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Rapid detection of the amphibian chytrid fungus (Batrachochytrium dendrobatidis) using in-situ DNA extraction and a handheld mobile thermocycler
  • Colleen Kamoroff,
  • Caren Goldberg,
  • Robert Grasso
Colleen Kamoroff
Yosemite National Park
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Caren Goldberg
Washington State University
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Robert Grasso
Yosemite National Park
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Peer review status:UNDER REVIEW

19 May 2020Submitted to Molecular Ecology Resources
30 Jun 2020Assigned to Editor
30 Jun 2020Submission Checks Completed
06 Jul 2020Reviewer(s) Assigned

Abstract

The amphibian chytrid fungus (Bd) has caused extinction of amphibian populations worldwide. Early and accurate Bd detection is essential for management and treatment of susceptible anurans. We analyzed the effectiveness of an in-situ DNA extraction along with handheld mobile quantitative PCR (qPCR) thermocycler to detect Bd on skin frog swabs, and to detect Bd in water samples using environmental DNA (eDNA). We collected duplicate eDNA samples and skin swabs from three Bd positive Rana sierrae populations. We processed one set of samples using a field protocol (a handheld thermocycler), and the other half using a standard lab protocol. We detected Bd DNA in all R. sierrae swabbed across all three sites using both the field and lab protocols. We also detected Bd DNA in eDNA samples collected at two of the three sites using both the field and lab protocols although the field and lab protocol failed to detect Bd eDNA at separate sites. The probability of detecting Bd DNA in the technical replicates was lower for the field protocol compared to samples extracted using the lab protocol, suggesting the field protocol has reduced sensitivity and may not detect low quantities of DNA. Our results suggest the field extraction protocol using a handheld qPCR platform is a promising tool for rapid detection of Bd in susceptible amphibian populations. The field protocol yielded accurate results in less than 60 minutes. However, the applied field protocol may be prone to false negatives when analyzing low-quantity DNA samples (i.e. eDNA).