Targeting the invaders – targeted detection of four priority freshwater invasive non-native species using environmental DNA

Rosetta C Blackman; Marco Benucci; Robert Donnelly; Bernd Hänfling; Lynsey R Harper; Helen Kimbell; Graham S Sellers; Andrew M Sheard; Hayley V Watson; Lori Lawson-Handley

doi:10.7287/peerj.preprints.27284v1

Targeting the invaders – targeted detection of four priority freshwater invasive non-native species using environmental DNA

Rosetta C Blackman ^1,2, Marco Benucci¹, Robert Donnelly¹, Bernd Hänfling¹, Lynsey R Harper¹, Helen Kimbell¹, Graham S Sellers¹, Andrew M Sheard³, Hayley V Watson¹, Lori Lawson-Handley¹

1 Evolutionary and Environmental Genomics Group (EvoHull), School of Environmental Sciences, University of Hull, Hull, UK

2 Department of Aquatic Ecology, eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland

3 Zurich, Switzerland

DOI: 10.7287/peerj.preprints.27284v1

Published: 2018-10-17
Accepted: 2018-10-17

Subject Areas: Biodiversity, Ecology, Molecular Biology, Freshwater Biology
Keywords: environmental DNA, eDNA, invasive non-native species, monitoring, targeted detection, standard PCR

Copyright: © 2018 Blackman 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: Blackman RC, Benucci M, Donnelly R, Hänfling B, Harper LR, Kimbell H, Sellers GS, Sheard AM, Watson HV, Lawson-Handley L. 2018. Targeting the invaders – targeted detection of four priority freshwater invasive non-native species using environmental DNA. PeerJ Preprints 6:e27284v1 https://doi.org/10.7287/peerj.preprints.27284v1

Abstract

Early detection is paramount for attempts to remove invasive non-native species (INNS). Traditional methods rely on physical sampling and morphological identification, which can be problematic when species are in low densities and/or are cryptic. The use of environmental DNA (eDNA) as a monitoring tool in freshwater systems is becoming increasingly acceptable and widely used for the detection of single species. Here we demonstrate the development and application of standard PCR primers for the detection of four freshwater invasive species which are high priority for monitoring in the UK and elsewhere: Dreissenid mussels; Dreissena rostriformis bugensis (Andrusov, 1987) and D. polymorpha (Pallas, 1771), and Gammarid shrimps; Dikerogammarus villosus (Sowinsky, 1984) and D. haemobaphes (Eichwald, 1843). We carried out a rigorous validation process for testing the new primers, including DNA detection and degradation rate experiments in mesocosm, and a field comparison with traditional monitoring protocols. We successfully detected all four target species in mesocosms, but success was higher for mussels than shrimps. eDNA from single individuals of both mussel species could be detected within four hours of the start of the experiment. By contrast, shrimp were only consistently detected at higher densities (20 individuals). In field trials, the two mussel species and D. haemobaphes were detected at all sites where the species are known to be present, and eDNA consistently outperformed traditional kick sampling for species detection. However, D. villosus eDNA was only detected in one of five sites where the species was confirmed by kick sampling. These results demonstrate the applicability of standard PCR for eDNA detection of freshwater invasive species, but also highlight the importance of differences between taxa in terms of the detection ability.