Evaluating environmental DNA as a tool for detecting an amphibian pathogen using an optimized extraction method
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CONSERVATION ECOLOGY – ORIGINAL RESEARCH
Evaluating environmental DNA as a tool for detecting an amphibian pathogen using an optimized extraction method Laura A. Brannelly1,2 · Daniel P. Wetzel1 · Michel E. B. Ohmer1 · Lydia Zimmerman1 · Veronica Saenz1 · Corinne L. Richards‑Zawacki1 Received: 21 July 2019 / Accepted: 26 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Environmental DNA (eDNA) detection is a valuable conservation tool that can be used to identify and monitor imperiled or invasive species and wildlife pathogens. Batrachochytrium pathogens are of global conservation concern because they are a leading cause of amphibian decline. While eDNA techniques have been used to detect Batrachochytrium DNA in the environment, a systematic comparison of extraction methods across environmental samples is lacking. In this study, we first compared eDNA extraction methods and found that a soil extraction kit (Qiagen PowerSoil) was the most effective for detecting Batrachochytrium dendrobatidis in water samples. The PowerSoil extraction had a minimum detection level of 100 zoospores and had a two- to four-fold higher detection probability than other commonly used extraction methods (e.g., QIAamp extraction, DNeasy+Qiashredder extraction method, respectively). Next, we used this extraction method on field-collected water and sediment samples and were able to detect pathogen DNA in both. While field-collected water filters were equivalent to amphibian skin swab samples in detecting the presence of pathogen DNA, the seasonal patterns in pathogen quantity were different between skin swabs and water samples. Detection rate was lowest in sediment samples. We also found that detection probability increases with the volume of water filtered. Our results indicate that water filter eDNA samples can be accurate in detecting pathogen presence at the habitat scale but their utility for quantifying pathogen loads in the environment appears limited. We suggest that eDNA techniques be used for early warning detection to guide animal sampling efforts. Keywords Amphibian · Chytridiomycosis · EDNA · Environmental detection · Extraction
Introduction The development and adaptation of DNA extraction methods to detect small quantities of DNA have opened the door for novel studies in conservation and biodiversity. One such Communicated by Joel Trexler. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00442-020-04743-4) contains supplementary material, which is available to authorized users. * Laura A. Brannelly [email protected] 1
Department of Biological Science, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
Melbourne Veterinary School, Faculty of Agricultural and Veterinary Sciences, University of Melbourne, Werribee, VIC, Australia
2
technique involves detecting small amounts of DNA from the environment. Environmental DNA (eDNA) detection involves extraction and downstream analyses of DNA fr
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