Table 2.
Basic geographic, ecosystem, and sampling information about the aquatic metaviromic (turquoise) studies, metatranscriptomic (coral) studies, and dsRNA sequencing (yellow) reviewed in this paper. Asterisk * denotes a temporal study in multiple locations.
| Region | Sampling Location |
Site Characteristics |
Sampling Scheme | Temporal/ Spatial |
Host or Viral Fractions Collected (Host-Fractionated/Unfractionated) |
Relative Abundance of Viral Reads in the Metatranscriptome | Reference | |
|---|---|---|---|---|---|---|---|---|
| Global | Multiple locations |
Deep sea | 133 locations | Spatial | Only viral fraction (RNA) | - | [57] | |
| Polar | West Antarctic Peninsula | Highly productive coastal area | 1 location | Temporal | Only viral fraction (RNA) | - | [24] | |
| Polar and temperate | Multiple locations |
Multiple site characteristics | 11 locations | Spatial | Only viral fraction (RNA) | - | [58] | |
| Temperate | Jericho Pier, Georgia Strait, Canada | Highly productive coastal area | 2 locations | Spatial | Only viral fraction (RNA) | - | [59] | |
| Temperate | Yangshan Harbour, Shanghai, China |
Brackish coastal area | 1 location | Spatial | Only viral fraction (RNA and DNA) | - | [11] | |
| Subtropical | Kane’ohe Bay, Hawai’i | Coastal area | 1 location | Spatial | Only viral fraction (RNA) | - | [60] | |
| Subpolar | Honshu, Japan Jamstec cruise |
Coastal and pelagic |
5 locations | Spatial | Host: Unfractionated >0.22 µm dsRNA + ssRNA metatranscriptomes Viral fraction (RNA) dsRNA + ssRNA viromes |
0.1% of ssRNA metatranscriptomes 1.3–36.6% of dsRNA metatranscriptomes |
[56] | |
| Polar | Chile Bay, Antarctica |
Highly productive coastal area | 1 location 2 samples, 3 weeks apart |
Temporal | Host: Fractionated 8 µm–0.22 µm fraction |
0.04–0.05% (rRNA depletion) |
[48] | |
| Temperate | Baltic sea Lake Torneträsk |
Eutrophic, mostly brackish | 11 location (2 depths) | Spatial | Host: Fractionated 200–3.0 µm 3.0–0.8 µm 0.8–0.1 µm + viral fraction (DNA) |
3.2% (separate rRNA depletion and poly-A selection libraries) |
[50] | |
| Temperate | Narragansett Bay (NB) Quantuck Bay (QB), USA |
Eutrophic (bloom) coastal | 2 locations NB - 5 samples during 4 weeks QB - 3 samples within a week |
Temporal * | Host: Fractionated QB 5–0.22 µm NB >5 µm |
0.043–2.4% (poly-A selection) |
[44] | |
| Temperate | Lake Tai, China | Hypereutrophic (bloom) lake | 9 locations 1 × monthly for 5 months |
Temporal * | Host: Unfractionated >0.22 µm |
0.02% (rRNA depletion) |
[46] | |
| Temperate | Owasco Lake Seneca Lake Cayuga Lake, USA |
Mezotrophic to eutrophic lakes | 3 locations 1 × monthly for 10 months |
Temporal * | Host: Fractionated 5–0.22 µm |
0.6% (rRNA depletion) |
[45] | |
| Temperate | California Current, USA | Oligotrophic, with upwelling | 1 location Every 4 h for 60 h |
Temporal | Host: Fractionated >5 µm 5–0.22 µm |
Not reported | [49] | |
| Temperate | Quantuck Bay (QB) Tiana Beach (TB), USA |
Eutrophic (bloom) coastal | 2 locations QB 1× weekly for 10 weeks TB—1× weekly for 8 weeks |
Temporal * | Host: Unfractionated >0.22 µm (for rRNA reduction) >1 µm (for poly-A selection) |
0.33–0.53% in rRNA depleted libraries 0.02–0.023% in poly-A selected libraries |
[47] | |
| Global | Multiple locations | Multiple site characteristics |
68 locations 2 depths |
Spatial | Host: Fractionated 2000–180 µm 180–20 µm 20–5 µm 5–0.8 µm |
0.0006% to 0.4% (poly-A selection) |
[18,51] |