Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Abstract

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.

Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

“…Untangling biases in species richness (under-or overestimation) from eDNA metabarcoding will require some reference to species present in the target system, which could come from calibration experiments using complex mesocosms with known species composition. Although there have been recent calls for standardized approaches in eDNA metabarcoding (Shu et al, 2020), it is unclear if standardized protocols are needed for purposes of measuring community composition or if protocols should be optimized for each system. 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).…”

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

“…All rights reserved DNA for metabarcoding applications. While water eDNA has been used for the study of protists, fito-and zooplankton or fish assemblages (e.g., Djurhuus et al, 2018;Massana et al, 2015;Shu, Ludwig, A., & Peng, 2020), its potential utility to analyse benthic communities is much less understood. Some authors (Koziol et al, 2019;Rey, Basurko, & Rodriguez-Ezpeleta, 2020) compared eDNA from water, sediment and settlement plates in port environments, finding clearly distinct community profiles.…”

Detecting fish assemblages with environmental DNA: Does protocol matter? Testing eDNA metabarcoding method robustness

“…This demonstrates the robustness and the replicability of the method, regardless of the differences between the two protocols, and therefore testifies that the two datasets could be analyzed together. The use of enclosed filters might have played an important role in the robustness of the method, because the filters used in both protocols had a larger surface of filtering membrane than most of the open filters used in the literature (reviewed in Shu et al (2020) and in Tsuji et al (2019)), allowing filtering a large volume of water (more than 30 L per sample). This also permitted us to overpass potential bias due to membrane clogging as we did not face clogging issues constraining the amount of filtered water.…”

“…In addition, the membrane composition also influences the quantity of eDNA retrieved (Deiner et al, 2018;Hinlo et al, 2017;Majaneva et al, 2018;Shu et al, 2020). The extraction step appears more consensual, with most studies processing eDNA with commercial DNA extraction kit (Lear et al, 2018;Tsuji et al, 2019;but see Turner et al, 2014 for alternatives).…”