.O. Box 52126, Victoria and Alfred Waterfront, Cape Town 8000, South Africa
*
Authors to whom correspondence should be addressed.
Academic Editors: Mathias Middelboe and Corina Brussaard
Received: 13 January 2017 / Revised: 13 March 2017 / Accepted: 13 March 2017 / Published: 17 March 2017
(This article belongs to the Special Issue Marine Viruses 2016)
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Abstract

The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order Caudovirales (59%), with the family Myoviridae being the most prevalent. The families Phycodnaviridae and Mimiviridae made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis. View Full-Text
Keywords: microbiome; viruses; prokaryote; eukaryote; NGS; diversity; phylotypes; eDNA; meDNA microbiome; viruses; prokaryote; eukaryote; NGS; diversity; phylotypes; eDNA; meDNA
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Flaviani, F.; Schroeder, D.C.; Balestreri, C.; Schroeder, J.L.; Moore, K.; Paszkiewicz, K.; Pfaff, M.C.; Rybicki, E.P. A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater. Viruses 2017, 9, 47.

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