An application of PCR-RFLP species identification assay for environmental DNA detection

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1 Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
2 Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
3 Estuary Research Center, Shimane University, Matsue, Shimane, Japan
4 Department of Evolutionary Studies of Biosystems, Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
5 Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Shiwa, Iwate, Japan
DOI
10.7287/peerj.preprints.27601v1
Published
Accepted
Subject Areas
Biodiversity, Conservation Biology, Ecology, Zoology, Freshwater Biology
Keywords
amphibian, environmental DNA, distribution range, species identification, monitoring survey, water sample, frog species, tadpole
Copyright
© 2019 Igawa et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Igawa T, Takahara T, Lau Q, Komaki S. 2019. An application of PCR-RFLP species identification assay for environmental DNA detection. PeerJ Preprints 7:e27601v1

Abstract

Recent advancement of eDNA methods for surveying species in aquatic ecosystems has been used for various organisms and contributed to monitoring and conservation of species and environments. Amphibians are one of the promising taxa which could be monitored efficiently by using eDNA. However, the cost of the eDNA detection can be quite high and requires instruments that are not usually installed in ecology laboratories. For aiding researchers foraying into eDNA studies of amphibians, especially those not specialized in molecular biology, we developed a cost efficient protocol using PCR-RFLP method. We attempted to detect eDNA of three Japanese Rana species (R. japonica, R. ornativentris, and R. tagoi tagoi) in various spatial scales including an area close to the Fukushima Nuclear Power Plant (FNPP) where the environment is recovering after the disaster in 2011. Our PCR-RFLP protocol was successful in detecting Rana species in static water in both laboratory and field; however, it could not detect Rana species in non-static water samples from the field. Even a more sensitive detection method (standard qPCR) was unable to detect frogs in all non-static water samples. We speculate that our new protocol is effective for frogs living in lentic habitats, but not for lotic habitats which may still require the gold standard of field observation for detection approach.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

PCR-RFLP and gel electrophoresis of field experiment (A)

DOI: 10.7287/peerj.preprints.27601v1/supp-1

Supplementary Table 1: Sample infomation

n/a qPCR not conducted; Rj = R. japonica; Ro = R. ornativentris; Rtt = R. t. tagoi

DOI: 10.7287/peerj.preprints.27601v1/supp-2