Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics

Abstract

Single-virus genomics (SVGs) has been successfully applied to ocean surface samples allowing the discovery of widespread dominant viruses overlooked for years by metagenomics, such as the uncultured virus vSAG 37-F6 infecting the ubiquitous Pelagibacter spp. In SVGs, one uncultured virus at a time is sorted from the environmental sample, whole-genome amplified, and sequenced. Here, we have applied SVGs to deep-ocean samples (200–4000 m depth) from global Malaspina and MEDIMAX expeditions, demonstrating the feasibility of this method in deep-ocean samples. A total of 1328 virus-like particles were sorted from the North Atlantic Ocean, the deep Mediterranean Sea, and the Pacific Ocean oxygen minimum zone (OMZ). For this proof of concept, sixty single viruses were selected at random for sequencing. Genome annotation identified 27 of these genomes as bona fide viruses, and detected three auxiliary metabolic genes involved in nucleotide biosynthesis and sugar metabolism. Massive protein profile analysis confirmed that these viruses represented novel viral groups not present in databases. Although they were not previously assembled by viromics, global fragment recruitment analysis showed a conserved profile of relative abundance of these viruses in all analyzed samples spanning different oceans. Altogether, these results reveal the feasibility in using SVGs in this vast environment to unveil the genomes of relevant viruses.

Comprehensive profiling of wastewater viromes by genomic sequencing

“…quality and function of freshwater systems (Numberger et al, 2022). And third, the advent of ultra-deep sequencing and computational methods, so far from public databases and seawater samples, has enabled the detection of large number of novel viruses, thus expanding considerably our knowledge of viral diversity (Edgar et al, 2022; Gregory et al, 2019; Martinez-Hernandez et al, 2022).…”

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles

“…Environmental viruses are more diverse than environmental bacteria, and genomic mutations occur frequently, leaving many challenges for high-resolution genome analysis [9]. Single-virus genome sequencing using FACS has been performed; however, it has some difficulties in sorting accuracy, and previous reports have recovered only a few dozen viral sequences mainly because of the low success rate of WGA [13][14][15]. Here, we developed a gel bead-based single-virus genomics platform and recovered a total of 1431 viral sequences from 93.2% of the isolated gel beads.…”

“…It should be noted that excluded contigs do not directly indicate viral sequence contamination since contigs derived from one viral species could be classified into multiple bins due to the lack of sequence information. Finally, we recovered 1431 vSAGs from 740 samples (96.3% of the total) by method (Ⅰ) and 691 samples (90.0% of the total) by method (Ⅱ), demonstrating a significantly higher recovery rate than conventional single-virus genomics [13][14][15]. Of the 105 samples with no viral sequences detected, 54 had small data sizes (less than 5,000 paired reads), and most of the remaining sequences were determined to contain fragmented reads of bacteria or viruses.…”

“…However, isolating nanometer-sized viral particles using FACS is technically challenging, and the efficiency of genome amplification was limited to 20% of sorted samples at most [13][14][15]. Therefore, the number of recovered vSAGs has been limited, and only the most abundant populations were recovered [16].…”

Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles

“…Among these viruses, those inhabiting the mesopelagic and deep marine environments have emerged as a subject of particular interest since these constitute the largest ecosystems on Earth and are crucial components of the global carbon cycle [5][6][7][8]. Despite the crucial ecological signi cance of viruses inhabiting dark ocean environments [5,[9][10][11], our comprehension of their diversity, abundance, and ecological roles remains signi cantly limited. This is even more dramatic with regard to those thriving in the permanently dark ocean under the polar Antarctic Ice Shelves.…”