Environmental DNA (eDNA) on a Budget: Results from a Novel Single Laboratory and Limited Dedicated Equipment eDNA Protocol

Authors: Kerry* Holcomb

Year: 2015 (xlvii)

Abstract

Forensic technologies, namely environmental DNA (eDNA), offers the promise of cost effective tools capable of producing precise and repeatable data that describe 1) the occurrence of target species (either exotic species or species of conservation concern), 2) community biodiversity (ranging from viruses and single cell organisms to vertebrates), and 3) the relative abundance or density of a species. I present results from a novel protocol that delivers quality eDNA-driven monitoring of invasive species at much lower cost than earlier methodologies. Costs are mitigated by avoiding the use of dedicated laboratory spaces and by using only a limited amount of dedicated equipment. To monitor whether cost reduction measures impair the quality of results, stringent quality control and quality assurance measures were built into the protocol. These measures assess both method and process type I and II errors, relative to a null hypothesis of no target DNA present. During 2014 and 2015, a total of 31 presence/absence samples and 31 collection negative controls were collected and processed for red swamp crayfish, Procambarus clarkii, at Ash Meadows NWR (to benefit endangered Warm Springs pupfish, Cyprinodon pectoralis nevadensis) and for blue tilapia, Oreochromis aureus, plus red swamp crayfish at the Muddy River, Nevada (to benefit endangered Moapa dace, ,i>Moapa coriacea). In addition, each set of samples included a negative extraction blank, PCR negative blank, and a PCR positive control. Target DNA contamination was not detected in any of the 259 PCR sample or control assays or in any of the extraction nor PCR blank assays. False negatives where produced in 3 of 9 known positive samples (33.3%), while all positive controls produced expected results. The observation of no false positives (no process nor method type I errors) and limited false negative results (process and/or method type II errors) supports the idea that dedicated laboratory space and equipment are not obligatory to the production of valuable eDNA results. While likely not appropriate for applications requiring a probability of contamination near zero, this protocol provides a tool to effect conservation at meaningful spatial and taxonomic scales without exceeding budget limitations.