Diversity and genomics of giant viruses in the North Pacific Subtropical Gyre

Abstract

Large double-stranded DNA viruses of the phylum Nucleocytoviricota, often referred to as “giant viruses,” are ubiquitous members of marine ecosystems that are important agents of mortality for eukaryotic plankton. Although giant viruses are known to be prevalent in marine systems, their activities in oligotrophic ocean waters remain unclear. Oligotrophic gyres constitute the majority of the ocean and assessing viral activities in these regions is therefore critical for understanding overall marine microbial processes. In this study, we generated 11 metagenome-assembled genomes (MAGs) of giant viruses from samples previously collected from Station ALOHA in the North Pacific Subtropical Gyre. Phylogenetic analyses revealed that they belong to the orders Imitervirales (n = 6), Algavirales (n = 4), and Pimascovirales (n = 1). Genome sizes ranged from ~119–574 kbp, and several of the genomes encoded predicted TCA cycle components, cytoskeletal proteins, collagen, rhodopsins, and proteins potentially involved in other cellular processes. Comparison with other marine metagenomes revealed that several have broad distribution across ocean basins and represent abundant viral constituents of pelagic surface waters. Our work sheds light on the diversity of giant viruses present in oligotrophic ocean waters across the globe.

Assessing the biogeography of marine giant viruses in four oceanic transects

“…Interestingly, we found that the recently-delineated family-level clade PM_01 was the most prevalent lineage of the Pimascovirales in the ocean, but no members of this group have been cultivated and their host range remains unknown. A recent study found a member of this lineage was prevalent in surface waters of Station ALOHA, consistent with the view that they are present in oligotrophic surface waters [ 58 ]. The only Asfuvirales virus found in our survey, GVMAG-M-3300027833-19 was recovered in the GA10 transect, which is located off the Atlantic coast of South Africa.…”

Assessing the biogeography of marine giant viruses in four oceanic transects

“…Interestingly, we found that the recently-delineated family-level clade PM_01 was the most prevalent lineage of the Pimascovirales in the ocean, but no members of this group have been cultivated and their host range remains unknown. A recent study found a member of this lineage was prevalent in surface waters of Station ALOHA, consistent with the view that they are present in oligotrophic surface waters [55]. The only Asfuvirales virus found in our survey, GVMAG-M-3300027833-19 was recovered in the GA10 transect, which is located off the Atlantic coast of South Africa.…”

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

“…Furthermore, numerous sequences assigned to NCLDV families exhibited significant similarity to various host proteins, including heat-shock proteins, tRNA synthetase, histone, and ubiquitin sequences, among others. Although these genes with eukaryotic homologs can potentially be encoded by NCLDV (Raoult et al, 2004;Boyer et al, 2009;de Souza et al, 2021;Ha et al, 2021;Farzad et al, 2022;Talbert et al, 2022), their abundance was significantly greater than those associated with the virus . CC-BY-NC-ND 4.0 International license perpetuity.…”

“…The average relative abundance was very uneven among families: Retroviridae dominated the eukaryotic viromes, accounting for 34.7% of reads assigned to eukaryotic viruses, followed by Mimiviridae at 23.5% (see Figure S1B and Table S4 at NCLDV families exhibited significant similarity to various host proteins, including heat-shock proteins, tRNA synthetase, histone, and ubiquitin sequences, among others. Although these genes with eukaryotic homologs can potentially be encoded by NCLDV (Raoult et al, 2004;Boyer et al, 2009;de Souza et al, 2021;Ha et al, 2021;Farzad et al, 2022;Talbert et al, 2022), their abundance was significantly greater than those associated with the virus replication, which lack close homologs in the host genomes (Koonin & Yutin, 2010). This could hint in the direction of these hits representing host sequences in the samples, which could partly explain why a large part of the apparently more dominant viral families identified across the viromes were DNA viruses, contrary to the common consensus, which states that RNA viruses dominate invertebrate viromes (Shi et al, 2016;Porter et al, 2019).…”