Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

Abstract

Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and

Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: a case study on a threatened amphibian

“…Consequently, ponds were represented by a single eDNA sample, for which 12 qPCR replicates were performed (Biggs et al, 2015). However, eDNA metabarcoding may require an entirely different workflow to enhance species detection (Harper et al, 2018; Harper et al, 2019).…”

“…Aquatic ecosystems are highly suited to eDNA studies as eDNA exists in multiple states with rapid modes of transport and degradation, increasing detectability of contemporary biodiversity (Rees et al, 2014; Barnes & Turner, 2015). Lentic systems provide further opportunities for eDNA research, being discrete water bodies with variable physicochemical properties that do not experience flow dynamics (Harper et al, 2019). Ponds in particular have enormous biodiversity and experimental virtue that has not been maximised in previous eDNA metabarcoding assessments of this habitat (Valentini et al, 2016; Evans et al, 2017; Klymus et al, 2017; Ushio et al, 2017; Bálint et al, 2018).…”

“…Consequently, ponds are model systems for experimental validation and examination of biogeographical patterns (De Meester et al, 2005). Habitat complexity and tools required for different taxa with associated bias (Evans et al, 2017) and cost (Valentini et al, 2016) once hindered exhaustive sampling of pond biodiversity (Hill et al, 2018), but eDNA metabarcoding may overcome these barriers (Harper et al, 2019).…”

Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals:

“…While many studies have shown the advantages of using eDNA metabarcoding in lotic (flowing streams and rivers; Balasingham et al, 2018) and lentic (still lakes and ponds; Harper et al, 2018;Hänfling et al, 2016;Perez et al, 2017) systems, they also raise concerns about the influence of flow in DNA dispersal in fast running water and the need to sample multiple locations in lentic waters.…”

Amphibian conservation in Scotland: A review of threats and opportunities

“…comm., May 2018; http://www.arc-trust.org/gcn-detectives). The potential, difficulties, challenges, and ways forward for monitoring freshwater pond biodiversity using eDNA have been discussed and reviewed by Harper, Buxton, et al ().…”