The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples

Abstract

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.

Figure 1. Breakdown of clustered GOS viral sequences by virus type (A) and functional classification of clustered bacteriophage sequences (B).

EV stands for eukaryotic virus and Hyp stands for hypothetical.

Figure 2. Phylogenetic trees of all GOS and publicly available psbA (A) and psbD (B) sequences.

BS indicates bootstrap values. GOS and public viral sequences are colored aqua and pink respectively. GOS and public prokaryotic sequences are navy blue and lime green respectively.

Figure 3. Phylogenetic trees of all GOS and publicly available pstS (A) and talC (B) sequences.

BS indicates bootstrap values. GOS and public viral sequences are colored aqua and pink respectively. GOS and public prokaryotic sequences are navy blue and lime green respectively. GOS eukaryotic sequences are colored yellow.

Figure 4. Distribution of GOS myovirus (a), podovirus (b) and siphovirus (c) sequences residing on scaffolds ≥5 kb across sampling locations.

The x-axis represents the relative abundance of normalized sequences per site, displayed as a percentage. Sampling locations and trophic status are displayed along the y-axis. Blue boxes indicate oligotrophic conditions, green boxes indicate mesotrophic conditions and red boxes indicate eutrophic conditions. Samples that are in close geographic proximity to each other share similarly colored histogram bars.

Figure 5. Recruitment of GOS sequences to the Prochlorococcus myophage P-SSM4 genome at 90% identity (B) and the distribution of these sequences across sampling locations (A).

The x-axis of the recruitment plot shows the position of sequence reads along the complete genome in base pairs and the y-axis represents percent identity. The x-axis of the histogram represents the relative abundance of normalized sequences per site, displayed as a percentage. Sampling locations and trophic status are displayed along the y-axis. Blue boxes indicate oligotrophic conditions, green boxes indicate mesotrophic conditions and red boxes indicate eutrophic conditions. Samples that are in close geographic proximity to each other share similarly colored histogram bars.