Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Abstract

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

“…It has been acknowledged that primer bias and differences in copy number of 18S (or mitochondrial abundance in the case of COI) hinder a direct quantitative relationship between number of reads (usually in the form of relative frequency within samples) and biomass of a given MOTU. Nevertheless, most studies analysing this relationship report a gross correlation, in the sense that more abundant species also tend to be represented by a higher relative or absolute number of reads (reviewed in Lejzerowicz et al, 2015;Barnes and Turner, 2016;Valentini et al, 2016;Bucklin et al, 2016). It can be added here that abundance estimation using traditional methods is not free of biases, either (Shelton et al, 2016).…”

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

“…Recent research has begun to validate metabarcoding as a time and cost‐efficient method for biodiversity surveys in terrestrial, freshwater, and marine ecosystems (Hirai, Kuriyama, Ichikawa, Hidaka, & Tsuda, 2015; Ji et al., 2013; Thomsen et al., 2012; Valentini et al., 2016). The results of metabarcoding studies depend on the markers used providing sufficient taxonomic coverage and resolution for the taxa of interest.…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…Sequencing of environmental samples such as seawater is now applied in a macrobial sense across a range of trophic levels ("microbes to mammals") (Trivedi et al, 2016;Valentini et al, 2016), and approaches used to inventory individuals (Ardura et al, 2013;Harada et al, 2015;Thompson et al, 2016) are being applied to assemblages (Carugati et al, 2015;Zimmermann et al, 2015;Aylagas et al, 2016). Studies demonstrate DNA metabarcoding to be a reliable method for biodiversity assessment with potential for inferring biotic indices for marine ecosystem quality assessment (Aylagas et al, 2014;Pawlowski et al, 2014;Cowart et al, 2015;Elbrecht and Leese, 2015;Visco et al, 2015;Ferrera et al, 2016).…”