title: A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater.
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 orderCaudovirales(59%), with the familyMyoviridaebeing the most prevalent. The familiesPhycodnaviridaeandMimiviridaemade 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.
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. flafla@mba.ac.uk.|Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK. flafla@mba.ac.uk.
authors.forename: Flavia
authors.initials: F
authors.lastname: Flaviani
authors.affiliation: Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK. dsch@mba.ac.uk.
authors.forename: Declan C
authors.initials: DC
authors.lastname: Schroeder
authors.affiliation: Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK. cecilia.balestreri@gmail.com.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Balestreri
authors.affiliation: Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UK. joanna.schroeder.uk@gmail.com.
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Schroeder
authors.affiliation: University of Exeter Sequencing Service, Biosciences, Stocker Rd., University of Exeter, Exeter EX4 4QD, UK. K.A.Moore@exeter.ac.uk.
authors.forename: Karen
authors.initials: K
authors.lastname: Moore
authors.affiliation: University of Exeter Sequencing Service, Biosciences, Stocker Rd., University of Exeter, Exeter EX4 4QD, UK. K.H.Paszkiewicz@exeter.ac.uk.
authors.forename: Konrad
authors.initials: K
authors.lastname: Paszkiewicz
authors.affiliation: Department of Environmental Affairs, Oceans and Coasts, P.O. Box 52126, Victoria and Alfred Waterfront, Cape Town 8000, South Africa. maya.pfaff@gmail.com.
authors.forename: Maya C
authors.initials: MC
authors.lastname: Pfaff
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. ed.rybicki@uct.ac.za.
authors.forename: Edward P
authors.initials: EP
authors.lastname: Rybicki
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D056890:Eukaryota / Q000145:classification* / Q000235:genetics; D064307:Microbiota; D012623:Seawater / Q000382:microbiology*; D014780:Viruses / Q000145:classification* / Q000235:genetics
keywords: NGS; diversity; eDNA; eukaryote; meDNA; microbiome; phylotypes; prokaryote; viruses