RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics
Abstract
:1. Introduction
2. Methodological Challenges in the Study of Aquatic RNA Viral Communities
3. Environmental RNA Metaviromics: Lytic Positive-Sense ssRNA Viruses Dominate Pelagic but Not Benthic RNA Viral Assemblages
4. Environmental (Viral) Metatranscriptomics: Sampling with Size Fractionation Improves Metatranscriptome Resolution and Uncovers the Role of ssRNA Viruses
5. Environmental dsRNA Sequencing: The Enrichment of dsRNA from Marine Samples Greatly Expands the Diversity of dsRNA Viruses
6. Holobiont Metatranscriptomics: Marine Macroalgae and Cultured Marine Protists Reveal the Broad Distribution of Non-Lytic Strategies in Marine RNA Viruses
7. Recommendations for Future Studies
8. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Method | Virus Nucleic Acid Detected | Shortcomings | Advantages | |
---|---|---|---|---|
Metaviromics or viral metagenomics | RNA or DNA viral genomes in the extracellular stage | RNA viruses targeted separately than DNA viruses Needs special enrichment for dsRNA and ssDNA Large DNA viruses are filtered out High-burst-size viruses can be overrepresented | Enriched for viral sequences, better assembly | |
Metatranscriptomics | Transcripts of (+) and (−) ssRNA, dsRNA, ssDNA, dsDNA | High background of nonviral sequences Potentially fragmented assemblies Misses low-titre viruses Does not distinguish between (+) ssRNA viral genome and transcripts | Captures all types of DNA and RNA viruses simultaneously Captures active infection (for DNA viruses) Can capture RNA viruses without capsids | |
dsRNA sequencing | ssRNA as replicative intermediate dsRNA genomes | Not as effective for (−) ssRNA and DNA viruses Cellular metatranscriptomes are removed in the enrichment process | Enriched for RNA viruses Can be used for detection of both extracellular (<0.22 µm fractions) and intracellular RNA viruses |
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] |
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Kolundžija, S.; Cheng, D.-Q.; Lauro, F.M. RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics. Viruses 2022, 14, 702. https://doi.org/10.3390/v14040702
Kolundžija S, Cheng D-Q, Lauro FM. RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics. Viruses. 2022; 14(4):702. https://doi.org/10.3390/v14040702
Chicago/Turabian StyleKolundžija, Sandra, Dong-Qiang Cheng, and Federico M. Lauro. 2022. "RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics" Viruses 14, no. 4: 702. https://doi.org/10.3390/v14040702
APA StyleKolundžija, S., Cheng, D.-Q., & Lauro, F. M. (2022). RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics. Viruses, 14(4), 702. https://doi.org/10.3390/v14040702