Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake
Abstract
:1. Introduction
2. Materials and Methods
2.1. Site Description
2.2. Sample Collection and Processing
2.3. Identification of Viral Reads
2.4. Diversity Analyses
2.5. Genomic Analyses
2.6. Comparison to Other Viral Communities
2.7. Data Availability
3. Results and Discussion
3.1. Viral Yield
3.2. Contrasting Environmental Conditions and Viral Populations Across Seasons
3.3. Genomic Analyses of Uncultured Viral Genomes
3.4. Comparisons to Other Sites
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Season | Cover (m) | Temperature (°C) | pH | Oxygen (mg L−1) | CH4 (µM) | SO4 (nM) | TN (mg L−1) | DOC (mg L−1) |
---|---|---|---|---|---|---|---|---|
Summer | none | Surface: 15 Bottom: 6 | 6 | Surface: 4.13 Bottom: <LD | Surface: 2.5 Bottom: 300 | 1.46 | 0.7 | 13.7 |
Winter | 0.5 m snow 0.6 m ice | Surface: 0 Bottom: 3.5 | 5 | <LD | 200 | 0.5 | 1.2 | 18.3 |
Genome Type | UViG | Contig ID | Length (bp) | Number of CDS | Summer Average Abundance | Winter Average Abundance | Putative Host Rank | Putative Viral Group |
---|---|---|---|---|---|---|---|---|
C | UViG3 | Ga0256681_10553986 | 63,992 | 103 | 2.18 | 0 | Firmicutes | Siphoviridae, Myoviridae (Lactococcus, Clostridium, Geobacillus phages) |
C | UViG4 | Ga0256681_10542696 | 34,037 | 36 | 7.61 | 0 | ||
C | UViG5 | Ga0256681_10559173 | 36,339 | 61 | 13.3 | 0 | Gammaproteobacteria | Podoviridae (Rhodoferax, Vibrio, Thalassomonas phages) |
C | UViG6 | Ga0256681_11263128 | 62,403 | 87 | 4.54 | 0 | Gammaproteobacteria | Podoviridae, Sophoviridae (Pseudomonas, Xanthomonas phages) |
C | UViG7 | Ga0256681_10579994 | 45,748 | 55 | 1.65 | 0 | ||
C | UViG8 | Ga0256681_10547172 | 42,853 | 61 | 8.45 | 0 | Gammaproteobacteria | Podoviridae (Acetinobacter, Aeromonas, Edwardsiella phages) |
C | UViG9 | Ga0256681_10567549 | 36,908 | 45 | 6.1 | 0 | Gammaproteobacteria | Podoviridae, Siphoviridae (Pseudoalteromonas, Marinomonas, Escherichia viruses) |
C | UViG10 | Ga0256681_10572110 | 37,103 | 56 | 1.63 | 0 | Alphaproteobacteria | Siphoviridae (Caulobacter viruses) |
C | UViG11 | Ga0256681_10539383 | 83,527 | 107 | 5.85 | 2.16 | Unknown | Unknown (Natrinema, Haloarcula viruses) |
P | vOTU12 | Ga0256681_11878260 | 12,576 | 13 | 0.37 | 0 | Gammaproteobacteria | Myoviridae (Pseudomonas, Stenotrophomonas, Xanthomonas phage) |
P | vOTU13 | Ga0256681_12578680 | 29,945 | 13 | 9.71 | 0 | (Bacteria, Archaea) | Unknown |
P | vOTU14 | Ga0256681_12584168 | 15,432 | 17 | 1.2 | 0 | Unknown | Unknown |
P | vOTU15 | Ga0256681_12612509 | 13,421 | 11 | 2.46 | 0 | (Bacteria) | Unknown |
P | vOTU16 | Ga0256681_10168136 | 15,698 | 15 | 0.89 | 0 | Betaproteobacteria (Polaromonas) | Unknown |
P | vOTU17 | Ga0256681_10683670 | 11,399 | 18 | 3.47 | 0 | Unknown | Unknown |
P | vOTU18 | Ga0256681_11428677 | 14,176 | 18 | 1.33 | 0 | (Bacteria, Archaea) | Unknown |
P | vOTU21 | Ga0256681_10088446 | 10,785 | 11 | 9.7 | 0 | (Bacteria, Archaea) | Unknown |
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Girard, C.; Langlois, V.; Vigneron, A.; Vincent, W.F.; Culley, A.I. Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake. Viruses 2020, 12, 1204. https://doi.org/10.3390/v12111204
Girard C, Langlois V, Vigneron A, Vincent WF, Culley AI. Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake. Viruses. 2020; 12(11):1204. https://doi.org/10.3390/v12111204
Chicago/Turabian StyleGirard, Catherine, Valérie Langlois, Adrien Vigneron, Warwick F. Vincent, and Alexander I. Culley. 2020. "Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake" Viruses 12, no. 11: 1204. https://doi.org/10.3390/v12111204