A pelagic microbiome (Viruses to protists) from a small cup of seawater

Flavia Flaviani, Declan C. Schroeder, Cecilia Balestreri, Joanna L. Schroeder, Karen Moore, Konrad Paszkiewicz, Maya C. Pfaff, Edward P. Rybicki

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

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.

Original languageEnglish (US)
Article number47
JournalViruses
Volume9
Issue number3
DOIs
StatePublished - Mar 17 2017

Bibliographical note

Funding Information:
Computations were performed using facilities provided by the University of Cape Town?s ICTS High Performance Computing team: http://hpc.uct.ac.za. Project was funded under National Research Foundation (NRF) grant to Ed Rybicki. (CPR20110717000020991). We would also like to thank Barney Balch for the opportunity to join the Coccolthophore Belt cruise. Declan Schroeder was funded by the FP7-OCEAN-2011 call, MicroB3 (grant number 287589) and the NERC eDNA award (grant number NE/N006151/1).

Publisher Copyright:
© 2017 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • Diversity
  • Eukaryote
  • Microbiome
  • NGS
  • Phylotypes
  • Prokaryote
  • Viruses
  • eDNA
  • meDNA

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