eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area
2.2. Water Temperature
2.3. Amphibian Sampling
2.4. Insect Sampling
2.5. Water Sampling
2.6. Sediment Sampling
2.7. Ranavirus Detection in Frogs, Tadpoles and Insects
2.8. Ranavirus Detection in Sediment
2.9. Ranavirus Detection in Water
2.10. Ranavirus Identification
3. Results
3.1. Field Observations
3.2. Ranavirus Detection in Organisms
3.3. Ranavirus Detection in Water
3.4. Ranavirus in Sediment
3.5. Ranavirus Identification
4. Discussion
4.1. Seasonal Dynamics of Ranavirus Epidemics in a Common Frog Population
4.2. Designing Pathogen Surveys Using eDNA and Occupancy Models
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Samples | Date | |||||
---|---|---|---|---|---|---|
10–11 June | 23–24 June | 08 July | 27 July | 15-16 August | 19 September | |
Tadpole alive | 5 (9–11) 1 | 5 (24–25) | 5 (30) | 5 (35–39) | 5 (39–41) | 5 (43–45) |
Tadpole dead | - | - | - | 10 (35–39) | - | |
Adult alive 2 | 5 | 5 | 5 | 0 | 1 | 5 |
Adult dead | 1 | - | - | - | - | - |
Terrestrial insects 3 | 1 | 1 | 1 | 1 | 1 | 1 |
Aquatic insects 4 | 1 | 1 | 1 | 1 | 1 | 1 |
Sediment 5 | 1 | 1 | 1 | 1 | 1 | 1 |
Water 6 | 1 | 1 | 1 | 1 | 1 | 1 |
Pathogen | Filter Mesh Water Collection | Volume of Water Sample | Field Sampling | Date | Occupancy Design | Reference |
---|---|---|---|---|---|---|
Chytrid | 0.45 µm Peristaltic pump | 0.05 to 2.3 L per site (filter clogged) | In shallow water (0.1 to 0.75 m deep) in known or likely amphibian habitats. 3 locations per site, 4 sites | 1 date | no | [21] |
Chytrid | 0.45 µm 50 mL syringe | <1 L per site (filter clogged) | Within 10 cm of the edge 1 location per site, 42 sites | 1 date | no | [22] |
Chytrid | 0.22 µm 60 mL syringe | 600 mL per site | Samples spaced evenly along the entire site circumference, but taken only from areas where frogs or tadpoles were present 30 samples of 20 mL combined, 20 sites | 4 dates | No, yes * | [23,63] |
Chytrid | 1.2 µm Hand pump | 500 to 1500 mL per site | Every 40 m along the shoreline. 5 samples of 50 mL combined, 13 sites | 1 date | no | [26] |
Chytrid | 0.22 µm 60 mL syringe | 20 mL to 2.4 L per site | In shallow water (5 and 20 cm below the water surface) 3 spatial replicates per site, 41 sites | 1 date | yes | [64] |
Ranavirus | 0.2 µm Disposable paper cup | 750 mL 250 mL × 3 per site | At 3 distinct locations (north, east and west) along the shore and surface (ca. 10 cm deep) 3 spatial replicates per site, 20 sites | 1 date | yes | [24] |
Ranavirus | 0.2 µm Disposable paper cup | 750 mL 250 mL × 3 per site | As above 8 sites | 16 dates | no | [27] |
Chytrids Ranavirus | 0.2 µm Hand pump | 0.6–1 L 150−250 mL × 4 per site | 4 locations approximately equidistant around the site (within 2 m of the edge and 20−40 cm below the surface), 4 spatial replicates per site; 21 sites | 3 dates | yes | [65] |
Ranavirus | 0.45 µm Sterile water-sample dipper | 2 L 100 mL × 20 combined | 20 locations equidistant around the site (within 0.5 m of the edge and 10 cm below the surface), 1 site | 6 dates | no | This study |
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Miaud, C.; Arnal, V.; Poulain, M.; Valentini, A.; Dejean, T. eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population. Viruses 2019, 11, 526. https://doi.org/10.3390/v11060526
Miaud C, Arnal V, Poulain M, Valentini A, Dejean T. eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population. Viruses. 2019; 11(6):526. https://doi.org/10.3390/v11060526
Chicago/Turabian StyleMiaud, Claude, Véronique Arnal, Marie Poulain, Alice Valentini, and Tony Dejean. 2019. "eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population" Viruses 11, no. 6: 526. https://doi.org/10.3390/v11060526