Title
Improving the Yield of Environmental DNA From Filtered Aquatic Samples
Start Date
26-10-2018 8:00 PM
End Date
26-10-2018 9:59 PM
Description
The analysis of environmental DNA (eDNA) is a promising conservation tool to provide information about the presence/absence of rare or invasive species that are difficult to physically locate. In aquatic environments, eDNA analysis has been successfully implemented to monitor a variety of species, however further research is needed to improve methodology used in eDNA analysis. The aim of the present study is to investigate the effect of the DNA extraction process and the effect of the filter preservation method on eDNA yield. We analyzed field-collected water samples for eDNA of the Eastern Hellbender, a fully-aquatic giant salamander that was once locally common but is now declining in its number. Water samples from sites of interest were filtered and the filters were stored in the laboratory until we extracted DNA from these filters and then performed quantitative PCR to detect Eastern Hellbender DNA. To improve eDNA recovery from filters, we tested whether the use of bead beating, where small silica beads are vortexed with the filter during DNA extraction, would increase eDNA yield by removing DNA trapped on the filters. In addition, we examined whether preservation of the filters in ethanol or storage at -20°C before extraction would yield more eDNA. We found that bead beating during DNA extraction significantly increased the estimated amount of eDNA extracted compared to controls and that preservation at -20°C also significantly increased estimated concentrations of eDNA obtained compared to preservation in ethanol.
Keywords
eastern hellbender, eDNA, bead beating
Type
Poster
Session
Poster session
Language
eng
Improving the Yield of Environmental DNA From Filtered Aquatic Samples
Elaine Langone Center, Terrace Room
The analysis of environmental DNA (eDNA) is a promising conservation tool to provide information about the presence/absence of rare or invasive species that are difficult to physically locate. In aquatic environments, eDNA analysis has been successfully implemented to monitor a variety of species, however further research is needed to improve methodology used in eDNA analysis. The aim of the present study is to investigate the effect of the DNA extraction process and the effect of the filter preservation method on eDNA yield. We analyzed field-collected water samples for eDNA of the Eastern Hellbender, a fully-aquatic giant salamander that was once locally common but is now declining in its number. Water samples from sites of interest were filtered and the filters were stored in the laboratory until we extracted DNA from these filters and then performed quantitative PCR to detect Eastern Hellbender DNA. To improve eDNA recovery from filters, we tested whether the use of bead beating, where small silica beads are vortexed with the filter during DNA extraction, would increase eDNA yield by removing DNA trapped on the filters. In addition, we examined whether preservation of the filters in ethanol or storage at -20°C before extraction would yield more eDNA. We found that bead beating during DNA extraction significantly increased the estimated amount of eDNA extracted compared to controls and that preservation at -20°C also significantly increased estimated concentrations of eDNA obtained compared to preservation in ethanol.
Comments
Related paper:
Hundermark, Emma and Takahashi, Mizuki. "Improving the Yield of Environmental DNA from Filtered Aquatic Samples." Conservation Genetics Resources (2018) .