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 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.

Marine Viruses: Key Players in Marine Ecosystems

“…A recent analysis of viral metagenomic sequence data from 43 surface ocean sites identified ~5500 populations of dsDNA viruses, of which only 39 could be affiliated to cultured viruses [ 22 ]. Even at very small scales, viral diversity may be high, as demonstrated by Flaviani et al [ 25 ], who found 254 unique virus phylotypes in a 250 mL oceanic water sample, supporting previous suggestions that local viral diversity is relatively similar to global diversity [ 22 ].…”

Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions

“…The development of long-read sequencing methods, preemptively deemed “third-generation sequencing”, may address many of the issues with short-read assembly and viral quantification. DNA barcoding has been suggested as a cheap, reliable method to quickly track virus populations, and has recently been shown to recapitulate general viral community structures using sample volumes no bigger than a cup of water [ 168 ]. New virus isolates can be discovered from sequencing of single aquatic viruses sorted by flow cytometry, [ 169 ], as closely related, hyper diverse viruses are suggested to be difficult to assemble from metagenomes [ 170 ].…”

Disentangling the mechanisms shaping the surface ocean microbiota

“…In the surface ocean, drastic changes in microbial species composition across space may point to strong changes in abiotic selection (as expected to occur across oceanographic fronts [74,75]), or high immigration. We identified 14 stations featuring abrupt changes in prokaryotic or picoeukaryotic community composition as well as 36 stations with a "unique" species composition.…”