The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection

Abstract

The field of environmental DNA (eDNA) analysis has rapidly developed over the past decade and the technique has become widely used for detecting aquatic macroorganisms in a variety of habitats. However, a variety of measurement protocols have been individually developed for different eDNA studies and this may lead to confusion for others who wish to incorporate eDNA analysis in their research. It is important therefore to synthesize the current status of—and future challenges to—the methodology of eDNA analysis. We here synthesized the protocols from total 438 published eDNA studies detecting aquatic macroorganisms were used to calculate the frequency of using each method in eDNA analysis steps. We found that the frequency of methods used converged to one or two methods for any analysis step. Furthermore, although the procedure with highest frequency is not always the best, it was shown that the eDNA collection by filtration and subsequent extraction/purification using a DNeasy Blood and Tissue DNA extraction kit (Qiagen, Hilden, Germany) or PowerWater DNA Extraction Kit (Qiagen) is the most common procedure. An understanding of the characteristics of commonly used methods can help those newly engaged in eDNA studies to understand the basic outline of eDNA analysis. Our review will be useful for the future improvement and development of analytical eDNA techniques of eDNA by sharing the recognition of methodological characteristic including advantages and disadvantages in major analytical techniques.

Application of Environmental DNA Metabarcoding to Spatiotemporal Finfish Community Assessment in a Temperate Embayment

“…Nylon filters (47 mm, 0.45 µm) were chosen initially for concentrating eDNA as they are hydrophilic, offer a relatively fast filtration speed, and have a small pore size to recover the majority of macroorganismal eDNA ranging from 1 to 10 µm (Turner et al, 2014). Although nylon filters are widely used (Thomsen et al, 2012;Stat et al, 2017;Stoeckle M. et al, 2017), other filter types are available (Kelly et al, 2014;Turner et al, 2014;Hinlo et al, 2017;Kelly et al, 2017;Lacoursière-Roussel et al, 2018;Tsuji et al, 2019). We compared the performance of nylon filters to that of polycarbonate filters, as the latter is most commonly used for concentrating microbial cells.…”

“…To better realize the potential for eDNA methods to address a wide range of ecological questions, spatiotemporal variations of eDNA in marine environments must be more thoroughly understood, and targeted studies addressing technical details regarding eDNA sample collection and processing are required. One such technical detail revolves around the choice of eDNA concentrating matrix -membrane filters, with both filter material and pore size playing important roles in eDNA capture (Djurhuus et al, 2017;Tsuji et al, 2019).…”

A practical guide to DNA metabarcoding for entomological ecologists

“…The widely used approach for retrieving eDNA from water samples involves filtration, ethanol precipitation, and centrifugation (Tsuji et al ., ). As a result, sampling biodiversity is constrained by the volume of processed water due to limitations of filter membranes (e.g.…”

“…For water eDNA samples, the use of filtration and DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany) is recommended by Deiner et al . () for eukaryote biodiversity surveys, because this combination showed good detection rates for both lotic and rare species (see also Tsuji et al ., ). Although the Qiagen DNeasy Blood & Tissue kit is widely used for terrestrial bulk invertebrates, the PowerPlant Kit performs better for benthic macroinvertebrates compared with two other tested kits, because it removes PCR inhibitors (Majaneva et al ., ).…”

Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

“…In recent years, environmental DNA (eDNA) metabarcoding (the simultaneous identification via next-generation sequencing of multiple taxa using DNA extracted from environmental samples, e.g., water, soil) has delivered on its initial potential and is now revolutionizing how we monitor biodiversity (Deiner et al 2017). The majority of eDNA metabarcoding applications have focused on monitoring fish and macroinvertebrates, with mammals being targeted in only 8% of vertebrate studies (Tsuji et al 2019). However, with the development of universal primers for vertebrates and mammals specifically, there has been a recent surge in studies tailored to detect and/or monitor mammalian communities in terrestrial and freshwater environments (e.g.…”