Critical considerations for the application of environmental DNA methods to detect aquatic species

By Caren S. Goldberg, C. Turner, K. Deiner, Katy E. Klymus, P. F. Thomsen, M. Murphy, Stephen F. Spear, A. McKee, S. Oyler‐McCance, R. Cornman and 10 more. 2016

879 citations recorded by the source corpus.

Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/93353772e91f4e8e5f96ad1abdaeeb807ce27ad8

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Citations in the corpus

A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish (2020, background): “Since eDNA-based biomonitoring is still a novel and rapidly advancing field, many aspects of eDNA methods await validation and adaptation to specific systems and research questions (DiazFerguson & Moyer, 2014; Goldberg et al., 2016).”
Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds (2020, background): “Age, physiology, life history and metabolic rate all play a role in the amount of eDNA released (eDNA shedding rate) from organisms into their surroundings (Barnes et al., 2014; Goldberg et al., 2016; Ruppert et al., 2019).”
eDNA Sampler: A fully integrated environmental DNA sampling system (2018, background): “Some protocols require samplers to transport volumes of water back to the laboratory, which limits sample size and introduces the possibility of DNA degradation before filtration or preservation can be performed (Goldberg et al., 2016).”
Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness (2020, background): “Still, best practices for eDNA metabarcoding are useful for minimizing contamination during sample and sequence processing and for maximizing yield with DNA capture, extraction, and amplification protocols (Goldberg et al., 2016).”
Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance (2021, background): “Therefore, where possible, it is preferable to avoid freezing samples in the ﬁeld and instead keep them chilled if they can be delivered to the lab within a reasonably short time (up to ~24 h [119,129]), where they can be immediately processed for ﬁltration and NA extraction (or storage).”
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, background): “In most cases, these studies deal with degraded DNA, thus are in urgent demand for short barcoding fragments for taxonomic identification (9,10).”
Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes (2020, methodology): “We followed a strict contamination control protocol in both field and laboratory stages (Goldberg et al., 2016; Valentini et al., 2016).”
From eDNA to citizen science: emerging tools for the early detection of invasive species (2020, methodology): “Protocols to minimize the risk of contamination, and to screen for its incidence, are integral in using eDNA to survey for invasive species (Goldberg et al. 2016).”
Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation (2018, background): “Sequencing platforms vary greatly with respect to their throughput, cost, error profile, and read structure (Goodwin et al. 2016).”
Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters (2020, background): “The sensitivity of eDNA assays will always be influenced by the filtered water volume, storage and extraction methods, and the number of PCR replicates performed, as well as both metabarcoding thresholds or qPCR detection thresholds (as also discussed by Goldberg et al., 2016; Harper et al., 2019).”
An environmental DNA‐based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica) (2017, background): “As the presence of contaminating DNA can significantly affect the validity of future studies, we strongly recommend that future research takes into consideration recently published guidelines for eDNA studies (Goldberg et al. 2016).”
The Elephant in the Lab (and Field): Contamination in Aquatic Environmental DNA Studies (2020, background): “Indeed, multiple papers over the past decade have indicated that the inclusion of controls throughout the entire eDNA workflow is required for strong inference about species presence (Darling and Mahon, 2011; Goldberg et al., 2016; Jerde, 2019; Sepulveda et al., 2019b).”