Marine DNA Viral Macro-and Micro-Diversity From Pole to Pole

Abstract

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow and metabolic outputs. However, ecosystem-level impacts of viral community diversity remains difficult to assess due to classification issues and few reference genomes. Here we establish a ~12-fold expanded global ocean DNA virome dataset of 195,728 60 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (interpopulation diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models. Results & Discussion: The dataset. The Global Ocean Viromes 2.0 (GOV 2.0) dataset is derived from 3.95 Tb of sequencing across 145 samples distributed throughout the world's oceans (Fig. 1A and Table S3; see Methods). These data build on the prior GOV dataset (Roux et al., 2016) by increased sequencing for mesopelagic samples (defined in our dataset as waters between 150m to 1,000m) and upgrading assemblies, both of which drastically improved sampling of the ocean viruses in these samples (results below). Additionally, we added 41 new samples derived from the Tara Oceans Polar Circle (TOPC) expedition, which traveled 25,000 km around the Arctic Ocean in 2013. These 41 Arctic Ocean viromes were generated to represent the most significantly climateimpacted region of the ocean, and an extreme environment. No such metagenome-based viral data exist for the Arctic region (Deming & Collins 2017), and more generally, for many planktonic organisms, systematic sampling is uneven throughout the Arctic Ocean (CAFF State of the Arctic Marine Biodiversity Report) due to geopolitical and physical challenges of sampling these regions. The first step to studying viral biodiversity from the assembled GOV 2.0 dataset (see Methods and Fig. S1A) was to identify contigs that likely derive from viruses using tools that collectively utilize homology to viral reference databases, probabilistic models on viral genomic features, and viral k-mer signatures (see Methods). These putative viral contigs were then assigned to 'populations', which are currently defined as viral contigs ≥10 kb where ≥70% of the shared genes have ≥95% average nucleotide identity (ANI) across its members (Brum et al., 2015; Roux et al., 2016; Roux et al., 2018; population definition also discussed below). This process identified 195,728 viral populations in the GOV 2.0 dataset, which is a ~12-fold increase over the 15,280 identified in the original GOV dataset and ass...

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