Single Cell Genomics Reveals Viruses Consumed by Marine Protists

Abstract

The predominant model of the role of viruses in the marine trophic web is that of the "viral shunt," where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.

Keywords: marine eukaryote; marine food web; microbial ecology; nanoeukaryote; phage; protist; virus.

FIGURE 1

Occurrence of bacterial and viral DNA in protistan SAGs sampled from the Gulf of Maine (A) and the Mediterranean Sea (C). Distribution of viral and bacterial DNA within cells with identifiable 18S rRNA genes sampled from the Gulf of Maine (B) and the Mediterranean Sea (D).

FIGURE 2

Box and whisker plots of abundance of viral sequences in SAGs from the Mediterranean and Gulf of Maine (A), abundance of viral sequences in different protist taxa (B), abundance of bacterial virus sequences in SAGs from the Mediterranean and Gulf of Maine (C), and abundance of bacterial virus sequences in SAGs from different protist taxa (D). Lowercase letters in plots (B) and (D) indicate results of a post hoc Tukey test.

FIGURE 3

Recovery of highly similar viral sequences from multiple Gulf of Maine protistan SAGs. Example networks containing two viruses recovered from multiple eukaryotic phyla. Connections indicate occurrence of viral sequences (triangles) within protist SAGs (circles) (A). Network diagram showing viral content of eukaryote cells containing at least one virus found in multiple phyla. Innermost circle of nodes represent viruses found in more than one SAG. Middle circle of nodes represents protist SAGs. Outer nodes are singleton viral sequences. Nodes are sized based on network connectivity, with larger nodes indicating higher connectivity (B).

FIGURE 4

Marine microbial food web with arrows indicating the flow of carbon. Red arrow highlights the proposed role of viruses as a link between viruses and phagotrophic protists.